---
_id: '6466'
abstract:
- lang: eng
text: "One of the most striking and consistent results in speciation genomics is
the heterogeneous divergence observed across the genomes of closely related species.
This pattern was initially attributed to different levels of gene exchange—with
divergence preserved at loci generating a barrier to gene flow but homogenized
at unlinked neutral loci. Although there is evidence to support this model, it
is now recognized that interpreting patterns of divergence across genomes is not
so straightforward. One \r\nproblem is that heterogenous divergence between populations
can also be generated by other processes (e.g. recurrent selective sweeps or background
selection) without any involvement of differential gene flow. Thus, integrated
studies that identify which loci are likely subject to divergent selection are
required to shed light on the interplay between selection and gene flow during
the early phases of speciation. In this issue of Molecular Ecology, Rifkin et
al. (2019) confront this challenge using a pair of sister morning glory species.
They wisely design their sampling to take the geographic context of individuals
into account, including geographically isolated (allopatric) and co‐occurring
(sympatric) populations. This enabled them to show that individuals are phenotypically
less differentiated in sympatry. They also found that the loci that resist introgression
are enriched for those most differentiated in allopatry and loci that exhibit
signals of divergent selection. One great strength of the \r\nstudy is the combination
of methods from population genetics and molecular evolution, including the development
of a model to simultaneously infer admixture proportions and selfing rates."
article_processing_charge: No
author:
- first_name: David
full_name: Field, David
id: 419049E2-F248-11E8-B48F-1D18A9856A87
last_name: Field
orcid: 0000-0002-4014-8478
- first_name: Christelle
full_name: Fraisse, Christelle
id: 32DF5794-F248-11E8-B48F-1D18A9856A87
last_name: Fraisse
orcid: 0000-0001-8441-5075
citation:
ama: Field D, Fraisse C. Breaking down barriers in morning glories. Molecular
ecology. 2019;28(7):1579-1581. doi:10.1111/mec.15048
apa: Field, D., & Fraisse, C. (2019). Breaking down barriers in morning glories.
Molecular Ecology. Wiley. https://doi.org/10.1111/mec.15048
chicago: Field, David, and Christelle Fraisse. “Breaking down Barriers in Morning
Glories.” Molecular Ecology. Wiley, 2019. https://doi.org/10.1111/mec.15048.
ieee: D. Field and C. Fraisse, “Breaking down barriers in morning glories,” Molecular
ecology, vol. 28, no. 7. Wiley, pp. 1579–1581, 2019.
ista: Field D, Fraisse C. 2019. Breaking down barriers in morning glories. Molecular
ecology. 28(7), 1579–1581.
mla: Field, David, and Christelle Fraisse. “Breaking down Barriers in Morning Glories.”
Molecular Ecology, vol. 28, no. 7, Wiley, 2019, pp. 1579–81, doi:10.1111/mec.15048.
short: D. Field, C. Fraisse, Molecular Ecology 28 (2019) 1579–1581.
date_created: 2019-05-19T21:59:15Z
date_published: 2019-04-01T00:00:00Z
date_updated: 2023-08-25T10:37:30Z
day: '01'
ddc:
- '580'
- '576'
department:
- _id: NiBa
doi: 10.1111/mec.15048
external_id:
isi:
- '000474808300001'
file:
- access_level: open_access
checksum: 521e3aff3e9263ddf2ffbfe0b6157715
content_type: application/pdf
creator: dernst
date_created: 2019-05-20T11:49:06Z
date_updated: 2020-07-14T12:47:31Z
file_id: '6472'
file_name: 2019_MolecularEcology_Field.pdf
file_size: 367711
relation: main_file
file_date_updated: 2020-07-14T12:47:31Z
has_accepted_license: '1'
intvolume: ' 28'
isi: 1
issue: '7'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: 1579-1581
publication: Molecular ecology
publication_identifier:
eissn:
- 1365294X
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: Breaking down barriers in morning glories
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 28
year: '2019'
...
---
_id: '6467'
abstract:
- lang: eng
text: Fitness interactions between mutations can influence a population’s evolution
in many different ways. While epistatic effects are difficult to measure precisely,
important information is captured by the mean and variance of log fitnesses for
individuals carrying different numbers of mutations. We derive predictions for
these quantities from a class of simple fitness landscapes, based on models of
optimizing selection on quantitative traits. We also explore extensions to the
models, including modular pleiotropy, variable effect sizes, mutational bias and
maladaptation of the wild type. We illustrate our approach by reanalysing a large
dataset of mutant effects in a yeast snoRNA (small nucleolar RNA). Though characterized
by some large epistatic effects, these data give a good overall fit to the non-epistatic
null model, suggesting that epistasis might have limited influence on the evolutionary
dynamics in this system. We also show how the amount of epistasis depends on both
the underlying fitness landscape and the distribution of mutations, and so is
expected to vary in consistent ways between new mutations, standing variation
and fixed mutations.
article_number: '0881'
article_processing_charge: No
article_type: original
author:
- first_name: Christelle
full_name: Fraisse, Christelle
id: 32DF5794-F248-11E8-B48F-1D18A9856A87
last_name: Fraisse
orcid: 0000-0001-8441-5075
- first_name: John J.
full_name: Welch, John J.
last_name: Welch
citation:
ama: Fraisse C, Welch JJ. The distribution of epistasis on simple fitness landscapes.
Biology Letters. 2019;15(4). doi:10.1098/rsbl.2018.0881
apa: Fraisse, C., & Welch, J. J. (2019). The distribution of epistasis on simple
fitness landscapes. Biology Letters. Royal Society of London. https://doi.org/10.1098/rsbl.2018.0881
chicago: Fraisse, Christelle, and John J. Welch. “The Distribution of Epistasis
on Simple Fitness Landscapes.” Biology Letters. Royal Society of London,
2019. https://doi.org/10.1098/rsbl.2018.0881.
ieee: C. Fraisse and J. J. Welch, “The distribution of epistasis on simple fitness
landscapes,” Biology Letters, vol. 15, no. 4. Royal Society of London,
2019.
ista: Fraisse C, Welch JJ. 2019. The distribution of epistasis on simple fitness
landscapes. Biology Letters. 15(4), 0881.
mla: Fraisse, Christelle, and John J. Welch. “The Distribution of Epistasis on Simple
Fitness Landscapes.” Biology Letters, vol. 15, no. 4, 0881, Royal Society
of London, 2019, doi:10.1098/rsbl.2018.0881.
short: C. Fraisse, J.J. Welch, Biology Letters 15 (2019).
date_created: 2019-05-19T21:59:15Z
date_published: 2019-04-03T00:00:00Z
date_updated: 2023-08-25T10:34:41Z
day: '03'
department:
- _id: BeVi
- _id: NiBa
doi: 10.1098/rsbl.2018.0881
ec_funded: 1
external_id:
isi:
- '000465405300010'
pmid:
- '31014191'
intvolume: ' 15'
isi: 1
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1098/rsbl.2018.0881
month: '04'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Biology Letters
publication_identifier:
eissn:
- 1744957X
issn:
- '17449561'
publication_status: published
publisher: Royal Society of London
quality_controlled: '1'
related_material:
link:
- relation: supplementary_material
url: https://dx.doi.org/10.6084/m9.figshare.c.4461008
record:
- id: '9798'
relation: research_data
status: public
- id: '9799'
relation: research_data
status: public
scopus_import: '1'
status: public
title: The distribution of epistasis on simple fitness landscapes
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 15
year: '2019'
...
---
_id: '6637'
abstract:
- lang: eng
text: The environment changes constantly at various time scales and, in order to
survive, species need to keep adapting. Whether these species succeed in avoiding
extinction is a major evolutionary question. Using a multilocus evolutionary model
of a mutation‐limited population adapting under strong selection, we investigate
the effects of the frequency of environmental fluctuations on adaptation. Our
results rely on an “adaptive‐walk” approximation and use mathematical methods
from evolutionary computation theory to investigate the interplay between fluctuation
frequency, the similarity of environments, and the number of loci contributing
to adaptation. First, we assume a linear additive fitness function, but later
generalize our results to include several types of epistasis. We show that frequent
environmental changes prevent populations from reaching a fitness peak, but they
may also prevent the large fitness loss that occurs after a single environmental
change. Thus, the population can survive, although not thrive, in a wide range
of conditions. Furthermore, we show that in a frequently changing environment,
the similarity of threats that a population faces affects the level of adaptation
that it is able to achieve. We check and supplement our analytical results with
simulations.
acknowledgement: The authors would like to thank to Tiago Paixao and Nick Barton for
useful comments and advice.
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Barbora
full_name: Trubenova, Barbora
id: 42302D54-F248-11E8-B48F-1D18A9856A87
last_name: Trubenova
orcid: 0000-0002-6873-2967
- first_name: 'Martin '
full_name: 'Krejca, Martin '
last_name: Krejca
- first_name: Per Kristian
full_name: Lehre, Per Kristian
last_name: Lehre
- first_name: Timo
full_name: Kötzing, Timo
last_name: Kötzing
citation:
ama: 'Trubenova B, Krejca M, Lehre PK, Kötzing T. Surfing on the seascape: Adaptation
in a changing environment. Evolution. 2019;73(7):1356-1374. doi:10.1111/evo.13784'
apa: 'Trubenova, B., Krejca, M., Lehre, P. K., & Kötzing, T. (2019). Surfing
on the seascape: Adaptation in a changing environment. Evolution. Wiley.
https://doi.org/10.1111/evo.13784'
chicago: 'Trubenova, Barbora, Martin Krejca, Per Kristian Lehre, and Timo Kötzing.
“Surfing on the Seascape: Adaptation in a Changing Environment.” Evolution.
Wiley, 2019. https://doi.org/10.1111/evo.13784.'
ieee: 'B. Trubenova, M. Krejca, P. K. Lehre, and T. Kötzing, “Surfing on the seascape:
Adaptation in a changing environment,” Evolution, vol. 73, no. 7. Wiley,
pp. 1356–1374, 2019.'
ista: 'Trubenova B, Krejca M, Lehre PK, Kötzing T. 2019. Surfing on the seascape:
Adaptation in a changing environment. Evolution. 73(7), 1356–1374.'
mla: 'Trubenova, Barbora, et al. “Surfing on the Seascape: Adaptation in a Changing
Environment.” Evolution, vol. 73, no. 7, Wiley, 2019, pp. 1356–74, doi:10.1111/evo.13784.'
short: B. Trubenova, M. Krejca, P.K. Lehre, T. Kötzing, Evolution 73 (2019) 1356–1374.
date_created: 2019-07-14T21:59:20Z
date_published: 2019-07-01T00:00:00Z
date_updated: 2023-08-29T06:31:14Z
day: '01'
ddc:
- '576'
department:
- _id: NiBa
doi: 10.1111/evo.13784
ec_funded: 1
external_id:
isi:
- '000474031600001'
file:
- access_level: open_access
checksum: 9831ca65def2d62498c7b08338b6d237
content_type: application/pdf
creator: apreinsp
date_created: 2019-07-16T06:08:31Z
date_updated: 2020-07-14T12:47:34Z
file_id: '6643'
file_name: 2019_Evolution_TrubenovaBarbora.pdf
file_size: 815416
relation: main_file
file_date_updated: 2020-07-14T12:47:34Z
has_accepted_license: '1'
intvolume: ' 73'
isi: 1
issue: '7'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-nd/4.0/
month: '07'
oa: 1
oa_version: Published Version
page: 1356-1374
project:
- _id: 25AEDD42-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '704172'
name: Rate of Adaptation in Changing Environment
- _id: 25B1EC9E-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '618091'
name: Speed of Adaptation in Population Genetics and Evolutionary Computation
publication: Evolution
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Surfing on the seascape: Adaptation in a changing environment'
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 73
year: '2019'
...
---
_id: '6680'
abstract:
- lang: eng
text: This paper analyzes how partial selfing in a large source population influences
its ability to colonize a new habitat via the introduction of a few founder individuals.
Founders experience inbreeding depression due to partially recessive deleterious
alleles as well as maladaptation to the new environment due to selection on a
large number of additive loci. I first introduce a simplified version of the Inbreeding
History Model (Kelly, 2007) in order to characterize mutation‐selection balance
in a large, partially selfing source population under selection involving multiple
non‐identical loci. I then use individual‐based simulations to study the eco‐evolutionary
dynamics of founders establishing in the new habitat under a model of hard selection.
The study explores how selfing rate shapes establishment probabilities of founders
via effects on both inbreeding depression and adaptability to the new environment,
and also distinguishes the effects of selfing on the initial fitness of founders
from its effects on the long‐term adaptive response of the populations they found.
A high rate of (but not complete) selfing is found to aid establishment over a
wide range of parameters, even in the absence of mate limitation. The sensitivity
of the results to assumptions about the nature of polygenic selection are discussed.
article_processing_charge: Yes (via OA deal)
author:
- first_name: Himani
full_name: Sachdeva, Himani
id: 42377A0A-F248-11E8-B48F-1D18A9856A87
last_name: Sachdeva
citation:
ama: Sachdeva H. Effect of partial selfing and polygenic selection on establishment
in a new habitat. Evolution. 2019;73(9):1729-1745. doi:10.1111/evo.13812
apa: Sachdeva, H. (2019). Effect of partial selfing and polygenic selection on establishment
in a new habitat. Evolution. Wiley. https://doi.org/10.1111/evo.13812
chicago: Sachdeva, Himani. “Effect of Partial Selfing and Polygenic Selection on
Establishment in a New Habitat.” Evolution. Wiley, 2019. https://doi.org/10.1111/evo.13812.
ieee: H. Sachdeva, “Effect of partial selfing and polygenic selection on establishment
in a new habitat,” Evolution, vol. 73, no. 9. Wiley, pp. 1729–1745, 2019.
ista: Sachdeva H. 2019. Effect of partial selfing and polygenic selection on establishment
in a new habitat. Evolution. 73(9), 1729–1745.
mla: Sachdeva, Himani. “Effect of Partial Selfing and Polygenic Selection on Establishment
in a New Habitat.” Evolution, vol. 73, no. 9, Wiley, 2019, pp. 1729–45,
doi:10.1111/evo.13812.
short: H. Sachdeva, Evolution 73 (2019) 1729–1745.
date_created: 2019-07-25T09:08:28Z
date_published: 2019-09-01T00:00:00Z
date_updated: 2023-08-29T06:43:58Z
day: '01'
ddc:
- '576'
department:
- _id: NiBa
doi: 10.1111/evo.13812
external_id:
isi:
- '000481300600001'
file:
- access_level: open_access
checksum: 772ce7035965153959b946a1033de1ca
content_type: application/pdf
creator: kschuh
date_created: 2019-09-17T10:56:27Z
date_updated: 2020-07-14T12:47:37Z
file_id: '6881'
file_name: 2019_Evolution_Sachdeva.pdf
file_size: 937573
relation: main_file
file_date_updated: 2020-07-14T12:47:37Z
has_accepted_license: '1'
intvolume: ' 73'
isi: 1
issue: '9'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
page: 1729-1745
publication: Evolution
publication_identifier:
eissn:
- 1558-5646
issn:
- 0014-3820
publication_status: published
publisher: Wiley
quality_controlled: '1'
related_material:
record:
- id: '9802'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Effect of partial selfing and polygenic selection on establishment in a new
habitat
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 73
year: '2019'
...
---
_id: '9804'
abstract:
- lang: eng
text: Evolutionary studies are often limited by missing data that are critical to
understanding the history of selection. Selection experiments, which reproduce
rapid evolution under controlled conditions, are excellent tools to study how
genomes evolve under selection. Here we present a genomic dissection of the Longshanks
selection experiment, in which mice were selectively bred over 20 generations
for longer tibiae relative to body mass, resulting in 13% longer tibiae in two
replicates. We synthesized evolutionary theory, genome sequences and molecular
genetics to understand the selection response and found that it involved both
polygenic adaptation and discrete loci of major effect, with the strongest loci
tending to be selected in parallel between replicates. We show that selection
may favor de-repression of bone growth through inactivating two limb enhancers
of an inhibitor, Nkx3-2. Our integrative genomic analyses thus show that it is
possible to connect individual base-pair changes to the overall selection response.
article_processing_charge: No
author:
- first_name: João Pl
full_name: Castro, João Pl
last_name: Castro
- first_name: Michelle N.
full_name: Yancoskie, Michelle N.
last_name: Yancoskie
- first_name: Marta
full_name: Marchini, Marta
last_name: Marchini
- first_name: Stefanie
full_name: Belohlavy, Stefanie
id: 43FE426A-F248-11E8-B48F-1D18A9856A87
last_name: Belohlavy
orcid: 0000-0002-9849-498X
- first_name: Layla
full_name: Hiramatsu, Layla
last_name: Hiramatsu
- first_name: Marek
full_name: Kučka, Marek
last_name: Kučka
- first_name: William H.
full_name: Beluch, William H.
last_name: Beluch
- first_name: Ronald
full_name: Naumann, Ronald
last_name: Naumann
- first_name: Isabella
full_name: Skuplik, Isabella
last_name: Skuplik
- first_name: John
full_name: Cobb, John
last_name: Cobb
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Campbell
full_name: Rolian, Campbell
last_name: Rolian
- first_name: Yingguang Frank
full_name: Chan, Yingguang Frank
last_name: Chan
citation:
ama: 'Castro JP, Yancoskie MN, Marchini M, et al. Data from: An integrative genomic
analysis of the Longshanks selection experiment for longer limbs in mice. 2019.
doi:10.5061/dryad.0q2h6tk'
apa: 'Castro, J. P., Yancoskie, M. N., Marchini, M., Belohlavy, S., Hiramatsu, L.,
Kučka, M., … Chan, Y. F. (2019). Data from: An integrative genomic analysis of
the Longshanks selection experiment for longer limbs in mice. Dryad. https://doi.org/10.5061/dryad.0q2h6tk'
chicago: 'Castro, João Pl, Michelle N. Yancoskie, Marta Marchini, Stefanie Belohlavy,
Layla Hiramatsu, Marek Kučka, William H. Beluch, et al. “Data from: An Integrative
Genomic Analysis of the Longshanks Selection Experiment for Longer Limbs in Mice.”
Dryad, 2019. https://doi.org/10.5061/dryad.0q2h6tk.'
ieee: 'J. P. Castro et al., “Data from: An integrative genomic analysis of
the Longshanks selection experiment for longer limbs in mice.” Dryad, 2019.'
ista: 'Castro JP, Yancoskie MN, Marchini M, Belohlavy S, Hiramatsu L, Kučka M, Beluch
WH, Naumann R, Skuplik I, Cobb J, Barton NH, Rolian C, Chan YF. 2019. Data from:
An integrative genomic analysis of the Longshanks selection experiment for longer
limbs in mice, Dryad, 10.5061/dryad.0q2h6tk.'
mla: 'Castro, João Pl, et al. Data from: An Integrative Genomic Analysis of the
Longshanks Selection Experiment for Longer Limbs in Mice. Dryad, 2019, doi:10.5061/dryad.0q2h6tk.'
short: J.P. Castro, M.N. Yancoskie, M. Marchini, S. Belohlavy, L. Hiramatsu, M.
Kučka, W.H. Beluch, R. Naumann, I. Skuplik, J. Cobb, N.H. Barton, C. Rolian, Y.F.
Chan, (2019).
date_created: 2021-08-06T11:52:54Z
date_published: 2019-06-06T00:00:00Z
date_updated: 2023-08-29T06:41:51Z
day: '06'
department:
- _id: NiBa
doi: 10.5061/dryad.0q2h6tk
main_file_link:
- open_access: '1'
url: https://doi.org/10.5061/dryad.0q2h6tk
month: '06'
oa: 1
oa_version: Published Version
publisher: Dryad
related_material:
record:
- id: '6713'
relation: used_in_publication
status: public
status: public
title: 'Data from: An integrative genomic analysis of the Longshanks selection experiment
for longer limbs in mice'
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2019'
...
---
_id: '9802'
abstract:
- lang: eng
text: This paper analyzes how partial selfing in a large source population influences
its ability to colonize a new habitat via the introduction of a few founder individuals.
Founders experience inbreeding depression due to partially recessive deleterious
alleles as well as maladaptation to the new environment due to selection on a
large number of additive loci. I first introduce a simplified version of the Inbreeding
History Model (Kelly, 2007) in order to characterize mutation-selection balance
in a large, partially selfing source population under selection involving multiple
non-identical loci. I then use individual-based simulations to study the eco-evolutionary
dynamics of founders establishing in the new habitat under a model of hard selection.
The study explores how selfing rate shapes establishment probabilities of founders
via effects on both inbreeding depression and adaptability to the new environment,
and also distinguishes the effects of selfing on the initial fitness of founders
from its effects on the long-term adaptive response of the populations they found.
A high rate of (but not complete) selfing is found to aid establishment over a
wide range of parameters, even in the absence of mate limitation. The sensitivity
of the results to assumptions about the nature of polygenic selection are discussed.
article_processing_charge: No
author:
- first_name: Himani
full_name: Sachdeva, Himani
id: 42377A0A-F248-11E8-B48F-1D18A9856A87
last_name: Sachdeva
citation:
ama: 'Sachdeva H. Data from: Effect of partial selfing and polygenic selection on
establishment in a new habitat. 2019. doi:10.5061/dryad.8tp0900'
apa: 'Sachdeva, H. (2019). Data from: Effect of partial selfing and polygenic selection
on establishment in a new habitat. Dryad. https://doi.org/10.5061/dryad.8tp0900'
chicago: 'Sachdeva, Himani. “Data from: Effect of Partial Selfing and Polygenic
Selection on Establishment in a New Habitat.” Dryad, 2019. https://doi.org/10.5061/dryad.8tp0900.'
ieee: 'H. Sachdeva, “Data from: Effect of partial selfing and polygenic selection
on establishment in a new habitat.” Dryad, 2019.'
ista: 'Sachdeva H. 2019. Data from: Effect of partial selfing and polygenic selection
on establishment in a new habitat, Dryad, 10.5061/dryad.8tp0900.'
mla: 'Sachdeva, Himani. Data from: Effect of Partial Selfing and Polygenic Selection
on Establishment in a New Habitat. Dryad, 2019, doi:10.5061/dryad.8tp0900.'
short: H. Sachdeva, (2019).
date_created: 2021-08-06T11:45:11Z
date_published: 2019-07-16T00:00:00Z
date_updated: 2023-08-29T06:43:57Z
day: '16'
department:
- _id: NiBa
doi: 10.5061/dryad.8tp0900
main_file_link:
- open_access: '1'
url: https://doi.org/10.5061/dryad.8tp0900
month: '07'
oa: 1
oa_version: Published Version
publisher: Dryad
related_material:
record:
- id: '6680'
relation: used_in_publication
status: public
status: public
title: 'Data from: Effect of partial selfing and polygenic selection on establishment
in a new habitat'
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2019'
...
---
_id: '6795'
abstract:
- lang: eng
text: The green‐beard effect is one proposed mechanism predicted to underpin the
evolu‐tion of altruistic behavior. It relies on the recognition and the selective
help of altruists to each other in order to promote and sustain altruistic behavior.
However, this mechanism has often been dismissed as unlikely or uncommon, as it
is assumed that both the signaling trait and altruistic trait need to be encoded
by the same gene or through tightly linked genes. Here, we use models of indirect
genetic effects (IGEs) to find the minimum correlation between the signaling and
altruistic trait required for the evolution of the latter. We show that this correlation
threshold depends on the strength of the interaction (influence of the green beard
on the expression of the altruistic trait), as well as the costs and benefits
of the altruistic behavior. We further show that this correlation does not necessarily
have to be high and support our analytical results by simulations.
article_processing_charge: No
article_type: original
author:
- first_name: Barbora
full_name: Trubenova, Barbora
id: 42302D54-F248-11E8-B48F-1D18A9856A87
last_name: Trubenova
orcid: 0000-0002-6873-2967
- first_name: Reinmar
full_name: Hager, Reinmar
last_name: Hager
citation:
ama: Trubenova B, Hager R. Green beards in the light of indirect genetic effects.
Ecology and Evolution. 2019;9(17):9597-9608. doi:10.1002/ece3.5484
apa: Trubenova, B., & Hager, R. (2019). Green beards in the light of indirect
genetic effects. Ecology and Evolution. Wiley. https://doi.org/10.1002/ece3.5484
chicago: Trubenova, Barbora, and Reinmar Hager. “Green Beards in the Light of Indirect
Genetic Effects.” Ecology and Evolution. Wiley, 2019. https://doi.org/10.1002/ece3.5484.
ieee: B. Trubenova and R. Hager, “Green beards in the light of indirect genetic
effects,” Ecology and Evolution, vol. 9, no. 17. Wiley, pp. 9597–9608,
2019.
ista: Trubenova B, Hager R. 2019. Green beards in the light of indirect genetic
effects. Ecology and Evolution. 9(17), 9597–9608.
mla: Trubenova, Barbora, and Reinmar Hager. “Green Beards in the Light of Indirect
Genetic Effects.” Ecology and Evolution, vol. 9, no. 17, Wiley, 2019, pp.
9597–608, doi:10.1002/ece3.5484.
short: B. Trubenova, R. Hager, Ecology and Evolution 9 (2019) 9597–9608.
date_created: 2019-08-11T21:59:24Z
date_published: 2019-09-01T00:00:00Z
date_updated: 2023-08-29T07:03:10Z
day: '01'
ddc:
- '576'
department:
- _id: NiBa
doi: 10.1002/ece3.5484
ec_funded: 1
external_id:
isi:
- '000479973400001'
file:
- access_level: open_access
checksum: adcb70af4901977d95b8747eeee01bd7
content_type: application/pdf
creator: dernst
date_created: 2019-08-12T07:30:30Z
date_updated: 2020-07-14T12:47:40Z
file_id: '6799'
file_name: 2019_EcologyEvolution_Trubenova.pdf
file_size: 2839636
relation: main_file
file_date_updated: 2020-07-14T12:47:40Z
has_accepted_license: '1'
intvolume: ' 9'
isi: 1
issue: '17'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
page: 9597-9608
project:
- _id: 25AEDD42-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '704172'
name: Rate of Adaptation in Changing Environment
publication: Ecology and Evolution
publication_identifier:
eissn:
- '20457758'
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: Green beards in the light of indirect genetic effects
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 9
year: '2019'
...
---
_id: '6831'
abstract:
- lang: eng
text: "* Understanding the mechanisms causing phenotypic differences between females
and males has long fascinated evolutionary biologists. An extensive literature
exists on animal sexual dimorphism but less information is known about sex differences
in plants, particularly the extent of geographical variation in sexual dimorphism
and its life‐cycle dynamics.\r\n* Here, we investigated patterns of genetically
based sexual dimorphism in vegetative and reproductive traits of a wind‐pollinated
dioecious plant, Rumex hastatulus, across three life‐cycle stages using open‐pollinated
families from 30 populations spanning the geographic range and chromosomal variation
(XY and XY1Y2) of the species.\r\n* The direction and degree of sexual dimorphism
was highly variable among populations and life‐cycle stages. Sex‐specific differences
in reproductive function explained a significant amount of temporal change in
sexual dimorphism. For several traits, geographical variation in sexual dimorphism
was associated with bioclimatic parameters, likely due to the differential responses
of the sexes to climate. We found no systematic differences in sexual dimorphism
between chromosome races.\r\n* Sex‐specific trait differences in dioecious plants
largely result from a balance between sexual and natural selection on resource
allocation. Our results indicate that abiotic factors associated with geographical
context also play a role in modifying sexual dimorphism during the plant life‐cycle."
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Gemma
full_name: Puixeu Sala, Gemma
id: 33AB266C-F248-11E8-B48F-1D18A9856A87
last_name: Puixeu Sala
orcid: 0000-0001-8330-1754
- first_name: Melinda
full_name: Pickup, Melinda
id: 2C78037E-F248-11E8-B48F-1D18A9856A87
last_name: Pickup
orcid: 0000-0001-6118-0541
- first_name: David
full_name: Field, David
last_name: Field
orcid: 0000-0002-4014-8478
- first_name: Spencer C.H.
full_name: Barrett, Spencer C.H.
last_name: Barrett
citation:
ama: 'Puixeu Sala G, Pickup M, Field D, Barrett SCH. Variation in sexual dimorphism
in a wind-pollinated plant: The influence of geographical context and life-cycle
dynamics. New Phytologist. 2019;224(3):1108-1120. doi:10.1111/nph.16050'
apa: 'Puixeu Sala, G., Pickup, M., Field, D., & Barrett, S. C. H. (2019). Variation
in sexual dimorphism in a wind-pollinated plant: The influence of geographical
context and life-cycle dynamics. New Phytologist. Wiley. https://doi.org/10.1111/nph.16050'
chicago: 'Puixeu Sala, Gemma, Melinda Pickup, David Field, and Spencer C.H. Barrett.
“Variation in Sexual Dimorphism in a Wind-Pollinated Plant: The Influence of Geographical
Context and Life-Cycle Dynamics.” New Phytologist. Wiley, 2019. https://doi.org/10.1111/nph.16050.'
ieee: 'G. Puixeu Sala, M. Pickup, D. Field, and S. C. H. Barrett, “Variation in
sexual dimorphism in a wind-pollinated plant: The influence of geographical context
and life-cycle dynamics,” New Phytologist, vol. 224, no. 3. Wiley, pp.
1108–1120, 2019.'
ista: 'Puixeu Sala G, Pickup M, Field D, Barrett SCH. 2019. Variation in sexual
dimorphism in a wind-pollinated plant: The influence of geographical context and
life-cycle dynamics. New Phytologist. 224(3), 1108–1120.'
mla: 'Puixeu Sala, Gemma, et al. “Variation in Sexual Dimorphism in a Wind-Pollinated
Plant: The Influence of Geographical Context and Life-Cycle Dynamics.” New
Phytologist, vol. 224, no. 3, Wiley, 2019, pp. 1108–20, doi:10.1111/nph.16050.'
short: G. Puixeu Sala, M. Pickup, D. Field, S.C.H. Barrett, New Phytologist 224
(2019) 1108–1120.
date_created: 2019-08-25T22:00:51Z
date_published: 2019-11-01T00:00:00Z
date_updated: 2023-08-29T07:17:07Z
day: '01'
ddc:
- '570'
department:
- _id: NiBa
- _id: BeVi
doi: 10.1111/nph.16050
ec_funded: 1
external_id:
isi:
- '000481376500001'
file:
- access_level: open_access
checksum: 6370e7567d96b7b562e77d8b89653f80
content_type: application/pdf
creator: apreinsp
date_created: 2019-08-27T12:44:54Z
date_updated: 2020-07-14T12:47:42Z
file_id: '6833'
file_name: 2019_NewPhytologist_Puixeu.pdf
file_size: 2314016
relation: main_file
file_date_updated: 2020-07-14T12:47:42Z
has_accepted_license: '1'
intvolume: ' 224'
isi: 1
issue: '3'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
page: 1108-1120
project:
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
publication: New Phytologist
publication_identifier:
eissn:
- 1469-8137
publication_status: published
publisher: Wiley
quality_controlled: '1'
related_material:
record:
- id: '9803'
relation: research_data
status: public
- id: '14058'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: 'Variation in sexual dimorphism in a wind-pollinated plant: The influence of
geographical context and life-cycle dynamics'
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 224
year: '2019'
...
---
_id: '9803'
abstract:
- lang: eng
text: Understanding the mechanisms causing phenotypic differences between females
and males has long fascinated evolutionary biologists. An extensive literature
exists on animal sexual dimorphism but less is known about sex differences in
plants, particularly the extent of geographical variation in sexual dimorphism
and its life-cycle dynamics. Here, we investigate patterns of genetically-based
sexual dimorphism in vegetative and reproductive traits of a wind-pollinated dioecious
plant, Rumex hastatulus, across three life-cycle stages using open-pollinated
families from 30 populations spanning the geographic range and chromosomal variation
(XY and XY1Y2) of the species. The direction and degree of sexual dimorphism was
highly variable among populations and life-cycle stages. Sex-specific differences
in reproductive function explained a significant amount of temporal change in
sexual dimorphism. For several traits, geographical variation in sexual dimorphism
was associated with bioclimatic parameters, likely due to the differential responses
of the sexes to climate. We found no systematic differences in sexual dimorphism
between chromosome races. Sex-specific trait differences in dioecious plants largely
result from a balance between sexual and natural selection on resource allocation.
Our results indicate that abiotic factors associated with geographical context
also play a role in modifying sexual dimorphism during the plant life cycle.
article_processing_charge: No
author:
- first_name: Gemma
full_name: Puixeu Sala, Gemma
id: 33AB266C-F248-11E8-B48F-1D18A9856A87
last_name: Puixeu Sala
orcid: 0000-0001-8330-1754
- first_name: Melinda
full_name: Pickup, Melinda
id: 2C78037E-F248-11E8-B48F-1D18A9856A87
last_name: Pickup
orcid: 0000-0001-6118-0541
- first_name: David
full_name: Field, David
last_name: Field
- first_name: Spencer C.H.
full_name: Barrett, Spencer C.H.
last_name: Barrett
citation:
ama: 'Puixeu Sala G, Pickup M, Field D, Barrett SCH. Data from: Variation in sexual
dimorphism in a wind-pollinated plant: the influence of geographical context and
life-cycle dynamics. 2019. doi:10.5061/dryad.n1701c9'
apa: 'Puixeu Sala, G., Pickup, M., Field, D., & Barrett, S. C. H. (2019). Data
from: Variation in sexual dimorphism in a wind-pollinated plant: the influence
of geographical context and life-cycle dynamics. Dryad. https://doi.org/10.5061/dryad.n1701c9'
chicago: 'Puixeu Sala, Gemma, Melinda Pickup, David Field, and Spencer C.H. Barrett.
“Data from: Variation in Sexual Dimorphism in a Wind-Pollinated Plant: The Influence
of Geographical Context and Life-Cycle Dynamics.” Dryad, 2019. https://doi.org/10.5061/dryad.n1701c9.'
ieee: 'G. Puixeu Sala, M. Pickup, D. Field, and S. C. H. Barrett, “Data from: Variation
in sexual dimorphism in a wind-pollinated plant: the influence of geographical
context and life-cycle dynamics.” Dryad, 2019.'
ista: 'Puixeu Sala G, Pickup M, Field D, Barrett SCH. 2019. Data from: Variation
in sexual dimorphism in a wind-pollinated plant: the influence of geographical
context and life-cycle dynamics, Dryad, 10.5061/dryad.n1701c9.'
mla: 'Puixeu Sala, Gemma, et al. Data from: Variation in Sexual Dimorphism in
a Wind-Pollinated Plant: The Influence of Geographical Context and Life-Cycle
Dynamics. Dryad, 2019, doi:10.5061/dryad.n1701c9.'
short: G. Puixeu Sala, M. Pickup, D. Field, S.C.H. Barrett, (2019).
date_created: 2021-08-06T11:48:42Z
date_published: 2019-07-22T00:00:00Z
date_updated: 2023-08-29T07:17:07Z
day: '22'
department:
- _id: NiBa
- _id: BeVi
doi: 10.5061/dryad.n1701c9
main_file_link:
- open_access: '1'
url: https://doi.org/10.5061/dryad.n1701c9
month: '07'
oa: 1
oa_version: Published Version
publisher: Dryad
related_material:
record:
- id: '14058'
relation: used_in_publication
status: public
- id: '6831'
relation: used_in_publication
status: public
status: public
title: 'Data from: Variation in sexual dimorphism in a wind-pollinated plant: the
influence of geographical context and life-cycle dynamics'
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2019'
...
---
_id: '6855'
abstract:
- lang: eng
text: Many traits of interest are highly heritable and genetically complex, meaning
that much of the variation they exhibit arises from differences at numerous loci
in the genome. Complex traits and their evolution have been studied for more than
a century, but only in the last decade have genome-wide association studies (GWASs)
in humans begun to reveal their genetic basis. Here, we bring these threads of
research together to ask how findings from GWASs can further our understanding
of the processes that give rise to heritable variation in complex traits and of
the genetic basis of complex trait evolution in response to changing selection
pressures (i.e., of polygenic adaptation). Conversely, we ask how evolutionary
thinking helps us to interpret findings from GWASs and informs related efforts
of practical importance.
article_processing_charge: No
author:
- first_name: Guy
full_name: Sella, Guy
last_name: Sella
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: Sella G, Barton NH. Thinking about the evolution of complex traits in the era
of genome-wide association studies. Annual Review of Genomics and Human Genetics.
2019;20:461-493. doi:10.1146/annurev-genom-083115-022316
apa: Sella, G., & Barton, N. H. (2019). Thinking about the evolution of complex
traits in the era of genome-wide association studies. Annual Review of Genomics
and Human Genetics. Annual Reviews. https://doi.org/10.1146/annurev-genom-083115-022316
chicago: Sella, Guy, and Nicholas H Barton. “Thinking about the Evolution of Complex
Traits in the Era of Genome-Wide Association Studies.” Annual Review of Genomics
and Human Genetics. Annual Reviews, 2019. https://doi.org/10.1146/annurev-genom-083115-022316.
ieee: G. Sella and N. H. Barton, “Thinking about the evolution of complex traits
in the era of genome-wide association studies,” Annual Review of Genomics and
Human Genetics, vol. 20. Annual Reviews, pp. 461–493, 2019.
ista: Sella G, Barton NH. 2019. Thinking about the evolution of complex traits in
the era of genome-wide association studies. Annual Review of Genomics and Human
Genetics. 20, 461–493.
mla: Sella, Guy, and Nicholas H. Barton. “Thinking about the Evolution of Complex
Traits in the Era of Genome-Wide Association Studies.” Annual Review of Genomics
and Human Genetics, vol. 20, Annual Reviews, 2019, pp. 461–93, doi:10.1146/annurev-genom-083115-022316.
short: G. Sella, N.H. Barton, Annual Review of Genomics and Human Genetics 20 (2019)
461–493.
date_created: 2019-09-07T14:28:29Z
date_published: 2019-07-05T00:00:00Z
date_updated: 2023-08-29T07:49:38Z
day: '05'
ddc:
- '576'
department:
- _id: NiBa
doi: 10.1146/annurev-genom-083115-022316
external_id:
isi:
- '000485148400020'
pmid:
- '31283361'
file:
- access_level: open_access
checksum: 23d3978cf4739a89ce2c3e779f9305ca
content_type: application/pdf
creator: dernst
date_created: 2019-09-09T07:22:12Z
date_updated: 2020-07-14T12:47:42Z
file_id: '6862'
file_name: 2019_AnnualReview_Sella.pdf
file_size: 411491
relation: main_file
file_date_updated: 2020-07-14T12:47:42Z
has_accepted_license: '1'
intvolume: ' 20'
isi: 1
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: 461-493
pmid: 1
publication: Annual Review of Genomics and Human Genetics
publication_identifier:
eissn:
- 1545-293X
issn:
- 1527-8204
publication_status: published
publisher: Annual Reviews
quality_controlled: '1'
scopus_import: '1'
status: public
title: Thinking about the evolution of complex traits in the era of genome-wide association
studies
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 20
year: '2019'
...
---
_id: '6858'
article_processing_charge: No
article_type: review
author:
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: Barton NH. Is speciation driven by cycles of mixing and isolation? National
Science Review. 2019;6(2):291-292. doi:10.1093/nsr/nwy113
apa: Barton, N. H. (2019). Is speciation driven by cycles of mixing and isolation?
National Science Review. Oxford University Press. https://doi.org/10.1093/nsr/nwy113
chicago: Barton, Nicholas H. “Is Speciation Driven by Cycles of Mixing and Isolation?”
National Science Review. Oxford University Press, 2019. https://doi.org/10.1093/nsr/nwy113.
ieee: N. H. Barton, “Is speciation driven by cycles of mixing and isolation?,” National
Science Review, vol. 6, no. 2. Oxford University Press, pp. 291–292, 2019.
ista: Barton NH. 2019. Is speciation driven by cycles of mixing and isolation? National
Science Review. 6(2), 291–292.
mla: Barton, Nicholas H. “Is Speciation Driven by Cycles of Mixing and Isolation?”
National Science Review, vol. 6, no. 2, Oxford University Press, 2019,
pp. 291–92, doi:10.1093/nsr/nwy113.
short: N.H. Barton, National Science Review 6 (2019) 291–292.
date_created: 2019-09-07T14:43:02Z
date_published: 2019-03-01T00:00:00Z
date_updated: 2023-08-29T07:51:09Z
day: '01'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1093/nsr/nwy113
external_id:
isi:
- '000467957400025'
file:
- access_level: open_access
checksum: 571d60fa21a568607d1fd04e119da88c
content_type: application/pdf
creator: dernst
date_created: 2020-10-02T09:16:44Z
date_updated: 2020-10-02T09:16:44Z
file_id: '8595'
file_name: 2019_NSR_Barton.pdf
file_size: 106463
relation: main_file
success: 1
file_date_updated: 2020-10-02T09:16:44Z
has_accepted_license: '1'
intvolume: ' 6'
isi: 1
issue: '2'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
page: 291-292
publication: National Science Review
publication_identifier:
eissn:
- 2053-714X
issn:
- 2095-5138
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Is speciation driven by cycles of mixing and isolation?
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 6
year: '2019'
...
---
_id: '6857'
abstract:
- lang: eng
text: "Gene Drives are regarded as future tools with a high potential for population
control. Due to their inherent ability to overcome the rules of Mendelian inheritance,
gene drives (GD) may spread genes rapidly through populations of sexually reproducing
organisms. A release of organisms carrying a GD would constitute a paradigm shift
in the handling of genetically modified organisms because gene drive organisms
(GDO) are designed to drive their transgenes into wild populations and thereby
increase the number of GDOs. The rapid development in this field and its focus
on wild populations demand a prospective risk assessment with a focus on exposure
related aspects. Presently, it is unclear how adequate risk management could be
guaranteed to limit the spread of GDs in time and space, in order to avoid potential
adverse effects in socio‐ecological systems.\r\n\r\nThe recent workshop on the
“Evaluation of Spatial and Temporal Control of Gene Drives” hosted by the Institute
of Safety/Security and Risk Sciences (ISR) in Vienna aimed at gaining some insight
into the potential population dynamic behavior of GDs and appropriate measures
of control. Scientists from France, Germany, England, and the USA discussed both
topics in this meeting on April 4–5, 2019. This article summarizes results of
the workshop."
article_number: '1900151'
article_processing_charge: No
article_type: original
author:
- first_name: B
full_name: Giese, B
last_name: Giese
- first_name: J L
full_name: Friess, J L
last_name: Friess
- first_name: 'M F '
full_name: 'Schetelig, M F '
last_name: Schetelig
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Philip
full_name: Messer, Philip
last_name: Messer
- first_name: Florence
full_name: Debarre, Florence
last_name: Debarre
- first_name: H
full_name: Meimberg, H
last_name: Meimberg
- first_name: N
full_name: Windbichler, N
last_name: Windbichler
- first_name: C
full_name: Boete, C
last_name: Boete
citation:
ama: 'Giese B, Friess JL, Schetelig MF, et al. Gene Drives: Dynamics and regulatory
matters – A report from the workshop “Evaluation of spatial and temporal control
of Gene Drives”, 4 – 5 April 2019, Vienna. BioEssays. 2019;41(11). doi:10.1002/bies.201900151'
apa: 'Giese, B., Friess, J. L., Schetelig, M. F., Barton, N. H., Messer, P., Debarre,
F., … Boete, C. (2019). Gene Drives: Dynamics and regulatory matters – A report
from the workshop “Evaluation of spatial and temporal control of Gene Drives”,
4 – 5 April 2019, Vienna. BioEssays. Wiley. https://doi.org/10.1002/bies.201900151'
chicago: 'Giese, B, J L Friess, M F Schetelig, Nicholas H Barton, Philip Messer,
Florence Debarre, H Meimberg, N Windbichler, and C Boete. “Gene Drives: Dynamics
and Regulatory Matters – A Report from the Workshop ‘Evaluation of Spatial and
Temporal Control of Gene Drives’, 4 – 5 April 2019, Vienna.” BioEssays.
Wiley, 2019. https://doi.org/10.1002/bies.201900151.'
ieee: 'B. Giese et al., “Gene Drives: Dynamics and regulatory matters – A
report from the workshop ‘Evaluation of spatial and temporal control of Gene Drives’,
4 – 5 April 2019, Vienna,” BioEssays, vol. 41, no. 11. Wiley, 2019.'
ista: 'Giese B, Friess JL, Schetelig MF, Barton NH, Messer P, Debarre F, Meimberg
H, Windbichler N, Boete C. 2019. Gene Drives: Dynamics and regulatory matters
– A report from the workshop “Evaluation of spatial and temporal control of Gene
Drives”, 4 – 5 April 2019, Vienna. BioEssays. 41(11), 1900151.'
mla: 'Giese, B., et al. “Gene Drives: Dynamics and Regulatory Matters – A Report
from the Workshop ‘Evaluation of Spatial and Temporal Control of Gene Drives’,
4 – 5 April 2019, Vienna.” BioEssays, vol. 41, no. 11, 1900151, Wiley,
2019, doi:10.1002/bies.201900151.'
short: B. Giese, J.L. Friess, M.F. Schetelig, N.H. Barton, P. Messer, F. Debarre,
H. Meimberg, N. Windbichler, C. Boete, BioEssays 41 (2019).
date_created: 2019-09-07T14:40:03Z
date_published: 2019-11-01T00:00:00Z
date_updated: 2023-08-30T06:56:26Z
day: '01'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1002/bies.201900151
external_id:
isi:
- '000489502000001'
file:
- access_level: open_access
checksum: 8cc7551bff70b2658f8d5630f228ee12
content_type: application/pdf
creator: dernst
date_created: 2019-10-11T06:59:26Z
date_updated: 2020-07-14T12:47:42Z
file_id: '6939'
file_name: 2019_BioEssays_Giese.pdf
file_size: 193248
relation: main_file
file_date_updated: 2020-07-14T12:47:42Z
has_accepted_license: '1'
intvolume: ' 41'
isi: 1
issue: '11'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
publication: BioEssays
publication_identifier:
eissn:
- 1521-1878
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Gene Drives: Dynamics and regulatory matters – A report from the workshop
“Evaluation of spatial and temporal control of Gene Drives”, 4 – 5 April 2019, Vienna'
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 41
year: '2019'
...
---
_id: '13067'
abstract:
- lang: eng
text: Genetic incompatibilities contribute to reproductive isolation between many
diverging populations, but it is still unclear to what extent they play a role
if divergence happens with gene flow. In contact zones between the "Crab" and
"Wave" ecotypes of the snail Littorina saxatilis divergent selection forms strong
barriers to gene flow, while the role of postzygotic barriers due to selection
against hybrids remains unclear. High embryo abortion rates in this species could
indicate the presence of such barriers. Postzygotic barriers might include genetic
incompatibilities (e.g. Dobzhansky-Muller incompatibilities) but also maladaptation,
both expected to be most pronounced in contact zones. In addition, embryo abortion
might reflect physiological stress on females and embryos independent of any genetic
stress. We examined all embryos of >500 females sampled outside and inside
contact zones of three populations in Sweden. Females' clutch size ranged from
0 to 1011 embryos (mean 130±123) and abortion rates varied between 0 and100% (mean
12%). We described female genotypes by using a hybrid index based on hundreds
of SNPs differentiated between ecotypes with which we characterised female genotypes.
We also calculated female SNP heterozygosity and inversion karyotype. Clutch size
did not vary with female hybrid index and abortion rates were only weakly related
to hybrid index in two sites but not at all in a third site. No additional variation
in abortion rate was explained by female SNP heterozygosity, but increased female
inversion heterozygosity added slightly to increased abortion. Our results show
only weak and probably biologically insignificant postzygotic barriers contributing
to ecotype divergence and the high and variable abortion rates were marginally,
if at all, explained by hybrid index of females.
article_processing_charge: No
author:
- first_name: Kerstin
full_name: Johannesson, Kerstin
last_name: Johannesson
- first_name: Zuzanna
full_name: Zagrodzka, Zuzanna
last_name: Zagrodzka
- first_name: Rui
full_name: Faria, Rui
last_name: Faria
- first_name: Anja M
full_name: Westram, Anja M
id: 3C147470-F248-11E8-B48F-1D18A9856A87
last_name: Westram
orcid: 0000-0003-1050-4969
- first_name: Roger
full_name: Butlin, Roger
last_name: Butlin
citation:
ama: 'Johannesson K, Zagrodzka Z, Faria R, Westram AM, Butlin R. Data from: Is embryo
abortion a postzygotic barrier to gene flow between Littorina ecotypes? 2019.
doi:10.5061/DRYAD.TB2RBNZWK'
apa: 'Johannesson, K., Zagrodzka, Z., Faria, R., Westram, A. M., & Butlin, R.
