---
OA_place: publisher
OA_type: hybrid
PlanS_conform: '1'
_id: '21841'
abstract:
- lang: eng
text: The long-standing notion that genotypes map to phenotypes through simple one
gene–one trait relationships continues to shape both research in the life sciences
and public understanding, with implications for policy and funding priorities.
Yet this paradigm is increasingly recognized as inadequate for explaining continuous
phenotypic variation and the complex genetic architectures of the genotype–phenotype
map. Modern genetics emerged from the early 20th-century synthesis of Mendelian
and biometric schools of heredity, with R.A. Fisher demonstrating early on how
multiple discrete loci could collectively produce continuous variation. Despite
this fundamental insight, Mendelism—with its focus on single genes and standardized
genetic backgrounds—became the dominant framework, shaping current genetics research
and molecular biology as well as science education. The advent of large-scale
genomic data has revealed yet again the limitations of this reductionist approach.
Evidence from quantitative genetics now shows that most phenotypes arise from
complex networks of many interdependent genes and their dynamic responses to environmental
perturbations. Here we trace the historical roots of how Mendelian classical genetics
departed from the biometric school to create the current predominant paradigm
in genetics, despite fundamentally unresolved issues. Moving on from this one-sided
paradigm will require systematic development of integrative, evolutionarily grounded
experimental approaches that better capture the multigenic and context-dependent
nature of inheritance. Achieving such an extended perspective will require methodological
innovation, including advances in large-scale (e.g. automated) phenotyping. Dedicated
research programs will be necessary to advance a new era of genetic research into
the complex mechanisms underlying phenotypic variation.
acknowledgement: We thank a variety of further colleagues for the many inspiring discussions
on the nature of heredity, especially the workshops in Berlin. Special thanks also
to the Stellenbosch Institute for Advanced Studies (STIAS) to provide DT the leisure
and freedom to write up the first version of this perspective. Thanks also to three
reviewers who have helped to improve the manuscript. Two dedicated symposia on the
topic were funded by the Max-Planck Society.
article_number: iyag024
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Diethard
full_name: Tautz, Diethard
last_name: Tautz
- first_name: Luisa F
full_name: Pallares, Luisa F
last_name: Pallares
- first_name: Leif
full_name: Andersson, Leif
last_name: Andersson
- first_name: Neda
full_name: Barghi, Neda
last_name: Barghi
- 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: Rachael
full_name: Bay, Rachael
last_name: Bay
- first_name: Yingguang Frank
full_name: Chan, Yingguang Frank
last_name: Chan
- first_name: Angela
full_name: Hancock, Angela
last_name: Hancock
- first_name: Tobias S
full_name: Kaiser, Tobias S
last_name: Kaiser
- first_name: Daniel
full_name: Koenig, Daniel
last_name: Koenig
- first_name: Zacharias
full_name: Kontarakis, Zacharias
last_name: Kontarakis
- first_name: Miriam
full_name: Liedvogel, Miriam
last_name: Liedvogel
- first_name: Juliette
full_name: de Meaux, Juliette
last_name: de Meaux
- first_name: Magnus
full_name: Nordborg, Magnus
last_name: Nordborg
- first_name: Abraham A
full_name: Palmer, Abraham A
last_name: Palmer
- first_name: Michael
full_name: Purugganan, Michael
last_name: Purugganan
- first_name: Christian
full_name: Schlötterer, Christian
last_name: Schlötterer
- first_name: Karl
full_name: Schmid, Karl
last_name: Schmid
- first_name: Didier Y R
full_name: Stainier, Didier Y R
last_name: Stainier
- first_name: Detlef
full_name: Weigel, Detlef
last_name: Weigel
- first_name: Jochen B W
full_name: Wolf, Jochen B W
last_name: Wolf
- first_name: Dieter
full_name: Ebert, Dieter
last_name: Ebert
- first_name: Greg
full_name: Gibson, Greg
last_name: Gibson
citation:
ama: 'Tautz D, Pallares LF, Andersson L, et al. Beyond Mendel: A call to revisit
the genotype–phenotype map through new experimental paradigms. Genetics.
2026;232(4). doi:10.1093/genetics/iyag024'
apa: 'Tautz, D., Pallares, L. F., Andersson, L., Barghi, N., Barton, N. H., Bay,
R., … Gibson, G. (2026). Beyond Mendel: A call to revisit the genotype–phenotype
map through new experimental paradigms. Genetics. Oxford University Press.
https://doi.org/10.1093/genetics/iyag024'
chicago: 'Tautz, Diethard, Luisa F Pallares, Leif Andersson, Neda Barghi, Nicholas
H Barton, Rachael Bay, Yingguang Frank Chan, et al. “Beyond Mendel: A Call to
Revisit the Genotype–Phenotype Map through New Experimental Paradigms.” Genetics.
