---
_id: '1336'
abstract:
- lang: eng
text: Evolutionary algorithms (EAs) form a popular optimisation paradigm inspired
by natural evolution. In recent years the field of evolutionary computation has
developed a rigorous analytical theory to analyse the runtimes of EAs on many
illustrative problems. Here we apply this theory to a simple model of natural
evolution. In the Strong Selection Weak Mutation (SSWM) evolutionary regime the
time between occurrences of new mutations is much longer than the time it takes
for a mutated genotype to take over the population. In this situation, the population
only contains copies of one genotype and evolution can be modelled as a stochastic
process evolving one genotype by means of mutation and selection between the resident
and the mutated genotype. The probability of accepting the mutated genotype then
depends on the change in fitness. We study this process, SSWM, from an algorithmic
perspective, quantifying its expected optimisation time for various parameters
and investigating differences to a similar evolutionary algorithm, the well-known
(1+1) EA. We show that SSWM can have a moderate advantage over the (1+1) EA at
crossing fitness valleys and study an example where SSWM outperforms the (1+1)
EA by taking advantage of information on the fitness gradient.
article_processing_charge: No
author:
- first_name: Tiago
full_name: Paixao, Tiago
id: 2C5658E6-F248-11E8-B48F-1D18A9856A87
last_name: Paixao
orcid: 0000-0003-2361-3953
- first_name: Jorge
full_name: Pérez Heredia, Jorge
last_name: Pérez Heredia
- first_name: Dirk
full_name: Sudholt, Dirk
last_name: Sudholt
- first_name: Barbora
full_name: Trubenova, Barbora
id: 42302D54-F248-11E8-B48F-1D18A9856A87
last_name: Trubenova
orcid: 0000-0002-6873-2967
citation:
ama: Paixao T, Pérez Heredia J, Sudholt D, Trubenova B. Towards a runtime comparison
of natural and artificial evolution. Algorithmica. 2017;78(2):681-713.
doi:10.1007/s00453-016-0212-1
apa: Paixao, T., Pérez Heredia, J., Sudholt, D., & Trubenova, B. (2017). Towards
a runtime comparison of natural and artificial evolution. Algorithmica.
Springer. https://doi.org/10.1007/s00453-016-0212-1
chicago: Paixao, Tiago, Jorge Pérez Heredia, Dirk Sudholt, and Barbora Trubenova.
“Towards a Runtime Comparison of Natural and Artificial Evolution.” Algorithmica.
Springer, 2017. https://doi.org/10.1007/s00453-016-0212-1.
ieee: T. Paixao, J. Pérez Heredia, D. Sudholt, and B. Trubenova, “Towards a runtime
comparison of natural and artificial evolution,” Algorithmica, vol. 78,
no. 2. Springer, pp. 681–713, 2017.
ista: Paixao T, Pérez Heredia J, Sudholt D, Trubenova B. 2017. Towards a runtime
comparison of natural and artificial evolution. Algorithmica. 78(2), 681–713.
mla: Paixao, Tiago, et al. “Towards a Runtime Comparison of Natural and Artificial
Evolution.” Algorithmica, vol. 78, no. 2, Springer, 2017, pp. 681–713,
doi:10.1007/s00453-016-0212-1.
short: T. Paixao, J. Pérez Heredia, D. Sudholt, B. Trubenova, Algorithmica 78 (2017)
681–713.
date_created: 2018-12-11T11:51:27Z
date_published: 2017-06-01T00:00:00Z
date_updated: 2023-09-20T11:14:42Z
day: '01'
ddc:
- '576'
department:
- _id: NiBa
- _id: CaGu
doi: 10.1007/s00453-016-0212-1
ec_funded: 1
external_id:
isi:
- '000400379500013'
file:
- access_level: open_access
checksum: 7873f665a0c598ac747c908f34cb14b9
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:10:19Z
date_updated: 2020-07-14T12:44:44Z
file_id: '4805'
file_name: IST-2016-658-v1+1_s00453-016-0212-1.pdf
file_size: 710206
relation: main_file
file_date_updated: 2020-07-14T12:44:44Z
has_accepted_license: '1'
intvolume: ' 78'
isi: 1
issue: '2'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: 681 - 713
project:
- _id: 25B1EC9E-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '618091'
name: Speed of Adaptation in Population Genetics and Evolutionary Computation
publication: Algorithmica
publication_identifier:
issn:
- '01784617'
publication_status: published
publisher: Springer
publist_id: '5931'
pubrep_id: '658'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Towards a runtime comparison of natural and artificial evolution
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 78
year: '2017'
...
---
_id: '1199'
abstract:
- lang: eng
text: Much of quantitative genetics is based on the ‘infinitesimal model’, under
which selection has a negligible effect on the genetic variance. This is typically
justified by assuming a very large number of loci with additive effects. However,
it applies even when genes interact, provided that the number of loci is large
enough that selection on each of them is weak relative to random drift. In the
long term, directional selection will change allele frequencies, but even then,
the effects of epistasis on the ultimate change in trait mean due to selection
may be modest. Stabilising selection can maintain many traits close to their optima,
even when the underlying alleles are weakly selected. However, the number of traits
that can be optimised is apparently limited to ~4Ne by the ‘drift load’, and this
is hard to reconcile with the apparent complexity of many organisms. Just as for
the mutation load, this limit can be evaded by a particular form of negative epistasis.
