---
_id: '20833'
abstract:
- lang: eng
text: Sex-chromosome systems are highly variable across animals, but how they transition
from one to another is not well understood. Diptera have undergone multiple sex-chromosome
turnovers and expansions while maintaining their general chromosomal content,
which makes them an ideal clade to study such transitions. We analysed more than
100 dipteran whole-genome assemblies and identified 4 new lineages that underwent
sex-chromosome turnover (in addition to the 5 previously reported). We find the
majority of turnovers happened in the group Schizophora, which tend to have fewer
genes on the F element (the chromosome homologous to the ancestral insect X chromosome)
than lower dipterans, a factor previously hypothesized to facilitate turnover.
Most derived X chromosomes have higher GC content than autosomes, consistent with
a high prevalence of male-achiasmy in Diptera. In addition, an excess of gene
movement out of the X is detected for most of these new X chromosomes, and many
of these moved genes have high testis expression in Drosophila, suggesting that
out-of-X gene movement contributes to the long-term demasculinization of X chromosomes.
article_processing_charge: No
author:
- first_name: Lorena Alexandra
full_name: Layana Franco, Lorena Alexandra
id: 02814589-eb8f-11eb-b029-a70074f3f18f
last_name: Layana Franco
orcid: 0000-0002-1253-6297
- first_name: Melissa A
full_name: Toups, Melissa A
id: 4E099E4E-F248-11E8-B48F-1D18A9856A87
last_name: Toups
orcid: 0000-0002-9752-7380
- first_name: Beatriz
full_name: Vicoso, Beatriz
id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
last_name: Vicoso
orcid: 0000-0002-4579-8306
citation:
ama: Layana Franco LA, Toups MA, Vicoso B. Research Data for “Causes and consequences
of sex-chromosome turnovers in Diptera.” 2026. doi:10.15479/AT-ISTA-20833
apa: Layana Franco, L. A., Toups, M. A., & Vicoso, B. (2026). Research Data
for “Causes and consequences of sex-chromosome turnovers in Diptera.” Institute
of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-20833
chicago: Layana Franco, Lorena Alexandra, Melissa A Toups, and Beatriz Vicoso. “Research
Data for ‘Causes and Consequences of Sex-Chromosome Turnovers in Diptera.’” Institute
of Science and Technology Austria, 2026. https://doi.org/10.15479/AT-ISTA-20833.
ieee: L. A. Layana Franco, M. A. Toups, and B. Vicoso, “Research Data for ‘Causes
and consequences of sex-chromosome turnovers in Diptera.’” Institute of Science
and Technology Austria, 2026.
ista: Layana Franco LA, Toups MA, Vicoso B. 2026. Research Data for ‘Causes and
consequences of sex-chromosome turnovers in Diptera’, Institute of Science and
Technology Austria, 10.15479/AT-ISTA-20833.
mla: Layana Franco, Lorena Alexandra, et al. Research Data for “Causes and Consequences
of Sex-Chromosome Turnovers in Diptera.” Institute of Science and Technology
Austria, 2026, doi:10.15479/AT-ISTA-20833.
short: L.A. Layana Franco, M.A. Toups, B. Vicoso, (2026).
corr_author: '1'
date_created: 2025-12-17T10:10:57Z
date_published: 2026-01-08T00:00:00Z
date_updated: 2026-01-08T13:49:40Z
day: '8'
department:
- _id: BeVi
doi: 10.15479/AT-ISTA-20833
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date_updated: 2025-12-17T10:10:11Z
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file_name: Supplementary_Datasets.zip
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file_size: 572362
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success: 1
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has_accepted_license: '1'
keyword:
- Schizophora
- sex chromosomes
- sex-chromosome turnover
- Diptera
- genomic features
- out-of-X movement.
month: '01'
oa: 1
oa_version: None
publisher: Institute of Science and Technology Austria
status: public
title: Research Data for 'Causes and consequences of sex-chromosome turnovers in Diptera'
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: 68b8ca59-c5b3-11ee-8790-cd641c68093d
year: '2026'
...
