---
_id: '39'
abstract:
- lang: eng
text: We study how a block of genome with a large number of weakly selected loci
introgresses under directional selection into a genetically homogeneous population.
We derive exact expressions for the expected rate of growth of any fragment of
the introduced block during the initial phase of introgression, and show that
the growth rate of a single-locus variant is largely insensitive to its own additive
effect, but depends instead on the combined effect of all loci within a characteristic
linkage scale. The expected growth rate of a fragment is highly correlated with
its long-term introgression probability in populations of moderate size, and can
hence identify variants that are likely to introgress across replicate populations.
We clarify how the introgression probability of an individual variant is determined
by the interplay between hitchhiking with relatively large fragments during the
early phase of introgression and selection on fine-scale variation within these,
which at longer times results in differential introgression probabilities for
beneficial and deleterious loci within successful fragments. By simulating individuals,
we also investigate how introgression probabilities at individual loci depend
on the variance of fitness effects, the net fitness of the introduced block, and
the size of the recipient population, and how this shapes the net advance under
selection. Our work suggests that even highly replicable substitutions may be
associated with a range of selective effects, which makes it challenging to fine
map the causal loci that underlie polygenic adaptation.
article_processing_charge: No
article_type: original
author:
- first_name: Himani
full_name: Sachdeva, Himani
id: 42377A0A-F248-11E8-B48F-1D18A9856A87
last_name: Sachdeva
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: Sachdeva H, Barton NH. Replicability of introgression under linked, polygenic
selection. Genetics. 2018;210(4):1411-1427. doi:10.1534/genetics.118.301429
apa: Sachdeva, H., & Barton, N. H. (2018). Replicability of introgression under
linked, polygenic selection. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.118.301429
chicago: Sachdeva, Himani, and Nicholas H Barton. “Replicability of Introgression
under Linked, Polygenic Selection.” Genetics. Genetics Society of America,
2018. https://doi.org/10.1534/genetics.118.301429.
ieee: H. Sachdeva and N. H. Barton, “Replicability of introgression under linked,
polygenic selection,” Genetics, vol. 210, no. 4. Genetics Society of America,
pp. 1411–1427, 2018.
ista: Sachdeva H, Barton NH. 2018. Replicability of introgression under linked,
polygenic selection. Genetics. 210(4), 1411–1427.
mla: Sachdeva, Himani, and Nicholas H. Barton. “Replicability of Introgression under
Linked, Polygenic Selection.” Genetics, vol. 210, no. 4, Genetics Society
of America, 2018, pp. 1411–27, doi:10.1534/genetics.118.301429.
short: H. Sachdeva, N.H. Barton, Genetics 210 (2018) 1411–1427.
date_created: 2018-12-11T11:44:18Z
date_published: 2018-12-04T00:00:00Z
date_updated: 2023-09-18T08:10:29Z
day: '04'
department:
- _id: NiBa
doi: 10.1534/genetics.118.301429
external_id:
isi:
- '000452315900021'
intvolume: ' 210'
isi: 1
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.biorxiv.org/content/10.1101/379578v1
month: '12'
oa: 1
oa_version: Preprint
page: 1411-1427
publication: Genetics
publication_identifier:
issn:
- '00166731'
publication_status: published
publisher: Genetics Society of America
quality_controlled: '1'
scopus_import: '1'
status: public
title: Replicability of introgression under linked, polygenic selection
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 210
year: '2018'
...
---
_id: '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: 2025-05-28T11:42:51Z
day: '01'
department:
- _id: NiBa
doi: 10.1534/genetics.116.196220
ec_funded: 1
external_id:
isi:
- '000395807200023'
intvolume: ' 205'
isi: 1
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.biorxiv.org/content/early/2016/09/23/076810
month: '03'
oa: 1
oa_version: Preprint
page: 1335 - 1351
project:
- _id: 25B07788-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '250152'
name: Limits to selection in biology and in evolutionary computation
publication: Genetics
publication_identifier:
issn:
- '00166731'
publication_status: published
publisher: Genetics Society of America
publist_id: '6307'
quality_controlled: '1'
related_material:
record:
- id: '200'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Inferring recent demography from isolation by distance of long shared sequence
blocks
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 205
year: '2017'
...