Oxford University Press, 2026. https://doi.org/10.1093/genetics/iyag024.'
ieee: 'D. Tautz et al., “Beyond Mendel: A call to revisit the genotype–phenotype
map through new experimental paradigms,” Genetics, vol. 232, no. 4. Oxford
University Press, 2026.'
ista: 'Tautz D, Pallares LF, Andersson L, Barghi N, Barton NH, Bay R, Chan YF, Hancock
A, Kaiser TS, Koenig D, Kontarakis Z, Liedvogel M, de Meaux J, Nordborg M, Palmer
AA, Purugganan M, Schlötterer C, Schmid K, Stainier DYR, Weigel D, Wolf JBW, Ebert
D, Gibson G. 2026. Beyond Mendel: A call to revisit the genotype–phenotype map
through new experimental paradigms. Genetics. 232(4), iyag024.'
mla: 'Tautz, Diethard, et al. “Beyond Mendel: A Call to Revisit the Genotype–Phenotype
Map through New Experimental Paradigms.” Genetics, vol. 232, no. 4, iyag024,
Oxford University Press, 2026, doi:10.1093/genetics/iyag024.'
short: D. Tautz, L.F. Pallares, L. Andersson, N. Barghi, N.H. Barton, R. Bay, Y.F.
Chan, A. Hancock, T.S. Kaiser, D. Koenig, Z. Kontarakis, M. Liedvogel, J. de Meaux,
M. Nordborg, A.A. Palmer, M. Purugganan, C. Schlötterer, K. Schmid, D.Y.R. Stainier,
D. Weigel, J.B.W. Wolf, D. Ebert, G. Gibson, Genetics 232 (2026).
date_created: 2026-05-07T08:53:40Z
date_published: 2026-04-01T00:00:00Z
date_updated: 2026-05-18T07:51:26Z
day: '01'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1093/genetics/iyag024
external_id:
pmid:
- '41701356'
file:
- access_level: open_access
checksum: 5a862c539f9dec4511277ad8927c549c
content_type: application/pdf
creator: dernst
date_created: 2026-05-18T07:48:45Z
date_updated: 2026-05-18T07:48:45Z
file_id: '21890'
file_name: 2026_Genetics_Tautz.pdf
file_size: 542844
relation: main_file
success: 1
file_date_updated: 2026-05-18T07:48:45Z
has_accepted_license: '1'
intvolume: ' 232'
issue: '4'
keyword:
- classic genetics
- quantitative genetics
- genotype–phenotype map
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
pmid: 1
publication: Genetics
publication_identifier:
eissn:
- 1943-2631
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Beyond Mendel: A call to revisit the genotype–phenotype map through new experimental
paradigms'
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: 232
year: '2026'
...
---
OA_place: publisher
OA_type: hybrid
_id: '20848'
abstract:
- lang: eng
text: 'Genetic variation that influences complex disease susceptibility is introduced
into the population by mutation and removed by natural selection and genetic drift.
This mutation–selection–drift balance (MSDB) shapes the prevalence of a disease
and its genetic architecture. To date, however, MSDB has been modeled only for
monogenic (Mendelian) diseases. Here, we develop an MSDB model for complex disease
susceptibility: we assume that genotype relates to disease risk according to the
canonical liability threshold model and that the selection on variants affecting
risk stems from the fitness cost of the disease. We focus on diseases that are
highly polygenic, entail a substantial fitness cost, and are neither extremely
common in the population nor exceedingly rare. The comparison of model predictions
with genome-wide association studies and other observations in humans indicates
that common genetic variation affecting complex disease susceptibility is little
affected by directional selection and instead shaped by pleiotropic stabilizing
selection on other traits. In turn, directional selection may exert a more substantial
effect on rare, large-effect variants. Our results also suggest that current estimates
of disease heritability are likely biased. The model thus provides a better understanding
of the evolutionary processes that shape the architecture and prevalence of complex
diseases.'
acknowledgement: We thank Nick Barton, Magnus Nordborg, John Novembre, Molly Przeworski,
and Himani Sachdeva for many helpful discussions and for comments on the manuscript,
and we thank Joshua Schraiber and 2 anonymous reviewers for comments on the manuscript.
We also thank members of the Sella, Przeworski and Andolfatto labs at Columbia University,
and the Berg, Novembre and Steinrücken labs at the University of Chicago, for feedback
on the work at various stages. This work was completed in part with resources provided
by the University of Chicago's Research Computing Center. This work was supported
by National Institutes of Health F32 grant GM126787 and R35 grant GM151257 to J.J.B.
and National Institutes of Health R01 grant GM115889 to G.S.
article_number: iyaf220
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Jeremy J.
full_name: Berg, Jeremy J.
last_name: Berg
- first_name: Xinyi
full_name: Li, Xinyi
last_name: Li
- first_name: Kellen
full_name: Riall, Kellen
last_name: Riall
- first_name: Laura
full_name: Hayward, Laura
id: fc885ee5-24bf-11eb-ad7b-bcc5104c0c1b
last_name: Hayward
- first_name: Guy
full_name: Sella, Guy
last_name: Sella
citation:
ama: Berg JJ, Li X, Riall K, Hayward L, Sella G. Mutation–selection–drift balance
models of complex diseases. Genetics. 2025;231(4). doi:10.1093/genetics/iyaf220
apa: Berg, J. J., Li, X., Riall, K., Hayward, L., & Sella, G. (2025). Mutation–selection–drift
balance models of complex diseases. Genetics. Oxford University Press.
https://doi.org/10.1093/genetics/iyaf220
chicago: Berg, Jeremy J., Xinyi Li, Kellen Riall, Laura Hayward, and Guy Sella.
“Mutation–Selection–Drift Balance Models of Complex Diseases.” Genetics.
