---
OA_place: repository
OA_type: green
_id: '21968'
abstract:
- lang: eng
text: Balancing selection, a form of selection that maintains genetic diversity,
is difficult to detect, and the importance of balancing selection for the maintenance
of genetic variation may be larger than often assumed. We model the possibility
that the diversity-promoting effects of balancing selection extend to other loci
that show sign epistasis with a locus under balancing selection. Rather than focusing
on overdominance, as was done in previous efforts, we explore the effects of negative
frequency dependence and show that this has important effects on the conditions
under which the diversity-promoting effect of epistasis can occur in diploids.
Our results show that not only recombination rate but also the dominance of sign
epistasis are key parameters that determine the maintenance of polymorphism beyond
the locus under direct balancing selection. We suggest that the effect we explore
may play a significant role, especially when balancing selection acts on major
effect loci.
acknowledgement: This work was funded by grants from the Swedish Research Council
(2023-03730 to G.A.) and the DOC fellowship from the Austrian Academy of Science
(26293 to K.K.).
article_processing_charge: No
author:
- first_name: Kseniia
full_name: Khudiakova, Kseniia
id: 4E6DC800-AE37-11E9-AC72-31CAE5697425
last_name: Khudiakova
orcid: 0000-0002-6246-1465
- 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: Goran
full_name: Arnqvist, Goran
last_name: Arnqvist
citation:
ama: Khudiakova K, Barton NH, Arnqvist G. Sign epistasis extends the effects of
balancing selection on genetic diversity. bioRxiv. doi:10.1101/2025.04.09.647826
apa: Khudiakova, K., Barton, N. H., & Arnqvist, G. (n.d.). Sign epistasis extends
the effects of balancing selection on genetic diversity. bioRxiv. https://doi.org/10.1101/2025.04.09.647826
chicago: Khudiakova, Kseniia, Nicholas H Barton, and Goran Arnqvist. “Sign Epistasis
Extends the Effects of Balancing Selection on Genetic Diversity.” BioRxiv,
n.d. https://doi.org/10.1101/2025.04.09.647826.
ieee: K. Khudiakova, N. H. Barton, and G. Arnqvist, “Sign epistasis extends the
effects of balancing selection on genetic diversity,” bioRxiv. .
ista: Khudiakova K, Barton NH, Arnqvist G. Sign epistasis extends the effects of
balancing selection on genetic diversity. bioRxiv, 10.1101/2025.04.09.647826.
mla: Khudiakova, Kseniia, et al. “Sign Epistasis Extends the Effects of Balancing
Selection on Genetic Diversity.” BioRxiv, doi:10.1101/2025.04.09.647826.
short: K. Khudiakova, N.H. Barton, G. Arnqvist, BioRxiv (n.d.).
corr_author: '1'
date_created: 2026-06-09T12:26:11Z
date_published: 2026-04-23T00:00:00Z
date_updated: 2026-06-12T12:43:34Z
day: '23'
department:
- _id: NiBa
- _id: JaMa
doi: 10.1101/2025.04.09.647826
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1101/2025.04.09.647826
month: '04'
oa: 1
oa_version: Preprint
project:
- _id: 34d33d68-11ca-11ed-8bc3-ec13763c0ca8
grant_number: '26293'
name: The impact of deleterious mutations on small populations
publication: bioRxiv
publication_status: draft
related_material:
record:
- id: '21918'
relation: dissertation_contains
status: public
status: public
title: Sign epistasis extends the effects of balancing selection on genetic diversity
tmp:
image: /images/cc_by_nc.png
legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode
name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
short: CC BY-NC (4.0)
type: preprint
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2026'
...
---
OA_type: closed access
_id: '21036'
abstract:
- lang: eng
text: 'Forests under livestock grazing sustain important ecosystem services but
face potential trade-offs between production and ecological integrity. While the
effects of grazing on individual forest attributes are well documented, their
integrated consequences remain poorly understood, particularly in temperate forest
ecosystems. We evaluated the combined influence of livestock grazing intensity
and canopy cover on individual attributes and ecosystem multifunctionality in
native Nothofagus forests of Tierra del Fuego, Argentina. Across eight ranches
spanning two agroecological regions (Ecotone and Mountain Range), we quantified
forest regeneration, understorey richness and biomass, and soil properties, integrating
them into a multifunctionality index. Using generalized linear mixed models, we
found strong context-dependence: in the Mountain Range, higher grazing intensity
reduced seedling and sapling density, organic matter content, coarse woody debris,
and overall multifunctionality. In the Ecotone, these effects of livestock use
intensity were attenuated, and canopy cover diminished sapling density and multifunctionality,
but moderate cover enhanced understorey. Our results extend multifunctionality
research from grazed grasslands to grazed temperate forests and show that ecological
responses and trade-offs vary across landscape units. We conclude that the Mountain
Range is more vulnerable to grazing, requiring stricter management, whereas the
Ecotone retains greater capacity to sustain multifunctionality under controlled
livestock use intensity. These findings underscore the importance of region-specific
silvopastoral strategies that reconcile food production with forest conservation
in southern Patagonia and comparable temperate forest landscapes worldwide.'
acknowledgement: We would like to thank Guillermo Ortiz (CADIC-CONICET) for his invaluable
support in the field and lab work. We are extremely grateful to the ranchers for
kindly allowing us access to their fields. Funding for this work was provided by
the Argentine National Scientific and Technical Research Council (CONICET) and the
National Agency for Scientific Promotion through project PICT 2019–675. PR was also
granted the Mobility Scholarship Program 2025 between Andalusian and Ibero-American
Universities (AUIP). VCA is co-supported by the Community of Madrid under the 2024
call for the ‘César Nombela’ research talent attraction programme (2024-T1/ECO-31335).
article_number: '110219'
article_processing_charge: No
article_type: original
author:
- first_name: Paula
full_name: Rodríguez, Paula
last_name: Rodríguez
- first_name: Verónica
full_name: Cruz Alonso, Verónica
last_name: Cruz Alonso
- first_name: Silvina
full_name: Romano, Silvina
last_name: Romano
- first_name: Gimena
full_name: Bustamante, Gimena
last_name: Bustamante
- first_name: Rosina Matilde
full_name: Soler Schaller, Rosina Matilde
id: 9e668447-8c32-11ed-b0c7-8dc2d7b80803
last_name: Soler Schaller
citation:
ama: Rodríguez P, Cruz Alonso V, Romano S, Bustamante G, Soler Schaller RM. Context-dependent
effects of livestock grazing on forest attributes and ecosystem multifunctionality
in Nothofagus forests. Agriculture, Ecosystems and Environment. 2026;400.
doi:10.1016/j.agee.2026.110219
apa: Rodríguez, P., Cruz Alonso, V., Romano, S., Bustamante, G., & Soler Schaller,
R. M. (2026). Context-dependent effects of livestock grazing on forest attributes
and ecosystem multifunctionality in Nothofagus forests. Agriculture, Ecosystems
and Environment. Elsevier. https://doi.org/10.1016/j.agee.2026.110219
chicago: Rodríguez, Paula, Verónica Cruz Alonso, Silvina Romano, Gimena Bustamante,
and Rosina Matilde Soler Schaller. “Context-Dependent Effects of Livestock Grazing
on Forest Attributes and Ecosystem Multifunctionality in Nothofagus Forests.”
Agriculture, Ecosystems and Environment. Elsevier, 2026. https://doi.org/10.1016/j.agee.2026.110219.
ieee: P. Rodríguez, V. Cruz Alonso, S. Romano, G. Bustamante, and R. M. Soler Schaller,
“Context-dependent effects of livestock grazing on forest attributes and ecosystem
multifunctionality in Nothofagus forests,” Agriculture, Ecosystems and Environment,
vol. 400. Elsevier, 2026.
ista: Rodríguez P, Cruz Alonso V, Romano S, Bustamante G, Soler Schaller RM. 2026.
Context-dependent effects of livestock grazing on forest attributes and ecosystem
multifunctionality in Nothofagus forests. Agriculture, Ecosystems and Environment.
400, 110219.
mla: Rodríguez, Paula, et al. “Context-Dependent Effects of Livestock Grazing on
Forest Attributes and Ecosystem Multifunctionality in Nothofagus Forests.” Agriculture,
Ecosystems and Environment, vol. 400, 110219, Elsevier, 2026, doi:10.1016/j.agee.2026.110219.
short: P. Rodríguez, V. Cruz Alonso, S. Romano, G. Bustamante, R.M. Soler Schaller,
Agriculture, Ecosystems and Environment 400 (2026).
das_tickbox: '1'
dataavailabilitystatement: The authors do not have permission to share data.
date_created: 2026-01-25T23:01:38Z
date_published: 2026-04-15T00:00:00Z
date_updated: 2026-07-27T11:01:30Z
day: '15'
department:
- _id: NiBa
doi: 10.1016/j.agee.2026.110219
intvolume: ' 400'
language:
- iso: eng
month: '04'
oa_version: None
publication: Agriculture, Ecosystems and Environment
publication_identifier:
issn:
- 0167-8809
publication_status: published
publisher: Elsevier
quality_controlled: '1'
researchdata_availability: no
scopus_import: '1'
status: public
supplementarymaterial: yes
title: Context-dependent effects of livestock grazing on forest attributes and ecosystem
multifunctionality in Nothofagus forests
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 400
year: '2026'
...
---
OA_place: publisher
OA_type: hybrid
PlanS_conform: '1'
_id: '21759'
abstract:
- lang: eng
text: 'Promoters and enhancers are cis-regulatory elements (CREs), DNA sequences
that bind transcription factor (TF) proteins to up- or down-regulate target genes.
Decades-long efforts yielded TF-DNA interaction models that predict how strongly
an individual TF binds arbitrary DNA sequences and how individual binding events
on the CRE combine to affect gene expression. These insights can be synthesized
into a global, biophysically realistic, and quantitative genotype-phenotype (GP)
map for gene regulation, a ‘holy grail’ for the application of evolutionary theory.
A global map provides a rare opportunity to simulate the long-term evolution of
regulatory sequences and pose several fundamental questions: How long does it
take to evolve CREs de novo? How many non-trivial regulatory functions exist in
sequence space? How connected are they? For which regulatory architecture is CRE
evolution most rapid and evolvable? In this article, the second of a two-part
series, we review the application of evolutionary concepts — epistasis, robustness,
evolvability, tunability, plasticity, and bet-hedging — to the evolution of gene
regulatory sequences. We then evaluate the potential for a unifying theory for
the evolution of regulatory sequences and identify key open challenges.'
acknowledgement: "We thank Calin Guet and Santiago Herrera-Álvarez for essential contributions
to this manuscript.\r\nE.M. acknowledges support from the APART-USA fellowship,
jointly funded by the Austrian Academy of Sciences (ÖAW) and the Institute of Science
and Technology Austria (ISTA). N.B. acknowledges funding from the ERC Advanced Grant
101055327 “HaplotypeStructure”.\r\nThis study was also supported by the European
Molecular Biology Laboratory (N.O.B., J.C.)."
article_number: '102472'
article_processing_charge: Yes (via OA deal)
article_type: review
author:
- first_name: Elia
full_name: Mascolo, Elia
id: 776a6ed0-a053-11f0-8635-80b95e0e0d53
last_name: Mascolo
orcid: 0000-0003-2977-7844
- first_name: Reka E
full_name: Körei, Reka E
id: 50FDE43E-AA30-11E9-A72B-8A12E6697425
last_name: Körei
- first_name: Noa O.
full_name: Borst, Noa O.
last_name: Borst
- 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: Justin
full_name: Crocker, Justin
last_name: Crocker
- first_name: Gašper
full_name: Tkačik, Gašper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkačik
orcid: 0000-0002-6699-1455
citation:
ama: 'Mascolo E, Körei RE, Borst NO, Barton NH, Crocker J, Tkačik G. Long-term evolution
of regulatory DNA sequences. Part 2: Theory and future challenges. Current
Opinion in Genetics and Development. 2026;98. doi:10.1016/j.gde.2026.102472'
apa: 'Mascolo, E., Körei, R. E., Borst, N. O., Barton, N. H., Crocker, J., &
Tkačik, G. (2026). Long-term evolution of regulatory DNA sequences. Part 2: Theory
and future challenges. Current Opinion in Genetics and Development. Elsevier.
https://doi.org/10.1016/j.gde.2026.102472'
chicago: 'Mascolo, Elia, Reka E Körei, Noa O. Borst, Nicholas H Barton, Justin Crocker,
and Gašper Tkačik. “Long-Term Evolution of Regulatory DNA Sequences. Part 2: Theory
and Future Challenges.” Current Opinion in Genetics and Development. Elsevier,
2026. https://doi.org/10.1016/j.gde.2026.102472.'
