---
_id: '1519'
abstract:
- lang: eng
text: Evolutionary biologists have an array of powerful theoretical techniques that
can accurately predict changes in the genetic composition of populations. Changes
in gene frequencies and genetic associations between loci can be tracked as they
respond to a wide variety of evolutionary forces. However, it is often less clear
how to decompose these various forces into components that accurately reflect
the underlying biology. Here, we present several issues that arise in the definition
and interpretation of selection and selection coefficients, focusing on insights
gained through the examination of selection coefficients in multilocus notation.
Using this notation, we discuss how its flexibility-which allows different biological
units to be identified as targets of selection-is reflected in the interpretation
of the coefficients that the notation generates. In many situations, it can be
difficult to agree on whether loci can be considered to be under "direct"
versus "indirect" selection, or to quantify this selection. We present
arguments for what the terms direct and indirect selection might best encompass,
considering a range of issues, from viability and sexual selection to kin selection.
We show how multilocus notation can discriminate between direct and indirect selection,
and describe when it can do so.
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: Maria
full_name: Servedio, Maria
last_name: Servedio
citation:
ama: Barton NH, Servedio M. The interpretation of selection coefficients. Evolution.
2015;69(5):1101-1112. doi:10.1111/evo.12641
apa: Barton, N. H., & Servedio, M. (2015). The interpretation of selection coefficients.
Evolution. Wiley. https://doi.org/10.1111/evo.12641
chicago: Barton, Nicholas H, and Maria Servedio. “The Interpretation of Selection
Coefficients.” Evolution. Wiley, 2015. https://doi.org/10.1111/evo.12641.
ieee: N. H. Barton and M. Servedio, “The interpretation of selection coefficients,”
Evolution, vol. 69, no. 5. Wiley, pp. 1101–1112, 2015.
ista: Barton NH, Servedio M. 2015. The interpretation of selection coefficients.
Evolution. 69(5), 1101–1112.
mla: Barton, Nicholas H., and Maria Servedio. “The Interpretation of Selection Coefficients.”
Evolution, vol. 69, no. 5, Wiley, 2015, pp. 1101–12, doi:10.1111/evo.12641.
short: N.H. Barton, M. Servedio, Evolution 69 (2015) 1101–1112.
corr_author: '1'
date_created: 2018-12-11T11:52:29Z
date_published: 2015-03-19T00:00:00Z
date_updated: 2025-09-23T13:53:01Z
day: '19'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1111/evo.12641
ec_funded: 1
external_id:
isi:
- '000354561600001'
file:
- access_level: open_access
checksum: fd8d23f476bc194419929b72ca265c02
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:10:34Z
date_updated: 2020-07-14T12:45:00Z
file_id: '4822'
file_name: IST-2016-560-v1+1_Interpreting_ML_coefficients_11.2.15_App.pdf
file_size: 188872
relation: main_file
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checksum: b774911e70044641d556e258efcb52ef
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:10:35Z
date_updated: 2020-07-14T12:45:00Z
file_id: '4823'
file_name: IST-2016-560-v1+2_Interpreting_ML_coefficients_11.2.15_mainText.pdf
file_size: 577415
relation: main_file
file_date_updated: 2020-07-14T12:45:00Z
has_accepted_license: '1'
intvolume: ' 69'
isi: 1
issue: '5'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Submitted Version
page: 1101 - 1112
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_status: published
publisher: Wiley
publist_id: '5656'
pubrep_id: '560'
quality_controlled: '1'
scopus_import: '1'
status: public
title: The interpretation of selection coefficients
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 69
year: '2015'
...
---
_id: '1542'
abstract:
- lang: eng
text: 'The theory of population genetics and evolutionary computation have been
evolving separately for nearly 30 years. Many results have been independently
obtained in both fields and many others are unique to its respective field. We
aim to bridge this gap by developing a unifying framework for evolutionary processes
that allows both evolutionary algorithms and population genetics models to be
cast in the same formal framework. The framework we present here decomposes the
evolutionary process into its several components in order to facilitate the identification
of similarities between different models. In particular, we propose a classification
of evolutionary operators based on the defining properties of the different components.
We cast several commonly used operators from both fields into this common framework.
Using this, we map different evolutionary and genetic algorithms to different
evolutionary regimes and identify candidates with the most potential for the translation
of results between the fields. This provides a unified description of evolutionary
processes and represents a stepping stone towards new tools and results to both
fields. '
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: Golnaz
full_name: Badkobeh, Golnaz
last_name: Badkobeh
- 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: Doğan
full_name: Çörüş, Doğan
last_name: Çörüş
- first_name: Duccuong
full_name: Dang, Duccuong
last_name: Dang
- first_name: Tobias
full_name: Friedrich, Tobias
last_name: Friedrich
- first_name: Per
full_name: Lehre, Per
last_name: Lehre
- first_name: Dirk
full_name: Sudholt, Dirk
last_name: Sudholt
- first_name: Andrew
full_name: Sutton, Andrew
last_name: Sutton
- 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, Badkobeh G, Barton NH, et al. Toward a unifying framework for evolutionary
processes. Journal of Theoretical Biology. 2015;383:28-43. doi:10.1016/j.jtbi.2015.07.011
apa: Paixao, T., Badkobeh, G., Barton, N. H., Çörüş, D., Dang, D., Friedrich, T.,
… Trubenova, B. (2015). Toward a unifying framework for evolutionary processes.
Journal of Theoretical Biology. Elsevier. https://doi.org/10.1016/j.jtbi.2015.07.011
chicago: Paixao, Tiago, Golnaz Badkobeh, Nicholas H Barton, Doğan Çörüş, Duccuong
Dang, Tobias Friedrich, Per Lehre, Dirk Sudholt, Andrew Sutton, and Barbora Trubenova.
“Toward a Unifying Framework for Evolutionary Processes.” Journal of Theoretical
Biology. Elsevier, 2015. https://doi.org/10.1016/j.jtbi.2015.07.011.
ieee: T. Paixao et al., “Toward a unifying framework for evolutionary processes,”
Journal of Theoretical Biology, vol. 383. Elsevier, pp. 28–43, 2015.
ista: Paixao T, Badkobeh G, Barton NH, Çörüş D, Dang D, Friedrich T, Lehre P, Sudholt
D, Sutton A, Trubenova B. 2015. Toward a unifying framework for evolutionary processes. Journal
of Theoretical Biology. 383, 28–43.
mla: Paixao, Tiago, et al. “Toward a Unifying Framework for Evolutionary Processes.”
Journal of Theoretical Biology, vol. 383, Elsevier, 2015, pp. 28–43, doi:10.1016/j.jtbi.2015.07.011.
short: T. Paixao, G. Badkobeh, N.H. Barton, D. Çörüş, D. Dang, T. Friedrich, P.
Lehre, D. Sudholt, A. Sutton, B. Trubenova, Journal of Theoretical Biology 383
(2015) 28–43.
corr_author: '1'
date_created: 2018-12-11T11:52:37Z
date_published: 2015-10-21T00:00:00Z
date_updated: 2025-09-23T14:55:02Z
day: '21'
ddc:
- '570'
department:
- _id: NiBa
- _id: CaGu
doi: 10.1016/j.jtbi.2015.07.011
ec_funded: 1
external_id:
isi:
- '000362056300005'
file:
- access_level: open_access
checksum: 33b60ecfea60764756a9ee9df5eb65ca
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:16:53Z
date_updated: 2020-07-14T12:45:01Z
file_id: '5244'
file_name: IST-2016-483-v1+1_1-s2.0-S0022519315003409-main.pdf
file_size: 595307
relation: main_file
file_date_updated: 2020-07-14T12:45:01Z
has_accepted_license: '1'
intvolume: ' 383'
isi: 1
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-nd/4.0/
month: '10'
oa: 1
oa_version: Published Version
page: 28 - 43
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: ' Journal of Theoretical Biology'
publication_status: published
publisher: Elsevier
publist_id: '5629'
pubrep_id: '483'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Toward a unifying framework for evolutionary processes
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 383
year: '2015'
...
---
_id: '1430'
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 their runtime 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
occurrence of new mutations is much longer than the time it takes for a new beneficial
mutation to take over the population. In this situation, the population only contains
copies of one genotype and evolution can be modelled as a (1+1)-type process where
the probability of accepting a new genotype (improvements or worsenings) depends
on the change in fitness. We present an initial runtime analysis of SSWM, quantifying
its performance for various parameters and investigating differences to the (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
arxiv: 1
author:
- first_name: Tiago
full_name: Paixao, Tiago
id: 2C5658E6-F248-11E8-B48F-1D18A9856A87
last_name: Paixao
orcid: 0000-0003-2361-3953
- first_name: Dirk
full_name: Sudholt, Dirk
last_name: Sudholt
- 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
citation:
ama: 'Paixao T, Sudholt D, Heredia J, Trubenova B. First steps towards a runtime
comparison of natural and artificial evolution. In: Proceedings of the 2015
Annual Conference on Genetic and Evolutionary Computation. ACM; 2015:1455-1462.
doi:10.1145/2739480.2754758'
apa: 'Paixao, T., Sudholt, D., Heredia, J., & Trubenova, B. (2015). First steps
towards a runtime comparison of natural and artificial evolution. In Proceedings
of the 2015 Annual Conference on Genetic and Evolutionary Computation (pp.
1455–1462). Madrid, Spain: ACM. https://doi.org/10.1145/2739480.2754758'
chicago: Paixao, Tiago, Dirk Sudholt, Jorge Heredia, and Barbora Trubenova. “First
Steps towards a Runtime Comparison of Natural and Artificial Evolution.” In Proceedings
of the 2015 Annual Conference on Genetic and Evolutionary Computation, 1455–62.