(2019). Data from: Is embryo abortion a postzygotic barrier to gene flow between
Littorina ecotypes? Dryad. https://doi.org/10.5061/DRYAD.TB2RBNZWK'
chicago: 'Johannesson, Kerstin, Zuzanna Zagrodzka, Rui Faria, Anja M Westram, and
Roger Butlin. “Data from: Is Embryo Abortion a Postzygotic Barrier to Gene Flow
between Littorina Ecotypes?” Dryad, 2019. https://doi.org/10.5061/DRYAD.TB2RBNZWK.'
ieee: 'K. Johannesson, Z. Zagrodzka, R. Faria, A. M. Westram, and R. Butlin, “Data
from: Is embryo abortion a postzygotic barrier to gene flow between Littorina
ecotypes?” Dryad, 2019.'
ista: 'Johannesson K, Zagrodzka Z, Faria R, Westram AM, Butlin R. 2019. Data from:
Is embryo abortion a postzygotic barrier to gene flow between Littorina ecotypes?,
Dryad, 10.5061/DRYAD.TB2RBNZWK.'
mla: 'Johannesson, Kerstin, et al. Data from: Is Embryo Abortion a Postzygotic
Barrier to Gene Flow between Littorina Ecotypes? Dryad, 2019, doi:10.5061/DRYAD.TB2RBNZWK.'
short: K. Johannesson, Z. Zagrodzka, R. Faria, A.M. Westram, R. Butlin, (2019).
date_created: 2023-05-23T16:36:27Z
date_published: 2019-12-02T00:00:00Z
date_updated: 2023-09-06T14:48:57Z
day: '02'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.5061/DRYAD.TB2RBNZWK
license: https://creativecommons.org/publicdomain/zero/1.0/
main_file_link:
- open_access: '1'
url: https://doi.org/10.5061/dryad.tb2rbnzwk
month: '12'
oa: 1
oa_version: Published Version
publisher: Dryad
related_material:
record:
- id: '7205'
relation: used_in_publication
status: public
status: public
title: 'Data from: Is embryo abortion a postzygotic barrier to gene flow between Littorina
ecotypes?'
tmp:
image: /images/cc_0.png
legal_code_url: https://creativecommons.org/publicdomain/zero/1.0/legalcode
name: Creative Commons Public Domain Dedication (CC0 1.0)
short: CC0 (1.0)
type: research_data_reference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2019'
...
---
_id: '7393'
abstract:
- lang: eng
text: The study of parallel ecological divergence provides important clues to the
operation of natural selection. Parallel divergence often occurs in heterogeneous
environments with different kinds of environmental gradients in different locations,
but the genomic basis underlying this process is unknown. We investigated the
genomics of rapid parallel adaptation in the marine snail Littorina saxatilis
in response to two independent environmental axes (crab-predation versus wave-action
and low-shore versus high-shore). Using pooled whole-genome resequencing, we show
that sharing of genomic regions of high differentiation between environments is
generally low but increases at smaller spatial scales. We identify different shared
genomic regions of divergence for each environmental axis and show that most of
these regions overlap with candidate chromosomal inversions. Several inversion
regions are divergent and polymorphic across many localities. We argue that chromosomal
inversions could store shared variation that fuels rapid parallel adaptation to
heterogeneous environments, possibly as balanced polymorphism shared by adaptive
gene flow.
article_number: eaav9963
article_processing_charge: No
article_type: original
author:
- first_name: Hernán E.
full_name: Morales, Hernán E.
last_name: Morales
- first_name: Rui
full_name: Faria, Rui
last_name: Faria
- first_name: Kerstin
full_name: Johannesson, Kerstin
last_name: Johannesson
- first_name: Tomas
full_name: Larsson, Tomas
last_name: Larsson
- first_name: Marina
full_name: Panova, Marina
last_name: Panova
- first_name: Anja M
full_name: Westram, Anja M
id: 3C147470-F248-11E8-B48F-1D18A9856A87
last_name: Westram
orcid: 0000-0003-1050-4969
- first_name: Roger K.
full_name: Butlin, Roger K.
last_name: Butlin
citation:
ama: 'Morales HE, Faria R, Johannesson K, et al. Genomic architecture of parallel
ecological divergence: Beyond a single environmental contrast. Science Advances.
2019;5(12). doi:10.1126/sciadv.aav9963'
apa: 'Morales, H. E., Faria, R., Johannesson, K., Larsson, T., Panova, M., Westram,
A. M., & Butlin, R. K. (2019). Genomic architecture of parallel ecological
divergence: Beyond a single environmental contrast. Science Advances. AAAS.
https://doi.org/10.1126/sciadv.aav9963'
chicago: 'Morales, Hernán E., Rui Faria, Kerstin Johannesson, Tomas Larsson, Marina
Panova, Anja M Westram, and Roger K. Butlin. “Genomic Architecture of Parallel
Ecological Divergence: Beyond a Single Environmental Contrast.” Science Advances.
AAAS, 2019. https://doi.org/10.1126/sciadv.aav9963.'
ieee: 'H. E. Morales et al., “Genomic architecture of parallel ecological
divergence: Beyond a single environmental contrast,” Science Advances,
vol. 5, no. 12. AAAS, 2019.'
ista: 'Morales HE, Faria R, Johannesson K, Larsson T, Panova M, Westram AM, Butlin
RK. 2019. Genomic architecture of parallel ecological divergence: Beyond a single
environmental contrast. Science Advances. 5(12), eaav9963.'
mla: 'Morales, Hernán E., et al. “Genomic Architecture of Parallel Ecological Divergence:
Beyond a Single Environmental Contrast.” Science Advances, vol. 5, no.
12, eaav9963, AAAS, 2019, doi:10.1126/sciadv.aav9963.'
short: H.E. Morales, R. Faria, K. Johannesson, T. Larsson, M. Panova, A.M. Westram,
R.K. Butlin, Science Advances 5 (2019).
date_created: 2020-01-29T15:58:27Z
date_published: 2019-12-04T00:00:00Z
date_updated: 2023-09-06T15:35:56Z
day: '04'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1126/sciadv.aav9963
ec_funded: 1
external_id:
isi:
- '000505069600008'
pmid:
- '31840052'
file:
- access_level: open_access
checksum: af99a5dcdc66c6d6102051faf3be48d8
content_type: application/pdf
creator: dernst
date_created: 2020-02-03T13:33:25Z
date_updated: 2020-07-14T12:47:57Z
file_id: '7442'
file_name: 2019_ScienceAdvances_Morales.pdf
file_size: 1869449
relation: main_file
file_date_updated: 2020-07-14T12:47:57Z
has_accepted_license: '1'
intvolume: ' 5'
isi: 1
issue: '12'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc/4.0/
month: '12'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
- _id: 265B41B8-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '797747'
name: Theoretical and empirical approaches to understanding Parallel Adaptation
publication: Science Advances
publication_identifier:
issn:
- 2375-2548
publication_status: published
publisher: AAAS
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Genomic architecture of parallel ecological divergence: Beyond a single environmental
contrast'
tmp:
image: /images/cc_by_nc.png
legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode
name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
short: CC BY-NC (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 5
year: '2019'
...
---
_id: '8281'
abstract:
- lang: eng
text: We review the history of population genetics, starting with its origins a
century ago from the synthesis between Mendel and Darwin's ideas, through to the
recent development of sophisticated schemes of inference from sequence data, based
on the coalescent. We explain the close relation between the coalescent and a
diffusion process, which we illustrate by their application to understand spatial
structure. We summarise the powerful methods available for analysis of multiple
loci, when linkage equilibrium can be assumed, and then discuss approaches to
the more challenging case, where associations between alleles require that we
follow genotype, rather than allele, frequencies. Though we can hardly cover the
whole of population genetics, we give an overview of the current state of the
subject, and future challenges to it.
article_processing_charge: No
author:
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Alison
full_name: Etheridge, Alison
last_name: Etheridge
citation:
ama: 'Barton NH, Etheridge A. Mathematical models in population genetics. In: Balding
D, Moltke I, Marioni J, eds. Handbook of Statistical Genomics. 4th ed.
Wiley; 2019:115-144. doi:10.1002/9781119487845.ch4'
apa: Barton, N. H., & Etheridge, A. (2019). Mathematical models in population
genetics. In D. Balding, I. Moltke, & J. Marioni (Eds.), Handbook of statistical
genomics (4th ed., pp. 115–144). Wiley. https://doi.org/10.1002/9781119487845.ch4
chicago: Barton, Nicholas H, and Alison Etheridge. “Mathematical Models in Population
Genetics.” In Handbook of Statistical Genomics, edited by David Balding,
Ida Moltke, and John Marioni, 4th ed., 115–44. Wiley, 2019. https://doi.org/10.1002/9781119487845.ch4.
ieee: N. H. Barton and A. Etheridge, “Mathematical models in population genetics,”
in Handbook of statistical genomics, 4th ed., D. Balding, I. Moltke, and
J. Marioni, Eds. Wiley, 2019, pp. 115–144.
ista: 'Barton NH, Etheridge A. 2019.Mathematical models in population genetics.
In: Handbook of statistical genomics. , 115–144.'
mla: Barton, Nicholas H., and Alison Etheridge. “Mathematical Models in Population
Genetics.” Handbook of Statistical Genomics, edited by David Balding et
al., 4th ed., Wiley, 2019, pp. 115–44, doi:10.1002/9781119487845.ch4.
short: N.H. Barton, A. Etheridge, in:, D. Balding, I. Moltke, J. Marioni (Eds.),
Handbook of Statistical Genomics, 4th ed., Wiley, 2019, pp. 115–144.
date_created: 2020-08-21T04:25:39Z
date_published: 2019-07-29T00:00:00Z
date_updated: 2023-09-08T11:24:15Z
day: '29'
ddc:
- '576'
department:
- _id: NiBa
doi: 10.1002/9781119487845.ch4
edition: '4'
editor:
- first_name: David
full_name: Balding, David
last_name: Balding
- first_name: Ida
full_name: Moltke, Ida
last_name: Moltke
- first_name: John
full_name: Marioni, John
last_name: Marioni
external_id:
isi:
- '000261343000003'
isi: 1
language:
- iso: eng
month: '07'
oa_version: None
page: 115-144
publication: Handbook of statistical genomics
publication_identifier:
isbn:
- '9781119429142'
publication_status: published
publisher: Wiley
quality_controlled: '1'
status: public
title: Mathematical models in population genetics
type: book_chapter
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2019'
...
---
_id: '9805'
abstract:
- lang: eng
text: The spread of adaptive alleles is fundamental to evolution, and in theory,
this process is well‐understood. However, only rarely can we follow this process—whether
it originates from the spread of a new mutation, or by introgression from another
population. In this issue of Molecular Ecology, Hanemaaijer et al. (2018) report
on a 25‐year long study of the mosquitoes Anopheles gambiae (Figure 1) and Anopheles
coluzzi in Mali, based on genotypes at 15 single‐nucleotide polymorphism (SNP).
The species are usually reproductively isolated from each other, but in 2002 and
2006, bursts of hybridization were observed, when F1 hybrids became abundant.
Alleles backcrossed from A. gambiae into A. coluzzi, but after the first event,
these declined over the following years. In contrast, after 2006, an insecticide
resistance allele that had established in A. gambiae spread into A. coluzzi, and
rose to high frequency there, over 6 years (~75 generations). Whole genome sequences
of 74 individuals showed that A. gambiae SNP from across the genome had become
common in the A. coluzzi population, but that most of these were clustered in
34 genes around the resistance locus. A new set of SNP from 25 of these genes
were assayed over time; over the 4 years since near‐fixation of the resistance
allele; some remained common, whereas others declined. What do these patterns
tell us about this introgression event?
article_processing_charge: No
author:
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: 'Barton NH. Data from: The consequences of an introgression event. 2019. doi:10.5061/dryad.2kb6fh4'
apa: 'Barton, N. H. (2019). Data from: The consequences of an introgression event.
Dryad. https://doi.org/10.5061/dryad.2kb6fh4'
chicago: 'Barton, Nicholas H. “Data from: The Consequences of an Introgression Event.”
Dryad, 2019. https://doi.org/10.5061/dryad.2kb6fh4.'
ieee: 'N. H. Barton, “Data from: The consequences of an introgression event.” Dryad,
2019.'
ista: 'Barton NH. 2019. Data from: The consequences of an introgression event, Dryad,
10.5061/dryad.2kb6fh4.'
mla: 'Barton, Nicholas H. Data from: The Consequences of an Introgression Event.
Dryad, 2019, doi:10.5061/dryad.2kb6fh4.'
short: N.H. Barton, (2019).
date_created: 2021-08-06T12:03:50Z
date_published: 2019-01-09T00:00:00Z
date_updated: 2023-09-19T10:06:07Z
day: '09'
department:
- _id: NiBa
doi: 10.5061/dryad.2kb6fh4
main_file_link:
- open_access: '1'
url: https://doi.org/10.5061/dryad.2kb6fh4
month: '01'
oa: 1
oa_version: Published Version
publisher: Dryad
related_material:
record:
- id: '40'
relation: used_in_publication
status: public
status: public
title: 'Data from: The consequences of an introgression event'
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2019'
...
---
_id: '6071'
abstract:
- lang: eng
text: 'Transcription factors, by binding to specific sequences on the DNA, control
the precise spatio-temporal expression of genes inside a cell. However, this specificity
is limited, leading to frequent incorrect binding of transcription factors that
might have deleterious consequences on the cell. By constructing a biophysical
model of TF-DNA binding in the context of gene regulation, I will first explore
how regulatory constraints can strongly shape the distribution of a population
in sequence space. Then, by directly linking this to a picture of multiple types
of transcription factors performing their functions simultaneously inside the
cell, I will explore the extent of regulatory crosstalk -- incorrect binding interactions
between transcription factors and binding sites that lead to erroneous regulatory
states -- and understand the constraints this places on the design of regulatory
systems. I will then develop a generic theoretical framework to investigate the
coevolution of multiple transcription factors and multiple binding sites, in the
context of a gene regulatory network that performs a certain function. As a particular
tractable version of this problem, I will consider the evolution of two transcription
factors when they transmit upstream signals to downstream target genes. Specifically,
I will describe the evolutionary steady states and the evolutionary pathways involved,
along with their timescales, of a system that initially undergoes a transcription
factor duplication event. To connect this important theoretical model to the prominent
biological event of transcription factor duplication giving rise to paralogous
families, I will then describe a bioinformatics analysis of C2H2 Zn-finger transcription
factors, a major family in humans, and focus on the patterns of evolution that
paralogs have undergone in their various protein domains in the recent past. '
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Roshan
full_name: Prizak, Roshan
id: 4456104E-F248-11E8-B48F-1D18A9856A87
last_name: Prizak
citation:
ama: Prizak R. Coevolution of transcription factors and their binding sites in sequence
space. 2019. doi:10.15479/at:ista:th6071
apa: Prizak, R. (2019). Coevolution of transcription factors and their binding
sites in sequence space. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:th6071
chicago: Prizak, Roshan. “Coevolution of Transcription Factors and Their Binding
Sites in Sequence Space.” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/at:ista:th6071.
ieee: R. Prizak, “Coevolution of transcription factors and their binding sites in
sequence space,” Institute of Science and Technology Austria, 2019.
ista: Prizak R. 2019. Coevolution of transcription factors and their binding sites
in sequence space. Institute of Science and Technology Austria.
mla: Prizak, Roshan. Coevolution of Transcription Factors and Their Binding Sites
in Sequence Space. Institute of Science and Technology Austria, 2019, doi:10.15479/at:ista:th6071.
short: R. Prizak, Coevolution of Transcription Factors and Their Binding Sites in
Sequence Space, Institute of Science and Technology Austria, 2019.
date_created: 2019-03-06T16:16:10Z
date_published: 2019-03-11T00:00:00Z
date_updated: 2023-09-22T10:00:48Z
day: '11'
ddc:
- '576'
degree_awarded: PhD
department:
- _id: GaTk
- _id: NiBa
doi: 10.15479/at:ista:th6071
file:
- access_level: open_access
checksum: e60a72de35d270b31f1a23d50f224ec0
content_type: application/pdf
creator: rprizak
date_created: 2019-03-06T16:05:07Z
date_updated: 2020-07-14T12:47:18Z
file_id: '6072'
file_name: Thesis_final_PDFA_RoshanPrizak.pdf
file_size: 20995465
relation: main_file
- access_level: closed
checksum: 67c2630333d05ebafef5f018863a8465
content_type: application/zip
creator: rprizak
date_created: 2019-03-06T16:09:39Z
date_updated: 2020-07-14T12:47:18Z
file_id: '6073'
file_name: thesis_v2_merge.zip
file_size: 85705272
relation: source_file
title: Latex files
file_date_updated: 2020-07-14T12:47:18Z
has_accepted_license: '1'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
page: '189'
project:
- _id: 254E9036-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P28844-B27
name: Biophysics of information processing in gene regulation
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '1358'
relation: part_of_dissertation
status: public
- id: '955'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Gašper
full_name: Tkačik, Gašper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkačik
orcid: 0000-0002-6699-1455
title: Coevolution of transcription factors and their binding sites in sequence space
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2019'
...
---
_id: '6856'
abstract:
- lang: eng
text: 'Plant mating systems play a key role in structuring genetic variation both
within and between species. In hybrid zones, the outcomes and dynamics of hybridization
are usually interpreted as the balance between gene flow and selection against
hybrids. Yet, mating systems can introduce selective forces that alter these expectations;
with diverse outcomes for the level and direction of gene flow depending on variation
in outcrossing and whether the mating systems of the species pair are the same
or divergent. We present a survey of hybridization in 133 species pairs from 41
plant families and examine how patterns of hybridization vary with mating system.
We examine if hybrid zone mode, level of gene flow, asymmetries in gene flow and
the frequency of reproductive isolating barriers vary in relation to mating system/s
of the species pair. We combine these results with a simulation model and examples
from the literature to address two general themes: (i) the two‐way interaction
between introgression and the evolution of reproductive systems, and (ii) how
mating system can facilitate or restrict interspecific gene flow. We conclude
that examining mating system with hybridization provides unique opportunities
to understand divergence and the processes underlying reproductive isolation.'
article_processing_charge: No
article_type: original
author:
- first_name: Melinda
full_name: Pickup, Melinda
id: 2C78037E-F248-11E8-B48F-1D18A9856A87
last_name: Pickup
orcid: 0000-0001-6118-0541
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Yaniv
full_name: Brandvain, Yaniv
last_name: Brandvain
- first_name: Christelle
full_name: Fraisse, Christelle
id: 32DF5794-F248-11E8-B48F-1D18A9856A87
last_name: Fraisse
orcid: 0000-0001-8441-5075
- first_name: Sarah
full_name: Yakimowski, Sarah
last_name: Yakimowski
- first_name: Tanmay
full_name: Dixit, Tanmay
last_name: Dixit
- first_name: Christian
full_name: Lexer, Christian
last_name: Lexer
- first_name: Eva
full_name: Cereghetti, Eva
id: 71AA91B4-05ED-11EA-8BEB-F5833E63BD63
last_name: Cereghetti
- first_name: David
full_name: Field, David
id: 419049E2-F248-11E8-B48F-1D18A9856A87
last_name: Field
orcid: 0000-0002-4014-8478
citation:
ama: 'Pickup M, Barton NH, Brandvain Y, et al. Mating system variation in hybrid
zones: Facilitation, barriers and asymmetries to gene flow. New Phytologist.
2019;224(3):1035-1047. doi:10.1111/nph.16180'
apa: 'Pickup, M., Barton, N. H., Brandvain, Y., Fraisse, C., Yakimowski, S., Dixit,
T., … Field, D. (2019). Mating system variation in hybrid zones: Facilitation,
barriers and asymmetries to gene flow. New Phytologist. Wiley. https://doi.org/10.1111/nph.16180'
chicago: 'Pickup, Melinda, Nicholas H Barton, Yaniv Brandvain, Christelle Fraisse,
Sarah Yakimowski, Tanmay Dixit, Christian Lexer, Eva Cereghetti, and David Field.
“Mating System Variation in Hybrid Zones: Facilitation, Barriers and Asymmetries
to Gene Flow.” New Phytologist. Wiley, 2019. https://doi.org/10.1111/nph.16180.'
ieee: 'M. Pickup et al., “Mating system variation in hybrid zones: Facilitation,
barriers and asymmetries to gene flow,” New Phytologist, vol. 224, no.
3. Wiley, pp. 1035–1047, 2019.'
ista: 'Pickup M, Barton NH, Brandvain Y, Fraisse C, Yakimowski S, Dixit T, Lexer
C, Cereghetti E, Field D. 2019. Mating system variation in hybrid zones: Facilitation,
barriers and asymmetries to gene flow. New Phytologist. 224(3), 1035–1047.'
mla: 'Pickup, Melinda, et al. “Mating System Variation in Hybrid Zones: Facilitation,
Barriers and Asymmetries to Gene Flow.” New Phytologist, vol. 224, no.
3, Wiley, 2019, pp. 1035–47, doi:10.1111/nph.16180.'
short: M. Pickup, N.H. Barton, Y. Brandvain, C. Fraisse, S. Yakimowski, T. Dixit,
C. Lexer, E. Cereghetti, D. Field, New Phytologist 224 (2019) 1035–1047.
date_created: 2019-09-07T14:35:40Z
date_published: 2019-11-01T00:00:00Z
date_updated: 2023-10-18T08:47:08Z
day: '01'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1111/nph.16180
ec_funded: 1
external_id:
pmid:
- '31505037'
file:
- access_level: open_access
checksum: 21e4c95599bbcaf7c483b89954658672
content_type: application/pdf
creator: dernst
date_created: 2019-11-13T08:15:05Z
date_updated: 2020-07-14T12:47:42Z
file_id: '7011'
file_name: 2019_NewPhytologist_Pickup.pdf
file_size: 1511958
relation: main_file
file_date_updated: 2020-07-14T12:47:42Z
has_accepted_license: '1'
intvolume: ' 224'
issue: '3'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
page: 1035-1047
pmid: 1
project:
- _id: 25B36484-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '329960'
name: Mating system and the evolutionary dynamics of hybrid zones
- _id: 2662AADE-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: M02463
name: Sex chromosomes and species barriers
publication: New Phytologist
publication_identifier:
eissn:
- 1469-8137
issn:
- 0028-646X
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Mating system variation in hybrid zones: Facilitation, barriers and asymmetries
to gene flow'
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 224
year: '2019'
...
---
_id: '6089'
abstract:
- lang: eng
text: Pleiotropy is the well-established idea that a single mutation affects multiple
phenotypes. If a mutation has opposite effects on fitness when expressed in different
contexts, then genetic conflict arises. Pleiotropic conflict is expected to reduce
the efficacy of selection by limiting the fixation of beneficial mutations through
adaptation, and the removal of deleterious mutations through purifying selection.
Although this has been widely discussed, in particular in the context of a putative
“gender load,” it has yet to be systematically quantified. In this work, we empirically
estimate to which extent different pleiotropic regimes impede the efficacy of
selection in Drosophila melanogaster. We use whole-genome polymorphism data from
a single African population and divergence data from D. simulans to estimate the
fraction of adaptive fixations (α), the rate of adaptation (ωA), and the direction
of selection (DoS). After controlling for confounding covariates, we find that
the different pleiotropic regimes have a relatively small, but significant, effect
on selection efficacy. Specifically, our results suggest that pleiotropic sexual
antagonism may restrict the efficacy of selection, but that this conflict can
be resolved by limiting the expression of genes to the sex where they are beneficial.
Intermediate levels of pleiotropy across tissues and life stages can also lead
to maladaptation in D. melanogaster, due to inefficient purifying selection combined
with low frequency of mutations that confer a selective advantage. Thus, our study
highlights the need to consider the efficacy of selection in the context of antagonistic
pleiotropy, and of genetic conflict in general.
article_processing_charge: No
author:
- first_name: Christelle
full_name: Fraisse, Christelle
id: 32DF5794-F248-11E8-B48F-1D18A9856A87
last_name: Fraisse
orcid: 0000-0001-8441-5075
- first_name: Gemma
full_name: Puixeu Sala, Gemma
id: 33AB266C-F248-11E8-B48F-1D18A9856A87
last_name: Puixeu Sala
orcid: 0000-0001-8330-1754
- first_name: Beatriz
full_name: Vicoso, Beatriz
id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
last_name: Vicoso
orcid: 0000-0002-4579-8306
citation:
ama: Fraisse C, Puixeu Sala G, Vicoso B. Pleiotropy modulates the efficacy of selection
in drosophila melanogaster. Molecular biology and evolution. 2019;36(3):500-515.
doi:10.1093/molbev/msy246
apa: Fraisse, C., Puixeu Sala, G., & Vicoso, B. (2019). Pleiotropy modulates
the efficacy of selection in drosophila melanogaster. Molecular Biology and
Evolution. Oxford University Press. https://doi.org/10.1093/molbev/msy246
chicago: Fraisse, Christelle, Gemma Puixeu Sala, and Beatriz Vicoso. “Pleiotropy
Modulates the Efficacy of Selection in Drosophila Melanogaster.” Molecular
Biology and Evolution. Oxford University Press, 2019. https://doi.org/10.1093/molbev/msy246.
ieee: C. Fraisse, G. Puixeu Sala, and B. Vicoso, “Pleiotropy modulates the efficacy
of selection in drosophila melanogaster,” Molecular biology and evolution,
vol. 36, no. 3. Oxford University Press, pp. 500–515, 2019.
ista: Fraisse C, Puixeu Sala G, Vicoso B. 2019. Pleiotropy modulates the efficacy
of selection in drosophila melanogaster. Molecular biology and evolution. 36(3),
500–515.
mla: Fraisse, Christelle, et al. “Pleiotropy Modulates the Efficacy of Selection
in Drosophila Melanogaster.” Molecular Biology and Evolution, vol. 36,
no. 3, Oxford University Press, 2019, pp. 500–15, doi:10.1093/molbev/msy246.
short: C. Fraisse, G. Puixeu Sala, B. Vicoso, Molecular Biology and Evolution 36
(2019) 500–515.
date_created: 2019-03-10T22:59:19Z
date_published: 2019-03-01T00:00:00Z
date_updated: 2024-02-21T13:59:17Z
day: '01'
department:
- _id: BeVi
- _id: NiBa
doi: 10.1093/molbev/msy246
external_id:
isi:
- '000462585100006'
pmid:
- '30590559'
intvolume: ' 36'
isi: 1
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pubmed/30590559
month: '03'
oa: 1
oa_version: Submitted Version
page: 500-515
pmid: 1
project:
- _id: 250ED89C-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P28842-B22
name: Sex chromosome evolution under male- and female- heterogamety
publication: Molecular biology and evolution
publication_identifier:
eissn:
- 1537-1719
issn:
- 0737-4038
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
related_material:
record:
- id: '5757'
relation: popular_science
status: public
scopus_import: '1'
status: public
title: Pleiotropy modulates the efficacy of selection in drosophila melanogaster
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 36
year: '2019'
...
---
_id: '6090'
abstract:
- lang: eng
text: Cells need to reliably sense external ligand concentrations to achieve various
biological functions such as chemotaxis or signaling. The molecular recognition
of ligands by surface receptors is degenerate in many systems, leading to crosstalk
between ligand-receptor pairs. Crosstalk is often thought of as a deviation from
optimal specific recognition, as the binding of noncognate ligands can interfere
with the detection of the receptor's cognate ligand, possibly leading to a false
triggering of a downstream signaling pathway. Here we quantify the optimal precision
of sensing the concentrations of multiple ligands by a collection of promiscuous
receptors. We demonstrate that crosstalk can improve precision in concentration
sensing and discrimination tasks. To achieve superior precision, the additional
information about ligand concentrations contained in short binding events of the
noncognate ligand should be exploited. We present a proofreading scheme to realize
an approximate estimation of multiple ligand concentrations that reaches a precision
close to the derived optimal bounds. Our results help rationalize the observed
ubiquity of receptor crosstalk in molecular sensing.
article_number: '022423'
article_processing_charge: No
author:
- first_name: Martín
full_name: Carballo-Pacheco, Martín
last_name: Carballo-Pacheco
- first_name: Jonathan
full_name: Desponds, Jonathan
last_name: Desponds
- first_name: Tatyana
full_name: Gavrilchenko, Tatyana
last_name: Gavrilchenko
- first_name: Andreas
full_name: Mayer, Andreas
last_name: Mayer
- first_name: Roshan
full_name: Prizak, Roshan
id: 4456104E-F248-11E8-B48F-1D18A9856A87
last_name: Prizak
- first_name: Gautam
full_name: Reddy, Gautam
last_name: Reddy
- first_name: Ilya
full_name: Nemenman, Ilya
last_name: Nemenman
- first_name: Thierry
full_name: Mora, Thierry
last_name: Mora
citation:
ama: Carballo-Pacheco M, Desponds J, Gavrilchenko T, et al. Receptor crosstalk improves
concentration sensing of multiple ligands. Physical Review E. 2019;99(2).
doi:10.1103/PhysRevE.99.022423
apa: Carballo-Pacheco, M., Desponds, J., Gavrilchenko, T., Mayer, A., Prizak, R.,
Reddy, G., … Mora, T. (2019). Receptor crosstalk improves concentration sensing
of multiple ligands. Physical Review E. American Physical Society. https://doi.org/10.1103/PhysRevE.99.022423
chicago: Carballo-Pacheco, Martín, Jonathan Desponds, Tatyana Gavrilchenko, Andreas
Mayer, Roshan Prizak, Gautam Reddy, Ilya Nemenman, and Thierry Mora. “Receptor
Crosstalk Improves Concentration Sensing of Multiple Ligands.” Physical Review
E. American Physical Society, 2019. https://doi.org/10.1103/PhysRevE.99.022423.
ieee: M. Carballo-Pacheco et al., “Receptor crosstalk improves concentration
sensing of multiple ligands,” Physical Review E, vol. 99, no. 2. American
Physical Society, 2019.
ista: Carballo-Pacheco M, Desponds J, Gavrilchenko T, Mayer A, Prizak R, Reddy G,
Nemenman I, Mora T. 2019. Receptor crosstalk improves concentration sensing of
multiple ligands. Physical Review E. 99(2), 022423.
mla: Carballo-Pacheco, Martín, et al. “Receptor Crosstalk Improves Concentration
Sensing of Multiple Ligands.” Physical Review E, vol. 99, no. 2, 022423,
American Physical Society, 2019, doi:10.1103/PhysRevE.99.022423.
short: M. Carballo-Pacheco, J. Desponds, T. Gavrilchenko, A. Mayer, R. Prizak, G.
Reddy, I. Nemenman, T. Mora, Physical Review E 99 (2019).
date_created: 2019-03-10T22:59:20Z
date_published: 2019-02-26T00:00:00Z
date_updated: 2024-02-28T13:12:06Z
day: '26'
department:
- _id: NiBa
- _id: GaTk
doi: 10.1103/PhysRevE.99.022423
external_id:
isi:
- '000459916500007'
intvolume: ' 99'
isi: 1
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.biorxiv.org/content/10.1101/448118v1.abstract
month: '02'
oa: 1
oa_version: Preprint
publication: Physical Review E
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Receptor crosstalk improves concentration sensing of multiple ligands
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 99
year: '2019'
...
---
_id: '6713'
abstract:
- lang: eng
text: Evolutionary studies are often limited by missing data that are critical to
understanding the history of selection. Selection experiments, which reproduce
rapid evolution under controlled conditions, are excellent tools to study how
genomes evolve under selection. Here we present a genomic dissection of the Longshanks
selection experiment, in which mice were selectively bred over 20 generations
for longer tibiae relative to body mass, resulting in 13% longer tibiae in two
replicates. We synthesized evolutionary theory, genome sequences and molecular
genetics to understand the selection response and found that it involved both
polygenic adaptation and discrete loci of major effect, with the strongest loci
tending to be selected in parallel between replicates. We show that selection
may favor de-repression of bone growth through inactivating two limb enhancers
of an inhibitor, Nkx3-2. Our integrative genomic analyses thus show that it is
possible to connect individual base-pair changes to the overall selection response.
article_number: e42014
article_processing_charge: No
author:
- first_name: João Pl
full_name: Castro, João Pl
last_name: Castro
- first_name: Michelle N.
full_name: Yancoskie, Michelle N.
last_name: Yancoskie
- first_name: Marta
full_name: Marchini, Marta
last_name: Marchini
- first_name: Stefanie
full_name: Belohlavy, Stefanie
id: 43FE426A-F248-11E8-B48F-1D18A9856A87
last_name: Belohlavy
orcid: 0000-0002-9849-498X
- first_name: Layla
full_name: Hiramatsu, Layla
last_name: Hiramatsu
- first_name: Marek
full_name: Kučka, Marek
last_name: Kučka
- first_name: William H.
full_name: Beluch, William H.
last_name: Beluch
- first_name: Ronald
full_name: Naumann, Ronald
last_name: Naumann
- first_name: Isabella
full_name: Skuplik, Isabella
last_name: Skuplik
- first_name: John
full_name: Cobb, John
last_name: Cobb
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Campbell
full_name: Rolian, Campbell
last_name: Rolian
- first_name: Yingguang Frank
full_name: Chan, Yingguang Frank
last_name: Chan
citation:
ama: Castro JP, Yancoskie MN, Marchini M, et al. An integrative genomic analysis
of the Longshanks selection experiment for longer limbs in mice. eLife.
2019;8. doi:10.7554/eLife.42014
apa: Castro, J. P., Yancoskie, M. N., Marchini, M., Belohlavy, S., Hiramatsu, L.,
Kučka, M., … Chan, Y. F. (2019). An integrative genomic analysis of the Longshanks
selection experiment for longer limbs in mice. ELife. eLife Sciences Publications.
https://doi.org/10.7554/eLife.42014
chicago: Castro, João Pl, Michelle N. Yancoskie, Marta Marchini, Stefanie Belohlavy,
Layla Hiramatsu, Marek Kučka, William H. Beluch, et al. “An Integrative Genomic
Analysis of the Longshanks Selection Experiment for Longer Limbs in Mice.” ELife.
eLife Sciences Publications, 2019. https://doi.org/10.7554/eLife.42014.
ieee: J. P. Castro et al., “An integrative genomic analysis of the Longshanks
selection experiment for longer limbs in mice,” eLife, vol. 8. eLife Sciences
Publications, 2019.
ista: Castro JP, Yancoskie MN, Marchini M, Belohlavy S, Hiramatsu L, Kučka M, Beluch
WH, Naumann R, Skuplik I, Cobb J, Barton NH, Rolian C, Chan YF. 2019. An integrative
genomic analysis of the Longshanks selection experiment for longer limbs in mice.
eLife. 8, e42014.
mla: Castro, João Pl, et al. “An Integrative Genomic Analysis of the Longshanks
Selection Experiment for Longer Limbs in Mice.” ELife, vol. 8, e42014,
eLife Sciences Publications, 2019, doi:10.7554/eLife.42014.
short: J.P. Castro, M.N. Yancoskie, M. Marchini, S. Belohlavy, L. Hiramatsu, M.
Kučka, W.H. Beluch, R. Naumann, I. Skuplik, J. Cobb, N.H. Barton, C. Rolian, Y.F.
Chan, ELife 8 (2019).
date_created: 2019-07-28T21:59:17Z
date_published: 2019-06-06T00:00:00Z
date_updated: 2024-03-28T23:30:23Z
day: '06'
ddc:
- '576'
department:
- _id: NiBa
doi: 10.7554/eLife.42014
external_id:
isi:
- '000473588700001'
pmid:
- '31169497'
file:
- access_level: open_access
checksum: fa0936fe58f0d9e3f8e75038570e5a17
content_type: application/pdf
creator: apreinsp
date_created: 2019-07-29T07:41:18Z
date_updated: 2020-07-14T12:47:38Z
file_id: '6721'
file_name: 2019_eLife_Castro.pdf
file_size: 6748249
relation: main_file
file_date_updated: 2020-07-14T12:47:38Z
has_accepted_license: '1'
intvolume: ' 8'
isi: 1
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
pmid: 1
publication: eLife
publication_status: published
publisher: eLife Sciences Publications
quality_controlled: '1'
related_material:
record:
- id: '9804'
relation: research_data
status: public
- id: '11388'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: An integrative genomic analysis of the Longshanks selection experiment for
longer limbs in mice
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 8
year: '2019'
...
---
_id: '315'
abstract:
- lang: eng
text: 'More than 100 years after Grigg’s influential analysis of species’ borders,
the causes of limits to species’ ranges still represent a puzzle that has never
been understood with clarity. The topic has become especially important recently
as many scientists have become interested in the potential for species’ ranges
to shift in response to climate change—and yet nearly all of those studies fail
to recognise or incorporate evolutionary genetics in a way that relates to theoretical
developments. I show that range margins can be understood based on just two measurable
parameters: (i) the fitness cost of dispersal—a measure of environmental heterogeneity—and
(ii) the strength of genetic drift, which reduces genetic diversity. Together,
these two parameters define an ‘expansion threshold’: adaptation fails when genetic
drift reduces genetic diversity below that required for adaptation to a heterogeneous
environment. When the key parameters drop below this expansion threshold locally,
a sharp range margin forms. When they drop below this threshold throughout the
species’ range, adaptation collapses everywhere, resulting in either extinction
or formation of a fragmented metapopulation. Because the effects of dispersal
differ fundamentally with dimension, the second parameter—the strength of genetic
drift—is qualitatively different compared to a linear habitat. In two-dimensional
habitats, genetic drift becomes effectively independent of selection. It decreases
with ‘neighbourhood size’—the number of individuals accessible by dispersal within
one generation. Moreover, in contrast to earlier predictions, which neglected
evolution of genetic variance and/or stochasticity in two dimensions, dispersal
into small marginal populations aids adaptation. This is because the reduction
of both genetic and demographic stochasticity has a stronger effect than the cost
of dispersal through increased maladaptation. The expansion threshold thus provides
a novel, theoretically justified, and testable prediction for formation of the
range margin and collapse of the species’ range.'
article_number: e2005372
author:
- first_name: Jitka
full_name: Polechova, Jitka
id: 3BBFB084-F248-11E8-B48F-1D18A9856A87
last_name: Polechova
orcid: 0000-0003-0951-3112
citation:
ama: Polechova J. Is the sky the limit? On the expansion threshold of a species’
range. PLoS Biology. 2018;16(6). doi:10.1371/journal.pbio.2005372
apa: Polechova, J. (2018). Is the sky the limit? On the expansion threshold of a
species’ range. PLoS Biology. Public Library of Science. https://doi.org/10.1371/journal.pbio.2005372
chicago: Polechova, Jitka. “Is the Sky the Limit? On the Expansion Threshold of
a Species’ Range.” PLoS Biology. Public Library of Science, 2018. https://doi.org/10.1371/journal.pbio.2005372.
ieee: J. Polechova, “Is the sky the limit? On the expansion threshold of a species’
range,” PLoS Biology, vol. 16, no. 6. Public Library of Science, 2018.
ista: Polechova J. 2018. Is the sky the limit? On the expansion threshold of a species’
range. PLoS Biology. 16(6), e2005372.
mla: Polechova, Jitka. “Is the Sky the Limit? On the Expansion Threshold of a Species’
Range.” PLoS Biology, vol. 16, no. 6, e2005372, Public Library of Science,
2018, doi:10.1371/journal.pbio.2005372.
short: J. Polechova, PLoS Biology 16 (2018).
date_created: 2018-12-11T11:45:46Z
date_published: 2018-06-15T00:00:00Z
date_updated: 2023-02-23T14:10:16Z
day: '15'
ddc:
- '576'
department:
- _id: NiBa
doi: 10.1371/journal.pbio.2005372
file:
- access_level: open_access
checksum: 908c52751bba30c55ed36789e5e4c84d
content_type: application/pdf
creator: dernst
date_created: 2019-01-22T08:30:03Z
date_updated: 2020-07-14T12:46:01Z
file_id: '5870'
file_name: 2017_PLOS_Polechova.pdf
file_size: 6968201
relation: main_file
file_date_updated: 2020-07-14T12:46:01Z
has_accepted_license: '1'
intvolume: ' 16'
issue: '6'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
publication: PLoS Biology
publication_identifier:
issn:
- '15449173'
publication_status: published
publisher: Public Library of Science
publist_id: '7550'
quality_controlled: '1'
related_material:
record:
- id: '9839'
relation: research_data
status: public
scopus_import: 1
status: public
title: Is the sky the limit? On the expansion threshold of a species’ range
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 16
year: '2018'
...
---
_id: '9837'
abstract:
- lang: eng
text: Both classical and recent studies suggest that chromosomal inversion polymorphisms
are important in adaptation and speciation. However, biases in discovery and reporting
of inversions make it difficult to assess their prevalence and biological importance.
Here, we use an approach based on linkage disequilibrium among markers genotyped
for samples collected across a transect between contrasting habitats to detect
chromosomal rearrangements de novo. We report 17 polymorphic rearrangements in
a single locality for the coastal marine snail, Littorina saxatilis. Patterns
of diversity in the field and of recombination in controlled crosses provide strong
evidence that at least the majority of these rearrangements are inversions. Most
show clinal changes in frequency between habitats, suggestive of divergent selection,
but only one appears to be fixed for different arrangements in the two habitats.
Consistent with widespread evidence for balancing selection on inversion polymorphisms,
we argue that a combination of heterosis and divergent selection can explain the
observed patterns and should be considered in other systems spanning environmental
gradients.
article_processing_charge: No
author:
- first_name: Rui
full_name: Faria, Rui
last_name: Faria
- first_name: Pragya
full_name: Chaube, Pragya
last_name: Chaube
- first_name: Hernán E.
full_name: Morales, Hernán E.
last_name: Morales
- first_name: Tomas
full_name: Larsson, Tomas
last_name: Larsson
- first_name: Alan R.
full_name: Lemmon, Alan R.
last_name: Lemmon
- first_name: Emily M.
full_name: Lemmon, Emily M.
last_name: Lemmon
- first_name: Marina
full_name: Rafajlović, Marina
last_name: Rafajlović
- first_name: Marina
full_name: Panova, Marina
last_name: Panova
- first_name: Mark
full_name: Ravinet, Mark
last_name: Ravinet
- first_name: Kerstin
full_name: Johannesson, Kerstin
last_name: Johannesson
- first_name: Anja M
full_name: Westram, Anja M
id: 3C147470-F248-11E8-B48F-1D18A9856A87
last_name: Westram
orcid: 0000-0003-1050-4969
- first_name: Roger K.
full_name: Butlin, Roger K.
last_name: Butlin
citation:
ama: 'Faria R, Chaube P, Morales HE, et al. Data from: Multiple chromosomal rearrangements
in a hybrid zone between Littorina saxatilis ecotypes. 2018. doi:10.5061/dryad.72cg113'
apa: 'Faria, R., Chaube, P., Morales, H. E., Larsson, T., Lemmon, A. R., Lemmon,
E. M., … Butlin, R. K. (2018). Data from: Multiple chromosomal rearrangements
in a hybrid zone between Littorina saxatilis ecotypes. Dryad. https://doi.org/10.5061/dryad.72cg113'
chicago: 'Faria, Rui, Pragya Chaube, Hernán E. Morales, Tomas Larsson, Alan R. Lemmon,
Emily M. Lemmon, Marina Rafajlović, et al. “Data from: Multiple Chromosomal Rearrangements
in a Hybrid Zone between Littorina Saxatilis Ecotypes.” Dryad, 2018. https://doi.org/10.5061/dryad.72cg113.'
ieee: 'R. Faria et al., “Data from: Multiple chromosomal rearrangements in
a hybrid zone between Littorina saxatilis ecotypes.” Dryad, 2018.'
ista: 'Faria R, Chaube P, Morales HE, Larsson T, Lemmon AR, Lemmon EM, Rafajlović
M, Panova M, Ravinet M, Johannesson K, Westram AM, Butlin RK. 2018. Data from:
Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis
ecotypes, Dryad, 10.5061/dryad.72cg113.'
mla: 'Faria, Rui, et al. Data from: Multiple Chromosomal Rearrangements in a
Hybrid Zone between Littorina Saxatilis Ecotypes. Dryad, 2018, doi:10.5061/dryad.72cg113.'
short: R. Faria, P. Chaube, H.E. Morales, T. Larsson, A.R. Lemmon, E.M. Lemmon,
M. Rafajlović, M. Panova, M. Ravinet, K. Johannesson, A.M. Westram, R.K. Butlin,
(2018).
date_created: 2021-08-09T12:46:39Z
date_published: 2018-10-09T00:00:00Z
date_updated: 2023-08-24T14:50:26Z
day: '09'
department:
- _id: NiBa
doi: 10.5061/dryad.72cg113
main_file_link:
- open_access: '1'
url: https://doi.org/10.5061/dryad.72cg113
month: '10'
oa: 1
oa_version: Published Version
publisher: Dryad
related_material:
record:
- id: '6095'
relation: used_in_publication
status: public
status: public
title: 'Data from: Multiple chromosomal rearrangements in a hybrid zone between Littorina
saxatilis ecotypes'
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2018'
...
---
_id: '423'
abstract:
- lang: eng
text: Herd immunity, a process in which resistant individuals limit the spread of
a pathogen among susceptible hosts has been extensively studied in eukaryotes.
Even though bacteria have evolved multiple immune systems against their phage
pathogens, herd immunity in bacteria remains unexplored. Here we experimentally
demonstrate that herd immunity arises during phage epidemics in structured and
unstructured Escherichia coli populations consisting of differing frequencies
of susceptible and resistant cells harboring CRISPR immunity. In addition, we
develop a mathematical model that quantifies how herd immunity is affected by
spatial population structure, bacterial growth rate, and phage replication rate.
Using our model we infer a general epidemiological rule describing the relative
speed of an epidemic in partially resistant spatially structured populations.
Our experimental and theoretical findings indicate that herd immunity may be important
in bacterial communities, allowing for stable coexistence of bacteria and their
phages and the maintenance of polymorphism in bacterial immunity.
acknowledgement: "We are grateful to Remy Chait for his help and assistance with establishing
our experimental setups and to Tobias Bergmiller for valuable insights into some
specific experimental details. We thank Luciano Marraffini for donating us the pCas9
plasmid used in this study. We also want to express our gratitude to Seth Barribeau,
Andrea Betancourt, Călin Guet, Mato Lagator, Tiago Paixão and Maroš Pleška for valuable
discussions on the manuscript. Finally, we would like to thank the \r\neditors and
reviewers for their helpful comments and suggestions."
article_number: e32035
article_processing_charge: No
author:
- first_name: Pavel
full_name: Payne, Pavel
id: 35F78294-F248-11E8-B48F-1D18A9856A87
last_name: Payne
orcid: 0000-0002-2711-9453
- first_name: Lukas
full_name: Geyrhofer, Lukas
last_name: Geyrhofer
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Jonathan P
full_name: Bollback, Jonathan P
id: 2C6FA9CC-F248-11E8-B48F-1D18A9856A87
last_name: Bollback
orcid: 0000-0002-4624-4612
citation:
ama: Payne P, Geyrhofer L, Barton NH, Bollback JP. CRISPR-based herd immunity can
limit phage epidemics in bacterial populations. eLife. 2018;7. doi:10.7554/eLife.32035
apa: Payne, P., Geyrhofer, L., Barton, N. H., & Bollback, J. P. (2018). CRISPR-based
herd immunity can limit phage epidemics in bacterial populations. ELife.
eLife Sciences Publications. https://doi.org/10.7554/eLife.32035
chicago: Payne, Pavel, Lukas Geyrhofer, Nicholas H Barton, and Jonathan P Bollback.
“CRISPR-Based Herd Immunity Can Limit Phage Epidemics in Bacterial Populations.”
ELife. eLife Sciences Publications, 2018. https://doi.org/10.7554/eLife.32035.
ieee: P. Payne, L. Geyrhofer, N. H. Barton, and J. P. Bollback, “CRISPR-based herd
immunity can limit phage epidemics in bacterial populations,” eLife, vol.
7. eLife Sciences Publications, 2018.
ista: Payne P, Geyrhofer L, Barton NH, Bollback JP. 2018. CRISPR-based herd immunity
can limit phage epidemics in bacterial populations. eLife. 7, e32035.
mla: Payne, Pavel, et al. “CRISPR-Based Herd Immunity Can Limit Phage Epidemics
in Bacterial Populations.” ELife, vol. 7, e32035, eLife Sciences Publications,
2018, doi:10.7554/eLife.32035.
short: P. Payne, L. Geyrhofer, N.H. Barton, J.P. Bollback, ELife 7 (2018).
date_created: 2018-12-11T11:46:23Z
date_published: 2018-03-09T00:00:00Z
date_updated: 2023-09-11T12:49:17Z
day: '09'
ddc:
- '576'
department:
- _id: NiBa
- _id: JoBo
doi: 10.7554/eLife.32035
ec_funded: 1
external_id:
isi:
- '000431035800001'
file:
- access_level: open_access
checksum: 447cf6e680bdc3c01062a8737d876569
content_type: application/pdf
creator: dernst
date_created: 2018-12-17T10:36:07Z
date_updated: 2020-07-14T12:46:25Z
file_id: '5689'
file_name: 2018_eLife_Payne.pdf
file_size: 3533881
relation: main_file
file_date_updated: 2020-07-14T12:46:25Z
has_accepted_license: '1'
intvolume: ' 7'
isi: 1
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
project:
- _id: 2578D616-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '648440'
name: Selective Barriers to Horizontal Gene Transfer
publication: eLife
publication_status: published
publisher: eLife Sciences Publications
publist_id: '7400'
quality_controlled: '1'
related_material:
record:
- id: '9840'
relation: research_data
status: public
scopus_import: '1'
status: public
title: CRISPR-based herd immunity can limit phage epidemics in bacterial populations
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 7
year: '2018'
...