ieee: 'E. Mascolo, R. E. Körei, N. O. Borst, N. H. Barton, J. Crocker, and G. Tkačik,
“Long-term evolution of regulatory DNA sequences. Part 2: Theory and future challenges,”
Current Opinion in Genetics and Development, vol. 98. Elsevier, 2026.'
ista: 'Mascolo E, Körei RE, Borst NO, Barton NH, Crocker J, Tkačik G. 2026. Long-term
evolution of regulatory DNA sequences. Part 2: Theory and future challenges. Current
Opinion in Genetics and Development. 98, 102472.'
mla: 'Mascolo, Elia, et al. “Long-Term Evolution of Regulatory DNA Sequences. Part
2: Theory and Future Challenges.” Current Opinion in Genetics and Development,
vol. 98, 102472, Elsevier, 2026, doi:10.1016/j.gde.2026.102472.'
short: E. Mascolo, R.E. Körei, N.O. Borst, N.H. Barton, J. Crocker, G. Tkačik, Current
Opinion in Genetics and Development 98 (2026).
corr_author: '1'
das_tickbox: '1'
dataavailabilitystatement: No data were used for the research described in the article.
date_created: 2026-04-26T22:01:46Z
date_published: 2026-06-01T00:00:00Z
date_updated: 2026-07-27T13:40:24Z
day: '01'
ddc:
- '570'
department:
- _id: GaTk
- _id: NiBa
doi: 10.1016/j.gde.2026.102472
file:
- access_level: open_access
checksum: ac8bbee61717bfe7116e312cc6825259
content_type: application/pdf
creator: dernst
date_created: 2026-07-27T13:39:59Z
date_updated: 2026-07-27T13:39:59Z
file_id: '22590'
file_name: 2026_CurrentOpinionGeneticsDev_Mascolo.pdf
file_size: 3190001
relation: main_file
success: 1
file_date_updated: 2026-07-27T13:39:59Z
has_accepted_license: '1'
intvolume: ' 98'
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
project:
- _id: bd6958e0-d553-11ed-ba76-86eba6a76c00
grant_number: '101055327'
name: Understanding the evolution of continuous genomes
publication: Current Opinion in Genetics and Development
publication_identifier:
eissn:
- 1879-0380
issn:
- 0959-437X
publication_status: published
publisher: Elsevier
quality_controlled: '1'
researchdata_availability: no
scopus_import: '1'
status: public
supplementarymaterial: no
title: 'Long-term evolution of regulatory DNA sequences. Part 2: Theory and future
challenges'
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: 98
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_type: closed access
_id: '20869'
abstract:
- lang: eng
text: "Premise: What maintains trait divergence in the face of gene flow? Two varieties
of wild snapdragon (Antirrhinum majus) characterized by divergent flower color
hybridize in their native range. Selection on flower color genes is indicated
by sharp clines, but the selective agents have not been demonstrated. Although
previous work has focused on pollinators, pigmentation genes can also contribute
to abiotic stress tolerance. We hypothesized that pigmentation in A. majus mediates
stress tolerance, which could contribute to hybrid zone maintenance through parental
niche divergence or hybrid maladaptation. Specifically, we tested whether morphotype
mediates drought tolerance in an experiment comparing magenta-flowered var. pseudomajus,
yellow-flowered var. striatum, and their pink-flowered hybrid cross.\r\nMethods:
We experimentally compared drought tolerance of each morphotype from allopatric
crosses within and between varieties using three greenhouse treatments. Control
plants were watered as needed, while drought-treated plants were watered half
as often, either from the transplant stage (“early” drought), or from flowering
onset (“late” drought).\r\nResults: Parental morphotypes responded identically
to drought in fitness and most phenotypic traits. However, hybrids had lower survival
(14%) under late drought stress than parental morphotypes (70%). All hybrids that
flowered in the late drought treatment died, compared to ~20% of flowering parental
morphotypes.\r\nConclusions: Hybrid maladaptation to abiotic stress could potentially
contribute to flower color divergence in the face of gene flow in A. majus. Further
research should test the relevance of our results to field conditions and explicitly
probe the role of flower color genes in drought tolerance."
acknowledgement: Thank you to Doug Schemske and Nick Barton forcritically reviewing
the manuscript, Beatriz Pablo Car-mona for assisting with data collection, Melinda
Pickupand Eva Cereghetti for seedlings, and Louise Arathoon,Ksenia Khudiakova, Georg
Rieckh, Daria Shiplina, andAnja Westram for help with experimental maintenance.We
sincerely thank the Associate Editor Brenda Grewelland two anonymous reviewers for
their thoughtfulcomments and suggestions, which substantially improved the clarity
and quality of our manuscript. C.B. receivedfunding from the European Union's Horizon
2020 researchand innovation programme under the Marie Skłodowska‐Curie Grant Agreement
No. 754411
article_number: e70129
article_processing_charge: No
article_type: original
author:
- first_name: Alexandre
full_name: Fuster‐Calvo, Alexandre
last_name: Fuster‐Calvo
- first_name: Coline C.
full_name: Jaworski, Coline C.
last_name: Jaworski
- first_name: Thomas
full_name: Ellis, Thomas
id: 3153D6D4-F248-11E8-B48F-1D18A9856A87
last_name: Ellis
orcid: 0000-0002-8511-0254
- first_name: Carina
full_name: Baskett, Carina
id: 3B4A7CE2-F248-11E8-B48F-1D18A9856A87
last_name: Baskett
orcid: 0000-0002-7354-8574
citation:
ama: Fuster‐Calvo A, Jaworski CC, Ellis T, Baskett C. Reduced fitness under drought
stress in F1 hybrids of Antirrhinum majus varieties with divergent flower colors.
American Journal of Botany. 2025;112(12). doi:10.1002/ajb2.70129
apa: Fuster‐Calvo, A., Jaworski, C. C., Ellis, T., & Baskett, C. (2025). Reduced
fitness under drought stress in F1 hybrids of Antirrhinum majus varieties with
divergent flower colors. American Journal of Botany. Wiley. https://doi.org/10.1002/ajb2.70129
chicago: Fuster‐Calvo, Alexandre, Coline C. Jaworski, Thomas Ellis, and Carina Baskett.
“Reduced Fitness under Drought Stress in F1 Hybrids of Antirrhinum Majus Varieties
with Divergent Flower Colors.” American Journal of Botany. Wiley, 2025.
https://doi.org/10.1002/ajb2.70129.
ieee: A. Fuster‐Calvo, C. C. Jaworski, T. Ellis, and C. Baskett, “Reduced fitness
under drought stress in F1 hybrids of Antirrhinum majus varieties with divergent
flower colors,” American Journal of Botany, vol. 112, no. 12. Wiley, 2025.
ista: Fuster‐Calvo A, Jaworski CC, Ellis T, Baskett C. 2025. Reduced fitness under
drought stress in F1 hybrids of Antirrhinum majus varieties with divergent flower
colors. American Journal of Botany. 112(12), e70129.
mla: Fuster‐Calvo, Alexandre, et al. “Reduced Fitness under Drought Stress in F1
Hybrids of Antirrhinum Majus Varieties with Divergent Flower Colors.” American
Journal of Botany, vol. 112, no. 12, e70129, Wiley, 2025, doi:10.1002/ajb2.70129.
short: A. Fuster‐Calvo, C.C. Jaworski, T. Ellis, C. Baskett, American Journal of
Botany 112 (2025).
date_created: 2025-12-29T12:14:26Z
date_published: 2025-12-01T00:00:00Z
date_updated: 2026-01-05T11:56:22Z
day: '01'
department:
- _id: NiBa
doi: 10.1002/ajb2.70129
ec_funded: 1
external_id:
pmid:
- '41327576 '
intvolume: ' 112'
issue: '12'
language:
- iso: eng
month: '12'
oa_version: None
pmid: 1
project:
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: American Journal of Botany
publication_identifier:
eissn:
- 1537-2197
issn:
- 0002-9122
publication_status: published
publisher: Wiley
quality_controlled: '1'
related_material:
link:
- relation: software
url: https://github.com/Alex-Fuster/hybrids_drought
scopus_import: '1'
status: public
title: Reduced fitness under drought stress in F1 hybrids of Antirrhinum majus varieties
with divergent flower colors
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 112
year: '2025'
...
---
OA_place: repository
OA_type: green
_id: '21322'
abstract:
- lang: eng
text: Habitat fragmentation poses a significant risk to population survival, causing
both demographic stochasticity and genetic drift within local populations to increase,
thereby increasing genetic load. Higher load causes population numbers to decline,
which reduces the efficiency of selection and further increases load, resulting
in a positive feedback that may drive entire populations to extinction. Here,
we investigate this eco-evolutionary feedback in a metapopulation consisting of
local demes connected via migration, with individuals subject to deleterious mutation
at a large number of loci. We first analyze the determinants of load under soft
selection, where population sizes are fixed, and then build on this to understand
hard selection, where population sizes and load coevolve. We show that under soft
selection, very little gene flow (less than one migrant per generation) is enough
to prevent fixation of deleterious alleles. By contrast, much higher levels of
migration are required to mitigate load and prevent extinction when selection
is hard, with critical migration thresholds for metapopulation persistence increasing
sharply as the genome-wide deleterious mutation rate becomes comparable to the
baseline population growth rate. Moreover, critical migration thresholds are highest
if deleterious mutations have intermediate selection coefficients but lower if
alleles are predominantly recessive rather than additive (due to more efficient
purging of recessive load within local populations). Our analysis is based on
a combination of analytical approximations and simulations, allowing for a more
comprehensive understanding of the factors influencing load and extinction in
fragmented populations.
acknowledgement: 'This research was partially funded by the Austrian Science Fund
(FWF P-32896B) and DOC Fellowships of the Austrian Academy of Sciences: grants 26380
(O.O.) and 26293 (K.K.). We thank Nick Barton for useful comments on the chapter
in O.O.’s thesis that led to this article.'
article_processing_charge: No
article_type: original
author:
- first_name: Oluwafunmilola O
full_name: Olusanya, Oluwafunmilola O
id: 41AD96DC-F248-11E8-B48F-1D18A9856A87
last_name: Olusanya
orcid: 0000-0003-1971-8314
- first_name: Kseniia
full_name: Khudiakova, Kseniia
id: 4E6DC800-AE37-11E9-AC72-31CAE5697425
last_name: Khudiakova
orcid: 0000-0002-6246-1465
- first_name: Himani
full_name: Sachdeva, Himani
id: 42377A0A-F248-11E8-B48F-1D18A9856A87
last_name: Sachdeva
citation:
ama: Olusanya OO, Khudiakova K, Sachdeva H. Genetic load, eco-evolutionary feedback,
and extinction in metapopulations. The American Naturalist. 2025;205(6):617-636.
doi:10.1086/735562
apa: Olusanya, O. O., Khudiakova, K., & Sachdeva, H. (2025). Genetic load, eco-evolutionary
feedback, and extinction in metapopulations. The American Naturalist. University
of Chicago Press. https://doi.org/10.1086/735562
chicago: Olusanya, Oluwafunmilola O, Kseniia Khudiakova, and Himani Sachdeva. “Genetic
Load, Eco-Evolutionary Feedback, and Extinction in Metapopulations.” The American
Naturalist. University of Chicago Press, 2025. https://doi.org/10.1086/735562.
ieee: O. O. Olusanya, K. Khudiakova, and H. Sachdeva, “Genetic load, eco-evolutionary
feedback, and extinction in metapopulations,” The American Naturalist,
vol. 205, no. 6. University of Chicago Press, pp. 617–636, 2025.
ista: Olusanya OO, Khudiakova K, Sachdeva H. 2025. Genetic load, eco-evolutionary
feedback, and extinction in metapopulations. The American Naturalist. 205(6),
617–636.
mla: Olusanya, Oluwafunmilola O., et al. “Genetic Load, Eco-Evolutionary Feedback,
and Extinction in Metapopulations.” The American Naturalist, vol. 205,
no. 6, University of Chicago Press, 2025, pp. 617–36, doi:10.1086/735562.
short: O.O. Olusanya, K. Khudiakova, H. Sachdeva, The American Naturalist 205 (2025)
617–636.
corr_author: '1'
date_created: 2026-02-18T10:47:18Z
date_published: 2025-06-01T00:00:00Z
date_updated: 2026-04-07T08:45:14Z
day: '01'
department:
- _id: JaMa
- _id: NiBa
doi: 10.1086/735562
external_id:
pmid:
- '40446297 '
intvolume: ' 205'
issue: '6'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1101/2023.12.02.569702
month: '06'
oa: 1
oa_version: Preprint
page: 617-636
pmid: 1
project:
- _id: c08d3278-5a5b-11eb-8a69-fdb09b55f4b8
grant_number: P32896
name: Causes and consequences of population fragmentation
- _id: 34c872fe-11ca-11ed-8bc3-8534b82131e6
grant_number: '26380'
name: Polygenic Adaptation in a Metapopulation
- _id: 34d33d68-11ca-11ed-8bc3-ec13763c0ca8
grant_number: '26293'
name: The impact of deleterious mutations on small populations
publication: The American Naturalist
publication_identifier:
eissn:
- 1537-5323
issn:
- 0003-0147
publication_status: published
publisher: University of Chicago Press
quality_controlled: '1'
related_material:
record:
- id: '14732'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: Genetic load, eco-evolutionary feedback, and extinction in metapopulations
type: journal_article
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
volume: 205
year: '2025'
...