ACM, 2015. https://doi.org/10.1145/2739480.2754758.
ieee: T. Paixao, D. Sudholt, J. Heredia, and B. Trubenova, “First steps towards
a runtime comparison of natural and artificial evolution,” in Proceedings of
the 2015 Annual Conference on Genetic and Evolutionary Computation, Madrid,
Spain, 2015, pp. 1455–1462.
ista: 'Paixao T, Sudholt D, Heredia J, Trubenova B. 2015. First steps towards a
runtime comparison of natural and artificial evolution. Proceedings of the 2015
Annual Conference on Genetic and Evolutionary Computation. GECCO: Genetic and
evolutionary computation conference, 1455–1462.'
mla: Paixao, Tiago, et al. “First Steps towards a Runtime Comparison of Natural
and Artificial Evolution.” Proceedings of the 2015 Annual Conference on Genetic
and Evolutionary Computation, ACM, 2015, pp. 1455–62, doi:10.1145/2739480.2754758.
short: T. Paixao, D. Sudholt, J. Heredia, B. Trubenova, in:, Proceedings of the
2015 Annual Conference on Genetic and Evolutionary Computation, ACM, 2015, pp.
1455–1462.
conference:
end_date: 2015-07-15
location: Madrid, Spain
name: 'GECCO: Genetic and evolutionary computation conference'
start_date: 2015-07-11
date_created: 2018-12-11T11:51:58Z
date_published: 2015-07-11T00:00:00Z
date_updated: 2025-09-23T08:50:33Z
day: '11'
department:
- _id: NiBa
- _id: CaGu
doi: 10.1145/2739480.2754758
ec_funded: 1
external_id:
arxiv:
- '1504.06260'
isi:
- '000358795700182'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1504.06260
month: '07'
oa: 1
oa_version: Preprint
page: 1455 - 1462
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 2015 Annual Conference on Genetic and Evolutionary
Computation
publication_status: published
publisher: ACM
publist_id: '5768'
quality_controlled: '1'
scopus_import: '1'
status: public
title: First steps towards a runtime comparison of natural and artificial evolution
type: conference
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
year: '2015'
...
---
_id: '1666'
abstract:
- lang: eng
text: Evolution of gene regulation is crucial for our understanding of the phenotypic
differences between species, populations and individuals. Sequence-specific binding
of transcription factors to the regulatory regions on the DNA is a key regulatory
mechanism that determines gene expression and hence heritable phenotypic variation.
We use a biophysical model for directional selection on gene expression to estimate
the rates of gain and loss of transcription factor binding sites (TFBS) in finite
populations under both point and insertion/deletion mutations. Our results show
that these rates are typically slow for a single TFBS in an isolated DNA region,
unless the selection is extremely strong. These rates decrease drastically with
increasing TFBS length or increasingly specific protein-DNA interactions, making
the evolution of sites longer than ∼ 10 bp unlikely on typical eukaryotic speciation
timescales. Similarly, evolution converges to the stationary distribution of binding
sequences very slowly, making the equilibrium assumption questionable. The availability
of longer regulatory sequences in which multiple binding sites can evolve simultaneously,
the presence of “pre-sites” or partially decayed old sites in the initial sequence,
and biophysical cooperativity between transcription factors, can all facilitate
gain of TFBS and reconcile theoretical calculations with timescales inferred from
comparative genomics.
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
- 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: Gasper
full_name: Tkacik, Gasper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
citation:
ama: Tugrul M, Paixao T, Barton NH, Tkačik G. Dynamics of transcription factor binding
site evolution. PLoS Genetics. 2015;11(11). doi:10.1371/journal.pgen.1005639
apa: Tugrul, M., Paixao, T., Barton, N. H., & Tkačik, G. (2015). Dynamics of
transcription factor binding site evolution. PLoS Genetics. Public Library
of Science. https://doi.org/10.1371/journal.pgen.1005639
chicago: Tugrul, Murat, Tiago Paixao, Nicholas H Barton, and Gašper Tkačik. “Dynamics
of Transcription Factor Binding Site Evolution.” PLoS Genetics. Public
Library of Science, 2015. https://doi.org/10.1371/journal.pgen.1005639.
ieee: M. Tugrul, T. Paixao, N. H. Barton, and G. Tkačik, “Dynamics of transcription
factor binding site evolution,” PLoS Genetics, vol. 11, no. 11. Public
Library of Science, 2015.
ista: Tugrul M, Paixao T, Barton NH, Tkačik G. 2015. Dynamics of transcription factor
binding site evolution. PLoS Genetics. 11(11).
mla: Tugrul, Murat, et al. “Dynamics of Transcription Factor Binding Site Evolution.”
PLoS Genetics, vol. 11, no. 11, Public Library of Science, 2015, doi:10.1371/journal.pgen.1005639.
short: M. Tugrul, T. Paixao, N.H. Barton, G. Tkačik, PLoS Genetics 11 (2015).
date_created: 2018-12-11T11:53:21Z
date_published: 2015-11-06T00:00:00Z
date_updated: 2026-04-09T10:52:40Z
day: '06'
ddc:
- '576'
department:
- _id: NiBa
- _id: CaGu
- _id: GaTk
doi: 10.1371/journal.pgen.1005639
ec_funded: 1
external_id:
isi:
- '000366179000022'
file:
- access_level: open_access
checksum: a4e72fca5ccf40ddacf4d08c8e46b554
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:07:58Z
date_updated: 2020-07-14T12:45:10Z
file_id: '4657'
file_name: IST-2016-463-v1+1_journal.pgen.1005639.pdf
file_size: 2580778
relation: main_file
file_date_updated: 2020-07-14T12:45:10Z
has_accepted_license: '1'
intvolume: ' 11'
isi: 1
issue: '11'
language:
- iso: eng
license: https://creativecommons.org/licenses/by/4.0/
month: '11'
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
publication: PLoS Genetics
publication_status: published
publisher: Public Library of Science
publist_id: '5483'
pubrep_id: '463'
quality_controlled: '1'
related_material:
record:
- id: '9712'
relation: research_data
status: public
- id: '1131'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Dynamics of transcription factor binding site 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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 11
year: '2015'
...
---
_id: '1681'
abstract:
- lang: eng
text: In many social situations, individuals endeavor to find the single best possible
partner, but are constrained to evaluate the candidates in sequence. Examples
include the search for mates, economic partnerships, or any other long-term ties
where the choice to interact involves two parties. Surprisingly, however, previous
theoretical work on mutual choice problems focuses on finding equilibrium solutions,
while ignoring the evolutionary dynamics of decisions. Empirically, this may be
of high importance, as some equilibrium solutions can never be reached unless
the population undergoes radical changes and a sufficient number of individuals
change their decisions simultaneously. To address this question, we apply a mutual
choice sequential search problem in an evolutionary game-theoretical model that
allows one to find solutions that are favored by evolution. As an example, we
study the influence of sequential search on the evolutionary dynamics of cooperation.
For this, we focus on the classic snowdrift game and the prisoner’s dilemma game.
article_processing_charge: No
article_type: original
author:
- first_name: Tadeas
full_name: Priklopil, Tadeas
id: 3C869AA0-F248-11E8-B48F-1D18A9856A87
last_name: Priklopil
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
citation:
ama: Priklopil T, Chatterjee K. Evolution of decisions in population games with
sequentially searching individuals. Games. 2015;6(4):413-437. doi:10.3390/g6040413
apa: Priklopil, T., & Chatterjee, K. (2015). Evolution of decisions in population
games with sequentially searching individuals. Games. MDPI. https://doi.org/10.3390/g6040413
chicago: Priklopil, Tadeas, and Krishnendu Chatterjee. “Evolution of Decisions in
Population Games with Sequentially Searching Individuals.” Games. MDPI,
2015. https://doi.org/10.3390/g6040413.
ieee: T. Priklopil and K. Chatterjee, “Evolution of decisions in population games
with sequentially searching individuals,” Games, vol. 6, no. 4. MDPI, pp.
413–437, 2015.
ista: Priklopil T, Chatterjee K. 2015. Evolution of decisions in population games
with sequentially searching individuals. Games. 6(4), 413–437.
mla: Priklopil, Tadeas, and Krishnendu Chatterjee. “Evolution of Decisions in Population
Games with Sequentially Searching Individuals.” Games, vol. 6, no. 4, MDPI,
2015, pp. 413–37, doi:10.3390/g6040413.
short: T. Priklopil, K. Chatterjee, Games 6 (2015) 413–437.
corr_author: '1'
date_created: 2018-12-11T11:53:26Z
date_published: 2015-09-29T00:00:00Z
date_updated: 2025-04-15T06:50:21Z
day: '29'
ddc:
- '000'
department:
- _id: NiBa
- _id: KrCh
doi: 10.3390/g6040413
ec_funded: 1
file:
- access_level: open_access
checksum: 912e1acbaf201100f447a43e4d5958bd
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:12:41Z
date_updated: 2020-07-14T12:45:12Z
file_id: '4959'
file_name: IST-2016-448-v1+1_games-06-00413.pdf
file_size: 518832
relation: main_file
file_date_updated: 2020-07-14T12:45:12Z
has_accepted_license: '1'
intvolume: ' 6'
issue: '4'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
page: 413 - 437
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
publication: Games
publication_identifier:
eissn:
- 2073-4336
publication_status: published
publisher: MDPI
publist_id: '5467'
pubrep_id: '448'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Evolution of decisions in population games with sequentially searching individuals
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: '2015'
...