---
_id: '9840'
abstract:
- lang: eng
text: Herd immunity, a process in which resistant individuals limit the spread of
a pathogen among susceptible hosts has been extensively studied in eukaryotes.
Even though bacteria have evolved multiple immune systems against their phage
pathogens, herd immunity in bacteria remains unexplored. Here we experimentally
demonstrate that herd immunity arises during phage epidemics in structured and
unstructured Escherichia coli populations consisting of differing frequencies
of susceptible and resistant cells harboring CRISPR immunity. In addition, we
develop a mathematical model that quantifies how herd immunity is affected by
spatial population structure, bacterial growth rate, and phage replication rate.
Using our model we infer a general epidemiological rule describing the relative
speed of an epidemic in partially resistant spatially structured populations.
Our experimental and theoretical findings indicate that herd immunity may be important
in bacterial communities, allowing for stable coexistence of bacteria and their
phages and the maintenance of polymorphism in bacterial immunity.
article_processing_charge: No
author:
- first_name: Pavel
full_name: Payne, Pavel
id: 35F78294-F248-11E8-B48F-1D18A9856A87
last_name: Payne
orcid: 0000-0002-2711-9453
- first_name: Lukas
full_name: Geyrhofer, Lukas
last_name: Geyrhofer
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Jonathan P
full_name: Bollback, Jonathan P
id: 2C6FA9CC-F248-11E8-B48F-1D18A9856A87
last_name: Bollback
orcid: 0000-0002-4624-4612
citation:
ama: 'Payne P, Geyrhofer L, Barton NH, Bollback JP. Data from: CRISPR-based herd
immunity limits phage epidemics in bacterial populations. 2018. doi:10.5061/dryad.42n44'
apa: 'Payne, P., Geyrhofer, L., Barton, N. H., & Bollback, J. P. (2018). Data
from: CRISPR-based herd immunity limits phage epidemics in bacterial populations.
Dryad. https://doi.org/10.5061/dryad.42n44'
chicago: 'Payne, Pavel, Lukas Geyrhofer, Nicholas H Barton, and Jonathan P Bollback.
“Data from: CRISPR-Based Herd Immunity Limits Phage Epidemics in Bacterial Populations.”
Dryad, 2018. https://doi.org/10.5061/dryad.42n44.'
ieee: 'P. Payne, L. Geyrhofer, N. H. Barton, and J. P. Bollback, “Data from: CRISPR-based
herd immunity limits phage epidemics in bacterial populations.” Dryad, 2018.'
ista: 'Payne P, Geyrhofer L, Barton NH, Bollback JP. 2018. Data from: CRISPR-based
herd immunity limits phage epidemics in bacterial populations, Dryad, 10.5061/dryad.42n44.'
mla: 'Payne, Pavel, et al. Data from: CRISPR-Based Herd Immunity Limits Phage
Epidemics in Bacterial Populations. Dryad, 2018, doi:10.5061/dryad.42n44.'
short: P. Payne, L. Geyrhofer, N.H. Barton, J.P. Bollback, (2018).
date_created: 2021-08-09T13:10:02Z
date_published: 2018-03-12T00:00:00Z
date_updated: 2023-09-11T12:49:17Z
day: '12'
department:
- _id: NiBa
- _id: JoBo
doi: 10.5061/dryad.42n44
main_file_link:
- open_access: '1'
url: https://doi.org/10.5061/dryad.42n44
month: '03'
oa: 1
oa_version: Published Version
publisher: Dryad
related_material:
record:
- id: '423'
relation: used_in_publication
status: public
status: public
title: 'Data from: CRISPR-based herd immunity limits phage epidemics in bacterial
populations'
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2018'
...
---
_id: '564'
abstract:
- lang: eng
text: "Maladapted individuals can only colonise a new habitat if they can evolve
a\r\npositive growth rate fast enough to avoid extinction, a process known as
evolutionary\r\nrescue. We treat log fitness at low density in the new habitat
as a\r\nsingle polygenic trait and thus use the infinitesimal model to follow
the evolution\r\nof the growth rate; this assumes that the trait values of offspring
of a\r\nsexual union are normally distributed around the mean of the parents’
trait\r\nvalues, with variance that depends only on the parents’ relatedness.
The\r\nprobability that a single migrant can establish depends on just two parameters:\r\nthe
mean and genetic variance of the trait in the source population.\r\nThe chance
of success becomes small if migrants come from a population\r\nwith mean growth
rate in the new habitat more than a few standard deviations\r\nbelow zero; this
chance depends roughly equally on the probability\r\nthat the initial founder
is unusually fit, and on the subsequent increase in\r\ngrowth rate of its offspring
as a result of selection. The loss of genetic variation\r\nduring the founding
event is substantial, but highly variable. With\r\ncontinued migration at rate
M, establishment is inevitable; when migration\r\nis rare, the expected time to
establishment decreases inversely with M.\r\nHowever, above a threshold migration
rate, the population may be trapped\r\nin a ‘sink’ state, in which adaptation
is held back by gene flow; above this\r\nthreshold, the expected time to establishment
increases exponentially with M. This threshold behaviour is captured by a deterministic
approximation,\r\nwhich assumes a Gaussian distribution of the trait in the founder
population\r\nwith mean and variance evolving deterministically. By assuming a
constant\r\ngenetic variance, we also develop a diffusion approximation for the
joint distribution\r\nof population size and trait mean, which extends to include
stabilising\r\nselection and density regulation. Divergence of the population
from its\r\nancestors causes partial reproductive isolation, which we measure
through\r\nthe reproductive value of migrants into the newly established population."
article_processing_charge: No
article_type: original
author:
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Alison
full_name: Etheridge, Alison
last_name: Etheridge
citation:
ama: Barton NH, Etheridge A. Establishment in a new habitat by polygenic adaptation.
Theoretical Population Biology. 2018;122(7):110-127. doi:10.1016/j.tpb.2017.11.007
apa: Barton, N. H., & Etheridge, A. (2018). Establishment in a new habitat by
polygenic adaptation. Theoretical Population Biology. Academic Press. https://doi.org/10.1016/j.tpb.2017.11.007
chicago: Barton, Nicholas H, and Alison Etheridge. “Establishment in a New Habitat
by Polygenic Adaptation.” Theoretical Population Biology. Academic Press,
2018. https://doi.org/10.1016/j.tpb.2017.11.007.
ieee: N. H. Barton and A. Etheridge, “Establishment in a new habitat by polygenic
adaptation,” Theoretical Population Biology, vol. 122, no. 7. Academic
Press, pp. 110–127, 2018.
ista: Barton NH, Etheridge A. 2018. Establishment in a new habitat by polygenic
adaptation. Theoretical Population Biology. 122(7), 110–127.
mla: Barton, Nicholas H., and Alison Etheridge. “Establishment in a New Habitat
by Polygenic Adaptation.” Theoretical Population Biology, vol. 122, no.
7, Academic Press, 2018, pp. 110–27, doi:10.1016/j.tpb.2017.11.007.
short: N.H. Barton, A. Etheridge, Theoretical Population Biology 122 (2018) 110–127.
date_created: 2018-12-11T11:47:12Z
date_published: 2018-07-01T00:00:00Z
date_updated: 2023-09-11T13:41:22Z
day: '01'
ddc:
- '519'
- '576'
department:
- _id: NiBa
doi: 10.1016/j.tpb.2017.11.007
ec_funded: 1
external_id:
isi:
- '000440392900014'
file:
- access_level: open_access
checksum: 0b96f6db47e3e91b5e7d103b847c239d
content_type: application/pdf
creator: nbarton
date_created: 2019-12-21T09:36:39Z
date_updated: 2020-07-14T12:47:09Z
file_id: '7199'
file_name: bartonetheridge.pdf
file_size: 2287682
relation: main_file
file_date_updated: 2020-07-14T12:47:09Z
has_accepted_license: '1'
intvolume: ' 122'
isi: 1
issue: '7'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Submitted Version
page: 110-127
project:
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
publication: Theoretical Population Biology
publication_status: published
publisher: Academic Press
publist_id: '7250'
quality_controlled: '1'
related_material:
record:
- id: '9842'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Establishment in a new habitat by polygenic adaptation
tmp:
image: /images/cc_by_nc.png
legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode
name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
short: CC BY-NC (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 122
year: '2018'
...
---
_id: '563'
abstract:
- lang: eng
text: "In continuous populations with local migration, nearby pairs of individuals
have on average more similar genotypes\r\nthan geographically well separated pairs.
A barrier to gene flow distorts this classical pattern of isolation by distance.
Genetic similarity is decreased for sample pairs on different sides of the barrier
and increased for pairs on the same side near the barrier. Here, we introduce
an inference scheme that utilizes this signal to detect and estimate the strength
of a linear barrier to gene flow in two-dimensions. We use a diffusion approximation
to model the effects of a barrier on the geographical spread of ancestry backwards
in time. This approach allows us to calculate the chance of recent coalescence
and probability of identity by descent. We introduce an inference scheme that
fits these theoretical results to the geographical covariance structure of bialleleic
genetic markers. It can estimate the strength of the barrier as well as several
demographic parameters. We investigate the power of our inference scheme to detect
barriers by applying it to a wide range of simulated data. We also showcase an
example application to a Antirrhinum majus (snapdragon) flower color hybrid zone,
where we do not detect any signal of a strong genome wide barrier to gene flow."
article_processing_charge: No
author:
- first_name: Harald
full_name: Ringbauer, Harald
id: 417FCFF4-F248-11E8-B48F-1D18A9856A87
last_name: Ringbauer
orcid: 0000-0002-4884-9682
- first_name: Alexander
full_name: Kolesnikov, Alexander
id: 2D157DB6-F248-11E8-B48F-1D18A9856A87
last_name: Kolesnikov
- first_name: David
full_name: Field, David
last_name: Field
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: Ringbauer H, Kolesnikov A, Field D, Barton NH. Estimating barriers to gene
flow from distorted isolation-by-distance patterns. Genetics. 2018;208(3):1231-1245.
doi:10.1534/genetics.117.300638
apa: Ringbauer, H., Kolesnikov, A., Field, D., & Barton, N. H. (2018). Estimating
barriers to gene flow from distorted isolation-by-distance patterns. Genetics.
Genetics Society of America. https://doi.org/10.1534/genetics.117.300638
chicago: Ringbauer, Harald, Alexander Kolesnikov, David Field, and Nicholas H Barton.
“Estimating Barriers to Gene Flow from Distorted Isolation-by-Distance Patterns.”
Genetics. Genetics Society of America, 2018. https://doi.org/10.1534/genetics.117.300638.
ieee: H. Ringbauer, A. Kolesnikov, D. Field, and N. H. Barton, “Estimating barriers
to gene flow from distorted isolation-by-distance patterns,” Genetics,
vol. 208, no. 3. Genetics Society of America, pp. 1231–1245, 2018.
ista: Ringbauer H, Kolesnikov A, Field D, Barton NH. 2018. Estimating barriers to
gene flow from distorted isolation-by-distance patterns. Genetics. 208(3), 1231–1245.
mla: Ringbauer, Harald, et al. “Estimating Barriers to Gene Flow from Distorted
Isolation-by-Distance Patterns.” Genetics, vol. 208, no. 3, Genetics Society
of America, 2018, pp. 1231–45, doi:10.1534/genetics.117.300638.
short: H. Ringbauer, A. Kolesnikov, D. Field, N.H. Barton, Genetics 208 (2018) 1231–1245.
date_created: 2018-12-11T11:47:12Z
date_published: 2018-03-01T00:00:00Z
date_updated: 2023-09-11T13:42:38Z
day: '01'
department:
- _id: NiBa
- _id: ChLa
doi: 10.1534/genetics.117.300638
external_id:
isi:
- '000426219600025'
intvolume: ' 208'
isi: 1
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.biorxiv.org/content/10.1101/205484v1
month: '03'
oa: 1
oa_version: Preprint
page: 1231-1245
publication: Genetics
publication_status: published
publisher: Genetics Society of America
publist_id: '7251'
quality_controlled: '1'
related_material:
record:
- id: '200'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Estimating barriers to gene flow from distorted isolation-by-distance patterns
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 208
year: '2018'
...
---
_id: '316'
abstract:
- lang: eng
text: 'Self-incompatibility (SI) is a genetically based recognition system that
functions to prevent self-fertilization and mating among related plants. An enduring
puzzle in SI is how the high diversity observed in nature arises and is maintained.
Based on the underlying recognition mechanism, SI can be classified into two main
groups: self- and non-self recognition. Most work has focused on diversification
within self-recognition systems despite expected differences between the two groups
in the evolutionary pathways and outcomes of diversification. Here, we use a deterministic
population genetic model and stochastic simulations to investigate how novel S-haplotypes
evolve in a gametophytic non-self recognition (SRNase/S Locus F-box (SLF)) SI
system. For this model the pathways for diversification involve either the maintenance
or breakdown of SI and can vary in the order of mutations of the female (SRNase)
and male (SLF) components. We show analytically that diversification can occur
with high inbreeding depression and self-pollination, but this varies with evolutionary
pathway and level of completeness (which determines the number of potential mating
partners in the population), and in general is more likely for lower haplotype
number. The conditions for diversification are broader in stochastic simulations
of finite population size. However, the number of haplotypes observed under high
inbreeding and moderate to high self-pollination is less than that commonly observed
in nature. Diversification was observed through pathways that maintain SI as well
as through self-compatible intermediates. Yet the lifespan of diversified haplotypes
was sensitive to their level of completeness. By examining diversification in
a non-self recognition SI system, this model extends our understanding of the
evolution and maintenance of haplotype diversity observed in a self recognition
system common in flowering plants.'
article_processing_charge: No
article_type: original
author:
- first_name: Katarina
full_name: Bodova, Katarina
id: 2BA24EA0-F248-11E8-B48F-1D18A9856A87
last_name: Bodova
orcid: 0000-0002-7214-0171
- first_name: Tadeas
full_name: Priklopil, Tadeas
id: 3C869AA0-F248-11E8-B48F-1D18A9856A87
last_name: Priklopil
- first_name: David
full_name: Field, David
id: 419049E2-F248-11E8-B48F-1D18A9856A87
last_name: Field
orcid: 0000-0002-4014-8478
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Melinda
full_name: Pickup, Melinda
id: 2C78037E-F248-11E8-B48F-1D18A9856A87
last_name: Pickup
orcid: 0000-0001-6118-0541
citation:
ama: Bodova K, Priklopil T, Field D, Barton NH, Pickup M. Evolutionary pathways
for the generation of new self-incompatibility haplotypes in a non-self recognition
system. Genetics. 2018;209(3):861-883. doi:10.1534/genetics.118.300748
apa: Bodova, K., Priklopil, T., Field, D., Barton, N. H., & Pickup, M. (2018).
Evolutionary pathways for the generation of new self-incompatibility haplotypes
in a non-self recognition system. Genetics. Genetics Society of America.
https://doi.org/10.1534/genetics.118.300748
chicago: Bodova, Katarina, Tadeas Priklopil, David Field, Nicholas H Barton, and
Melinda Pickup. “Evolutionary Pathways for the Generation of New Self-Incompatibility
Haplotypes in a Non-Self Recognition System.” Genetics. Genetics Society
of America, 2018. https://doi.org/10.1534/genetics.118.300748.
ieee: K. Bodova, T. Priklopil, D. Field, N. H. Barton, and M. Pickup, “Evolutionary
pathways for the generation of new self-incompatibility haplotypes in a non-self
recognition system,” Genetics, vol. 209, no. 3. Genetics Society of America,
pp. 861–883, 2018.
ista: Bodova K, Priklopil T, Field D, Barton NH, Pickup M. 2018. Evolutionary pathways
for the generation of new self-incompatibility haplotypes in a non-self recognition
system. Genetics. 209(3), 861–883.
mla: Bodova, Katarina, et al. “Evolutionary Pathways for the Generation of New Self-Incompatibility
Haplotypes in a Non-Self Recognition System.” Genetics, vol. 209, no. 3,
Genetics Society of America, 2018, pp. 861–83, doi:10.1534/genetics.118.300748.
short: K. Bodova, T. Priklopil, D. Field, N.H. Barton, M. Pickup, Genetics 209 (2018)
861–883.
date_created: 2018-12-11T11:45:47Z
date_published: 2018-07-01T00:00:00Z
date_updated: 2023-09-11T13:57:43Z
day: '01'
department:
- _id: NiBa
- _id: GaTk
doi: 10.1534/genetics.118.300748
ec_funded: 1
external_id:
isi:
- '000437171700017'
intvolume: ' 209'
isi: 1
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.biorxiv.org/node/80098.abstract
month: '07'
oa: 1
oa_version: Preprint
page: 861-883
project:
- _id: 25B36484-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '329960'
name: Mating system and the evolutionary dynamics of hybrid zones
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publication: Genetics
publication_status: published
publisher: Genetics Society of America
quality_controlled: '1'
related_material:
link:
- description: News on IST Homepage
relation: press_release
url: https://ist.ac.at/en/news/recognizing-others-but-not-yourself-new-insights-into-the-evolution-of-plant-mating/
record:
- id: '9813'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Evolutionary pathways for the generation of new self-incompatibility haplotypes
in a non-self recognition system
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 209
year: '2018'
...
---
_id: '9813'
abstract:
- lang: eng
text: 'File S1 contains figures that clarify the following features: (i) effect
of population size on the average number/frequency of SI classes, (ii) changes
in the minimal completeness deficit in time for a single class, and (iii) diversification
diagrams for all studied pathways, including the summary figure for k = 8. File
S2 contains the code required for a stochastic simulation of the SLF system with
an example. This file also includes the output in the form of figures and tables.'
article_processing_charge: No
author:
- first_name: Katarína
full_name: Bod'ová, Katarína
id: 2BA24EA0-F248-11E8-B48F-1D18A9856A87
last_name: Bod'ová
orcid: 0000-0002-7214-0171
- first_name: Tadeas
full_name: Priklopil, Tadeas
id: 3C869AA0-F248-11E8-B48F-1D18A9856A87
last_name: Priklopil
- first_name: David
full_name: Field, David
id: 419049E2-F248-11E8-B48F-1D18A9856A87
last_name: Field
orcid: 0000-0002-4014-8478
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Melinda
full_name: Pickup, Melinda
id: 2C78037E-F248-11E8-B48F-1D18A9856A87
last_name: Pickup
orcid: 0000-0001-6118-0541
citation:
ama: Bodova K, Priklopil T, Field D, Barton NH, Pickup M. Supplemental material
for Bodova et al., 2018. 2018. doi:10.25386/genetics.6148304.v1
apa: Bodova, K., Priklopil, T., Field, D., Barton, N. H., & Pickup, M. (2018).
Supplemental material for Bodova et al., 2018. Genetics Society of America. https://doi.org/10.25386/genetics.6148304.v1
chicago: Bodova, Katarina, Tadeas Priklopil, David Field, Nicholas H Barton, and
Melinda Pickup. “Supplemental Material for Bodova et Al., 2018.” Genetics Society
of America, 2018. https://doi.org/10.25386/genetics.6148304.v1.
ieee: K. Bodova, T. Priklopil, D. Field, N. H. Barton, and M. Pickup, “Supplemental
material for Bodova et al., 2018.” Genetics Society of America, 2018.
ista: Bodova K, Priklopil T, Field D, Barton NH, Pickup M. 2018. Supplemental material
for Bodova et al., 2018, Genetics Society of America, 10.25386/genetics.6148304.v1.
mla: Bodova, Katarina, et al. Supplemental Material for Bodova et Al., 2018.
Genetics Society of America, 2018, doi:10.25386/genetics.6148304.v1.
short: K. Bodova, T. Priklopil, D. Field, N.H. Barton, M. Pickup, (2018).
date_created: 2021-08-06T13:04:32Z
date_published: 2018-04-30T00:00:00Z
date_updated: 2023-09-11T13:57:42Z
day: '30'
department:
- _id: NiBa
- _id: GaTk
doi: 10.25386/genetics.6148304.v1
main_file_link:
- open_access: '1'
url: https://doi.org/10.25386/genetics.6148304.v1
month: '04'
oa: 1
oa_version: Published Version
publisher: Genetics Society of America
related_material:
record:
- id: '316'
relation: used_in_publication
status: public
status: public
title: Supplemental material for Bodova et al., 2018
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2018'
...
---
_id: '723'
abstract:
- lang: eng
text: Escaping local optima is one of the major obstacles to function optimisation.
Using the metaphor of a fitness landscape, local optima correspond to hills separated
by fitness valleys that have to be overcome. We define a class of fitness valleys
of tunable difficulty by considering their length, representing the Hamming path
between the two optima and their depth, the drop in fitness. For this function
class we present a runtime comparison between stochastic search algorithms using
different search strategies. The (1+1) EA is a simple and well-studied evolutionary
algorithm that has to jump across the valley to a point of higher fitness because
it does not accept worsening moves (elitism). In contrast, the Metropolis algorithm
and the Strong Selection Weak Mutation (SSWM) algorithm, a famous process in population
genetics, are both able to cross the fitness valley by accepting worsening moves.
We show that the runtime of the (1+1) EA depends critically on the length of the
valley while the runtimes of the non-elitist algorithms depend crucially on the
depth of the valley. Moreover, we show that both SSWM and Metropolis can also
efficiently optimise a rugged function consisting of consecutive valleys.
article_processing_charge: No
author:
- first_name: Pietro
full_name: Oliveto, Pietro
last_name: Oliveto
- first_name: Tiago
full_name: Paixao, Tiago
id: 2C5658E6-F248-11E8-B48F-1D18A9856A87
last_name: Paixao
orcid: 0000-0003-2361-3953
- first_name: Jorge
full_name: Pérez Heredia, Jorge
last_name: Pérez Heredia
- first_name: Dirk
full_name: Sudholt, Dirk
last_name: Sudholt
- first_name: Barbora
full_name: Trubenova, Barbora
id: 42302D54-F248-11E8-B48F-1D18A9856A87
last_name: Trubenova
orcid: 0000-0002-6873-2967
citation:
ama: Oliveto P, Paixao T, Pérez Heredia J, Sudholt D, Trubenova B. How to escape
local optima in black box optimisation when non elitism outperforms elitism. Algorithmica.
2018;80(5):1604-1633. doi:10.1007/s00453-017-0369-2
apa: Oliveto, P., Paixao, T., Pérez Heredia, J., Sudholt, D., & Trubenova, B.
(2018). How to escape local optima in black box optimisation when non elitism
outperforms elitism. Algorithmica. Springer. https://doi.org/10.1007/s00453-017-0369-2
chicago: Oliveto, Pietro, Tiago Paixao, Jorge Pérez Heredia, Dirk Sudholt, and Barbora
Trubenova. “How to Escape Local Optima in Black Box Optimisation When Non Elitism
Outperforms Elitism.” Algorithmica. Springer, 2018. https://doi.org/10.1007/s00453-017-0369-2.
ieee: P. Oliveto, T. Paixao, J. Pérez Heredia, D. Sudholt, and B. Trubenova, “How
to escape local optima in black box optimisation when non elitism outperforms
elitism,” Algorithmica, vol. 80, no. 5. Springer, pp. 1604–1633, 2018.
ista: Oliveto P, Paixao T, Pérez Heredia J, Sudholt D, Trubenova B. 2018. How to
escape local optima in black box optimisation when non elitism outperforms elitism.
Algorithmica. 80(5), 1604–1633.
mla: Oliveto, Pietro, et al. “How to Escape Local Optima in Black Box Optimisation
When Non Elitism Outperforms Elitism.” Algorithmica, vol. 80, no. 5, Springer,
2018, pp. 1604–33, doi:10.1007/s00453-017-0369-2.
short: P. Oliveto, T. Paixao, J. Pérez Heredia, D. Sudholt, B. Trubenova, Algorithmica
80 (2018) 1604–1633.
date_created: 2018-12-11T11:48:09Z
date_published: 2018-05-01T00:00:00Z
date_updated: 2023-09-11T14:11:35Z
day: '01'
ddc:
- '576'
department:
- _id: NiBa
- _id: CaGu
doi: 10.1007/s00453-017-0369-2
ec_funded: 1
external_id:
isi:
- '000428239300010'
file:
- access_level: open_access
checksum: 7d92f5d7be81e387edeec4f06442791c
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:08:14Z
date_updated: 2020-07-14T12:47:54Z
file_id: '4674'
file_name: IST-2018-1014-v1+1_2018_Paixao_Escape.pdf
file_size: 691245
relation: main_file
file_date_updated: 2020-07-14T12:47:54Z
has_accepted_license: '1'
intvolume: ' 80'
isi: 1
issue: '5'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
page: 1604 - 1633
project:
- _id: 25B1EC9E-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '618091'
name: Speed of Adaptation in Population Genetics and Evolutionary Computation
publication: Algorithmica
publication_status: published
publisher: Springer
publist_id: '6957'
pubrep_id: '1014'
quality_controlled: '1'
scopus_import: '1'
status: public
title: How to escape local optima in black box optimisation when non elitism outperforms
elitism
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 80
year: '2018'
...
---
_id: '282'
abstract:
- lang: eng
text: Adaptive introgression is common in nature and can be driven by selection
acting on multiple, linked genes. We explore the effects of polygenic selection
on introgression under the infinitesimal model with linkage. This model assumes
that the introgressing block has an effectively infinite number of genes, each
with an infinitesimal effect on the trait under selection. The block is assumed
to introgress under directional selection within a native population that is genetically
homogeneous. We use individual-based simulations and a branching process approximation
to compute various statistics of the introgressing block, and explore how these
depend on parameters such as the map length and initial trait value associated
with the introgressing block, the genetic variability along the block, and the
strength of selection. Our results show that the introgression dynamics of a block
under infinitesimal selection is qualitatively different from the dynamics of
neutral introgression. We also find that in the long run, surviving descendant
blocks are likely to have intermediate lengths, and clarify how the length is
shaped by the interplay between linkage and infinitesimal selection. Our results
suggest that it may be difficult to distinguish introgression of single loci from
that of genomic blocks with multiple, tightly linked and weakly selected loci.
article_processing_charge: No
author:
- first_name: Himani
full_name: Sachdeva, Himani
id: 42377A0A-F248-11E8-B48F-1D18A9856A87
last_name: Sachdeva
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: Sachdeva H, Barton NH. Introgression of a block of genome under infinitesimal
selection. Genetics. 2018;209(4):1279-1303. doi:10.1534/genetics.118.301018
apa: Sachdeva, H., & Barton, N. H. (2018). Introgression of a block of genome
under infinitesimal selection. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.118.301018
chicago: Sachdeva, Himani, and Nicholas H Barton. “Introgression of a Block of Genome
under Infinitesimal Selection.” Genetics. Genetics Society of America,
2018. https://doi.org/10.1534/genetics.118.301018.
ieee: H. Sachdeva and N. H. Barton, “Introgression of a block of genome under infinitesimal
selection,” Genetics, vol. 209, no. 4. Genetics Society of America, pp.
1279–1303, 2018.
ista: Sachdeva H, Barton NH. 2018. Introgression of a block of genome under infinitesimal
selection. Genetics. 209(4), 1279–1303.
mla: Sachdeva, Himani, and Nicholas H. Barton. “Introgression of a Block of Genome
under Infinitesimal Selection.” Genetics, vol. 209, no. 4, Genetics Society
of America, 2018, pp. 1279–303, doi:10.1534/genetics.118.301018.
short: H. Sachdeva, N.H. Barton, Genetics 209 (2018) 1279–1303.
date_created: 2018-12-11T11:45:36Z
date_published: 2018-08-01T00:00:00Z
date_updated: 2023-09-13T08:22:32Z
day: '01'
department:
- _id: NiBa
doi: 10.1534/genetics.118.301018
external_id:
isi:
- '000440014100020'
intvolume: ' 209'
isi: 1
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.biorxiv.org/content/early/2017/11/30/227082
month: '08'
oa: 1
oa_version: Submitted Version
page: 1279 - 1303
publication: Genetics
publication_status: published
publisher: Genetics Society of America
publist_id: '7617'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Introgression of a block of genome under infinitesimal selection
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 209
year: '2018'
...
---
_id: '39'
abstract:
- lang: eng
text: We study how a block of genome with a large number of weakly selected loci
introgresses under directional selection into a genetically homogeneous population.
We derive exact expressions for the expected rate of growth of any fragment of
the introduced block during the initial phase of introgression, and show that
the growth rate of a single-locus variant is largely insensitive to its own additive
effect, but depends instead on the combined effect of all loci within a characteristic
linkage scale. The expected growth rate of a fragment is highly correlated with
its long-term introgression probability in populations of moderate size, and can
hence identify variants that are likely to introgress across replicate populations.
We clarify how the introgression probability of an individual variant is determined
by the interplay between hitchhiking with relatively large fragments during the
early phase of introgression and selection on fine-scale variation within these,
which at longer times results in differential introgression probabilities for
beneficial and deleterious loci within successful fragments. By simulating individuals,
we also investigate how introgression probabilities at individual loci depend
on the variance of fitness effects, the net fitness of the introduced block, and
the size of the recipient population, and how this shapes the net advance under
selection. Our work suggests that even highly replicable substitutions may be
associated with a range of selective effects, which makes it challenging to fine
map the causal loci that underlie polygenic adaptation.
article_processing_charge: No
article_type: original
author:
- first_name: Himani
full_name: Sachdeva, Himani
id: 42377A0A-F248-11E8-B48F-1D18A9856A87
last_name: Sachdeva
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: Sachdeva H, Barton NH. Replicability of introgression under linked, polygenic
selection. Genetics. 2018;210(4):1411-1427. doi:10.1534/genetics.118.301429
apa: Sachdeva, H., & Barton, N. H. (2018). Replicability of introgression under
linked, polygenic selection. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.118.301429
chicago: Sachdeva, Himani, and Nicholas H Barton. “Replicability of Introgression
under Linked, Polygenic Selection.” Genetics. Genetics Society of America,
2018. https://doi.org/10.1534/genetics.118.301429.
ieee: H. Sachdeva and N. H. Barton, “Replicability of introgression under linked,
polygenic selection,” Genetics, vol. 210, no. 4. Genetics Society of America,
pp. 1411–1427, 2018.
ista: Sachdeva H, Barton NH. 2018. Replicability of introgression under linked,
polygenic selection. Genetics. 210(4), 1411–1427.
mla: Sachdeva, Himani, and Nicholas H. Barton. “Replicability of Introgression under
Linked, Polygenic Selection.” Genetics, vol. 210, no. 4, Genetics Society
of America, 2018, pp. 1411–27, doi:10.1534/genetics.118.301429.
short: H. Sachdeva, N.H. Barton, Genetics 210 (2018) 1411–1427.
date_created: 2018-12-11T11:44:18Z
date_published: 2018-12-04T00:00:00Z
date_updated: 2023-09-18T08:10:29Z
day: '04'
department:
- _id: NiBa
doi: 10.1534/genetics.118.301429
external_id:
isi:
- '000452315900021'
intvolume: ' 210'
isi: 1
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.biorxiv.org/content/10.1101/379578v1
month: '12'
oa: 1
oa_version: Preprint
page: 1411-1427
publication: Genetics
publication_identifier:
issn:
- '00166731'
publication_status: published
publisher: Genetics Society of America
quality_controlled: '1'
scopus_import: '1'
status: public
title: Replicability of introgression under linked, polygenic selection
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 210
year: '2018'
...
---
_id: '38'
abstract:
- lang: eng
text: 'Genomes of closely-related species or populations often display localized
regions of enhanced relative sequence divergence, termed genomic islands. It has
been proposed that these islands arise through selective sweeps and/or barriers
to gene flow. Here, we genetically dissect a genomic island that controls flower
color pattern differences between two subspecies of Antirrhinum majus, A.m.striatum
and A.m.pseudomajus, and relate it to clinal variation across a natural hybrid
zone. We show that selective sweeps likely raised relative divergence at two tightly-linked
MYB-like transcription factors, leading to distinct flower patterns in the two
subspecies. The two patterns provide alternate floral guides and create a strong
barrier to gene flow where populations come into contact. This barrier affects
the selected flower color genes and tightlylinked loci, but does not extend outside
of this domain, allowing gene flow to lower relative divergence for the rest of
the chromosome. Thus, both selective sweeps and barriers to gene flow play a role
in shaping genomic islands: sweeps cause elevation in relative divergence, while
heterogeneous gene flow flattens the surrounding "sea," making the island of divergence
stand out. By showing how selective sweeps establish alternative adaptive phenotypes
that lead to barriers to gene flow, our study sheds light on possible mechanisms
leading to reproductive isolation and speciation.'
acknowledgement: ' ERC Grant 201252 (to N.H.B.)'
article_processing_charge: No
author:
- first_name: Hugo
full_name: Tavares, Hugo
last_name: Tavares
- first_name: Annabel
full_name: Whitley, Annabel
last_name: Whitley
- first_name: David
full_name: Field, David
id: 419049E2-F248-11E8-B48F-1D18A9856A87
last_name: Field
orcid: 0000-0002-4014-8478
- first_name: Desmond
full_name: Bradley, Desmond
last_name: Bradley
- first_name: Matthew
full_name: Couchman, Matthew
last_name: Couchman
- first_name: Lucy
full_name: Copsey, Lucy
last_name: Copsey
- first_name: Joane
full_name: Elleouet, Joane
last_name: Elleouet
- first_name: Monique
full_name: Burrus, Monique
last_name: Burrus
- first_name: Christophe
full_name: Andalo, Christophe
last_name: Andalo
- first_name: Miaomiao
full_name: Li, Miaomiao
last_name: Li
- first_name: Qun
full_name: Li, Qun
last_name: Li
- first_name: Yongbiao
full_name: Xue, Yongbiao
last_name: Xue
- first_name: Alexandra B
full_name: Rebocho, Alexandra B
last_name: Rebocho
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Enrico
full_name: Coen, Enrico
last_name: Coen
citation:
ama: Tavares H, Whitley A, Field D, et al. Selection and gene flow shape genomic
islands that control floral guides. PNAS. 2018;115(43):11006-11011. doi:10.1073/pnas.1801832115
apa: Tavares, H., Whitley, A., Field, D., Bradley, D., Couchman, M., Copsey, L.,
… Coen, E. (2018). Selection and gene flow shape genomic islands that control
floral guides. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1801832115
chicago: Tavares, Hugo, Annabel Whitley, David Field, Desmond Bradley, Matthew Couchman,
Lucy Copsey, Joane Elleouet, et al. “Selection and Gene Flow Shape Genomic Islands
That Control Floral Guides.” PNAS. National Academy of Sciences, 2018.
https://doi.org/10.1073/pnas.1801832115.
ieee: H. Tavares et al., “Selection and gene flow shape genomic islands that
control floral guides,” PNAS, vol. 115, no. 43. National Academy of Sciences,
pp. 11006–11011, 2018.
ista: Tavares H, Whitley A, Field D, Bradley D, Couchman M, Copsey L, Elleouet J,
Burrus M, Andalo C, Li M, Li Q, Xue Y, Rebocho AB, Barton NH, Coen E. 2018. Selection
and gene flow shape genomic islands that control floral guides. PNAS. 115(43),
11006–11011.
mla: Tavares, Hugo, et al. “Selection and Gene Flow Shape Genomic Islands That Control
Floral Guides.” PNAS, vol. 115, no. 43, National Academy of Sciences, 2018,
pp. 11006–11, doi:10.1073/pnas.1801832115.
short: H. Tavares, A. Whitley, D. Field, D. Bradley, M. Couchman, L. Copsey, J.
Elleouet, M. Burrus, C. Andalo, M. Li, Q. Li, Y. Xue, A.B. Rebocho, N.H. Barton,
E. Coen, PNAS 115 (2018) 11006–11011.
date_created: 2018-12-11T11:44:18Z
date_published: 2018-10-23T00:00:00Z
date_updated: 2023-09-18T08:36:49Z
day: '23'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1073/pnas.1801832115
external_id:
isi:
- '000448040500065'
pmid:
- '30297406'
file:
- access_level: open_access
checksum: d2305d0cc81dbbe4c1c677d64ad6f6d1
content_type: application/pdf
creator: dernst
date_created: 2018-12-17T08:44:03Z
date_updated: 2020-07-14T12:46:16Z
file_id: '5683'
file_name: 11006.full.pdf
file_size: 1911302
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file_date_updated: 2020-07-14T12:46:16Z
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intvolume: ' 115'
isi: 1
issue: '43'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
page: 11006 - 11011
pmid: 1
publication: PNAS
publication_identifier:
issn:
- '00278424'
publication_status: published
publisher: National Academy of Sciences
publist_id: '8017'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Selection and gene flow shape genomic islands that control floral guides
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 115
year: '2018'
...
---
_id: '40'
abstract:
- lang: eng
text: Hanemaaijer et al. (Molecular Ecology, 27, 2018) describe the genetic consequences
of the introgression of an insecticide resistance allele into a mosquito population.
Linked alleles initially increased, but many of these later declined. It is hard
to determine whether this decline was due to counter‐selection, rather than simply
to chance.
article_processing_charge: Yes (via OA deal)
article_type: letter_note
author:
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: Barton NH. The consequences of an introgression event. Molecular Ecology.
2018;27(24):4973-4975. doi:10.1111/mec.14950
apa: Barton, N. H. (2018). The consequences of an introgression event. Molecular
Ecology. Wiley. https://doi.org/10.1111/mec.14950
chicago: Barton, Nicholas H. “The Consequences of an Introgression Event.” Molecular
Ecology. Wiley, 2018. https://doi.org/10.1111/mec.14950.
ieee: N. H. Barton, “The consequences of an introgression event,” Molecular Ecology,
vol. 27, no. 24. Wiley, pp. 4973–4975, 2018.
ista: Barton NH. 2018. The consequences of an introgression event. Molecular Ecology.
27(24), 4973–4975.
mla: Barton, Nicholas H. “The Consequences of an Introgression Event.” Molecular
Ecology, vol. 27, no. 24, Wiley, 2018, pp. 4973–75, doi:10.1111/mec.14950.
short: N.H. Barton, Molecular Ecology 27 (2018) 4973–4975.
date_created: 2018-12-11T11:44:18Z
date_published: 2018-12-31T00:00:00Z
date_updated: 2023-09-19T10:06:08Z
day: '31'
ddc:
- '576'
department:
- _id: NiBa
doi: 10.1111/mec.14950
external_id:
isi:
- '000454600500001'
pmid:
- '30599087'
file:
- access_level: open_access
content_type: application/pdf
creator: apreinsp
date_created: 2019-07-19T06:54:46Z
date_updated: 2020-07-14T12:46:22Z
file_id: '6652'
file_name: 2018_MolecularEcology_BartonNick.pdf
file_size: 295452
relation: main_file
file_date_updated: 2020-07-14T12:46:22Z
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intvolume: ' 27'
isi: 1
issue: '24'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
page: 4973-4975
pmid: 1
publication: Molecular Ecology
publication_identifier:
issn:
- 1365294X
publication_status: published
publisher: Wiley
publist_id: '8014'
quality_controlled: '1'
related_material:
record:
- id: '9805'
relation: research_data
status: public
scopus_import: '1'
status: public
title: The consequences of an introgression event
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 27
year: '2018'
...
---
_id: '565'
abstract:
- lang: eng
text: 'We re-examine the model of Kirkpatrick and Barton for the spread of an inversion
into a local population. This model assumes that local selection maintains alleles
at two or more loci, despite immigration of alternative alleles at these loci
from another population. We show that an inversion is favored because it prevents
the breakdown of linkage disequilibrium generated by migration; the selective
advantage of an inversion is proportional to the amount of recombination between
the loci involved, as in other cases where inversions are selected for. We derive
expressions for the rate of spread of an inversion; when the loci covered by the
inversion are tightly linked, these conditions deviate substantially from those
proposed previously, and imply that an inversion can then have only a small advantage. '
article_processing_charge: No
article_type: original
author:
- first_name: Brian
full_name: Charlesworth, Brian
last_name: Charlesworth
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: Charlesworth B, Barton NH. The spread of an inversion with migration and selection.
Genetics. 2018;208(1):377-382. doi:10.1534/genetics.117.300426
apa: Charlesworth, B., & Barton, N. H. (2018). The spread of an inversion with
migration and selection. Genetics. Genetics . https://doi.org/10.1534/genetics.117.300426
chicago: Charlesworth, Brian, and Nicholas H Barton. “The Spread of an Inversion
with Migration and Selection.” Genetics. Genetics , 2018. https://doi.org/10.1534/genetics.117.300426.
ieee: B. Charlesworth and N. H. Barton, “The spread of an inversion with migration
and selection,” Genetics, vol. 208, no. 1. Genetics , pp. 377–382, 2018.
ista: Charlesworth B, Barton NH. 2018. The spread of an inversion with migration
and selection. Genetics. 208(1), 377–382.
mla: Charlesworth, Brian, and Nicholas H. Barton. “The Spread of an Inversion with
Migration and Selection.” Genetics, vol. 208, no. 1, Genetics , 2018, pp.
377–82, doi:10.1534/genetics.117.300426.
short: B. Charlesworth, N.H. Barton, Genetics 208 (2018) 377–382.
date_created: 2018-12-11T11:47:12Z
date_published: 2018-01-01T00:00:00Z
date_updated: 2023-09-19T10:12:31Z
day: '01'
department:
- _id: NiBa
doi: 10.1534/genetics.117.300426
external_id:
isi:
- '000419356300025'
pmid:
- '29158424'
intvolume: ' 208'
isi: 1
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5753870/
month: '01'
oa: 1
oa_version: Published Version
page: 377 - 382
pmid: 1
publication: Genetics
publication_status: published
publisher: 'Genetics '
publist_id: '7249'
quality_controlled: '1'
scopus_import: '1'
status: public
title: The spread of an inversion with migration and selection
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 208
year: '2018'
...
---
_id: '430'
abstract:
- lang: eng
text: In this issue of GENETICS, a new method for detecting natural selection on
polygenic traits is developed and applied to sev- eral human examples ( Racimo
et al. 2018 ). By de fi nition, many loci contribute to variation in polygenic
traits, and a challenge for evolutionary ge neticists has been that these traits
can evolve by small, nearly undetectable shifts in allele frequencies across each
of many, typically unknown, loci. Recently, a helpful remedy has arisen. Genome-wide
associ- ation studies (GWAS) have been illuminating sets of loci that can be interrogated
jointly for c hanges in allele frequencies. By aggregating small signal s of change
across many such loci, directional natural selection is now in principle detect-
able using genetic data, even for highly polygenic traits. This is an exciting
arena of progress – with these methods, tests can be made for selection associated
with traits, and we can now study selection in what may be its most prevalent
mode. The continuing fast pace of GWAS publications suggest there will be many
more polygenic tests of selection in the near future, as every new GWAS is an
opportunity for an accom- panying test of polygenic selection. However, it is
important to be aware of complications th at arise in interpretation, especially
given that these studies may easily be misinter- preted both in and outside the
evolutionary genetics commu- nity. Here, we provide context for understanding
polygenic tests and urge caution regarding how these results are inter- preted
and reported upon more broadly.
article_processing_charge: No
author:
- first_name: John
full_name: Novembre, John
last_name: Novembre
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: Novembre J, Barton NH. Tread lightly interpreting polygenic tests of selection.
Genetics. 2018;208(4):1351-1355. doi:10.1534/genetics.118.300786
apa: Novembre, J., & Barton, N. H. (2018). Tread lightly interpreting polygenic
tests of selection. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.118.300786
chicago: Novembre, John, and Nicholas H Barton. “Tread Lightly Interpreting Polygenic
Tests of Selection.” Genetics. Genetics Society of America, 2018. https://doi.org/10.1534/genetics.118.300786.
ieee: J. Novembre and N. H. Barton, “Tread lightly interpreting polygenic tests
of selection,” Genetics, vol. 208, no. 4. Genetics Society of America,
pp. 1351–1355, 2018.
ista: Novembre J, Barton NH. 2018. Tread lightly interpreting polygenic tests of
selection. Genetics. 208(4), 1351–1355.
mla: Novembre, John, and Nicholas H. Barton. “Tread Lightly Interpreting Polygenic
Tests of Selection.” Genetics, vol. 208, no. 4, Genetics Society of America,
2018, pp. 1351–55, doi:10.1534/genetics.118.300786.
short: J. Novembre, N.H. Barton, Genetics 208 (2018) 1351–1355.
date_created: 2018-12-11T11:46:26Z
date_published: 2018-04-01T00:00:00Z
date_updated: 2023-09-19T10:17:30Z
day: '01'
ddc:
- '576'
department:
- _id: NiBa
doi: 10.1534/genetics.118.300786
external_id:
isi:
- '000429094400005'
file:
- access_level: open_access
checksum: 3d838dc285df394376555b794b6a5ad1
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:12:40Z
date_updated: 2020-07-14T12:46:26Z
file_id: '4958'
file_name: IST-2018-1012-v1+1_2018_Barton_Tread.pdf
file_size: 500129
relation: main_file
file_date_updated: 2020-07-14T12:46:26Z
has_accepted_license: '1'
intvolume: ' 208'
isi: 1
issue: '4'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: 1351 - 1355
publication: Genetics
publication_status: published
publisher: Genetics Society of America
publist_id: '7393'
pubrep_id: '1012'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Tread lightly interpreting polygenic tests of selection
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 208
year: '2018'
...
---
_id: '607'
abstract:
- lang: eng
text: We study the Fokker-Planck equation derived in the large system limit of the
Markovian process describing the dynamics of quantitative traits. The Fokker-Planck
equation is posed on a bounded domain and its transport and diffusion coefficients
vanish on the domain's boundary. We first argue that, despite this degeneracy,
the standard no-flux boundary condition is valid. We derive the weak formulation
of the problem and prove the existence and uniqueness of its solutions by constructing
the corresponding contraction semigroup on a suitable function space. Then, we
prove that for the parameter regime with high enough mutation rate the problem
exhibits a positive spectral gap, which implies exponential convergence to equilibrium.Next,
we provide a simple derivation of the so-called Dynamic Maximum Entropy (DynMaxEnt)
method for approximation of observables (moments) of the Fokker-Planck solution,
which can be interpreted as a nonlinear Galerkin approximation. The limited applicability
of the DynMaxEnt method inspires us to introduce its modified version that is
valid for the whole range of admissible parameters. Finally, we present several
numerical experiments to demonstrate the performance of both the original and
modified DynMaxEnt methods. We observe that in the parameter regimes where both
methods are valid, the modified one exhibits slightly better approximation properties
compared to the original one.
acknowledgement: "JH and PM are funded by KAUST baseline funds and grant no. 1000000193
.\r\nWe thank Nicholas Barton (IST Austria) for his useful comments and suggestions.
\r\n\r\n"
article_processing_charge: No
author:
- first_name: Katarina
full_name: Bodova, Katarina
id: 2BA24EA0-F248-11E8-B48F-1D18A9856A87
last_name: Bodova
orcid: 0000-0002-7214-0171
- first_name: Jan
full_name: Haskovec, Jan
last_name: Haskovec
- first_name: Peter
full_name: Markowich, Peter
last_name: Markowich
citation:
ama: 'Bodova K, Haskovec J, Markowich P. Well posedness and maximum entropy approximation
for the dynamics of quantitative traits. Physica D: Nonlinear Phenomena.
2018;376-377:108-120. doi:10.1016/j.physd.2017.10.015'
apa: 'Bodova, K., Haskovec, J., & Markowich, P. (2018). Well posedness and maximum
entropy approximation for the dynamics of quantitative traits. Physica D: Nonlinear
Phenomena. Elsevier. https://doi.org/10.1016/j.physd.2017.10.015'
chicago: 'Bodova, Katarina, Jan Haskovec, and Peter Markowich. “Well Posedness and
Maximum Entropy Approximation for the Dynamics of Quantitative Traits.” Physica
D: Nonlinear Phenomena. Elsevier, 2018. https://doi.org/10.1016/j.physd.2017.10.015.'
ieee: 'K. Bodova, J. Haskovec, and P. Markowich, “Well posedness and maximum entropy
approximation for the dynamics of quantitative traits,” Physica D: Nonlinear
Phenomena, vol. 376–377. Elsevier, pp. 108–120, 2018.'
ista: 'Bodova K, Haskovec J, Markowich P. 2018. Well posedness and maximum entropy
approximation for the dynamics of quantitative traits. Physica D: Nonlinear Phenomena.