---
_id: '18712'
abstract:
- lang: eng
text: 'This file contains the code associated with the manuscript ''Effect of assortative
mating and sexual selection on polygenic barriers to gene flow''. '
acknowledged_ssus:
- _id: ScienComp
article_processing_charge: No
author:
- first_name: Parvathy
full_name: Surendranadh, Parvathy
id: 455235B8-F248-11E8-B48F-1D18A9856A87
last_name: Surendranadh
orcid: 0000-0001-6395-386X
- first_name: Himani
full_name: Sachdeva, Himani
last_name: Sachdeva
citation:
ama: Surendranadh P, Sachdeva H. Mathematica notebook and Fortran code for “Effect
of assortative mating and sexual selection on polygenic barriers to gene flow.”
2025. doi:10.15479/AT:ISTA:17344
apa: Surendranadh, P., & Sachdeva, H. (2025). Mathematica notebook and Fortran
code for “Effect of assortative mating and sexual selection on polygenic barriers
to gene flow.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:17344
chicago: Surendranadh, Parvathy, and Himani Sachdeva. “Mathematica Notebook and
Fortran Code for ‘Effect of Assortative Mating and Sexual Selection on Polygenic
Barriers to Gene Flow.’” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT:ISTA:17344.
ieee: P. Surendranadh and H. Sachdeva, “Mathematica notebook and Fortran code for
‘Effect of assortative mating and sexual selection on polygenic barriers to gene
flow.’” Institute of Science and Technology Austria, 2025.
ista: Surendranadh P, Sachdeva H. 2025. Mathematica notebook and Fortran code for
‘Effect of assortative mating and sexual selection on polygenic barriers to gene
flow’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:17344.
mla: Surendranadh, Parvathy, and Himani Sachdeva. Mathematica Notebook and Fortran
Code for “Effect of Assortative Mating and Sexual Selection on Polygenic Barriers
to Gene Flow.” Institute of Science and Technology Austria, 2025, doi:10.15479/AT:ISTA:17344.
short: P. Surendranadh, H. Sachdeva, (2025).
corr_author: '1'
date_created: 2025-01-01T15:28:27Z
date_published: 2025-01-07T00:00:00Z
date_updated: 2025-12-30T08:44:12Z
day: '07'
ddc:
- '576'
department:
- _id: GradSch
- _id: NiBa
doi: 10.15479/AT:ISTA:17344
file:
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checksum: 9c5f91876014706990a0728c3675cd2a
content_type: application/zip
creator: psurendr
date_created: 2025-01-02T12:30:27Z
date_updated: 2025-01-02T12:30:27Z
file_id: '18722'
file_name: Codes.zip
file_size: 326835
relation: main_file
success: 1
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date_created: 2025-01-02T12:30:39Z
date_updated: 2025-01-02T12:30:39Z
file_id: '18723'
file_name: ReadMe.txt
file_size: 620
relation: main_file
success: 1
file_date_updated: 2025-01-02T12:30:39Z
has_accepted_license: '1'
month: '01'
oa: 1
oa_version: Published Version
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '19876'
relation: used_in_publication
status: public
status: public
title: Mathematica notebook and Fortran code for 'Effect of assortative mating and
sexual selection on polygenic barriers to gene flow'
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: research_data
user_id: 9947682f-b9fa-11ee-9c4a-b3ffaafe6614
year: '2025'
...
---
OA_place: publisher
OA_type: hybrid
_id: '19438'
abstract:
- lang: eng
text: "Polymorphic short insertions and deletions (INDELs \r\n 50 bp) are abundant,
although less common than single nucleotide polymorphisms (SNPs). Evidence from
model organisms shows INDELs to be more strongly influenced by purifying selection
than SNPs. Partly for this reason, INDELs are rarely used as markers for demographic
processes or to detect divergent selection. Here, we compared INDELs and SNPs
in the intertidal snail Littorina saxatilis, focussing on hybrid zones between
ecotypes, in order to test the utility of INDELs in the detection of divergent
selection. We computed INDEL and SNP site frequency spectra using capture sequencing
data. We assessed the impact of divergent selection by analyzing allele frequency
clines across habitat boundaries. We also examined the influence of GC-biased
gene conversion because it may be confounded with signatures of selection. We
show evidence that short INDELs are affected more by purifying selection than
SNPs, but part of the observed site frequency spectra difference can be attributed
to GC-biased gene conversion. We did not find a difference in the impact of divergent
selection between short INDELs and SNPs. Short INDELs and SNPs were similarly
distributed across the genome and so are likely to respond to indirect selection
in the same way. A few regions likely affected by divergent selection were revealed
by INDELs and not by SNPs. Short INDELs can be useful (additional) genetic markers
helping to identify genomic regions important for adaptation and population divergence."
acknowledgement: "This work was supported by the Natural Environment Research Council
(NE/K014021/1), European Research Council (ERC-2015-AdG-693030- BARRIERS) and Swedish
Research Council VR (2018-03695) and we are also very grateful for the support of
the Linnaeus Centre for Marine Evolutionary Biology at the University of Gothenburg.\r\nWe
thank the Swedish Bioinformatics Advisory Program organized by SciLifeLab for feedback
and assistance on the variant calling pipeline and Alan Le Moan for helpful discussions.
R.K.B. and A.M.W. contributed equally to this work. We are also very grateful to
Tomas Larsson and Marina Panova for their bioinformatic analyses on the genome and
the annotation. The bioinformatic analyses were performed on resources at the University
of Sheffield’s High Performance Computing cluster, ShARC. We thank two anonymous
reviewers for helpful comments on a previous version."
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Samuel
full_name: Perini, Samuel
last_name: Perini
- first_name: Kerstin
full_name: Johannesson, Kerstin
last_name: Johannesson
- first_name: Roger K.
full_name: Butlin, Roger K.
last_name: Butlin
- first_name: Anja M
full_name: Westram, Anja M
id: 3C147470-F248-11E8-B48F-1D18A9856A87
last_name: Westram
orcid: 0000-0003-1050-4969
citation:
ama: Perini S, Johannesson K, Butlin RK, Westram AM. Short INDELs and SNPs as markers
of evolutionary processes in hybrid zones. Journal of Evolutionary Biology.
2025;38(3):367-378. doi:10.1093/jeb/voaf002
apa: Perini, S., Johannesson, K., Butlin, R. K., & Westram, A. M. (2025). Short
INDELs and SNPs as markers of evolutionary processes in hybrid zones. Journal
of Evolutionary Biology. Oxford University Press. https://doi.org/10.1093/jeb/voaf002
chicago: Perini, Samuel, Kerstin Johannesson, Roger K. Butlin, and Anja M Westram.
“Short INDELs and SNPs as Markers of Evolutionary Processes in Hybrid Zones.”
Journal of Evolutionary Biology. Oxford University Press, 2025. https://doi.org/10.1093/jeb/voaf002.
ieee: S. Perini, K. Johannesson, R. K. Butlin, and A. M. Westram, “Short INDELs
and SNPs as markers of evolutionary processes in hybrid zones,” Journal of
Evolutionary Biology, vol. 38, no. 3. Oxford University Press, pp. 367–378,
2025.
ista: Perini S, Johannesson K, Butlin RK, Westram AM. 2025. Short INDELs and SNPs
as markers of evolutionary processes in hybrid zones. Journal of Evolutionary
Biology. 38(3), 367–378.
mla: Perini, Samuel, et al. “Short INDELs and SNPs as Markers of Evolutionary Processes
in Hybrid Zones.” Journal of Evolutionary Biology, vol. 38, no. 3, Oxford
University Press, 2025, pp. 367–78, doi:10.1093/jeb/voaf002.
short: S. Perini, K. Johannesson, R.K. Butlin, A.M. Westram, Journal of Evolutionary
Biology 38 (2025) 367–378.
corr_author: '1'
date_created: 2025-03-23T23:01:25Z
date_published: 2025-03-01T00:00:00Z
date_updated: 2025-09-30T11:19:56Z
day: '01'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1093/jeb/voaf002
external_id:
isi:
- '001415267900001'
pmid:
- '39803902'
file:
- access_level: open_access
checksum: 01408e626a4131bfec5ffc70b0af9129
content_type: application/pdf
creator: dernst
date_created: 2025-04-03T11:53:06Z
date_updated: 2025-04-03T11:53:06Z
file_id: '19469'
file_name: 2025_JourEvolBiology_Perini.pdf
file_size: 12826085
relation: main_file
success: 1
file_date_updated: 2025-04-03T11:53:06Z
has_accepted_license: '1'
intvolume: ' 38'
isi: 1
issue: '3'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
page: 367-378
pmid: 1
publication: Journal of Evolutionary Biology
publication_identifier:
eissn:
- 1420-9101
issn:
- 1010-061X
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Short INDELs and SNPs as markers of evolutionary processes in hybrid zones
tmp:
image: /images/cc_by_nc.png
legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode
name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
short: CC BY-NC (4.0)
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 38
year: '2025'
...
---
OA_place: publisher
OA_type: hybrid
PlanS_conform: '1'
_id: '19442'
abstract:
- lang: eng
text: "1. Climate change is expected to induce shifts in the composition, structure
and functioning of Arctic tundra ecosystems. Increases in the frequency and severity
of tundra fires have the potential to catalyse vegetation transitions with far-reaching
local, regional and global consequences.\r\n2. We propose that post-fire tundra
recovery, coupled with climate change, may not necessarily lead to pre-fire conditions.
Our hypothesis, based on surveys and literature, suggests two climate–fire driven
trajectories. One trajectory results in increased woody vegetation under low fire
frequency; the other results in grass dominance under high frequency.\r\n3. Future
research should address uncertainties regarding possible tundra ecosystem shifts
linked to fires, using methods that encompass greater temporal and spatial scales
than previously addressed. More case studies, especially in underrepresented regions
and ecosystem types, are essential to broaden the empirical basis for forecasts
and potential fire management strategies.\r\n4. Synthesis. Our review synthesises
current knowledge on post-fire vegetation trajectories in Arctic tundra ecosystems,
highlighting potential transitions and alternative ecosystem states and their
implications. We discuss challenges in defining and predicting these trajectories
as well as future directions."
acknowledgement: We would like to express our sincere gratitude to all the data providers
who carried out fieldwork in different regions of the Arctic and published their
data, which we used for our meta-analysis. We recognise the hard work and dedication
of these individuals, without whom this paper would not have been possible. We are
grateful to the editor and the anonymous reviewer for their time and valuable feedback
on this manuscript. We particularly appreciate the detailed and constructive comments
provided by reviewer Mara Baudena, which significantly strengthened our work. We
also acknowledge the Indigenous peoples and rural communities of the Arctic, whose
traditional knowledge, rights, and interests are integral to the stewardship and
study of these ecosystems. This work was funded in part by the U.S. National Aeronautics
and Space Administration (NASA) grant 80NSSC22K1256 (GVF). Open Access funding enabled
and organized by Projekt DEAL.
article_processing_charge: Yes (via OA deal)
article_type: review
author:
- first_name: Ramona Julia
full_name: Heim, Ramona Julia
last_name: Heim
- first_name: Adrian V.
full_name: Rocha, Adrian V.
last_name: Rocha
- first_name: Vitalii
full_name: Zemlianskii, Vitalii
last_name: Zemlianskii
- first_name: Kirsten
full_name: Barrett, Kirsten
last_name: Barrett
- first_name: Helga
full_name: Bültmann, Helga
last_name: Bültmann
- first_name: Amy
full_name: Breen, Amy
last_name: Breen
- first_name: Gerald Verner
full_name: Frost, Gerald Verner
last_name: Frost
- first_name: Teresa Nettleton
full_name: Hollingsworth, Teresa Nettleton
last_name: Hollingsworth
- first_name: Randi
full_name: Jandt, Randi
last_name: Jandt
- first_name: Maria
full_name: Kozlova, Maria
last_name: Kozlova
- first_name: Anastasiya
full_name: Kurka, Anastasiya
last_name: Kurka
- first_name: Mark Torre
full_name: Jorgenson, Mark Torre
last_name: Jorgenson
- first_name: Simon M.