---
_id: '1699'
abstract:
- lang: eng
text: By hybridization and backcrossing, alleles can surmount species boundaries
and be incorporated into the genome of a related species. This introgression of
genes is of particular evolutionary relevance if it involves the transfer of adaptations
between populations. However, any beneficial allele will typically be associated
with other alien alleles that are often deleterious and hamper the introgression
process. In order to describe the introgression of an adaptive allele, we set
up a stochastic model with an explicit genetic makeup of linked and unlinked deleterious
alleles. Based on the theory of reducible multitype branching processes, we derive
a recursive expression for the establishment probability of the beneficial allele
after a single hybridization event. We furthermore study the probability that
slightly deleterious alleles hitchhike to fixation. The key to the analysis is
a split of the process into a stochastic phase in which the advantageous alleles
establishes and a deterministic phase in which it sweeps to fixation. We thereafter
apply the theory to a set of biologically relevant scenarios such as introgression
in the presence of many unlinked or few closely linked deleterious alleles. A
comparison to computer simulations shows that the approximations work well over
a large parameter range.
acknowledgement: This work was made possible with financial support by the Vienna
Science and Technology Fund (WWTF), by the Deutsche Forschungsgemeinschaft (DFG),
Research Unit 1078 Natural selection in structured populations, by the Austrian
Science Fund (FWF) via funding for the Vienna Graduate School for Population Genetics,
and by a “For Women in Science” fellowship (L’Oréal Österreich in cooperation with
the Austrian Commission for UNESCO and the Austrian Academy of Sciences with financial
support from the Federal Ministry for Science and Research Austria).
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
- first_name: Derek
full_name: Setter, Derek
last_name: Setter
- first_name: Joachim
full_name: Hermisson, Joachim
last_name: Hermisson
citation:
ama: Uecker H, Setter D, Hermisson J. Adaptive gene introgression after secondary
contact. Journal of Mathematical Biology. 2015;70(7):1523-1580. doi:10.1007/s00285-014-0802-y
apa: Uecker, H., Setter, D., & Hermisson, J. (2015). Adaptive gene introgression
after secondary contact. Journal of Mathematical Biology. Springer. https://doi.org/10.1007/s00285-014-0802-y
chicago: Uecker, Hildegard, Derek Setter, and Joachim Hermisson. “Adaptive Gene
Introgression after Secondary Contact.” Journal of Mathematical Biology.
Springer, 2015. https://doi.org/10.1007/s00285-014-0802-y.
ieee: H. Uecker, D. Setter, and J. Hermisson, “Adaptive gene introgression after
secondary contact,” Journal of Mathematical Biology, vol. 70, no. 7. Springer,
pp. 1523–1580, 2015.
ista: Uecker H, Setter D, Hermisson J. 2015. Adaptive gene introgression after secondary
contact. Journal of Mathematical Biology. 70(7), 1523–1580.
mla: Uecker, Hildegard, et al. “Adaptive Gene Introgression after Secondary Contact.”
Journal of Mathematical Biology, vol. 70, no. 7, Springer, 2015, pp. 1523–80,
doi:10.1007/s00285-014-0802-y.
short: H. Uecker, D. Setter, J. Hermisson, Journal of Mathematical Biology 70 (2015)
1523–1580.
corr_author: '1'
date_created: 2018-12-11T11:53:32Z
date_published: 2015-06-01T00:00:00Z
date_updated: 2025-09-23T07:31:45Z
day: '01'
ddc:
- '576'
department:
- _id: NiBa
doi: 10.1007/s00285-014-0802-y
external_id:
isi:
- '000354196800003'
file:
- access_level: open_access
checksum: 00e3a67bda05d4cc165b3a48b41ef9ad
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:14:27Z
date_updated: 2020-07-14T12:45:12Z
file_id: '5079'
file_name: IST-2016-458-v1+1_s00285-014-0802-y.pdf
file_size: 1321527
relation: main_file
file_date_updated: 2020-07-14T12:45:12Z
has_accepted_license: '1'
intvolume: ' 70'
isi: 1
issue: '7'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: 1523 - 1580
project:
- _id: 25B67606-B435-11E9-9278-68D0E5697425
name: Evolutionary rescue
publication: Journal of Mathematical Biology
publication_status: published
publisher: Springer
publist_id: '5442'
pubrep_id: '458'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Adaptive gene introgression after secondary contact
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 70
year: '2015'
...
---
_id: '1703'
abstract:
- lang: eng
text: Vegetation clearing and land-use change have depleted many natural plant communities
to the point where restoration is required. A major impediment to the success
of rebuilding complex vegetation communities is having regular access to sufficient
quantities of high-quality seed. Seed-production areas (SPAs) can help generate
this seed, but these must be underpinned by a broad genetic base to maximise the
evolutionary potential of restored populations. However, genetic bottlenecks can
occur at the collection, establishment and production stages in SPAs, requiring
genetic evaluation. This is especially relevant for species that may take many
years before a return on SPA investment is realised. Two recently established
yellow box (Eucalyptus melliodora A.Cunn. ex Schauer, Myrtaceae) SPAs were evaluated
to determine whether genetic bottlenecks had occurred between seed collection
and SPA establishment. No evidence was found to suggest that a significant loss
of genetic diversity had occurred at this stage, although there was a significant
difference in diversity between the two SPAs. Complex population genetic structure
was also observed in the seed used to source the SPAs, with up to eight groups
identified. Plant survival in the SPAs was influenced by seed collection location
but not by SPA location and was not associated with genetic diversity. There were
also no associations between genetic diversity and plant growth. These data highlighted
the importance of chance events when establishing SPAs and indicated that the
two yellow box SPAs are likely to provide genetically diverse seed sources for
future restoration projects, especially by pooling seed from both SPAs.
article_processing_charge: No
author:
- first_name: Linda
full_name: Broadhurst, Linda
last_name: Broadhurst
- first_name: Graham
full_name: Fifield, Graham
last_name: Fifield
- first_name: Bindi
full_name: Vanzella, Bindi
last_name: Vanzella
- first_name: Melinda
full_name: Pickup, Melinda
id: 2C78037E-F248-11E8-B48F-1D18A9856A87
last_name: Pickup
orcid: 0000-0001-6118-0541
citation:
ama: Broadhurst L, Fifield G, Vanzella B, Pickup M. An evaluation of the genetic
structure of seed sources and the maintenance of genetic diversity during establishment
of two yellow box (Eucalyptus melliodora) seed-production areas. Australian
Journal of Botany. 2015;63(5):455-466. doi:10.1071/BT15023
apa: Broadhurst, L., Fifield, G., Vanzella, B., & Pickup, M. (2015). An evaluation
of the genetic structure of seed sources and the maintenance of genetic diversity
during establishment of two yellow box (Eucalyptus melliodora) seed-production
areas. Australian Journal of Botany. CSIRO. https://doi.org/10.1071/BT15023
chicago: Broadhurst, Linda, Graham Fifield, Bindi Vanzella, and Melinda Pickup.
“An Evaluation of the Genetic Structure of Seed Sources and the Maintenance of
Genetic Diversity during Establishment of Two Yellow Box (Eucalyptus Melliodora)
Seed-Production Areas.” Australian Journal of Botany. CSIRO, 2015. https://doi.org/10.1071/BT15023.
ieee: L. Broadhurst, G. Fifield, B. Vanzella, and M. Pickup, “An evaluation of the
genetic structure of seed sources and the maintenance of genetic diversity during
establishment of two yellow box (Eucalyptus melliodora) seed-production areas,”
Australian Journal of Botany, vol. 63, no. 5. CSIRO, pp. 455–466, 2015.
ista: Broadhurst L, Fifield G, Vanzella B, Pickup M. 2015. An evaluation of the
genetic structure of seed sources and the maintenance of genetic diversity during
establishment of two yellow box (Eucalyptus melliodora) seed-production areas.
Australian Journal of Botany. 63(5), 455–466.
mla: Broadhurst, Linda, et al. “An Evaluation of the Genetic Structure of Seed Sources
and the Maintenance of Genetic Diversity during Establishment of Two Yellow Box
(Eucalyptus Melliodora) Seed-Production Areas.” Australian Journal of Botany,
vol. 63, no. 5, CSIRO, 2015, pp. 455–66, doi:10.1071/BT15023.
short: L. Broadhurst, G. Fifield, B. Vanzella, M. Pickup, Australian Journal of
Botany 63 (2015) 455–466.
date_created: 2018-12-11T11:53:34Z
date_published: 2015-05-26T00:00:00Z
date_updated: 2025-09-23T07:51:07Z
day: '26'
department:
- _id: NiBa
doi: 10.1071/BT15023
external_id:
isi:
- '000363276500009'
intvolume: ' 63'
isi: 1
issue: '5'
language:
- iso: eng
month: '05'
oa_version: None
page: 455 - 466
publication: Australian Journal of Botany
publication_status: published
publisher: CSIRO
publist_id: '5434'
quality_controlled: '1'
scopus_import: '1'
status: public
title: An evaluation of the genetic structure of seed sources and the maintenance
of genetic diversity during establishment of two yellow box (Eucalyptus melliodora)
seed-production areas
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 63
year: '2015'
...