Oxford University Press, 2025. https://doi.org/10.1093/genetics/iyaf220.
ieee: J. J. Berg, X. Li, K. Riall, L. Hayward, and G. Sella, “Mutation–selection–drift
balance models of complex diseases,” Genetics, vol. 231, no. 4. Oxford
University Press, 2025.
ista: Berg JJ, Li X, Riall K, Hayward L, Sella G. 2025. Mutation–selection–drift
balance models of complex diseases. Genetics. 231(4), iyaf220.
mla: Berg, Jeremy J., et al. “Mutation–Selection–Drift Balance Models of Complex
Diseases.” Genetics, vol. 231, no. 4, iyaf220, Oxford University Press,
2025, doi:10.1093/genetics/iyaf220.
short: J.J. Berg, X. Li, K. Riall, L. Hayward, G. Sella, Genetics 231 (2025).
date_created: 2025-12-21T23:01:34Z
date_published: 2025-12-01T00:00:00Z
date_updated: 2025-12-29T11:29:16Z
day: '01'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1093/genetics/iyaf220
external_id:
pmid:
- '41073879'
file:
- access_level: open_access
checksum: b02eb6b78028b8bef435edc8435a8468
content_type: application/pdf
creator: dernst
date_created: 2025-12-29T11:27:51Z
date_updated: 2025-12-29T11:27:51Z
file_id: '20863'
file_name: 2025_Genetics_Berg.pdf
file_size: 1182339
relation: main_file
success: 1
file_date_updated: 2025-12-29T11:27:51Z
has_accepted_license: '1'
intvolume: ' 231'
issue: '4'
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
pmid: 1
publication: Genetics
publication_identifier:
eissn:
- 1943-2631
issn:
- 0016-6731
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Mutation–selection–drift balance models of complex diseases
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 231
year: '2025'
...
---
OA_place: publisher
OA_type: hybrid
_id: '18936'
abstract:
- lang: eng
text: A major obstacle to predictive understanding of evolution stems from the complexity
of biological systems, which prevents detailed characterization of key evolutionary
properties. Here, we highlight some of the major sources of complexity that arise
when relating molecular mechanisms to their evolutionary consequences and ask
whether accounting for every mechanistic detail is important to accurately predict
evolutionary outcomes. To do this, we developed a mechanistic model of a bacterial
promoter regulated by 2 proteins, allowing us to connect any promoter genotype
to 6 phenotypes that capture the dynamics of gene expression following an environmental
switch. Accounting for the mechanisms that govern how this system works enabled
us to provide an in-depth picture of how regulated bacterial promoters might evolve.
More importantly, we used the model to explore which factors that contribute to
the complexity of this system are essential for understanding its evolution, and
which can be simplified without information loss. We found that several key evolutionary
properties—the distribution of phenotypic and fitness effects of mutations, the
evolutionary trajectories during selection for regulation—can be accurately captured
without accounting for all, or even most, parameters of the system. Our findings
point to the need for a mechanistic approach to studying evolution, as it enables
tackling biological complexity and in doing so improves the ability to predict
evolutionary outcomes.
acknowledgement: "The authors thank Nick Barton, Stepan Denisov, Claudia Igler, Srdjan
Sarikas, Anna Staron, and the anonymous reviewers for useful comments and discussions
that helped improve our work.\r\nFunding for this work was provided by the Wellcome
Trust–Royal Society Sir Henry Dale Fellowship (216779/Z/19/Z) and the Royal Society
Research Grant (RG\\R2\\232522) to M.L."
article_number: iyae191
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Rok
full_name: Grah, Rok
id: 483E70DE-F248-11E8-B48F-1D18A9856A87
last_name: Grah
orcid: 0000-0003-2539-3560
- first_name: Calin C
full_name: Guet, Calin C
id: 47F8433E-F248-11E8-B48F-1D18A9856A87
last_name: Guet
orcid: 0000-0001-6220-2052
- first_name: Gašper
full_name: Tkačik, Gašper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkačik
orcid: 0000-0002-6699-1455
- first_name: Mato
full_name: Lagator, Mato
id: 345D25EC-F248-11E8-B48F-1D18A9856A87
last_name: Lagator
citation:
ama: 'Grah R, Guet CC, Tkačik G, Lagator M. Linking molecular mechanisms to their
evolutionary consequences: a primer. Genetics. 2025;229(2). doi:10.1093/genetics/iyae191'
apa: 'Grah, R., Guet, C. C., Tkačik, G., & Lagator, M. (2025). Linking molecular
mechanisms to their evolutionary consequences: a primer. Genetics. Oxford
University Press. https://doi.org/10.1093/genetics/iyae191'
chicago: 'Grah, Rok, Calin C Guet, Gašper Tkačik, and Mato Lagator. “Linking Molecular
Mechanisms to Their Evolutionary Consequences: A Primer.” Genetics. Oxford
University Press, 2025. https://doi.org/10.1093/genetics/iyae191.'
ieee: 'R. Grah, C. C. Guet, G. Tkačik, and M. Lagator, “Linking molecular mechanisms
to their evolutionary consequences: a primer,” Genetics, vol. 229, no.
