---
_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: 2025-04-15T06:50:00Z
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: '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
license: https://creativecommons.org/licenses/by/4.0/
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: '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: '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: 2025-04-15T07:17:08Z
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: '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: 2025-04-15T07:11:03Z
day: '12'
department:
- _id: NiBa
doi: 10.15479/AT:ISTA:95
file:
- access_level: open_access
checksum: fc6aab51439f2622ba6df8632e66fd4f
content_type: text/csv
creator: system
date_created: 2018-12-12T13:02:41Z
date_updated: 2020-07-14T12:47:07Z
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file_size: 122048
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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
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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
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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'
license: https://creativecommons.org/publicdomain/zero/1.0/
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: '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: 2025-04-15T07:11:04Z
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
license: https://creativecommons.org/licenses/by-nc/4.0/
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: '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 Society of America. 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 Society of America, 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 Society of America,
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 Society of
America, 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: 2025-06-03T11:31:54Z
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 Society of America
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: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 208
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: 2025-04-15T08:18:38Z
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
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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
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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
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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
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file_name: FileS5.txt
file_size: 2495437
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creator: cfraisse
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creator: cfraisse
date_created: 2018-12-19T14:19:50Z
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date_updated: 2020-07-14T12:47:11Z
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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: '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
arxiv: 1
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.'
corr_author: '1'
date_created: 2018-12-11T11:47:28Z
date_published: 2018-08-01T00:00:00Z
date_updated: 2024-10-09T20:58:45Z
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: '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: 2025-04-15T08:22:22Z
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: '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: '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: 2025-04-15T08:17:50Z
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: '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: 2025-07-10T11:52:32Z
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
relation: main_file
file_date_updated: 2020-07-14T12:46:16Z
has_accepted_license: '1'
intvolume: ' 115'
isi: 1
issue: '43'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-nd/4.0/
month: '10'
oa: 1
oa_version: Published Version
page: 11006 - 11011
pmid: 1
publication: PNAS
publication_identifier:
issn:
- 0027-8424
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: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 115
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: 2025-07-10T11:52:33Z
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:
- 0016-6731
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: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 210
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.
corr_author: '1'
date_created: 2018-12-11T11:44:18Z
date_published: 2018-12-31T00:00:00Z
date_updated: 2025-07-10T11:52:34Z
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
has_accepted_license: '1'
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:
- 1365-294X
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: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 27
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: 2025-03-31T16:00:24Z
day: '09'
ddc:
- '576'
department:
- _id: NiBa
- _id: JoBo
doi: 10.7554/eLife.32035
ec_funded: 1
external_id:
isi:
- '000431035800001'
file:
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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
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intvolume: ' 7'
isi: 1
language:
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month: '03'
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oa_version: Published Version
project:
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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'
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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: '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
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file_date_updated: 2020-07-14T12:46:26Z
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intvolume: ' 208'
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issue: '4'
language:
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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'
...
---
OA_place: publisher
_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.
corr_author: '1'
date_created: 2018-12-11T11:45:10Z
date_published: 2018-02-21T00:00:00Z
date_updated: 2026-04-08T14:06:37Z
day: '21'
ddc:
- '576'
degree_awarded: PhD
department:
- _id: NiBa
doi: 10.15479/AT:ISTA:th_963
file:
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checksum: 8cc534d2b528ae017acf80874cce48c9
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creator: system
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file_name: IST-2018-963-v1+1_thesis.pdf
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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: ba8df636-2132-11f1-aed0-ed93e2281fdd
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.
corr_author: '1'
date_created: 2018-12-11T11:47:12Z
date_published: 2018-03-01T00:00:00Z
date_updated: 2026-04-08T14:06:35Z
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: '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: 2025-07-10T11:50:13Z
day: '01'
ddc:
- '576'
department:
- _id: NiBa
doi: 10.1534/genetics.116.193946
ec_funded: 1
external_id:
isi:
- '000393677300025'
file:
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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:
- 0016-6731
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: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 205
year: '2017'
...