---
_id: '537'
abstract:
- lang: eng
text: Transgenerational effects are broader than only parental relationships. Despite
mounting evidence that multigenerational effects alter phenotypic and life-history
traits, our understanding of how they combine to determine fitness is not well
developed because of the added complexity necessary to study them. Here, we derive
a quantitative genetic model of adaptation to an extraordinary new environment
by an additive genetic component, phenotypic plasticity, maternal and grandmaternal
effects. We show how, at equilibrium, negative maternal and negative grandmaternal
effects maximize expected population mean fitness. We define negative transgenerational
effects as those that have a negative effect on trait expression in the subsequent
generation, that is, they slow, or potentially reverse, the expected evolutionary
dynamic. When maternal effects are positive, negative grandmaternal effects are
preferred. As expected under Mendelian inheritance, the grandmaternal effects
have a lower impact on fitness than the maternal effects, but this dual inheritance
model predicts a more complex relationship between maternal and grandmaternal
effects to constrain phenotypic variance and so maximize expected population mean
fitness in the offspring.
article_processing_charge: No
author:
- first_name: Roshan
full_name: Prizak, Roshan
id: 4456104E-F248-11E8-B48F-1D18A9856A87
last_name: Prizak
- first_name: Thomas
full_name: Ezard, Thomas
last_name: Ezard
- first_name: Rebecca
full_name: Hoyle, Rebecca
last_name: Hoyle
citation:
ama: Prizak R, Ezard T, Hoyle R. Fitness consequences of maternal and grandmaternal
effects. Ecology and Evolution. 2014;4(15):3139-3145. doi:10.1002/ece3.1150
apa: Prizak, R., Ezard, T., & Hoyle, R. (2014). Fitness consequences of maternal
and grandmaternal effects. Ecology and Evolution. Wiley-Blackwell. https://doi.org/10.1002/ece3.1150
chicago: Prizak, Roshan, Thomas Ezard, and Rebecca Hoyle. “Fitness Consequences
of Maternal and Grandmaternal Effects.” Ecology and Evolution. Wiley-Blackwell,
2014. https://doi.org/10.1002/ece3.1150.
ieee: R. Prizak, T. Ezard, and R. Hoyle, “Fitness consequences of maternal and grandmaternal
effects,” Ecology and Evolution, vol. 4, no. 15. Wiley-Blackwell, pp. 3139–3145,
2014.
ista: Prizak R, Ezard T, Hoyle R. 2014. Fitness consequences of maternal and grandmaternal
effects. Ecology and Evolution. 4(15), 3139–3145.
mla: Prizak, Roshan, et al. “Fitness Consequences of Maternal and Grandmaternal
Effects.” Ecology and Evolution, vol. 4, no. 15, Wiley-Blackwell, 2014,
pp. 3139–45, doi:10.1002/ece3.1150.
short: R. Prizak, T. Ezard, R. Hoyle, Ecology and Evolution 4 (2014) 3139–3145.
date_created: 2018-12-11T11:47:02Z
date_published: 2014-07-19T00:00:00Z
date_updated: 2025-09-29T13:17:53Z
day: '19'
ddc:
- '530'
- '571'
department:
- _id: NiBa
- _id: GaTk
doi: 10.1002/ece3.1150
external_id:
isi:
- '000340575000015'
file:
- access_level: open_access
checksum: e32abf75a248e7a11811fd7f60858769
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:11:31Z
date_updated: 2020-07-14T12:46:38Z
file_id: '4886'
file_name: IST-2018-934-v1+1_Prizak_et_al-2014-Ecology_and_Evolution.pdf
file_size: 621582
relation: main_file
file_date_updated: 2020-07-14T12:46:38Z
has_accepted_license: '1'
intvolume: ' 4'
isi: 1
issue: '15'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: 3139 - 3145
publication: Ecology and Evolution
publication_status: published
publisher: Wiley-Blackwell
publist_id: '7280'
pubrep_id: '934'
scopus_import: '1'
status: public
title: Fitness consequences of maternal and grandmaternal 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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 4
year: '2014'
...
---
_id: '2168'
abstract:
- lang: eng
text: Many species have an essentially continuous distribution in space, in which
there are no natural divisions between randomly mating subpopulations. Yet, the
standard approach to modelling these populations is to impose an arbitrary grid
of demes, adjusting deme sizes and migration rates in an attempt to capture the
important features of the population. Such indirect methods are required because
of the failure of the classical models of isolation by distance, which have been
shown to have major technical flaws. A recently introduced model of extinction
and recolonisation in two dimensions solves these technical problems, and provides
a rigorous technical foundation for the study of populations evolving in a spatial
continuum. The coalescent process for this model is simply stated, but direct
simulation is very inefficient for large neighbourhood sizes. We present efficient
and exact algorithms to simulate this coalescent process for arbitrary sample
sizes and numbers of loci, and analyse these algorithms in detail.
article_processing_charge: No
author:
- first_name: Jerome
full_name: Kelleher, Jerome
last_name: Kelleher
- 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: 'Kelleher J, Etheridge A, Barton NH. Coalescent simulation in continuous space:
Algorithms for large neighbourhood size. Theoretical Population Biology.
2014;95:13-23. doi:10.1016/j.tpb.2014.05.001'
apa: 'Kelleher, J., Etheridge, A., & Barton, N. H. (2014). Coalescent simulation
in continuous space: Algorithms for large neighbourhood size. Theoretical Population
Biology. Academic Press. https://doi.org/10.1016/j.tpb.2014.05.001'
chicago: 'Kelleher, Jerome, Alison Etheridge, and Nicholas H Barton. “Coalescent
Simulation in Continuous Space: Algorithms for Large Neighbourhood Size.” Theoretical
Population Biology. Academic Press, 2014. https://doi.org/10.1016/j.tpb.2014.05.001.'
ieee: 'J. Kelleher, A. Etheridge, and N. H. Barton, “Coalescent simulation in continuous
space: Algorithms for large neighbourhood size,” Theoretical Population Biology,
vol. 95. Academic Press, pp. 13–23, 2014.'
ista: 'Kelleher J, Etheridge A, Barton NH. 2014. Coalescent simulation in continuous
space: Algorithms for large neighbourhood size. Theoretical Population Biology.
95, 13–23.'
mla: 'Kelleher, Jerome, et al. “Coalescent Simulation in Continuous Space: Algorithms
for Large Neighbourhood Size.” Theoretical Population Biology, vol. 95,
Academic Press, 2014, pp. 13–23, doi:10.1016/j.tpb.2014.05.001.'
short: J. Kelleher, A. Etheridge, N.H. Barton, Theoretical Population Biology 95
(2014) 13–23.
date_created: 2018-12-11T11:56:06Z
date_published: 2014-08-01T00:00:00Z
date_updated: 2025-09-29T11:39:51Z
day: '01'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1016/j.tpb.2014.05.001
ec_funded: 1
external_id:
isi:
- '000339460300002'
file:
- access_level: open_access
checksum: 979d7a8034e9df198f068f0d251f31bd
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:10:49Z
date_updated: 2020-07-14T12:45:31Z
file_id: '4839'
file_name: IST-2015-391-v1+1_1-s2.0-S0040580914000355-main.pdf
file_size: 569005
relation: main_file
file_date_updated: 2020-07-14T12:45:31Z
has_accepted_license: '1'
intvolume: ' 95'
isi: 1
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
page: 13 - 23
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: '4816'
pubrep_id: '391'
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Coalescent simulation in continuous space: Algorithms for large neighbourhood
size'
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 95
year: '2014'
...
---
_id: '2169'
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: 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: Barton NH, Novak S, Paixao T. Diverse forms of selection in evolution and computer
science. PNAS. 2014;111(29):10398-10399. doi:10.1073/pnas.1410107111
apa: Barton, N. H., Novak, S., & Paixao, T. (2014). Diverse forms of selection
in evolution and computer science. PNAS. National Academy of Sciences.
https://doi.org/10.1073/pnas.1410107111
chicago: Barton, Nicholas H, Sebastian Novak, and Tiago Paixao. “Diverse Forms of
Selection in Evolution and Computer Science.” PNAS. National Academy of
Sciences, 2014. https://doi.org/10.1073/pnas.1410107111.
ieee: N. H. Barton, S. Novak, and T. Paixao, “Diverse forms of selection in evolution
and computer science,” PNAS, vol. 111, no. 29. National Academy of Sciences,
pp. 10398–10399, 2014.
ista: Barton NH, Novak S, Paixao T. 2014. Diverse forms of selection in evolution
and computer science. PNAS. 111(29), 10398–10399.
mla: Barton, Nicholas H., et al. “Diverse Forms of Selection in Evolution and Computer
Science.” PNAS, vol. 111, no. 29, National Academy of Sciences, 2014, pp.
10398–99, doi:10.1073/pnas.1410107111.
short: N.H. Barton, S. Novak, T. Paixao, PNAS 111 (2014) 10398–10399.
corr_author: '1'
date_created: 2018-12-11T11:56:07Z
date_published: 2014-07-22T00:00:00Z
date_updated: 2025-09-29T11:39:19Z
day: '22'
department:
- _id: NiBa
doi: 10.1073/pnas.1410107111
external_id:
isi:
- '000339310700017'
intvolume: ' 111'
isi: 1
issue: '29'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4115508/
month: '07'
oa: 1
oa_version: Submitted Version
page: 10398 - 10399
publication: PNAS
publication_status: published
publisher: National Academy of Sciences
publist_id: '4815'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Diverse forms of selection in evolution and computer science
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 111
year: '2014'
...