2. Oxford University Press, 2025.'
ista: 'Grah R, Guet CC, Tkačik G, Lagator M. 2025. Linking molecular mechanisms
to their evolutionary consequences: a primer. Genetics. 229(2), iyae191.'
mla: 'Grah, Rok, et al. “Linking Molecular Mechanisms to Their Evolutionary Consequences:
A Primer.” Genetics, vol. 229, no. 2, iyae191, Oxford University Press,
2025, doi:10.1093/genetics/iyae191.'
short: R. Grah, C.C. Guet, G. Tkačik, M. Lagator, Genetics 229 (2025).
corr_author: '1'
date_created: 2025-01-29T08:21:35Z
date_published: 2025-02-01T00:00:00Z
date_updated: 2025-05-19T14:08:02Z
day: '01'
ddc:
- '570'
department:
- _id: CaGu
- _id: GaTk
doi: 10.1093/genetics/iyae191
external_id:
isi:
- '001379194200001'
pmid:
- '39601269'
file:
- access_level: open_access
checksum: f730e416795969449ef49d97b82ac494
content_type: application/pdf
creator: dernst
date_created: 2025-04-16T09:41:04Z
date_updated: 2025-04-16T09:41:04Z
file_id: '19580'
file_name: 2025_Genetics_Grah.pdf
file_size: 1511688
relation: main_file
success: 1
file_date_updated: 2025-04-16T09:41:04Z
has_accepted_license: '1'
intvolume: ' 229'
isi: 1
issue: '2'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
pmid: 1
publication: Genetics
publication_identifier:
eissn:
- 1943-2631
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Linking molecular mechanisms to their evolutionary consequences: a primer'
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: 229
year: '2025'
...
---
_id: '14452'
abstract:
- lang: eng
text: The classical infinitesimal model is a simple and robust model for the inheritance
of quantitative traits. In this model, a quantitative trait is expressed as the
sum of a genetic and an environmental component, and the genetic component of
offspring traits within a family follows a normal distribution around the average
of the parents’ trait values, and has a variance that is independent of the parental
traits. In previous work, we showed that when trait values are determined by the
sum of a large number of additive Mendelian factors, each of small effect, one
can justify the infinitesimal model as a limit of Mendelian inheritance. In this
paper, we show that this result extends to include dominance. We define the model
in terms of classical quantities of quantitative genetics, before justifying it
as a limit of Mendelian inheritance as the number, M, of underlying loci tends
to infinity. As in the additive case, the multivariate normal distribution of
trait values across the pedigree can be expressed in terms of variance components
in an ancestral population and probabilities of identity by descent determined
by the pedigree. Now, with just first-order dominance effects, we require two-,
three-, and four-way identities. We also show that, even if we condition on parental
trait values, the “shared” and “residual” components of trait values within each
family will be asymptotically normally distributed as the number of loci tends
to infinity, with an error of order 1/M−−√. We illustrate our results with some
numerical examples.
acknowledgement: NHB was supported in part by ERC Grants 250152 and 101055327. AV
was partly supported by the chaire Modélisation Mathématique et Biodiversité of
Veolia Environment—Ecole Polytechnique—Museum National d’Histoire Naturelle—Fondation
X.
article_number: iyad133
article_processing_charge: Yes (in subscription journal)
article_type: original
arxiv: 1
author:
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Alison M.
full_name: Etheridge, Alison M.
last_name: Etheridge
- first_name: Amandine
full_name: Véber, Amandine
last_name: Véber
citation:
ama: Barton NH, Etheridge AM, Véber A. The infinitesimal model with dominance. Genetics.
2023;225(2). doi:10.1093/genetics/iyad133
apa: Barton, N. H., Etheridge, A. M., & Véber, A. (2023). The infinitesimal
model with dominance. Genetics. Oxford University Press. https://doi.org/10.1093/genetics/iyad133
chicago: Barton, Nicholas H, Alison M. Etheridge, and Amandine Véber. “The Infinitesimal
Model with Dominance.” Genetics. Oxford University Press, 2023. https://doi.org/10.1093/genetics/iyad133.
ieee: N. H. Barton, A. M. Etheridge, and A. Véber, “The infinitesimal model with
dominance,” Genetics, vol. 225, no. 2. Oxford University Press, 2023.
ista: Barton NH, Etheridge AM, Véber A. 2023. The infinitesimal model with dominance.
Genetics. 225(2), iyad133.
mla: Barton, Nicholas H., et al. “The Infinitesimal Model with Dominance.” Genetics,
vol. 225, no. 2, iyad133, Oxford University Press, 2023, doi:10.1093/genetics/iyad133.
short: N.H. Barton, A.M. Etheridge, A. Véber, Genetics 225 (2023).
date_created: 2023-10-29T23:01:15Z
date_published: 2023-10-01T00:00:00Z
date_updated: 2025-09-09T13:07:07Z
day: '01'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1093/genetics/iyad133
ec_funded: 1
external_id:
arxiv:
- '2211.03515'
isi:
- '001148042000008'
file:
- access_level: open_access
checksum: 3f65b1fbe813e2f4dbb5d2b5e891844a
content_type: application/pdf
creator: dernst
date_created: 2023-10-30T12:57:53Z
date_updated: 2023-10-30T12:57:53Z
file_id: '14469'
file_name: 2023_Genetics_Barton.pdf
file_size: 1439032
relation: main_file
success: 1
file_date_updated: 2023-10-30T12:57:53Z
has_accepted_license: '1'
intvolume: ' 225'
isi: 1
issue: '2'
language:
- iso: eng
month: '10'
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: bd6958e0-d553-11ed-ba76-86eba6a76c00
grant_number: '101055327'
name: Understanding the evolution of continuous genomes
publication: Genetics
publication_identifier:
eissn:
- 1943-2631
issn:
- 0016-6731
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
related_material:
record:
- id: '12949'
relation: research_data
status: public
scopus_import: '1'
status: public
title: The infinitesimal model with dominance
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: 225
year: '2023'
...