376–377, 108–120.'
mla: 'Bodova, Katarina, et al. “Well Posedness and Maximum Entropy Approximation
for the Dynamics of Quantitative Traits.” Physica D: Nonlinear Phenomena,
vol. 376–377, Elsevier, 2018, pp. 108–20, doi:10.1016/j.physd.2017.10.015.'
short: 'K. Bodova, J. Haskovec, P. Markowich, Physica D: Nonlinear Phenomena 376–377
(2018) 108–120.'
date_created: 2018-12-11T11:47:28Z
date_published: 2018-08-01T00:00:00Z
date_updated: 2023-09-19T10:38:34Z
day: '01'
department:
- _id: NiBa
- _id: GaTk
doi: 10.1016/j.physd.2017.10.015
external_id:
arxiv:
- '1704.08757'
isi:
- '000437962900012'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1704.08757
month: '08'
oa: 1
oa_version: Submitted Version
page: 108-120
publication: 'Physica D: Nonlinear Phenomena'
publication_status: published
publisher: Elsevier
publist_id: '7198'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Well posedness and maximum entropy approximation for the dynamics of quantitative
traits
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 376-377
year: '2018'
...
---
_id: '200'
abstract:
- lang: eng
text: This thesis is concerned with the inference of current population structure
based on geo-referenced genetic data. The underlying idea is that population structure
affects its spatial genetic structure. Therefore, genotype information can be
utilized to estimate important demographic parameters such as migration rates.
These indirect estimates of population structure have become very attractive,
as genotype data is now widely available. However, there also has been much concern
about these approaches. Importantly, genetic structure can be influenced by many
complex patterns, which often cannot be disentangled. Moreover, many methods merely
fit heuristic patterns of genetic structure, and do not build upon population
genetics theory. Here, I describe two novel inference methods that address these
shortcomings. In Chapter 2, I introduce an inference scheme based on a new type
of signal, identity by descent (IBD) blocks. Recently, it has become feasible
to detect such long blocks of genome shared between pairs of samples. These blocks
are direct traces of recent coalescence events. As such, they contain ample signal
for inferring recent demography. I examine sharing of IBD blocks in two-dimensional
populations with local migration. Using a diffusion approximation, I derive formulas
for an isolation by distance pattern of long IBD blocks and show that sharing
of long IBD blocks approaches rapid exponential decay for growing sample distance.
I describe an inference scheme based on these results. It can robustly estimate
the dispersal rate and population density, which is demonstrated on simulated
data. I also show an application to estimate mean migration and the rate of recent
population growth within Eastern Europe. Chapter 3 is about a novel method to
estimate barriers to gene flow in a two dimensional population. This inference
scheme utilizes geographically localized allele frequency fluctuations - a classical
isolation by distance signal. The strength of these local fluctuations increases
on average next to a barrier, and there is less correlation across it. I again
use a framework of diffusion of ancestral lineages to model this effect, and provide
an efficient numerical implementation to fit the results to geo-referenced biallelic
SNP data. This inference scheme is able to robustly estimate strong barriers to
gene flow, as tests on simulated data confirm.
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Harald
full_name: Ringbauer, Harald
id: 417FCFF4-F248-11E8-B48F-1D18A9856A87
last_name: Ringbauer
orcid: 0000-0002-4884-9682
citation:
ama: Ringbauer H. Inferring recent demography from spatial genetic structure. 2018.
doi:10.15479/AT:ISTA:th_963
apa: Ringbauer, H. (2018). Inferring recent demography from spatial genetic structure.
Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_963
chicago: Ringbauer, Harald. “Inferring Recent Demography from Spatial Genetic Structure.”
Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:th_963.
ieee: H. Ringbauer, “Inferring recent demography from spatial genetic structure,”
Institute of Science and Technology Austria, 2018.
ista: Ringbauer H. 2018. Inferring recent demography from spatial genetic structure.
Institute of Science and Technology Austria.
mla: Ringbauer, Harald. Inferring Recent Demography from Spatial Genetic Structure.
Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:th_963.
short: H. Ringbauer, Inferring Recent Demography from Spatial Genetic Structure,
Institute of Science and Technology Austria, 2018.
date_created: 2018-12-11T11:45:10Z
date_published: 2018-02-21T00:00:00Z
date_updated: 2023-09-20T12:00:56Z
day: '21'
ddc:
- '576'
degree_awarded: PhD
department:
- _id: NiBa
doi: 10.15479/AT:ISTA:th_963
file:
- access_level: open_access
checksum: 8cc534d2b528ae017acf80874cce48c9
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:14:55Z
date_updated: 2020-07-14T12:45:23Z
file_id: '5111'
file_name: IST-2018-963-v1+1_thesis.pdf
file_size: 5792935
relation: main_file
- access_level: closed
checksum: 6af18d7e5a7e2728ceda2f41ee24f628
content_type: application/zip
creator: dernst
date_created: 2019-04-05T09:30:12Z
date_updated: 2020-07-14T12:45:23Z
file_id: '6224'
file_name: 2018_thesis_ringbauer_source.zip
file_size: 113365
relation: source_file
file_date_updated: 2020-07-14T12:45:23Z
has_accepted_license: '1'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
page: '146'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
publist_id: '7713'
pubrep_id: '963'
related_material:
record:
- id: '563'
relation: part_of_dissertation
status: public
- id: '1074'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
title: Inferring recent demography from spatial genetic structure
tmp:
image: /images/cc_by_nc.png
legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode
name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
short: CC BY-NC (4.0)
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2018'
...
---
_id: '139'
abstract:
- lang: eng
text: 'Genome-scale diversity data are increasingly available in a variety of biological
systems, and can be used to reconstruct the past evolutionary history of species
divergence. However, extracting the full demographic information from these data
is not trivial, and requires inferential methods that account for the diversity
of coalescent histories throughout the genome. Here, we evaluate the potential
and limitations of one such approach. We reexamine a well-known system of mussel
sister species, using the joint site frequency spectrum (jSFS) of synonymousmutations
computed either fromexome capture or RNA-seq, in an Approximate Bayesian Computation
(ABC) framework. We first assess the best sampling strategy (number of: individuals,
loci, and bins in the jSFS), and show that model selection is robust to variation
in the number of individuals and loci. In contrast, different binning choices
when summarizing the jSFS, strongly affect the results: including classes of low
and high frequency shared polymorphisms can more effectively reveal recent migration
events. We then take advantage of the flexibility of ABC to compare more realistic
models of speciation, including variation in migration rates through time (i.e.,
periodic connectivity) and across genes (i.e., genome-wide heterogeneity in migration
rates). We show that these models were consistently selected as the most probable,
suggesting that mussels have experienced a complex history of gene flow during
divergence and that the species boundary is semi-permeable. Our work provides
a comprehensive evaluation of ABC demographic inference in mussels based on the
coding jSFS, and supplies guidelines for employing different sequencing techniques
and sampling strategies. We emphasize, perhaps surprisingly, that inferences are
less limited by the volume of data, than by the way in which they are analyzed.'
article_number: '30083438'
article_processing_charge: No
author:
- first_name: Christelle
full_name: Fraisse, Christelle
id: 32DF5794-F248-11E8-B48F-1D18A9856A87
last_name: Fraisse
orcid: 0000-0001-8441-5075
- first_name: Camille
full_name: Roux, Camille
last_name: Roux
- first_name: Pierre
full_name: Gagnaire, Pierre
last_name: Gagnaire
- first_name: Jonathan
full_name: Romiguier, Jonathan
last_name: Romiguier
- first_name: Nicolas
full_name: Faivre, Nicolas
last_name: Faivre
- first_name: John
full_name: Welch, John
last_name: Welch
- first_name: Nicolas
full_name: Bierne, Nicolas
last_name: Bierne
citation:
ama: 'Fraisse C, Roux C, Gagnaire P, et al. The divergence history of European blue
mussel species reconstructed from Approximate Bayesian Computation: The effects
of sequencing techniques and sampling strategies. PeerJ. 2018;2018(7).
doi:10.7717/peerj.5198'
apa: 'Fraisse, C., Roux, C., Gagnaire, P., Romiguier, J., Faivre, N., Welch, J.,
& Bierne, N. (2018). The divergence history of European blue mussel species
reconstructed from Approximate Bayesian Computation: The effects of sequencing
techniques and sampling strategies. PeerJ. PeerJ. https://doi.org/10.7717/peerj.5198'
chicago: 'Fraisse, Christelle, Camille Roux, Pierre Gagnaire, Jonathan Romiguier,
Nicolas Faivre, John Welch, and Nicolas Bierne. “The Divergence History of European
Blue Mussel Species Reconstructed from Approximate Bayesian Computation: The Effects
of Sequencing Techniques and Sampling Strategies.” PeerJ. PeerJ, 2018.
https://doi.org/10.7717/peerj.5198.'
ieee: 'C. Fraisse et al., “The divergence history of European blue mussel
species reconstructed from Approximate Bayesian Computation: The effects of sequencing
techniques and sampling strategies,” PeerJ, vol. 2018, no. 7. PeerJ, 2018.'
ista: 'Fraisse C, Roux C, Gagnaire P, Romiguier J, Faivre N, Welch J, Bierne N.
2018. The divergence history of European blue mussel species reconstructed from
Approximate Bayesian Computation: The effects of sequencing techniques and sampling
strategies. PeerJ. 2018(7), 30083438.'
mla: 'Fraisse, Christelle, et al. “The Divergence History of European Blue Mussel
Species Reconstructed from Approximate Bayesian Computation: The Effects of Sequencing
Techniques and Sampling Strategies.” PeerJ, vol. 2018, no. 7, 30083438,
PeerJ, 2018, doi:10.7717/peerj.5198.'
short: C. Fraisse, C. Roux, P. Gagnaire, J. Romiguier, N. Faivre, J. Welch, N. Bierne,
PeerJ 2018 (2018).
date_created: 2018-12-11T11:44:50Z
date_published: 2018-07-30T00:00:00Z
date_updated: 2023-10-17T12:25:28Z
day: '30'
ddc:
- '576'
department:
- _id: BeVi
- _id: NiBa
doi: 10.7717/peerj.5198
external_id:
isi:
- '000440484800002'
file:
- access_level: open_access
checksum: 7d55ae22598a1c70759cd671600cff53
content_type: application/pdf
creator: dernst
date_created: 2018-12-18T09:42:11Z
date_updated: 2020-07-14T12:44:48Z
file_id: '5739'
file_name: 2018_PeerJ_Fraisse.pdf
file_size: 1480792
relation: main_file
file_date_updated: 2020-07-14T12:44:48Z
has_accepted_license: '1'
intvolume: ' 2018'
isi: 1
issue: '7'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
publication: PeerJ
publication_status: published
publisher: PeerJ
publist_id: '7784'
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'The divergence history of European blue mussel species reconstructed from
Approximate Bayesian Computation: The effects of sequencing techniques and sampling
strategies'
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 2018
year: '2018'
...
---
_id: '33'
abstract:
- lang: eng
text: Secondary contact is the reestablishment of gene flow between sister populations
that have diverged. For instance, at the end of the Quaternary glaciations in
Europe, secondary contact occurred during the northward expansion of the populations
which had found refugia in the southern peninsulas. With the advent of multi-locus
markers, secondary contact can be investigated using various molecular signatures
including gradients of allele frequency, admixture clines, and local increase
of genetic differentiation. We use coalescent simulations to investigate if molecular
data provide enough information to distinguish between secondary contact following
range expansion and an alternative evolutionary scenario consisting of a barrier
to gene flow in an isolation-by-distance model. We find that an excess of linkage
disequilibrium and of genetic diversity at the suture zone is a unique signature
of secondary contact. We also find that the directionality index ψ, which was
proposed to study range expansion, is informative to distinguish between the two
hypotheses. However, although evidence for secondary contact is usually conveyed
by statistics related to admixture coefficients, we find that they can be confounded
by isolation-by-distance. We recommend to account for the spatial repartition
of individuals when investigating secondary contact in order to better reflect
the complex spatio-temporal evolution of populations and species.
acknowledgement: 'Johanna Bertl was supported by the Vienna Graduate School of Population
Genetics (Austrian Science Fund (FWF): W1225-B20) and worked on this project while
employed at the Department of Statistics and Operations Research, University of
Vienna, Austria. This article was developed in the framework of the Grenoble Alpes
Data Institute, which is supported by the French National Research Agency under
the “Investissments d’avenir” program (ANR-15-IDEX-02).'
article_number: e5325
article_processing_charge: No
author:
- first_name: Johanna
full_name: Bertl, Johanna
last_name: Bertl
- first_name: Harald
full_name: Ringbauer, Harald
id: 417FCFF4-F248-11E8-B48F-1D18A9856A87
last_name: Ringbauer
orcid: 0000-0002-4884-9682
- first_name: Michaël
full_name: Blum, Michaël
last_name: Blum
citation:
ama: Bertl J, Ringbauer H, Blum M. Can secondary contact following range expansion
be distinguished from barriers to gene flow? PeerJ. 2018;2018(10). doi:10.7717/peerj.5325
apa: Bertl, J., Ringbauer, H., & Blum, M. (2018). Can secondary contact following
range expansion be distinguished from barriers to gene flow? PeerJ. PeerJ.
https://doi.org/10.7717/peerj.5325
chicago: Bertl, Johanna, Harald Ringbauer, and Michaël Blum. “Can Secondary Contact
Following Range Expansion Be Distinguished from Barriers to Gene Flow?” PeerJ.
PeerJ, 2018. https://doi.org/10.7717/peerj.5325.
ieee: J. Bertl, H. Ringbauer, and M. Blum, “Can secondary contact following range
expansion be distinguished from barriers to gene flow?,” PeerJ, vol. 2018,
no. 10. PeerJ, 2018.
ista: Bertl J, Ringbauer H, Blum M. 2018. Can secondary contact following range
expansion be distinguished from barriers to gene flow? PeerJ. 2018(10), e5325.
mla: Bertl, Johanna, et al. “Can Secondary Contact Following Range Expansion Be
Distinguished from Barriers to Gene Flow?” PeerJ, vol. 2018, no. 10, e5325,
PeerJ, 2018, doi:10.7717/peerj.5325.
short: J. Bertl, H. Ringbauer, M. Blum, PeerJ 2018 (2018).
date_created: 2018-12-11T11:44:16Z
date_published: 2018-10-01T00:00:00Z
date_updated: 2023-10-17T12:24:43Z
day: '01'
ddc:
- '576'
department:
- _id: NiBa
doi: 10.7717/peerj.5325
external_id:
isi:
- '000447204400001'
pmid:
- '30294507'
file:
- access_level: open_access
checksum: 3334886c4b39678db4c4b74299ca14ba
content_type: application/pdf
creator: dernst
date_created: 2018-12-17T10:46:06Z
date_updated: 2020-07-14T12:46:06Z
file_id: '5692'
file_name: 2018_PeerJ_Bertl.pdf
file_size: 1328344
relation: main_file
file_date_updated: 2020-07-14T12:46:06Z
has_accepted_license: '1'
intvolume: ' 2018'
isi: 1
issue: '10'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
pmid: 1
publication: PeerJ
publication_status: published
publisher: PeerJ
publist_id: '8022'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Can secondary contact following range expansion be distinguished from barriers
to gene flow?
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 2018
year: '2018'
...
---
_id: '286'
abstract:
- lang: eng
text: 'Pedigree and sibship reconstruction are important methods in quantifying
relationships and fitness of individuals in natural populations. Current methods
employ a Markov chain-based algorithm to explore plausible possible pedigrees
iteratively. This provides accurate results, but is time-consuming. Here, we develop
a method to infer sibship and paternity relationships from half-sibling arrays
of known maternity using hierarchical clustering. Given 50 or more unlinked SNP
markers and empirically derived error rates, the method performs as well as the
widely used package Colony, but is faster by two orders of magnitude. Using simulations,
we show that the method performs well across contrasting mating scenarios, even
when samples are large. We then apply the method to open-pollinated arrays of
the snapdragon Antirrhinum majus and find evidence for a high degree of multiple
mating. Although we focus on diploid SNP data, the method does not depend on marker
type and as such has broad applications in nonmodel systems. '
acknowledgement: 'ERC, Grant/Award Number: 250152'
article_processing_charge: No
author:
- first_name: Thomas
full_name: Ellis, Thomas
id: 3153D6D4-F248-11E8-B48F-1D18A9856A87
last_name: Ellis
orcid: 0000-0002-8511-0254
- first_name: David
full_name: Field, David
id: 419049E2-F248-11E8-B48F-1D18A9856A87
last_name: Field
orcid: 0000-0002-4014-8478
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: Ellis T, Field D, Barton NH. Efficient inference of paternity and sibship inference
given known maternity via hierarchical clustering. Molecular Ecology Resources.
2018;18(5):988-999. doi:10.1111/1755-0998.12782
apa: Ellis, T., Field, D., & Barton, N. H. (2018). Efficient inference of paternity
and sibship inference given known maternity via hierarchical clustering. Molecular
Ecology Resources. Wiley. https://doi.org/10.1111/1755-0998.12782
chicago: Ellis, Thomas, David Field, and Nicholas H Barton. “Efficient Inference
of Paternity and Sibship Inference given Known Maternity via Hierarchical Clustering.”
Molecular Ecology Resources. Wiley, 2018. https://doi.org/10.1111/1755-0998.12782.
ieee: T. Ellis, D. Field, and N. H. Barton, “Efficient inference of paternity and
sibship inference given known maternity via hierarchical clustering,” Molecular
Ecology Resources, vol. 18, no. 5. Wiley, pp. 988–999, 2018.
ista: Ellis T, Field D, Barton NH. 2018. Efficient inference of paternity and sibship
inference given known maternity via hierarchical clustering. Molecular Ecology
Resources. 18(5), 988–999.
mla: Ellis, Thomas, et al. “Efficient Inference of Paternity and Sibship Inference
given Known Maternity via Hierarchical Clustering.” Molecular Ecology Resources,
vol. 18, no. 5, Wiley, 2018, pp. 988–99, doi:10.1111/1755-0998.12782.
short: T. Ellis, D. Field, N.H. Barton, Molecular Ecology Resources 18 (2018) 988–999.
date_created: 2018-12-11T11:45:37Z
date_published: 2018-09-01T00:00:00Z
date_updated: 2024-02-21T13:45:00Z
day: '01'
department:
- _id: NiBa
doi: 10.1111/1755-0998.12782
ec_funded: 1
external_id:
isi:
- '000441753000007'
intvolume: ' 18'
isi: 1
issue: '5'
language:
- iso: eng
month: '09'
oa_version: None
page: 988 - 999
project:
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
publication: Molecular Ecology Resources
publication_status: published
publisher: Wiley
quality_controlled: '1'
related_material:
record:
- id: '5583'
relation: popular_science
status: public
scopus_import: '1'
status: public
title: Efficient inference of paternity and sibship inference given known maternity
via hierarchical clustering
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 18
year: '2018'
...
---
_id: '5583'
abstract:
- lang: eng
text: "Data and scripts are provided in support of the manuscript \"Efficient inference
of paternity and sibship inference given known maternity via hierarchical clustering\",
and the associated Python package FAPS, available from www.github.com/ellisztamas/faps.\r\n\r\nSimulation
scripts cover:\r\n1. Performance under different mating scenarios.\r\n2. Comparison
with Colony2.\r\n3. Effect of changing the number of Monte Carlo draws\r\n\r\nThe
final script covers the analysis of half-sib arrays from wild-pollinated seed
in an Antirrhinum majus hybrid zone."
article_processing_charge: No
author:
- first_name: Thomas
full_name: Ellis, Thomas
id: 3153D6D4-F248-11E8-B48F-1D18A9856A87
last_name: Ellis
orcid: 0000-0002-8511-0254
citation:
ama: Ellis T. Data and Python scripts supporting Python package FAPS. 2018. doi:10.15479/AT:ISTA:95
apa: Ellis, T. (2018). Data and Python scripts supporting Python package FAPS. Institute
of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:95
chicago: Ellis, Thomas. “Data and Python Scripts Supporting Python Package FAPS.”
Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:95.
ieee: T. Ellis, “Data and Python scripts supporting Python package FAPS.” Institute
of Science and Technology Austria, 2018.
ista: Ellis T. 2018. Data and Python scripts supporting Python package FAPS, Institute
of Science and Technology Austria, 10.15479/AT:ISTA:95.
mla: Ellis, Thomas. Data and Python Scripts Supporting Python Package FAPS.
Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:95.
short: T. Ellis, (2018).
contributor:
- first_name: David
id: 419049E2-F248-11E8-B48F-1D18A9856A87
last_name: Field
- first_name: Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
datarep_id: '95'
date_created: 2018-12-12T12:31:39Z
date_published: 2018-02-12T00:00:00Z
date_updated: 2024-02-21T13:45:01Z
day: '12'
department:
- _id: NiBa
doi: 10.15479/AT:ISTA:95
file:
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checksum: fc6aab51439f2622ba6df8632e66fd4f
content_type: text/csv
creator: system
date_created: 2018-12-12T13:02:41Z
date_updated: 2020-07-14T12:47:07Z
file_id: '5606'
file_name: IST-2018-95-v1+1_amajus_GPS_2012.csv
file_size: 122048
relation: main_file
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checksum: 92347586ae4f8a6eb7c04354797bf314
content_type: text/csv
creator: system
date_created: 2018-12-12T13:02:42Z
date_updated: 2020-07-14T12:47:07Z
file_id: '5607'
file_name: IST-2018-95-v1+2_offspring_SNPs_2012.csv
file_size: 235980
relation: main_file
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checksum: 3300813645a54e6c5c39f41917228354
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creator: system
date_created: 2018-12-12T13:02:43Z
date_updated: 2020-07-14T12:47:07Z
file_id: '5608'
file_name: IST-2018-95-v1+3_parents_SNPs_2012.csv
file_size: 311712
relation: main_file
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creator: system
date_created: 2018-12-12T13:02:44Z
date_updated: 2020-07-14T12:47:07Z
file_id: '5609'
file_name: IST-2018-95-v1+4_faps_scripts.zip
file_size: 342090
relation: main_file
file_date_updated: 2020-07-14T12:47:07Z
has_accepted_license: '1'
month: '02'
oa: 1
oa_version: Published Version
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '286'
relation: research_paper
status: public
status: public
title: Data and Python scripts supporting Python package FAPS
tmp:
image: /images/cc_0.png
legal_code_url: https://creativecommons.org/publicdomain/zero/1.0/legalcode
name: Creative Commons Public Domain Dedication (CC0 1.0)
short: CC0 (1.0)
type: research_data
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2018'
...
---
_id: '5757'
abstract:
- lang: eng
text: "File S1. Variant Calling Format file of the ingroup: 197 haploid sequences
of D. melanogaster from Zambia (Africa) aligned to the D. melanogaster 5.57 reference
genome.\r\n\r\nFile S2. Variant Calling Format file of the outgroup: 1 haploid
sequence of D. simulans aligned to the D. melanogaster 5.57 reference genome.\r\n\r\nFile
S3. Annotations of each transcript in coding regions with SNPeff: Ps (# of synonymous
polymorphic sites); Pn (# of non-synonymous polymorphic sites); Ds (# of synonymous
divergent sites); Dn (# of non-synonymous divergent sites); DoS; ⍺ MK . All variants
were included.\r\n\r\nFile S4. Annotations of each transcript in non-coding regions
with SNPeff: Ps (# of synonymous polymorphic sites); Pu (# of UTR polymorphic
sites); Ds (# of synonymous divergent sites); Du (# of UTR divergent sites); DoS;
⍺ MK . All variants were included.\r\n\r\nFile S5. Annotations of each transcript
in coding regions with SNPGenie: Ps (# of synonymous polymorphic sites); πs (synonymous
diversity); Ss_p (total # of synonymous sites in the polymorphism data); Pn (#
of non-synonymous polymorphic sites); πn (non-synonymous diversity); Sn_p (total
# of non-synonymous sites in the polymorphism data); Ds (# of synonymous divergent
sites); ks (synonymous evolutionary rate); Ss_d (total # of synonymous sites in
the divergence data); Dn (# of non-synonymous divergent sites); kn (non-synonymous
evolutionary rate); Sn_d (total # of non-\r\nsynonymous sites in the divergence
data); DoS; ⍺ MK . All variants were included.\r\n\r\nFile S6. Gene expression
values (RPKM summed over all transcripts) for each sample. Values were quantile-normalized
across all samples.\r\n\r\nFile S7. Final dataset with all covariates, ⍺ MK ,
ωA MK and DoS for coding sites, excluding variants below 5% frequency.\r\n\r\nFile
S8. Final dataset with all covariates, ⍺ MK , ωA MK and DoS for non-coding sites,
excluding variants below 5%\r\nfrequency.\r\n\r\nFile S9. Final dataset with all
covariates, ⍺ EWK , ωA EWK and deleterious SFS for coding sites obtained with
the Eyre-Walker and Keightley method on binned data and using all variants."
article_processing_charge: No
author:
- first_name: Christelle
full_name: Fraisse, Christelle
id: 32DF5794-F248-11E8-B48F-1D18A9856A87
last_name: Fraisse
orcid: 0000-0001-8441-5075
citation:
ama: Fraisse C. Supplementary Files for “Pleiotropy modulates the efficacy of selection
in Drosophila melanogaster.” 2018. doi:10.15479/at:ista:/5757
apa: Fraisse, C. (2018). Supplementary Files for “Pleiotropy modulates the efficacy
of selection in Drosophila melanogaster.” Institute of Science and Technology
Austria. https://doi.org/10.15479/at:ista:/5757
chicago: Fraisse, Christelle. “Supplementary Files for ‘Pleiotropy Modulates the
Efficacy of Selection in Drosophila Melanogaster.’” Institute of Science and Technology
Austria, 2018. https://doi.org/10.15479/at:ista:/5757.
ieee: C. Fraisse, “Supplementary Files for ‘Pleiotropy modulates the efficacy of
selection in Drosophila melanogaster.’” Institute of Science and Technology Austria,
2018.
ista: Fraisse C. 2018. Supplementary Files for ‘Pleiotropy modulates the efficacy
of selection in Drosophila melanogaster’, Institute of Science and Technology
Austria, 10.15479/at:ista:/5757.
mla: Fraisse, Christelle. Supplementary Files for “Pleiotropy Modulates the Efficacy
of Selection in Drosophila Melanogaster.” Institute of Science and Technology
Austria, 2018, doi:10.15479/at:ista:/5757.
short: C. Fraisse, (2018).
contributor:
- first_name: Christelle
id: 32DF5794-F248-11E8-B48F-1D18A9856A87
last_name: Fraisse
- first_name: Gemma
id: 33AB266C-F248-11E8-B48F-1D18A9856A87
last_name: Puixeu Sala
- first_name: Beatriz
id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
last_name: Vicoso
orcid: 0000-0002-4579-8306
date_created: 2018-12-19T14:22:35Z
date_published: 2018-12-19T00:00:00Z
date_updated: 2024-02-21T13:59:18Z
day: '19'
ddc:
- '576'
department:
- _id: BeVi
- _id: NiBa
doi: 10.15479/at:ista:/5757
ec_funded: 1
file:
- access_level: open_access
checksum: aed7ee9ca3f4dc07d8a66945f68e13cd
content_type: application/zip
creator: cfraisse
date_created: 2018-12-19T14:19:52Z
date_updated: 2020-07-14T12:47:11Z
file_id: '5758'
file_name: FileS1.zip
file_size: 369837892
relation: main_file
- access_level: open_access
checksum: 3592e467b4d8206650860b612d6e12f3
content_type: application/zip
creator: cfraisse
date_created: 2018-12-19T14:19:49Z
date_updated: 2020-07-14T12:47:11Z
file_id: '5759'
file_name: FileS2.zip
file_size: 84856909
relation: main_file
- access_level: open_access
checksum: c37ac5d5437c457338afc128c1240655
content_type: text/plain
creator: cfraisse
date_created: 2018-12-19T14:19:49Z
date_updated: 2020-07-14T12:47:11Z
file_id: '5760'
file_name: FileS3.txt
file_size: 881133
relation: main_file
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checksum: 943dfd14da61817441e33e3e3cb8cdb9
content_type: text/plain
creator: cfraisse
date_created: 2018-12-19T14:19:49Z
date_updated: 2020-07-14T12:47:11Z
file_id: '5761'
file_name: FileS4.txt
file_size: 883742
relation: main_file
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checksum: 1c669b6c4690ec1bbca3e2da9f566d17
content_type: text/plain
creator: cfraisse
date_created: 2018-12-19T14:19:49Z
date_updated: 2020-07-14T12:47:11Z
file_id: '5762'
file_name: FileS5.txt
file_size: 2495437
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checksum: f40f661b987ca6fb6b47f650cbbb04e6
content_type: text/plain
creator: cfraisse
date_created: 2018-12-19T14:19:50Z
date_updated: 2020-07-14T12:47:11Z
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file_name: FileS6.txt
file_size: 15913457
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checksum: 25f41e5b8a075669c6c88d4c6713bf6f
content_type: text/plain
creator: cfraisse
date_created: 2018-12-19T14:19:50Z
date_updated: 2020-07-14T12:47:11Z
file_id: '5764'
file_name: FileS7.txt
file_size: 2584120
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content_type: text/plain
creator: cfraisse
date_created: 2018-12-19T14:19:50Z
date_updated: 2020-07-14T12:47:11Z
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file_name: FileS8.txt
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checksum: 0fe7a58a030b11bf3b9c8ff7a7addcae
content_type: text/plain
creator: cfraisse
date_created: 2018-12-19T14:19:50Z
date_updated: 2020-07-14T12:47:11Z
file_id: '5766'
file_name: FileS9.txt
file_size: 100737
relation: main_file
file_date_updated: 2020-07-14T12:47:11Z
has_accepted_license: '1'
keyword:
- (mal)adaptation
- pleiotropy
- selective constraint
- evo-devo
- gene expression
- Drosophila melanogaster
month: '12'
oa: 1
oa_version: Published Version
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '6089'
relation: research_paper
status: public
status: public
title: Supplementary Files for "Pleiotropy modulates the efficacy of selection in
Drosophila melanogaster"
type: research_data
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2018'
...
---
_id: '1112'
abstract:
- lang: eng
text: There has been renewed interest in modelling the behaviour of evolutionary
algorithms by more traditional mathematical objects, such as ordinary differential
equations or Markov chains. The advantage is that the analysis becomes greatly
facilitated due to the existence of well established methods. However, this typically
comes at the cost of disregarding information about the process. Here, we introduce
the use of stochastic differential equations (SDEs) for the study of EAs. SDEs
can produce simple analytical results for the dynamics of stochastic processes,
unlike Markov chains which can produce rigorous but unwieldy expressions about
the dynamics. On the other hand, unlike ordinary differential equations (ODEs),
they do not discard information about the stochasticity of the process. We show
that these are especially suitable for the analysis of fixed budget scenarios
and present analogs of the additive and multiplicative drift theorems for SDEs.
We exemplify the use of these methods for two model algorithms ((1+1) EA and RLS)
on two canonical problems(OneMax and LeadingOnes).
author:
- first_name: Tiago
full_name: Paixao, Tiago
id: 2C5658E6-F248-11E8-B48F-1D18A9856A87
last_name: Paixao
orcid: 0000-0003-2361-3953
- first_name: Jorge
full_name: Pérez Heredia, Jorge
last_name: Pérez Heredia
citation:
ama: 'Paixao T, Pérez Heredia J. An application of stochastic differential equations
to evolutionary algorithms. In: Proceedings of the 14th ACM/SIGEVO Conference
on Foundations of Genetic Algorithms. ACM; 2017:3-11. doi:10.1145/3040718.3040729'
apa: 'Paixao, T., & Pérez Heredia, J. (2017). An application of stochastic differential
equations to evolutionary algorithms. In Proceedings of the 14th ACM/SIGEVO
Conference on Foundations of Genetic Algorithms (pp. 3–11). Copenhagen, Denmark:
ACM. https://doi.org/10.1145/3040718.3040729'
chicago: Paixao, Tiago, and Jorge Pérez Heredia. “An Application of Stochastic Differential
Equations to Evolutionary Algorithms.” In Proceedings of the 14th ACM/SIGEVO
Conference on Foundations of Genetic Algorithms, 3–11. ACM, 2017. https://doi.org/10.1145/3040718.3040729.
ieee: T. Paixao and J. Pérez Heredia, “An application of stochastic differential
equations to evolutionary algorithms,” in Proceedings of the 14th ACM/SIGEVO
Conference on Foundations of Genetic Algorithms, Copenhagen, Denmark, 2017,
pp. 3–11.
ista: 'Paixao T, Pérez Heredia J. 2017. An application of stochastic differential
equations to evolutionary algorithms. Proceedings of the 14th ACM/SIGEVO Conference
on Foundations of Genetic Algorithms. FOGA: Foundations of Genetic Algorithms,
3–11.'
mla: Paixao, Tiago, and Jorge Pérez Heredia. “An Application of Stochastic Differential
Equations to Evolutionary Algorithms.” Proceedings of the 14th ACM/SIGEVO Conference
on Foundations of Genetic Algorithms, ACM, 2017, pp. 3–11, doi:10.1145/3040718.3040729.
short: T. Paixao, J. Pérez Heredia, in:, Proceedings of the 14th ACM/SIGEVO Conference
on Foundations of Genetic Algorithms, ACM, 2017, pp. 3–11.
conference:
end_date: 2017-01-15
location: Copenhagen, Denmark
name: 'FOGA: Foundations of Genetic Algorithms'
start_date: 2017-01-12
date_created: 2018-12-11T11:50:12Z
date_published: 2017-01-12T00:00:00Z
date_updated: 2021-01-12T06:48:22Z
day: '12'
department:
- _id: NiBa
doi: 10.1145/3040718.3040729
language:
- iso: eng
month: '01'
oa_version: None
page: 3 - 11
publication: Proceedings of the 14th ACM/SIGEVO Conference on Foundations of Genetic
Algorithms
publication_identifier:
isbn:
- 978-145034651-1
publication_status: published
publisher: ACM
publist_id: '6255'
quality_controlled: '1'
scopus_import: 1
status: public
title: An application of stochastic differential equations to evolutionary algorithms
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2017'
...
---
_id: '1191'
abstract:
- lang: eng
text: Variation in genotypes may be responsible for differences in dispersal rates,
directional biases, and growth rates of individuals. These traits may favor certain
genotypes and enhance their spatiotemporal spreading into areas occupied by the
less advantageous genotypes. We study how these factors influence the speed of
spreading in the case of two competing genotypes under the assumption that spatial
variation of the total population is small compared to the spatial variation of
the frequencies of the genotypes in the population. In that case, the dynamics
of the frequency of one of the genotypes is approximately described by a generalized
Fisher–Kolmogorov–Petrovskii–Piskunov (F–KPP) equation. This generalized F–KPP
equation with (nonlinear) frequency-dependent diffusion and advection terms admits
traveling wave solutions that characterize the invasion of the dominant genotype.
Our existence results generalize the classical theory for traveling waves for
the F–KPP with constant coefficients. Moreover, in the particular case of the
quadratic (monostable) nonlinear growth–decay rate in the generalized F–KPP we
study in detail the influence of the variance in diffusion and mean displacement
rates of the two genotypes on the minimal wave propagation speed.
acknowledgement: "We thank Nick Barton, Katarína Bod’ová, and Sr\r\n-\r\ndan Sarikas
for constructive feed-\r\nback and support. Furthermore, we would like to express
our deep gratitude to the anonymous referees (one\r\nof whom, Jimmy Garnier, agreed
to reveal his identity) and the editor Max Souza, for very helpful and\r\ndetailed
comments and suggestions that significantly helped us to improve the manuscript.
This project has\r\nreceived funding from the European Union’s Seventh Framework
Programme for research, technological\r\ndevelopment and demonstration under Grant
Agreement 618091 Speed of Adaptation in Population Genet-\r\nics and Evolutionary
Computation (SAGE) and the European Research Council (ERC) Grant No. 250152\r\n(SN),
from the Scientific Grant Agency of the Slovak Republic under the Grant 1/0459/13
and by the Slovak\r\nResearch and Development Agency under the Contract No. APVV-14-0378
(RK). RK would also like to\r\nthank IST Austria for its hospitality during the
work on this project."
author:
- first_name: Richard
full_name: Kollár, Richard
last_name: Kollár
- first_name: Sebastian
full_name: Novak, Sebastian
id: 461468AE-F248-11E8-B48F-1D18A9856A87
last_name: Novak
citation:
ama: Kollár R, Novak S. Existence of traveling waves for the generalized F–KPP equation.
Bulletin of Mathematical Biology. 2017;79(3):525-559. doi:10.1007/s11538-016-0244-3
apa: Kollár, R., & Novak, S. (2017). Existence of traveling waves for the generalized
F–KPP equation. Bulletin of Mathematical Biology. Springer. https://doi.org/10.1007/s11538-016-0244-3
chicago: Kollár, Richard, and Sebastian Novak. “Existence of Traveling Waves for
the Generalized F–KPP Equation.” Bulletin of Mathematical Biology. Springer,
2017. https://doi.org/10.1007/s11538-016-0244-3.
ieee: R. Kollár and S. Novak, “Existence of traveling waves for the generalized
F–KPP equation,” Bulletin of Mathematical Biology, vol. 79, no. 3. Springer,
pp. 525–559, 2017.
ista: Kollár R, Novak S. 2017. Existence of traveling waves for the generalized
F–KPP equation. Bulletin of Mathematical Biology. 79(3), 525–559.
mla: Kollár, Richard, and Sebastian Novak. “Existence of Traveling Waves for the
Generalized F–KPP Equation.” Bulletin of Mathematical Biology, vol. 79,
no. 3, Springer, 2017, pp. 525–59, doi:10.1007/s11538-016-0244-3.
short: R. Kollár, S. Novak, Bulletin of Mathematical Biology 79 (2017) 525–559.
date_created: 2018-12-11T11:50:38Z
date_published: 2017-03-01T00:00:00Z
date_updated: 2021-01-12T06:48:58Z
day: '01'
department:
- _id: NiBa
doi: 10.1007/s11538-016-0244-3
ec_funded: 1
intvolume: ' 79'
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1607.00944
month: '03'
oa: 1
oa_version: Preprint
page: 525-559
project:
- _id: 25B1EC9E-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '618091'
name: Speed of Adaptation in Population Genetics and Evolutionary Computation
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
publication: Bulletin of Mathematical Biology
publication_status: published
publisher: Springer
publist_id: '6160'
quality_controlled: '1'
scopus_import: 1
status: public
title: Existence of traveling waves for the generalized F–KPP equation
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 79
year: '2017'
...
---
_id: '570'
abstract:
- lang: eng
text: 'Most phenotypes are determined by molecular systems composed of specifically
interacting molecules. However, unlike for individual components, little is known
about the distributions of mutational effects of molecular systems as a whole.
We ask how the distribution of mutational effects of a transcriptional regulatory
system differs from the distributions of its components, by first independently,
and then simultaneously, mutating a transcription factor and the associated promoter
it represses. We find that the system distribution exhibits increased phenotypic
variation compared to individual component distributions - an effect arising from
intermolecular epistasis between the transcription factor and its DNA-binding
site. In large part, this epistasis can be qualitatively attributed to the structure
of the transcriptional regulatory system and could therefore be a common feature
in prokaryotes. Counter-intuitively, intermolecular epistasis can alleviate the
constraints of individual components, thereby increasing phenotypic variation
that selection could act on and facilitating adaptive evolution. '
article_number: e28921
author:
- first_name: Mato
full_name: Lagator, Mato
id: 345D25EC-F248-11E8-B48F-1D18A9856A87
last_name: Lagator
- first_name: Srdjan
full_name: Sarikas, Srdjan
id: 35F0286E-F248-11E8-B48F-1D18A9856A87
last_name: Sarikas
- first_name: Hande
full_name: Acar, Hande
id: 2DDF136A-F248-11E8-B48F-1D18A9856A87
last_name: Acar
orcid: 0000-0003-1986-9753
- first_name: Jonathan P
full_name: Bollback, Jonathan P
id: 2C6FA9CC-F248-11E8-B48F-1D18A9856A87
last_name: Bollback
orcid: 0000-0002-4624-4612
- first_name: Calin C
full_name: Guet, Calin C
id: 47F8433E-F248-11E8-B48F-1D18A9856A87
last_name: Guet
orcid: 0000-0001-6220-2052
citation:
ama: Lagator M, Sarikas S, Acar H, Bollback JP, Guet CC. Regulatory network structure
determines patterns of intermolecular epistasis. eLife. 2017;6. doi:10.7554/eLife.28921
apa: Lagator, M., Sarikas, S., Acar, H., Bollback, J. P., & Guet, C. C. (2017).
Regulatory network structure determines patterns of intermolecular epistasis.
ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.28921
chicago: Lagator, Mato, Srdjan Sarikas, Hande Acar, Jonathan P Bollback, and Calin
C Guet. “Regulatory Network Structure Determines Patterns of Intermolecular Epistasis.”
ELife. eLife Sciences Publications, 2017. https://doi.org/10.7554/eLife.28921.
ieee: M. Lagator, S. Sarikas, H. Acar, J. P. Bollback, and C. C. Guet, “Regulatory
network structure determines patterns of intermolecular epistasis,” eLife,
vol. 6. eLife Sciences Publications, 2017.
ista: Lagator M, Sarikas S, Acar H, Bollback JP, Guet CC. 2017. Regulatory network
structure determines patterns of intermolecular epistasis. eLife. 6, e28921.
mla: Lagator, Mato, et al. “Regulatory Network Structure Determines Patterns of
Intermolecular Epistasis.” ELife, vol. 6, e28921, eLife Sciences Publications,
2017, doi:10.7554/eLife.28921.
short: M. Lagator, S. Sarikas, H. Acar, J.P. Bollback, C.C. Guet, ELife 6 (2017).
date_created: 2018-12-11T11:47:14Z
date_published: 2017-11-13T00:00:00Z
date_updated: 2021-01-12T08:03:15Z
day: '13'
ddc:
- '576'
department:
- _id: CaGu
- _id: JoBo
- _id: NiBa
doi: 10.7554/eLife.28921
ec_funded: 1
file:
- access_level: open_access
checksum: 273ab17f33305e4eaafd911ff88e7c5b
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:14:42Z
date_updated: 2020-07-14T12:47:10Z
file_id: '5096'
file_name: IST-2017-918-v1+1_elife-28921-figures-v3.pdf
file_size: 8453470
relation: main_file
- access_level: open_access
checksum: b433f90576c7be597cd43367946f8e7f
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:14:43Z
date_updated: 2020-07-14T12:47:10Z
file_id: '5097'
file_name: IST-2017-918-v1+2_elife-28921-v3.pdf
file_size: 1953221
relation: main_file
file_date_updated: 2020-07-14T12:47:10Z
has_accepted_license: '1'
intvolume: ' 6'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
- _id: 2578D616-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '648440'
name: Selective Barriers to Horizontal Gene Transfer
publication: eLife
publication_identifier:
issn:
- 2050084X
publication_status: published
publisher: eLife Sciences Publications
publist_id: '7244'
pubrep_id: '918'
quality_controlled: '1'
scopus_import: 1
status: public
title: Regulatory network structure determines patterns of intermolecular epistasis
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 6
year: '2017'
...
---
_id: '611'
abstract:
- lang: eng
text: Small RNAs (sRNAs) regulate genes in plants and animals. Here, we show that
population-wide differences in color patterns in snapdragon flowers are caused
by an inverted duplication that generates sRNAs. The complexity and size of the
transcripts indicate that the duplication represents an intermediate on the pathway
to microRNA evolution. The sRNAs repress a pigment biosynthesis gene, creating
a yellow highlight at the site of pollinator entry. The inverted duplication exhibits
steep clines in allele frequency in a natural hybrid zone, showing that the allele
is under selection. Thus, regulatory interactions of evolutionarily recent sRNAs
can be acted upon by selection and contribute to the evolution of phenotypic diversity.
author:
- first_name: Desmond
full_name: Bradley, Desmond
last_name: Bradley
- first_name: Ping
full_name: Xu, Ping
last_name: Xu
- first_name: Irina
full_name: Mohorianu, Irina
last_name: Mohorianu
- first_name: Annabel
full_name: Whibley, Annabel
last_name: Whibley
- first_name: David
full_name: Field, David
id: 419049E2-F248-11E8-B48F-1D18A9856A87
last_name: Field
orcid: 0000-0002-4014-8478
- first_name: Hugo
full_name: Tavares, Hugo
last_name: Tavares
- first_name: Matthew
full_name: Couchman, Matthew
last_name: Couchman
- first_name: Lucy
full_name: Copsey, Lucy
last_name: Copsey
- first_name: Rosemary
full_name: Carpenter, Rosemary
last_name: Carpenter
- first_name: Miaomiao
full_name: Li, Miaomiao
last_name: Li
- first_name: Qun
full_name: Li, Qun
last_name: Li
- first_name: Yongbiao
full_name: Xue, Yongbiao
last_name: Xue
- first_name: Tamas
full_name: Dalmay, Tamas
last_name: Dalmay
- first_name: Enrico
full_name: Coen, Enrico
last_name: Coen
citation:
ama: Bradley D, Xu P, Mohorianu I, et al. Evolution of flower color pattern through
selection on regulatory small RNAs. Science. 2017;358(6365):925-928. doi:10.1126/science.aao3526
apa: Bradley, D., Xu, P., Mohorianu, I., Whibley, A., Field, D., Tavares, H., …
Coen, E. (2017). Evolution of flower color pattern through selection on regulatory
small RNAs. Science. American Association for the Advancement of Science.
https://doi.org/10.1126/science.aao3526
chicago: Bradley, Desmond, Ping Xu, Irina Mohorianu, Annabel Whibley, David Field,
Hugo Tavares, Matthew Couchman, et al. “Evolution of Flower Color Pattern through
Selection on Regulatory Small RNAs.” Science. American Association for
the Advancement of Science, 2017. https://doi.org/10.1126/science.aao3526.
ieee: D. Bradley et al., “Evolution of flower color pattern through selection
on regulatory small RNAs,” Science, vol. 358, no. 6365. American Association
for the Advancement of Science, pp. 925–928, 2017.
ista: Bradley D, Xu P, Mohorianu I, Whibley A, Field D, Tavares H, Couchman M, Copsey
L, Carpenter R, Li M, Li Q, Xue Y, Dalmay T, Coen E. 2017. Evolution of flower
color pattern through selection on regulatory small RNAs. Science. 358(6365),
925–928.
mla: Bradley, Desmond, et al. “Evolution of Flower Color Pattern through Selection
on Regulatory Small RNAs.” Science, vol. 358, no. 6365, American Association
for the Advancement of Science, 2017, pp. 925–28, doi:10.1126/science.aao3526.
short: D. Bradley, P. Xu, I. Mohorianu, A. Whibley, D. Field, H. Tavares, M. Couchman,
L. Copsey, R. Carpenter, M. Li, Q. Li, Y. Xue, T. Dalmay, E. Coen, Science 358
(2017) 925–928.
date_created: 2018-12-11T11:47:29Z
date_published: 2017-11-17T00:00:00Z
date_updated: 2021-01-12T08:06:10Z
day: '17'
department:
- _id: NiBa
doi: 10.1126/science.aao3526
intvolume: ' 358'
issue: '6365'
language:
- iso: eng
month: '11'
oa_version: None
page: 925 - 928
publication: Science
publication_identifier:
issn:
- '00368075'
publication_status: published
publisher: American Association for the Advancement of Science
publist_id: '7193'
quality_controlled: '1'
scopus_import: 1
status: public
title: Evolution of flower color pattern through selection on regulatory small RNAs
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 358
year: '2017'
...
---
_id: '626'
abstract:
- lang: eng
text: 'Our focus here is on the infinitesimal model. In this model, one or several
quantitative traits are described as the sum of a genetic and a non-genetic component,
the first being distributed within families as a normal random variable centred
at the average of the parental genetic components, and with a variance independent
of the parental traits. Thus, the variance that segregates within families is
not perturbed by selection, and can be predicted from the variance components.