---
_id: '21116'
abstract:
- lang: eng
text: Sex-chromosome systems are highly variable across animals, but how they transition
from one to another is not well understood. Diptera have undergone multiple sex-chromosome
turnovers and expansions while maintaining their general chromosomal content,
which makes them an ideal clade to study such transitions. We analyzed more than
100 dipteran whole-genome assemblies and identified 4 new lineages that underwent
sex-chromosome turnover (in addition to the 5 previously reported). We find that
the majority of turnovers happened in the group Schizophora, which tend to have
fewer genes on Muller element F (the chromosome homologous to the ancestral insect
X chromosome) than lower dipterans, a factor previously hypothesized to facilitate
turnover. Most derived X chromosomes have higher GC content than autosomes, consistent
with a high prevalence of male achiasmy in Diptera. In addition, an excess of
gene movement out of the X is detected for most of these new X chromosomes, and
many of these moved genes have high testis expression in Drosophila, suggesting
that out-of-X gene movement contributes to the long-term demasculinization of
X chromosomes.
article_processing_charge: No
author:
- first_name: Lorena Alexandra
full_name: Layana Franco, Lorena Alexandra
id: 02814589-eb8f-11eb-b029-a70074f3f18f
last_name: Layana Franco
orcid: 0000-0002-1253-6297
- first_name: Melissa A
full_name: Toups, Melissa A
id: 4E099E4E-F248-11E8-B48F-1D18A9856A87
last_name: Toups
orcid: 0000-0002-9752-7380
- first_name: Beatriz
full_name: Vicoso, Beatriz
id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
last_name: Vicoso
orcid: 0000-0002-4579-8306
citation:
ama: Layana Franco LA, Toups MA, Vicoso B. Research Data for “Causes and consequences
of sex-chromosome turnovers in Diptera.” 2026. doi:10.15479/AT-ISTA-21116
apa: Layana Franco, L. A., Toups, M. A., & Vicoso, B. (2026). Research Data
for “Causes and consequences of sex-chromosome turnovers in Diptera.” Institute
of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-21116
chicago: Layana Franco, Lorena Alexandra, Melissa A Toups, and Beatriz Vicoso. “Research
Data for ‘Causes and Consequences of Sex-Chromosome Turnovers in Diptera.’” Institute
of Science and Technology Austria, 2026. https://doi.org/10.15479/AT-ISTA-21116.
ieee: L. A. Layana Franco, M. A. Toups, and B. Vicoso, “Research Data for ‘Causes
and consequences of sex-chromosome turnovers in Diptera.’” Institute of Science
and Technology Austria, 2026.
ista: Layana Franco LA, Toups MA, Vicoso B. 2026. Research Data for ‘Causes and
consequences of sex-chromosome turnovers in Diptera’, Institute of Science and
Technology Austria, 10.15479/AT-ISTA-21116.
mla: Layana Franco, Lorena Alexandra, et al. Research Data for “Causes and Consequences
of Sex-Chromosome Turnovers in Diptera.” Institute of Science and Technology
Austria, 2026, doi:10.15479/AT-ISTA-21116.
short: L.A. Layana Franco, M.A. Toups, B. Vicoso, (2026).
corr_author: '1'
date_created: 2026-01-30T11:04:14Z
date_published: 2026-01-02T00:00:00Z
date_updated: 2026-02-12T12:58:00Z
day: '2'
department:
- _id: BeVi
doi: 10.15479/AT-ISTA-21116
file:
- access_level: open_access
checksum: 0b79be6229f2ad9ac117ef00fc4f5c0e
content_type: text/plain
creator: llayanaf
date_created: 2026-01-30T11:00:24Z
date_updated: 2026-01-30T11:00:24Z
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file_name: README.txt
file_size: 1201
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success: 1
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content_type: application/zip
creator: llayanaf
date_created: 2026-01-30T11:00:36Z
date_updated: 2026-01-30T11:00:36Z
file_id: '21118'
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file_size: 572403
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content_type: application/zip
creator: llayanaf
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date_updated: 2026-01-30T11:00:48Z
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file_name: Supplementary_Datasets.zip
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relation: main_file
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content_type: application/zip
creator: llayanaf
date_created: 2026-01-30T11:00:56Z
date_updated: 2026-01-30T11:00:56Z
file_id: '21120'
file_name: Perl_scripts.zip
file_size: 4575
relation: main_file
success: 1
file_date_updated: 2026-01-30T11:00:56Z
has_accepted_license: '1'
keyword:
- Schizophora
- sex chromosomes
- sex-chromosome turnover
- Diptera
- genomic features
- out-of-X movement.
month: '01'
oa: 1
oa_version: Published Version
publisher: Institute of Science and Technology Austria
status: public
title: Research Data for "Causes and consequences of sex-chromosome turnovers in Diptera"
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: 68b8ca59-c5b3-11ee-8790-cd641c68093d
year: '2026'
...