---
_id: '11411'
abstract:
- lang: eng
text: Many studies have quantified the distribution of heterozygosity and relatedness
in natural populations, but few have examined the demographic processes driving
these patterns. In this study, we take a novel approach by studying how population
structure affects both pairwise identity and the distribution of heterozygosity
in a natural population of the self-incompatible plant Antirrhinum majus. Excess
variance in heterozygosity between individuals is due to identity disequilibrium,
which reflects the variance in inbreeding between individuals; it is measured
by the statistic g2. We calculated g2 together with FST and pairwise relatedness
(Fij) using 91 SNPs in 22,353 individuals collected over 11 years. We find that
pairwise Fij declines rapidly over short spatial scales, and the excess variance
in heterozygosity between individuals reflects significant variation in inbreeding.
Additionally, we detect an excess of individuals with around half the average
heterozygosity, indicating either selfing or matings between close relatives.
We use 2 types of simulation to ask whether variation in heterozygosity is consistent
with fine-scale spatial population structure. First, by simulating offspring using
parents drawn from a range of spatial scales, we show that the known pollen dispersal
kernel explains g2. Second, we simulate a 1,000-generation pedigree using the
known dispersal and spatial distribution and find that the resulting g2 is consistent
with that observed from the field data. In contrast, a simulated population with
uniform density underestimates g2, indicating that heterogeneous density promotes
identity disequilibrium. Our study shows that heterogeneous density and leptokurtic
dispersal can together explain the distribution of heterozygosity.
acknowledged_ssus:
- _id: ScienComp
acknowledgement: "Part of this work was funded by Marie Curie COFUND Doctoral Fellowship
and Austrian Science Fund FWF (grant P32166).\r\nWe thank the many volunteers and
friends who have contributed to data collection in the field site over the years,
in particular those who have managed field seasons: Barbora Trubenova, Maria Clara
Melo, Tom Ellis, Eva Cereghetti, Lenka Matejovicova, Beatriz Pablo Carmona. Frederic
Ferrer and Eva Salmerón Mateu have been immensely helpful with logistics at our
informal field station, El Serrat de Planoles. We thank Sean Stankowski for technical
help in\r\nproducing figure 1. This research was also supported by the Scientific
Service Units (SSU) of IST Austria through resources provided by Scientific Computing
(SciComp)."
article_number: iyac083
article_processing_charge: No
article_type: original
author:
- first_name: Parvathy
full_name: Surendranadh, Parvathy
id: 455235B8-F248-11E8-B48F-1D18A9856A87
last_name: Surendranadh
orcid: 0000-0001-6395-386X
- first_name: Louise S
full_name: Arathoon, Louise S
id: 2CFCFF98-F248-11E8-B48F-1D18A9856A87
last_name: Arathoon
orcid: 0000-0003-1771-714X
- first_name: Carina
full_name: Baskett, Carina
id: 3B4A7CE2-F248-11E8-B48F-1D18A9856A87
last_name: Baskett
orcid: 0000-0002-7354-8574
- first_name: David
full_name: Field, David
id: 419049E2-F248-11E8-B48F-1D18A9856A87
last_name: Field
orcid: 0000-0002-4014-8478
- first_name: Melinda
full_name: Pickup, Melinda
id: 2C78037E-F248-11E8-B48F-1D18A9856A87
last_name: Pickup
orcid: 0000-0001-6118-0541
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: Surendranadh P, Arathoon LS, Baskett C, Field D, Pickup M, Barton NH. Effects
of fine-scale population structure on the distribution of heterozygosity in a
long-term study of Antirrhinum majus. Genetics. 2022;221(3). doi:10.1093/genetics/iyac083
apa: Surendranadh, P., Arathoon, L. S., Baskett, C., Field, D., Pickup, M., &
Barton, N. H. (2022). Effects of fine-scale population structure on the distribution
of heterozygosity in a long-term study of Antirrhinum majus. Genetics.
Oxford University Press. https://doi.org/10.1093/genetics/iyac083
chicago: Surendranadh, Parvathy, Louise S Arathoon, Carina Baskett, David Field,
Melinda Pickup, and Nicholas H Barton. “Effects of Fine-Scale Population Structure
on the Distribution of Heterozygosity in a Long-Term Study of Antirrhinum Majus.”
Genetics. Oxford University Press, 2022. https://doi.org/10.1093/genetics/iyac083.
ieee: P. Surendranadh, L. S. Arathoon, C. Baskett, D. Field, M. Pickup, and N. H.
Barton, “Effects of fine-scale population structure on the distribution of heterozygosity
in a long-term study of Antirrhinum majus,” Genetics, vol. 221, no. 3.
Oxford University Press, 2022.
ista: Surendranadh P, Arathoon LS, Baskett C, Field D, Pickup M, Barton NH. 2022.