A more robust limit is set by the variance in reproductive success. This suggests
that selection accumulates information most efficiently in the infinitesimal regime,
when selection on individual alleles is weak, and comparable with random drift.
A review of evidence on selection strength suggests that although most variance
in fitness may be because of alleles with large Nes, substantial amounts of adaptation
may be because of alleles in the infinitesimal regime, in which epistasis has
modest effects.
article_processing_charge: No
author:
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: Barton NH. How does epistasis influence the response to selection? Heredity.
2017;118:96-109. doi:10.1038/hdy.2016.109
apa: Barton, N. H. (2017). How does epistasis influence the response to selection?
Heredity. Nature Publishing Group. https://doi.org/10.1038/hdy.2016.109
chicago: Barton, Nicholas H. “How Does Epistasis Influence the Response to Selection?”
Heredity. Nature Publishing Group, 2017. https://doi.org/10.1038/hdy.2016.109.
ieee: N. H. Barton, “How does epistasis influence the response to selection?,” Heredity,
vol. 118. Nature Publishing Group, pp. 96–109, 2017.
ista: Barton NH. 2017. How does epistasis influence the response to selection? Heredity.
118, 96–109.
mla: Barton, Nicholas H. “How Does Epistasis Influence the Response to Selection?”
Heredity, vol. 118, Nature Publishing Group, 2017, pp. 96–109, doi:10.1038/hdy.2016.109.
short: N.H. Barton, Heredity 118 (2017) 96–109.
date_created: 2018-12-11T11:50:40Z
date_published: 2017-01-01T00:00:00Z
date_updated: 2023-09-20T11:17:47Z
day: '01'
department:
- _id: NiBa
doi: 10.1038/hdy.2016.109
ec_funded: 1
external_id:
isi:
- '000392229100011'
intvolume: ' 118'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5176114/
month: '01'
oa: 1
oa_version: Submitted Version
page: 96 - 109
project:
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
publication: Heredity
publication_status: published
publisher: Nature Publishing Group
publist_id: '6151'
quality_controlled: '1'
related_material:
record:
- id: '9710'
relation: research_data
status: public
scopus_import: '1'
status: public
title: How does epistasis influence the response to selection?
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 118
year: '2017'
...
---
_id: '1169'
abstract:
- lang: eng
text: Dispersal is a crucial factor in natural evolution, since it determines the
habitat experienced by any population and defines the spatial scale of interactions
between individuals. There is compelling evidence for systematic differences in
dispersal characteristics within the same population, i.e., genotype-dependent
dispersal. The consequences of genotype-dependent dispersal on other evolutionary
phenomena, however, are poorly understood. In this article we investigate the
effect of genotype-dependent dispersal on spatial gene frequency patterns, using
a generalization of the classical diffusion model of selection and dispersal.
Dispersal is characterized by the variance of dispersal (diffusion coefficient)
and the mean displacement (directional advection term). We demonstrate that genotype-dependent
dispersal may change the qualitative behavior of Fisher waves, which change from
being “pulled” to being “pushed” wave fronts as the discrepancy in dispersal between
genotypes increases. The speed of any wave is partitioned into components due
to selection, genotype-dependent variance of dispersal, and genotype-dependent
mean displacement. We apply our findings to wave fronts maintained by selection
against heterozygotes. Furthermore, we identify a benefit of increased variance
of dispersal, quantify its effect on the speed of the wave, and discuss the implications
for the evolution of dispersal strategies.
article_processing_charge: No
author:
- first_name: Sebastian
full_name: Novak, Sebastian
id: 461468AE-F248-11E8-B48F-1D18A9856A87
last_name: Novak
orcid: 0000-0002-2519-824X
- first_name: Richard
full_name: Kollár, Richard
last_name: Kollár
citation:
ama: Novak S, Kollár R. Spatial gene frequency waves under genotype dependent dispersal.
Genetics. 2017;205(1):367-374. doi:10.1534/genetics.116.193946
apa: Novak, S., & Kollár, R. (2017). Spatial gene frequency waves under genotype
dependent dispersal. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.116.193946
chicago: Novak, Sebastian, and Richard Kollár. “Spatial Gene Frequency Waves under
Genotype Dependent Dispersal.” Genetics. Genetics Society of America, 2017.
https://doi.org/10.1534/genetics.116.193946.
ieee: S. Novak and R. Kollár, “Spatial gene frequency waves under genotype dependent
dispersal,” Genetics, vol. 205, no. 1. Genetics Society of America, pp.