---
_id: '2170'
abstract:
- lang: eng
text: ' Short-read sequencing technologies have in principle made it feasible to
draw detailed inferences about the recent history of any organism. In practice,
however, this remains challenging due to the difficulty of genome assembly in
most organisms and the lack of statistical methods powerful enough to discriminate
between recent, nonequilibrium histories. We address both the assembly and inference
challenges. We develop a bioinformatic pipeline for generating outgroup-rooted
alignments of orthologous sequence blocks from de novo low-coverage short-read
data for a small number of genomes, and show how such sequence blocks can be used
to fit explicit models of population divergence and admixture in a likelihood
framework. To illustrate our approach, we reconstruct the Pleistocene history
of an oak-feeding insect (the oak gallwasp Biorhiza pallida), which, in common
with many other taxa, was restricted during Pleistocene ice ages to a longitudinal
series of southern refugia spanning the Western Palaearctic. Our analysis of sequence
blocks sampled from a single genome from each of three major glacial refugia reveals
support for an unexpected history dominated by recent admixture. Despite the fact
that 80% of the genome is affected by admixture during the last glacial cycle,
we are able to infer the deeper divergence history of these populations. These
inferences are robust to variation in block length, mutation model and the sampling
location of individual genomes within refugia. This combination of de novo assembly
and numerical likelihood calculation provides a powerful framework for estimating
recent population history that can be applied to any organism without the need
for prior genetic resources.'
acknowledgement: This work was funded by NERC grants to G Stone, J Nicholls, K Lohse
and N Barton (NE/J010499, NBAF375, NE/E014453/1 and NER/B/S2003/00856).
article_processing_charge: No
author:
- first_name: Jack
full_name: Hearn, Jack
last_name: Hearn
- first_name: Graham
full_name: Stone, Graham
last_name: Stone
- first_name: Lynsey
full_name: Bunnefeld, Lynsey
last_name: Bunnefeld
- first_name: James
full_name: Nicholls, James
last_name: Nicholls
- 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: Konrad
full_name: Lohse, Konrad
last_name: Lohse
citation:
ama: Hearn J, Stone G, Bunnefeld L, Nicholls J, Barton NH, Lohse K. Likelihood-based
inference of population history from low-coverage de novo genome assemblies. Molecular
Ecology. 2014;23(1):198-211. doi:10.1111/mec.12578
apa: Hearn, J., Stone, G., Bunnefeld, L., Nicholls, J., Barton, N. H., & Lohse,
K. (2014). Likelihood-based inference of population history from low-coverage
de novo genome assemblies. Molecular Ecology. Wiley-Blackwell. https://doi.org/10.1111/mec.12578
chicago: Hearn, Jack, Graham Stone, Lynsey Bunnefeld, James Nicholls, Nicholas H
Barton, and Konrad Lohse. “Likelihood-Based Inference of Population History from
Low-Coverage de Novo Genome Assemblies.” Molecular Ecology. Wiley-Blackwell,
2014. https://doi.org/10.1111/mec.12578.
ieee: J. Hearn, G. Stone, L. Bunnefeld, J. Nicholls, N. H. Barton, and K. Lohse,
“Likelihood-based inference of population history from low-coverage de novo genome
assemblies,” Molecular Ecology, vol. 23, no. 1. Wiley-Blackwell, pp. 198–211,
2014.
ista: Hearn J, Stone G, Bunnefeld L, Nicholls J, Barton NH, Lohse K. 2014. Likelihood-based
inference of population history from low-coverage de novo genome assemblies. Molecular
Ecology. 23(1), 198–211.
mla: Hearn, Jack, et al. “Likelihood-Based Inference of Population History from
Low-Coverage de Novo Genome Assemblies.” Molecular Ecology, vol. 23, no.
1, Wiley-Blackwell, 2014, pp. 198–211, doi:10.1111/mec.12578.
short: J. Hearn, G. Stone, L. Bunnefeld, J. Nicholls, N.H. Barton, K. Lohse, Molecular
Ecology 23 (2014) 198–211.
date_created: 2018-12-11T11:56:07Z
date_published: 2014-01-01T00:00:00Z
date_updated: 2025-09-29T11:38:51Z
day: '01'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1111/mec.12578
external_id:
isi:
- '000330950900017'
file:
- access_level: open_access
checksum: 4de1ab255976a8ae77eb0e55ad62ecc9
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:07:52Z
date_updated: 2020-07-14T12:45:31Z
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file_name: IST-2016-559-v1+1_Hearn_et_al.pdf
file_size: 807444
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checksum: 01a8073e071c088500425f910b0f1f71
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:07:53Z
date_updated: 2020-07-14T12:45:31Z
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file_size: 1518088
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file_date_updated: 2020-07-14T12:45:31Z
has_accepted_license: '1'
intvolume: ' 23'
isi: 1
issue: '1'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Submitted Version
page: 198 - 211
publication: Molecular Ecology
publication_status: published
publisher: Wiley-Blackwell
publist_id: '4814'
pubrep_id: '559'
quality_controlled: '1'
related_material:
record:
- id: '9754'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Likelihood-based inference of population history from low-coverage de novo
genome assemblies
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 23
year: '2014'
...
---
_id: '2174'
abstract:
- lang: eng
text: 'When polygenic traits are under stabilizing selection, many different combinations
of alleles allow close adaptation to the optimum. If alleles have equal effects,
all combinations that result in the same deviation from the optimum are equivalent.
Furthermore, the genetic variance that is maintained by mutation-selection balance
is 2μ/S per locus, where μ is the mutation rate and S the strength of stabilizing
selection. In reality, alleles vary in their effects, making the fitness landscape
asymmetric and complicating analysis of the equilibria. We show that that the
resulting genetic variance depends on the fraction of alleles near fixation, which
contribute by 2μ/S, and on the total mutational effects of alleles that are at
intermediate frequency. The inpplayfi between stabilizing selection and mutation
leads to a sharp transition: alleles with effects smaller than a threshold value
of 2 remain polymorphic, whereas those with larger effects are fixed. The genetic
load in equilibrium is less than for traits of equal effects, and the fitness
equilibria are more similar. We find p the optimum is displaced, alleles with
effects close to the threshold value sweep first, and their rate of increase is
bounded by Long-term response leads in general to well-adapted traits, unlike
the case of equal effects that often end up at a suboptimal fitness peak. However,
the particular peaks to which the populations converge are extremely sensitive
to the initial states and to the speed of the shift of the optimum trait value.'
article_processing_charge: No
arxiv: 1
author:
- first_name: Harold
full_name: De Vladar, Harold
last_name: De Vladar
- 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: De Vladar H, Barton NH. Stability and response of polygenic traits to stabilizing
selection and mutation. Genetics. 2014;197(2):749-767. doi:10.1534/genetics.113.159111
apa: De Vladar, H., & Barton, N. H. (2014). Stability and response of polygenic
traits to stabilizing selection and mutation. Genetics. Genetics Society
of America. https://doi.org/10.1534/genetics.113.159111
chicago: De Vladar, Harold, and Nicholas H Barton. “Stability and Response of Polygenic
Traits to Stabilizing Selection and Mutation.” Genetics. Genetics Society
of America, 2014. https://doi.org/10.1534/genetics.113.159111.
ieee: H. De Vladar and N. H. Barton, “Stability and response of polygenic traits
to stabilizing selection and mutation,” Genetics, vol. 197, no. 2. Genetics
Society of America, pp. 749–767, 2014.
ista: De Vladar H, Barton NH. 2014. Stability and response of polygenic traits to
stabilizing selection and mutation. Genetics. 197(2), 749–767.
mla: De Vladar, Harold, and Nicholas H. Barton. “Stability and Response of Polygenic
Traits to Stabilizing Selection and Mutation.” Genetics, vol. 197, no.
2, Genetics Society of America, 2014, pp. 749–67, doi:10.1534/genetics.113.159111.
short: H. De Vladar, N.H. Barton, Genetics 197 (2014) 749–767.
corr_author: '1'
date_created: 2018-12-11T11:56:08Z
date_published: 2014-06-01T00:00:00Z
date_updated: 2025-09-29T11:37:14Z
day: '01'
department:
- _id: NiBa
doi: 10.1534/genetics.113.159111
ec_funded: 1
external_id:
arxiv:
- '1404.1017'
isi:
- '000338697000027'
intvolume: ' 197'
isi: 1
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1404.1017
month: '06'
oa: 1
oa_version: Submitted Version
page: 749 - 767
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: '4809'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Stability and response of polygenic traits to stabilizing selection and mutation
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 197
year: '2014'
...
---
_id: '2252'
abstract:
- lang: eng
text: The pattern of inheritance and mechanism of sex determination can have important
evolutionary consequences. We studied probabilistic sex determination in the ciliate
Tetrahymena thermophila, which was previously shown to cause evolution of skewed
sex ratios. We find that the genetic background alters the sex determination patterns
of mat alleles in heterozygotes and that allelic interaction can differentially
influence the expression probability of the 7 sexes. We quantify the dominance
relationships between several mat alleles and find that A-type alleles, which
specify sex I, are indeed recessive to B-type alleles, which are unable to specify
that sex. Our results provide additional support for the presence of modifier
loci and raise implications for the dynamics of sex ratios in populations of T.
thermophila.
article_processing_charge: No
author:
- first_name: Sujal
full_name: Phadke, Sujal
last_name: Phadke
- first_name: Tiago
full_name: Paixao, Tiago
id: 2C5658E6-F248-11E8-B48F-1D18A9856A87
last_name: Paixao
orcid: 0000-0003-2361-3953
- first_name: Tuan
full_name: Pham, Tuan
last_name: Pham
- first_name: Stephanie
full_name: Pham, Stephanie
last_name: Pham
- first_name: Rebecca
full_name: Zufall, Rebecca
last_name: Zufall
citation:
ama: Phadke S, Paixao T, Pham T, Pham S, Zufall R. Genetic background alters dominance
relationships between mat alleles in the ciliate Tetrahymena Thermophila. Journal
of Heredity. 2014;105(1):130-135. doi:10.1093/jhered/est063
apa: Phadke, S., Paixao, T., Pham, T., Pham, S., & Zufall, R. (2014). Genetic
background alters dominance relationships between mat alleles in the ciliate Tetrahymena
Thermophila. Journal of Heredity. Oxford University Press. https://doi.org/10.1093/jhered/est063
chicago: Phadke, Sujal, Tiago Paixao, Tuan Pham, Stephanie Pham, and Rebecca Zufall.
“Genetic Background Alters Dominance Relationships between Mat Alleles in the
Ciliate Tetrahymena Thermophila.” Journal of Heredity. Oxford University
Press, 2014. https://doi.org/10.1093/jhered/est063.
ieee: S. Phadke, T. Paixao, T. Pham, S. Pham, and R. Zufall, “Genetic background
alters dominance relationships between mat alleles in the ciliate Tetrahymena
Thermophila,” Journal of Heredity, vol. 105, no. 1. Oxford University Press,
pp. 130–135, 2014.
ista: Phadke S, Paixao T, Pham T, Pham S, Zufall R. 2014. Genetic background alters
dominance relationships between mat alleles in the ciliate Tetrahymena Thermophila.