---
OA_place: publisher
OA_type: hybrid
PlanS_conform: '1'
_id: '21161'
abstract:
- lang: eng
text: In many species, sex-biased expression is widespread and thought to contribute
to sexual dimorphism. While bulk RNA-sequencing has been instrumental in identifying
strongly sex-biased genes, it lacks resolution to assess variation across cell-types
and tissue compartments. Using single-nucleus expression data from the Fly Cell
Atlas, we investigate sex differences in adult Drosophila melanogaster. We find
that differences in cell-type composition between the sexes are not a major source
of sex-bias, as for the vast majority of genes, the degree of sex-bias is similar
regardless of whether sex differences in cell-type composition are controlled
for or not. Our analysis confirms a deficit of X-linked male-biased genes in the
body’s somatic tissues that is widespread across cell-types. We also find the
excess of X-linked female-biased genes to be associated with nervous system cells
in the head but with epithelial cells in the body’s somatic tissues, showing that
single-nucleus data crucially resolves sex-bias at the cell-type level. We investigate
dosage compensation (DC) across 15 tissues and 17 cell-types. We observe that
it varies throughout the body. Surprisingly, we observe a lack of DC in a cluster
of main cells within the male accessory glands. This result highlights the importance
of understanding context-dependent DC.
acknowledged_ssus:
- _id: ScienComp
- _id: Bio
acknowledgement: This work was partly funded by an Austrian Science Foundation FWF
ESPRIT fellowship (10.55776/ESP6331524) to C.B. We would like to thank the Vicoso
group for their invaluable input and discussions throughout this work. We thank
Filip Ruzicka for his insightful comments on the manuscript. All computational resources
were provided by the Scientific Computing Unit at ISTA. This research was also supported
through resources provided by the Imaging & Optics Facility (IOF) at ISTA.
article_number: '20252471'
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Carolina
full_name: De Castro Barbosa Rodrigues Barata, Carolina
id: 20565186-803f-11ed-ab7e-96a4ff7694ef
last_name: De Castro Barbosa Rodrigues Barata
orcid: 0000-0003-1945-2245
- first_name: Beatriz
full_name: Vicoso, Beatriz
id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
last_name: Vicoso
orcid: 0000-0002-4579-8306
citation:
ama: de Castro Barbosa Rodrigues Barata C, Vicoso B. Single-nucleus resolution of
sex-biased expression and dosage compensation in Drosophila melanogaster. Proceedings
of the Royal Society B Biological Sciences. 2026;293(2063). doi:10.1098/rspb.2025.2471
apa: de Castro Barbosa Rodrigues Barata, C., & Vicoso, B. (2026). Single-nucleus
resolution of sex-biased expression and dosage compensation in Drosophila melanogaster.
Proceedings of the Royal Society B Biological Sciences. Royal Society of
London. https://doi.org/10.1098/rspb.2025.2471
chicago: Castro Barbosa Rodrigues Barata, Carolina de, and Beatriz Vicoso. “Single-Nucleus
Resolution of Sex-Biased Expression and Dosage Compensation in Drosophila Melanogaster.”
Proceedings of the Royal Society B Biological Sciences. Royal Society of
London, 2026. https://doi.org/10.1098/rspb.2025.2471.
ieee: C. de Castro Barbosa Rodrigues Barata and B. Vicoso, “Single-nucleus resolution
of sex-biased expression and dosage compensation in Drosophila melanogaster,”
Proceedings of the Royal Society B Biological Sciences, vol. 293, no. 2063.
Royal Society of London, 2026.
ista: de Castro Barbosa Rodrigues Barata C, Vicoso B. 2026. Single-nucleus resolution
of sex-biased expression and dosage compensation in Drosophila melanogaster. Proceedings
of the Royal Society B Biological Sciences. 293(2063), 20252471.
mla: de Castro Barbosa Rodrigues Barata, Carolina, and Beatriz Vicoso. “Single-Nucleus
Resolution of Sex-Biased Expression and Dosage Compensation in Drosophila Melanogaster.”