367–374, 2017.
ista: Novak S, Kollár R. 2017. Spatial gene frequency waves under genotype dependent
dispersal. Genetics. 205(1), 367–374.
mla: Novak, Sebastian, and Richard Kollár. “Spatial Gene Frequency Waves under Genotype
Dependent Dispersal.” Genetics, vol. 205, no. 1, Genetics Society of America,
2017, pp. 367–74, doi:10.1534/genetics.116.193946.
short: S. Novak, R. Kollár, Genetics 205 (2017) 367–374.
date_created: 2018-12-11T11:50:31Z
date_published: 2017-01-01T00:00:00Z
date_updated: 2023-09-20T11:24:21Z
day: '01'
ddc:
- '576'
department:
- _id: NiBa
doi: 10.1534/genetics.116.193946
ec_funded: 1
external_id:
isi:
- '000393677300025'
file:
- access_level: open_access
checksum: 7c8ab79cda1f92760bbbbe0f53175bfc
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:10:43Z
date_updated: 2020-07-14T12:44:37Z
file_id: '4833'
file_name: IST-2016-727-v1+1_SFC_Genetics_final.pdf
file_size: 361500
relation: main_file
file_date_updated: 2020-07-14T12:44:37Z
has_accepted_license: '1'
intvolume: ' 205'
isi: 1
issue: '1'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Submitted Version
page: 367 - 374
project:
- _id: 25B1EC9E-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '618091'
name: Speed of Adaptation in Population Genetics and Evolutionary Computation
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
publication: Genetics
publication_identifier:
issn:
- '00166731'
publication_status: published
publisher: Genetics Society of America
publist_id: '6188'
pubrep_id: '727'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Spatial gene frequency waves under genotype dependent dispersal
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 205
year: '2017'
...
---
_id: '1111'
abstract:
- lang: eng
text: Adaptation depends critically on the effects of new mutations and their dependency
on the genetic background in which they occur. These two factors can be summarized
by the fitness landscape. However, it would require testing all mutations in all
backgrounds, making the definition and analysis of fitness landscapes mostly inaccessible.
Instead of postulating a particular fitness landscape, we address this problem
by considering general classes of landscapes and calculating an upper limit for
the time it takes for a population to reach a fitness peak, circumventing the
need to have full knowledge about the fitness landscape. We analyze populations
in the weak-mutation regime and characterize the conditions that enable them to
quickly reach the fitness peak as a function of the number of sites under selection.
We show that for additive landscapes there is a critical selection strength enabling
populations to reach high-fitness genotypes, regardless of the distribution of
effects. This threshold scales with the number of sites under selection, effectively
setting a limit to adaptation, and results from the inevitable increase in deleterious
mutational pressure as the population adapts in a space of discrete genotypes.
Furthermore, we show that for the class of all unimodal landscapes this condition
is sufficient but not necessary for rapid adaptation, as in some highly epistatic
landscapes the critical strength does not depend on the number of sites under
selection; effectively removing this barrier to adaptation.
article_processing_charge: No
article_type: original
author:
- first_name: Jorge
full_name: Heredia, Jorge
last_name: Heredia
- first_name: Barbora
full_name: Trubenova, Barbora
id: 42302D54-F248-11E8-B48F-1D18A9856A87
last_name: Trubenova
orcid: 0000-0002-6873-2967
- first_name: Dirk
full_name: Sudholt, Dirk
last_name: Sudholt
- first_name: Tiago
full_name: Paixao, Tiago
id: 2C5658E6-F248-11E8-B48F-1D18A9856A87
last_name: Paixao
orcid: 0000-0003-2361-3953
citation:
ama: Heredia J, Trubenova B, Sudholt D, Paixao T. Selection limits to adaptive walks
on correlated landscapes. Genetics. 2017;205(2):803-825. doi:10.1534/genetics.116.189340
apa: Heredia, J., Trubenova, B., Sudholt, D., & Paixao, T. (2017). Selection
limits to adaptive walks on correlated landscapes. Genetics. Genetics Society
of America. https://doi.org/10.1534/genetics.116.189340
chicago: Heredia, Jorge, Barbora Trubenova, Dirk Sudholt, and Tiago Paixao. “Selection
Limits to Adaptive Walks on Correlated Landscapes.” Genetics. Genetics
Society of America, 2017. https://doi.org/10.1534/genetics.116.189340.
ieee: J. Heredia, B. Trubenova, D. Sudholt, and T. Paixao, “Selection limits to
adaptive walks on correlated landscapes,” Genetics, vol. 205, no. 2. Genetics
Society of America, pp. 803–825, 2017.
ista: Heredia J, Trubenova B, Sudholt D, Paixao T. 2017. Selection limits to adaptive
walks on correlated landscapes. Genetics. 205(2), 803–825.
mla: Heredia, Jorge, et al. “Selection Limits to Adaptive Walks on Correlated Landscapes.”