Journal of Heredity. 105(1), 130–135.
mla: Phadke, Sujal, et al. “Genetic Background Alters Dominance Relationships between
Mat Alleles in the Ciliate Tetrahymena Thermophila.” Journal of Heredity,
vol. 105, no. 1, Oxford University Press, 2014, pp. 130–35, doi:10.1093/jhered/est063.
short: S. Phadke, T. Paixao, T. Pham, S. Pham, R. Zufall, Journal of Heredity 105
(2014) 130–135.
corr_author: '1'
date_created: 2018-12-11T11:56:35Z
date_published: 2014-01-01T00:00:00Z
date_updated: 2025-09-29T11:16:03Z
day: '01'
department:
- _id: NiBa
doi: 10.1093/jhered/est063
external_id:
isi:
- '000328427800013'
intvolume: ' 105'
isi: 1
issue: '1'
language:
- iso: eng
month: '01'
oa_version: None
page: 130 - 135
publication: Journal of Heredity
publication_identifier:
issn:
- 0022-1503
publication_status: published
publisher: Oxford University Press
publist_id: '4695'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Genetic background alters dominance relationships between mat alleles in the
ciliate Tetrahymena Thermophila
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 105
year: '2014'
...
---
_id: '1932'
abstract:
- lang: eng
text: The existence of complex (multiple-step) genetic adaptations that are "irreducible"
(i.e., all partial combinations are less fit than the original genotype) is one
of the longest standing problems in evolutionary biology. In standard genetics
parlance, these adaptations require the crossing of a wide adaptive valley of
deleterious intermediate stages. Here, we demonstrate, using a simple model, that
evolution can cross wide valleys to produce "irreducibly complex" adaptations
by making use of previously cryptic mutations. When revealed by an evolutionary
capacitor, previously cryptic mutants have higher initial frequencies than do
new mutations, bringing them closer to a valley-crossing saddle in allele frequency
space. Moreover, simple combinatorics implies an enormous number of candidate
combinations exist within available cryptic genetic variation. We model the dynamics
of crossing of a wide adaptive valley after a capacitance event using both numerical
simulations and analytical approximations. Although individual valley crossing
events become less likely as valleys widen, by taking the combinatorics of genotype
space into account, we see that revealing cryptic variation can cause the frequent
evolution of complex adaptations.
acknowledgement: "Funded by National Institutes of Health. Grant Numbers: R01GM076041,
R01GM104040 \r\n\r\nSimons Foundation\r\n\r\n"
article_processing_charge: No
arxiv: 1
author:
- first_name: Meredith
full_name: Trotter, Meredith
last_name: Trotter
- first_name: Daniel
full_name: Weissman, Daniel
id: 2D0CE020-F248-11E8-B48F-1D18A9856A87
last_name: Weissman
- first_name: Grant
full_name: Peterson, Grant
last_name: Peterson
- first_name: Kayla
full_name: Peck, Kayla
last_name: Peck
- first_name: Joanna
full_name: Masel, Joanna
last_name: Masel
citation:
ama: Trotter M, Weissman D, Peterson G, Peck K, Masel J. Cryptic genetic variation
can make "irreducible complexity" a common mode of adaptation
in sexual populations. Evolution. 2014;68(12):3357-3367. doi:10.1111/evo.12517
apa: Trotter, M., Weissman, D., Peterson, G., Peck, K., & Masel, J. (2014).
Cryptic genetic variation can make "irreducible complexity"
a common mode of adaptation in sexual populations. Evolution. Wiley-Blackwell.
https://doi.org/10.1111/evo.12517
chicago: Trotter, Meredith, Daniel Weissman, Grant Peterson, Kayla Peck, and Joanna
Masel. “Cryptic Genetic Variation Can Make "Irreducible Complexity"
a Common Mode of Adaptation in Sexual Populations.” Evolution. Wiley-Blackwell,
2014. https://doi.org/10.1111/evo.12517.
ieee: M. Trotter, D. Weissman, G. Peterson, K. Peck, and J. Masel, “Cryptic genetic
variation can make "irreducible complexity" a common mode of
adaptation in sexual populations,” Evolution, vol. 68, no. 12. Wiley-Blackwell,
pp. 3357–3367, 2014.
ista: Trotter M, Weissman D, Peterson G, Peck K, Masel J. 2014. Cryptic genetic
variation can make "irreducible complexity" a common mode of
adaptation in sexual populations. Evolution. 68(12), 3357–3367.
mla: Trotter, Meredith, et al. “Cryptic Genetic Variation Can Make "Irreducible
Complexity" a Common Mode of Adaptation in Sexual Populations.” Evolution,
vol. 68, no. 12, Wiley-Blackwell, 2014, pp. 3357–67, doi:10.1111/evo.12517.
short: M. Trotter, D. Weissman, G. Peterson, K. Peck, J. Masel, Evolution 68 (2014)
3357–3367.
date_created: 2018-12-11T11:54:47Z
date_published: 2014-12-01T00:00:00Z
date_updated: 2025-09-29T12:10:43Z
day: '01'
department:
- _id: NiBa
doi: 10.1111/evo.12517
ec_funded: 1
external_id:
arxiv:
- '1310.6077'
isi:
- '000346075600001'
intvolume: ' 68'
isi: 1
issue: '12'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1310.6077
month: '12'
oa: 1
oa_version: Submitted Version
page: 3357 - 3367
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_status: published
publisher: Wiley-Blackwell
publist_id: '5162'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Cryptic genetic variation can make "irreducible complexity" a common
mode of adaptation in sexual populations
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 68
year: '2014'
...
---
_id: '1936'
abstract:
- lang: eng
text: 'The social intelligence hypothesis states that the need to cope with complexities
of social life has driven the evolution of advanced cognitive abilities. It is
usually invoked in the context of challenges arising from complex intragroup structures,
hierarchies, and alliances. However, a fundamental aspect of group living remains
largely unexplored as a driving force in cognitive evolution: the competition
between individuals searching for resources (producers) and conspecifics that
parasitize their findings (scroungers). In populations of social foragers, abilities
that enable scroungers to steal by outsmarting producers, and those allowing producers
to prevent theft by outsmarting scroungers, are likely to be beneficial and may
fuel a cognitive arms race. Using analytical theory and agent-based simulations,
we present a general model for such a race that is driven by the producer-scrounger
game and show that the race''s plausibility is dramatically affected by the nature
of the evolving abilities. If scrounging and scrounging avoidance rely on separate,
strategy-specific cognitive abilities, arms races are short-lived and have a limited
effect on cognition. However, general cognitive abilities that facilitate both
scrounging and scrounging avoidance undergo stable, long-lasting arms races. Thus,
ubiquitous foraging interactions may lead to the evolution of general cognitive
abilities in social animals, without the requirement of complex intragroup structures.'
article_processing_charge: No
author:
- first_name: Michal
full_name: Arbilly, Michal
last_name: Arbilly
- first_name: Daniel
full_name: Weissman, Daniel
id: 2D0CE020-F248-11E8-B48F-1D18A9856A87
last_name: Weissman
- first_name: Marcus
full_name: Feldman, Marcus
last_name: Feldman
- first_name: Uri
full_name: Grodzinski, Uri
last_name: Grodzinski
citation:
ama: Arbilly M, Weissman D, Feldman M, Grodzinski U. An arms race between producers
and scroungers can drive the evolution of social cognition. Behavioral Ecology.
2014;25(3):487-495. doi:10.1093/beheco/aru002
apa: Arbilly, M., Weissman, D., Feldman, M., & Grodzinski, U. (2014). An arms
race between producers and scroungers can drive the evolution of social cognition.
Behavioral Ecology. Oxford University Press. https://doi.org/10.1093/beheco/aru002
chicago: Arbilly, Michal, Daniel Weissman, Marcus Feldman, and Uri Grodzinski. “An
Arms Race between Producers and Scroungers Can Drive the Evolution of Social Cognition.”
Behavioral Ecology. Oxford University Press, 2014. https://doi.org/10.1093/beheco/aru002.
ieee: M. Arbilly, D. Weissman, M. Feldman, and U. Grodzinski, “An arms race between
producers and scroungers can drive the evolution of social cognition,” Behavioral
Ecology, vol. 25, no. 3. Oxford University Press, pp. 487–495, 2014.
ista: Arbilly M, Weissman D, Feldman M, Grodzinski U. 2014. An arms race between
producers and scroungers can drive the evolution of social cognition. Behavioral
Ecology. 25(3), 487–495.
mla: Arbilly, Michal, et al. “An Arms Race between Producers and Scroungers Can
Drive the Evolution of Social Cognition.” Behavioral Ecology, vol. 25,
no. 3, Oxford University Press, 2014, pp. 487–95, doi:10.1093/beheco/aru002.
short: M. Arbilly, D. Weissman, M. Feldman, U. Grodzinski, Behavioral Ecology 25
(2014) 487–495.
date_created: 2018-12-11T11:54:48Z
date_published: 2014-02-13T00:00:00Z
date_updated: 2025-09-29T12:07:50Z
day: '13'
department:
- _id: NiBa
doi: 10.1093/beheco/aru002
ec_funded: 1
external_id:
isi:
- '000336486100012'
intvolume: ' 25'
isi: 1
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4014306/
month: '02'
oa: 1
oa_version: Submitted Version
page: 487 - 495
project:
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
publication: Behavioral Ecology
publication_status: published
publisher: Oxford University Press
publist_id: '5157'
quality_controlled: '1'
scopus_import: '1'
status: public
title: An arms race between producers and scroungers can drive the evolution of social
cognition
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 25
year: '2014'
...