Proceedings of the Royal Society B Biological Sciences, vol. 293, no. 2063,
20252471, Royal Society of London, 2026, doi:10.1098/rspb.2025.2471.
short: C. de Castro Barbosa Rodrigues Barata, B. Vicoso, Proceedings of the Royal
Society B Biological Sciences 293 (2026).
corr_author: '1'
date_created: 2026-02-08T23:02:49Z
date_published: 2026-01-28T00:00:00Z
date_updated: 2026-02-16T09:27:33Z
day: '28'
ddc:
- '570'
department:
- _id: BeVi
doi: 10.1098/rspb.2025.2471
external_id:
pmid:
- '41592777'
file:
- access_level: open_access
checksum: d76afebca0a6f112df0146ae2d929f36
content_type: application/pdf
creator: dernst
date_created: 2026-02-16T09:26:02Z
date_updated: 2026-02-16T09:26:02Z
file_id: '21226'
file_name: 2026_RoyalSocPubProceedingsB_Barata.pdf
file_size: 2230841
relation: main_file
success: 1
file_date_updated: 2026-02-16T09:26:02Z
has_accepted_license: '1'
intvolume: ' 293'
issue: '2063'
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 90ef7108-16d5-11f0-9cad-e6e116913473
grant_number: ESP 6331524
name: Does genetic drift set a limit on the adaptive evolution of sex-biased expression?
publication: Proceedings of the Royal Society B Biological Sciences
publication_identifier:
eissn:
- 1471-2954
publication_status: published
publisher: Royal Society of London
quality_controlled: '1'
scopus_import: '1'
status: public
title: Single-nucleus resolution of sex-biased expression and dosage compensation
in Drosophila melanogaster
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: 293
year: '2026'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
PlanS_conform: '1'
_id: '21409'
abstract:
- lang: eng
text: Meiotic drivers are selfish genetic elements that gain transmission advantages
by distorting equal, Mendelian segregation. For decades, biologists have considered
meiotic drivers as interesting, albeit esoteric, case studies. It is now clear,
however, that meiotic drive is more common and phylogenetically widespread than
previously supposed. Indeed, intensive study of a few well-known cases has begun
to reveal the evolutionary genomic consequences of meiotic drive. We argue here
that many features of genome evolution, content, and organization that are seemingly
inexplicable by organismal adaptation or nearly neutral processes are instead
best accounted for by recurrent histories of meiotic drive. We review how meiotic
drive can affect the evolution of sequences, gene copy numbers, genes with functions
in meiosis and gametogenesis, signatures of “selection,” chromosome rearrangements,
and karyotype evolution. We also explore the interactions of meiotic drive elements
with other classes of selfish genetic elements, including satellite DNAs, transposable
elements, and with the endogenous host genes involved in drive suppression. Finally,
we argue that some aspects of drive-mediated genome evolution are now sufficiently
well established that we might reverse the direction of discovery—rather than
ask how drive affects genome evolution, we can use genome data to discover new
putative drive elements.
acknowledgement: "This review is a product of the SMBE satellite workshop and the
SNSF Scientific Exchange on the Genomic Consequences of Meiotic Drive. We thank
the Society for Molecular Biology and Evolution (satellite grant to A.M.L., A.K.L.,
R.L.U., D.C.P.), the Swiss National Science Foundation (Schweizerischer Nationalfonds
zur Förderung der Wissenschaftlichen Forschung IZSEZ0_217501 to A.K.L.), and the
National Science Foundation Division of Molecular and Cellular Biosciences (NSF
MCB Conference grant 2312190 to R.L.U.) for their generous support of the workshop.\r\n\r\nWe
also thank the following for their support of individual authors: National Science
Foundation Division of Molecular and Cellular Biosciences (NSF MCB CAREER 2047052
to R.L.U.), Division of Environmental Biology (NSF DEB-2344468 to L.F., NSF DEB-1737824
to K.A.D.), National Institute of General Medical Sciences (NIH R35GM119515 to A.M.L.,
NIH R01GM148442 to D.C.P.), European Research Council (PGErepro to L.R.), Fundação
de Amparo à Pesquisa do Estado de São Paulo (FAPESP 2020/06188-5 to A.B.S.M.F.),
Royal Society (DHF\\R1\\180120 to L.R.), Wissenschaftskolleg zu Berlin (support
for D.C.P.), and Vetenskapsrådet (Swedish Research Council VR grant number 2021-0429
to A.A.V.)."