Genetics, vol. 205, no. 2, Genetics Society of America, 2017, pp. 803–25,
doi:10.1534/genetics.116.189340.
short: J. Heredia, B. Trubenova, D. Sudholt, T. Paixao, Genetics 205 (2017) 803–825.
date_created: 2018-12-11T11:50:12Z
date_published: 2017-02-01T00:00:00Z
date_updated: 2023-09-20T11:35:03Z
day: '01'
department:
- _id: NiBa
doi: 10.1534/genetics.116.189340
ec_funded: 1
external_id:
isi:
- '000394144900025'
pmid:
- '27881471'
intvolume: ' 205'
isi: 1
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1534/genetics.116.189340
month: '02'
oa: 1
oa_version: Published Version
page: 803 - 825
pmid: 1
project:
- _id: 25B1EC9E-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '618091'
name: Speed of Adaptation in Population Genetics and Evolutionary Computation
publication: Genetics
publication_identifier:
issn:
- '00166731'
publication_status: published
publisher: Genetics Society of America
publist_id: '6256'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Selection limits to adaptive walks on correlated landscapes
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 205
year: '2017'
...
---
_id: '1077'
abstract:
- lang: eng
text: Viral capsids are structurally constrained by interactions among the amino
acids (AAs) of their constituent proteins. Therefore, epistasis is expected to
evolve among physically interacting sites and to influence the rates of substitution.
To study the evolution of epistasis, we focused on the major structural protein
of the fX174 phage family by first reconstructing the ancestral protein sequences
of 18 species using a Bayesian statistical framework. The inferred ancestral reconstruction
differed at eight AAs, for a total of 256 possible ancestral haplotypes. For each
ancestral haplotype and the extant species, we estimated, in silico, the distribution
of free energies and epistasis of the capsid structure. We found that free energy
has not significantly increased but epistasis has. We decomposed epistasis up
to fifth order and found that higher-order epistasis sometimes compensates pairwise
interactions making the free energy seem additive. The dN/dS ratio is low, suggesting
strong purifying selection, and that structure is under stabilizing selection.
We synthesized phages carrying ancestral haplotypes of the coat protein gene and
measured their fitness experimentally. Our findings indicate that stabilizing
mutations can have higher fitness, and that fitness optima do not necessarily
coincide with energy minima.
article_number: '20160139'
article_processing_charge: Yes (in subscription journal)
author:
- first_name: Rodrigo A
full_name: Fernandes Redondo, Rodrigo A
id: 409D5C96-F248-11E8-B48F-1D18A9856A87
last_name: Fernandes Redondo
orcid: 0000-0002-5837-2793
- first_name: Harold
full_name: Vladar, Harold
id: 2A181218-F248-11E8-B48F-1D18A9856A87
last_name: Vladar
orcid: 0000-0002-5985-7653
- first_name: Tomasz
full_name: Włodarski, Tomasz
last_name: Włodarski
- first_name: Jonathan P
full_name: Bollback, Jonathan P
id: 2C6FA9CC-F248-11E8-B48F-1D18A9856A87
last_name: Bollback
orcid: 0000-0002-4624-4612
citation:
ama: Fernandes Redondo RA, de Vladar H, Włodarski T, Bollback JP. Evolutionary interplay
between structure, energy and epistasis in the coat protein of the ϕX174 phage
family. Journal of the Royal Society Interface. 2017;14(126). doi:10.1098/rsif.2016.0139
apa: Fernandes Redondo, R. A., de Vladar, H., Włodarski, T., & Bollback, J.
P. (2017). Evolutionary interplay between structure, energy and epistasis in the
coat protein of the ϕX174 phage family. Journal of the Royal Society Interface.
Royal Society of London. https://doi.org/10.1098/rsif.2016.0139
chicago: Fernandes Redondo, Rodrigo A, Harold de Vladar, Tomasz Włodarski, and Jonathan
P Bollback. “Evolutionary Interplay between Structure, Energy and Epistasis in
the Coat Protein of the ΦX174 Phage Family.” Journal of the Royal Society Interface.
Royal Society of London, 2017. https://doi.org/10.1098/rsif.2016.0139.
ieee: R. A. Fernandes Redondo, H. de Vladar, T. Włodarski, and J. P. Bollback, “Evolutionary
interplay between structure, energy and epistasis in the coat protein of the ϕX174
phage family,” Journal of the Royal Society Interface, vol. 14, no. 126.
Royal Society of London, 2017.
ista: Fernandes Redondo RA, de Vladar H, Włodarski T, Bollback JP. 2017. Evolutionary
interplay between structure, energy and epistasis in the coat protein of the ϕX174
phage family. Journal of the Royal Society Interface. 14(126), 20160139.
mla: Fernandes Redondo, Rodrigo A., et al. “Evolutionary Interplay between Structure,
Energy and Epistasis in the Coat Protein of the ΦX174 Phage Family.” Journal
of the Royal Society Interface, vol. 14, no. 126, 20160139, Royal Society
of London, 2017, doi:10.1098/rsif.2016.0139.
short: R.A. Fernandes Redondo, H. de Vladar, T. Włodarski, J.P. Bollback, Journal
of the Royal Society Interface 14 (2017).