---
_id: '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: '1169'
abstract:
- lang: eng
text: Dispersal is a crucial factor in natural evolution, since it determines the
habitat experienced by any population and defines the spatial scale of interactions
between individuals. There is compelling evidence for systematic differences in
dispersal characteristics within the same population, i.e., genotype-dependent
dispersal. The consequences of genotype-dependent dispersal on other evolutionary
phenomena, however, are poorly understood. In this article we investigate the
effect of genotype-dependent dispersal on spatial gene frequency patterns, using
a generalization of the classical diffusion model of selection and dispersal.
Dispersal is characterized by the variance of dispersal (diffusion coefficient)
and the mean displacement (directional advection term). We demonstrate that genotype-dependent
dispersal may change the qualitative behavior of Fisher waves, which change from
being “pulled” to being “pushed” wave fronts as the discrepancy in dispersal between
genotypes increases. The speed of any wave is partitioned into components due
to selection, genotype-dependent variance of dispersal, and genotype-dependent
mean displacement. We apply our findings to wave fronts maintained by selection
against heterozygotes. Furthermore, we identify a benefit of increased variance
of dispersal, quantify its effect on the speed of the wave, and discuss the implications
for the evolution of dispersal strategies.
article_processing_charge: No
author:
- first_name: Sebastian
full_name: Novak, Sebastian
id: 461468AE-F248-11E8-B48F-1D18A9856A87
last_name: Novak
orcid: 0000-0002-2519-824X
- first_name: Richard
full_name: Kollár, Richard
last_name: Kollár
citation:
ama: Novak S, Kollár R. Spatial gene frequency waves under genotype dependent dispersal.
Genetics. 2017;205(1):367-374. doi:10.1534/genetics.116.193946
apa: Novak, S., & Kollár, R. (2017). Spatial gene frequency waves under genotype
dependent dispersal. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.116.193946
chicago: Novak, Sebastian, and Richard Kollár. “Spatial Gene Frequency Waves under
Genotype Dependent Dispersal.” Genetics. Genetics Society of America, 2017.
https://doi.org/10.1534/genetics.116.193946.
ieee: S. Novak and R. Kollár, “Spatial gene frequency waves under genotype dependent
dispersal,” Genetics, vol. 205, no. 1. Genetics Society of America, pp.
367–374, 2017.
ista: Novak S, Kollár R. 2017. Spatial gene frequency waves under genotype dependent
dispersal. Genetics. 205(1), 367–374.
mla: Novak, Sebastian, and Richard Kollár. “Spatial Gene Frequency Waves under Genotype
Dependent Dispersal.” Genetics, vol. 205, no. 1, Genetics Society of America,
2017, pp. 367–74, doi:10.1534/genetics.116.193946.
short: S. Novak, R. Kollár, Genetics 205 (2017) 367–374.
date_created: 2018-12-11T11:50:31Z
date_published: 2017-01-01T00:00:00Z
date_updated: 2025-05-28T11:42:46Z
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: '6161'
abstract:
- lang: eng
text: 'The tra-1 gene is a terminal regulator of somatic sex in Caenorhabditis elegans:
high tra-1 activity elicits female development, low tra-1 activity elicits male
development. To investigate the function and evolution of tra- 1, we examined
the tra-1 gene from the closely related nematode C. briggsae. Ce-tra-1 and Cb-tra-1
are unusually divergent. Each gene generates two transcripts, but only one of
these is present in both species. This common transcript encodes TRA-1A, which
shows only 44% amino acid identity between the species, a figure much lower than
that for previously compared genes. A Cb-tra-1 transgene rescues many tissues
of tra-1(null) mutants of C. elegans but not the somatic gonad or germ line. This
transgene also causes nongonadal feminization of XO animals, indicating incorrect
sexual regulation. Alignment of Ce-TRA-1A and Cb-TRA-1A defined several conserved
regions likely to be important for tra-1 function. The phenotype differences between
Ce-tra- 1(null) mutants rescued by Cb-tra-1 transgenes and wild-type C. elegans
indicate significant divergence of regulatory regions. These molecular and functional
studies suggest that evolution of sex determination in nematodes is rapid and
genetically complex.'