article_number: msag020
article_processing_charge: Yes
article_type: original
author:
- first_name: Daven C.
full_name: Presgraves, Daven C.
last_name: Presgraves
- first_name: R. Kelly
full_name: Dawe, R. Kelly
last_name: Dawe
- first_name: Kelly A.
full_name: Dyer, Kelly A.
last_name: Dyer
- first_name: Lila
full_name: Fishman, Lila
last_name: Fishman
- first_name: Soumitra A.
full_name: Bhide, Soumitra A.
last_name: Bhide
- first_name: Sasha L.
full_name: Bradshaw, Sasha L.
last_name: Bradshaw
- first_name: Meghan J.
full_name: Brady, Meghan J.
last_name: Brady
- first_name: Alejandro
full_name: Burga, Alejandro
last_name: Burga
- first_name: Cécile
full_name: Courret, Cécile
last_name: Courret
- first_name: Brandon L.
full_name: Fagen, Brandon L.
last_name: Fagen
- first_name: Ana Beatriz Stein
full_name: Machado Ferretti, Ana Beatriz Stein
last_name: Machado Ferretti
- first_name: Réka K
full_name: Kelemen, Réka K
id: 48D3F8DE-F248-11E8-B48F-1D18A9856A87
last_name: Kelemen
orcid: 0000-0002-8489-9281
- first_name: Jun
full_name: Kitano, Jun
last_name: Kitano
- first_name: Yiran
full_name: Liu, Yiran
last_name: Liu
- first_name: Emiliano
full_name: Martí, Emiliano
last_name: Martí
- first_name: Theresa
full_name: Erlenbach, Theresa
last_name: Erlenbach
- first_name: Josephine A.
full_name: Reinhardt, Josephine A.
last_name: Reinhardt
- first_name: Laura
full_name: Ross, Laura
last_name: Ross
- first_name: Jan Niklas
full_name: Runge, Jan Niklas
last_name: Runge
- first_name: Callie M.
full_name: Swanepoel, Callie M.
last_name: Swanepoel
- first_name: Beatriz
full_name: Vicoso, Beatriz
id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
last_name: Vicoso
orcid: 0000-0002-4579-8306
- first_name: Aaron A.
full_name: Vogan, Aaron A.
last_name: Vogan
- first_name: Anna K.
full_name: Lindholm, Anna K.
last_name: Lindholm
- first_name: Amanda M.
full_name: Larracuente, Amanda M.
last_name: Larracuente
- first_name: Robert L.
full_name: Unckless, Robert L.
last_name: Unckless
citation:
ama: Presgraves DC, Dawe RK, Dyer KA, et al. The evolutionary genomics of meiotic
drive. Molecular Biology and Evolution. 2026;43(2). doi:10.1093/molbev/msag020
apa: Presgraves, D. C., Dawe, R. K., Dyer, K. A., Fishman, L., Bhide, S. A., Bradshaw,
S. L., … Unckless, R. L. (2026). The evolutionary genomics of meiotic drive. Molecular
Biology and Evolution. Oxford University Press. https://doi.org/10.1093/molbev/msag020
chicago: Presgraves, Daven C., R. Kelly Dawe, Kelly A. Dyer, Lila Fishman, Soumitra
A. Bhide, Sasha L. Bradshaw, Meghan J. Brady, et al. “The Evolutionary Genomics
of Meiotic Drive.” Molecular Biology and Evolution. Oxford University Press,
2026. https://doi.org/10.1093/molbev/msag020.
ieee: D. C. Presgraves et al., “The evolutionary genomics of meiotic drive,”
Molecular Biology and Evolution, vol. 43, no. 2. Oxford University Press,
2026.
ista: Presgraves DC, Dawe RK, Dyer KA, Fishman L, Bhide SA, Bradshaw SL, Brady MJ,
Burga A, Courret C, Fagen BL, Machado Ferretti ABS, Kelemen RK, Kitano J, Liu
Y, Martí E, Erlenbach T, Reinhardt JA, Ross L, Runge JN, Swanepoel CM, Vicoso
B, Vogan AA, Lindholm AK, Larracuente AM, Unckless RL. 2026. The evolutionary
genomics of meiotic drive. Molecular Biology and Evolution. 43(2), msag020.
mla: Presgraves, Daven C., et al. “The Evolutionary Genomics of Meiotic Drive.”