date_created: 2018-12-11T11:50:01Z
date_published: 2017-01-04T00:00:00Z
date_updated: 2023-09-20T11:56:34Z
day: '04'
ddc:
- '570'
department:
- _id: NiBa
- _id: JoBo
doi: 10.1098/rsif.2016.0139
ec_funded: 1
external_id:
isi:
- '000393380400001'
file:
- access_level: open_access
content_type: application/pdf
creator: dernst
date_created: 2019-01-18T09:14:02Z
date_updated: 2019-01-18T09:14:02Z
file_id: '5843'
file_name: 2017_JRSI_Redondo.pdf
file_size: 1092015
relation: main_file
success: 1
file_date_updated: 2019-01-18T09:14:02Z
has_accepted_license: '1'
intvolume: ' 14'
isi: 1
issue: '126'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
project:
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
- _id: 2578D616-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '648440'
name: Selective Barriers to Horizontal Gene Transfer
publication: Journal of the Royal Society Interface
publication_identifier:
issn:
- '17425689'
publication_status: published
publisher: Royal Society of London
publist_id: '6303'
quality_controlled: '1'
related_material:
record:
- id: '9864'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Evolutionary interplay between structure, energy and epistasis in the coat
protein of the ϕX174 phage family
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 14
year: '2017'
...
---
_id: '1074'
abstract:
- lang: eng
text: Recently it has become feasible to detect long blocks of nearly identical
sequence shared between pairs of genomes. These IBD blocks are direct traces of
recent coalescence events and, as such, contain ample signal to infer recent demography.
Here, we examine sharing of such blocks in two-dimensional populations with local
migration. Using a diffusion approximation to trace genetic ancestry, we derive
analytical formulae for patterns of isolation by distance of IBD blocks, which
can also incorporate recent population density changes. We introduce an inference
scheme that uses a composite likelihood approach to fit these formulae. We then
extensively evaluate our theory and inference method on a range of scenarios using
simulated data. We first validate the diffusion approximation by showing that
the theoretical results closely match the simulated block sharing patterns. We
then demonstrate that our inference scheme can accurately and robustly infer dispersal
rate and effective density, as well as bounds on recent dynamics of population
density. To demonstrate an application, we use our estimation scheme to explore
the fit of a diffusion model to Eastern European samples in the POPRES data set.
We show that ancestry diffusing with a rate of σ ≈ 50–100 km/√gen during the last
centuries, combined with accelerating population growth, can explain the observed
exponential decay of block sharing with increasing pairwise sample distance.
article_processing_charge: No
author:
- first_name: Harald
full_name: Ringbauer, Harald
id: 417FCFF4-F248-11E8-B48F-1D18A9856A87
last_name: Ringbauer
orcid: 0000-0002-4884-9682
- first_name: Graham
full_name: Coop, Graham
last_name: Coop
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: Ringbauer H, Coop G, Barton NH. Inferring recent demography from isolation
by distance of long shared sequence blocks. Genetics. 2017;205(3):1335-1351.
doi:10.1534/genetics.116.196220
apa: Ringbauer, H., Coop, G., & Barton, N. H. (2017). Inferring recent demography
from isolation by distance of long shared sequence blocks. Genetics. Genetics
Society of America. https://doi.org/10.1534/genetics.116.196220
chicago: Ringbauer, Harald, Graham Coop, and Nicholas H Barton. “Inferring Recent
Demography from Isolation by Distance of Long Shared Sequence Blocks.” Genetics.
Genetics Society of America, 2017. https://doi.org/10.1534/genetics.116.196220.
ieee: H. Ringbauer, G. Coop, and N. H. Barton, “Inferring recent demography from
isolation by distance of long shared sequence blocks,” Genetics, vol. 205,
no. 3. Genetics Society of America, pp. 1335–1351, 2017.
ista: Ringbauer H, Coop G, Barton NH. 2017. Inferring recent demography from isolation
by distance of long shared sequence blocks. Genetics. 205(3), 1335–1351.
mla: Ringbauer, Harald, et al. “Inferring Recent Demography from Isolation by Distance
of Long Shared Sequence Blocks.” Genetics, vol. 205, no. 3, Genetics Society
of America, 2017, pp. 1335–51, doi:10.1534/genetics.116.196220.
short: H. Ringbauer, G. Coop, N.H. Barton, Genetics 205 (2017) 1335–1351.
date_created: 2018-12-11T11:50:00Z
date_published: 2017-03-01T00:00:00Z
date_updated: 2023-09-20T12:00:56Z
day: '01'
department:
- _id: NiBa
doi: 10.1534/genetics.116.196220
ec_funded: 1
external_id:
isi:
- '000395807200023'
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isi: 1
issue: '3'
language:
- iso: eng
main_file_link:
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url: http://www.biorxiv.org/content/early/2016/09/23/076810
month: '03'
oa: 1
oa_version: Preprint
page: 1335 - 1351
project:
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
publication: Genetics
publication_identifier:
issn:
- '00166731'
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publisher: Genetics Society of America
publist_id: '6307'
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title: Inferring recent demography from isolation by distance of long shared sequence
blocks
type: journal_article
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volume: 205
year: '2017'
...