---
_id: '2023'
abstract:
- lang: eng
text: 'Understanding the evolution of dispersal is essential for understanding and
predicting the dynamics of natural populations. Two main factors are known to
influence dispersal evolution: spatio-temporal variation in the environment and
relatedness between individuals. However, the relation between these factors is
still poorly understood, and they are usually treated separately. In this article,
I present a theoretical framework that contains and connects effects of both environmental
variation and relatedness, and reproduces and extends their known features. Spatial
habitat variation selects for balanced dispersal strategies, whereby the population
is kept at an ideal free distribution. Within this class of dispersal strategies,
I explain how increased dispersal is promoted by perturbations to the dispersal
type frequencies. An explicit formula shows the magnitude of the selective advantage
of increased dispersal in terms of the spatial variability in the frequencies
of the different dispersal strategies present. These variances are capable of
capturing various sources of stochasticity and hence establish a common scale
for their effects on the evolution of dispersal. The results furthermore indicate
an alternative approach to identifying effects of relatedness on dispersal evolution.'
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. Habitat heterogeneities versus spatial type frequency variances as
driving forces of dispersal evolution. Ecology and Evolution. 2014;4(24):4589-4597.
doi:10.1002/ece3.1289
apa: Novak, S. (2014). Habitat heterogeneities versus spatial type frequency variances
as driving forces of dispersal evolution. Ecology and Evolution. Wiley-Blackwell.
https://doi.org/10.1002/ece3.1289
chicago: Novak, Sebastian. “Habitat Heterogeneities versus Spatial Type Frequency
Variances as Driving Forces of Dispersal Evolution.” Ecology and Evolution.
Wiley-Blackwell, 2014. https://doi.org/10.1002/ece3.1289.
ieee: S. Novak, “Habitat heterogeneities versus spatial type frequency variances
as driving forces of dispersal evolution,” Ecology and Evolution, vol.
4, no. 24. Wiley-Blackwell, pp. 4589–4597, 2014.
ista: Novak S. 2014. Habitat heterogeneities versus spatial type frequency variances
as driving forces of dispersal evolution. Ecology and Evolution. 4(24), 4589–4597.
mla: Novak, Sebastian. “Habitat Heterogeneities versus Spatial Type Frequency Variances
as Driving Forces of Dispersal Evolution.” Ecology and Evolution, vol.
4, no. 24, Wiley-Blackwell, 2014, pp. 4589–97, doi:10.1002/ece3.1289.
short: S. Novak, Ecology and Evolution 4 (2014) 4589–4597.
corr_author: '1'
date_created: 2018-12-11T11:55:16Z
date_published: 2014-11-27T00:00:00Z
date_updated: 2026-04-09T14:25:34Z
day: '27'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1002/ece3.1289
ec_funded: 1
external_id:
isi:
- '000346736200003'
file:
- access_level: open_access
checksum: 9ab43db1b0fede7bfe560ed77e177b76
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:12:28Z
date_updated: 2020-07-14T12:45:25Z
file_id: '4946'
file_name: IST-2016-462-v1+1_Novak-2014-Ecology_and_Evolution.pdf
file_size: 118813
relation: main_file
file_date_updated: 2020-07-14T12:45:25Z
has_accepted_license: '1'
intvolume: ' 4'
isi: 1
issue: '24'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
page: 4589 - 4597
project:
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
publication: Ecology and Evolution
publication_status: published
publisher: Wiley-Blackwell
publist_id: '5049'
pubrep_id: '462'
quality_controlled: '1'
related_material:
record:
- id: '1125'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Habitat heterogeneities versus spatial type frequency variances as driving
forces of dispersal 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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 4
year: '2014'
...
---
_id: '1896'
abstract:
- lang: eng
text: 'Biopolymer length regulation is a complex process that involves a large number
of biological, chemical, and physical subprocesses acting simultaneously across
multiple spatial and temporal scales. An illustrative example important for genomic
stability is the length regulation of telomeres - nucleoprotein structures at
the ends of linear chromosomes consisting of tandemly repeated DNA sequences and
a specialized set of proteins. Maintenance of telomeres is often facilitated by
the enzyme telomerase but, particularly in telomerase-free systems, the maintenance
of chromosomal termini depends on alternative lengthening of telomeres (ALT) mechanisms
mediated by recombination. Various linear and circular DNA structures were identified
to participate in ALT, however, dynamics of the whole process is still poorly
understood. We propose a chemical kinetics model of ALT with kinetic rates systematically
derived from the biophysics of DNA diffusion and looping. The reaction system
is reduced to a coagulation-fragmentation system by quasi-steady-state approximation.
The detailed treatment of kinetic rates yields explicit formulas for expected
size distributions of telomeres that demonstrate the key role played by the J
factor, a quantitative measure of bending of polymers. The results are in agreement
with experimental data and point out interesting phenomena: an appearance of very
long telomeric circles if the total telomere density exceeds a critical value
(excess mass) and a nonlinear response of the telomere size distributions to the
amount of telomeric DNA in the system. The results can be of general importance
for understanding dynamics of telomeres in telomerase-independent systems as this
mode of telomere maintenance is similar to the situation in tumor cells lacking
telomerase activity. Furthermore, due to its universality, the model may also
serve as a prototype of an interaction between linear and circular DNA structures
in various settings.'
acknowledgement: The work was supported by the VEGA Grant No. 1/0459/13 (R.K. and
K.B.).
article_number: '032701'
article_processing_charge: No
arxiv: 1
author:
- first_name: Richard
full_name: Kollár, Richard
last_name: Kollár
- 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: Jozef
full_name: Nosek, Jozef
last_name: Nosek
- first_name: Ľubomír
full_name: Tomáška, Ľubomír
last_name: Tomáška
citation:
ama: Kollár R, Bodova K, Nosek J, Tomáška Ľ. Mathematical model of alternative mechanism
of telomere length maintenance. Physical Review E Statistical Nonlinear and
Soft Matter Physics. 2014;89(3). doi:10.1103/PhysRevE.89.032701
apa: Kollár, R., Bodova, K., Nosek, J., & Tomáška, Ľ. (2014). Mathematical model
of alternative mechanism of telomere length maintenance. Physical Review E
Statistical Nonlinear and Soft Matter Physics. American Institute of Physics.
https://doi.org/10.1103/PhysRevE.89.032701
chicago: Kollár, Richard, Katarina Bodova, Jozef Nosek, and Ľubomír Tomáška. “Mathematical
Model of Alternative Mechanism of Telomere Length Maintenance.” Physical Review
E Statistical Nonlinear and Soft Matter Physics. American Institute of Physics,
2014. https://doi.org/10.1103/PhysRevE.89.032701.
ieee: R. Kollár, K. Bodova, J. Nosek, and Ľ. Tomáška, “Mathematical model of alternative
mechanism of telomere length maintenance,” Physical Review E Statistical Nonlinear
and Soft Matter Physics, vol. 89, no. 3. American Institute of Physics, 2014.
ista: Kollár R, Bodova K, Nosek J, Tomáška Ľ. 2014. Mathematical model of alternative
mechanism of telomere length maintenance. Physical Review E Statistical Nonlinear
and Soft Matter Physics. 89(3), 032701.
mla: Kollár, Richard, et al. “Mathematical Model of Alternative Mechanism of Telomere
Length Maintenance.” Physical Review E Statistical Nonlinear and Soft Matter
Physics, vol. 89, no. 3, 032701, American Institute of Physics, 2014, doi:10.1103/PhysRevE.89.032701.
short: R. Kollár, K. Bodova, J. Nosek, Ľ. Tomáška, Physical Review E Statistical
Nonlinear and Soft Matter Physics 89 (2014).
date_created: 2018-12-11T11:54:35Z
date_published: 2014-03-04T00:00:00Z
date_updated: 2025-09-29T13:03:34Z
day: '04'
department:
- _id: NiBa
- _id: GaTk
doi: 10.1103/PhysRevE.89.032701
external_id:
arxiv:
- '1402.0430'
isi:
- '000332274100002'
intvolume: ' 89'
isi: 1
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1402.0430
month: '03'
oa: 1
oa_version: Submitted Version
publication: Physical Review E Statistical Nonlinear and Soft Matter Physics
publication_status: published
publisher: American Institute of Physics
publist_id: '5198'
scopus_import: '1'
status: public
title: Mathematical model of alternative mechanism of telomere length maintenance
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 89
year: '2014'
...
---
_id: '1908'
abstract:
- lang: eng
text: In large populations, multiple beneficial mutations may be simultaneously
spreading. In asexual populations, these mutations must either arise on the same
background or compete against each other. In sexual populations, recombination
can bring together beneficial alleles from different backgrounds, but tightly
linked alleles may still greatly interfere with each other. We show for well-mixed
populations that when this interference is strong, the genome can be seen as consisting
of many effectively asexual stretches linked together. The rate at which beneficial
alleles fix is thus roughly proportional to the rate of recombination and depends
only logarithmically on the mutation supply and the strength of selection. Our
scaling arguments also allow us to predict, with reasonable accuracy, the fitness
distribution of fixed mutations when the mutational effect sizes are broad. We
focus on the regime in which crossovers occur more frequently than beneficial
mutations, as is likely to be the case for many natural populations.
article_processing_charge: No
arxiv: 1
author:
- first_name: Daniel
full_name: Weissman, Daniel
id: 2D0CE020-F248-11E8-B48F-1D18A9856A87
last_name: Weissman
- first_name: Oskar
full_name: Hallatschek, Oskar
last_name: Hallatschek
citation:
ama: Weissman D, Hallatschek O. The rate of adaptation in large sexual populations
with linear chromosomes. Genetics. 2014;196(4):1167-1183. doi:10.1534/genetics.113.160705
apa: Weissman, D., & Hallatschek, O. (2014). The rate of adaptation in large
sexual populations with linear chromosomes. Genetics. Genetics Society
of America. https://doi.org/10.1534/genetics.113.160705
chicago: Weissman, Daniel, and Oskar Hallatschek. “The Rate of Adaptation in Large
Sexual Populations with Linear Chromosomes.” Genetics. Genetics Society
of America, 2014. https://doi.org/10.1534/genetics.113.160705.
ieee: D. Weissman and O. Hallatschek, “The rate of adaptation in large sexual populations
with linear chromosomes,” Genetics, vol. 196, no. 4. Genetics Society of
America, pp. 1167–1183, 2014.
ista: Weissman D, Hallatschek O. 2014. The rate of adaptation in large sexual populations
with linear chromosomes. Genetics. 196(4), 1167–1183.
mla: Weissman, Daniel, and Oskar Hallatschek. “The Rate of Adaptation in Large Sexual
Populations with Linear Chromosomes.” Genetics, vol. 196, no. 4, Genetics
Society of America, 2014, pp. 1167–83, doi:10.1534/genetics.113.160705.
short: D. Weissman, O. Hallatschek, Genetics 196 (2014) 1167–1183.
corr_author: '1'
date_created: 2018-12-11T11:54:39Z
date_published: 2014-04-01T00:00:00Z
date_updated: 2025-09-29T12:27:03Z
day: '01'
department:
- _id: NiBa
doi: 10.1534/genetics.113.160705
ec_funded: 1
external_id:
arxiv:
- '1307.0737'
isi:
- '000334179300022'
intvolume: ' 196'
isi: 1
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1307.0737
month: '04'
oa: 1
oa_version: Submitted Version
page: 1167 - 1183
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: '5187'
quality_controlled: '1'
scopus_import: '1'
status: public
title: The rate of adaptation in large sexual populations with linear chromosomes
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 196
year: '2014'
...