Molecular Biology and Evolution, vol. 43, no. 2, msag020, Oxford University
Press, 2026, doi:10.1093/molbev/msag020.
short: D.C. Presgraves, R.K. Dawe, K.A. Dyer, L. Fishman, S.A. Bhide, S.L. Bradshaw,
M.J. Brady, A. Burga, C. Courret, B.L. Fagen, A.B.S. Machado Ferretti, R.K. Kelemen,
J. Kitano, Y. Liu, E. Martí, T. Erlenbach, J.A. Reinhardt, L. Ross, J.N. Runge,
C.M. Swanepoel, B. Vicoso, A.A. Vogan, A.K. Lindholm, A.M. Larracuente, R.L. Unckless,
Molecular Biology and Evolution 43 (2026).
date_created: 2026-03-08T23:01:45Z
date_published: 2026-02-02T00:00:00Z
date_updated: 2026-03-09T10:33:04Z
day: '02'
ddc:
- '570'
department:
- _id: BeVi
doi: 10.1093/molbev/msag020
external_id:
pmid:
- '41589062'
file:
- access_level: open_access
checksum: 406e7cca0f2536d3bb877032fc837f9b
content_type: application/pdf
creator: dernst
date_created: 2026-03-09T10:32:02Z
date_updated: 2026-03-09T10:32:02Z
file_id: '21414'
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file_size: 4533829
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month: '02'
oa: 1
oa_version: Published Version
pmid: 1
publication: Molecular Biology and Evolution
publication_identifier:
eissn:
- 1537-1719
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: The evolutionary genomics of meiotic drive
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: 43
year: '2026'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
_id: '21486'
abstract:
- lang: eng
text: Sex-chromosome systems are highly variable across animals, but how they transition
from one to another is not well understood. Diptera have undergone multiple sex-chromosome
turnovers and expansions while maintaining their general chromosomal content,
which makes them an ideal clade to study such transitions. We analyzed more than
100 dipteran whole-genome assemblies and identified 4 new lineages that underwent
sex-chromosome turnover (in addition to the 5 previously reported). We find that
the majority of turnovers happened in the group Schizophora, which tend to have
fewer genes on Muller element F (the chromosome homologous to the ancestral insect
X chromosome) than lower dipterans, a factor previously hypothesized to facilitate
turnover. Most derived X chromosomes have higher GC content than autosomes, consistent
with a high prevalence of male achiasmy in Diptera. In addition, an excess of
gene movement out of the X is detected for most of these new X chromosomes, and
many of these moved genes have high testis expression in Drosophila, suggesting
that out-of-X gene movement contributes to the long-term demasculinization of
X chromosomes.
acknowledgement: This work was supported by a grant from the Austrian Science Fund
(FWF, grant number PAT 8748323) to B.V. We thank the Vicoso group for their feedback
on an early version of the manuscript. We are grateful to Kamil Jaron and Julia
Gries for helpful discussions and for sharing their unpublished work. Computational
resources and support were provided by the Scientific Computing Unit at ISTA.
article_number: qrag003
article_processing_charge: Yes
article_type: original
author:
- first_name: Lorena Alexandra
full_name: Layana Franco, Lorena Alexandra
id: 02814589-eb8f-11eb-b029-a70074f3f18f
last_name: Layana Franco
orcid: 0000-0002-1253-6297
- first_name: Melissa A
full_name: Toups, Melissa A
id: 4E099E4E-F248-11E8-B48F-1D18A9856A87
last_name: Toups
orcid: 0000-0002-9752-7380
- first_name: Beatriz
full_name: Vicoso, Beatriz
id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
last_name: Vicoso
orcid: 0000-0002-4579-8306
citation:
ama: Layana Franco LA, Toups MA, Vicoso B. Causes and consequences of sex-chromosome
turnovers in Diptera. Evolution Letters. 2026. doi:10.1093/evlett/qrag003
apa: Layana Franco, L. A., Toups, M. A., & Vicoso, B. (2026). Causes and consequences
of sex-chromosome turnovers in Diptera. Evolution Letters. Oxford University
Press. https://doi.org/10.1093/evlett/qrag003
chicago: Layana Franco, Lorena Alexandra, Melissa A Toups, and Beatriz Vicoso. “Causes
and Consequences of Sex-Chromosome Turnovers in Diptera.” Evolution Letters.