This does not necessarily imply that the trait distribution across the whole population
should be Gaussian, and indeed selection or population structure may have a substantial
effect on the overall trait distribution. One of our main aims is to identify
some general conditions on the allelic effects for the infinitesimal model to
be accurate. We first review the long history of the infinitesimal model in quantitative
genetics. Then we formulate the model at the phenotypic level in terms of individual
trait values and relationships between individuals, but including different evolutionary
processes: genetic drift, recombination, selection, mutation, population structure,
…. We give a range of examples of its application to evolutionary questions related
to stabilising selection, assortative mating, effective population size and response
to selection, habitat preference and speciation. We provide a mathematical justification
of the model as the limit as the number M of underlying loci tends to infinity
of a model with Mendelian inheritance, mutation and environmental noise, when
the genetic component of the trait is purely additive. We also show how the model
generalises to include epistatic effects. We prove in particular that, within
each family, the genetic components of the individual trait values in the current
generation are indeed normally distributed with a variance independent of ancestral
traits, up to an error of order 1∕M. Simulations suggest that in some cases the
convergence may be as fast as 1∕M.'
author:
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Alison
full_name: Etheridge, Alison
last_name: Etheridge
- first_name: Amandine
full_name: Véber, Amandine
last_name: Véber
citation:
ama: 'Barton NH, Etheridge A, Véber A. The infinitesimal model: Definition derivation
and implications. Theoretical Population Biology. 2017;118:50-73. doi:10.1016/j.tpb.2017.06.001'
apa: 'Barton, N. H., Etheridge, A., & Véber, A. (2017). The infinitesimal model:
Definition derivation and implications. Theoretical Population Biology.
Academic Press. https://doi.org/10.1016/j.tpb.2017.06.001'
chicago: 'Barton, Nicholas H, Alison Etheridge, and Amandine Véber. “The Infinitesimal
Model: Definition Derivation and Implications.” Theoretical Population Biology.
Academic Press, 2017. https://doi.org/10.1016/j.tpb.2017.06.001.'
ieee: 'N. H. Barton, A. Etheridge, and A. Véber, “The infinitesimal model: Definition
derivation and implications,” Theoretical Population Biology, vol. 118.
Academic Press, pp. 50–73, 2017.'
ista: 'Barton NH, Etheridge A, Véber A. 2017. The infinitesimal model: Definition
derivation and implications. Theoretical Population Biology. 118, 50–73.'
mla: 'Barton, Nicholas H., et al. “The Infinitesimal Model: Definition Derivation
and Implications.” Theoretical Population Biology, vol. 118, Academic Press,
2017, pp. 50–73, doi:10.1016/j.tpb.2017.06.001.'
short: N.H. Barton, A. Etheridge, A. Véber, Theoretical Population Biology 118 (2017)
50–73.
date_created: 2018-12-11T11:47:34Z
date_published: 2017-12-01T00:00:00Z
date_updated: 2021-01-12T08:06:50Z
day: '01'
ddc:
- '576'
department:
- _id: NiBa
doi: 10.1016/j.tpb.2017.06.001
ec_funded: 1
file:
- access_level: open_access
checksum: 7dd02bfcfe8f244f4a6c19091aedf2c8
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:12:45Z
date_updated: 2020-07-14T12:47:25Z
file_id: '4964'
file_name: IST-2017-908-v1+1_1-s2.0-S0040580917300886-main_1_.pdf
file_size: 1133924
relation: main_file
file_date_updated: 2020-07-14T12:47:25Z
has_accepted_license: '1'
intvolume: ' 118'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
page: 50 - 73
project:
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
publication: Theoretical Population Biology
publication_identifier:
issn:
- '00405809'
publication_status: published
publisher: Academic Press
publist_id: '7169'
pubrep_id: '908'
quality_controlled: '1'
scopus_import: 1
status: public
title: 'The infinitesimal model: Definition derivation and implications'
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 118
year: '2017'
...
---
_id: '9849'
abstract:
- lang: eng
text: This text provides additional information about the model, a derivation of
the analytic results in Eq (4), and details about simulations of an additional
parameter set.
article_processing_charge: No
author:
- first_name: Marta
full_name: Lukacisinova, Marta
id: 4342E402-F248-11E8-B48F-1D18A9856A87
last_name: Lukacisinova
orcid: 0000-0002-2519-8004
- first_name: Sebastian
full_name: Novak, Sebastian
id: 461468AE-F248-11E8-B48F-1D18A9856A87
last_name: Novak
- first_name: Tiago
full_name: Paixao, Tiago
id: 2C5658E6-F248-11E8-B48F-1D18A9856A87
last_name: Paixao
orcid: 0000-0003-2361-3953
citation:
ama: Lukacisinova M, Novak S, Paixao T. Modelling and simulation details. 2017.
doi:10.1371/journal.pcbi.1005609.s001
apa: Lukacisinova, M., Novak, S., & Paixao, T. (2017). Modelling and simulation
details. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1005609.s001
chicago: Lukacisinova, Marta, Sebastian Novak, and Tiago Paixao. “Modelling and
Simulation Details.” Public Library of Science, 2017. https://doi.org/10.1371/journal.pcbi.1005609.s001.
ieee: M. Lukacisinova, S. Novak, and T. Paixao, “Modelling and simulation details.”
Public Library of Science, 2017.
ista: Lukacisinova M, Novak S, Paixao T. 2017. Modelling and simulation details,
Public Library of Science, 10.1371/journal.pcbi.1005609.s001.
mla: Lukacisinova, Marta, et al. Modelling and Simulation Details. Public
Library of Science, 2017, doi:10.1371/journal.pcbi.1005609.s001.
short: M. Lukacisinova, S. Novak, T. Paixao, (2017).
date_created: 2021-08-09T14:02:34Z
date_published: 2017-07-18T00:00:00Z
date_updated: 2023-02-23T12:55:39Z
day: '18'
department:
- _id: ToBo
- _id: NiBa
- _id: CaGu
doi: 10.1371/journal.pcbi.1005609.s001
month: '07'
oa_version: Published Version
publisher: Public Library of Science
related_material:
record:
- id: '696'
relation: used_in_publication
status: public
status: public
title: Modelling and simulation details
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2017'
...
---
_id: '9850'
abstract:
- lang: eng
text: In this text, we discuss how a cost of resistance and the possibility of lethal
mutations impact our model.
article_processing_charge: No
author:
- first_name: Marta
full_name: Lukacisinova, Marta
id: 4342E402-F248-11E8-B48F-1D18A9856A87
last_name: Lukacisinova
orcid: 0000-0002-2519-8004
- first_name: Sebastian
full_name: Novak, Sebastian
id: 461468AE-F248-11E8-B48F-1D18A9856A87
last_name: Novak
- first_name: Tiago
full_name: Paixao, Tiago
id: 2C5658E6-F248-11E8-B48F-1D18A9856A87
last_name: Paixao
orcid: 0000-0003-2361-3953
citation:
ama: Lukacisinova M, Novak S, Paixao T. Extensions of the model. 2017. doi:10.1371/journal.pcbi.1005609.s002
apa: Lukacisinova, M., Novak, S., & Paixao, T. (2017). Extensions of the model.
Public Library of Science. https://doi.org/10.1371/journal.pcbi.1005609.s002
chicago: Lukacisinova, Marta, Sebastian Novak, and Tiago Paixao. “Extensions of
the Model.” Public Library of Science, 2017. https://doi.org/10.1371/journal.pcbi.1005609.s002.
ieee: M. Lukacisinova, S. Novak, and T. Paixao, “Extensions of the model.” Public
Library of Science, 2017.
ista: Lukacisinova M, Novak S, Paixao T. 2017. Extensions of the model, Public Library
of Science, 10.1371/journal.pcbi.1005609.s002.
mla: Lukacisinova, Marta, et al. Extensions of the Model. Public Library
of Science, 2017, doi:10.1371/journal.pcbi.1005609.s002.
short: M. Lukacisinova, S. Novak, T. Paixao, (2017).
date_created: 2021-08-09T14:05:24Z
date_published: 2017-07-18T00:00:00Z
date_updated: 2023-02-23T12:55:39Z
day: '18'
department:
- _id: ToBo
- _id: CaGu
- _id: NiBa
doi: 10.1371/journal.pcbi.1005609.s002
month: '07'
oa_version: Published Version
publisher: Public Library of Science
related_material:
record:
- id: '696'
relation: used_in_publication
status: public
status: public
title: Extensions of the model
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2017'
...
---
_id: '9851'
abstract:
- lang: eng
text: Based on the intuitive derivation of the dynamics of SIM allele frequency
pM in the main text, we present a heuristic prediction for the long-term SIM allele
frequencies with χ > 1 stresses and compare it to numerical simulations.
article_processing_charge: No
author:
- first_name: Marta
full_name: Lukacisinova, Marta
id: 4342E402-F248-11E8-B48F-1D18A9856A87
last_name: Lukacisinova
orcid: 0000-0002-2519-8004
- first_name: Sebastian
full_name: Novak, Sebastian
id: 461468AE-F248-11E8-B48F-1D18A9856A87
last_name: Novak
- first_name: Tiago
full_name: Paixao, Tiago
id: 2C5658E6-F248-11E8-B48F-1D18A9856A87
last_name: Paixao
orcid: 0000-0003-2361-3953
citation:
ama: Lukacisinova M, Novak S, Paixao T. Heuristic prediction for multiple stresses.
2017. doi:10.1371/journal.pcbi.1005609.s003
apa: Lukacisinova, M., Novak, S., & Paixao, T. (2017). Heuristic prediction
for multiple stresses. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1005609.s003
chicago: Lukacisinova, Marta, Sebastian Novak, and Tiago Paixao. “Heuristic Prediction
for Multiple Stresses.” Public Library of Science, 2017. https://doi.org/10.1371/journal.pcbi.1005609.s003.
ieee: M. Lukacisinova, S. Novak, and T. Paixao, “Heuristic prediction for multiple
stresses.” Public Library of Science, 2017.
ista: Lukacisinova M, Novak S, Paixao T. 2017. Heuristic prediction for multiple
stresses, Public Library of Science, 10.1371/journal.pcbi.1005609.s003.
mla: Lukacisinova, Marta, et al. Heuristic Prediction for Multiple Stresses.
Public Library of Science, 2017, doi:10.1371/journal.pcbi.1005609.s003.
short: M. Lukacisinova, S. Novak, T. Paixao, (2017).
date_created: 2021-08-09T14:08:14Z
date_published: 2017-07-18T00:00:00Z
date_updated: 2023-02-23T12:55:39Z
day: '18'
department:
- _id: ToBo
- _id: CaGu
- _id: NiBa
doi: 10.1371/journal.pcbi.1005609.s003
month: '07'
oa_version: Published Version
publisher: Public Library of Science
related_material:
record:
- id: '696'
relation: used_in_publication
status: public
status: public
title: Heuristic prediction for multiple stresses
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2017'
...
---
_id: '9852'
abstract:
- lang: eng
text: We show how different combination strategies affect the fraction of individuals
that are multi-resistant.
article_processing_charge: No
author:
- first_name: Marta
full_name: Lukacisinova, Marta
id: 4342E402-F248-11E8-B48F-1D18A9856A87
last_name: Lukacisinova
orcid: 0000-0002-2519-8004
- first_name: Sebastian
full_name: Novak, Sebastian
id: 461468AE-F248-11E8-B48F-1D18A9856A87
last_name: Novak
- first_name: Tiago
full_name: Paixao, Tiago
id: 2C5658E6-F248-11E8-B48F-1D18A9856A87
last_name: Paixao
orcid: 0000-0003-2361-3953
citation:
ama: Lukacisinova M, Novak S, Paixao T. Resistance frequencies for different combination
strategies. 2017. doi:10.1371/journal.pcbi.1005609.s004
apa: Lukacisinova, M., Novak, S., & Paixao, T. (2017). Resistance frequencies
for different combination strategies. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1005609.s004
chicago: Lukacisinova, Marta, Sebastian Novak, and Tiago Paixao. “Resistance Frequencies
for Different Combination Strategies.” Public Library of Science, 2017. https://doi.org/10.1371/journal.pcbi.1005609.s004.
ieee: M. Lukacisinova, S. Novak, and T. Paixao, “Resistance frequencies for different
combination strategies.” Public Library of Science, 2017.
ista: Lukacisinova M, Novak S, Paixao T. 2017. Resistance frequencies for different
combination strategies, Public Library of Science, 10.1371/journal.pcbi.1005609.s004.
mla: Lukacisinova, Marta, et al. Resistance Frequencies for Different Combination
Strategies. Public Library of Science, 2017, doi:10.1371/journal.pcbi.1005609.s004.
short: M. Lukacisinova, S. Novak, T. Paixao, (2017).
date_created: 2021-08-09T14:11:40Z
date_published: 2017-07-18T00:00:00Z
date_updated: 2023-02-23T12:55:39Z
day: '18'
department:
- _id: ToBo
- _id: CaGu
- _id: NiBa
doi: 10.1371/journal.pcbi.1005609.s004
month: '07'
oa_version: Published Version
publisher: Public Library of Science
related_material:
record:
- id: '696'
relation: used_in_publication
status: public
status: public
title: Resistance frequencies for different combination strategies
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2017'
...
---
_id: '6291'
abstract:
- lang: eng
text: Bacteria and their pathogens – phages – are the most abundant living entities
on Earth. Throughout their coevolution, bacteria have evolved multiple immune
systems to overcome the ubiquitous threat from the phages. Although the molecu-
lar details of these immune systems’ functions are relatively well understood,
their epidemiological consequences for the phage-bacterial communities have been
largely neglected. In this thesis we employed both experimental and theoretical
methods to explore whether herd and social immunity may arise in bacterial popu-
lations. Using our experimental system consisting of Escherichia coli strains
with a CRISPR based immunity to the T7 phage we show that herd immunity arises
in phage-bacterial communities and that it is accentuated when the populations
are spatially structured. By fitting a mathematical model, we inferred expressions
for the herd immunity threshold and the velocity of spread of a phage epidemic
in partially resistant bacterial populations, which both depend on the bacterial
growth rate, phage burst size and phage latent period. We also investigated the
poten- tial for social immunity in Streptococcus thermophilus and its phage 2972
using a bioinformatic analysis of potentially coding short open reading frames
with a signalling signature, encoded within the CRISPR associated genes. Subsequently,
we tested one identified potentially signalling peptide and found that its addition
to a phage-challenged culture increases probability of survival of bacteria two
fold, although the results were only marginally significant. Together, these results
demonstrate that the ubiquitous arms races between bacteria and phages have further
consequences at the level of the population.
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Pavel
full_name: Payne, Pavel
id: 35F78294-F248-11E8-B48F-1D18A9856A87
last_name: Payne
orcid: 0000-0002-2711-9453
citation:
ama: Payne P. Bacterial herd and social immunity to phages. 2017.
apa: Payne, P. (2017). Bacterial herd and social immunity to phages. Institute
of Science and Technology Austria.
chicago: Payne, Pavel. “Bacterial Herd and Social Immunity to Phages.” Institute
of Science and Technology Austria, 2017.
ieee: P. Payne, “Bacterial herd and social immunity to phages,” Institute of Science
and Technology Austria, 2017.
ista: Payne P. 2017. Bacterial herd and social immunity to phages. Institute of
Science and Technology Austria.
mla: Payne, Pavel. Bacterial Herd and Social Immunity to Phages. Institute
of Science and Technology Austria, 2017.
short: P. Payne, Bacterial Herd and Social Immunity to Phages, Institute of Science
and Technology Austria, 2017.
date_created: 2019-04-09T15:16:45Z
date_published: 2017-02-01T00:00:00Z
date_updated: 2023-09-07T12:00:00Z
day: '01'
ddc:
- '570'
degree_awarded: PhD
department:
- _id: NiBa
- _id: JoBo
file:
- access_level: closed
checksum: a0fc5c26a89c0ea759947ffba87d0d8f
content_type: application/pdf
creator: dernst
date_created: 2019-04-09T15:15:32Z
date_updated: 2020-07-14T12:47:27Z
file_id: '6292'
file_name: thesis_pavel_payne_final_w_signature_page.pdf
file_size: 3025175
relation: main_file
- access_level: open_access
checksum: af531e921a7f64a9e0af4cd8783b2226
content_type: application/pdf
creator: dernst
date_created: 2021-02-22T13:45:59Z
date_updated: 2021-02-22T13:45:59Z
file_id: '9187'
file_name: 2017_Payne_Thesis.pdf
file_size: 3111536
relation: main_file
success: 1
file_date_updated: 2021-02-22T13:45:59Z
has_accepted_license: '1'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
page: '83'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
status: public
supervisor:
- first_name: Jonathan P
full_name: Bollback, Jonathan P
id: 2C6FA9CC-F248-11E8-B48F-1D18A9856A87
last_name: Bollback
orcid: 0000-0002-4624-4612
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
title: Bacterial herd and social immunity to phages
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2017'
...
---
_id: '9842'
abstract:
- lang: eng
text: Mathematica notebooks used to generate figures.
article_processing_charge: No
author:
- first_name: Alison
full_name: Etheridge, Alison
last_name: Etheridge
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: 'Etheridge A, Barton NH. Data for: Establishment in a new habitat by polygenic
adaptation. 2017. doi:10.17632/nw68fxzjpm.1'
apa: 'Etheridge, A., & Barton, N. H. (2017). Data for: Establishment in a new
habitat by polygenic adaptation. Mendeley Data. https://doi.org/10.17632/nw68fxzjpm.1'
chicago: 'Etheridge, Alison, and Nicholas H Barton. “Data for: Establishment in
a New Habitat by Polygenic Adaptation.” Mendeley Data, 2017. https://doi.org/10.17632/nw68fxzjpm.1.'
ieee: 'A. Etheridge and N. H. Barton, “Data for: Establishment in a new habitat
by polygenic adaptation.” Mendeley Data, 2017.'
ista: 'Etheridge A, Barton NH. 2017. Data for: Establishment in a new habitat by
polygenic adaptation, Mendeley Data, 10.17632/nw68fxzjpm.1.'
mla: 'Etheridge, Alison, and Nicholas H. Barton. Data for: Establishment in a
New Habitat by Polygenic Adaptation. Mendeley Data, 2017, doi:10.17632/nw68fxzjpm.1.'
short: A. Etheridge, N.H. Barton, (2017).
date_created: 2021-08-09T13:18:55Z
date_published: 2017-12-29T00:00:00Z
date_updated: 2023-09-11T13:41:21Z
day: '29'
department:
- _id: NiBa
doi: 10.17632/nw68fxzjpm.1
main_file_link:
- open_access: '1'
url: https://doi.org/10.17632/nw68fxzjpm.1
month: '12'
oa: 1
oa_version: Published Version
publisher: Mendeley Data
related_material:
record:
- id: '564'
relation: used_in_publication
status: public
status: public
title: 'Data for: Establishment in a new habitat by polygenic adaptation'
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2017'
...
---
_id: '1351'
abstract:
- lang: eng
text: The behaviour of gene regulatory networks (GRNs) is typically analysed using
simulation-based statistical testing-like methods. In this paper, we demonstrate
that we can replace this approach by a formal verification-like method that gives
higher assurance and scalability. We focus on Wagner’s weighted GRN model with
varying weights, which is used in evolutionary biology. In the model, weight parameters
represent the gene interaction strength that may change due to genetic mutations.
For a property of interest, we synthesise the constraints over the parameter space
that represent the set of GRNs satisfying the property. We experimentally show
that our parameter synthesis procedure computes the mutational robustness of GRNs—an
important problem of interest in evolutionary biology—more efficiently than the
classical simulation method. We specify the property in linear temporal logic.
We employ symbolic bounded model checking and SMT solving to compute the space
of GRNs that satisfy the property, which amounts to synthesizing a set of linear
constraints on the weights.
article_processing_charge: No
author:
- first_name: Mirco
full_name: Giacobbe, Mirco
id: 3444EA5E-F248-11E8-B48F-1D18A9856A87
last_name: Giacobbe
orcid: 0000-0001-8180-0904
- first_name: Calin C
full_name: Guet, Calin C
id: 47F8433E-F248-11E8-B48F-1D18A9856A87
last_name: Guet
orcid: 0000-0001-6220-2052
- first_name: Ashutosh
full_name: Gupta, Ashutosh
id: 335E5684-F248-11E8-B48F-1D18A9856A87
last_name: Gupta
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Tiago
full_name: Paixao, Tiago
id: 2C5658E6-F248-11E8-B48F-1D18A9856A87
last_name: Paixao
orcid: 0000-0003-2361-3953
- first_name: Tatjana
full_name: Petrov, Tatjana
id: 3D5811FC-F248-11E8-B48F-1D18A9856A87
last_name: Petrov
orcid: 0000-0002-9041-0905
citation:
ama: Giacobbe M, Guet CC, Gupta A, Henzinger TA, Paixao T, Petrov T. Model checking
the evolution of gene regulatory networks. Acta Informatica. 2017;54(8):765-787.
doi:10.1007/s00236-016-0278-x
apa: Giacobbe, M., Guet, C. C., Gupta, A., Henzinger, T. A., Paixao, T., & Petrov,
T. (2017). Model checking the evolution of gene regulatory networks. Acta Informatica.
Springer. https://doi.org/10.1007/s00236-016-0278-x
chicago: Giacobbe, Mirco, Calin C Guet, Ashutosh Gupta, Thomas A Henzinger, Tiago
Paixao, and Tatjana Petrov. “Model Checking the Evolution of Gene Regulatory Networks.”
Acta Informatica. Springer, 2017. https://doi.org/10.1007/s00236-016-0278-x.
ieee: M. Giacobbe, C. C. Guet, A. Gupta, T. A. Henzinger, T. Paixao, and T. Petrov,
“Model checking the evolution of gene regulatory networks,” Acta Informatica,
vol. 54, no. 8. Springer, pp. 765–787, 2017.
ista: Giacobbe M, Guet CC, Gupta A, Henzinger TA, Paixao T, Petrov T. 2017. Model
checking the evolution of gene regulatory networks. Acta Informatica. 54(8), 765–787.
mla: Giacobbe, Mirco, et al. “Model Checking the Evolution of Gene Regulatory Networks.”
Acta Informatica, vol. 54, no. 8, Springer, 2017, pp. 765–87, doi:10.1007/s00236-016-0278-x.
short: M. Giacobbe, C.C. Guet, A. Gupta, T.A. Henzinger, T. Paixao, T. Petrov, Acta
Informatica 54 (2017) 765–787.
date_created: 2018-12-11T11:51:32Z
date_published: 2017-12-01T00:00:00Z
date_updated: 2023-09-20T11:06:03Z
day: '01'
ddc:
- '006'
- '576'
department:
- _id: ToHe
- _id: CaGu
- _id: NiBa
doi: 10.1007/s00236-016-0278-x
ec_funded: 1
external_id:
isi:
- '000414343200003'
file:
- access_level: open_access
checksum: 4e661d9135d7f8c342e8e258dee76f3e
content_type: application/pdf
creator: dernst
date_created: 2019-01-17T15:57:29Z
date_updated: 2020-07-14T12:44:46Z
file_id: '5841'
file_name: 2017_ActaInformatica_Giacobbe.pdf
file_size: 755241
relation: main_file
file_date_updated: 2020-07-14T12:44:46Z
has_accepted_license: '1'
intvolume: ' 54'
isi: 1
issue: '8'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
page: 765 - 787
project:
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 25F42A32-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Z211
name: The Wittgenstein Prize
- _id: 25B1EC9E-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '618091'
name: Speed of Adaptation in Population Genetics and Evolutionary Computation
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
publication: Acta Informatica
publication_identifier:
issn:
- '00015903'
publication_status: published
publisher: Springer
publist_id: '5898'
pubrep_id: '649'
quality_controlled: '1'
related_material:
record:
- id: '1835'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: Model checking the evolution of gene regulatory networks
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 54
year: '2017'
...
---
_id: '1336'
abstract:
- lang: eng
text: Evolutionary algorithms (EAs) form a popular optimisation paradigm inspired
by natural evolution. In recent years the field of evolutionary computation has
developed a rigorous analytical theory to analyse the runtimes of EAs on many
illustrative problems. Here we apply this theory to a simple model of natural
evolution. In the Strong Selection Weak Mutation (SSWM) evolutionary regime the
time between occurrences of new mutations is much longer than the time it takes
for a mutated genotype to take over the population. In this situation, the population
only contains copies of one genotype and evolution can be modelled as a stochastic
process evolving one genotype by means of mutation and selection between the resident
and the mutated genotype. The probability of accepting the mutated genotype then
depends on the change in fitness. We study this process, SSWM, from an algorithmic
perspective, quantifying its expected optimisation time for various parameters
and investigating differences to a similar evolutionary algorithm, the well-known
(1+1) EA. We show that SSWM can have a moderate advantage over the (1+1) EA at
crossing fitness valleys and study an example where SSWM outperforms the (1+1)
EA by taking advantage of information on the fitness gradient.
article_processing_charge: No
author:
- first_name: Tiago
full_name: Paixao, Tiago
id: 2C5658E6-F248-11E8-B48F-1D18A9856A87
last_name: Paixao
orcid: 0000-0003-2361-3953
- first_name: Jorge
full_name: Pérez Heredia, Jorge
last_name: Pérez Heredia
- first_name: Dirk
full_name: Sudholt, Dirk
last_name: Sudholt
- first_name: Barbora
full_name: Trubenova, Barbora
id: 42302D54-F248-11E8-B48F-1D18A9856A87
last_name: Trubenova
orcid: 0000-0002-6873-2967
citation:
ama: Paixao T, Pérez Heredia J, Sudholt D, Trubenova B. Towards a runtime comparison
of natural and artificial evolution. Algorithmica. 2017;78(2):681-713.
doi:10.1007/s00453-016-0212-1
apa: Paixao, T., Pérez Heredia, J., Sudholt, D., & Trubenova, B. (2017). Towards
a runtime comparison of natural and artificial evolution. Algorithmica.
Springer. https://doi.org/10.1007/s00453-016-0212-1
chicago: Paixao, Tiago, Jorge Pérez Heredia, Dirk Sudholt, and Barbora Trubenova.
“Towards a Runtime Comparison of Natural and Artificial Evolution.” Algorithmica.
Springer, 2017. https://doi.org/10.1007/s00453-016-0212-1.
ieee: T. Paixao, J. Pérez Heredia, D. Sudholt, and B. Trubenova, “Towards a runtime
comparison of natural and artificial evolution,” Algorithmica, vol. 78,
no. 2. Springer, pp. 681–713, 2017.
ista: Paixao T, Pérez Heredia J, Sudholt D, Trubenova B. 2017. Towards a runtime
comparison of natural and artificial evolution. Algorithmica. 78(2), 681–713.
mla: Paixao, Tiago, et al. “Towards a Runtime Comparison of Natural and Artificial
Evolution.” Algorithmica, vol. 78, no. 2, Springer, 2017, pp. 681–713,
doi:10.1007/s00453-016-0212-1.
short: T. Paixao, J. Pérez Heredia, D. Sudholt, B. Trubenova, Algorithmica 78 (2017)
681–713.
date_created: 2018-12-11T11:51:27Z
date_published: 2017-06-01T00:00:00Z
date_updated: 2023-09-20T11:14:42Z
day: '01'
ddc:
- '576'
department:
- _id: NiBa
- _id: CaGu
doi: 10.1007/s00453-016-0212-1
ec_funded: 1
external_id:
isi:
- '000400379500013'
file:
- access_level: open_access
checksum: 7873f665a0c598ac747c908f34cb14b9
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:10:19Z
date_updated: 2020-07-14T12:44:44Z
file_id: '4805'
file_name: IST-2016-658-v1+1_s00453-016-0212-1.pdf
file_size: 710206
relation: main_file
file_date_updated: 2020-07-14T12:44:44Z
has_accepted_license: '1'
intvolume: ' 78'
isi: 1
issue: '2'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: 681 - 713
project:
- _id: 25B1EC9E-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '618091'
name: Speed of Adaptation in Population Genetics and Evolutionary Computation
publication: Algorithmica
publication_identifier:
issn:
- '01784617'
publication_status: published
publisher: Springer
publist_id: '5931'
pubrep_id: '658'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Towards a runtime comparison of natural and artificial evolution
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 78
year: '2017'
...
---
_id: '1199'
abstract:
- lang: eng
text: Much of quantitative genetics is based on the ‘infinitesimal model’, under
which selection has a negligible effect on the genetic variance. This is typically
justified by assuming a very large number of loci with additive effects. However,
it applies even when genes interact, provided that the number of loci is large
enough that selection on each of them is weak relative to random drift. In the
long term, directional selection will change allele frequencies, but even then,
the effects of epistasis on the ultimate change in trait mean due to selection
may be modest. Stabilising selection can maintain many traits close to their optima,
even when the underlying alleles are weakly selected. However, the number of traits
that can be optimised is apparently limited to ~4Ne by the ‘drift load’, and this
is hard to reconcile with the apparent complexity of many organisms. Just as for
the mutation load, this limit can be evaded by a particular form of negative epistasis.
A more robust limit is set by the variance in reproductive success. This suggests
that selection accumulates information most efficiently in the infinitesimal regime,
when selection on individual alleles is weak, and comparable with random drift.
A review of evidence on selection strength suggests that although most variance
in fitness may be because of alleles with large Nes, substantial amounts of adaptation
may be because of alleles in the infinitesimal regime, in which epistasis has
modest effects.
article_processing_charge: No
author:
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: Barton NH. How does epistasis influence the response to selection? Heredity.
2017;118:96-109. doi:10.1038/hdy.2016.109
apa: Barton, N. H. (2017). How does epistasis influence the response to selection?
Heredity. Nature Publishing Group. https://doi.org/10.1038/hdy.2016.109
chicago: Barton, Nicholas H. “How Does Epistasis Influence the Response to Selection?”
Heredity. Nature Publishing Group, 2017. https://doi.org/10.1038/hdy.2016.109.
ieee: N. H. Barton, “How does epistasis influence the response to selection?,” Heredity,
vol. 118. Nature Publishing Group, pp. 96–109, 2017.
ista: Barton NH. 2017. How does epistasis influence the response to selection? Heredity.
118, 96–109.
mla: Barton, Nicholas H. “How Does Epistasis Influence the Response to Selection?”
Heredity, vol. 118, Nature Publishing Group, 2017, pp. 96–109, doi:10.1038/hdy.2016.109.
short: N.H. Barton, Heredity 118 (2017) 96–109.
date_created: 2018-12-11T11:50:40Z
date_published: 2017-01-01T00:00:00Z
date_updated: 2023-09-20T11:17:47Z
day: '01'
department:
- _id: NiBa
doi: 10.1038/hdy.2016.109
ec_funded: 1
external_id:
isi:
- '000392229100011'
intvolume: ' 118'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5176114/
month: '01'
oa: 1
oa_version: Submitted Version
page: 96 - 109
project:
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
publication: Heredity
publication_status: published
publisher: Nature Publishing Group
publist_id: '6151'
quality_controlled: '1'
related_material:
record:
- id: '9710'
relation: research_data
status: public
scopus_import: '1'
status: public
title: How does epistasis influence the response to selection?
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 118
year: '2017'
...
---
_id: '1169'
abstract:
- lang: eng
text: Dispersal is a crucial factor in natural evolution, since it determines the
habitat experienced by any population and defines the spatial scale of interactions
between individuals. There is compelling evidence for systematic differences in
dispersal characteristics within the same population, i.e., genotype-dependent
dispersal. The consequences of genotype-dependent dispersal on other evolutionary
phenomena, however, are poorly understood. In this article we investigate the
effect of genotype-dependent dispersal on spatial gene frequency patterns, using
a generalization of the classical diffusion model of selection and dispersal.
Dispersal is characterized by the variance of dispersal (diffusion coefficient)
and the mean displacement (directional advection term). We demonstrate that genotype-dependent
dispersal may change the qualitative behavior of Fisher waves, which change from
being “pulled” to being “pushed” wave fronts as the discrepancy in dispersal between
genotypes increases. The speed of any wave is partitioned into components due
to selection, genotype-dependent variance of dispersal, and genotype-dependent
mean displacement. We apply our findings to wave fronts maintained by selection
against heterozygotes. Furthermore, we identify a benefit of increased variance
of dispersal, quantify its effect on the speed of the wave, and discuss the implications
for the evolution of dispersal strategies.
article_processing_charge: No
author:
- first_name: Sebastian
full_name: Novak, Sebastian
id: 461468AE-F248-11E8-B48F-1D18A9856A87
last_name: Novak
orcid: 0000-0002-2519-824X
- first_name: Richard
full_name: Kollár, Richard
last_name: Kollár
citation:
ama: Novak S, Kollár R. Spatial gene frequency waves under genotype dependent dispersal.
Genetics. 2017;205(1):367-374. doi:10.1534/genetics.116.193946
apa: Novak, S., & Kollár, R. (2017). Spatial gene frequency waves under genotype
dependent dispersal. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.116.193946
chicago: Novak, Sebastian, and Richard Kollár. “Spatial Gene Frequency Waves under
Genotype Dependent Dispersal.” Genetics. Genetics Society of America, 2017.
https://doi.org/10.1534/genetics.116.193946.
ieee: S. Novak and R. Kollár, “Spatial gene frequency waves under genotype dependent
dispersal,” Genetics, vol. 205, no. 1. Genetics Society of America, pp.
367–374, 2017.
ista: Novak S, Kollár R. 2017. Spatial gene frequency waves under genotype dependent
dispersal. Genetics. 205(1), 367–374.
mla: Novak, Sebastian, and Richard Kollár. “Spatial Gene Frequency Waves under Genotype
Dependent Dispersal.” Genetics, vol. 205, no. 1, Genetics Society of America,
2017, pp. 367–74, doi:10.1534/genetics.116.193946.
short: S. Novak, R. Kollár, Genetics 205 (2017) 367–374.
date_created: 2018-12-11T11:50:31Z
date_published: 2017-01-01T00:00:00Z
date_updated: 2023-09-20T11:24:21Z
day: '01'
ddc:
- '576'
department:
- _id: NiBa
doi: 10.1534/genetics.116.193946
ec_funded: 1
external_id:
isi:
- '000393677300025'
file:
- access_level: open_access
checksum: 7c8ab79cda1f92760bbbbe0f53175bfc
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:10:43Z
date_updated: 2020-07-14T12:44:37Z
file_id: '4833'
file_name: IST-2016-727-v1+1_SFC_Genetics_final.pdf
file_size: 361500
relation: main_file
file_date_updated: 2020-07-14T12:44:37Z
has_accepted_license: '1'
intvolume: ' 205'
isi: 1
issue: '1'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Submitted Version
page: 367 - 374
project:
- _id: 25B1EC9E-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '618091'
name: Speed of Adaptation in Population Genetics and Evolutionary Computation
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
publication: Genetics
publication_identifier:
issn:
- '00166731'
publication_status: published
publisher: Genetics Society of America
publist_id: '6188'
pubrep_id: '727'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Spatial gene frequency waves under genotype dependent dispersal
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 205
year: '2017'
...
---
_id: '1111'
abstract:
- lang: eng
text: Adaptation depends critically on the effects of new mutations and their dependency
on the genetic background in which they occur. These two factors can be summarized
by the fitness landscape. However, it would require testing all mutations in all
backgrounds, making the definition and analysis of fitness landscapes mostly inaccessible.
Instead of postulating a particular fitness landscape, we address this problem
by considering general classes of landscapes and calculating an upper limit for
the time it takes for a population to reach a fitness peak, circumventing the
need to have full knowledge about the fitness landscape. We analyze populations
in the weak-mutation regime and characterize the conditions that enable them to
quickly reach the fitness peak as a function of the number of sites under selection.
We show that for additive landscapes there is a critical selection strength enabling
populations to reach high-fitness genotypes, regardless of the distribution of
effects. This threshold scales with the number of sites under selection, effectively
setting a limit to adaptation, and results from the inevitable increase in deleterious
mutational pressure as the population adapts in a space of discrete genotypes.
Furthermore, we show that for the class of all unimodal landscapes this condition
is sufficient but not necessary for rapid adaptation, as in some highly epistatic
landscapes the critical strength does not depend on the number of sites under
selection; effectively removing this barrier to adaptation.
article_processing_charge: No
article_type: original
author:
- first_name: Jorge
full_name: Heredia, Jorge
last_name: Heredia
- first_name: Barbora
full_name: Trubenova, Barbora
id: 42302D54-F248-11E8-B48F-1D18A9856A87
last_name: Trubenova
orcid: 0000-0002-6873-2967
- first_name: Dirk
full_name: Sudholt, Dirk
last_name: Sudholt
- first_name: Tiago
full_name: Paixao, Tiago
id: 2C5658E6-F248-11E8-B48F-1D18A9856A87
last_name: Paixao
orcid: 0000-0003-2361-3953
citation:
ama: Heredia J, Trubenova B, Sudholt D, Paixao T. Selection limits to adaptive walks
on correlated landscapes. Genetics. 2017;205(2):803-825. doi:10.1534/genetics.116.189340
apa: Heredia, J., Trubenova, B., Sudholt, D., & Paixao, T. (2017). Selection
limits to adaptive walks on correlated landscapes. Genetics. Genetics Society
of America. https://doi.org/10.1534/genetics.116.189340
chicago: Heredia, Jorge, Barbora Trubenova, Dirk Sudholt, and Tiago Paixao. “Selection
Limits to Adaptive Walks on Correlated Landscapes.” Genetics. Genetics
Society of America, 2017. https://doi.org/10.1534/genetics.116.189340.
ieee: J. Heredia, B. Trubenova, D. Sudholt, and T. Paixao, “Selection limits to
adaptive walks on correlated landscapes,” Genetics, vol. 205, no. 2. Genetics
Society of America, pp. 803–825, 2017.
ista: Heredia J, Trubenova B, Sudholt D, Paixao T. 2017. Selection limits to adaptive
walks on correlated landscapes. Genetics. 205(2), 803–825.
mla: Heredia, Jorge, et al. “Selection Limits to Adaptive Walks on Correlated Landscapes.”
Genetics, vol. 205, no. 2, Genetics Society of America, 2017, pp. 803–25,
doi:10.1534/genetics.116.189340.
short: J. Heredia, B. Trubenova, D. Sudholt, T. Paixao, Genetics 205 (2017) 803–825.
date_created: 2018-12-11T11:50:12Z
date_published: 2017-02-01T00:00:00Z
date_updated: 2023-09-20T11:35:03Z
day: '01'
department:
- _id: NiBa
doi: 10.1534/genetics.116.189340
ec_funded: 1
external_id:
isi:
- '000394144900025'
pmid:
- '27881471'
intvolume: ' 205'
isi: 1
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1534/genetics.116.189340
month: '02'
oa: 1
oa_version: Published Version
page: 803 - 825
pmid: 1
project:
- _id: 25B1EC9E-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '618091'
name: Speed of Adaptation in Population Genetics and Evolutionary Computation
publication: Genetics
publication_identifier:
issn:
- '00166731'
publication_status: published
publisher: Genetics Society of America
publist_id: '6256'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Selection limits to adaptive walks on correlated landscapes
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 205
year: '2017'
...
---
_id: '1077'
abstract:
- lang: eng
text: Viral capsids are structurally constrained by interactions among the amino
acids (AAs) of their constituent proteins. Therefore, epistasis is expected to
evolve among physically interacting sites and to influence the rates of substitution.
To study the evolution of epistasis, we focused on the major structural protein
of the fX174 phage family by first reconstructing the ancestral protein sequences
of 18 species using a Bayesian statistical framework. The inferred ancestral reconstruction
differed at eight AAs, for a total of 256 possible ancestral haplotypes. For each
ancestral haplotype and the extant species, we estimated, in silico, the distribution
of free energies and epistasis of the capsid structure. We found that free energy
has not significantly increased but epistasis has. We decomposed epistasis up
to fifth order and found that higher-order epistasis sometimes compensates pairwise
interactions making the free energy seem additive. The dN/dS ratio is low, suggesting
strong purifying selection, and that structure is under stabilizing selection.
We synthesized phages carrying ancestral haplotypes of the coat protein gene and
measured their fitness experimentally. Our findings indicate that stabilizing
mutations can have higher fitness, and that fitness optima do not necessarily
coincide with energy minima.
article_number: '20160139'
article_processing_charge: Yes (in subscription journal)
author:
- first_name: Rodrigo A
full_name: Fernandes Redondo, Rodrigo A
id: 409D5C96-F248-11E8-B48F-1D18A9856A87
last_name: Fernandes Redondo
orcid: 0000-0002-5837-2793
- first_name: Harold
full_name: Vladar, Harold
id: 2A181218-F248-11E8-B48F-1D18A9856A87
last_name: Vladar
orcid: 0000-0002-5985-7653
- first_name: Tomasz
full_name: Włodarski, Tomasz
last_name: Włodarski
- first_name: Jonathan P
full_name: Bollback, Jonathan P
id: 2C6FA9CC-F248-11E8-B48F-1D18A9856A87
last_name: Bollback
orcid: 0000-0002-4624-4612
citation:
ama: Fernandes Redondo RA, de Vladar H, Włodarski T, Bollback JP. Evolutionary interplay
between structure, energy and epistasis in the coat protein of the ϕX174 phage
family. Journal of the Royal Society Interface. 2017;14(126). doi:10.1098/rsif.2016.0139
apa: Fernandes Redondo, R. A., de Vladar, H., Włodarski, T., & Bollback, J.
P. (2017). Evolutionary interplay between structure, energy and epistasis in the
coat protein of the ϕX174 phage family. Journal of the Royal Society Interface.
Royal Society of London. https://doi.org/10.1098/rsif.2016.0139
chicago: Fernandes Redondo, Rodrigo A, Harold de Vladar, Tomasz Włodarski, and Jonathan
P Bollback. “Evolutionary Interplay between Structure, Energy and Epistasis in
the Coat Protein of the ΦX174 Phage Family.” Journal of the Royal Society Interface.
Royal Society of London, 2017. https://doi.org/10.1098/rsif.2016.0139.
ieee: R. A. Fernandes Redondo, H. de Vladar, T. Włodarski, and J. P. Bollback, “Evolutionary
interplay between structure, energy and epistasis in the coat protein of the ϕX174
phage family,” Journal of the Royal Society Interface, vol. 14, no. 126.
Royal Society of London, 2017.
ista: Fernandes Redondo RA, de Vladar H, Włodarski T, Bollback JP. 2017. Evolutionary
interplay between structure, energy and epistasis in the coat protein of the ϕX174
phage family. Journal of the Royal Society Interface. 14(126), 20160139.
mla: Fernandes Redondo, Rodrigo A., et al. “Evolutionary Interplay between Structure,
Energy and Epistasis in the Coat Protein of the ΦX174 Phage Family.” Journal
of the Royal Society Interface, vol. 14, no. 126, 20160139, Royal Society
of London, 2017, doi:10.1098/rsif.2016.0139.
short: R.A. Fernandes Redondo, H. de Vladar, T. Włodarski, J.P. Bollback, Journal
of the Royal Society Interface 14 (2017).
date_created: 2018-12-11T11:50:01Z
date_published: 2017-01-04T00:00:00Z
date_updated: 2023-09-20T11:56:34Z
day: '04'
ddc:
- '570'
department:
- _id: NiBa
- _id: JoBo
doi: 10.1098/rsif.2016.0139
ec_funded: 1
external_id:
isi:
- '000393380400001'
file:
- access_level: open_access
content_type: application/pdf
creator: dernst
date_created: 2019-01-18T09:14:02Z
date_updated: 2019-01-18T09:14:02Z
file_id: '5843'
file_name: 2017_JRSI_Redondo.pdf
file_size: 1092015
relation: main_file
success: 1
file_date_updated: 2019-01-18T09:14:02Z
has_accepted_license: '1'
intvolume: ' 14'
isi: 1
issue: '126'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
project:
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
- _id: 2578D616-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '648440'
name: Selective Barriers to Horizontal Gene Transfer
publication: Journal of the Royal Society Interface
publication_identifier:
issn:
- '17425689'
publication_status: published
publisher: Royal Society of London
publist_id: '6303'
quality_controlled: '1'
related_material:
record:
- id: '9864'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Evolutionary interplay between structure, energy and epistasis in the coat
protein of the ϕX174 phage family
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 14
year: '2017'
...
---
_id: '1074'
abstract:
- lang: eng
text: Recently it has become feasible to detect long blocks of nearly identical
sequence shared between pairs of genomes. These IBD blocks are direct traces of
recent coalescence events and, as such, contain ample signal to infer recent demography.
Here, we examine sharing of such blocks in two-dimensional populations with local
migration. Using a diffusion approximation to trace genetic ancestry, we derive
analytical formulae for patterns of isolation by distance of IBD blocks, which
can also incorporate recent population density changes. We introduce an inference
scheme that uses a composite likelihood approach to fit these formulae. We then
extensively evaluate our theory and inference method on a range of scenarios using
simulated data. We first validate the diffusion approximation by showing that
the theoretical results closely match the simulated block sharing patterns. We
then demonstrate that our inference scheme can accurately and robustly infer dispersal
rate and effective density, as well as bounds on recent dynamics of population
density. To demonstrate an application, we use our estimation scheme to explore
the fit of a diffusion model to Eastern European samples in the POPRES data set.
We show that ancestry diffusing with a rate of σ ≈ 50–100 km/√gen during the last
centuries, combined with accelerating population growth, can explain the observed
exponential decay of block sharing with increasing pairwise sample distance.
article_processing_charge: No
author:
- first_name: Harald
full_name: Ringbauer, Harald
id: 417FCFF4-F248-11E8-B48F-1D18A9856A87
last_name: Ringbauer
orcid: 0000-0002-4884-9682
- first_name: Graham
full_name: Coop, Graham
last_name: Coop
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: Ringbauer H, Coop G, Barton NH. Inferring recent demography from isolation
by distance of long shared sequence blocks. Genetics. 2017;205(3):1335-1351.
doi:10.1534/genetics.116.196220
apa: Ringbauer, H., Coop, G., & Barton, N. H. (2017). Inferring recent demography
from isolation by distance of long shared sequence blocks. Genetics. Genetics
Society of America. https://doi.org/10.1534/genetics.116.196220
chicago: Ringbauer, Harald, Graham Coop, and Nicholas H Barton. “Inferring Recent
Demography from Isolation by Distance of Long Shared Sequence Blocks.” Genetics.
Genetics Society of America, 2017. https://doi.org/10.1534/genetics.116.196220.
ieee: H. Ringbauer, G. Coop, and N. H. Barton, “Inferring recent demography from
isolation by distance of long shared sequence blocks,” Genetics, vol. 205,
no. 3. Genetics Society of America, pp. 1335–1351, 2017.
ista: Ringbauer H, Coop G, Barton NH. 2017. Inferring recent demography from isolation
by distance of long shared sequence blocks. Genetics. 205(3), 1335–1351.
mla: Ringbauer, Harald, et al. “Inferring Recent Demography from Isolation by Distance
of Long Shared Sequence Blocks.” Genetics, vol. 205, no. 3, Genetics Society
of America, 2017, pp. 1335–51, doi:10.1534/genetics.116.196220.
short: H. Ringbauer, G. Coop, N.H. Barton, Genetics 205 (2017) 1335–1351.
date_created: 2018-12-11T11:50:00Z
date_published: 2017-03-01T00:00:00Z
date_updated: 2023-09-20T12:00:56Z
day: '01'
department:
- _id: NiBa
doi: 10.1534/genetics.116.196220
ec_funded: 1
external_id:
isi:
- '000395807200023'
intvolume: ' 205'
isi: 1
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.biorxiv.org/content/early/2016/09/23/076810
month: '03'
oa: 1
oa_version: Preprint
page: 1335 - 1351
project:
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
publication: Genetics
publication_identifier:
issn:
- '00166731'
publication_status: published
publisher: Genetics Society of America
publist_id: '6307'
quality_controlled: '1'
related_material:
record:
- id: '200'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Inferring recent demography from isolation by distance of long shared sequence
blocks
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 205
year: '2017'
...
---
_id: '1063'
abstract:
- lang: eng
text: Severe environmental change can drive a population extinct unless the population
adapts in time to the new conditions (“evolutionary rescue”). How does biparental
sexual reproduction influence the chances of population persistence compared to
clonal reproduction or selfing? In this article, we set up a one‐locus two‐allele
model for adaptation in diploid species, where rescue is contingent on the establishment
of the mutant homozygote. Reproduction can occur by random mating, selfing, or
clonally. Random mating generates and destroys the rescue mutant; selfing is efficient
at generating it but at the same time depletes the heterozygote, which can lead
to a low mutant frequency in the standing genetic variation. Due to these (and
other) antagonistic effects, we find a nontrivial dependence of population survival
on the rate of sex/selfing, which is strongly influenced by the dominance coefficient
of the mutation before and after the environmental change. Importantly, since
mating with the wild‐type breaks the mutant homozygote up, a slow decay of the
wild‐type population size can impede rescue in randomly mating populations.
article_processing_charge: No
author:
- first_name: Hildegard
full_name: Uecker, Hildegard
id: 2DB8F68A-F248-11E8-B48F-1D18A9856A87
last_name: Uecker
orcid: 0000-0001-9435-2813
citation:
ama: Uecker H. Evolutionary rescue in randomly mating, selfing, and clonal populations.