author:
- first_name: Mario
full_name: de Bono, Mario
id: 4E3FF80E-F248-11E8-B48F-1D18A9856A87
last_name: de Bono
orcid: 0000-0001-8347-0443
- first_name: J.
full_name: Hodgkin, J.
last_name: Hodgkin
citation:
ama: 'de Bono M, Hodgkin J. Evolution of sex determination in Caenorhabditis: Unusually
high divergence of tra-1 and its functional consequences. Genetics. 1996;144(2):587-595.'
apa: 'de Bono, M., & Hodgkin, J. (1996). Evolution of sex determination in Caenorhabditis:
Unusually high divergence of tra-1 and its functional consequences. Genetics.
Genetics Society of America.'
chicago: 'Bono, Mario de, and J. Hodgkin. “Evolution of Sex Determination in Caenorhabditis:
Unusually High Divergence of Tra-1 and Its Functional Consequences.” Genetics.
Genetics Society of America, 1996.'
ieee: 'M. de Bono and J. Hodgkin, “Evolution of sex determination in Caenorhabditis:
Unusually high divergence of tra-1 and its functional consequences,” Genetics,
vol. 144, no. 2. Genetics Society of America, pp. 587–595, 1996.'
ista: 'de Bono M, Hodgkin J. 1996. Evolution of sex determination in Caenorhabditis:
Unusually high divergence of tra-1 and its functional consequences. Genetics.
144(2), 587–595.'
mla: 'de Bono, Mario, and J. Hodgkin. “Evolution of Sex Determination in Caenorhabditis:
Unusually High Divergence of Tra-1 and Its Functional Consequences.” Genetics,
vol. 144, no. 2, Genetics Society of America, 1996, pp. 587–95.'
short: M. de Bono, J. Hodgkin, Genetics 144 (1996) 587–595.
date_created: 2019-03-21T11:50:37Z
date_published: 1996-10-01T00:00:00Z
date_updated: 2021-01-12T08:06:28Z
day: '01'
extern: '1'
external_id:
pmid:
- '8889522'
intvolume: ' 144'
issue: '2'
keyword:
- amino acid sequence
- article
- caenorhabditis elegans
- evolution
- genetic variability
- nonhuman
- priority journal
- sex determination
- Amino Acid Sequence
- Animals
- Animals
- Genetically Modified
- Base Sequence
- Caenorhabditis
- Caenorhabditis elegans
- Caenorhabditis elegans Proteins
- DNA
- Helminth
- DNA-Binding Proteins
- Evolution
- Molecular
- Female
- Helminth Proteins
- Membrane Proteins
- Molecular Sequence Data
- Mutagenesis
- RNA
- Messenger
- Sequence Homology
- Amino Acid
- Sex Determination (Analysis)
- Transcription Factors
- Transgenes
- Turner Syndrome
- Animalia
- Caenorhabditis
- Caenorhabditis briggsae
- Caenorhabditis elegans
- Nematoda
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1207552/
month: '10'
oa: 1
oa_version: Published Version
page: 587-595
pmid: 1
publication: Genetics
publication_identifier:
issn:
- '00166731'
publication_status: published
publisher: Genetics Society of America
quality_controlled: '1'
status: public
title: 'Evolution of sex determination in Caenorhabditis: Unusually high divergence
of tra-1 and its functional consequences'
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 144
year: '1996'
...