Effects of fine-scale population structure on the distribution of heterozygosity
in a long-term study of Antirrhinum majus. Genetics. 221(3), iyac083.
mla: Surendranadh, Parvathy, et al. “Effects of Fine-Scale Population Structure
on the Distribution of Heterozygosity in a Long-Term Study of Antirrhinum Majus.”
Genetics, vol. 221, no. 3, iyac083, Oxford University Press, 2022, doi:10.1093/genetics/iyac083.
short: P. Surendranadh, L.S. Arathoon, C. Baskett, D. Field, M. Pickup, N.H. Barton,
Genetics 221 (2022).
corr_author: '1'
date_created: 2022-05-26T13:44:50Z
date_published: 2022-07-01T00:00:00Z
date_updated: 2026-04-07T13:28:29Z
day: '01'
ddc:
- '576'
department:
- _id: GradSch
- _id: NiBa
doi: 10.1093/genetics/iyac083
external_id:
isi:
- '000803735800001'
pmid:
- '35639938'
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file_size: 885374
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creator: larathoo
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date_updated: 2022-05-26T12:48:21Z
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file_name: SupplementalMaterial.pdf
file_size: 1401704
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intvolume: ' 221'
isi: 1
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language:
- iso: eng
month: '07'
oa: 1
oa_version: Submitted Version
pmid: 1
project:
- _id: 05959E1C-7A3F-11EA-A408-12923DDC885E
grant_number: P32166
name: Snapdragon Speciation
publication: Genetics
publication_identifier:
eissn:
- 1943-2631
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
related_material:
record:
- id: '9192'
relation: research_data
status: public
- id: '11321'
relation: research_data
status: public
- id: '14651'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Effects of fine-scale population structure on the distribution of heterozygosity
in a long-term study of Antirrhinum majus
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 221
year: '2022'
...
---
_id: '7400'
abstract:
- lang: eng
text: 'Suppressed recombination allows divergence between homologous sex chromosomes
and the functionality of their genes. Here, we reveal patterns of the earliest
stages of sex-chromosome evolution in the diploid dioecious herb Mercurialis annua
on the basis of cytological analysis, de novo genome assembly and annotation,
genetic mapping, exome resequencing of natural populations, and transcriptome
analysis. The genome assembly contained 34,105 expressed genes, of which 10,076
were assigned to linkage groups. Genetic mapping and exome resequencing of individuals
across the species range both identified the largest linkage group, LG1, as the
sex chromosome. Although the sex chromosomes of M. annua are karyotypically homomorphic,
we estimate that about one-third of the Y chromosome, containing 568 transcripts
and spanning 22.3 cM in the corresponding female map, has ceased recombining.
Nevertheless, we found limited evidence for Y-chromosome degeneration in terms
of gene loss and pseudogenization, and most X- and Y-linked genes appear to have
diverged in the period subsequent to speciation between M. annua and its sister
species M. huetii, which shares the same sex-determining region. Taken together,
our results suggest that the M. annua Y chromosome has at least two evolutionary
strata: a small old stratum shared with M. huetii, and a more recent larger stratum
that is probably unique to M. annua and that stopped recombining ∼1 MYA. Patterns
of gene expression within the nonrecombining region are consistent with the idea
that sexually antagonistic selection may have played a role in favoring suppressed
recombination.'
article_processing_charge: No
article_type: original
author:
- first_name: Paris
full_name: Veltsos, Paris
last_name: Veltsos
- first_name: Kate E.
full_name: Ridout, Kate E.
last_name: Ridout
- first_name: Melissa A
full_name: Toups, Melissa A
id: 4E099E4E-F248-11E8-B48F-1D18A9856A87
last_name: Toups
orcid: 0000-0002-9752-7380
- first_name: Santiago C.
full_name: González-Martínez, Santiago C.
last_name: González-Martínez
- first_name: Aline
full_name: Muyle, Aline
last_name: Muyle
- first_name: Olivier
full_name: Emery, Olivier
last_name: Emery
- first_name: Pasi
full_name: Rastas, Pasi
last_name: Rastas
- first_name: Vojtech
full_name: Hudzieczek, Vojtech
last_name: Hudzieczek
- first_name: Roman
full_name: Hobza, Roman
last_name: Hobza
- first_name: Boris
full_name: Vyskot, Boris
last_name: Vyskot
- first_name: Gabriel A. B.
full_name: Marais, Gabriel A. B.
last_name: Marais
- first_name: Dmitry A.
full_name: Filatov, Dmitry A.
last_name: Filatov
- first_name: John R.
full_name: Pannell, John R.
last_name: Pannell
citation:
ama: Veltsos P, Ridout KE, Toups MA, et al. Early sex-chromosome evolution in the
diploid dioecious plant Mercurialis annua. Genetics. 2019;212(3):815-835.
doi:10.1534/genetics.119.302045
apa: Veltsos, P., Ridout, K. E., Toups, M. A., González-Martínez, S. C., Muyle,
A., Emery, O., … Pannell, J. R. (2019). Early sex-chromosome evolution in the
diploid dioecious plant Mercurialis annua. Genetics. Genetics Society of
America. https://doi.org/10.1534/genetics.119.302045
chicago: Veltsos, Paris, Kate E. Ridout, Melissa A Toups, Santiago C. González-Martínez,
Aline Muyle, Olivier Emery, Pasi Rastas, et al. “Early Sex-Chromosome Evolution
in the Diploid Dioecious Plant Mercurialis Annua.” Genetics. Genetics Society
of America, 2019. https://doi.org/10.1534/genetics.119.302045.
ieee: P. Veltsos et al., “Early sex-chromosome evolution in the diploid dioecious
plant Mercurialis annua,” Genetics, vol. 212, no. 3. Genetics Society of
America, pp. 815–835, 2019.
ista: Veltsos P, Ridout KE, Toups MA, González-Martínez SC, Muyle A, Emery O, Rastas
P, Hudzieczek V, Hobza R, Vyskot B, Marais GAB, Filatov DA, Pannell JR. 2019.