Evolution. 2017;71(4):845-858. doi:10.1111/evo.13191
apa: Uecker, H. (2017). Evolutionary rescue in randomly mating, selfing, and clonal
populations. Evolution. Wiley-Blackwell. https://doi.org/10.1111/evo.13191
chicago: Uecker, Hildegard. “Evolutionary Rescue in Randomly Mating, Selfing, and
Clonal Populations.” Evolution. Wiley-Blackwell, 2017. https://doi.org/10.1111/evo.13191.
ieee: H. Uecker, “Evolutionary rescue in randomly mating, selfing, and clonal populations,”
Evolution, vol. 71, no. 4. Wiley-Blackwell, pp. 845–858, 2017.
ista: Uecker H. 2017. Evolutionary rescue in randomly mating, selfing, and clonal
populations. Evolution. 71(4), 845–858.
mla: Uecker, Hildegard. “Evolutionary Rescue in Randomly Mating, Selfing, and Clonal
Populations.” Evolution, vol. 71, no. 4, Wiley-Blackwell, 2017, pp. 845–58,
doi:10.1111/evo.13191.
short: H. Uecker, Evolution 71 (2017) 845–858.
date_created: 2018-12-11T11:49:57Z
date_published: 2017-04-01T00:00:00Z
date_updated: 2023-09-20T12:10:32Z
day: '01'
department:
- _id: NiBa
doi: 10.1111/evo.13191
ec_funded: 1
external_id:
isi:
- '000398545200003'
intvolume: ' 71'
isi: 1
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://biorxiv.org/content/early/2016/10/14/081042
month: '04'
oa: 1
oa_version: Submitted Version
page: 845 - 858
project:
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
publication: Evolution
publication_identifier:
issn:
- '00143820'
publication_status: published
publisher: Wiley-Blackwell
publist_id: '6327'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Evolutionary rescue in randomly mating, selfing, and clonal populations
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 71
year: '2017'
...
---
_id: '990'
abstract:
- lang: eng
text: Assortative mating is an important driver of speciation in populations with
gene flow and is predicted to evolve under certain conditions in few-locus models.
However, the evolution of assortment is less understood for mating based on quantitative
traits, which are often characterized by high genetic variability and extensive
linkage disequilibrium between trait loci. We explore this scenario for a two-deme
model with migration, by considering a single polygenic trait subject to divergent
viability selection across demes, as well as assortative mating and sexual selection
within demes, and investigate how trait divergence is shaped by various evolutionary
forces. Our analysis reveals the existence of sharp thresholds of assortment strength,
at which divergence increases dramatically. We also study the evolution of assortment
via invasion of modifiers of mate discrimination and show that the ES assortment
strength has an intermediate value under a range of migration-selection parameters,
even in diverged populations, due to subtle effects which depend sensitively on
the extent of phenotypic variation within these populations. The evolutionary
dynamics of the polygenic trait is studied using the hypergeometric and infinitesimal
models. We further investigate the sensitivity of our results to the assumptions
of the hypergeometric model, using individual-based simulations.
article_processing_charge: No
author:
- first_name: Himani
full_name: Sachdeva, Himani
id: 42377A0A-F248-11E8-B48F-1D18A9856A87
last_name: Sachdeva
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: Sachdeva H, Barton NH. Divergence and evolution of assortative mating in a
polygenic trait model of speciation with gene flow. Evolution; International
Journal of Organic Evolution. 2017;71(6):1478-1493. doi:10.1111/evo.13252
apa: Sachdeva, H., & Barton, N. H. (2017). Divergence and evolution of assortative
mating in a polygenic trait model of speciation with gene flow. Evolution;
International Journal of Organic Evolution. Wiley-Blackwell. https://doi.org/10.1111/evo.13252
chicago: Sachdeva, Himani, and Nicholas H Barton. “Divergence and Evolution of Assortative
Mating in a Polygenic Trait Model of Speciation with Gene Flow.” Evolution;
International Journal of Organic Evolution. Wiley-Blackwell, 2017. https://doi.org/10.1111/evo.13252.
ieee: H. Sachdeva and N. H. Barton, “Divergence and evolution of assortative mating
in a polygenic trait model of speciation with gene flow,” Evolution; International
Journal of Organic Evolution, vol. 71, no. 6. Wiley-Blackwell, pp. 1478–1493,
2017.
ista: Sachdeva H, Barton NH. 2017. Divergence and evolution of assortative mating
in a polygenic trait model of speciation with gene flow. Evolution; International
Journal of Organic Evolution. 71(6), 1478–1493.
mla: Sachdeva, Himani, and Nicholas H. Barton. “Divergence and Evolution of Assortative
Mating in a Polygenic Trait Model of Speciation with Gene Flow.” Evolution;
International Journal of Organic Evolution, vol. 71, no. 6, Wiley-Blackwell,
2017, pp. 1478–93, doi:10.1111/evo.13252.
short: H. Sachdeva, N.H. Barton, Evolution; International Journal of Organic Evolution
71 (2017) 1478–1493.
date_created: 2018-12-11T11:49:34Z
date_published: 2017-06-01T00:00:00Z
date_updated: 2023-09-22T09:55:13Z
day: '01'
ddc:
- '576'
department:
- _id: NiBa
doi: 10.1111/evo.13252
ec_funded: 1
external_id:
isi:
- '000403014800005'
pmid:
- '28419447'
file:
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checksum: 6d4c38cb1347fd43620d1736c6df5c79
content_type: application/pdf
creator: dernst
date_created: 2019-04-17T07:37:04Z
date_updated: 2020-07-14T12:48:18Z
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intvolume: ' 71'
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language:
- iso: eng
month: '06'
oa: 1
oa_version: Submitted Version
page: '1478 - 1493 '
pmid: 1
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
publication: Evolution; International Journal of Organic Evolution
publication_identifier:
issn:
- '00143820'
publication_status: published
publisher: Wiley-Blackwell
publist_id: '6409'
pubrep_id: '977'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Divergence and evolution of assortative mating in a polygenic trait model of
speciation with gene flow
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 71
year: '2017'
...
---
_id: '954'
abstract:
- lang: eng
text: Understanding the relation between genotype and phenotype remains a major
challenge. The difficulty of predicting individual mutation effects, and particularly
the interactions between them, has prevented the development of a comprehensive
theory that links genotypic changes to their phenotypic effects. We show that
a general thermodynamic framework for gene regulation, based on a biophysical
understanding of protein-DNA binding, accurately predicts the sign of epistasis
in a canonical cis-regulatory element consisting of overlapping RNA polymerase
and repressor binding sites. Sign and magnitude of individual mutation effects
are sufficient to predict the sign of epistasis and its environmental dependence.
Thus, the thermodynamic model offers the correct null prediction for epistasis
between mutations across DNA-binding sites. Our results indicate that a predictive
theory for the effects of cis-regulatory mutations is possible from first principles,
as long as the essential molecular mechanisms and the constraints these impose
on a biological system are accounted for.
article_number: e25192
article_processing_charge: Yes
author:
- first_name: Mato
full_name: Lagator, Mato
id: 345D25EC-F248-11E8-B48F-1D18A9856A87
last_name: Lagator
- first_name: Tiago
full_name: Paixao, Tiago
id: 2C5658E6-F248-11E8-B48F-1D18A9856A87
last_name: Paixao
orcid: 0000-0003-2361-3953
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Jonathan P
full_name: Bollback, Jonathan P
id: 2C6FA9CC-F248-11E8-B48F-1D18A9856A87
last_name: Bollback
orcid: 0000-0002-4624-4612
- first_name: Calin C
full_name: Guet, Calin C
id: 47F8433E-F248-11E8-B48F-1D18A9856A87
last_name: Guet
orcid: 0000-0001-6220-2052
citation:
ama: Lagator M, Paixao T, Barton NH, Bollback JP, Guet CC. On the mechanistic nature
of epistasis in a canonical cis-regulatory element. eLife. 2017;6. doi:10.7554/eLife.25192
apa: Lagator, M., Paixao, T., Barton, N. H., Bollback, J. P., & Guet, C. C.
(2017). On the mechanistic nature of epistasis in a canonical cis-regulatory element.
ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.25192
chicago: Lagator, Mato, Tiago Paixao, Nicholas H Barton, Jonathan P Bollback, and
Calin C Guet. “On the Mechanistic Nature of Epistasis in a Canonical Cis-Regulatory
Element.” ELife. eLife Sciences Publications, 2017. https://doi.org/10.7554/eLife.25192.
ieee: M. Lagator, T. Paixao, N. H. Barton, J. P. Bollback, and C. C. Guet, “On the
mechanistic nature of epistasis in a canonical cis-regulatory element,” eLife,
vol. 6. eLife Sciences Publications, 2017.
ista: Lagator M, Paixao T, Barton NH, Bollback JP, Guet CC. 2017. On the mechanistic
nature of epistasis in a canonical cis-regulatory element. eLife. 6, e25192.
mla: Lagator, Mato, et al. “On the Mechanistic Nature of Epistasis in a Canonical
Cis-Regulatory Element.” ELife, vol. 6, e25192, eLife Sciences Publications,
2017, doi:10.7554/eLife.25192.
short: M. Lagator, T. Paixao, N.H. Barton, J.P. Bollback, C.C. Guet, ELife 6 (2017).
date_created: 2018-12-11T11:49:23Z
date_published: 2017-05-18T00:00:00Z
date_updated: 2023-09-22T10:01:17Z
day: '18'
ddc:
- '576'
department:
- _id: CaGu
- _id: NiBa
- _id: JoBo
doi: 10.7554/eLife.25192
ec_funded: 1
external_id:
isi:
- '000404024800001'
file:
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checksum: 59cdd4400fb41280122d414fea971546
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:17:49Z
date_updated: 2020-07-14T12:48:16Z
file_id: '5306'
file_name: IST-2017-841-v1+1_elife-25192-v2.pdf
file_size: 2441529
relation: main_file
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checksum: b69024880558b858eb8c5d47a92b6377
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:17:50Z
date_updated: 2020-07-14T12:48:16Z
file_id: '5307'
file_name: IST-2017-841-v1+2_elife-25192-figures-v2.pdf
file_size: 3752660
relation: main_file
file_date_updated: 2020-07-14T12:48:16Z
has_accepted_license: '1'
intvolume: ' 6'
isi: 1
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
project:
- _id: 25B1EC9E-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '618091'
name: Speed of Adaptation in Population Genetics and Evolutionary Computation
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
- _id: 2578D616-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '648440'
name: Selective Barriers to Horizontal Gene Transfer
publication: eLife
publication_identifier:
issn:
- 2050084X
publication_status: published
publisher: eLife Sciences Publications
publist_id: '6460'
pubrep_id: '841'
quality_controlled: '1'
scopus_import: '1'
status: public
title: On the mechanistic nature of epistasis in a canonical cis-regulatory element
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 6
year: '2017'
...
---
_id: '955'
abstract:
- lang: eng
text: 'Gene expression is controlled by networks of regulatory proteins that interact
specifically with external signals and DNA regulatory sequences. These interactions
force the network components to co-evolve so as to continually maintain function.
Yet, existing models of evolution mostly focus on isolated genetic elements. In
contrast, we study the essential process by which regulatory networks grow: the
duplication and subsequent specialization of network components. We synthesize
a biophysical model of molecular interactions with the evolutionary framework
to find the conditions and pathways by which new regulatory functions emerge.
We show that specialization of new network components is usually slow, but can
be drastically accelerated in the presence of regulatory crosstalk and mutations
that promote promiscuous interactions between network components.'
article_number: '216'
article_processing_charge: Yes (in subscription journal)
author:
- first_name: Tamar
full_name: Friedlander, Tamar
id: 36A5845C-F248-11E8-B48F-1D18A9856A87
last_name: Friedlander
- first_name: Roshan
full_name: Prizak, Roshan
id: 4456104E-F248-11E8-B48F-1D18A9856A87
last_name: Prizak
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Gasper
full_name: Tkacik, Gasper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
citation:
ama: Friedlander T, Prizak R, Barton NH, Tkačik G. Evolution of new regulatory functions
on biophysically realistic fitness landscapes. Nature Communications. 2017;8(1).
doi:10.1038/s41467-017-00238-8
apa: Friedlander, T., Prizak, R., Barton, N. H., & Tkačik, G. (2017). Evolution
of new regulatory functions on biophysically realistic fitness landscapes. Nature
Communications. Nature Publishing Group. https://doi.org/10.1038/s41467-017-00238-8
chicago: Friedlander, Tamar, Roshan Prizak, Nicholas H Barton, and Gašper Tkačik.
“Evolution of New Regulatory Functions on Biophysically Realistic Fitness Landscapes.”
Nature Communications. Nature Publishing Group, 2017. https://doi.org/10.1038/s41467-017-00238-8.
ieee: T. Friedlander, R. Prizak, N. H. Barton, and G. Tkačik, “Evolution of new
regulatory functions on biophysically realistic fitness landscapes,” Nature
Communications, vol. 8, no. 1. Nature Publishing Group, 2017.
ista: Friedlander T, Prizak R, Barton NH, Tkačik G. 2017. Evolution of new regulatory
functions on biophysically realistic fitness landscapes. Nature Communications.
8(1), 216.
mla: Friedlander, Tamar, et al. “Evolution of New Regulatory Functions on Biophysically
Realistic Fitness Landscapes.” Nature Communications, vol. 8, no. 1, 216,
Nature Publishing Group, 2017, doi:10.1038/s41467-017-00238-8.
short: T. Friedlander, R. Prizak, N.H. Barton, G. Tkačik, Nature Communications
8 (2017).
date_created: 2018-12-11T11:49:23Z
date_published: 2017-08-09T00:00:00Z
date_updated: 2023-09-22T10:00:49Z
day: '09'
ddc:
- '539'
- '576'
department:
- _id: GaTk
- _id: NiBa
doi: 10.1038/s41467-017-00238-8
ec_funded: 1
external_id:
isi:
- '000407198800005'
file:
- access_level: open_access
checksum: 29a1b5db458048d3bd5c67e0e2a56818
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creator: system
date_created: 2018-12-12T10:14:14Z
date_updated: 2020-07-14T12:48:16Z
file_id: '5064'
file_name: IST-2017-864-v1+1_s41467-017-00238-8.pdf
file_size: 998157
relation: main_file
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content_type: application/pdf
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file_id: '5065'
file_name: IST-2017-864-v1+2_41467_2017_238_MOESM1_ESM.pdf
file_size: 9715993
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has_accepted_license: '1'
intvolume: ' 8'
isi: 1
issue: '1'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
- _id: 254E9036-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P28844-B27
name: Biophysics of information processing in gene regulation
publication: Nature Communications
publication_identifier:
issn:
- '20411723'
publication_status: published
publisher: Nature Publishing Group
publist_id: '6459'
pubrep_id: '864'
quality_controlled: '1'
related_material:
record:
- id: '6071'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Evolution of new regulatory functions on biophysically realistic fitness landscapes
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 8
year: '2017'
...
---
_id: '953'
abstract:
- lang: eng
text: 'The role of natural selection in the evolution of adaptive phenotypes has
undergone constant probing by evolutionary biologists, employing both theoretical
and empirical approaches. As Darwin noted, natural selection can act together
with other processes, including random changes in the frequencies of phenotypic
differences that are not under strong selection, and changes in the environment,
which may reflect evolutionary changes in the organisms themselves. As understanding
of genetics developed after 1900, the new genetic discoveries were incorporated
into evolutionary biology. The resulting general principles were summarized by
Julian Huxley in his 1942 book Evolution: the modern synthesis. Here, we examine
how recent advances in genetics, developmental biology and molecular biology,
including epigenetics, relate to today''s understanding of the evolution of adaptations.
We illustrate how careful genetic studies have repeatedly shown that apparently
puzzling results in a wide diversity of organisms involve processes that are consistent
with neo-Darwinism. They do not support important roles in adaptation for processes
such as directed mutation or the inheritance of acquired characters, and therefore
no radical revision of our understanding of the mechanism of adaptive evolution
is needed.'
article_number: '20162864'
article_processing_charge: No
author:
- first_name: Deborah
full_name: Charlesworth, Deborah
last_name: Charlesworth
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Brian
full_name: Charlesworth, Brian
last_name: Charlesworth
citation:
ama: Charlesworth D, Barton NH, Charlesworth B. The sources of adaptive evolution.
Proceedings of the Royal Society of London Series B Biological Sciences.
2017;284(1855). doi:10.1098/rspb.2016.2864
apa: Charlesworth, D., Barton, N. H., & Charlesworth, B. (2017). The sources
of adaptive evolution. Proceedings of the Royal Society of London Series B
Biological Sciences. Royal Society, The. https://doi.org/10.1098/rspb.2016.2864
chicago: Charlesworth, Deborah, Nicholas H Barton, and Brian Charlesworth. “The
Sources of Adaptive Evolution.” Proceedings of the Royal Society of London
Series B Biological Sciences. Royal Society, The, 2017. https://doi.org/10.1098/rspb.2016.2864.
ieee: D. Charlesworth, N. H. Barton, and B. Charlesworth, “The sources of adaptive
evolution,” Proceedings of the Royal Society of London Series B Biological
Sciences, vol. 284, no. 1855. Royal Society, The, 2017.
ista: Charlesworth D, Barton NH, Charlesworth B. 2017. The sources of adaptive evolution.
Proceedings of the Royal Society of London Series B Biological Sciences. 284(1855),
20162864.
mla: Charlesworth, Deborah, et al. “The Sources of Adaptive Evolution.” Proceedings
of the Royal Society of London Series B Biological Sciences, vol. 284, no.
1855, 20162864, Royal Society, The, 2017, doi:10.1098/rspb.2016.2864.
short: D. Charlesworth, N.H. Barton, B. Charlesworth, Proceedings of the Royal Society
of London Series B Biological Sciences 284 (2017).
date_created: 2018-12-11T11:49:23Z
date_published: 2017-05-31T00:00:00Z
date_updated: 2023-09-22T10:01:48Z
day: '31'
department:
- _id: NiBa
doi: 10.1098/rspb.2016.2864
external_id:
isi:
- '000405148800021'
pmid:
- '28566483'
intvolume: ' 284'
isi: 1
issue: '1855'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5454256/
month: '05'
oa: 1
oa_version: Submitted Version
pmid: 1
publication: Proceedings of the Royal Society of London Series B Biological Sciences
publication_status: published
publisher: Royal Society, The
publist_id: '6462'
quality_controlled: '1'
scopus_import: '1'
status: public
title: The sources of adaptive evolution
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 284
year: '2017'
...
---
_id: '952'
abstract:
- lang: eng
text: A novel strategy for controlling the spread of arboviral diseases such as
dengue, Zika and chikungunya is to transform mosquito populations with virus-suppressing
Wolbachia. In general, Wolbachia transinfected into mosquitoes induce fitness
costs through lower viability or fecundity. These maternally inherited bacteria
also produce a frequency-dependent advantage for infected females by inducing
cytoplasmic incompatibility (CI), which kills the embryos produced by uninfected
females mated to infected males. These competing effects, a frequency-dependent
advantage and frequency-independent costs, produce bistable Wolbachia frequency
dynamics. Above a threshold frequency, denoted pˆ, CI drives fitness-decreasing
Wolbachia transinfections through local populations; but below pˆ, infection frequencies
tend to decline to zero. If pˆ is not too high, CI also drives spatial spread
once infections become established over sufficiently large areas. We illustrate
how simple models provide testable predictions concerning the spatial and temporal
dynamics of Wolbachia introductions, focusing on rate of spatial spread, the shape
of spreading waves, and the conditions for initiating spread from local introductions.
First, we consider the robustness of diffusion-based predictions to incorporating
two important features of wMel-Aedes aegypti biology that may be inconsistent
with the diffusion approximations, namely fast local dynamics induced by complete
CI (i.e., all embryos produced from incompatible crosses die) and long-tailed,
non-Gaussian dispersal. With complete CI, our numerical analyses show that long-tailed
dispersal changes wave-width predictions only slightly; but it can significantly
reduce wave speed relative to the diffusion prediction; it also allows smaller
local introductions to initiate spatial spread. Second, we use approximations
for pˆ and dispersal distances to predict the outcome of 2013 releases of wMel-infected
Aedes aegypti in Cairns, Australia, Third, we describe new data from Ae. aegypti
populations near Cairns, Australia that demonstrate long-distance dispersal and
provide an approximate lower bound on pˆ for wMel in northeastern Australia. Finally,
we apply our analyses to produce operational guidelines for efficient transformation
of vector populations over large areas. We demonstrate that even very slow spatial
spread, on the order of 10-20 m/month (as predicted), can produce area-wide population
transformation within a few years following initial releases covering about 20-30%
of the target area.
article_processing_charge: No
author:
- first_name: Michael
full_name: Turelli, Michael
last_name: Turelli
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: 'Turelli M, Barton NH. Deploying dengue-suppressing Wolbachia: Robust models
predict slow but effective spatial spread in Aedes aegypti. Theoretical Population
Biology. 2017;115:45-60. doi:10.1016/j.tpb.2017.03.003'
apa: 'Turelli, M., & Barton, N. H. (2017). Deploying dengue-suppressing Wolbachia:
Robust models predict slow but effective spatial spread in Aedes aegypti. Theoretical
Population Biology. Elsevier. https://doi.org/10.1016/j.tpb.2017.03.003'
chicago: 'Turelli, Michael, and Nicholas H Barton. “Deploying Dengue-Suppressing
Wolbachia: Robust Models Predict Slow but Effective Spatial Spread in Aedes Aegypti.”
Theoretical Population Biology. Elsevier, 2017. https://doi.org/10.1016/j.tpb.2017.03.003.'
ieee: 'M. Turelli and N. H. Barton, “Deploying dengue-suppressing Wolbachia: Robust
models predict slow but effective spatial spread in Aedes aegypti,” Theoretical
Population Biology, vol. 115. Elsevier, pp. 45–60, 2017.'
ista: 'Turelli M, Barton NH. 2017. Deploying dengue-suppressing Wolbachia: Robust
models predict slow but effective spatial spread in Aedes aegypti. Theoretical
Population Biology. 115, 45–60.'
mla: 'Turelli, Michael, and Nicholas H. Barton. “Deploying Dengue-Suppressing Wolbachia:
Robust Models Predict Slow but Effective Spatial Spread in Aedes Aegypti.” Theoretical
Population Biology, vol. 115, Elsevier, 2017, pp. 45–60, doi:10.1016/j.tpb.2017.03.003.'
short: M. Turelli, N.H. Barton, Theoretical Population Biology 115 (2017) 45–60.
date_created: 2018-12-11T11:49:22Z
date_published: 2017-06-01T00:00:00Z
date_updated: 2023-09-22T10:02:21Z
day: '01'
ddc:
- '576'
department:
- _id: NiBa
doi: 10.1016/j.tpb.2017.03.003
external_id:
pmid:
- '28411063'
file:
- access_level: open_access
checksum: 9aeff86fa7de69f7a15cf4fc60d57d01
content_type: application/pdf
creator: dernst
date_created: 2019-04-17T06:39:45Z
date_updated: 2020-07-14T12:48:16Z
file_id: '6327'
file_name: 2017_TheoreticalPopulationBio_Turelli.pdf
file_size: 2073856
relation: main_file
file_date_updated: 2020-07-14T12:48:16Z
has_accepted_license: '1'
intvolume: ' 115'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Submitted Version
page: 45 - 60
pmid: 1
publication: Theoretical Population Biology
publication_identifier:
issn:
- '00405809'
publication_status: published
publisher: Elsevier
publist_id: '6463'
pubrep_id: '972'
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Deploying dengue-suppressing Wolbachia: Robust models predict slow but effective
spatial spread in Aedes aegypti'
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 115
year: '2017'
...
---
_id: '951'
abstract:
- lang: eng
text: Dengue-suppressing Wolbachia strains are promising tools for arbovirus control,
particularly as they have the potential to self-spread following local introductions.
To test this, we followed the frequency of the transinfected Wolbachia strain
wMel through Ae. aegypti in Cairns, Australia, following releases at 3 nonisolated
locations within the city in early 2013. Spatial spread was analysed graphically
using interpolation and by fitting a statistical model describing the position
and width of the wave. For the larger 2 of the 3 releases (covering 0.97 km2 and
0.52 km2), we observed slow but steady spatial spread, at about 100–200 m per
year, roughly consistent with theoretical predictions. In contrast, the smallest
release (0.11 km2) produced erratic temporal and spatial dynamics, with little
evidence of spread after 2 years. This is consistent with the prediction concerning
fitness-decreasing Wolbachia transinfections that a minimum release area is needed
to achieve stable local establishment and spread in continuous habitats. Our graphical
and likelihood analyses produced broadly consistent estimates of wave speed and
wave width. Spread at all sites was spatially heterogeneous, suggesting that environmental
heterogeneity will affect large-scale Wolbachia transformations of urban mosquito
populations. The persistence and spread of Wolbachia in release areas meeting
minimum area requirements indicates the promise of successful large-scale population
transfo
article_number: e2001894
article_processing_charge: No
author:
- first_name: Tom
full_name: Schmidt, Tom
last_name: Schmidt
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Gordana
full_name: Rasic, Gordana
last_name: Rasic
- first_name: Andrew
full_name: Turley, Andrew
last_name: Turley
- first_name: Brian
full_name: Montgomery, Brian
last_name: Montgomery
- first_name: Inaki
full_name: Iturbe Ormaetxe, Inaki
last_name: Iturbe Ormaetxe
- first_name: Peter
full_name: Cook, Peter
last_name: Cook
- first_name: Peter
full_name: Ryan, Peter
last_name: Ryan
- first_name: Scott
full_name: Ritchie, Scott
last_name: Ritchie
- first_name: Ary
full_name: Hoffmann, Ary
last_name: Hoffmann
- first_name: Scott
full_name: O’Neill, Scott
last_name: O’Neill
- first_name: Michael
full_name: Turelli, Michael
last_name: Turelli
citation:
ama: Schmidt T, Barton NH, Rasic G, et al. Local introduction and heterogeneous
spatial spread of dengue-suppressing Wolbachia through an urban population of
Aedes Aegypti. PLoS Biology. 2017;15(5). doi:10.1371/journal.pbio.2001894
apa: Schmidt, T., Barton, N. H., Rasic, G., Turley, A., Montgomery, B., Iturbe Ormaetxe,
I., … Turelli, M. (2017). Local introduction and heterogeneous spatial spread
of dengue-suppressing Wolbachia through an urban population of Aedes Aegypti.
PLoS Biology. Public Library of Science. https://doi.org/10.1371/journal.pbio.2001894
chicago: Schmidt, Tom, Nicholas H Barton, Gordana Rasic, Andrew Turley, Brian Montgomery,
Inaki Iturbe Ormaetxe, Peter Cook, et al. “Local Introduction and Heterogeneous
Spatial Spread of Dengue-Suppressing Wolbachia through an Urban Population of
Aedes Aegypti.” PLoS Biology. Public Library of Science, 2017. https://doi.org/10.1371/journal.pbio.2001894.
ieee: T. Schmidt et al., “Local introduction and heterogeneous spatial spread
of dengue-suppressing Wolbachia through an urban population of Aedes Aegypti,”
PLoS Biology, vol. 15, no. 5. Public Library of Science, 2017.
ista: Schmidt T, Barton NH, Rasic G, Turley A, Montgomery B, Iturbe Ormaetxe I,
Cook P, Ryan P, Ritchie S, Hoffmann A, O’Neill S, Turelli M. 2017. Local introduction
and heterogeneous spatial spread of dengue-suppressing Wolbachia through an urban
population of Aedes Aegypti. PLoS Biology. 15(5), e2001894.
mla: Schmidt, Tom, et al. “Local Introduction and Heterogeneous Spatial Spread of
Dengue-Suppressing Wolbachia through an Urban Population of Aedes Aegypti.” PLoS
Biology, vol. 15, no. 5, e2001894, Public Library of Science, 2017, doi:10.1371/journal.pbio.2001894.
short: T. Schmidt, N.H. Barton, G. Rasic, A. Turley, B. Montgomery, I. Iturbe Ormaetxe,
P. Cook, P. Ryan, S. Ritchie, A. Hoffmann, S. O’Neill, M. Turelli, PLoS Biology
15 (2017).
date_created: 2018-12-11T11:49:22Z
date_published: 2017-05-30T00:00:00Z
date_updated: 2023-09-22T10:02:52Z
day: '30'
ddc:
- '576'
department:
- _id: NiBa
doi: 10.1371/journal.pbio.2001894
external_id:
isi:
- '000402520000012'
file:
- access_level: open_access
checksum: 107d290bd1159ec77b734eb2824b01c8
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:08:30Z
date_updated: 2020-07-14T12:48:16Z
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file_name: IST-2017-843-v1+1_journal.pbio.2001894.pdf
file_size: 5541206
relation: main_file
file_date_updated: 2020-07-14T12:48:16Z
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intvolume: ' 15'
isi: 1
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language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
publication: PLoS Biology
publication_identifier:
issn:
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publication_status: published
publisher: Public Library of Science
publist_id: '6464'
pubrep_id: '843'
quality_controlled: '1'
related_material:
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relation: research_data
status: public
- id: '9857'
relation: research_data
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- id: '9858'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Local introduction and heterogeneous spatial spread of dengue-suppressing Wolbachia
through an urban population of Aedes Aegypti
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 15
year: '2017'
...
---
_id: '9858'
article_processing_charge: No
author:
- first_name: Tom
full_name: Schmidt, Tom
last_name: Schmidt
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Gordana
full_name: Rasic, Gordana
last_name: Rasic
- first_name: Andrew
full_name: Turley, Andrew
last_name: Turley
- first_name: Brian
full_name: Montgomery, Brian
last_name: Montgomery
- first_name: Inaki
full_name: Iturbe Ormaetxe, Inaki
last_name: Iturbe Ormaetxe
- first_name: Peter
full_name: Cook, Peter
last_name: Cook
- first_name: Peter
full_name: Ryan, Peter
last_name: Ryan
- first_name: Scott
full_name: Ritchie, Scott
last_name: Ritchie
- first_name: Ary
full_name: Hoffmann, Ary
last_name: Hoffmann
- first_name: Scott
full_name: O’Neill, Scott
last_name: O’Neill
- first_name: Michael
full_name: Turelli, Michael
last_name: Turelli
citation:
ama: Schmidt T, Barton NH, Rasic G, et al. Excel file with data on mosquito densities,
Wolbachia infection status and housing characteristics. 2017. doi:10.1371/journal.pbio.2001894.s016
apa: Schmidt, T., Barton, N. H., Rasic, G., Turley, A., Montgomery, B., Iturbe Ormaetxe,
I., … Turelli, M. (2017). Excel file with data on mosquito densities, Wolbachia
infection status and housing characteristics. Public Library of Science. https://doi.org/10.1371/journal.pbio.2001894.s016
chicago: Schmidt, Tom, Nicholas H Barton, Gordana Rasic, Andrew Turley, Brian Montgomery,
Inaki Iturbe Ormaetxe, Peter Cook, et al. “Excel File with Data on Mosquito Densities,
Wolbachia Infection Status and Housing Characteristics.” Public Library of Science,
2017. https://doi.org/10.1371/journal.pbio.2001894.s016.
ieee: T. Schmidt et al., “Excel file with data on mosquito densities, Wolbachia
infection status and housing characteristics.” Public Library of Science, 2017.
ista: Schmidt T, Barton NH, Rasic G, Turley A, Montgomery B, Iturbe Ormaetxe I,
Cook P, Ryan P, Ritchie S, Hoffmann A, O’Neill S, Turelli M. 2017. Excel file
with data on mosquito densities, Wolbachia infection status and housing characteristics,
Public Library of Science, 10.1371/journal.pbio.2001894.s016.
mla: Schmidt, Tom, et al. Excel File with Data on Mosquito Densities, Wolbachia
Infection Status and Housing Characteristics. Public Library of Science, 2017,
doi:10.1371/journal.pbio.2001894.s016.
short: T. Schmidt, N.H. Barton, G. Rasic, A. Turley, B. Montgomery, I. Iturbe Ormaetxe,
P. Cook, P. Ryan, S. Ritchie, A. Hoffmann, S. O’Neill, M. Turelli, (2017).
date_created: 2021-08-10T07:47:07Z
date_published: 2017-05-30T00:00:00Z
date_updated: 2023-09-22T10:02:51Z
day: '30'
department:
- _id: NiBa
doi: 10.1371/journal.pbio.2001894.s016
month: '05'
oa_version: Published Version
publisher: Public Library of Science
related_material:
record:
- id: '951'
relation: used_in_publication
status: public
status: public
title: Excel file with data on mosquito densities, Wolbachia infection status and
housing characteristics
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2017'
...
---
_id: '9857'
article_processing_charge: No
author:
- first_name: Tom
full_name: Schmidt, Tom
last_name: Schmidt
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Gordana
full_name: Rasic, Gordana
last_name: Rasic
- first_name: Andrew
full_name: Turley, Andrew
last_name: Turley
- first_name: Brian
full_name: Montgomery, Brian
last_name: Montgomery
- first_name: Inaki
full_name: Iturbe Ormaetxe, Inaki
last_name: Iturbe Ormaetxe
- first_name: Peter
full_name: Cook, Peter
last_name: Cook
- first_name: Peter
full_name: Ryan, Peter
last_name: Ryan
- first_name: Scott
full_name: Ritchie, Scott
last_name: Ritchie
- first_name: Ary
full_name: Hoffmann, Ary
last_name: Hoffmann
- first_name: Scott
full_name: O’Neill, Scott
last_name: O’Neill
- first_name: Michael
full_name: Turelli, Michael
last_name: Turelli
citation:
ama: Schmidt T, Barton NH, Rasic G, et al. Supporting information concerning observed
wMel frequencies and analyses of habitat variables. 2017. doi:10.1371/journal.pbio.2001894.s015
apa: Schmidt, T., Barton, N. H., Rasic, G., Turley, A., Montgomery, B., Iturbe Ormaetxe,
I., … Turelli, M. (2017). Supporting information concerning observed wMel frequencies
and analyses of habitat variables. Public Library of Science . https://doi.org/10.1371/journal.pbio.2001894.s015
chicago: Schmidt, Tom, Nicholas H Barton, Gordana Rasic, Andrew Turley, Brian Montgomery,
Inaki Iturbe Ormaetxe, Peter Cook, et al. “Supporting Information Concerning Observed
WMel Frequencies and Analyses of Habitat Variables.” Public Library of Science
, 2017. https://doi.org/10.1371/journal.pbio.2001894.s015.
ieee: T. Schmidt et al., “Supporting information concerning observed wMel
frequencies and analyses of habitat variables.” Public Library of Science , 2017.
ista: Schmidt T, Barton NH, Rasic G, Turley A, Montgomery B, Iturbe Ormaetxe I,
Cook P, Ryan P, Ritchie S, Hoffmann A, O’Neill S, Turelli M. 2017. Supporting
information concerning observed wMel frequencies and analyses of habitat variables,
Public Library of Science , 10.1371/journal.pbio.2001894.s015.
mla: Schmidt, Tom, et al. Supporting Information Concerning Observed WMel Frequencies
and Analyses of Habitat Variables. Public Library of Science , 2017, doi:10.1371/journal.pbio.2001894.s015.
short: T. Schmidt, N.H. Barton, G. Rasic, A. Turley, B. Montgomery, I. Iturbe Ormaetxe,
P. Cook, P. Ryan, S. Ritchie, A. Hoffmann, S. O’Neill, M. Turelli, (2017).
date_created: 2021-08-10T07:41:52Z
date_published: 2017-05-30T00:00:00Z
date_updated: 2023-09-22T10:02:51Z
day: '30'
department:
- _id: NiBa
doi: 10.1371/journal.pbio.2001894.s015
month: '05'
oa_version: Published Version
publisher: 'Public Library of Science '
related_material:
record:
- id: '951'
relation: used_in_publication
status: public
status: public
title: Supporting information concerning observed wMel frequencies and analyses of
habitat variables
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2017'
...
---
_id: '9856'
article_processing_charge: No
author:
- first_name: Tom
full_name: Schmidt, Tom
last_name: Schmidt
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Gordana
full_name: Rasic, Gordana
last_name: Rasic
- first_name: Andrew
full_name: Turley, Andrew
last_name: Turley
- first_name: Brian
full_name: Montgomery, Brian
last_name: Montgomery
- first_name: Inaki
full_name: Iturbe Ormaetxe, Inaki
last_name: Iturbe Ormaetxe
- first_name: Peter
full_name: Cook, Peter
last_name: Cook
- first_name: Peter
full_name: Ryan, Peter
last_name: Ryan
- first_name: Scott
full_name: Ritchie, Scott
last_name: Ritchie
- first_name: Ary
full_name: Hoffmann, Ary
last_name: Hoffmann
- first_name: Scott
full_name: O’Neill, Scott
last_name: O’Neill
- first_name: Michael
full_name: Turelli, Michael
last_name: Turelli
citation:
ama: Schmidt T, Barton NH, Rasic G, et al. Supporting Information concerning additional
likelihood analyses and results. 2017. doi:10.1371/journal.pbio.2001894.s014
apa: Schmidt, T., Barton, N. H., Rasic, G., Turley, A., Montgomery, B., Iturbe Ormaetxe,
I., … Turelli, M. (2017). Supporting Information concerning additional likelihood
analyses and results. Public Library of Science. https://doi.org/10.1371/journal.pbio.2001894.s014
chicago: Schmidt, Tom, Nicholas H Barton, Gordana Rasic, Andrew Turley, Brian Montgomery,
Inaki Iturbe Ormaetxe, Peter Cook, et al. “Supporting Information Concerning Additional
Likelihood Analyses and Results.” Public Library of Science, 2017. https://doi.org/10.1371/journal.pbio.2001894.s014.
ieee: T. Schmidt et al., “Supporting Information concerning additional likelihood
analyses and results.” Public Library of Science, 2017.
ista: Schmidt T, Barton NH, Rasic G, Turley A, Montgomery B, Iturbe Ormaetxe I,
Cook P, Ryan P, Ritchie S, Hoffmann A, O’Neill S, Turelli M. 2017. Supporting
Information concerning additional likelihood analyses and results, Public Library
of Science, 10.1371/journal.pbio.2001894.s014.
mla: Schmidt, Tom, et al. Supporting Information Concerning Additional Likelihood
Analyses and Results. Public Library of Science, 2017, doi:10.1371/journal.pbio.2001894.s014.
short: T. Schmidt, N.H. Barton, G. Rasic, A. Turley, B. Montgomery, I. Iturbe Ormaetxe,
P. Cook, P. Ryan, S. Ritchie, A. Hoffmann, S. O’Neill, M. Turelli, (2017).
date_created: 2021-08-10T07:36:04Z
date_published: 2017-05-30T00:00:00Z
date_updated: 2023-09-22T10:02:51Z
day: '30'
department:
- _id: NiBa
doi: 10.1371/journal.pbio.2001894.s014
month: '05'
oa_version: Published Version
publisher: Public Library of Science
related_material:
record:
- id: '951'
relation: used_in_publication
status: public
status: public
title: Supporting Information concerning additional likelihood analyses and results
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2017'
...
---
_id: '910'
abstract:
- lang: eng
text: "Frequency-independent selection is generally considered as a force that acts
to reduce the genetic variation in evolving populations, yet rigorous arguments
for this idea are scarce. When selection fluctuates in time, it is unclear whether
frequency-independent selection may maintain genetic polymorphism without invoking
additional mechanisms. We show that constant frequency-independent selection with
arbitrary epistasis on a well-mixed haploid population eliminates genetic variation
if we assume linkage equilibrium between alleles. To this end, we introduce the
notion of frequency-independent selection at the level of alleles, which is sufficient
to prove our claim and contains the notion of frequency-independent selection
on haploids. When selection and recombination are weak but of the same order,
there may be strong linkage disequilibrium; numerical calculations show that stable
equilibria are highly unlikely. Using the example of a diallelic two-locus model,
we then demonstrate that frequency-independent selection that fluctuates in time
can maintain stable polymorphism if linkage disequilibrium changes its sign periodically.
We put our findings in the context of results from the existing literature and
point out those scenarios in which the possible role of frequency-independent
selection in maintaining genetic variation remains unclear.\r\n"
article_processing_charge: No
author:
- first_name: Sebastian
full_name: Novak, Sebastian
id: 461468AE-F248-11E8-B48F-1D18A9856A87
last_name: Novak
orcid: 0000-0002-2519-824X
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: Novak S, Barton NH. When does frequency-independent selection maintain genetic
variation? Genetics. 2017;207(2):653-668. doi:10.1534/genetics.117.300129
apa: Novak, S., & Barton, N. H. (2017). When does frequency-independent selection
maintain genetic variation? Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.117.300129
chicago: Novak, Sebastian, and Nicholas H Barton. “When Does Frequency-Independent
Selection Maintain Genetic Variation?” Genetics. Genetics Society of America,
2017. https://doi.org/10.1534/genetics.117.300129.
ieee: S. Novak and N. H. Barton, “When does frequency-independent selection maintain
genetic variation?,” Genetics, vol. 207, no. 2. Genetics Society of America,
pp. 653–668, 2017.
ista: Novak S, Barton NH. 2017. When does frequency-independent selection maintain
genetic variation? Genetics. 207(2), 653–668.
mla: Novak, Sebastian, and Nicholas H. Barton. “When Does Frequency-Independent
Selection Maintain Genetic Variation?” Genetics, vol. 207, no. 2, Genetics
Society of America, 2017, pp. 653–68, doi:10.1534/genetics.117.300129.
short: S. Novak, N.H. Barton, Genetics 207 (2017) 653–668.
date_created: 2018-12-11T11:49:09Z
date_published: 2017-10-01T00:00:00Z
date_updated: 2023-09-26T15:49:15Z
day: '01'
ddc:
- '576'
department:
- _id: NiBa
doi: 10.1534/genetics.117.300129
ec_funded: 1
external_id:
isi:
- '000412232600019'
file:
- access_level: open_access
checksum: f7c32dabf52e6d9e709d9203761e39fd
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:17:12Z
date_updated: 2020-07-14T12:48:15Z
file_id: '5264'
file_name: IST-2018-974-v1+1_manuscript.pdf
file_size: 494268
relation: main_file
file_date_updated: 2020-07-14T12:48:15Z
has_accepted_license: '1'
intvolume: ' 207'
isi: 1
issue: '2'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Submitted Version
page: 653 - 668
project:
- _id: 25B1EC9E-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '618091'
name: Speed of Adaptation in Population Genetics and Evolutionary Computation
publication: Genetics
publication_status: published
publisher: Genetics Society of America
publist_id: '6533'
pubrep_id: '974'
quality_controlled: '1'
scopus_import: '1'
status: public
title: When does frequency-independent selection maintain genetic variation?
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 207
year: '2017'
...
---
_id: '614'
abstract:
- lang: eng
text: 'Moths and butterflies (Lepidoptera) usually have a pair of differentiated
WZ sex chromosomes. However, in most lineages outside of the division Ditrysia,
as well as in the sister order Trichoptera, females lack a W chromosome. The W
is therefore thought to have been acquired secondarily. Here we compare the genomes
of three Lepidoptera species (one Dytrisia and two non-Dytrisia) to test three
models accounting for the origin of the W: (1) a Z-autosome fusion; (2) a sex
chromosome turnover; and (3) a non-canonical mechanism (e.g., through the recruitment
of a B chromosome). We show that the gene content of the Z is highly conserved
across Lepidoptera (rejecting a sex chromosome turnover) and that very few genes
moved onto the Z in the common ancestor of the Ditrysia (arguing against a Z-autosome
fusion). Our comparative genomics analysis therefore supports the secondary acquisition
of the Lepidoptera W by a non-canonical mechanism, and it confirms the extreme
stability of well-differentiated sex chromosomes.'
article_number: '1486'
article_processing_charge: No
article_type: original
author:
- first_name: Christelle
full_name: Fraisse, Christelle
id: 32DF5794-F248-11E8-B48F-1D18A9856A87
last_name: Fraisse
orcid: 0000-0001-8441-5075
- first_name: Marion A
full_name: Picard, Marion A
id: 2C921A7A-F248-11E8-B48F-1D18A9856A87
last_name: Picard
orcid: 0000-0002-8101-2518
- first_name: Beatriz
full_name: Vicoso, Beatriz
id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
last_name: Vicoso
orcid: 0000-0002-4579-8306
citation:
ama: Fraisse C, Picard MAL, Vicoso B. The deep conservation of the Lepidoptera Z
chromosome suggests a non canonical origin of the W. Nature Communications.
2017;8(1). doi:10.1038/s41467-017-01663-5
apa: Fraisse, C., Picard, M. A. L., & Vicoso, B. (2017). The deep conservation
of the Lepidoptera Z chromosome suggests a non canonical origin of the W. Nature
Communications. Nature Publishing Group. https://doi.org/10.1038/s41467-017-01663-5
chicago: Fraisse, Christelle, Marion A L Picard, and Beatriz Vicoso. “The Deep Conservation
of the Lepidoptera Z Chromosome Suggests a Non Canonical Origin of the W.” Nature
Communications. Nature Publishing Group, 2017. https://doi.org/10.1038/s41467-017-01663-5.
ieee: C. Fraisse, M. A. L. Picard, and B. Vicoso, “The deep conservation of the
Lepidoptera Z chromosome suggests a non canonical origin of the W,” Nature
Communications, vol. 8, no. 1. Nature Publishing Group, 2017.
ista: Fraisse C, Picard MAL, Vicoso B. 2017. The deep conservation of the Lepidoptera
Z chromosome suggests a non canonical origin of the W. Nature Communications.
8(1), 1486.
mla: Fraisse, Christelle, et al. “The Deep Conservation of the Lepidoptera Z Chromosome
Suggests a Non Canonical Origin of the W.” Nature Communications, vol.
8, no. 1, 1486, Nature Publishing Group, 2017, doi:10.1038/s41467-017-01663-5.
short: C. Fraisse, M.A.L. Picard, B. Vicoso, Nature Communications 8 (2017).
date_created: 2018-12-11T11:47:30Z
date_published: 2017-12-01T00:00:00Z
date_updated: 2024-02-21T13:47:47Z
day: '01'
ddc:
- '570'
- '576'
department:
- _id: BeVi
- _id: NiBa
doi: 10.1038/s41467-017-01663-5
external_id:
pmid:
- '29133797'
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checksum: 4da2651303c8afc2f7fc419be42a2433
content_type: application/pdf
creator: dernst
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file_id: '7562'
file_name: 2017_NatureComm_Fraisse.pdf
file_size: 1201520
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file_date_updated: 2020-07-14T12:47:20Z
has_accepted_license: '1'
intvolume: ' 8'
issue: '1'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 250ED89C-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P28842-B22
name: Sex chromosome evolution under male- and female- heterogamety
publication: Nature Communications
publication_identifier:
issn:
- '20411723'
publication_status: published
publisher: Nature Publishing Group
publist_id: '7190'
pubrep_id: '910'
quality_controlled: '1'
related_material:
record:
- id: '7163'
relation: popular_science
status: public
scopus_import: 1
status: public
title: The deep conservation of the Lepidoptera Z chromosome suggests a non canonical
origin of the W
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 8
year: '2017'
...
---
_id: '7163'
abstract:
- lang: eng
text: The de novo genome assemblies generated for this study, and the associated
metadata.
article_processing_charge: No
author:
- first_name: Christelle
full_name: Fraisse, Christelle
id: 32DF5794-F248-11E8-B48F-1D18A9856A87
last_name: Fraisse
orcid: 0000-0001-8441-5075
citation:
ama: Fraisse C. Supplementary Files for “The deep conservation of the Lepidoptera
Z chromosome suggests a non canonical origin of the W.” 2017. doi:10.15479/AT:ISTA:7163
apa: Fraisse, C. (2017). Supplementary Files for “The deep conservation of the Lepidoptera
Z chromosome suggests a non canonical origin of the W.” Institute of Science and
Technology Austria. https://doi.org/10.15479/AT:ISTA:7163
chicago: Fraisse, Christelle. “Supplementary Files for ‘The Deep Conservation of
the Lepidoptera Z Chromosome Suggests a Non Canonical Origin of the W.’” Institute
of Science and Technology Austria, 2017. https://doi.org/10.15479/AT:ISTA:7163.
ieee: C. Fraisse, “Supplementary Files for ‘The deep conservation of the Lepidoptera
Z chromosome suggests a non canonical origin of the W.’” Institute of Science
and Technology Austria, 2017.
ista: Fraisse C. 2017. Supplementary Files for ‘The deep conservation of the Lepidoptera
Z chromosome suggests a non canonical origin of the W’, Institute of Science and
Technology Austria, 10.15479/AT:ISTA:7163.
mla: Fraisse, Christelle. Supplementary Files for “The Deep Conservation of the
Lepidoptera Z Chromosome Suggests a Non Canonical Origin of the W.” Institute
of Science and Technology Austria, 2017, doi:10.15479/AT:ISTA:7163.
short: C. Fraisse, (2017).
contributor:
- first_name: Christelle
id: 32DF5794-F248-11E8-B48F-1D18A9856A87
last_name: Fraisse
orcid: 0000-0001-8441-5075
- first_name: Marion A L
id: 2C921A7A-F248-11E8-B48F-1D18A9856A87
last_name: Picard
orcid: 0000-0002-8101-2518
- first_name: Beatriz
id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
last_name: Vicoso
orcid: 0000-0002-4579-8306
date_created: 2019-12-09T23:03:03Z
date_published: 2017-12-01T00:00:00Z
date_updated: 2024-02-21T13:47:47Z
day: '01'
ddc:
- '576'
department:
- _id: BeVi
- _id: NiBa
doi: 10.15479/AT:ISTA:7163
file:
- access_level: open_access
checksum: 3cae8a2e3cbf8703399b9c483aaba7f3
content_type: application/zip
creator: cfraisse
date_created: 2019-12-10T08:46:46Z
date_updated: 2020-07-14T12:47:50Z
file_id: '7164'
file_name: Vicoso_Cohridella_Ndegeerella_Tsylvina_genome_assemblies.zip
file_size: 841375478
relation: main_file
file_date_updated: 2020-07-14T12:47:50Z
has_accepted_license: '1'
month: '12'
oa: 1
oa_version: Published Version
project:
- _id: 250ED89C-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P28842-B22
name: Sex chromosome evolution under male- and female- heterogamety
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '614'
relation: research_paper
status: public
status: public
title: Supplementary Files for "The deep conservation of the Lepidoptera Z chromosome
suggests a non canonical origin of the W"
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: research_data
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2017'
...