Oxford University Press, 2026. https://doi.org/10.1093/evlett/qrag003.
ieee: L. A. Layana Franco, M. A. Toups, and B. Vicoso, “Causes and consequences
of sex-chromosome turnovers in Diptera,” Evolution Letters. Oxford University
Press, 2026.
ista: Layana Franco LA, Toups MA, Vicoso B. 2026. Causes and consequences of sex-chromosome
turnovers in Diptera. Evolution Letters., qrag003.
mla: Layana Franco, Lorena Alexandra, et al. “Causes and Consequences of Sex-Chromosome
Turnovers in Diptera.” Evolution Letters, qrag003, Oxford University Press,
2026, doi:10.1093/evlett/qrag003.
short: L.A. Layana Franco, M.A. Toups, B. Vicoso, Evolution Letters (2026).
corr_author: '1'
date_created: 2026-03-23T15:05:42Z
date_published: 2026-03-12T00:00:00Z
date_updated: 2026-03-24T07:14:08Z
day: '12'
ddc:
- '570'
department:
- _id: BeVi
- _id: GradSch
doi: 10.1093/evlett/qrag003
has_accepted_license: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1093/evlett/qrag003
month: '03'
oa: 1
oa_version: Published Version
project:
- _id: 8ed82125-16d5-11f0-9cad-fbcae312235b
grant_number: PAT 8748323
name: Sex chromosomes in evolution and development
publication: Evolution Letters
publication_identifier:
eissn:
- 2056-3744
publication_status: epub_ahead
publisher: Oxford University Press
quality_controlled: '1'
status: public
title: Causes and consequences of sex-chromosome turnovers in Diptera
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
year: '2026'
...
---
OA_place: publisher
OA_type: hybrid
PlanS_conform: '1'
_id: '20009'
abstract:
- lang: eng
text: The suppression of recombination between young X and Y chromosomes is a crucial
step in their evolution, but why it occurs is not known. The detailed characterization
of the polymorphic sex chromosomes of the fourspine stickleback by Liu et al.
promises to shed new light on this longstanding question.
acknowledgement: I thank the Vicoso group for in-depth discussions of the original
article highlighted here. This work was supported by an Austrian Research Fund (FWF)
grant to B.V. (PAT 8748323).
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Beatriz
full_name: Vicoso, Beatriz
id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
last_name: Vicoso
orcid: 0000-0002-4579-8306
citation:
ama: Vicoso B. Sex chromosome evolution in action in fourspine sticklebacks. Trends
in Ecology and Evolution. 2025;40(8):728-730. doi:10.1016/j.tree.2025.06.010
apa: Vicoso, B. (2025). Sex chromosome evolution in action in fourspine sticklebacks.
Trends in Ecology and Evolution. Elsevier. https://doi.org/10.1016/j.tree.2025.06.010
chicago: Vicoso, Beatriz. “Sex Chromosome Evolution in Action in Fourspine Sticklebacks.”
Trends in Ecology and Evolution. Elsevier, 2025. https://doi.org/10.1016/j.tree.2025.06.010.
ieee: B. Vicoso, “Sex chromosome evolution in action in fourspine sticklebacks,”
Trends in Ecology and Evolution, vol. 40, no. 8. Elsevier, pp. 728–730,
2025.
ista: Vicoso B. 2025. Sex chromosome evolution in action in fourspine sticklebacks.
Trends in Ecology and Evolution. 40(8), 728–730.
mla: Vicoso, Beatriz. “Sex Chromosome Evolution in Action in Fourspine Sticklebacks.”