Early sex-chromosome evolution in the diploid dioecious plant Mercurialis annua.
Genetics. 212(3), 815–835.
mla: Veltsos, Paris, et al. “Early Sex-Chromosome Evolution in the Diploid Dioecious
Plant Mercurialis Annua.” Genetics, vol. 212, no. 3, Genetics Society of
America, 2019, pp. 815–35, doi:10.1534/genetics.119.302045.
short: P. Veltsos, K.E. Ridout, M.A. Toups, S.C. González-Martínez, A. Muyle, O.
Emery, P. Rastas, V. Hudzieczek, R. Hobza, B. Vyskot, G.A.B. Marais, D.A. Filatov,
J.R. Pannell, Genetics 212 (2019) 815–835.
date_created: 2020-01-29T16:15:44Z
date_published: 2019-07-01T00:00:00Z
date_updated: 2026-06-18T19:18:06Z
day: '01'
ddc:
- '570'
department:
- _id: BeVi
doi: 10.1534/genetics.119.302045
ec_funded: 1
external_id:
isi:
- '000474809300015'
pmid:
- '31113811'
intvolume: ' 212'
isi: 1
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1534/genetics.119.302045
month: '07'
oa: 1
oa_version: Published Version
page: 815-835
pmid: 1
project:
- _id: 250BDE62-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '715257'
name: Prevalence and Influence of Sexual Antagonism on Genome Evolution
publication: Genetics
publication_identifier:
eissn:
- 1943-2631
issn:
- 0016-6731
publication_status: published
publisher: Genetics Society of America
quality_controlled: '1'
scopus_import: '1'
status: public
title: Early sex-chromosome evolution in the diploid dioecious plant Mercurialis annua
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 212
year: '2019'
...
---
OA_type: closed access
_id: '4251'
abstract:
- lang: eng
text: In finite populations subject to selection, genetic drift generates negative
linkage disequilibrium, on average, even if selection acts independently (i.e.
multiplicatively) upon all loci. Negative disequilibrium reduces the variance
in fitness and hence, by FISHER's Fundamental Theorem (1930), slows the rate of
increase in mean fitness. Modifiers that increase recombination eliminate the
negative disequilibria that impede selection and consequently increase in frequency
by 'hitch-hiking'. In addition, recombinant progeny are more fit on average than
non-recombinant progeny when there is negative linkage disequilibrium and loci
interact multiplicatively. For both these reasons, stochastic fluctuations in
linkage disequilibrium in finite populations favor the evolution of increased
rates of recombination, even in the absence of epistatic interactions among loci
and even when disequilibrium is initially absent. The method developed within
this paper quantifies the strength of selection on a modifier allele that increases
recombination due to stochastically generated linkage disequilibria. The analysis
indicates that, in a population subject to multiplicative selection, genetic associations
generated by drift do select for increased recombination, a result that is confirmed
by Monte Carlo simulations. Selection for a modifier that increases recombination
is highest when linkage among all loci is tight, when beneficial alleles rise
from low to high frequency, and when the population size is small.
article_processing_charge: No
article_type: original
author:
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
- first_name: Sarah
full_name: Otto, Sarah
last_name: Otto
citation:
ama: Barton NH, Otto S. Evolution of recombination due to random drift. Genetics.
2005;169(4):2353-2370. doi:10.1534/genetics.104.032821
apa: Barton, N. H., & Otto, S. (2005). Evolution of recombination due to random
drift. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.104.032821
chicago: Barton, Nicholas H, and Sarah Otto. “Evolution of Recombination Due to
Random Drift.” Genetics. Genetics Society of America, 2005. https://doi.org/10.1534/genetics.104.032821.
ieee: N. H. Barton and S. Otto, “Evolution of recombination due to random drift,”
Genetics, vol. 169, no. 4. Genetics Society of America, pp. 2353–2370,
2005.
ista: Barton NH, Otto S. 2005. Evolution of recombination due to random drift. Genetics.
169(4), 2353–2370.
mla: Barton, Nicholas H., and Sarah Otto. “Evolution of Recombination Due to Random
Drift.” Genetics, vol. 169, no. 4, Genetics Society of America, 2005, pp.
2353–70, doi:10.1534/genetics.104.032821.
short: N.H. Barton, S. Otto, Genetics 169 (2005) 2353–2370.
das_tickbox: '1'
date_created: 2018-12-11T12:07:51Z
date_published: 2005-03-01T00:00:00Z
date_updated: 2026-07-03T08:18:26Z
day: '01'
doi: 10.1534/genetics.104.032821
extern: '1'
external_id:
pmid:
- '15687279'
intvolume: ' 169'
issue: '4'
language:
- iso: eng
month: '03'
oa_version: None
page: 2353 - 2370
pmid: 1
publication: Genetics
publication_identifier:
eissn:
- 1943-2631
issn:
- 0016-6731
publication_status: published
publisher: Genetics Society of America
publist_id: '1846'
status: public
title: Evolution of recombination due to random drift
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 169
year: '2005'
...