---
_id: '696'
abstract:
- lang: eng
text: Mutator strains are expected to evolve when the availability and effect of
beneficial mutations are high enough to counteract the disadvantage from deleterious
mutations that will inevitably accumulate. As the population becomes more adapted
to its environment, both availability and effect of beneficial mutations necessarily
decrease and mutation rates are predicted to decrease. It has been shown that
certain molecular mechanisms can lead to increased mutation rates when the organism
finds itself in a stressful environment. While this may be a correlated response
to other functions, it could also be an adaptive mechanism, raising mutation rates
only when it is most advantageous. Here, we use a mathematical model to investigate
the plausibility of the adaptive hypothesis. We show that such a mechanism can
be mantained if the population is subjected to diverse stresses. By simulating
various antibiotic treatment schemes, we find that combination treatments can
reduce the effectiveness of second-order selection on stress-induced mutagenesis.
We discuss the implications of our results to strategies of antibiotic therapy.
article_number: e1005609
article_type: original
author:
- first_name: Marta
full_name: Lukacisinova, Marta
id: 4342E402-F248-11E8-B48F-1D18A9856A87
last_name: Lukacisinova
orcid: 0000-0002-2519-8004
- first_name: Sebastian
full_name: Novak, Sebastian
id: 461468AE-F248-11E8-B48F-1D18A9856A87
last_name: Novak
orcid: 0000-0002-2519-824X
- first_name: Tiago
full_name: Paixao, Tiago
id: 2C5658E6-F248-11E8-B48F-1D18A9856A87
last_name: Paixao
orcid: 0000-0003-2361-3953
citation:
ama: 'Lukacisinova M, Novak S, Paixao T. Stress induced mutagenesis: Stress diversity
facilitates the persistence of mutator genes. PLoS Computational Biology.
2017;13(7). doi:10.1371/journal.pcbi.1005609'
apa: 'Lukacisinova, M., Novak, S., & Paixao, T. (2017). Stress induced mutagenesis:
Stress diversity facilitates the persistence of mutator genes. PLoS Computational
Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1005609'
chicago: 'Lukacisinova, Marta, Sebastian Novak, and Tiago Paixao. “Stress Induced
Mutagenesis: Stress Diversity Facilitates the Persistence of Mutator Genes.” PLoS
Computational Biology. Public Library of Science, 2017. https://doi.org/10.1371/journal.pcbi.1005609.'
ieee: 'M. Lukacisinova, S. Novak, and T. Paixao, “Stress induced mutagenesis: Stress
diversity facilitates the persistence of mutator genes,” PLoS Computational
Biology, vol. 13, no. 7. Public Library of Science, 2017.'
ista: 'Lukacisinova M, Novak S, Paixao T. 2017. Stress induced mutagenesis: Stress
diversity facilitates the persistence of mutator genes. PLoS Computational Biology.
13(7), e1005609.'
mla: 'Lukacisinova, Marta, et al. “Stress Induced Mutagenesis: Stress Diversity
Facilitates the Persistence of Mutator Genes.” PLoS Computational Biology,
vol. 13, no. 7, e1005609, Public Library of Science, 2017, doi:10.1371/journal.pcbi.1005609.'
short: M. Lukacisinova, S. Novak, T. Paixao, PLoS Computational Biology 13 (2017).
date_created: 2018-12-11T11:47:58Z
date_published: 2017-07-18T00:00:00Z
date_updated: 2024-03-28T23:30:28Z
day: '18'
ddc:
- '576'
department:
- _id: ToBo
- _id: NiBa
- _id: CaGu
doi: 10.1371/journal.pcbi.1005609
ec_funded: 1
file:
- access_level: open_access
checksum: 9143c290fa6458ed2563bff4b295554a
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:15:01Z
date_updated: 2020-07-14T12:47:46Z
file_id: '5117'
file_name: IST-2017-894-v1+1_journal.pcbi.1005609.pdf
file_size: 3775716
relation: main_file
file_date_updated: 2020-07-14T12:47:46Z
has_accepted_license: '1'
intvolume: ' 13'
issue: '7'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
project:
- _id: 25B1EC9E-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '618091'
name: Speed of Adaptation in Population Genetics and Evolutionary Computation
publication: PLoS Computational Biology
publication_identifier:
issn:
- 1553734X
publication_status: published
publisher: Public Library of Science
publist_id: '7004'
pubrep_id: '894'
quality_controlled: '1'
related_material:
record:
- id: '9849'
relation: research_data
status: public
- id: '9850'
relation: research_data
status: public
- id: '9851'
relation: research_data
status: public
- id: '9852'
relation: research_data
status: public
- id: '6263'
relation: dissertation_contains
status: public
scopus_import: 1
status: public
title: 'Stress induced mutagenesis: Stress diversity facilitates the persistence of
mutator genes'
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 13
year: '2017'
...
---
_id: '1172'
abstract:
- lang: eng
text: A central issue in cell biology is the physico-chemical basis of organelle
biogenesis in intracellular trafficking pathways, its most impressive manifestation
being the biogenesis of Golgi cisternae. At a basic level, such morphologically
and chemically distinct compartments should arise from an interplay between the
molecular transport and chemical maturation. Here, we formulate analytically tractable,
minimalist models, that incorporate this interplay between transport and chemical
progression in physical space, and explore the conditions for de novo biogenesis
of distinct cisternae. We propose new quantitative measures that can discriminate
between the various models of transport in a qualitative manner-this includes
measures of the dynamics in steady state and the dynamical response to perturbations
of the kind amenable to live-cell imaging.
acknowledgement: H.S. thanks NCBS for hospitality. We thank Vivek Malhotra and Mukund
Thattai for critical discussions and suggestions.
article_number: '38840'
author:
- first_name: Himani
full_name: Sachdeva, Himani
id: 42377A0A-F248-11E8-B48F-1D18A9856A87
last_name: Sachdeva
- first_name: Mustansir
full_name: Barma, Mustansir
last_name: Barma
- first_name: Madan
full_name: Rao, Madan
last_name: Rao
citation:
ama: Sachdeva H, Barma M, Rao M. Nonequilibrium description of de novo biogenesis
and transport through Golgi-like cisternae. Scientific Reports. 2016;6.
doi:10.1038/srep38840
apa: Sachdeva, H., Barma, M., & Rao, M. (2016). Nonequilibrium description of
de novo biogenesis and transport through Golgi-like cisternae. Scientific Reports.
Nature Publishing Group. https://doi.org/10.1038/srep38840
chicago: Sachdeva, Himani, Mustansir Barma, and Madan Rao. “Nonequilibrium Description
of de Novo Biogenesis and Transport through Golgi-like Cisternae.” Scientific
Reports. Nature Publishing Group, 2016. https://doi.org/10.1038/srep38840.
ieee: H. Sachdeva, M. Barma, and M. Rao, “Nonequilibrium description of de novo
biogenesis and transport through Golgi-like cisternae,” Scientific Reports,
vol. 6. Nature Publishing Group, 2016.
ista: Sachdeva H, Barma M, Rao M. 2016. Nonequilibrium description of de novo biogenesis
and transport through Golgi-like cisternae. Scientific Reports. 6, 38840.
mla: Sachdeva, Himani, et al. “Nonequilibrium Description of de Novo Biogenesis
and Transport through Golgi-like Cisternae.” Scientific Reports, vol. 6,
38840, Nature Publishing Group, 2016, doi:10.1038/srep38840.
short: H. Sachdeva, M. Barma, M. Rao, Scientific Reports 6 (2016).
date_created: 2018-12-11T11:50:32Z
date_published: 2016-12-19T00:00:00Z
date_updated: 2021-01-12T06:48:50Z
day: '19'
ddc:
- '576'
department:
- _id: NiBa
doi: 10.1038/srep38840
file:
- access_level: open_access
checksum: cb378732da885ea4959ec5b845fb6e52
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:12:56Z
date_updated: 2020-07-14T12:44:37Z
file_id: '4977'
file_name: IST-2017-737-v1+1_srep38840.pdf
file_size: 760967
relation: main_file
file_date_updated: 2020-07-14T12:44:37Z
has_accepted_license: '1'
intvolume: ' 6'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
publication: Scientific Reports
publication_status: published
publisher: Nature Publishing Group
publist_id: '6183'
pubrep_id: '737'
quality_controlled: '1'
scopus_import: 1
status: public
title: Nonequilibrium description of de novo biogenesis and transport through Golgi-like
cisternae
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 6
year: '2016'
...
---
_id: '1195'
abstract:
- lang: eng
text: 'The genetic analysis of experimentally evolving populations typically relies
on short reads from pooled individuals (Pool-Seq). While this method provides
reliable allele frequency estimates, the underlying haplotype structure remains
poorly characterized. With small population sizes and adaptive variants that start
from low frequencies, the interpretation of selection signatures in most Evolve
and Resequencing studies remains challenging. To facilitate the characterization
of selection targets, we propose a new approach that reconstructs selected haplotypes
from replicated time series, using Pool-Seq data. We identify selected haplotypes
through the correlated frequencies of alleles carried by them. Computer simulations
indicate that selected haplotype-blocks of several Mb can be reconstructed with
high confidence and low error rates, even when allele frequencies change only
by 20% across three replicates. Applying this method to real data from D. melanogaster
populations adapting to a hot environment, we identify a selected haplotype-block
of 6.93 Mb. We confirm the presence of this haplotype-block in evolved populations
by experimental haplotyping, demonstrating the power and accuracy of our haplotype
reconstruction from Pool-Seq data. We propose that the combination of allele frequency
estimates with haplotype information will provide the key to understanding the
dynamics of adaptive alleles. '
acknowledgement: "The authors thank all members of the Institute of Population\r\nGenetics
for discussion and support on the project and par-\r\nticularly N. Barghi for helpful
comments on earlier versions of\r\nthe manuscript. This work was supported
\ by the European\r\nResearch Council (ERC) grants “ArchAdapt” and “250152”."
author:
- first_name: Susan
full_name: Franssen, Susan
last_name: Franssen
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Christian
full_name: Schlötterer, Christian
last_name: Schlötterer
citation:
ama: Franssen S, Barton NH, Schlötterer C. Reconstruction of haplotype-blocks selected
during experimental evolution. Molecular Biology and Evolution. 2016;34(1):174-184.
doi:10.1093/molbev/msw210
apa: Franssen, S., Barton, N. H., & Schlötterer, C. (2016). Reconstruction of
haplotype-blocks selected during experimental evolution. Molecular Biology
and Evolution. Oxford University Press. https://doi.org/10.1093/molbev/msw210
chicago: Franssen, Susan, Nicholas H Barton, and Christian Schlötterer. “Reconstruction
of Haplotype-Blocks Selected during Experimental Evolution.” Molecular Biology
and Evolution. Oxford University Press, 2016. https://doi.org/10.1093/molbev/msw210.
ieee: S. Franssen, N. H. Barton, and C. Schlötterer, “Reconstruction of haplotype-blocks
selected during experimental evolution.,” Molecular Biology and Evolution,
vol. 34, no. 1. Oxford University Press, pp. 174–184, 2016.
ista: Franssen S, Barton NH, Schlötterer C. 2016. Reconstruction of haplotype-blocks
selected during experimental evolution. Molecular Biology and Evolution. 34(1),
174–184.
mla: Franssen, Susan, et al. “Reconstruction of Haplotype-Blocks Selected during
Experimental Evolution.” Molecular Biology and Evolution, vol. 34, no.
1, Oxford University Press, 2016, pp. 174–84, doi:10.1093/molbev/msw210.
short: S. Franssen, N.H. Barton, C. Schlötterer, Molecular Biology and Evolution
34 (2016) 174–184.
date_created: 2018-12-11T11:50:39Z
date_published: 2016-10-03T00:00:00Z
date_updated: 2021-01-12T06:49:00Z
day: '03'
ddc:
- '576'
department:
- _id: NiBa
doi: 10.1093/molbev/msw210
ec_funded: 1
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date_created: 2018-12-12T10:16:37Z
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creator: system
date_created: 2018-12-12T10:16:38Z
date_updated: 2020-07-14T12:44:38Z
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creator: system
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file_size: 50705
relation: main_file
file_date_updated: 2020-07-14T12:44:38Z
has_accepted_license: '1'
intvolume: ' 34'
issue: '1'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Submitted Version
page: 174 - 184
project:
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
publication: Molecular Biology and Evolution
publication_status: published
publisher: Oxford University Press
publist_id: '6155'
pubrep_id: '770'
quality_controlled: '1'
scopus_import: 1
status: public
title: Reconstruction of haplotype-blocks selected during experimental evolution.
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 34
year: '2016'
...
---
_id: '1224'
abstract:
- lang: eng
text: Sexual dimorphism in resource allocation is expected to change during the
life cycle of dioecious plants because of temporal differences between the sexes
in reproductive investment. Given the potential for sex-specific differences in
reproductive costs, resource availability may contribute to variation in reproductive
allocation in females and males. Here, we used Rumex hastatulus, a dioecious,
wind-pollinated annual plant, to investigate whether sexual dimorphism varies
with life-history stage and nutrient availability, and determine whether allocation
patterns differ depending on reproductive commitment. To examine if the costs
of reproduction varied between the sexes, reproduction was either allowed or prevented
through bud removal, and biomass allocation was measured at maturity. In a second
experiment to assess variation in sexual dimorphism across the life cycle, and
whether this varied with resource availability, plants were grown in high and
low nutrients and allocation to roots, aboveground vegetative growth and reproduction
were measured at three developmental stages. Males prevented from reproducing
compensated with increased above- and belowground allocation to a much larger
degree than females, suggesting that male reproductive costs reduce vegetative
growth. The proportional allocation to roots, reproductive structures and aboveground
vegetative growth varied between the sexes and among life-cycle stages, but not
with nutrient treatment. Females allocated proportionally more resources to roots
than males at peak flowering, but this pattern was reversed at reproductive maturity
under low-nutrient conditions. Our study illustrates the importance of temporal
dynamics in sex-specific resource allocation and provides support for high male
reproductive costs in wind-pollinated plants.
author:
- first_name: Zachary
full_name: Teitel, Zachary
last_name: Teitel
- first_name: Melinda
full_name: Pickup, Melinda
id: 2C78037E-F248-11E8-B48F-1D18A9856A87
last_name: Pickup
orcid: 0000-0001-6118-0541
- first_name: David
full_name: Field, David
id: 419049E2-F248-11E8-B48F-1D18A9856A87
last_name: Field
orcid: 0000-0002-4014-8478
- first_name: Spencer
full_name: Barrett, Spencer
last_name: Barrett
citation:
ama: Teitel Z, Pickup M, Field D, Barrett S. The dynamics of resource allocation
and costs of reproduction in a sexually dimorphic, wind-pollinated dioecious plant.
Plant Biology. 2016;18(1):98-103. doi:10.1111/plb.12336
apa: Teitel, Z., Pickup, M., Field, D., & Barrett, S. (2016). The dynamics of
resource allocation and costs of reproduction in a sexually dimorphic, wind-pollinated
dioecious plant. Plant Biology. Wiley-Blackwell. https://doi.org/10.1111/plb.12336
chicago: Teitel, Zachary, Melinda Pickup, David Field, and Spencer Barrett. “The
Dynamics of Resource Allocation and Costs of Reproduction in a Sexually Dimorphic,
Wind-Pollinated Dioecious Plant.” Plant Biology. Wiley-Blackwell, 2016.
https://doi.org/10.1111/plb.12336.
ieee: Z. Teitel, M. Pickup, D. Field, and S. Barrett, “The dynamics of resource
allocation and costs of reproduction in a sexually dimorphic, wind-pollinated
dioecious plant,” Plant Biology, vol. 18, no. 1. Wiley-Blackwell, pp. 98–103,
2016.
ista: Teitel Z, Pickup M, Field D, Barrett S. 2016. The dynamics of resource allocation
and costs of reproduction in a sexually dimorphic, wind-pollinated dioecious plant.
Plant Biology. 18(1), 98–103.
mla: Teitel, Zachary, et al. “The Dynamics of Resource Allocation and Costs of Reproduction
in a Sexually Dimorphic, Wind-Pollinated Dioecious Plant.” Plant Biology,
vol. 18, no. 1, Wiley-Blackwell, 2016, pp. 98–103, doi:10.1111/plb.12336.
short: Z. Teitel, M. Pickup, D. Field, S. Barrett, Plant Biology 18 (2016) 98–103.
date_created: 2018-12-11T11:50:48Z
date_published: 2016-01-01T00:00:00Z
date_updated: 2021-01-12T06:49:12Z
day: '01'
department:
- _id: NiBa
doi: 10.1111/plb.12336
intvolume: ' 18'
issue: '1'
language:
- iso: eng
month: '01'
oa_version: None
page: 98 - 103
publication: Plant Biology
publication_status: published
publisher: Wiley-Blackwell
publist_id: '6110'
quality_controlled: '1'
scopus_import: 1
status: public
title: The dynamics of resource allocation and costs of reproduction in a sexually
dimorphic, wind-pollinated dioecious plant
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 18
year: '2016'
...
---
_id: '1241'
abstract:
- lang: eng
text: 'How likely is it that a population escapes extinction through adaptive evolution?
The answer to this question is of great relevance in conservation biology, where
we aim at species’ rescue and the maintenance of biodiversity, and in agriculture
and medicine, where we seek to hamper the emergence of pesticide or drug resistance.
By reshuffling the genome, recombination has two antagonistic effects on the probability
of evolutionary rescue: It generates and it breaks up favorable gene combinations.
Which of the two effects prevails depends on the fitness effects of mutations
and on the impact of stochasticity on the allele frequencies. In this article,
we analyze a mathematical model for rescue after a sudden environmental change
when adaptation is contingent on mutations at two loci. The analysis reveals a
complex nonlinear dependence of population survival on recombination. We moreover
find that, counterintuitively, a fast eradication of the wild type can promote
rescue in the presence of recombination. The model also shows that two-step rescue
is not unlikely to happen and can even be more likely than single-step rescue
(where adaptation relies on a single mutation), depending on the circumstances.'
acknowledgement: This work was made possible by a “For Women in Science” fellowship
(L’Oréal Österreich in cooperation with the Austrian Commission for the United Nations
Educational, Scientific, and Cultural Organization and the Austrian Academy of Sciences
with financial support from the Federal Ministry for Science and Research Austria)
and European Research Council grant 250152 (to Nick Barton).
author:
- first_name: Hildegard
full_name: Uecker, Hildegard
id: 2DB8F68A-F248-11E8-B48F-1D18A9856A87
last_name: Uecker
orcid: 0000-0001-9435-2813
- first_name: Joachim
full_name: Hermisson, Joachim
last_name: Hermisson
citation:
ama: Uecker H, Hermisson J. The role of recombination in evolutionary rescue. Genetics.
2016;202(2):721-732. doi:10.1534/genetics.115.180299
apa: Uecker, H., & Hermisson, J. (2016). The role of recombination in evolutionary
rescue. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.115.180299
chicago: Uecker, Hildegard, and Joachim Hermisson. “The Role of Recombination in
Evolutionary Rescue.” Genetics. Genetics Society of America, 2016. https://doi.org/10.1534/genetics.115.180299.
ieee: H. Uecker and J. Hermisson, “The role of recombination in evolutionary rescue,”
Genetics, vol. 202, no. 2. Genetics Society of America, pp. 721–732, 2016.
ista: Uecker H, Hermisson J. 2016. The role of recombination in evolutionary rescue.
Genetics. 202(2), 721–732.
mla: Uecker, Hildegard, and Joachim Hermisson. “The Role of Recombination in Evolutionary
Rescue.” Genetics, vol. 202, no. 2, Genetics Society of America, 2016,
pp. 721–32, doi:10.1534/genetics.115.180299.
short: H. Uecker, J. Hermisson, Genetics 202 (2016) 721–732.
date_created: 2018-12-11T11:50:54Z
date_published: 2016-02-01T00:00:00Z
date_updated: 2023-02-21T10:24:19Z
day: '01'
department:
- _id: NiBa
doi: 10.1534/genetics.115.180299
ec_funded: 1
intvolume: ' 202'
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://biorxiv.org/content/early/2015/07/06/022020.abstract
month: '02'
oa: 1
oa_version: Preprint
page: 721 - 732
project:
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
- _id: 25B67606-B435-11E9-9278-68D0E5697425
name: L'OREAL Fellowship
publication: Genetics
publication_status: published
publisher: Genetics Society of America
publist_id: '6091'
quality_controlled: '1'
scopus_import: 1
status: public
title: The role of recombination in evolutionary rescue
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 202
year: '2016'
...
---
_id: '1349'
abstract:
- lang: eng
text: Crossing fitness valleys is one of the major obstacles to function optimization.
In this paper we investigate how the structure of the fitness valley, namely its
depth d and length ℓ, influence the runtime of different strategies for crossing
these valleys. We present a runtime comparison between the (1+1) EA and two non-elitist
nature-inspired algorithms, Strong Selection Weak Mutation (SSWM) and the Metropolis
algorithm. While the (1+1) EA has to jump across the valley to a point of higher
fitness because it does not accept decreasing moves, the non-elitist algorithms
may cross the valley by accepting worsening moves. We show that while the runtime
of the (1+1) EA algorithm depends critically on the length of the valley, the
runtimes of the non-elitist algorithms depend crucially only on the depth of the
valley. In particular, the expected runtime of both SSWM and Metropolis is polynomial
in ℓ and exponential in d while the (1+1) EA is efficient only for valleys of
small length. Moreover, we show that both SSWM and Metropolis can also efficiently
optimize a rugged function consisting of consecutive valleys.
author:
- first_name: Pietro
full_name: Oliveto, Pietro
last_name: Oliveto
- first_name: Tiago
full_name: Paixao, Tiago
id: 2C5658E6-F248-11E8-B48F-1D18A9856A87
last_name: Paixao
orcid: 0000-0003-2361-3953
- first_name: Jorge
full_name: Heredia, Jorge
last_name: Heredia
- first_name: Dirk
full_name: Sudholt, Dirk
last_name: Sudholt
- first_name: Barbora
full_name: Trubenova, Barbora
id: 42302D54-F248-11E8-B48F-1D18A9856A87
last_name: Trubenova
orcid: 0000-0002-6873-2967
citation:
ama: 'Oliveto P, Paixao T, Heredia J, Sudholt D, Trubenova B. When non-elitism outperforms
elitism for crossing fitness valleys. In: Proceedings of the Genetic and Evolutionary
Computation Conference 2016 . ACM; 2016:1163-1170. doi:10.1145/2908812.2908909'
apa: 'Oliveto, P., Paixao, T., Heredia, J., Sudholt, D., & Trubenova, B. (2016).
When non-elitism outperforms elitism for crossing fitness valleys. In Proceedings
of the Genetic and Evolutionary Computation Conference 2016 (pp. 1163–1170).
Denver, CO, USA: ACM. https://doi.org/10.1145/2908812.2908909'
chicago: Oliveto, Pietro, Tiago Paixao, Jorge Heredia, Dirk Sudholt, and Barbora
Trubenova. “When Non-Elitism Outperforms Elitism for Crossing Fitness Valleys.”
In Proceedings of the Genetic and Evolutionary Computation Conference 2016
, 1163–70. ACM, 2016. https://doi.org/10.1145/2908812.2908909.
ieee: P. Oliveto, T. Paixao, J. Heredia, D. Sudholt, and B. Trubenova, “When non-elitism
outperforms elitism for crossing fitness valleys,” in Proceedings of the Genetic
and Evolutionary Computation Conference 2016 , Denver, CO, USA, 2016, pp.
1163–1170.
ista: 'Oliveto P, Paixao T, Heredia J, Sudholt D, Trubenova B. 2016. When non-elitism
outperforms elitism for crossing fitness valleys. Proceedings of the Genetic and
Evolutionary Computation Conference 2016 . GECCO: Genetic and evolutionary computation
conference, 1163–1170.'
mla: Oliveto, Pietro, et al. “When Non-Elitism Outperforms Elitism for Crossing
Fitness Valleys.” Proceedings of the Genetic and Evolutionary Computation Conference
2016 , ACM, 2016, pp. 1163–70, doi:10.1145/2908812.2908909.
short: P. Oliveto, T. Paixao, J. Heredia, D. Sudholt, B. Trubenova, in:, Proceedings
of the Genetic and Evolutionary Computation Conference 2016 , ACM, 2016, pp. 1163–1170.
conference:
end_date: 2016-07-24
location: Denver, CO, USA
name: 'GECCO: Genetic and evolutionary computation conference'
start_date: 2016-07-20
date_created: 2018-12-11T11:51:31Z
date_published: 2016-07-20T00:00:00Z
date_updated: 2021-01-12T06:50:03Z
day: '20'
ddc:
- '576'
department:
- _id: NiBa
- _id: CaGu
doi: 10.1145/2908812.2908909
ec_funded: 1
file:
- access_level: open_access
checksum: a1896e39e4113f2711e46b435d5f3e69
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:16:27Z
date_updated: 2020-07-14T12:44:45Z
file_id: '5214'
file_name: IST-2016-650-v1+1_p1163-oliveto.pdf
file_size: 979026
relation: main_file
file_date_updated: 2020-07-14T12:44:45Z
has_accepted_license: '1'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: 1163 - 1170
project:
- _id: 25B1EC9E-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '618091'
name: Speed of Adaptation in Population Genetics and Evolutionary Computation
publication: 'Proceedings of the Genetic and Evolutionary Computation Conference 2016 '
publication_status: published
publisher: ACM
publist_id: '5900'
pubrep_id: '650'
quality_controlled: '1'
scopus_import: 1
status: public
title: When non-elitism outperforms elitism for crossing fitness valleys
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: conference
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
year: '2016'
...
---
_id: '1359'
abstract:
- lang: eng
text: "The role of gene interactions in the evolutionary process has long\r\nbeen
controversial. Although some argue that they are not of\r\nimportance, because
most variation is additive, others claim that\r\ntheir effect in the long term
can be substantial. Here, we focus on\r\nthe long-term effects of genetic interactions
under directional\r\nselection assuming no mutation or dominance, and that epistasis
is\r\nsymmetrical overall. We ask by how much the mean of a complex\r\ntrait can
be increased by selection and analyze two extreme\r\nregimes, in which either
drift or selection dominate the dynamics\r\nof allele frequencies. In both scenarios,
epistatic interactions affect\r\nthe long-term response to selection by modulating
the additive\r\ngenetic variance. When drift dominates, we extend Robertson\r\n’\r\ns\r\n[Robertson
A (1960)\r\nProc R Soc Lond B Biol Sci\r\n153(951):234\r\n−\r\n249]\r\nargument
to show that, for any form of epistasis, the total response\r\nof a haploid population
is proportional to the initial total genotypic\r\nvariance. In contrast, the total
response of a diploid population is\r\nincreased by epistasis, for a given initial
genotypic variance. When\r\nselection dominates, we show that the total selection
response can\r\nonly be increased by epistasis when s\r\nome initially deleterious
alleles\r\nbecome favored as the genetic background changes. We find a sim-\r\nple
approximation for this effect and show that, in this regime, it is\r\nthe structure
of the genotype - phenotype map that matters and not\r\nthe variance components
of the population."
article_processing_charge: No
article_type: original
author:
- first_name: Tiago
full_name: Paixao, Tiago
id: 2C5658E6-F248-11E8-B48F-1D18A9856A87
last_name: Paixao
orcid: 0000-0003-2361-3953
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: Paixao T, Barton NH. The effect of gene interactions on the long-term response
to selection. PNAS. 2016;113(16):4422-4427. doi:10.1073/pnas.1518830113
apa: Paixao, T., & Barton, N. H. (2016). The effect of gene interactions on
the long-term response to selection. PNAS. National Academy of Sciences.
https://doi.org/10.1073/pnas.1518830113
chicago: Paixao, Tiago, and Nicholas H Barton. “The Effect of Gene Interactions
on the Long-Term Response to Selection.” PNAS. National Academy of Sciences,
2016. https://doi.org/10.1073/pnas.1518830113.
ieee: T. Paixao and N. H. Barton, “The effect of gene interactions on the long-term
response to selection,” PNAS, vol. 113, no. 16. National Academy of Sciences,
pp. 4422–4427, 2016.
ista: Paixao T, Barton NH. 2016. The effect of gene interactions on the long-term
response to selection. PNAS. 113(16), 4422–4427.
mla: Paixao, Tiago, and Nicholas H. Barton. “The Effect of Gene Interactions on
the Long-Term Response to Selection.” PNAS, vol. 113, no. 16, National
Academy of Sciences, 2016, pp. 4422–27, doi:10.1073/pnas.1518830113.
short: T. Paixao, N.H. Barton, PNAS 113 (2016) 4422–4427.
date_created: 2018-12-11T11:51:34Z
date_published: 2016-04-19T00:00:00Z
date_updated: 2021-01-12T06:50:08Z
day: '19'
department:
- _id: NiBa
- _id: CaGu
doi: 10.1073/pnas.1518830113
ec_funded: 1
external_id:
pmid:
- '27044080'
intvolume: ' 113'
issue: '16'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4843425/
month: '04'
oa: 1
oa_version: Published Version
page: 4422 - 4427
pmid: 1
project:
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
- _id: 25B1EC9E-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '618091'
name: Speed of Adaptation in Population Genetics and Evolutionary Computation
publication: PNAS
publication_status: published
publisher: National Academy of Sciences
publist_id: '5886'
quality_controlled: '1'
scopus_import: 1
status: public
title: The effect of gene interactions on the long-term response to selection
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 113
year: '2016'
...
---
_id: '1356'
author:
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: Barton NH. Sewall Wright on evolution in Mendelian populations and the “Shifting
Balance.” Genetics. 2016;202(1):3-4. doi:10.1534/genetics.115.184796
apa: Barton, N. H. (2016). Sewall Wright on evolution in Mendelian populations and
the “Shifting Balance.” Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.115.184796
chicago: Barton, Nicholas H. “Sewall Wright on Evolution in Mendelian Populations
and the ‘Shifting Balance.’” Genetics. Genetics Society of America, 2016.
https://doi.org/10.1534/genetics.115.184796.
ieee: N. H. Barton, “Sewall Wright on evolution in Mendelian populations and the
‘Shifting Balance,’” Genetics, vol. 202, no. 1. Genetics Society of America,
pp. 3–4, 2016.
ista: Barton NH. 2016. Sewall Wright on evolution in Mendelian populations and the
“Shifting Balance”. Genetics. 202(1), 3–4.
mla: Barton, Nicholas H. “Sewall Wright on Evolution in Mendelian Populations and
the ‘Shifting Balance.’” Genetics, vol. 202, no. 1, Genetics Society of
America, 2016, pp. 3–4, doi:10.1534/genetics.115.184796.
short: N.H. Barton, Genetics 202 (2016) 3–4.
date_created: 2018-12-11T11:51:33Z
date_published: 2016-01-05T00:00:00Z
date_updated: 2021-01-12T06:50:07Z
day: '05'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1534/genetics.115.184796
file:
- access_level: open_access
checksum: 3562b89c821a4be84edf2b6ebd870cf5
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:08:26Z
date_updated: 2020-07-14T12:44:46Z
file_id: '4687'
file_name: IST-2017-769-v1+1_SewallWright1931.pdf
file_size: 112674
relation: main_file
file_date_updated: 2020-07-14T12:44:46Z
has_accepted_license: '1'
intvolume: ' 202'
issue: '1'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Submitted Version
page: 3 - 4
publication: Genetics
publication_status: published
publisher: Genetics Society of America
publist_id: '5889'
pubrep_id: '769'
quality_controlled: '1'
scopus_import: 1
status: public
title: Sewall Wright on evolution in Mendelian populations and the “Shifting Balance”
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 202
year: '2016'
...
---
_id: '1357'
author:
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: Barton NH. Richard Hudson and Norman Kaplan on the coalescent process. Genetics.
2016;202(3):865-866. doi:10.1534/genetics.116.187542
apa: Barton, N. H. (2016). Richard Hudson and Norman Kaplan on the coalescent process.
Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.116.187542
chicago: Barton, Nicholas H. “Richard Hudson and Norman Kaplan on the Coalescent
Process.” Genetics. Genetics Society of America, 2016. https://doi.org/10.1534/genetics.116.187542.
ieee: N. H. Barton, “Richard Hudson and Norman Kaplan on the coalescent process,”
Genetics, vol. 202, no. 3. Genetics Society of America, pp. 865–866, 2016.
ista: Barton NH. 2016. Richard Hudson and Norman Kaplan on the coalescent process.
Genetics. 202(3), 865–866.
mla: Barton, Nicholas H. “Richard Hudson and Norman Kaplan on the Coalescent Process.”
Genetics, vol. 202, no. 3, Genetics Society of America, 2016, pp. 865–66,
doi:10.1534/genetics.116.187542.
short: N.H. Barton, Genetics 202 (2016) 865–866.
date_created: 2018-12-11T11:51:33Z
date_published: 2016-03-01T00:00:00Z
date_updated: 2021-01-12T06:50:07Z
day: '01'
ddc:
- '576'
department:
- _id: NiBa
doi: 10.1534/genetics.116.187542
file:
- access_level: open_access
checksum: b2174bab2de1d1142900062a150f35c9
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:15:09Z
date_updated: 2020-07-14T12:44:46Z
file_id: '5127'
file_name: IST-2017-768-v1+1_Hudson-Kaplan-1988.pdf
file_size: 130779
relation: main_file
file_date_updated: 2020-07-14T12:44:46Z
has_accepted_license: '1'
intvolume: ' 202'
issue: '3'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Submitted Version
page: 865 - 866
publication: Genetics
publication_status: published
publisher: Genetics Society of America
publist_id: '5888'
pubrep_id: '768'
quality_controlled: '1'
scopus_import: 1
status: public
title: Richard Hudson and Norman Kaplan on the coalescent process
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 202
year: '2016'
...
---
_id: '1409'
author:
- first_name: Richard
full_name: Abbott, Richard
last_name: Abbott
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Jeffrey
full_name: Good, Jeffrey
last_name: Good
citation:
ama: Abbott R, Barton NH, Good J. Genomics of hybridization and its evolutionary
consequences. Molecular Ecology. 2016;25(11):2325-2332. doi:10.1111/mec.13685
apa: Abbott, R., Barton, N. H., & Good, J. (2016). Genomics of hybridization
and its evolutionary consequences. Molecular Ecology. Wiley-Blackwell.
https://doi.org/10.1111/mec.13685
chicago: Abbott, Richard, Nicholas H Barton, and Jeffrey Good. “Genomics of Hybridization
and Its Evolutionary Consequences.” Molecular Ecology. Wiley-Blackwell,
2016. https://doi.org/10.1111/mec.13685.
ieee: R. Abbott, N. H. Barton, and J. Good, “Genomics of hybridization and its evolutionary
consequences,” Molecular Ecology, vol. 25, no. 11. Wiley-Blackwell, pp.
2325–2332, 2016.
ista: Abbott R, Barton NH, Good J. 2016. Genomics of hybridization and its evolutionary
consequences. Molecular Ecology. 25(11), 2325–2332.
mla: Abbott, Richard, et al. “Genomics of Hybridization and Its Evolutionary Consequences.”
Molecular Ecology, vol. 25, no. 11, Wiley-Blackwell, 2016, pp. 2325–32,
doi:10.1111/mec.13685.
short: R. Abbott, N.H. Barton, J. Good, Molecular Ecology 25 (2016) 2325–2332.
date_created: 2018-12-11T11:51:51Z
date_published: 2016-06-08T00:00:00Z
date_updated: 2021-01-12T06:50:33Z
day: '08'
ddc:
- '576'
department:
- _id: NiBa
doi: 10.1111/mec.13685
file:
- access_level: open_access
checksum: ede7d0b8a471754f71f17e2b20f3135b
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:10:12Z
date_updated: 2020-07-14T12:44:53Z
file_id: '4797'
file_name: IST-2017-772-v1+1_AbbotEtAl2016-3.pdf
file_size: 226137
relation: main_file
file_date_updated: 2020-07-14T12:44:53Z
has_accepted_license: '1'
intvolume: ' 25'
issue: '11'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Submitted Version
page: 2325 - 2332
publication: Molecular Ecology
publication_status: published
publisher: Wiley-Blackwell
publist_id: '5798'
pubrep_id: '772'
quality_controlled: '1'
scopus_import: 1
status: public
title: Genomics of hybridization and its evolutionary consequences
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 25
year: '2016'
...
---
_id: '1420'
abstract:
- lang: eng
text: 'Selection, mutation, and random drift affect the dynamics of allele frequencies
and consequently of quantitative traits. While the macroscopic dynamics of quantitative
traits can be measured, the underlying allele frequencies are typically unobserved.
Can we understand how the macroscopic observables evolve without following these
microscopic processes? This problem has been studied previously by analogy with
statistical mechanics: the allele frequency distribution at each time point is
approximated by the stationary form, which maximizes entropy. We explore the limitations
of this method when mutation is small (4Nμ < 1) so that populations are typically
close to fixation, and we extend the theory in this regime to account for changes
in mutation strength. We consider a single diallelic locus either under directional
selection or with overdominance and then generalize to multiple unlinked biallelic
loci with unequal effects. We find that the maximum-entropy approximation is remarkably
accurate, even when mutation and selection change rapidly. '
article_processing_charge: No
author:
- first_name: Katarína
full_name: Bod'ová, Katarína
id: 2BA24EA0-F248-11E8-B48F-1D18A9856A87
last_name: Bod'ová
orcid: 0000-0002-7214-0171
- first_name: Gasper
full_name: Tkacik, Gasper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: Bodova K, Tkačik G, Barton NH. A general approximation for the dynamics of
quantitative traits. Genetics. 2016;202(4):1523-1548. doi:10.1534/genetics.115.184127
apa: Bodova, K., Tkačik, G., & Barton, N. H. (2016). A general approximation
for the dynamics of quantitative traits. Genetics. Genetics Society of
America. https://doi.org/10.1534/genetics.115.184127
chicago: Bodova, Katarina, Gašper Tkačik, and Nicholas H Barton. “A General Approximation
for the Dynamics of Quantitative Traits.” Genetics. Genetics Society of
America, 2016. https://doi.org/10.1534/genetics.115.184127.
ieee: K. Bodova, G. Tkačik, and N. H. Barton, “A general approximation for the dynamics
of quantitative traits,” Genetics, vol. 202, no. 4. Genetics Society of
America, pp. 1523–1548, 2016.
ista: Bodova K, Tkačik G, Barton NH. 2016. A general approximation for the dynamics
of quantitative traits. Genetics. 202(4), 1523–1548.
mla: Bodova, Katarina, et al. “A General Approximation for the Dynamics of Quantitative
Traits.” Genetics, vol. 202, no. 4, Genetics Society of America, 2016,
pp. 1523–48, doi:10.1534/genetics.115.184127.
short: K. Bodova, G. Tkačik, N.H. Barton, Genetics 202 (2016) 1523–1548.
date_created: 2018-12-11T11:51:55Z
date_published: 2016-04-06T00:00:00Z
date_updated: 2022-08-01T10:49:55Z
day: '06'
department:
- _id: GaTk
- _id: NiBa
doi: 10.1534/genetics.115.184127
ec_funded: 1
external_id:
arxiv:
- '1510.08344'
intvolume: ' 202'
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1510.08344
month: '04'
oa: 1
oa_version: Preprint
page: 1523 - 1548
project:
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
- _id: 255008E4-B435-11E9-9278-68D0E5697425
grant_number: RGP0065/2012
name: Information processing and computation in fish groups
publication: Genetics
publication_status: published
publisher: Genetics Society of America
publist_id: '5787'
quality_controlled: '1'
scopus_import: '1'
status: public
title: A general approximation for the dynamics of quantitative traits
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 202
year: '2016'
...
---
_id: '1518'
abstract:
- lang: eng
text: The inference of demographic history from genome data is hindered by a lack
of efficient computational approaches. In particular, it has proved difficult
to exploit the information contained in the distribution of genealogies across
the genome. We have previously shown that the generating function (GF) of genealogies
can be used to analytically compute likelihoods of demographic models from configurations
of mutations in short sequence blocks (Lohse et al. 2011). Although the GF has
a simple, recursive form, the size of such likelihood calculations explodes quickly
with the number of individuals and applications of this framework have so far
been mainly limited to small samples (pairs and triplets) for which the GF can
be written by hand. Here we investigate several strategies for exploiting the
inherent symmetries of the coalescent. In particular, we show that the GF of genealogies
can be decomposed into a set of equivalence classes that allows likelihood calculations
from nontrivial samples. Using this strategy, we automated blockwise likelihood
calculations for a general set of demographic scenarios in Mathematica. These
histories may involve population size changes, continuous migration, discrete
divergence, and admixture between multiple populations. To give a concrete example,
we calculate the likelihood for a model of isolation with migration (IM), assuming
two diploid samples without phase and outgroup information. We demonstrate the
new inference scheme with an analysis of two individual butterfly genomes from
the sister species Heliconius melpomene rosina and H. cydno.
acknowledgement: "We thank Lynsey Bunnefeld for discussions throughout the project
and Joshua Schraiber and one anonymous reviewer\r\nfor constructive comments on
an earlier version of this manuscript. This work was supported by funding from the\r\nUnited
Kingdom Natural Environment Research Council (to K.L.) (NE/I020288/1) and a grant
from the European\r\nResearch Council (250152) (to N.H.B.)."
article_processing_charge: No
article_type: original
author:
- first_name: Konrad
full_name: Lohse, Konrad
last_name: Lohse
- first_name: Martin
full_name: Chmelik, Martin
id: 3624234E-F248-11E8-B48F-1D18A9856A87
last_name: Chmelik
- first_name: Simon
full_name: Martin, Simon
last_name: Martin
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: Lohse K, Chmelik M, Martin S, Barton NH. Efficient strategies for calculating
blockwise likelihoods under the coalescent. Genetics. 2016;202(2):775-786.
doi:10.1534/genetics.115.183814
apa: Lohse, K., Chmelik, M., Martin, S., & Barton, N. H. (2016). Efficient strategies
for calculating blockwise likelihoods under the coalescent. Genetics. Genetics
Society of America. https://doi.org/10.1534/genetics.115.183814
chicago: Lohse, Konrad, Martin Chmelik, Simon Martin, and Nicholas H Barton. “Efficient
Strategies for Calculating Blockwise Likelihoods under the Coalescent.” Genetics.
Genetics Society of America, 2016. https://doi.org/10.1534/genetics.115.183814.
ieee: K. Lohse, M. Chmelik, S. Martin, and N. H. Barton, “Efficient strategies for
calculating blockwise likelihoods under the coalescent,” Genetics, vol.
202, no. 2. Genetics Society of America, pp. 775–786, 2016.
ista: Lohse K, Chmelik M, Martin S, Barton NH. 2016. Efficient strategies for calculating
blockwise likelihoods under the coalescent. Genetics. 202(2), 775–786.
mla: Lohse, Konrad, et al. “Efficient Strategies for Calculating Blockwise Likelihoods
under the Coalescent.” Genetics, vol. 202, no. 2, Genetics Society of America,
2016, pp. 775–86, doi:10.1534/genetics.115.183814.
short: K. Lohse, M. Chmelik, S. Martin, N.H. Barton, Genetics 202 (2016) 775–786.
date_created: 2018-12-11T11:52:29Z
date_published: 2016-02-01T00:00:00Z
date_updated: 2022-05-24T09:16:22Z
day: '01'
ddc:
- '570'
department:
- _id: KrCh
- _id: NiBa
doi: 10.1534/genetics.115.183814
ec_funded: 1
external_id:
pmid:
- '26715666'
file:
- access_level: open_access
checksum: 41c9b5d72e7fe4624dd22dfe622337d5
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:16:51Z
date_updated: 2020-07-14T12:45:00Z
file_id: '5241'
file_name: IST-2016-561-v1+1_Lohse_et_al_Genetics_2015.pdf
file_size: 957466
relation: main_file
file_date_updated: 2020-07-14T12:45:00Z
has_accepted_license: '1'
intvolume: ' 202'
issue: '2'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Preprint
page: 775 - 786
pmid: 1
project:
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
publication: Genetics
publication_status: published
publisher: Genetics Society of America
publist_id: '5658'
pubrep_id: '561'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Efficient strategies for calculating blockwise likelihoods under the coalescent
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 202
year: '2016'
...
---
_id: '1631'
abstract:
- lang: eng
text: 'Ancestral processes are fundamental to modern population genetics and spatial
structure has been the subject of intense interest for many years. Despite this
interest, almost nothing is known about the distribution of the locations of pedigree
or genetic ancestors. Using both spatially continuous and stepping-stone models,
we show that the distribution of pedigree ancestors approaches a travelling wave,
for which we develop two alternative approximations. The speed and width of the
wave are sensitive to the local details of the model. After a short time, genetic
ancestors spread far more slowly than pedigree ancestors, ultimately diffusing
out with radius ## rather than spreading at constant speed. In contrast to the
wave of pedigree ancestors, the spread of genetic ancestry is insensitive to the
local details of the models.'
author:
- first_name: Jerome
full_name: Kelleher, Jerome
last_name: Kelleher
- first_name: Alison
full_name: Etheridge, Alison
last_name: Etheridge
- first_name: Amandine
full_name: Véber, Amandine
last_name: Véber
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: Kelleher J, Etheridge A, Véber A, Barton NH. Spread of pedigree versus genetic
ancestry in spatially distributed populations. Theoretical Population Biology.
2016;108:1-12. doi:10.1016/j.tpb.2015.10.008
apa: Kelleher, J., Etheridge, A., Véber, A., & Barton, N. H. (2016). Spread
of pedigree versus genetic ancestry in spatially distributed populations. Theoretical
Population Biology. Academic Press. https://doi.org/10.1016/j.tpb.2015.10.008
chicago: Kelleher, Jerome, Alison Etheridge, Amandine Véber, and Nicholas H Barton.
“Spread of Pedigree versus Genetic Ancestry in Spatially Distributed Populations.”
Theoretical Population Biology. Academic Press, 2016. https://doi.org/10.1016/j.tpb.2015.10.008.
ieee: J. Kelleher, A. Etheridge, A. Véber, and N. H. Barton, “Spread of pedigree
versus genetic ancestry in spatially distributed populations,” Theoretical
Population Biology, vol. 108. Academic Press, pp. 1–12, 2016.
ista: Kelleher J, Etheridge A, Véber A, Barton NH. 2016. Spread of pedigree versus
genetic ancestry in spatially distributed populations. Theoretical Population
Biology. 108, 1–12.
mla: Kelleher, Jerome, et al. “Spread of Pedigree versus Genetic Ancestry in Spatially
Distributed Populations.” Theoretical Population Biology, vol. 108, Academic
Press, 2016, pp. 1–12, doi:10.1016/j.tpb.2015.10.008.
short: J. Kelleher, A. Etheridge, A. Véber, N.H. Barton, Theoretical Population
Biology 108 (2016) 1–12.
date_created: 2018-12-11T11:53:08Z
date_published: 2016-04-01T00:00:00Z
date_updated: 2021-01-12T06:52:07Z
day: '01'
ddc:
- '576'
department:
- _id: NiBa
doi: 10.1016/j.tpb.2015.10.008
ec_funded: 1
file:
- access_level: open_access
checksum: 6a65ba187994d4ad86c1c509e0ff482a
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:11:12Z
date_updated: 2020-07-14T12:45:07Z
file_id: '4865'
file_name: IST-2016-465-v1+1_1-s2.0-S0040580915001094-main.pdf
file_size: 1684043
relation: main_file
file_date_updated: 2020-07-14T12:45:07Z
has_accepted_license: '1'
intvolume: ' 108'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: 1 - 12
project:
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
publication: Theoretical Population Biology
publication_status: published
publisher: Academic Press
publist_id: '5524'
pubrep_id: '465'
quality_controlled: '1'
scopus_import: 1
status: public
title: Spread of pedigree versus genetic ancestry in spatially distributed populations
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 108
year: '2016'
...