---
_id: '1063'
abstract:
- lang: eng
text: Severe environmental change can drive a population extinct unless the population
adapts in time to the new conditions (“evolutionary rescue”). How does biparental
sexual reproduction influence the chances of population persistence compared to
clonal reproduction or selfing? In this article, we set up a one‐locus two‐allele
model for adaptation in diploid species, where rescue is contingent on the establishment
of the mutant homozygote. Reproduction can occur by random mating, selfing, or
clonally. Random mating generates and destroys the rescue mutant; selfing is efficient
at generating it but at the same time depletes the heterozygote, which can lead
to a low mutant frequency in the standing genetic variation. Due to these (and
other) antagonistic effects, we find a nontrivial dependence of population survival
on the rate of sex/selfing, which is strongly influenced by the dominance coefficient
of the mutation before and after the environmental change. Importantly, since
mating with the wild‐type breaks the mutant homozygote up, a slow decay of the
wild‐type population size can impede rescue in randomly mating populations.
article_processing_charge: No
author:
- first_name: Hildegard
full_name: Uecker, Hildegard
id: 2DB8F68A-F248-11E8-B48F-1D18A9856A87
last_name: Uecker
orcid: 0000-0001-9435-2813
citation:
ama: Uecker H. Evolutionary rescue in randomly mating, selfing, and clonal populations.
Evolution. 2017;71(4):845-858. doi:10.1111/evo.13191
apa: Uecker, H. (2017). Evolutionary rescue in randomly mating, selfing, and clonal
populations. Evolution. Wiley-Blackwell. https://doi.org/10.1111/evo.13191
chicago: Uecker, Hildegard. “Evolutionary Rescue in Randomly Mating, Selfing, and
Clonal Populations.” Evolution. Wiley-Blackwell, 2017. https://doi.org/10.1111/evo.13191.
ieee: H. Uecker, “Evolutionary rescue in randomly mating, selfing, and clonal populations,”
Evolution, vol. 71, no. 4. Wiley-Blackwell, pp. 845–858, 2017.
ista: Uecker H. 2017. Evolutionary rescue in randomly mating, selfing, and clonal
populations. Evolution. 71(4), 845–858.
mla: Uecker, Hildegard. “Evolutionary Rescue in Randomly Mating, Selfing, and Clonal
Populations.” Evolution, vol. 71, no. 4, Wiley-Blackwell, 2017, pp. 845–58,
doi:10.1111/evo.13191.
short: H. Uecker, Evolution 71 (2017) 845–858.
date_created: 2018-12-11T11:49:57Z
date_published: 2017-04-01T00:00:00Z
date_updated: 2023-09-20T12:10:32Z
day: '01'
department:
- _id: NiBa
doi: 10.1111/evo.13191
ec_funded: 1
external_id:
isi:
- '000398545200003'
intvolume: ' 71'
isi: 1
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://biorxiv.org/content/early/2016/10/14/081042
month: '04'
oa: 1
oa_version: Submitted Version
page: 845 - 858
project:
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
publication: Evolution
publication_identifier:
issn:
- '00143820'
publication_status: published
publisher: Wiley-Blackwell
publist_id: '6327'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Evolutionary rescue in randomly mating, selfing, and clonal populations
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 71
year: '2017'
...
---
_id: '990'
abstract:
- lang: eng
text: Assortative mating is an important driver of speciation in populations with
gene flow and is predicted to evolve under certain conditions in few-locus models.
However, the evolution of assortment is less understood for mating based on quantitative
traits, which are often characterized by high genetic variability and extensive
linkage disequilibrium between trait loci. We explore this scenario for a two-deme
model with migration, by considering a single polygenic trait subject to divergent
viability selection across demes, as well as assortative mating and sexual selection
within demes, and investigate how trait divergence is shaped by various evolutionary
forces. Our analysis reveals the existence of sharp thresholds of assortment strength,
at which divergence increases dramatically. We also study the evolution of assortment
via invasion of modifiers of mate discrimination and show that the ES assortment
strength has an intermediate value under a range of migration-selection parameters,
even in diverged populations, due to subtle effects which depend sensitively on
the extent of phenotypic variation within these populations. The evolutionary
dynamics of the polygenic trait is studied using the hypergeometric and infinitesimal
models. We further investigate the sensitivity of our results to the assumptions
of the hypergeometric model, using individual-based simulations.
article_processing_charge: No
author:
- first_name: Himani
full_name: Sachdeva, Himani
id: 42377A0A-F248-11E8-B48F-1D18A9856A87
last_name: Sachdeva
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: Sachdeva H, Barton NH. Divergence and evolution of assortative mating in a
polygenic trait model of speciation with gene flow. Evolution; International
Journal of Organic Evolution. 2017;71(6):1478-1493. doi:10.1111/evo.13252
apa: Sachdeva, H., & Barton, N. H. (2017). Divergence and evolution of assortative
mating in a polygenic trait model of speciation with gene flow. Evolution;
International Journal of Organic Evolution. Wiley-Blackwell. https://doi.org/10.1111/evo.13252
chicago: Sachdeva, Himani, and Nicholas H Barton. “Divergence and Evolution of Assortative
Mating in a Polygenic Trait Model of Speciation with Gene Flow.” Evolution;
International Journal of Organic Evolution. Wiley-Blackwell, 2017. https://doi.org/10.1111/evo.13252.