---
OA_type: closed access
_id: '3151'
abstract:
- lang: eng
text: Biosynthesis of most peptide hormones and neuropeptides requires proteolytic
excision of the active peptide from inactive proprotein precursors, an activity
carried out by subtilisin-like proprotein convertases (SPCs) in constitutive or
regulated secretory pathways. The Drosophila amontillado (amon) gene encodes a
homolog of the mammalian PC2 protein, an SPC that functions in the regulated secretory
pathway in neuroendocrine tissues. We have identified amon mutants by isolating
ethylmethanesulfonate (EMS)-induced lethal and visible mutations that define two
complementation groups in the amon interval at 97D1 of the third chromosome. DNA
sequencing identified the amon complementation group and the DNA sequence change
for each of the nine amon alleles isolated. amon mutants display partial embryonic
lethality, are defective in larval growth, and arrest during the first to second
instar larval molt. Mutant larvae can be rescued by heat-shock-induced expression
of the amon protein. Rescued larvae arrest at the subsequent larval molt, suggesting
that amon is also required for the second to third instar larval molt. Our data
indicate that the amon proprotein convertase is required during embryogenesis
and larval development in Drosophila and support the hypothesis that AMON acts
to proteolytically process peptide hormones that regulate hatching, larval growth,
and larval ecdysis.
article_processing_charge: No
article_type: original
author:
- first_name: Lowell
full_name: Rayburn, Lowell
last_name: Rayburn
- first_name: Holly
full_name: Gooding, Holly
last_name: Gooding
- first_name: Semil
full_name: Choksi, Semil
last_name: Choksi
- first_name: Dhea
full_name: Maloney, Dhea
last_name: Maloney
- first_name: Ambrose
full_name: Kidd, Ambrose
last_name: Kidd
- first_name: Daria E
full_name: Siekhaus, Daria E
id: 3D224B9E-F248-11E8-B48F-1D18A9856A87
last_name: Siekhaus
orcid: 0000-0001-8323-8353
- first_name: Michael
full_name: Bender, Michael
last_name: Bender
citation:
ama: Rayburn L, Gooding H, Choksi S, et al. Amontillado, the Drosophila homolog
of the prohormone processing protease PC2, is required during embryogenesis and
early larval development. Genetics. 2003;163(1):227-237. doi:10.1093/genetics/163.1.227
apa: Rayburn, L., Gooding, H., Choksi, S., Maloney, D., Kidd, A., Siekhaus, D. E.,
& Bender, M. (2003). Amontillado, the Drosophila homolog of the prohormone
processing protease PC2, is required during embryogenesis and early larval development.
Genetics. Oxford Academic. https://doi.org/10.1093/genetics/163.1.227
chicago: Rayburn, Lowell, Holly Gooding, Semil Choksi, Dhea Maloney, Ambrose Kidd,
Daria E Siekhaus, and Michael Bender. “Amontillado, the Drosophila Homolog of
the Prohormone Processing Protease PC2, Is Required during Embryogenesis and Early
Larval Development.” Genetics. Oxford Academic, 2003. https://doi.org/10.1093/genetics/163.1.227.
ieee: L. Rayburn et al., “Amontillado, the Drosophila homolog of the prohormone
processing protease PC2, is required during embryogenesis and early larval development,”
Genetics, vol. 163, no. 1. Oxford Academic, pp. 227–237, 2003.
ista: Rayburn L, Gooding H, Choksi S, Maloney D, Kidd A, Siekhaus DE, Bender M.
2003. Amontillado, the Drosophila homolog of the prohormone processing protease
PC2, is required during embryogenesis and early larval development. Genetics.
163(1), 227–237.
mla: Rayburn, Lowell, et al. “Amontillado, the Drosophila Homolog of the Prohormone
Processing Protease PC2, Is Required during Embryogenesis and Early Larval Development.”
Genetics, vol. 163, no. 1, Oxford Academic, 2003, pp. 227–37, doi:10.1093/genetics/163.1.227.
short: L. Rayburn, H. Gooding, S. Choksi, D. Maloney, A. Kidd, D.E. Siekhaus, M.
Bender, Genetics 163 (2003) 227–237.
date_created: 2018-12-11T12:01:41Z
date_published: 2003-01-01T00:00:00Z
date_updated: 2026-05-22T08:38:04Z
day: '01'
doi: 10.1093/genetics/163.1.227
extern: '1'
external_id:
pmid:
- '12586710'
intvolume: ' 163'
issue: '1'
language:
- iso: eng
month: '01'
oa_version: None
page: 227 - 237
pmid: 1
publication: Genetics
publication_identifier:
eissn:
- 1943-2631
issn:
- 0016-6731
publication_status: published
publisher: Oxford Academic
publist_id: '3545'
quality_controlled: '1'
status: public
title: Amontillado, the Drosophila homolog of the prohormone processing protease PC2,
is required during embryogenesis and early larval development
type: journal_article
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
volume: 163
year: '2003'
...