---
_id: '1158'
abstract:
- lang: eng
text: Speciation results from the progressive accumulation of mutations that decrease
the probability of mating between parental populations or reduce the fitness of
hybrids—the so-called species barriers. The speciation genomic literature, however,
is mainly a collection of case studies, each with its own approach and specificities,
such that a global view of the gradual process of evolution from one to two species
is currently lacking. Of primary importance is the prevalence of gene flow between
diverging entities, which is central in most species concepts and has been widely
discussed in recent years. Here, we explore the continuum of speciation thanks
to a comparative analysis of genomic data from 61 pairs of populations/species
of animals with variable levels of divergence. Gene flow between diverging gene
pools is assessed under an approximate Bayesian computation (ABC) framework. We
show that the intermediate "grey zone" of speciation, in which taxonomy
is often controversial, spans from 0.5% to 2% of net synonymous divergence, irrespective
of species life history traits or ecology. Thanks to appropriate modeling of among-locus
variation in genetic drift and introgression rate, we clarify the status of the
majority of ambiguous cases and uncover a number of cryptic species. Our analysis
also reveals the high incidence in animals of semi-isolated species (when some
but not all loci are affected by barriers to gene flow) and highlights the intrinsic
difficulty, both statistical and conceptual, of delineating species in the grey
zone of speciation.
acknowledgement: "European Research Council (ERC) https://erc.europa.eu/ (grant number
ERC grant 232971). PopPhyl project. The funder had no role in study design, data
collection and analysis, decision to publish, or preparation of the manuscript.
French National Research Agency (ANR) http://www.agence-nationale-recherche.fr/en/project-based-funding-to-advance-french-research/
(grant number ANR-12-BSV7- 0011). HYSEA project.\r\nWe thank Aude Darracq, Vincent
Castric, Pierre-Alexandre Gagnaire, Xavier Vekemans, and John Welch for insightful
discussions. The computations were performed at the Vital-IT (http://www.vital-it.ch)
Center for high-performance computing of the SIB Swiss Institute of Bioinformatics
and the ISEM computing cluster at the platform Montpellier Bioinformatique et Biodiversité."
article_number: e2000234
author:
- first_name: Camille
full_name: Roux, Camille
last_name: Roux
- first_name: Christelle
full_name: Fraisse, Christelle
id: 32DF5794-F248-11E8-B48F-1D18A9856A87
last_name: Fraisse
orcid: 0000-0001-8441-5075
- first_name: Jonathan
full_name: Romiguier, Jonathan
last_name: Romiguier
- first_name: Youann
full_name: Anciaux, Youann
last_name: Anciaux
- first_name: Nicolas
full_name: Galtier, Nicolas
last_name: Galtier
- first_name: Nicolas
full_name: Bierne, Nicolas
last_name: Bierne
citation:
ama: Roux C, Fraisse C, Romiguier J, Anciaux Y, Galtier N, Bierne N. Shedding light
on the grey zone of speciation along a continuum of genomic divergence. PLoS
Biology. 2016;14(12). doi:10.1371/journal.pbio.2000234
apa: Roux, C., Fraisse, C., Romiguier, J., Anciaux, Y., Galtier, N., & Bierne,
N. (2016). Shedding light on the grey zone of speciation along a continuum of
genomic divergence. PLoS Biology. Public Library of Science. https://doi.org/10.1371/journal.pbio.2000234
chicago: Roux, Camille, Christelle Fraisse, Jonathan Romiguier, Youann Anciaux,
Nicolas Galtier, and Nicolas Bierne. “Shedding Light on the Grey Zone of Speciation
along a Continuum of Genomic Divergence.” PLoS Biology. Public Library
of Science, 2016. https://doi.org/10.1371/journal.pbio.2000234.
ieee: C. Roux, C. Fraisse, J. Romiguier, Y. Anciaux, N. Galtier, and N. Bierne,
“Shedding light on the grey zone of speciation along a continuum of genomic divergence,”
PLoS Biology, vol. 14, no. 12. Public Library of Science, 2016.
ista: Roux C, Fraisse C, Romiguier J, Anciaux Y, Galtier N, Bierne N. 2016. Shedding
light on the grey zone of speciation along a continuum of genomic divergence.
PLoS Biology. 14(12), e2000234.
mla: Roux, Camille, et al. “Shedding Light on the Grey Zone of Speciation along
a Continuum of Genomic Divergence.” PLoS Biology, vol. 14, no. 12, e2000234,
Public Library of Science, 2016, doi:10.1371/journal.pbio.2000234.
short: C. Roux, C. Fraisse, J. Romiguier, Y. Anciaux, N. Galtier, N. Bierne, PLoS
Biology 14 (2016).
date_created: 2018-12-11T11:50:28Z
date_published: 2016-12-27T00:00:00Z
date_updated: 2023-02-23T14:11:16Z
day: '27'
ddc:
- '576'
department:
- _id: BeVi
- _id: NiBa
doi: 10.1371/journal.pbio.2000234
file:
- access_level: open_access
checksum: 2bab63b068a9840efd532b9ae583f9bb
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:15:42Z
date_updated: 2020-07-14T12:44:36Z
file_id: '5164'
file_name: IST-2017-742-v1+1_journal.pbio.2000234.pdf
file_size: 2494348
relation: main_file
file_date_updated: 2020-07-14T12:44:36Z
has_accepted_license: '1'
intvolume: ' 14'
issue: '12'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
publication: PLoS Biology
publication_status: published
publisher: Public Library of Science
publist_id: '6200'
pubrep_id: '742'
quality_controlled: '1'
related_material:
record:
- id: '9862'
relation: research_data
status: public
- id: '9863'
relation: research_data
status: public
scopus_import: 1
status: public
title: Shedding light on the grey zone of speciation along a continuum of genomic
divergence
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 14
year: '2016'
...
---
_id: '9862'
article_processing_charge: No
author:
- first_name: Camille
full_name: Roux, Camille
last_name: Roux
- first_name: Christelle
full_name: Fraisse, Christelle
id: 32DF5794-F248-11E8-B48F-1D18A9856A87
last_name: Fraisse
orcid: 0000-0001-8441-5075
- first_name: Jonathan
full_name: Romiguier, Jonathan
last_name: Romiguier
- first_name: Youann
full_name: Anciaux, Youann
last_name: Anciaux
- first_name: Nicolas
full_name: Galtier, Nicolas
last_name: Galtier
- first_name: Nicolas
full_name: Bierne, Nicolas
last_name: Bierne
citation:
ama: Roux C, Fraisse C, Romiguier J, Anciaux Y, Galtier N, Bierne N. Simulation
study to test the robustness of ABC in face of recent times of divergence. 2016.
doi:10.1371/journal.pbio.2000234.s016
apa: Roux, C., Fraisse, C., Romiguier, J., Anciaux, Y., Galtier, N., & Bierne,
N. (2016). Simulation study to test the robustness of ABC in face of recent times
of divergence. Public Library of Science. https://doi.org/10.1371/journal.pbio.2000234.s016
chicago: Roux, Camille, Christelle Fraisse, Jonathan Romiguier, Youann Anciaux,
Nicolas Galtier, and Nicolas Bierne. “Simulation Study to Test the Robustness
of ABC in Face of Recent Times of Divergence.” Public Library of Science, 2016.
https://doi.org/10.1371/journal.pbio.2000234.s016.
ieee: C. Roux, C. Fraisse, J. Romiguier, Y. Anciaux, N. Galtier, and N. Bierne,
“Simulation study to test the robustness of ABC in face of recent times of divergence.”
Public Library of Science, 2016.
ista: Roux C, Fraisse C, Romiguier J, Anciaux Y, Galtier N, Bierne N. 2016. Simulation
study to test the robustness of ABC in face of recent times of divergence, Public
Library of Science, 10.1371/journal.pbio.2000234.s016.
mla: Roux, Camille, et al. Simulation Study to Test the Robustness of ABC in
Face of Recent Times of Divergence. Public Library of Science, 2016, doi:10.1371/journal.pbio.2000234.s016.
short: C. Roux, C. Fraisse, J. Romiguier, Y. Anciaux, N. Galtier, N. Bierne, (2016).
date_created: 2021-08-10T08:20:17Z
date_updated: 2023-02-21T16:21:20Z
day: '27'
department:
- _id: BeVi
- _id: NiBa
doi: 10.1371/journal.pbio.2000234.s016
month: '12'
oa_version: Published Version
publisher: Public Library of Science
related_material:
record:
- id: '1158'
relation: used_in_publication
status: public
status: public
title: Simulation study to test the robustness of ABC in face of recent times of divergence
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2016'
...
---
_id: '9863'
article_processing_charge: No
author:
- first_name: Camille
full_name: Roux, Camille
last_name: Roux
- first_name: Christelle
full_name: Fraisse, Christelle
id: 32DF5794-F248-11E8-B48F-1D18A9856A87
last_name: Fraisse
orcid: 0000-0001-8441-5075
- first_name: Jonathan
full_name: Romiguier, Jonathan
last_name: Romiguier
- first_name: Youann
full_name: Anciaux, Youann
last_name: Anciaux
- first_name: Nicolas
full_name: Galtier, Nicolas
last_name: Galtier
- first_name: Nicolas
full_name: Bierne, Nicolas
last_name: Bierne
citation:
ama: Roux C, Fraisse C, Romiguier J, Anciaux Y, Galtier N, Bierne N. Accessions
of surveyed individuals, geographic locations and summary statistics. 2016. doi:10.1371/journal.pbio.2000234.s017
apa: Roux, C., Fraisse, C., Romiguier, J., Anciaux, Y., Galtier, N., & Bierne,
N. (2016). Accessions of surveyed individuals, geographic locations and summary
statistics. Public Library of Science. https://doi.org/10.1371/journal.pbio.2000234.s017
chicago: Roux, Camille, Christelle Fraisse, Jonathan Romiguier, Youann Anciaux,
Nicolas Galtier, and Nicolas Bierne. “Accessions of Surveyed Individuals, Geographic
Locations and Summary Statistics.” Public Library of Science, 2016. https://doi.org/10.1371/journal.pbio.2000234.s017.
ieee: C. Roux, C. Fraisse, J. Romiguier, Y. Anciaux, N. Galtier, and N. Bierne,
“Accessions of surveyed individuals, geographic locations and summary statistics.”
Public Library of Science, 2016.
ista: Roux C, Fraisse C, Romiguier J, Anciaux Y, Galtier N, Bierne N. 2016. Accessions
of surveyed individuals, geographic locations and summary statistics, Public Library
of Science, 10.1371/journal.pbio.2000234.s017.
mla: Roux, Camille, et al. Accessions of Surveyed Individuals, Geographic Locations
and Summary Statistics. Public Library of Science, 2016, doi:10.1371/journal.pbio.2000234.s017.
short: C. Roux, C. Fraisse, J. Romiguier, Y. Anciaux, N. Galtier, N. Bierne, (2016).
date_created: 2021-08-10T08:22:52Z
date_updated: 2023-02-21T16:21:20Z
day: '27'
department:
- _id: BeVi
- _id: NiBa
doi: 10.1371/journal.pbio.2000234.s017
month: '12'
oa_version: Published Version
publisher: Public Library of Science
related_material:
record:
- id: '1158'
relation: used_in_publication
status: public
status: public
title: Accessions of surveyed individuals, geographic locations and summary statistics
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2016'
...
---
_id: '1125'
abstract:
- lang: eng
text: "Natural environments are never constant but subject to spatial and temporal
change on\r\nall scales, increasingly so due to human activity. Hence, it is crucial
to understand the\r\nimpact of environmental variation on evolutionary processes.
In this thesis, I present\r\nthree topics that share the common theme of environmental
variation, yet illustrate its\r\neffect from different perspectives.\r\nFirst,
I show how a temporally fluctuating environment gives rise to second-order\r\nselection
on a modifier for stress-induced mutagenesis. Without fluctuations, when\r\npopulations
are adapted to their environment, mutation rates are minimized. I argue\r\nthat
a stress-induced mutator mechanism may only be maintained if the population is\r\nrepeatedly
subjected to diverse environmental challenges, and I outline implications of\r\nthe
presented results to antibiotic treatment strategies.\r\nSecond, I discuss my
work on the evolution of dispersal. Besides reproducing\r\nknown results about
the effect of heterogeneous habitats on dispersal, it identifies\r\nspatial changes
in dispersal type frequencies as a source for selection for increased\r\npropensities
to disperse. This concept contains effects of relatedness that are known\r\nto
promote dispersal, and I explain how it identifies other forces selecting for
dispersal\r\nand puts them on a common scale.\r\nThird, I analyse genetic variances
of phenotypic traits under multivariate stabilizing\r\nselection. For the case
of constant environments, I generalize known formulae of\r\nequilibrium variances
to multiple traits and discuss how the genetic variance of a focal\r\ntrait is
influenced by selection on background traits. I conclude by presenting ideas and\r\npreliminary
work aiming at including environmental fluctuations in the form of moving\r\ntrait
optima into the model."
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Sebastian
full_name: Novak, Sebastian
id: 461468AE-F248-11E8-B48F-1D18A9856A87
last_name: Novak
orcid: 0000-0002-2519-824X
citation:
ama: Novak S. Evolutionary proccesses in variable emvironments. 2016.
apa: Novak, S. (2016). Evolutionary proccesses in variable emvironments.
Institute of Science and Technology Austria.
chicago: Novak, Sebastian. “Evolutionary Proccesses in Variable Emvironments.” Institute
of Science and Technology Austria, 2016.
ieee: S. Novak, “Evolutionary proccesses in variable emvironments,” Institute of
Science and Technology Austria, 2016.
ista: Novak S. 2016. Evolutionary proccesses in variable emvironments. Institute
of Science and Technology Austria.
mla: Novak, Sebastian. Evolutionary Proccesses in Variable Emvironments.
Institute of Science and Technology Austria, 2016.
short: S. Novak, Evolutionary Proccesses in Variable Emvironments, Institute of
Science and Technology Austria, 2016.
date_created: 2018-12-11T11:50:17Z
date_published: 2016-07-01T00:00:00Z
date_updated: 2023-09-07T11:55:53Z
day: '01'
ddc:
- '576'
degree_awarded: PhD
department:
- _id: NiBa
file:
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checksum: 81dcc838dfcf7aa0b1a27ecf4fe2da4e
content_type: application/pdf
creator: dernst
date_created: 2019-08-13T09:01:00Z
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file_name: Novak_thesis.pdf
file_size: 3564901
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creator: dernst
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language:
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month: '07'
oa: 1
oa_version: Published Version
page: '124'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
publist_id: '6235'
related_material:
record:
- id: '2023'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
title: Evolutionary proccesses in variable emvironments
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2016'
...
---
_id: '1358'
abstract:
- lang: eng
text: 'Gene regulation relies on the specificity of transcription factor (TF)–DNA
interactions. Limited specificity may lead to crosstalk: a regulatory state in
which a gene is either incorrectly activated due to noncognate TF–DNA interactions
or remains erroneously inactive. As each TF can have numerous interactions with
noncognate cis-regulatory elements, crosstalk is inherently a global problem,
yet has previously not been studied as such. We construct a theoretical framework
to analyse the effects of global crosstalk on gene regulation. We find that crosstalk
presents a significant challenge for organisms with low-specificity TFs, such
as metazoans. Crosstalk is not easily mitigated by known regulatory schemes acting
at equilibrium, including variants of cooperativity and combinatorial regulation.
Our results suggest that crosstalk imposes a previously unexplored global constraint
on the functioning and evolution of regulatory networks, which is qualitatively
distinct from the known constraints that act at the level of individual gene regulatory
elements.'
article_number: '12307'
author:
- first_name: Tamar
full_name: Friedlander, Tamar
id: 36A5845C-F248-11E8-B48F-1D18A9856A87
last_name: Friedlander
- first_name: Roshan
full_name: Prizak, Roshan
id: 4456104E-F248-11E8-B48F-1D18A9856A87
last_name: Prizak
- first_name: Calin C
full_name: Guet, Calin C
id: 47F8433E-F248-11E8-B48F-1D18A9856A87
last_name: Guet
orcid: 0000-0001-6220-2052
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Gasper
full_name: Tkacik, Gasper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
citation:
ama: Friedlander T, Prizak R, Guet CC, Barton NH, Tkačik G. Intrinsic limits to
gene regulation by global crosstalk. Nature Communications. 2016;7. doi:10.1038/ncomms12307
apa: Friedlander, T., Prizak, R., Guet, C. C., Barton, N. H., & Tkačik, G. (2016).
Intrinsic limits to gene regulation by global crosstalk. Nature Communications.
Nature Publishing Group. https://doi.org/10.1038/ncomms12307
chicago: Friedlander, Tamar, Roshan Prizak, Calin C Guet, Nicholas H Barton, and
Gašper Tkačik. “Intrinsic Limits to Gene Regulation by Global Crosstalk.” Nature
Communications. Nature Publishing Group, 2016. https://doi.org/10.1038/ncomms12307.
ieee: T. Friedlander, R. Prizak, C. C. Guet, N. H. Barton, and G. Tkačik, “Intrinsic
limits to gene regulation by global crosstalk,” Nature Communications,
vol. 7. Nature Publishing Group, 2016.
ista: Friedlander T, Prizak R, Guet CC, Barton NH, Tkačik G. 2016. Intrinsic limits
to gene regulation by global crosstalk. Nature Communications. 7, 12307.
mla: Friedlander, Tamar, et al. “Intrinsic Limits to Gene Regulation by Global Crosstalk.”
Nature Communications, vol. 7, 12307, Nature Publishing Group, 2016, doi:10.1038/ncomms12307.
short: T. Friedlander, R. Prizak, C.C. Guet, N.H. Barton, G. Tkačik, Nature Communications
7 (2016).
date_created: 2018-12-11T11:51:34Z
date_published: 2016-08-04T00:00:00Z
date_updated: 2023-09-07T12:53:49Z
day: '04'
ddc:
- '576'
department:
- _id: GaTk
- _id: NiBa
- _id: CaGu
doi: 10.1038/ncomms12307
ec_funded: 1
file:
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checksum: fe3f3a1526d180b29fe691ab11435b78
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creator: system
date_created: 2018-12-12T10:12:01Z
date_updated: 2020-07-14T12:44:46Z
file_id: '4919'
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file_size: 861805
relation: main_file
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creator: system
date_created: 2018-12-12T10:12:02Z
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file_id: '4920'
file_name: IST-2016-627-v1+2_ncomms12307-s1.pdf
file_size: 1084703
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file_date_updated: 2020-07-14T12:44:46Z
has_accepted_license: '1'
intvolume: ' 7'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
- _id: 254E9036-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P28844-B27
name: Biophysics of information processing in gene regulation
publication: Nature Communications
publication_status: published
publisher: Nature Publishing Group
publist_id: '5887'
pubrep_id: '627'
quality_controlled: '1'
related_material:
record:
- id: '6071'
relation: dissertation_contains
status: public
scopus_import: 1
status: public
title: Intrinsic limits to gene regulation by global crosstalk
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 7
year: '2016'
...
---
_id: '9710'
abstract:
- lang: eng
text: Much of quantitative genetics is based on the ‘infinitesimal model’, under
which selection has a negligible effect on the genetic variance. This is typically
justified by assuming a very large number of loci with additive effects. However,
it applies even when genes interact, provided that the number of loci is large
enough that selection on each of them is weak relative to random drift. In the
long term, directional selection will change allele frequencies, but even then,
the effects of epistasis on the ultimate change in trait mean due to selection
may be modest. Stabilising selection can maintain many traits close to their optima,
even when the underlying alleles are weakly selected. However, the number of traits
that can be optimised is apparently limited to ~4Ne by the ‘drift load’, and this
is hard to reconcile with the apparent complexity of many organisms. Just as for
the mutation load, this limit can be evaded by a particular form of negative epistasis.
A more robust limit is set by the variance in reproductive success. This suggests
that selection accumulates information most efficiently in the infinitesimal regime,
when selection on individual alleles is weak, and comparable with random drift.
A review of evidence on selection strength suggests that although most variance
in fitness may be because of alleles with large Nes, substantial amounts of adaptation
may be because of alleles in the infinitesimal regime, in which epistasis has
modest effects.
article_processing_charge: No
author:
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: 'Barton NH. Data from: How does epistasis influence the response to selection?
2016. doi:10.5061/dryad.s5s7r'
apa: 'Barton, N. H. (2016). Data from: How does epistasis influence the response
to selection? Dryad. https://doi.org/10.5061/dryad.s5s7r'
chicago: 'Barton, Nicholas H. “Data from: How Does Epistasis Influence the Response
to Selection?” Dryad, 2016. https://doi.org/10.5061/dryad.s5s7r.'
ieee: 'N. H. Barton, “Data from: How does epistasis influence the response to selection?”
Dryad, 2016.'
ista: 'Barton NH. 2016. Data from: How does epistasis influence the response to
selection?, Dryad, 10.5061/dryad.s5s7r.'
mla: 'Barton, Nicholas H. Data from: How Does Epistasis Influence the Response
to Selection? Dryad, 2016, doi:10.5061/dryad.s5s7r.'
short: N.H. Barton, (2016).
date_created: 2021-07-23T11:45:47Z
date_published: 2016-09-23T00:00:00Z
date_updated: 2023-09-20T11:17:47Z
day: '23'
department:
- _id: NiBa
doi: 10.5061/dryad.s5s7r
main_file_link:
- open_access: '1'
url: https://doi.org/10.5061/dryad.s5s7r
month: '09'
oa: 1
oa_version: Published Version
publisher: Dryad
related_material:
record:
- id: '1199'
relation: used_in_publication
status: public
status: public
title: 'Data from: How does epistasis influence the response to selection?'
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2016'
...
---
_id: '9864'
abstract:
- lang: eng
text: Viral capsids are structurally constrained by interactions among the amino
acids (AAs) of their constituent proteins. Therefore, epistasis is expected to
evolve among physically interacting sites and to influence the rates of substitution.
To study the evolution of epistasis, we focused on the major structural protein
of the ϕX174 phage family by, first, reconstructing the ancestral protein sequences
of 18 species using a Bayesian statistical framework. The inferred ancestral reconstruction
differed at eight AAs, for a total of 256 possible ancestral haplotypes. For each
ancestral haplotype and the extant species, we estimated, in silico, the distribution
of free energies and epistasis of the capsid structure. We found that free energy
has not significantly increased but epistasis has. We decomposed epistasis up
to fifth order and found that higher-order epistasis sometimes compensates pairwise
interactions making the free energy seem additive. The dN/dS ratio is low, suggesting
strong purifying selection, and that structure is under stabilizing selection.
We synthesized phages carrying ancestral haplotypes of the coat protein gene and
measured their fitness experimentally. Our findings indicate that stabilizing
mutations can have higher fitness, and that fitness optima do not necessarily
coincide with energy minima.
article_processing_charge: No
author:
- first_name: Rodrigo A
full_name: Fernandes Redondo, Rodrigo A
id: 409D5C96-F248-11E8-B48F-1D18A9856A87
last_name: Fernandes Redondo
orcid: 0000-0002-5837-2793
- first_name: Harold
full_name: de Vladar, Harold
id: 2A181218-F248-11E8-B48F-1D18A9856A87
last_name: de Vladar
orcid: 0000-0002-5985-7653
- first_name: Tomasz
full_name: Włodarski, Tomasz
last_name: Włodarski
- first_name: Jonathan P
full_name: Bollback, Jonathan P
id: 2C6FA9CC-F248-11E8-B48F-1D18A9856A87
last_name: Bollback
orcid: 0000-0002-4624-4612
citation:
ama: Fernandes Redondo RA, de Vladar H, Włodarski T, Bollback JP. Data from evolutionary
interplay between structure, energy and epistasis in the coat protein of the ϕX174
phage family. 2016. doi:10.6084/m9.figshare.4315652.v1
apa: Fernandes Redondo, R. A., de Vladar, H., Włodarski, T., & Bollback, J.
P. (2016). Data from evolutionary interplay between structure, energy and epistasis
in the coat protein of the ϕX174 phage family. The Royal Society. https://doi.org/10.6084/m9.figshare.4315652.v1
chicago: Fernandes Redondo, Rodrigo A, Harold de Vladar, Tomasz Włodarski, and Jonathan
P Bollback. “Data from Evolutionary Interplay between Structure, Energy and Epistasis
in the Coat Protein of the ΦX174 Phage Family.” The Royal Society, 2016. https://doi.org/10.6084/m9.figshare.4315652.v1.
ieee: R. A. Fernandes Redondo, H. de Vladar, T. Włodarski, and J. P. Bollback, “Data
from evolutionary interplay between structure, energy and epistasis in the coat
protein of the ϕX174 phage family.” The Royal Society, 2016.
ista: Fernandes Redondo RA, de Vladar H, Włodarski T, Bollback JP. 2016. Data from
evolutionary interplay between structure, energy and epistasis in the coat protein
of the ϕX174 phage family, The Royal Society, 10.6084/m9.figshare.4315652.v1.
mla: Fernandes Redondo, Rodrigo A., et al. Data from Evolutionary Interplay between
Structure, Energy and Epistasis in the Coat Protein of the ΦX174 Phage Family.
The Royal Society, 2016, doi:10.6084/m9.figshare.4315652.v1.
short: R.A. Fernandes Redondo, H. de Vladar, T. Włodarski, J.P. Bollback, (2016).
date_created: 2021-08-10T08:29:47Z
date_published: 2016-12-14T00:00:00Z
date_updated: 2023-09-20T11:56:33Z
day: '14'
department:
- _id: NiBa
- _id: JoBo
doi: 10.6084/m9.figshare.4315652.v1
main_file_link:
- open_access: '1'
url: https://doi.org/10.6084/m9.figshare.4315652.v1
month: '12'
oa: 1
oa_version: Published Version
publisher: The Royal Society
related_material:
record:
- id: '1077'
relation: used_in_publication
status: public
status: public
title: Data from evolutionary interplay between structure, energy and epistasis in
the coat protein of the ϕX174 phage family
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2016'
...
---
_id: '1382'
abstract:
- lang: eng
text: Background and aims Angiosperms display remarkable diversity in flower colour,
implying that transitions between pigmentation phenotypes must have been common.
Despite progress in understanding transitions between anthocyanin (blue, purple,
pink or red) and unpigmented (white) flowers, little is known about the evolutionary
patterns of flower-colour transitions in lineages with both yellow and anthocyanin-pigmented
flowers. This study investigates the relative rates of evolutionary transitions
between different combinations of yellow- and anthocyanin-pigmentation phenotypes
in the tribe Antirrhineae. Methods We surveyed taxonomic literature for data on
anthocyanin and yellow floral pigmentation for 369 species across the tribe. We
then reconstructed the phylogeny of 169 taxa and used phylogenetic comparative
methods to estimate transition rates among pigmentation phenotypes across the
phylogeny. Key Results In contrast to previous studies we found a bias towards
transitions involving a gain in pigmentation, although transitions to phenotypes
with both anthocyanin and yellow taxa are nevertheless extremely rare. Despite
the dominance of yellow and anthocyanin-pigmented taxa, transitions between these
phenotypes are constrained to move through a white intermediate stage, whereas
transitions to double-pigmentation are very rare. The most abundant transitions
are between anthocyanin-pigmented and unpigmented flowers, and similarly the most
abundant polymorphic taxa were those with anthocyanin-pigmented and unpigmented
flowers. Conclusions Our findings show that pigment evolution is limited by the
presence of other floral pigments. This interaction between anthocyanin and yellow
pigments constrains the breadth of potential floral diversity observed in nature.
In particular, they suggest that selection has repeatedly acted to promote the
spread of single-pigmented phenotypes across the Antirrhineae phylogeny. Furthermore,
the correlation between transition rates and polymorphism suggests that the forces
causing and maintaining variance in the short term reflect evolutionary processes
on longer time scales.
acknowledgement: We thank Melinda Pickup, Spencer Barrett, Nick Barton and four anonymous
reviewers for helpful discussions on previous versions of this manuscript. We also thank Jana Porsche for
her efforts in tracking down the more obscure references.
author:
- first_name: Thomas
full_name: Ellis, Thomas
id: 3153D6D4-F248-11E8-B48F-1D18A9856A87
last_name: Ellis
orcid: 0000-0002-8511-0254
- first_name: David
full_name: Field, David
id: 419049E2-F248-11E8-B48F-1D18A9856A87
last_name: Field
orcid: 0000-0002-4014-8478
citation:
ama: Ellis T, Field D. Repeated gains in yellow and anthocyanin pigmentation in
flower colour transitions in the Antirrhineae. Annals of Botany. 2016;117(7):1133-1140.
doi:10.1093/aob/mcw043
apa: Ellis, T., & Field, D. (2016). Repeated gains in yellow and anthocyanin
pigmentation in flower colour transitions in the Antirrhineae. Annals of Botany.
Oxford University Press. https://doi.org/10.1093/aob/mcw043
chicago: Ellis, Thomas, and David Field. “Repeated Gains in Yellow and Anthocyanin
Pigmentation in Flower Colour Transitions in the Antirrhineae.” Annals of Botany.
Oxford University Press, 2016. https://doi.org/10.1093/aob/mcw043.
ieee: T. Ellis and D. Field, “Repeated gains in yellow and anthocyanin pigmentation
in flower colour transitions in the Antirrhineae,” Annals of Botany, vol.
117, no. 7. Oxford University Press, pp. 1133–1140, 2016.
ista: Ellis T, Field D. 2016. Repeated gains in yellow and anthocyanin pigmentation
in flower colour transitions in the Antirrhineae. Annals of Botany. 117(7), 1133–1140.
mla: Ellis, Thomas, and David Field. “Repeated Gains in Yellow and Anthocyanin Pigmentation
in Flower Colour Transitions in the Antirrhineae.” Annals of Botany, vol.
117, no. 7, Oxford University Press, 2016, pp. 1133–40, doi:10.1093/aob/mcw043.
short: T. Ellis, D. Field, Annals of Botany 117 (2016) 1133–1140.
date_created: 2018-12-11T11:51:42Z
date_published: 2016-06-01T00:00:00Z
date_updated: 2024-02-21T13:49:53Z
day: '1'
department:
- _id: NiBa
doi: 10.1093/aob/mcw043
intvolume: ' 117'
issue: '7'
language:
- iso: eng
month: '06'
oa_version: None
page: 1133 - 1140
publication: Annals of Botany
publication_status: published
publisher: Oxford University Press
publist_id: '5828'
quality_controlled: '1'
related_material:
record:
- id: '5550'
relation: popular_science
status: public
scopus_import: 1
status: public
title: Repeated gains in yellow and anthocyanin pigmentation in flower colour transitions
in the Antirrhineae
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 117
year: '2016'
...
---
_id: '5550'
abstract:
- lang: eng
text: "We collected flower colour information on species in the tribe Antirrhineae
from taxonomic literature. We also retreived molecular data from GenBank for as
many of these species as possible to estimate phylogenetic relationships among
these taxa. We then used the R package 'diversitree' to examine patterns of evolutionary
transitions between anthocyanin and yellow pigmentation across the phylogeny.\r\n\r\nFor
full details of the methods see:\r\nEllis TJ and Field DL \"Repeated gains in
yellow and anthocyanin pigmentation in flower colour transitions in the Antirrhineae”,
Annals of Botany (in press)"
article_processing_charge: No
author:
- first_name: Thomas
full_name: Ellis, Thomas
id: 3153D6D4-F248-11E8-B48F-1D18A9856A87
last_name: Ellis
orcid: 0000-0002-8511-0254
- first_name: David
full_name: Field, David
id: 419049E2-F248-11E8-B48F-1D18A9856A87
last_name: Field
orcid: 0000-0002-4014-8478
citation:
ama: Ellis T, Field D. Flower colour data and phylogeny (NEXUS) files. 2016. doi:10.15479/AT:ISTA:34
apa: Ellis, T., & Field, D. (2016). Flower colour data and phylogeny (NEXUS)
files. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:34
chicago: Ellis, Thomas, and David Field. “Flower Colour Data and Phylogeny (NEXUS)
Files.” Institute of Science and Technology Austria, 2016. https://doi.org/10.15479/AT:ISTA:34.
ieee: T. Ellis and D. Field, “Flower colour data and phylogeny (NEXUS) files.” Institute
of Science and Technology Austria, 2016.
ista: Ellis T, Field D. 2016. Flower colour data and phylogeny (NEXUS) files, Institute
of Science and Technology Austria, 10.15479/AT:ISTA:34.
mla: Ellis, Thomas, and David Field. Flower Colour Data and Phylogeny (NEXUS)
Files. Institute of Science and Technology Austria, 2016, doi:10.15479/AT:ISTA:34.
short: T. Ellis, D. Field, (2016).
datarep_id: '34'
date_created: 2018-12-12T12:31:29Z
date_published: 2016-02-19T00:00:00Z
date_updated: 2024-02-21T13:49:54Z
day: '19'
ddc:
- '576'
department:
- _id: NiBa
doi: 10.15479/AT:ISTA:34
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date_created: 2018-12-12T13:02:27Z
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publisher: Institute of Science and Technology Austria
publist_id: '5828'
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relation: research_paper
status: public
status: public
title: Flower colour data and phylogeny (NEXUS) files
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year: '2016'
...
---
_id: '1398'
abstract:
- lang: eng
text: Hybrid zones represent evolutionary laboratories, where recombination brings
together alleles in combinations which have not previously been tested by selection.
This provides an excellent opportunity to test the effect of molecular variation
on fitness, and how this variation is able to spread through populations in a
natural context. The snapdragon Antirrhinum majus is polymorphic in the wild for
two loci controlling the distribution of yellow and magenta floral pigments. Where
the yellow A. m. striatum and the magenta A. m. pseudomajus meet along a valley
in the Spanish Pyrenees they form a stable hybrid zone Alleles at these loci recombine
to give striking transgressive variation for flower colour. The sharp transition
in phenotype over ~1km implies strong selection maintaining the hybrid zone. An
indirect assay of pollinator visitation in the field found that pollinators forage
in a positive-frequency dependent manner on Antirrhinum, matching previous data
on fruit set. Experimental arrays and paternity analysis of wild-pollinated seeds
demonstrated assortative mating for pigmentation alleles, and that pollinator
behaviour alone is sufficient to explain this pattern. Selection by pollinators
should be sufficiently strong to maintain the hybrid zone, although other mechanisms
may be at work. At a broader scale I examined evolutionary transitions between
yellow and anthocyanin pigmentation in the tribe Antirrhinae, and found that selection
has acted strate that pollinators are a major determinant of reproductive success
and mating patterns in wild Antirrhinum.
acknowledgement: "I am indebted to many people for their support during my PhD, but
I particularly wish to thank Nick Barton for his guidance and intuition, and for
encouraging me to take the time to look beyond the immediate topic of my PhD to
understand the broader context. I am also especially grateful to David Field his
bottomless patience, invaluable advice on experimental design, analysis and scientific
writing, and for tireless work on the population surveys and genomic work without
most of my thesis could not have happened. \r\n\r\nIt has been a pleasure to work
with the combined strengths of the groups at The John Innes Centre, University of
Toulouse and IST Austria. Thanks to Enrico Coen and his group for hosting me in
Norwich in 2011 and especially for setting up the tag experiment. \r\n\r\nI thank
David Field, Desmond Bradley and Maria Clara Melo-Hurtado for organising field collections,
as well as Monique Burrus and Christophe Andalo and a large number of volunteers
for their e ff orts helping with the field work. Furthermore I thank Coline Jaworski
for providing seeds and for her input into the design of the experimental arrays,
and Matthew Couchman for maintaining the database of. \r\n\r\nIn addition to those
mentioned above, I am grateful to Melinda Pickup, Spencer Barrett, and four anonymous
reviewers for their insightful comments on sections of this manuscript. I also thank
Jana Porsche for her e ff orts in tracking down the more obscure references for
chapter 5, and Jon Bollback for his advice about the analysis. \r\n\r\nI am indebted
to Jon Ågren for his patience whilst I finished this thesis, and to Sylvia Cremer
and Magnus Nordborg for taking the time to read and evaluate the thesis given a
shorter deadline than was fair. \r\n\r\nA very positive aspect of my PhD has been
the supportive atmosphere of IST. In particular, I have come to appreciate the enormous
support from our group assistants Nicole Hotzy, Julia Asimakis, Christine Ostermann
and Jerneja Beslagic. I also thank Christian Chaloupka and Stefan Hipfinger for
their enthusiasm and readiness to help where possible in setting up our greenhouse
and experiments. "
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Thomas
full_name: Ellis, Thomas
id: 3153D6D4-F248-11E8-B48F-1D18A9856A87
last_name: Ellis
orcid: 0000-0002-8511-0254
citation:
ama: Ellis T. The role of pollinator-mediated selection in the maintenance of a
flower color polymorphism in an Antirrhinum majus hybrid zone. 2016. doi:10.15479/AT:ISTA:TH_526
apa: Ellis, T. (2016). The role of pollinator-mediated selection in the maintenance
of a flower color polymorphism in an Antirrhinum majus hybrid zone. Institute
of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:TH_526
chicago: Ellis, Thomas. “The Role of Pollinator-Mediated Selection in the Maintenance
of a Flower Color Polymorphism in an Antirrhinum Majus Hybrid Zone.” Institute
of Science and Technology Austria, 2016. https://doi.org/10.15479/AT:ISTA:TH_526 .
ieee: T. Ellis, “The role of pollinator-mediated selection in the maintenance of
a flower color polymorphism in an Antirrhinum majus hybrid zone,” Institute of
Science and Technology Austria, 2016.
ista: Ellis T. 2016. The role of pollinator-mediated selection in the maintenance
of a flower color polymorphism in an Antirrhinum majus hybrid zone. Institute
of Science and Technology Austria.
mla: Ellis, Thomas. The Role of Pollinator-Mediated Selection in the Maintenance
of a Flower Color Polymorphism in an Antirrhinum Majus Hybrid Zone. Institute
of Science and Technology Austria, 2016, doi:10.15479/AT:ISTA:TH_526 .
short: T. Ellis, The Role of Pollinator-Mediated Selection in the Maintenance of
a Flower Color Polymorphism in an Antirrhinum Majus Hybrid Zone, Institute of
Science and Technology Austria, 2016.
date_created: 2018-12-11T11:51:47Z
date_published: 2016-02-18T00:00:00Z
date_updated: 2024-02-21T13:51:39Z
day: '18'
ddc:
- '576'
degree_awarded: PhD
department:
- _id: NiBa
doi: '10.15479/AT:ISTA:TH_526 '
file:
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publication_status: published
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status: public
supervisor:
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
title: The role of pollinator-mediated selection in the maintenance of a flower color
polymorphism in an Antirrhinum majus hybrid zone
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2016'
...
---
_id: '1131'
abstract:
- lang: eng
text: "Evolution of gene regulation is important for phenotypic evolution and diversity.
Sequence-specific binding of regulatory proteins is one of the key regulatory
mechanisms determining gene expression. Although there has been intense interest
in evolution of regulatory binding sites in the last decades, a theoretical understanding
is far from being complete. In this thesis, I aim at a better understanding of
the evolution of transcriptional regulatory binding sequences by using biophysical
and population genetic models.\r\nIn the first part of the thesis, I discuss how
to formulate the evolutionary dynamics of binding se- quences in a single isolated
binding site and in promoter/enhancer regions. I develop a theoretical framework
bridging between a thermodynamical model for transcription and a mutation-selection-drift
model for monomorphic populations. I mainly address the typical evolutionary rates,
and how they de- pend on biophysical parameters (e.g. binding length and specificity)
and population genetic parameters (e.g. population size and selection strength).\r\nIn
the second part of the thesis, I analyse empirical data for a better evolutionary
and biophysical understanding of sequence-specific binding of bacterial RNA polymerase.
First, I infer selection on regulatory and non-regulatory binding sites of RNA
polymerase in the E. coli K12 genome. Second, I infer the chemical potential of
RNA polymerase, an important but unknown physical parameter defining the threshold
energy for strong binding. Furthermore, I try to understand the relation between
the lac promoter sequence diversity and the LacZ activity variation among 20 bacterial
isolates by constructing a simple but biophysically motivated gene expression
model. Lastly, I lay out a statistical framework to predict adaptive point mutations
in de novo promoter evolution in a selection experiment."
acknowledgement: This PhD thesis may not have been completed without the help and
care I received from some peo- ple during my PhD life. I am especially grateful
to Tiago Paixao, Gasper Tkacik, Nick Barton, not only for their scientific advices
but also for their patience and support. I thank Calin Guet and Jonathan Bollback
for allowing me to “play around” in their labs and get some experience on experimental
evolution. I thank Magdalena Steinrueck and Fabienne Jesse for collaborating and
sharing their experimental data with me. I thank Johannes Jaeger for reviewing my
thesis. I thank all members of Barton group (aka bartonians) for their feedback,
and all workers of IST Austria for making the best working conditions. Lastly, I
thank two special women, Nejla Sag ̆lam and Setenay Dog ̆an, for their continuous
support and encouragement. I truly had a great chance of having right people around
me.
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Murat
full_name: Tugrul, Murat
id: 37C323C6-F248-11E8-B48F-1D18A9856A87
last_name: Tugrul
orcid: 0000-0002-8523-0758
citation:
ama: Tugrul M. Evolution of transcriptional regulatory sequences. 2016.
apa: Tugrul, M. (2016). Evolution of transcriptional regulatory sequences.
Institute of Science and Technology Austria.
chicago: Tugrul, Murat. “Evolution of Transcriptional Regulatory Sequences.” Institute
of Science and Technology Austria, 2016.
ieee: M. Tugrul, “Evolution of transcriptional regulatory sequences,” Institute
of Science and Technology Austria, 2016.
ista: Tugrul M. 2016. Evolution of transcriptional regulatory sequences. Institute
of Science and Technology Austria.
mla: Tugrul, Murat. Evolution of Transcriptional Regulatory Sequences. Institute
of Science and Technology Austria, 2016.
short: M. Tugrul, Evolution of Transcriptional Regulatory Sequences, Institute of
Science and Technology Austria, 2016.
date_created: 2018-12-11T11:50:19Z
date_published: 2016-07-01T00:00:00Z
date_updated: 2024-02-21T13:50:34Z
day: '01'
ddc:
- '576'
degree_awarded: PhD
department:
- _id: NiBa
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creator: dernst
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date_updated: 2021-02-22T11:45:20Z
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file_name: 2016_Tugrul_Thesis.pdf
file_size: 3880811
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language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: '89'
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
publist_id: '6229'
related_material:
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relation: part_of_dissertation
status: public
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status: public
status: public
supervisor:
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
title: Evolution of transcriptional regulatory sequences
type: dissertation
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
year: '2016'
...
---
_id: '5553'
abstract:
- lang: eng
text: "Genotypic, phenotypic and demographic data for 2128 wild snapdragons and
1127 open-pollinated progeny from a natural hybrid zone, collected as part of
Tom Ellis' PhD thesis (submitted) February 2016).\r\n\r\nTissue samples were sent
to LGC Genomics in Berlin for DNA extraction, and genotyping at 70 SNP markers
by KASPR genotyping. 29 of these SNPs failed to amplify reliably, and have been
removed from this dataset.\r\n\r\nOther data were retreived from an online database
of this population at www.antspec.org."
article_processing_charge: No
author:
- first_name: David
full_name: Field, David
id: 419049E2-F248-11E8-B48F-1D18A9856A87
last_name: Field
orcid: 0000-0002-4014-8478
- first_name: Thomas
full_name: Ellis, Thomas
id: 3153D6D4-F248-11E8-B48F-1D18A9856A87
last_name: Ellis
orcid: 0000-0002-8511-0254
citation:
ama: Field D, Ellis T. Inference of mating patterns among wild snapdragons in a
natural hybrid zone in 2012. 2016. doi:10.15479/AT:ISTA:37
apa: Field, D., & Ellis, T. (2016). Inference of mating patterns among wild
snapdragons in a natural hybrid zone in 2012. Institute of Science and Technology
Austria. https://doi.org/10.15479/AT:ISTA:37
chicago: Field, David, and Thomas Ellis. “Inference of Mating Patterns among Wild
Snapdragons in a Natural Hybrid Zone in 2012.” Institute of Science and Technology
Austria, 2016. https://doi.org/10.15479/AT:ISTA:37.
ieee: D. Field and T. Ellis, “Inference of mating patterns among wild snapdragons
in a natural hybrid zone in 2012.” Institute of Science and Technology Austria,
2016.
ista: Field D, Ellis T. 2016. Inference of mating patterns among wild snapdragons
in a natural hybrid zone in 2012, Institute of Science and Technology Austria,
10.15479/AT:ISTA:37.
mla: Field, David, and Thomas Ellis. Inference of Mating Patterns among Wild
Snapdragons in a Natural Hybrid Zone in 2012. Institute of Science and Technology
Austria, 2016, doi:10.15479/AT:ISTA:37.
short: D. Field, T. Ellis, (2016).
contributor:
- contributor_type: project_manager
first_name: Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
datarep_id: '37'
date_created: 2018-12-12T12:31:30Z
date_published: 2016-02-19T00:00:00Z
date_updated: 2024-02-21T13:51:14Z
day: '19'
ddc:
- '576'
department:
- _id: NiBa
doi: 10.15479/AT:ISTA:37
file:
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creator: system
date_created: 2018-12-12T13:03:02Z
date_updated: 2020-07-14T12:47:01Z
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file_size: 132808
relation: main_file
file_date_updated: 2020-07-14T12:47:01Z
has_accepted_license: '1'
keyword:
- paternity assignment
- pedigree
- matting patterns
- assortative mating
- Antirrhinum majus
- frequency-dependent selection
- plant-pollinator interaction
month: '02'
oa: 1
oa_version: Published Version
publisher: Institute of Science and Technology Austria
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title: Inference of mating patterns among wild snapdragons in a natural hybrid zone
in 2012
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user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2016'
...
---
_id: '5551'
abstract:
- lang: eng
text: "Data from array experiments investigating pollinator behaviour on snapdragons
in controlled conditions, and their effect on plant mating. Data were collected
as part of Tom Ellis' PhD thesis , submitted February 2016.\r\n\r\nWe placed a
total of 36 plants in a grid inside a closed organza tent, with a single hive
of commercially bred bumblebees (Bombus hortorum). We used only the yellow-flowered
Antirrhinum majus striatum and the magenta-flowered Antirrhinum majus pseudomajus,
at ratios of 6:36, 12:24, 18:18, 24:12 and 30:6.\r\n\r\nAfter 24 hours to learn
how to deal with snapdragons, I observed pollinators foraging on plants, and recorded
the transitions between plants. Thereafter seeds on plants were allowed to develops.
A sample of these were grown to maturity when their flower colour could be determined,
and they were scored as yellow, magenta, or hybrid."
article_processing_charge: No
author:
- first_name: Thomas
full_name: Ellis, Thomas
id: 3153D6D4-F248-11E8-B48F-1D18A9856A87
last_name: Ellis
orcid: 0000-0002-8511-0254
citation:
ama: Ellis T. Data on pollinator observations and offpsring phenotypes. 2016. doi:10.15479/AT:ISTA:35
apa: Ellis, T. (2016). Data on pollinator observations and offpsring phenotypes.
Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:35
chicago: Ellis, Thomas. “Data on Pollinator Observations and Offpsring Phenotypes.”
Institute of Science and Technology Austria, 2016. https://doi.org/10.15479/AT:ISTA:35.
ieee: T. Ellis, “Data on pollinator observations and offpsring phenotypes.” Institute
of Science and Technology Austria, 2016.
ista: Ellis T. 2016. Data on pollinator observations and offpsring phenotypes, Institute
of Science and Technology Austria, 10.15479/AT:ISTA:35.
mla: Ellis, Thomas. Data on Pollinator Observations and Offpsring Phenotypes.
Institute of Science and Technology Austria, 2016, doi:10.15479/AT:ISTA:35.
short: T. Ellis, (2016).
contributor:
- first_name: David
id: 419049E2-F248-11E8-B48F-1D18A9856A87
last_name: Field
- first_name: Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
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date_created: 2018-12-12T12:31:29Z
date_published: 2016-02-19T00:00:00Z
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doi: 10.15479/AT:ISTA:35
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