full_name: Landhäusser, Simon M.
last_name: Landhäusser
- first_name: Michael Mark
full_name: Loranty, Michael Mark
last_name: Loranty
- first_name: Eric A.
full_name: Miller, Eric A.
last_name: Miller
- first_name: Kenji
full_name: Narita, Kenji
last_name: Narita
- first_name: Evgeniya
full_name: Pravdolyubova, Evgeniya
id: 0b30719b-13f0-11ed-ab2a-94498bc6a278
last_name: Pravdolyubova
- first_name: Norbert
full_name: Hölzel, Norbert
last_name: Hölzel
- first_name: Gabriela
full_name: Schaepman-Strub, Gabriela
last_name: Schaepman-Strub
citation:
ama: Heim RJ, Rocha AV, Zemlianskii V, et al. Arctic tundra ecosystems under fire—Alternative
ecosystem states in a changing climate? Journal of Ecology. 2025;113(5):1042-1056.
doi:10.1111/1365-2745.70022
apa: Heim, R. J., Rocha, A. V., Zemlianskii, V., Barrett, K., Bültmann, H., Breen,
A., … Schaepman-Strub, G. (2025). Arctic tundra ecosystems under fire—Alternative
ecosystem states in a changing climate? Journal of Ecology. Wiley. https://doi.org/10.1111/1365-2745.70022
chicago: Heim, Ramona Julia, Adrian V. Rocha, Vitalii Zemlianskii, Kirsten Barrett,
Helga Bültmann, Amy Breen, Gerald Verner Frost, et al. “Arctic Tundra Ecosystems
under Fire—Alternative Ecosystem States in a Changing Climate?” Journal of
Ecology. Wiley, 2025. https://doi.org/10.1111/1365-2745.70022.
ieee: R. J. Heim et al., “Arctic tundra ecosystems under fire—Alternative
ecosystem states in a changing climate?,” Journal of Ecology, vol. 113,
no. 5. Wiley, pp. 1042–1056, 2025.
ista: Heim RJ, Rocha AV, Zemlianskii V, Barrett K, Bültmann H, Breen A, Frost GV,
Hollingsworth TN, Jandt R, Kozlova M, Kurka A, Jorgenson MT, Landhäusser SM, Loranty
MM, Miller EA, Narita K, Pravdolyubova E, Hölzel N, Schaepman-Strub G. 2025. Arctic
tundra ecosystems under fire—Alternative ecosystem states in a changing climate?
Journal of Ecology. 113(5), 1042–1056.
mla: Heim, Ramona Julia, et al. “Arctic Tundra Ecosystems under Fire—Alternative
Ecosystem States in a Changing Climate?” Journal of Ecology, vol. 113,
no. 5, Wiley, 2025, pp. 1042–56, doi:10.1111/1365-2745.70022.
short: R.J. Heim, A.V. Rocha, V. Zemlianskii, K. Barrett, H. Bültmann, A. Breen,
G.V. Frost, T.N. Hollingsworth, R. Jandt, M. Kozlova, A. Kurka, M.T. Jorgenson,
S.M. Landhäusser, M.M. Loranty, E.A. Miller, K. Narita, E. Pravdolyubova, N. Hölzel,
G. Schaepman-Strub, Journal of Ecology 113 (2025) 1042–1056.
date_created: 2025-03-23T23:01:27Z
date_published: 2025-05-01T00:00:00Z
date_updated: 2025-12-30T08:09:47Z
day: '01'
ddc:
- '550'
- '570'
department:
- _id: NiBa
doi: 10.1111/1365-2745.70022
external_id:
isi:
- '001443422900001'
file:
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checksum: e2785ae265e211b4dc7fc9c5b7744948
content_type: application/pdf
creator: dernst
date_created: 2025-12-30T08:08:18Z
date_updated: 2025-12-30T08:08:18Z
file_id: '20890'
file_name: 2025_JournEcology_Heim.pdf
file_size: 2662766
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file_date_updated: 2025-12-30T08:08:18Z
has_accepted_license: '1'
intvolume: ' 113'
isi: 1
issue: '5'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
page: 1042-1056
publication: Journal of Ecology
publication_identifier:
eissn:
- 1365-2745
issn:
- 0022-0477
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: Arctic tundra ecosystems under fire—Alternative ecosystem states in a changing
climate?
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: 113
year: '2025'
...
---
OA_type: closed access
_id: '19641'
abstract:
- lang: eng
text: Mycorrhizal and saprotrophic macromycetes contribute strongly to the carbon
and nitrogen cycles of forest ecosystems, often studied by tracing stable isotope
composition of carbon and nitrogen. The phenomenon of the saprotrophic-mycorrhizal
divide highlights the difference in the stable isotope composition of fruiting
bodies of mycorrhizal and saprotrophic fungi. Much less is known about the isotopic
composition of the mycelium, which plays an important role in the formation of
the soil organic matter and fuels the fungal trophic channel in soil food webs.
In this study, we assessed whether the saprotrophic-mycorrhizal divide in the
natural δ13С and δ15N values can be traced throughout entire fungal organisms.
This hypothesis was tested using 16 species of ectomycorrhizal and six species
of saprotrophic basidiomycetous fungi. We showed that not only fruiting bodies,
but also the mycelium of ectomycorrhizal and saprotrophic fungi differs in the
δ13C and δ15N values. In both ectomycorrhizal and saprotrophic fungi, the δ13C
and δ15N values increased from mycelium to hymenophores and correlated positively
with the total N content in the corresponding tissues. The differences between
ectomycorrhizal and saprotrophic mycelium can be used to reconstruct the fungal-driven
belowground carbon and nitrogen allocation, and the contribution of saprotrophic
and mycorrhizal fungi to soil food webs.
acknowledgement: We thank Sergey Tsurikov for the help with stable isotope analysis.
Dr. Jacob D. Wickham (IEE RAS) kindly improved the English of the manuscript. This
work was supported by the Russian Science Foundation (project №. 22–14–00363).
article_number: '32'
article_processing_charge: No
article_type: original
author:
- first_name: A. G.
full_name: Zuev, A. G.
last_name: Zuev
- first_name: A. V.
full_name: Alexandrova, A. V.
last_name: Alexandrova
- first_name: V. A.
full_name: Litvinskiy, V. A.
last_name: Litvinskiy
- first_name: Evgeniya
full_name: Pravdolyubova, Evgeniya
id: 0b30719b-13f0-11ed-ab2a-94498bc6a278
last_name: Pravdolyubova
- first_name: A. V.
full_name: Tiunov, A. V.
last_name: Tiunov
citation:
ama: 'Zuev AG, Alexandrova AV, Litvinskiy VA, Pravdolyubova E, Tiunov AV. Saprotrophic-mycorrhizal
divide in stable isotope composition throughout the whole fungus: From mycelium
to hymenophore. Mycorrhiza. 2025;35(2). doi:10.1007/s00572-025-01203-w'
apa: 'Zuev, A. G., Alexandrova, A. V., Litvinskiy, V. A., Pravdolyubova, E., &
Tiunov, A. V. (2025). Saprotrophic-mycorrhizal divide in stable isotope composition
throughout the whole fungus: From mycelium to hymenophore. Mycorrhiza.
Springer Nature. https://doi.org/10.1007/s00572-025-01203-w'
chicago: 'Zuev, A. G., A. V. Alexandrova, V. A. Litvinskiy, Evgeniya Pravdolyubova,
and A. V. Tiunov. “Saprotrophic-Mycorrhizal Divide in Stable Isotope Composition
throughout the Whole Fungus: From Mycelium to Hymenophore.” Mycorrhiza.
Springer Nature, 2025. https://doi.org/10.1007/s00572-025-01203-w.'
ieee: 'A. G. Zuev, A. V. Alexandrova, V. A. Litvinskiy, E. Pravdolyubova, and A.
V. Tiunov, “Saprotrophic-mycorrhizal divide in stable isotope composition throughout
the whole fungus: From mycelium to hymenophore,” Mycorrhiza, vol. 35, no.
2. Springer Nature, 2025.'
ista: 'Zuev AG, Alexandrova AV, Litvinskiy VA, Pravdolyubova E, Tiunov AV. 2025.
Saprotrophic-mycorrhizal divide in stable isotope composition throughout the whole
fungus: From mycelium to hymenophore. Mycorrhiza. 35(2), 32.'
mla: 'Zuev, A. G., et al. “Saprotrophic-Mycorrhizal Divide in Stable Isotope Composition
throughout the Whole Fungus: From Mycelium to Hymenophore.” Mycorrhiza,
vol. 35, no. 2, 32, Springer Nature, 2025, doi:10.1007/s00572-025-01203-w.'
short: A.G. Zuev, A.V. Alexandrova, V.A. Litvinskiy, E. Pravdolyubova, A.V. Tiunov,
Mycorrhiza 35 (2025).
date_created: 2025-05-04T22:02:32Z
date_published: 2025-04-01T00:00:00Z
date_updated: 2025-09-30T12:24:12Z
day: '01'
department:
- _id: NiBa
doi: 10.1007/s00572-025-01203-w
external_id:
isi:
- '001467249900001'
pmid:
- '40232310'
intvolume: ' 35'
isi: 1
issue: '2'
language:
- iso: eng
month: '04'
oa_version: None
pmid: 1
publication: Mycorrhiza
publication_identifier:
eissn:
- 1432-1890
issn:
- 0940-6360
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Saprotrophic-mycorrhizal divide in stable isotope composition throughout the
whole fungus: From mycelium to hymenophore'
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 35
year: '2025'
...
---
OA_type: closed access
_id: '19671'
abstract:
- lang: eng
text: Silvopastoral use in native forests could impact population dynamics of key
tree species, with contrasting effects at different life cycle stages. Prior studies
in South American temperate forests have mainly focused on initial stages, lacking
a comprehensive understanding of the entire life cycle within productive systems.
We assessed the population dynamics of two key species of mixed forests in northern
Patagonia (Austrocedrus chilensis and Nothofagus dombeyi) under two silvopastoral
use intensities (high vs. low), using demographic techniques and population projection
models. Over 3 years, we quantified vital rates (survival, fertility, growth,
reversion and stasis) and used matrix models to calculate deterministic population
growth rates (λ). High-intensity silvopastoral use had predominantly negative
effects on the elements of the projection matrices of A. chilensis, whereas N.
dombeyi exhibited mostly positive or no changes. As a result, projections indicated
slight population decreases for A. chilensis (mostly λ < 1) at high silvopastoral
use levels compared to low levels, while N. dombeyi showed similar projections
(λ ≅ 1) between use levels. Decreased λ for A. chilensis resulted mainly from
lower adult tree survival, while early life stages had limited influence on λ
for these long-lived species. In summary, silvopastoral use affects population
dynamics of key tree species of these mixed forests of northern Patagonia, with
implications for sustainable management. Our findings highlight the importance
of considering the entire life cycle and suggest targeted practices to enhance
A. chilensis populations.
acknowledgement: We would like to express our sincere gratitude to the owners of the
estates, Lisandro and Oscar Lanfré, Roberto Criado and Yayo Tillería, for allowing
us to conduct our research on their properties and for generously sharing their
time and knowledge throughout these years. We are also deeply thankful to our field
assistants, Matías Scotti, Clara Pissolito, Noel Szudruk, Mariano Varela, Ian Mott,
Brisa Guenuleo, Nicolás Bistolfi, Facundo Gómez and Belén Vallerga, who tirelessly
collaborated in the arduous tasks of monitoring and data collection, even in challenging
weather conditions. We are grateful to CONICET for providing the doctoral scholarship
to D. Arpigiani. This study received partial financial support from the Agencia
MINCyT (PICT 2015-1692) and the Universidad Nacional de Río Negro (PI 40-B-478),
Argentina.
article_number: e70058
article_processing_charge: No
article_type: original
author:
- first_name: Daniela
full_name: Arpigiani, Daniela
last_name: Arpigiani
- first_name: Valeria
full_name: Aschero, Valeria
last_name: Aschero
- first_name: Rosina Matilde
full_name: Soler Schaller, Rosina Matilde
id: 9e668447-8c32-11ed-b0c7-8dc2d7b80803
last_name: Soler Schaller
- first_name: Mariano M.
full_name: Amoroso, Mariano M.
last_name: Amoroso
citation:
ama: Arpigiani D, Aschero V, Soler Schaller RM, Amoroso MM. A life-cycle approach
to understand consequences of silvopastoral use on two native tree species of
Northern Patagonia. Austral Ecology. 2025;50(4). doi:10.1111/aec.70058
apa: Arpigiani, D., Aschero, V., Soler Schaller, R. M., & Amoroso, M. M. (2025).