---
_id: '1909'
abstract:
- lang: eng
text: 'Summary: Phenotypes are often environmentally dependent, which requires organisms
to track environmental change. The challenge for organisms is to construct phenotypes
using the most accurate environmental cue. Here, we use a quantitative genetic
model of adaptation by additive genetic variance, within- and transgenerational
plasticity via linear reaction norms and indirect genetic effects respectively.
We show how the relative influence on the eventual phenotype of these components
depends on the predictability of environmental change (fast or slow, sinusoidal
or stochastic) and the developmental lag τ between when the environment is perceived
and when selection acts. We then decompose expected mean fitness into three components
(variance load, adaptation and fluctuation load) to study the fitness costs of
within- and transgenerational plasticity. A strongly negative maternal effect
coefficient m minimizes the variance load, but a strongly positive m minimises
the fluctuation load. The adaptation term is maximized closer to zero, with positive
or negative m preferred under different environmental scenarios. Phenotypic plasticity
is higher when τ is shorter and when the environment changes frequently between
seasonal extremes. Expected mean population fitness is highest away from highest
observed levels of phenotypic plasticity. Within- and transgenerational plasticity
act in concert to deliver well-adapted phenotypes, which emphasizes the need to
study both simultaneously when investigating phenotypic evolution.'
acknowledgement: 'Engineering and Physical Sciences Research Council. Grant Number:
EP/H031928/1'
article_processing_charge: No
author:
- first_name: Thomas
full_name: Ezard, Thomas
last_name: Ezard
- first_name: Roshan
full_name: Prizak, Roshan
id: 4456104E-F248-11E8-B48F-1D18A9856A87
last_name: Prizak
- first_name: Rebecca
full_name: Hoyle, Rebecca
last_name: Hoyle
citation:
ama: Ezard T, Prizak R, Hoyle R. The fitness costs of adaptation via phenotypic
plasticity and maternal effects. Functional Ecology. 2014;28(3):693-701.
doi:10.1111/1365-2435.12207
apa: Ezard, T., Prizak, R., & Hoyle, R. (2014). The fitness costs of adaptation
via phenotypic plasticity and maternal effects. Functional Ecology. Wiley-Blackwell.
https://doi.org/10.1111/1365-2435.12207
chicago: Ezard, Thomas, Roshan Prizak, and Rebecca Hoyle. “The Fitness Costs of
Adaptation via Phenotypic Plasticity and Maternal Effects.” Functional Ecology.
Wiley-Blackwell, 2014. https://doi.org/10.1111/1365-2435.12207.
ieee: T. Ezard, R. Prizak, and R. Hoyle, “The fitness costs of adaptation via phenotypic
plasticity and maternal effects,” Functional Ecology, vol. 28, no. 3. Wiley-Blackwell,
pp. 693–701, 2014.
ista: Ezard T, Prizak R, Hoyle R. 2014. The fitness costs of adaptation via phenotypic
plasticity and maternal effects. Functional Ecology. 28(3), 693–701.
mla: Ezard, Thomas, et al. “The Fitness Costs of Adaptation via Phenotypic Plasticity
and Maternal Effects.” Functional Ecology, vol. 28, no. 3, Wiley-Blackwell,
2014, pp. 693–701, doi:10.1111/1365-2435.12207.
short: T. Ezard, R. Prizak, R. Hoyle, Functional Ecology 28 (2014) 693–701.
date_created: 2018-12-11T11:54:40Z
date_published: 2014-06-01T00:00:00Z
date_updated: 2025-09-29T12:26:34Z
day: '01'
ddc:
- '570'
department:
- _id: NiBa
- _id: GaTk
doi: 10.1111/1365-2435.12207
external_id:
isi:
- '000335954900016'
file:
- access_level: open_access
checksum: 3cbe8623174709a8ceec2103246f8fe0
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:15:45Z
date_updated: 2020-07-14T12:45:20Z
file_id: '5167'
file_name: IST-2016-419-v1+1_Ezard_et_al-2014-Functional_Ecology.pdf
file_size: 536154
relation: main_file
file_date_updated: 2020-07-14T12:45:20Z
has_accepted_license: '1'
intvolume: ' 28'
isi: 1
issue: '3'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: 693 - 701
publication: Functional Ecology
publication_status: published
publisher: Wiley-Blackwell
publist_id: '5186'
pubrep_id: '419'
scopus_import: '1'
status: public
title: The fitness costs of adaptation via phenotypic plasticity and maternal 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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 28
year: '2014'
...
---
_id: '9754'
abstract:
- lang: eng
text: Short-read sequencing technologies have in principle made it feasible to draw
detailed inferences about the recent history of any organism. In practice, however,
this remains challenging due to the difficulty of genome assembly in most organisms
and the lack of statistical methods powerful enough to discriminate among recent,
non-equilibrium histories. We address both the assembly and inference challenges.
We develop a bioinformatic pipeline for generating outgroup-rooted alignments
of orthologous sequence blocks from de novo low-coverage short-read data for a
small number of genomes, and show how such sequence blocks can be used to fit
explicit models of population divergence and admixture in a likelihood framework.
To illustrate our approach, we reconstruct the Pleistocene history of an oak-feeding
insect (the oak gallwasp Biorhiza pallida) which, in common with many other taxa,
was restricted during Pleistocene ice ages to a longitudinal series of southern
refugia spanning theWestern Palaearctic. Our analysis of sequence blocks sampled
from a single genome from each of three major glacial refugia reveals support
for an unexpected history dominated by recent admixture. Despite the fact that
80% of the genome is affected by admixture during the last glacial cycle, we are
able to infer the deeper divergence history of these populations. These inferences
are robust to variation in block length, mutation model, and the sampling location
of individual genomes within refugia. This combination of de novo assembly and
numerical likelihood calculation provides a powerful framework for estimating
recent population history that can be applied to any organism without the need
for prior genetic resources.
article_processing_charge: No
author:
- first_name: Jack
full_name: Hearn, Jack
last_name: Hearn
- first_name: Graham
full_name: Stone, Graham
last_name: Stone
- 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: Konrad
full_name: Lohse, Konrad
last_name: Lohse
- first_name: Lynsey
full_name: Bunnefeld, Lynsey
last_name: Bunnefeld
citation:
ama: 'Hearn J, Stone G, Barton NH, Lohse K, Bunnefeld L. Data from: Likelihood-based
inference of population history from low coverage de novo genome assemblies. 2013.
doi:10.5061/dryad.r3r60'
apa: 'Hearn, J., Stone, G., Barton, N. H., Lohse, K., & Bunnefeld, L. (2013).
Data from: Likelihood-based inference of population history from low coverage
de novo genome assemblies. Dryad. https://doi.org/10.5061/dryad.r3r60'
chicago: 'Hearn, Jack, Graham Stone, Nicholas H Barton, Konrad Lohse, and Lynsey
Bunnefeld. “Data from: Likelihood-Based Inference of Population History from Low
Coverage de Novo Genome Assemblies.” Dryad, 2013. https://doi.org/10.5061/dryad.r3r60.'
ieee: 'J. Hearn, G. Stone, N. H. Barton, K. Lohse, and L. Bunnefeld, “Data from:
Likelihood-based inference of population history from low coverage de novo genome
assemblies.” Dryad, 2013.'
ista: 'Hearn J, Stone G, Barton NH, Lohse K, Bunnefeld L. 2013. Data from: Likelihood-based
inference of population history from low coverage de novo genome assemblies, Dryad,
10.5061/dryad.r3r60.'
mla: 'Hearn, Jack, et al. Data from: Likelihood-Based Inference of Population
History from Low Coverage de Novo Genome Assemblies. Dryad, 2013, doi:10.5061/dryad.r3r60.'
short: J. Hearn, G. Stone, N.H. Barton, K. Lohse, L. Bunnefeld, (2013).
date_created: 2021-07-30T08:31:22Z
date_published: 2013-10-01T00:00:00Z
date_updated: 2025-09-29T11:38:51Z
day: '01'
department:
- _id: NiBa
doi: 10.5061/dryad.r3r60
main_file_link:
- open_access: '1'
url: https://doi.org/10.5061/dryad.r3r60
month: '10'
oa: 1
oa_version: Published Version
publisher: Dryad
related_material:
record:
- id: '2170'
relation: used_in_publication
status: public
status: public
title: 'Data from: Likelihood-based inference of population history from low coverage
de novo genome assemblies'
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2013'
...