ieee: H. Sachdeva and N. H. Barton, “Divergence and evolution of assortative mating
in a polygenic trait model of speciation with gene flow,” Evolution; International
Journal of Organic Evolution, vol. 71, no. 6. Wiley-Blackwell, pp. 1478–1493,
2017.
ista: Sachdeva H, Barton NH. 2017. Divergence and evolution of assortative mating
in a polygenic trait model of speciation with gene flow. Evolution; International
Journal of Organic Evolution. 71(6), 1478–1493.
mla: Sachdeva, Himani, and Nicholas H. Barton. “Divergence and Evolution of Assortative
Mating in a Polygenic Trait Model of Speciation with Gene Flow.” Evolution;
International Journal of Organic Evolution, vol. 71, no. 6, Wiley-Blackwell,
2017, pp. 1478–93, doi:10.1111/evo.13252.
short: H. Sachdeva, N.H. Barton, Evolution; International Journal of Organic Evolution
71 (2017) 1478–1493.
date_created: 2018-12-11T11:49:34Z
date_published: 2017-06-01T00:00:00Z
date_updated: 2023-09-22T09:55:13Z
day: '01'
ddc:
- '576'
department:
- _id: NiBa
doi: 10.1111/evo.13252
ec_funded: 1
external_id:
isi:
- '000403014800005'
pmid:
- '28419447'
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page: '1478 - 1493 '
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call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
publication: Evolution; International Journal of Organic Evolution
publication_identifier:
issn:
- '00143820'
publication_status: published
publisher: Wiley-Blackwell
publist_id: '6409'
pubrep_id: '977'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Divergence and evolution of assortative mating in a polygenic trait model of
speciation with gene flow
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 71
year: '2017'
...
---
_id: '954'
abstract:
- lang: eng
text: Understanding the relation between genotype and phenotype remains a major
challenge. The difficulty of predicting individual mutation effects, and particularly
the interactions between them, has prevented the development of a comprehensive
theory that links genotypic changes to their phenotypic effects. We show that
a general thermodynamic framework for gene regulation, based on a biophysical
understanding of protein-DNA binding, accurately predicts the sign of epistasis
in a canonical cis-regulatory element consisting of overlapping RNA polymerase
and repressor binding sites. Sign and magnitude of individual mutation effects
are sufficient to predict the sign of epistasis and its environmental dependence.
Thus, the thermodynamic model offers the correct null prediction for epistasis
between mutations across DNA-binding sites. Our results indicate that a predictive
theory for the effects of cis-regulatory mutations is possible from first principles,
as long as the essential molecular mechanisms and the constraints these impose
on a biological system are accounted for.
article_number: e25192
article_processing_charge: Yes
author:
- first_name: Mato
full_name: Lagator, Mato
id: 345D25EC-F248-11E8-B48F-1D18A9856A87
last_name: Lagator
- first_name: Tiago
full_name: Paixao, Tiago
id: 2C5658E6-F248-11E8-B48F-1D18A9856A87
last_name: Paixao
orcid: 0000-0003-2361-3953
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Jonathan P
full_name: Bollback, Jonathan P
id: 2C6FA9CC-F248-11E8-B48F-1D18A9856A87
last_name: Bollback
orcid: 0000-0002-4624-4612
- first_name: Calin C
full_name: Guet, Calin C
id: 47F8433E-F248-11E8-B48F-1D18A9856A87
last_name: Guet
orcid: 0000-0001-6220-2052
citation:
ama: Lagator M, Paixao T, Barton NH, Bollback JP, Guet CC. On the mechanistic nature
of epistasis in a canonical cis-regulatory element. eLife. 2017;6. doi:10.7554/eLife.25192
apa: Lagator, M., Paixao, T., Barton, N. H., Bollback, J. P., & Guet, C. C.
(2017). On the mechanistic nature of epistasis in a canonical cis-regulatory element.
ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.25192
chicago: Lagator, Mato, Tiago Paixao, Nicholas H Barton, Jonathan P Bollback, and
Calin C Guet. “On the Mechanistic Nature of Epistasis in a Canonical Cis-Regulatory
Element.” ELife. eLife Sciences Publications, 2017. https://doi.org/10.7554/eLife.25192.
ieee: M. Lagator, T. Paixao, N. H. Barton, J. P. Bollback, and C. C. Guet, “On the
mechanistic nature of epistasis in a canonical cis-regulatory element,” eLife,
vol. 6. eLife Sciences Publications, 2017.
ista: Lagator M, Paixao T, Barton NH, Bollback JP, Guet CC. 2017. On the mechanistic
nature of epistasis in a canonical cis-regulatory element. eLife. 6, e25192.
mla: Lagator, Mato, et al. “On the Mechanistic Nature of Epistasis in a Canonical
Cis-Regulatory Element.” ELife, vol. 6, e25192, eLife Sciences Publications,
2017, doi:10.7554/eLife.25192.
short: M. Lagator, T. Paixao, N.H. Barton, J.P. Bollback, C.C. Guet, ELife 6 (2017).
date_created: 2018-12-11T11:49:23Z
date_published: 2017-05-18T00:00:00Z
date_updated: 2023-09-22T10:01:17Z
day: '18'
ddc:
- '576'
department:
- _id: CaGu
- _id: NiBa
- _id: JoBo
doi: 10.7554/eLife.25192
ec_funded: 1
external_id:
isi:
- '000404024800001'
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language:
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month: '05'
oa: 1
oa_version: Published Version
project:
- _id: 25B1EC9E-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '618091'
name: Speed of Adaptation in Population Genetics and Evolutionary Computation
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
- _id: 2578D616-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '648440'
name: Selective Barriers to Horizontal Gene Transfer
publication: eLife
publication_identifier:
issn:
- 2050084X
publication_status: published
publisher: eLife Sciences Publications
publist_id: '6460'
pubrep_id: '841'
quality_controlled: '1'
scopus_import: '1'
status: public
title: On the mechanistic nature of epistasis in a canonical cis-regulatory element
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
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year: '2017'
...
---
_id: '955'
abstract:
- lang: eng
text: 'Gene expression is controlled by networks of regulatory proteins that interact
specifically with external signals and DNA regulatory sequences. These interactions
force the network components to co-evolve so as to continually maintain function.
Yet, existing models of evolution mostly focus on isolated genetic elements. In
contrast, we study the essential process by which regulatory networks grow: the
duplication and subsequent specialization of network components. We synthesize
a biophysical model of molecular interactions with the evolutionary framework
to find the conditions and pathways by which new regulatory functions emerge.
We show that specialization of new network components is usually slow, but can
be drastically accelerated in the presence of regulatory crosstalk and mutations
that promote promiscuous interactions between network components.'
article_number: '216'
article_processing_charge: Yes (in subscription journal)
author:
- first_name: Tamar
full_name: Friedlander, Tamar
id: 36A5845C-F248-11E8-B48F-1D18A9856A87
last_name: Friedlander
- first_name: Roshan
full_name: Prizak, Roshan
id: 4456104E-F248-11E8-B48F-1D18A9856A87
last_name: Prizak
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Gasper
full_name: Tkacik, Gasper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkacik
orcid: 0000-0002-6699-1455
citation:
ama: Friedlander T, Prizak R, Barton NH, Tkačik G. Evolution of new regulatory functions
on biophysically realistic fitness landscapes. Nature Communications. 2017;8(1).
doi:10.1038/s41467-017-00238-8
apa: Friedlander, T., Prizak, R., Barton, N. H., & Tkačik, G. (2017). Evolution
of new regulatory functions on biophysically realistic fitness landscapes. Nature
Communications. Nature Publishing Group. https://doi.org/10.1038/s41467-017-00238-8
chicago: Friedlander, Tamar, Roshan Prizak, Nicholas H Barton, and Gašper Tkačik.
“Evolution of New Regulatory Functions on Biophysically Realistic Fitness Landscapes.”
Nature Communications. Nature Publishing Group, 2017. https://doi.org/10.1038/s41467-017-00238-8.
ieee: T. Friedlander, R. Prizak, N. H. Barton, and G. Tkačik, “Evolution of new
regulatory functions on biophysically realistic fitness landscapes,” Nature
Communications, vol. 8, no. 1. Nature Publishing Group, 2017.
ista: Friedlander T, Prizak R, Barton NH, Tkačik G. 2017. Evolution of new regulatory
functions on biophysically realistic fitness landscapes. Nature Communications.
8(1), 216.
mla: Friedlander, Tamar, et al. “Evolution of New Regulatory Functions on Biophysically
Realistic Fitness Landscapes.” Nature Communications, vol. 8, no. 1, 216,
Nature Publishing Group, 2017, doi:10.1038/s41467-017-00238-8.
short: T. Friedlander, R. Prizak, N.H. Barton, G. Tkačik, Nature Communications
8 (2017).
date_created: 2018-12-11T11:49:23Z
date_published: 2017-08-09T00:00:00Z
date_updated: 2023-09-22T10:00:49Z
day: '09'
ddc:
- '539'
- '576'
department:
- _id: GaTk
- _id: NiBa
doi: 10.1038/s41467-017-00238-8
ec_funded: 1
external_id:
isi:
- '000407198800005'
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month: '08'
oa: 1
oa_version: Published Version
project:
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call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
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scopus_import: '1'
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title: Evolution of new regulatory functions on biophysically realistic fitness landscapes
tmp:
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...