A life-cycle approach to understand consequences of silvopastoral use on two native
tree species of Northern Patagonia. Austral Ecology. Wiley. https://doi.org/10.1111/aec.70058
chicago: Arpigiani, Daniela, Valeria Aschero, Rosina Matilde Soler Schaller, and
Mariano M. Amoroso. “A Life-Cycle Approach to Understand Consequences of Silvopastoral
Use on Two Native Tree Species of Northern Patagonia.” Austral Ecology.
Wiley, 2025. https://doi.org/10.1111/aec.70058.
ieee: D. Arpigiani, V. Aschero, R. M. Soler Schaller, and M. M. Amoroso, “A life-cycle
approach to understand consequences of silvopastoral use on two native tree species
of Northern Patagonia,” Austral Ecology, vol. 50, no. 4. Wiley, 2025.
ista: Arpigiani D, Aschero V, Soler Schaller RM, Amoroso MM. 2025. A life-cycle
approach to understand consequences of silvopastoral use on two native tree species
of Northern Patagonia. Austral Ecology. 50(4), e70058.
mla: Arpigiani, Daniela, et al. “A Life-Cycle Approach to Understand Consequences
of Silvopastoral Use on Two Native Tree Species of Northern Patagonia.” Austral
Ecology, vol. 50, no. 4, e70058, Wiley, 2025, doi:10.1111/aec.70058.
short: D. Arpigiani, V. Aschero, R.M. Soler Schaller, M.M. Amoroso, Austral Ecology
50 (2025).
date_created: 2025-05-11T22:02:41Z
date_published: 2025-04-01T00:00:00Z
date_updated: 2025-09-30T12:31:04Z
day: '01'
department:
- _id: NiBa
doi: 10.1111/aec.70058
external_id:
isi:
- '001476761500001'
intvolume: ' 50'
isi: 1
issue: '4'
language:
- iso: eng
month: '04'
oa_version: None
publication: Austral Ecology
publication_identifier:
eissn:
- 1442-9993
issn:
- 1442-9985
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: A life-cycle approach to understand consequences of silvopastoral use on two
native tree species of Northern Patagonia
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 50
year: '2025'
...
---
OA_place: publisher
OA_type: hybrid
_id: '19876'
abstract:
- lang: eng
text: "Assortative mating and sexual selection are widespread in nature and can
play an important role in speciation by facilitating the buildup and maintenance
of reproductive isolation (RI). However, their contribution to genome-wide suppression
of gene flow during RI is rarely quantified.\r\nHere, we consider a polygenic
“magic” trait that is divergently selected across two populations connected by
migration, while also serving as the basis of assortative mating, thus generating
sexual selection on one or both sexes. We obtain theoretical predictions for divergence
at\r\nindividual trait loci by assuming that the effect of all other loci on any
locus can be encapsulated via an effective migration rate, which bears a simple
relationship to measurable fitness components of migrants and various early-generation
hybrids. Our analysis clarifies how “tipping\r\npoints” (characterized by an abrupt
collapse of adaptive divergence) arise, and when assortative mating can shift
the critical level of migration beyond which divergence collapses. We quantify
the relative contributions of viability and sexual selection to genome-wide barriers
to gene\r\nflow and discuss how these depend on existing divergence levels. Our
results suggest that effective migration rates provide a useful way of understanding
genomic divergence, even in scenarios involving multiple, interacting mechanisms
of RI. "
acknowledged_ssus:
- _id: ScienComp
acknowledgement: We thank Nick Barton for useful comments on the manuscript. This
research was supported by the Scientific Service Units (SSU) of Institute of Science
and Technology Austria (ISTA) through resources provided by Scientific Computing
(SciComp).
article_processing_charge: Yes (via OA deal)
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: Himani
full_name: Sachdeva, Himani
last_name: Sachdeva
citation:
ama: Surendranadh P, Sachdeva H. Effect of assortative mating and sexual selection
on polygenic barriers to gene flow. Evolution. 2025;79(7):1185-1198. doi:10.1093/evolut/qpaf047
apa: Surendranadh, P., & Sachdeva, H. (2025). Effect of assortative mating and
sexual selection on polygenic barriers to gene flow. Evolution. Oxford
University Press. https://doi.org/10.1093/evolut/qpaf047
chicago: Surendranadh, Parvathy, and Himani Sachdeva. “Effect of Assortative Mating
and Sexual Selection on Polygenic Barriers to Gene Flow.” Evolution. Oxford
University Press, 2025. https://doi.org/10.1093/evolut/qpaf047.
ieee: P. Surendranadh and H. Sachdeva, “Effect of assortative mating and sexual
selection on polygenic barriers to gene flow,” Evolution, vol. 79, no.
7. Oxford University Press, pp. 1185–1198, 2025.
ista: Surendranadh P, Sachdeva H. 2025. Effect of assortative mating and sexual
selection on polygenic barriers to gene flow. Evolution. 79(7), 1185–1198.
mla: Surendranadh, Parvathy, and Himani Sachdeva. “Effect of Assortative Mating
and Sexual Selection on Polygenic Barriers to Gene Flow.” Evolution, vol.
79, no. 7, Oxford University Press, 2025, pp. 1185–98, doi:10.1093/evolut/qpaf047.
short: P. Surendranadh, H. Sachdeva, Evolution 79 (2025) 1185–1198.
corr_author: '1'
date_created: 2025-06-23T13:51:00Z
date_published: 2025-07-01T00:00:00Z
date_updated: 2025-12-30T08:44:13Z
day: '01'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1093/evolut/qpaf047
external_id:
isi:
- '001490646300001'
file:
- access_level: open_access
checksum: 288ca936cef794d68a55356e70671846
content_type: application/pdf
creator: dernst
date_created: 2025-12-30T08:43:33Z
date_updated: 2025-12-30T08:43:33Z
file_id: '20898'
file_name: 2025_Evolution_Surendranadh.pdf
file_size: 2784295
relation: main_file
success: 1
file_date_updated: 2025-12-30T08:43:33Z
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intvolume: ' 79'
isi: 1
issue: '7'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: 1185-1198
publication: Evolution
publication_identifier:
eissn:
- 1558-5646
issn:
- 0014-3820
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
related_material:
record:
- id: '18712'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Effect of assortative mating and sexual selection on polygenic barriers to
gene flow
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: 79
year: '2025'
...
---
OA_place: publisher
OA_type: hybrid
PlanS_conform: '1'
_id: '20102'
abstract:
- lang: eng
text: 'Speciation is rarely observable directly. A way forward is to compare pairs
of ecotypes that evolved in parallel in similar contexts but have reached different
degrees of reproductive isolation. Such comparisons are possible in the marine
snail Littorina saxatilis by contrasting barriers to gene flow between parallel
ecotypes in Spain and Sweden. In both countries, divergent ecotypes have evolved
to withstand either crab predation or wave action. Here, we explore transects
spanning contact zones between the Crab and the Wave ecotypes using low-coverage
whole-genome sequencing, morphological and behavioural traits. Despite parallel
phenotypic divergence, distinct patterns of differentiation between the ecotypes
emerged: a continuous cline in Sweden indicating a weak barrier to gene flow,
but two highly genetically and phenotypically divergent, and partly spatially
overlapping clusters in Spain suggesting a much stronger barrier to gene flow.
The absence of Spanish early-generation hybrids supported strong isolation, but
a low level of gene flow is evident from molecular data. In both countries, highly
differentiated loci were located in both shared and country-specific chromosomal
inversions but were also present in collinear regions. Despite being considered
the same species and showing similar levels of phenotypic divergence, the Spanish
ecotypes are much closer to full reproductive isolation than the Swedish ones.
Barriers to gene flow of very different strengths between ecotypes within the
same species might be explained by dissimilarities in the spatial arrangement
of habitats, the selection gradients or the ages of the systems.'
acknowledgement: 'This study was supported by European Research Council grant 693030-BARRIERS
to RKB; the Swedish Research Council (grant number 2021-04191) to KJ; the Portuguese
Foundation for Science and Technology (FCT: 2020.00275.CEECIND and PTDC/BIA-EVL/1614/2021)
to RF; grant PID2022-137935NB-I00 by MICIU/AEI/ 10.13039/501100011033/and ERDF/EU
(ED431C 2020-05) to JG, grant PID2021-124930NB-I00 funded by MICIU/AEI/ 10.13039/501100011033/and
ERDF/EU to ERA, Xunta de Galicia (ED431C 2024/22), Centro singular de Investigación
de Galicia accreditation 2024-2027 (ED431G 2023/07), ‘ERDF A way of making Europe’
and Norwegian Research Council RCN, project 315287 to AMW.'
article_number: e70025
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Francesca
full_name: Raffini, Francesca
last_name: Raffini
- first_name: Aurélien
full_name: De Jode, Aurélien
last_name: De Jode
- first_name: Kerstin
full_name: Johannesson, Kerstin
last_name: Johannesson
- first_name: Rui
full_name: Faria, Rui
last_name: Faria
- first_name: Zuzanna B.
full_name: Zagrodzka, Zuzanna B.
last_name: Zagrodzka
- first_name: Anja M
full_name: Westram, Anja M
id: 3C147470-F248-11E8-B48F-1D18A9856A87
last_name: Westram
orcid: 0000-0003-1050-4969
- first_name: Juan
full_name: Galindo, Juan
last_name: Galindo
- first_name: Emilio
full_name: Rolán-Alvarez, Emilio
last_name: Rolán-Alvarez
- first_name: Roger K.
full_name: Butlin, Roger K.
last_name: Butlin
citation:
ama: Raffini F, De Jode A, Johannesson K, et al. Phenotypic divergence and genomic
architecture between parallel ecotypes at two different points on the speciation
continuum in a marine snail. Molecular Ecology. 2025;34(21). doi:10.1111/mec.70025
apa: Raffini, F., De Jode, A., Johannesson, K., Faria, R., Zagrodzka, Z. B., Westram,
A. M., … Butlin, R. K. (2025). Phenotypic divergence and genomic architecture
between parallel ecotypes at two different points on the speciation continuum
in a marine snail. Molecular Ecology. Wiley. https://doi.org/10.1111/mec.70025
chicago: Raffini, Francesca, Aurélien De Jode, Kerstin Johannesson, Rui Faria, Zuzanna
B. Zagrodzka, Anja M Westram, Juan Galindo, Emilio Rolán-Alvarez, and Roger K.
Butlin. “Phenotypic Divergence and Genomic Architecture between Parallel Ecotypes
at Two Different Points on the Speciation Continuum in a Marine Snail.” Molecular
Ecology. Wiley, 2025. https://doi.org/10.1111/mec.70025.
ieee: F. Raffini et al., “Phenotypic divergence and genomic architecture
between parallel ecotypes at two different points on the speciation continuum
in a marine snail,” Molecular Ecology, vol. 34, no. 21. Wiley, 2025.
ista: Raffini F, De Jode A, Johannesson K, Faria R, Zagrodzka ZB, Westram AM, Galindo
J, Rolán-Alvarez E, Butlin RK. 2025. Phenotypic divergence and genomic architecture
between parallel ecotypes at two different points on the speciation continuum
in a marine snail. Molecular Ecology. 34(21), e70025.
mla: Raffini, Francesca, et al. “Phenotypic Divergence and Genomic Architecture
between Parallel Ecotypes at Two Different Points on the Speciation Continuum
in a Marine Snail.” Molecular Ecology, vol. 34, no. 21, e70025, Wiley,
2025, doi:10.1111/mec.70025.
short: F. Raffini, A. De Jode, K. Johannesson, R. Faria, Z.B. Zagrodzka, A.M. Westram,
J. Galindo, E. Rolán-Alvarez, R.K. Butlin, Molecular Ecology 34 (2025).
date_created: 2025-08-03T22:01:31Z
date_published: 2025-11-01T00:00:00Z
date_updated: 2025-12-30T09:25:45Z
day: '01'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1111/mec.70025
external_id:
isi:
- '001538172800001'
file:
- access_level: open_access
checksum: ec01edda64cfbc6cbc8adf300f719644
content_type: application/pdf
creator: dernst
date_created: 2025-12-30T09:25:17Z
date_updated: 2025-12-30T09:25:17Z
file_id: '20906'
file_name: 2025_MolecEcology_Raffini.pdf
file_size: 2767745
relation: main_file
success: 1
file_date_updated: 2025-12-30T09:25:17Z
has_accepted_license: '1'
intvolume: ' 34'
isi: 1
issue: '21'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
publication: Molecular Ecology
publication_identifier:
eissn:
- 1365-294X
issn:
- 0962-1083
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: Phenotypic divergence and genomic architecture between parallel ecotypes at
two different points on the speciation continuum in a marine snail
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: 34
year: '2025'
...
---
OA_place: publisher
OA_type: hybrid
_id: '20325'
abstract:
- lang: eng
text: Inferring genealogical relationships of wild populations is useful because
it gives direct estimates of mating patterns and variance in reproductive success.
Inference can be improved by including information about parentage shared between
siblings, or by modelling phenotypes or population data related to mating. However,
we currently lack a framework to infer parent–offspring relationships, sibships
and population parameters in a single analysis. To address this, we here extend
a previous method, Fractional Analysis of Paternity and Sibships, to include population
data for the case where one parent is known. We illustrate this with the example
of pollen dispersal in a natural hybrid zone population of the snapdragon Antirrhinum
majus. Pollen dispersal is leptokurtic, with half of mating events occurring within
30 m, but with a long tail of mating events up to 859 m. Using simulations, we
find that both sibship and population information substantially improve pedigree
reconstruction, and that we can expect to resolve median dispersal distances with
high accuracy.
acknowledgement: 'We thank a large number of field volunteers for maintaining the
population sampling, and Tom White for assistance with seed collection. We thank
Sylvia Rebel for plating tissue for DNA extraction, as well as Sean Stankowski and
two anonymous reviewers for feedback on the manuscript. '
article_number: e70051
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Thomas
full_name: Ellis, Thomas
id: 3153D6D4-F248-11E8-B48F-1D18A9856A87
last_name: Ellis
orcid: 0000-0002-8511-0254
- first_name: David
full_name: Field, David
id: 419049E2-F248-11E8-B48F-1D18A9856A87
last_name: Field
orcid: 0000-0002-4014-8478
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: Ellis T, Field D, Barton NH. Joint estimation of paternity, sibships and pollen
dispersal in a snapdragon hybrid zone. Molecular Ecology. 2025;34(15).
doi:10.1111/mec.70051
apa: Ellis, T., Field, D., & Barton, N. H. (2025). Joint estimation of paternity,
sibships and pollen dispersal in a snapdragon hybrid zone. Molecular Ecology.
Wiley. https://doi.org/10.1111/mec.70051
chicago: Ellis, Thomas, David Field, and Nicholas H Barton. “Joint Estimation of
Paternity, Sibships and Pollen Dispersal in a Snapdragon Hybrid Zone.” Molecular
Ecology. Wiley, 2025. https://doi.org/10.1111/mec.70051.
ieee: T. Ellis, D. Field, and N. H. Barton, “Joint estimation of paternity, sibships
and pollen dispersal in a snapdragon hybrid zone,” Molecular Ecology, vol.
34, no. 15. Wiley, 2025.
ista: Ellis T, Field D, Barton NH. 2025. Joint estimation of paternity, sibships
and pollen dispersal in a snapdragon hybrid zone. Molecular Ecology. 34(15), e70051.
mla: Ellis, Thomas, et al. “Joint Estimation of Paternity, Sibships and Pollen Dispersal
in a Snapdragon Hybrid Zone.” Molecular Ecology, vol. 34, no. 15, e70051,
Wiley, 2025, doi:10.1111/mec.70051.
short: T. Ellis, D. Field, N.H. Barton, Molecular Ecology 34 (2025).
corr_author: '1'
date_created: 2025-09-10T05:42:23Z
date_published: 2025-09-02T00:00:00Z
date_updated: 2025-12-30T10:12:34Z
day: '02'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1111/mec.70051
external_id:
isi:
- '001542913000001'
pmid:
- '40751392'
file:
- access_level: open_access
checksum: 5059ad4d74e6327b84b5282a39d36774
content_type: application/pdf
creator: dernst
date_created: 2025-12-30T10:12:17Z
date_updated: 2025-12-30T10:12:17Z
file_id: '20911'
file_name: 2025_MolecularEcology_Ellis.pdf
file_size: 1698605
relation: main_file
success: 1
file_date_updated: 2025-12-30T10:12:17Z
has_accepted_license: '1'
intvolume: ' 34'
isi: 1
issue: '15'
language:
- iso: eng
month: '09'
oa: 1
oa_version: Published Version
pmid: 1
publication: Molecular Ecology
publication_identifier:
eissn:
- 1365-294X
issn:
- 0962-1083
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: Joint estimation of paternity, sibships and pollen dispersal in a snapdragon
hybrid zone
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: 34
year: '2025'
...
---
OA_place: publisher
OA_type: hybrid
PlanS_conform: '1'
_id: '20330'
abstract:
- lang: eng
text: The evolution of sexual dimorphism (the difference in average trait values
between females and males, SD), is often thought to be constrained by shared genetic
architecture between the sexes. Indeed, it is commonly expected that SD should
negatively correlate with the intersex correlation (the genetic correlation between
effects of segregating variants in females and males, r fm), either because (1)
traits with ancestrally low r fm are less constrained in their ability to respond
to sex-specific selection and thus evolve to be more dimorphic, or because (2)
sex-specific selection, driving sexual dimorphism evolution, also acts to reduce
r fm. Despite the intuitive appeal and prominence of these ideas, their generality
and the conditions in which they hold remain unclear. Here, we develop models
incorporating sex-specific stabilizing selection, mutation and genetic drift to
examine the relationship between r fm and SD. We show that the two commonly-discussed
mechanisms with the potential to generate a negative correlation between SD and
r fm could just as easily generate a positive association, since the standard
line of reasoning hinges on a hidden assumption that sex-specific adaptation more
frequently favors increased dimorphism than reduced dimorphism. Our results provide,
to our knowledge, the first mechanistic framework for understanding the conditions
under which a correlation between r fm and SD may arise and offer a compelling
explanation for inconsistent empirical evidence. We also make the intriguing observation
that—even when selection between the two sexes is identical—drift generates nonzero
SD. We quantify this effect and discuss its significance.
acknowledgement: We thank Tim Connallon for useful discussions and correspondence,
Himani Sachdeva and Nick Barton for comments on the manuscript and the Scientific
Computing unit at ISTA for technical support. GP is the recipient of a DOC Fellowship
of the Austrian Academy of Sciences at the Institute of Science and Technology Austria
(DOC 25817) and received funding from the European Union’s Horizon 2020 research
and innovation program under the Marie Skłodowska-Curie Grant (agreement no. 665385).
LH received funding from the European Research Council, under the HaplotypeStructure
Grant (grant no. 101055327) to Nick Barton.
article_number: iyaf175
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Gemma
full_name: Puixeu Sala, Gemma
id: 33AB266C-F248-11E8-B48F-1D18A9856A87
last_name: Puixeu Sala
orcid: 0000-0001-8330-1754
- first_name: Laura
full_name: Hayward, Laura
id: fc885ee5-24bf-11eb-ad7b-bcc5104c0c1b
last_name: Hayward
citation:
ama: 'Puixeu Sala G, Hayward L. The relationship between sexual dimorphism and intersex
correlation: Do models support intuition? Genetics. 2025;231(3). doi:10.1093/genetics/iyaf175'
apa: 'Puixeu Sala, G., & Hayward, L. (2025). The relationship between sexual
dimorphism and intersex correlation: Do models support intuition? Genetics.
Oxford University Press. https://doi.org/10.1093/genetics/iyaf175'
chicago: 'Puixeu Sala, Gemma, and Laura Hayward. “The Relationship between Sexual
Dimorphism and Intersex Correlation: Do Models Support Intuition?” Genetics.
Oxford University Press, 2025. https://doi.org/10.1093/genetics/iyaf175.'
ieee: 'G. Puixeu Sala and L. Hayward, “The relationship between sexual dimorphism
and intersex correlation: Do models support intuition?,” Genetics, vol.
231, no. 3. Oxford University Press, 2025.'
ista: 'Puixeu Sala G, Hayward L. 2025. The relationship between sexual dimorphism
and intersex correlation: Do models support intuition? Genetics. 231(3), iyaf175.'
mla: 'Puixeu Sala, Gemma, and Laura Hayward. “The Relationship between Sexual Dimorphism
and Intersex Correlation: Do Models Support Intuition?” Genetics, vol.
231, no. 3, iyaf175, Oxford University Press, 2025, doi:10.1093/genetics/iyaf175.'
short: G. Puixeu Sala, L. Hayward, Genetics 231 (2025).
corr_author: '1'
date_created: 2025-09-10T05:48:04Z
date_published: 2025-11-01T00:00:00Z
date_updated: 2026-01-05T13:04:07Z
day: '01'
ddc:
- '570'
department:
- _id: BeVi
- _id: NiBa
doi: 10.1093/genetics/iyaf175
ec_funded: 1
external_id:
isi:
- '001598595000001'
file:
- access_level: open_access
checksum: bbb73bbf8617812d4d8db4af92be9538
content_type: application/pdf
creator: dernst
date_created: 2026-01-05T13:03:18Z
date_updated: 2026-01-05T13:03:18Z
file_id: '20946'
file_name: 2025_Genetics_Puixeu.pdf
file_size: 1550562
relation: main_file
success: 1
file_date_updated: 2026-01-05T13:03:18Z
has_accepted_license: '1'
intvolume: ' 231'
isi: 1
issue: '3'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
project:
- _id: 9B9DFC9E-BA93-11EA-9121-9846C619BF3A
grant_number: '25817'
name: 'Sexual conflict: resolution, constraints and biomedical implications'
- _id: 2564DBCA-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '665385'
name: International IST Doctoral Program
- _id: bd6958e0-d553-11ed-ba76-86eba6a76c00
grant_number: '101055327'
name: Understanding the evolution of continuous genomes
publication: Genetics
publication_identifier:
issn:
- 1943-2631
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'The relationship between sexual dimorphism and intersex correlation: Do models
support intuition?'
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: 231
year: '2025'
...
---
OA_type: closed access
_id: '20429'
abstract:
- lang: eng
text: Plant–plant interactions are key to understanding ecosystem services and shaping
restoration strategies, as they can produce either negative or positive effects,
determining species establishment and growth. Recognizing these interactions during
early-life stages provides valuable insights for restoration in human-disturbed
areas. One promising approach is nucleation planting, which establishes small
clusters of native species in strategically selected sites, being particularly
useful in sites with large herbivores. In southern Patagonia, livestock production
has historically been the main economic activity, severely impacting extensive
areas of Nothofagus antarctica forest through grazing and intentional burning
to increase forage. In this context, nucleation planting with Berberis microphylla,
a non-palatable shrub, could foster forest recovery in degraded sites. To evaluate
this, we conducted an experiment testing the response of trees to varying shrub
number, while also assessing intraspecific effects in both species. We measured
survival, biomass, and functional traits. Results showed that the combination
of four shrubs surrounding a single tree maintained tree survival at levels comparable
to trees growing alone, while seedlings exhibited conspecific negative plant number
dependence. Additionally, B. microphylla increased its below- to above-ground
biomass ratio under higher plant number, indicating resource reallocation and
niche differentiation through spatial separation of root systems.
article_processing_charge: No
article_type: original
author:
- first_name: Gimena Noemí
full_name: Bustamante, Gimena Noemí
last_name: Bustamante
- first_name: Miriam Elisabet
full_name: Arena, Miriam Elisabet
last_name: Arena
- first_name: Luciano
full_name: Selzer, Luciano
last_name: Selzer
- first_name: Matthew
full_name: Ruggirello, Matthew
last_name: Ruggirello
- first_name: Paula
full_name: Rodríguez, Paula
last_name: Rodríguez
- first_name: Samuele
full_name: Pedrazzani, Samuele
last_name: Pedrazzani
- first_name: Jose Antonio
full_name: Navarro-Cano, Jose Antonio
last_name: Navarro-Cano
- first_name: Rosina Matilde
full_name: Soler Schaller, Rosina Matilde
id: 9e668447-8c32-11ed-b0c7-8dc2d7b80803
last_name: Soler Schaller
citation:
ama: 'Bustamante GN, Arena ME, Selzer L, et al. Biotic interactions between trees
and colonizing shrubs: Implications for active restoration in southern Patagonian
forests. Plant Ecology. 2025;226:1301-1313. doi:10.1007/s11258-025-01568-0'
apa: 'Bustamante, G. N., Arena, M. E., Selzer, L., Ruggirello, M., Rodríguez, P.,
Pedrazzani, S., … Soler Schaller, R. M. (2025). Biotic interactions between trees
and colonizing shrubs: Implications for active restoration in southern Patagonian
forests. Plant Ecology. Springer Nature. https://doi.org/10.1007/s11258-025-01568-0'
chicago: 'Bustamante, Gimena Noemí, Miriam Elisabet Arena, Luciano Selzer, Matthew
Ruggirello, Paula Rodríguez, Samuele Pedrazzani, Jose Antonio Navarro-Cano, and
Rosina Matilde Soler Schaller. “Biotic Interactions between Trees and Colonizing
Shrubs: Implications for Active Restoration in Southern Patagonian Forests.” Plant
Ecology. Springer Nature, 2025. https://doi.org/10.1007/s11258-025-01568-0.'
ieee: 'G. N. Bustamante et al., “Biotic interactions between trees and colonizing
shrubs: Implications for active restoration in southern Patagonian forests,” Plant
Ecology, vol. 226. Springer Nature, pp. 1301–1313, 2025.'
ista: 'Bustamante GN, Arena ME, Selzer L, Ruggirello M, Rodríguez P, Pedrazzani
S, Navarro-Cano JA, Soler Schaller RM. 2025. Biotic interactions between trees
and colonizing shrubs: Implications for active restoration in southern Patagonian
forests. Plant Ecology. 226, 1301–1313.'
mla: 'Bustamante, Gimena Noemí, et al. “Biotic Interactions between Trees and Colonizing
Shrubs: Implications for Active Restoration in Southern Patagonian Forests.” Plant
Ecology, vol. 226, Springer Nature, 2025, pp. 1301–13, doi:10.1007/s11258-025-01568-0.'
short: G.N. Bustamante, M.E. Arena, L. Selzer, M. Ruggirello, P. Rodríguez, S. Pedrazzani,
J.A. Navarro-Cano, R.M. Soler Schaller, Plant Ecology 226 (2025) 1301–1313.
date_created: 2025-10-05T22:01:36Z
date_published: 2025-12-01T00:00:00Z
date_updated: 2026-01-05T13:23:57Z
day: '01'
department:
- _id: NiBa
doi: 10.1007/s11258-025-01568-0
external_id:
isi:
- '001581599800001'
intvolume: ' 226'
isi: 1
language:
- iso: eng
month: '12'
oa_version: None
page: 1301-1313
publication: Plant Ecology
publication_identifier:
eissn:
- 1573-5052
issn:
- 1385-0237
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Biotic interactions between trees and colonizing shrubs: Implications for
active restoration in southern Patagonian forests'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 226
year: '2025'
...
---
OA_place: repository
OA_type: green
_id: '20531'
abstract:
- lang: eng
text: Genetic drift is potentially an important component of selection for sex,
as it is a source of statistical associations between alleles at selected loci.
By increasing local drift, population structure may thus amplify the evolutionary
advantage of sex. However, most previous models have focused either on haploid
populations or on diploid populations without spatial structure. In this article,
we use two- and three-locus analytical models and multilocus simulations to explore
selection for sex in a diploid population structured according to the island model,
in the presence of recurrent deleterious mutations. Our results show that selection
generally favors an intermediate rate of sex that decreases as the direct cost
of sex increases and increases moderately as the degree of population structure
increases. Selection for sex is generated by multiple effects involving genetic
associations within and between loci. When selection occurs at many loci, it is
generally dominated by interference effects involving deleterious alleles at different
loci, captured by our three-locus model. In our multilocus simulations, we observed
an irreversible spread of asexual mutants under strong costs of sex, and when
deleterious mutations are partially recessive. However, population structure may
prevent this spread of asexual mutants when dispersal rates are sufficiently small.
acknowledgement: L.F. is funded by the NOMIS-ISTA Fellowship Program. We thank Colin
Olito and two anonymous reviewers for helpful comments, and the bioinformatics and
computing services at Roscoff’s Biological Station (Abims platform) and at Institute
of Science and Technology Austria for computing time.
article_processing_charge: No
article_type: original
author:
- first_name: Louise
full_name: Fouqueau, Louise
id: 1676e173-8143-11ed-8927-fe165216a93f
last_name: Fouqueau
orcid: 0000-0003-0371-9339
- first_name: Denis
full_name: Roze, Denis
last_name: Roze
citation:
ama: Fouqueau L, Roze D. Deleterious mutations and selection for sex in spatially
structured, diploid populations. Evolution. 2025;79(10):2167-2180. doi:10.1093/evolut/qpaf143
apa: Fouqueau, L., & Roze, D. (2025). Deleterious mutations and selection for
sex in spatially structured, diploid populations. Evolution. Oxford University
Press. https://doi.org/10.1093/evolut/qpaf143
chicago: Fouqueau, Louise, and Denis Roze. “Deleterious Mutations and Selection
for Sex in Spatially Structured, Diploid Populations.” Evolution. Oxford
University Press, 2025. https://doi.org/10.1093/evolut/qpaf143.
ieee: L. Fouqueau and D. Roze, “Deleterious mutations and selection for sex in spatially
structured, diploid populations,” Evolution, vol. 79, no. 10. Oxford University
Press, pp. 2167–2180, 2025.
ista: Fouqueau L, Roze D. 2025. Deleterious mutations and selection for sex in spatially
structured, diploid populations. Evolution. 79(10), 2167–2180.
mla: Fouqueau, Louise, and Denis Roze. “Deleterious Mutations and Selection for
Sex in Spatially Structured, Diploid Populations.” Evolution, vol. 79,
no. 10, Oxford University Press, 2025, pp. 2167–80, doi:10.1093/evolut/qpaf143.
short: L. Fouqueau, D. Roze, Evolution 79 (2025) 2167–2180.
date_created: 2025-10-26T23:01:34Z
date_published: 2025-10-17T00:00:00Z
date_updated: 2025-12-01T15:03:54Z
day: '17'
department:
- _id: NiBa
doi: 10.1093/evolut/qpaf143
external_id:
isi:
- '001547542300001'
pmid:
- '40668071'
intvolume: ' 79'
isi: 1
issue: '10'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1101/2025.01.22.634382
month: '10'
oa: 1
oa_version: Preprint
page: 2167-2180
pmid: 1
project:
- _id: 9B861AAC-BA93-11EA-9121-9846C619BF3A
name: NOMIS Fellowship Program
publication: Evolution
publication_identifier:
eissn:
- 1558-5646
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Deleterious mutations and selection for sex in spatially structured, diploid
populations
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 79
year: '2025'
...
---
OA_place: publisher
_id: '20694'
abstract:
- lang: eng
text: "Understanding the mechanisms underlying speciation is a central aim of evolutionary
biology.\r\nA persistent challenge in the field is to identify loci that contribute
to reproductive isolation,\r\nwhile disentangling signals of selection from demography,
linkage and intrinsic genomic\r\nfeatures. Traditional population genomic approaches
that rely on site-based statistics in\r\narbitrary fixed windows face inherent
limitations, as they conflate historical and\r\ncontemporary processes of divergence
and overlook haplotype structure. Recent advances in\r\nwhole-genome sequencing
and methods to infer ancestral recombination graphs (ARGs) now\r\noffer the opportunity
to study genealogical relationships explicitly, revealing how lineages\r\ncoalesce
and recombine through time. By directly analysing haplotype clustering by species\r\nor
phenotype and their patterns of coalescence, ARG-based methods show promise for\r\ndiagnosing
sweeps, identifying barrier loci maintained under divergent selection amid gene\r\nflow,
and tracing their evolutionary history.\r\nIn this thesis, I explore the utility
of genealogical approaches for studying species\r\ndivergence. In chapter 2, I
propose a conceptual framework for defining haplotype blocks\r\nthrough the structure
of the ARG, using simulations and empirical data to highlight how\r\ngenealogical
processes generate rich and often overlooked haplotypic patterns.\r\nIn chapter
3, I examine the genomic basis of a key evolutionary innovation in marine\r\nsnails
Littorina. These snails offer a unique opportunity to study an innovation because
they\r\ninclude a very recent transition from egg-laying to live bearing, yet
snails with the different\r\nreproductive modes are not reciprocally monophyletic.
I exploited this by using topology\r\nclustering in ARG-derived local genealogical
trees to pinpoint narrow genomic regions or\r\nhaplotype blocks that carry swept
alleles, thus revealing that the transition from egg-laying\r\nto live-bearing
involves multiple, live-bearer-specific sweeps.\r\nChapter 4 establishes a population-scale,
phased genomic resource for Antirrhinum\r\nmajus, using cost-effective haplotagging,
then optimizes imputation from low-coverage data\r\nagainst high-accuracy KASP
sequencing to maximize sequence completeness with modest\r\naccuracy trade-offs
against a traditional short-read sequence pipeline. A hybrid phasing\r\nstrategy
combines molecular phasing with statistical phasing to generate phased whole\r\ngenome
sequences of 1084 Antirrhinum individuals at a fraction of long-read sequencing\r\ncosts.\r\nIn
chapter 5, I analyse hybridising populations from two replicate hybrid zones to
find\r\na parallel genetic basis of flower colour, amidst the noise in genomic
differentiation landscape\r\ndriven by variation in demographic history. While
outlier genome scans of FST failed to dissect\r\nthe causes of differentiation,
ARG-based topology clustering revealed a reuse of colour\r\nassociated haplotypes
across hybrid zones. In addition to the biological insight, this chapter\r\nalso
presents a comparison of the latest ARG inference tools, showing that signals
of\r\nAbstract\r\nviii\r\ntopological clustering qualitatively agree between methods,
despite differences in the tree\r\nsequences.\r\nNext, in chapter 6, by leveraging
~1000 individuals in one of the hybrid zones, I\r\nintegrated genome-wide association
studies of floral pigmentation with genealogical\r\ninference, to test for additional
colour loci, and confirm the effect of previously described loci.\r\nThis work
demonstrates that flower colour variation is driven by a small number of large
effect\r\nloci, while also hinting at the presence of a new candidate regulatory
factor.\r\nFinally in chapter 7, in a preliminary analysis, I begin to dissect
the genomic island of\r\nspeciation around Rosea/Eluta to understand its evolutionary
origins. My results show that it\r\nconsists of 5 highly divergent loci, each
of which is associated with flower colour. Using\r\npatterns of coalescence in
genealogical trees, I find evidence of staggered selective sweeps\r\nand a persistent
localized barrier to gene flow within an otherwise permeable genome.\r\nTogether,
these chapters add to the increasing pool of studies using genealogical\r\napproaches
to complement and extend site-based statistics to use haplotype structures in\r\nspeciation
research. By tracking haplotypes directly and connecting genealogical clustering
to\r\npopulation processes, ARG-based inference promises to provide new insights
into how local\r\nselective pressures, demographic history, and long-term barriers
interact to shape the\r\ngenomic architecture of divergence. By underscoring the
value of ARGs in revealing the finescale origins and maintenance of biodiversity,
this thesis presents cautious optimism about\r\nthe benefits of using genealogical
inference to learn more than what site-based statistics\r\ncould tell us."
acknowledged_ssus:
- _id: ScienComp
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Arka
full_name: Pal, Arka
id: 6AAB2240-CA9A-11E9-9C1A-D9D1E5697425
last_name: Pal
orcid: 0000-0002-4530-8469
citation:
ama: Pal A. Using genealogies to study the genomic basis of species divergence.
2025. doi:10.15479/AT-ISTA-20694
apa: Pal, A. (2025). Using genealogies to study the genomic basis of species
divergence. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-20694
chicago: Pal, Arka. “Using Genealogies to Study the Genomic Basis of Species Divergence.”
Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-20694.
ieee: A. Pal, “Using genealogies to study the genomic basis of species divergence,”
Institute of Science and Technology Austria, 2025.
ista: Pal A. 2025. Using genealogies to study the genomic basis of species divergence.
Institute of Science and Technology Austria.
mla: Pal, Arka. Using Genealogies to Study the Genomic Basis of Species Divergence.
Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-20694.
short: A. Pal, Using Genealogies to Study the Genomic Basis of Species Divergence,
Institute of Science and Technology Austria, 2025.
corr_author: '1'
date_created: 2025-11-25T13:19:11Z
date_published: 2025-11-25T00:00:00Z
date_updated: 2026-04-28T13:20:36Z
day: '25'
ddc:
- '576'
- '578'
degree_awarded: PhD
department:
- _id: GradSch
- _id: NiBa
doi: 10.15479/AT-ISTA-20694
file:
- access_level: open_access
checksum: 7a10a738d58524aebb5dcbd9b34c21c5
content_type: application/pdf
creator: apal
date_created: 2025-12-01T13:53:36Z
date_updated: 2026-03-01T23:30:03Z
embargo: 2026-03-01
file_id: '20721'
file_name: 2025_Pal_Arka_Thesis.pdf
file_size: 42723135
relation: main_file
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checksum: 166d832b08d0434ce407f8f3cb930fe5
content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document
creator: apal
date_created: 2025-12-01T13:53:39Z
date_updated: 2026-03-01T23:30:03Z
embargo_to: open_access
file_id: '20722'
file_name: 2025_Pal_Arka_Thesis.docx
file_size: 60632116
relation: source_file
file_date_updated: 2026-03-01T23:30:03Z
has_accepted_license: '1'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
page: '268'
project:
- _id: bd6958e0-d553-11ed-ba76-86eba6a76c00
grant_number: '101055327'
name: Understanding the evolution of continuous genomes
- _id: 05959E1C-7A3F-11EA-A408-12923DDC885E
grant_number: P32166
name: Snapdragon Speciation
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '12159'
relation: part_of_dissertation
status: public
- id: '14796'
relation: part_of_dissertation
status: public
- id: '20190'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
title: Using genealogies to study the genomic basis of species divergence
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: dissertation
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2025'
...
---
OA_place: publisher
OA_type: hybrid
PlanS_conform: '1'
_id: '20190'
abstract:
- lang: eng
text: 'A major goal of speciation research is identifying loci that underpin barriers
to gene flow. Population genomics takes a ‘bottom-up’ approach, scanning the genome
for molecular signatures of processes that drive or maintain divergence. However,
interpreting the ‘genomic landscape’ of speciation is complicated, because genome
scans conflate multiple processes, most of which are not informative about gene
flow. However, studying replicated population contrasts, including multiple incidences
of secondary contact, can strengthen inferences. In this paper, we use linked-read
sequencing (haplotagging), FST scans and genealogical methods to characterise
the genomic landscape associated with replicate hybrid zone formation. We studied
two flower colour varieties of the common snapdragon, Antirrhinum majus subspecies
majus, that form secondary hybrid zones in multiple independent valleys in the
Pyrenees. Consistent with past work, we found very low differentiation at one
well-studied zone (Planoles). However, at a second zone (Avellanet), we found
stronger differentiation and greater heterogeneity, which we argue is due to differences
in the amount of introgression following secondary contact. Topology weighting
of genealogical trees identified loci where haplotype diversity was associated
with the two snapdragon varieties. Two of the strongest associations were at previously
identified flower colour loci: Flavia, that affects yellow pigmentation, and Rosea/Eluta,
two linked loci that affect magenta pigmentation. Preliminary analysis of coalescence
times provides additional evidence for selective sweeps at these loci and barriers
to gene flow. Our study highlights the impact of demographic history on the differentiation
landscape, emphasising the need to distinguish between historical divergence and
recent introgression.'
acknowledged_ssus:
- _id: ScienComp
acknowledgement: 'We thank ESEB Godfrey Hewitt Mobility Award for supporting AP’s
research stay at UC Davis. We thank Tom Ellis, Parvathy Surendranadh, and other
Barton Group and Coop Lab members for stimulating discussions. We are grateful to
all the interns and volunteers who have helped us with fieldwork. We thank Eva Salmerón
Mateu for her assistance in fieldwork logistics at the field station, El Serrat.
We are grateful to Enrico Coen and his research group for providing the Antirrhinum
molle PoolSeq data used in the allele polarisation. We are also thankful to Enrico
Coen and Cristophe Thébaud for discovering the Avellanet hybrid zone, followed up
with sampling led by D.L.F. in 2017. The study was supported by Austrian Science
Fund (FWF) Grant (Snapdragon Speciation P32166, awarded to D.L.F.); ERC (Advanced
Grant HaplotypeStructure 101055327, awarded to NHB); ERC (POC Grant 101069216, awarded
to Y.F.C.) and the National Institutes of Health (NIH R35 GM136290, awarded to G.C.).
Y.F.C. was supported by the Max Planck Society. Computing infrastructure for bioinformatics
and analyses was provided by ISTA High Performance Cluster. '
article_number: e70067
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Arka
full_name: Pal, Arka
id: 6AAB2240-CA9A-11E9-9C1A-D9D1E5697425
last_name: Pal
orcid: 0000-0002-4530-8469
- first_name: Daria
full_name: Shipilina, Daria
id: 428A94B0-F248-11E8-B48F-1D18A9856A87
last_name: Shipilina
orcid: 0000-0002-1145-9226
- first_name: Alan
full_name: Le Moan, Alan
last_name: Le Moan
- first_name: Adrian J.
full_name: Mcnairn, Adrian J.
last_name: Mcnairn
- first_name: Jennifer K.
full_name: Grenier, Jennifer K.
last_name: Grenier
- first_name: Marek
full_name: Kucka, Marek
last_name: Kucka
- first_name: Graham
full_name: Coop, Graham
last_name: Coop
- first_name: Yingguang Frank
full_name: Chan, Yingguang Frank
last_name: Chan
- 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: David
full_name: Field, David
id: 419049E2-F248-11E8-B48F-1D18A9856A87
last_name: Field
orcid: 0000-0002-4014-8478
- first_name: Sean
full_name: Stankowski, Sean
id: 43161670-5719-11EA-8025-FABC3DDC885E
last_name: Stankowski
citation:
ama: Pal A, Shipilina D, Le Moan A, et al. Genealogical analysis of replicate flower
colour hybrid zones in Antirrhinum. Molecular Ecology. 2025;34(22). doi:10.1111/mec.70067
apa: Pal, A., Shipilina, D., Le Moan, A., Mcnairn, A. J., Grenier, J. K., Kucka,
M., … Stankowski, S. (2025). Genealogical analysis of replicate flower colour
hybrid zones in Antirrhinum. Molecular Ecology. Wiley. https://doi.org/10.1111/mec.70067
chicago: Pal, Arka, Daria Shipilina, Alan Le Moan, Adrian J. Mcnairn, Jennifer K.
Grenier, Marek Kucka, Graham Coop, et al. “Genealogical Analysis of Replicate
Flower Colour Hybrid Zones in Antirrhinum.” Molecular Ecology. Wiley, 2025.
https://doi.org/10.1111/mec.70067.
ieee: A. Pal et al., “Genealogical analysis of replicate flower colour hybrid
zones in Antirrhinum,” Molecular Ecology, vol. 34, no. 22. Wiley, 2025.
ista: Pal A, Shipilina D, Le Moan A, Mcnairn AJ, Grenier JK, Kucka M, Coop G, Chan
YF, Barton NH, Field D, Stankowski S. 2025. Genealogical analysis of replicate
flower colour hybrid zones in Antirrhinum. Molecular Ecology. 34(22), e70067.
mla: Pal, Arka, et al. “Genealogical Analysis of Replicate Flower Colour Hybrid
Zones in Antirrhinum.” Molecular Ecology, vol. 34, no. 22, e70067, Wiley,
2025, doi:10.1111/mec.70067.
short: A. Pal, D. Shipilina, A. Le Moan, A.J. Mcnairn, J.K. Grenier, M. Kucka, G.
Coop, Y.F. Chan, N.H. Barton, D. Field, S. Stankowski, Molecular Ecology 34 (2025).
corr_author: '1'
date_created: 2025-08-17T22:01:37Z
date_published: 2025-11-01T00:00:00Z
date_updated: 2026-08-02T22:30:45Z
day: '01'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1111/mec.70067
external_id:
isi:
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creator: dernst
date_created: 2026-01-05T13:47:47Z
date_updated: 2026-01-05T13:47:47Z
file_id: '20958'
file_name: 2025_MolecEcology_Pal.pdf
file_size: 9886694
relation: main_file
success: 1
file_date_updated: 2026-01-05T13:47:47Z
has_accepted_license: '1'
intvolume: ' 34'
isi: 1
issue: '22'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
project:
- _id: 05959E1C-7A3F-11EA-A408-12923DDC885E
grant_number: P32166
name: Snapdragon Speciation
- _id: bd6958e0-d553-11ed-ba76-86eba6a76c00
grant_number: '101055327'
name: Understanding the evolution of continuous genomes
publication: Molecular Ecology
publication_identifier:
eissn:
- 1365-294X
issn:
- 0962-1083
publication_status: published
publisher: Wiley
quality_controlled: '1'
related_material:
link:
- description: News on ISTA website
relation: press_release
url: https://ista.ac.at/en/news/snapdragon-secrets/
record:
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relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Genealogical analysis of replicate flower colour hybrid zones in Antirrhinum
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: ba8df636-2132-11f1-aed0-ed93e2281fdd
volume: 34
year: '2025'
...
---
OA_type: green
_id: '21967'
abstract:
- lang: eng
text: "Selection against deleterious mutations, called purifying selection, plays
a central role in evolution and acts in all populations. It is known that the
genetic patterns observed in genomic regions undergoing purifying selection differ
from those resulting from neutral evolution. However, a comprehensive understanding
of the underlying mechanisms shaping those patterns is still lacking.\r\n\r\nIn
the present work, we use simulations combined with a genealogical approach to
identify the effect of purifying selection on the ancestry and thus on the genetic
diversity. Our analysis relies on the postulate that the genealogy belongs to
the universality class of Beta-coalescents. Under this assumption, we derive statistics
measuring the distortion of the genealogy. This approach allows us to consider
a wide range of regimes (i.e. arbitrary selection and mutation strengths) and
uncover a rich phase diagram. We find that, for strong selection, the limiting
genealogy is given by Kingman’s coalescent on a polynomial timescale. As selection
gets weaker, Muller’s ratchet starts operating, setting off the emergence of multiple
mergers in the genealogical structures. Our results show that while multiple-merger
coalescents are often interpreted as the signature of selective sweeps in rapidly
adapting populations, these structures can also appear in the context of Muller’s
ratchet."
acknowledgement: This work was supported by the Austrian Academy of Science, DOC fellowship
No 26293 (K.K.) and the European Union’s Horizon 2020 research and innovation programme
under the Marie Skłodowska-Curie grant agreement No 101034413 (J.T.). Simulations
were performed on the ISTA High-performance Computing Cluster.
article_processing_charge: No
author:
- first_name: Kseniia
full_name: Khudiakova, Kseniia
id: 4E6DC800-AE37-11E9-AC72-31CAE5697425
last_name: Khudiakova
orcid: 0000-0002-6246-1465
- first_name: Florin
full_name: Boenkost, Florin
last_name: Boenkost
- first_name: Julie N
full_name: Tourniaire, Julie N
id: 5dc06dd8-8e51-11ec-9170-8d9c450cc216
last_name: Tourniaire
citation:
ama: Khudiakova K, Boenkost F, Tourniaire JN. Genealogies under purifying selection.
bioRxiv. doi:10.1101/2024.10.15.618444
apa: Khudiakova, K., Boenkost, F., & Tourniaire, J. N. (n.d.). Genealogies under
purifying selection. bioRxiv. https://doi.org/10.1101/2024.10.15.618444
chicago: Khudiakova, Kseniia, Florin Boenkost, and Julie N Tourniaire. “Genealogies
under Purifying Selection.” BioRxiv, n.d. https://doi.org/10.1101/2024.10.15.618444.
ieee: K. Khudiakova, F. Boenkost, and J. N. Tourniaire, “Genealogies under purifying
selection,” bioRxiv. .
ista: Khudiakova K, Boenkost F, Tourniaire JN. Genealogies under purifying selection.
bioRxiv, 10.1101/2024.10.15.618444.
mla: Khudiakova, Kseniia, et al. “Genealogies under Purifying Selection.” BioRxiv,
doi:10.1101/2024.10.15.618444.
short: K. Khudiakova, F. Boenkost, J.N. Tourniaire, BioRxiv (n.d.).
corr_author: '1'
date_created: 2026-06-09T12:14:08Z
date_published: 2024-10-18T00:00:00Z
date_updated: 2026-06-12T12:43:34Z
day: '18'
department:
- _id: NiBa
- _id: JaMa
doi: 10.1101/2024.10.15.618444
ec_funded: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1101/2024.10.15.618444
month: '10'
oa: 1
oa_version: Preprint
project:
- _id: 34d33d68-11ca-11ed-8bc3-ec13763c0ca8
grant_number: '26293'
name: The impact of deleterious mutations on small populations
- _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c
call_identifier: H2020
grant_number: '101034413'
name: 'IST-BRIDGE: International postdoctoral program'
publication: bioRxiv
publication_status: draft
related_material:
record:
- id: '21918'
relation: dissertation_contains
status: public
status: public
title: Genealogies under purifying selection
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: preprint
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2024'
...