Trends in Ecology and Evolution, vol. 40, no. 8, Elsevier, 2025, pp. 728–30,
doi:10.1016/j.tree.2025.06.010.
short: B. Vicoso, Trends in Ecology and Evolution 40 (2025) 728–730.
corr_author: '1'
date_created: 2025-07-13T22:01:23Z
date_published: 2025-08-01T00:00:00Z
date_updated: 2025-12-30T09:22:29Z
day: '01'
ddc:
- '570'
department:
- _id: BeVi
doi: 10.1016/j.tree.2025.06.010
external_id:
isi:
- '001550437400006'
file:
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checksum: 0a7c6e8600c878dac7082681e4409b50
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creator: dernst
date_created: 2025-12-30T09:21:14Z
date_updated: 2025-12-30T09:21:14Z
file_id: '20905'
file_name: 2025_TrendsEcoloEvolution_Vicoso.pdf
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success: 1
file_date_updated: 2025-12-30T09:21:14Z
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intvolume: ' 40'
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language:
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month: '08'
oa: 1
oa_version: Published Version
page: 728-730
project:
- _id: 8ed82125-16d5-11f0-9cad-fbcae312235b
grant_number: PAT 8748323
name: Sex chromosomes in evolution and development
publication: Trends in Ecology and Evolution
publication_identifier:
issn:
- 0169-5347
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Sex chromosome evolution in action in fourspine sticklebacks
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: 40
year: '2025'
...
---
OA_place: publisher
OA_type: hybrid
PlanS_conform: '1'
_id: '20044'
abstract:
- lang: eng
text: Genetic trade-offs—which occur when variants that are beneficial in some contexts
of natural selection are harmful in others—can influence a wide range of evolutionary
phenomena, from the maintenance of genetic variation to the evolution of aging
and sex differences. An extensive body of evolutionary theory has focused on the
consequences of such trade-offs, and recent analyses of Fisher’s geometric model
have further quantified the expected proportion of new mutations that exhibit
trade-offs. However, the theory remains silent regarding the prevalence of trade-offs
among the variants that contribute to adaptation. Here, we extend Fisher’s geometric
model to predict the prevalence of trade-offs among the adaptive mutations that
become established or fixed in a population. We consider trade-offs between sexes,
habitats, fitness components, and temporally fluctuating environments. In all
4 scenarios, trade-off alleles are consistently under-represented among established
relative to new beneficial mutations—an effect that arises from the greater susceptibility
of trade-off alleles to genetic drift. Adaptation during a population size decline
exacerbates this deficit of trade-offs among established mutations, whereas population
expansions dampen it. Consequently, threatened populations should primarily adapt
using unconditionally beneficial alleles, while invasive populations are more
prone to adaptation using variants that exhibit trade-offs.
acknowledgement: 'Support for this research came from the European Society of Evolutionary
Biology (ESEB) through a “Special Topics Network” grant. Further financial support
came from the European Research Council (ERC-2023-STG916 #101117517, to C.O.), the
Swedish Research Council (#2022-03603, to C.O.; #2020‑03123, to E.I.S.), the Research
Council of Norway (Norges forskningsråd #302619, to D.G.), the Alexander von Humboldt
Foundation and the GenEvo graduate school (to H.K.), the Foundation for Zoological
Research and the Birgitta Sintring Foundation (#S2024-0007, to M.K.Z.), a postdoctoral
fellowship from the Consejo Nacional de Humanidades, Ciencias y Tecnología (to A.N.B.),
and a H2020 Marie Skłodowska-Curie COFUND Action fellowship (#101034413, to F.R.).
We wish to express our deepest gratitude to Lotte de Vries for extensive discussion
of the project, rederiving some of our results, and providing comments on an earlier
version of the manuscript, and to the European Society of Evolutionary Biology (ESEB)
for a “Special Topics Network” grant that supported workshops that initiated this
collaboration and facilitated many new ideas and friendships. We also thank two
anonymous reviewers for their thoughtful comments and suggestions that helped us
to substantially improve upon the original version of the article.'
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Tim
full_name: Connallon, Tim
last_name: Connallon
- first_name: Peter
full_name: Czuppon, Peter
last_name: Czuppon
- first_name: Colin
full_name: Olito, Colin
last_name: Olito
- first_name: Debora
full_name: Goedert, Debora
last_name: Goedert
- first_name: Hanna
full_name: Kokko, Hanna
last_name: Kokko
- first_name: Angela
full_name: Nava-Bolaños, Angela
last_name: Nava-Bolaños
- first_name: Sofie
full_name: Nilén, Sofie
last_name: Nilén
- first_name: Erik I
full_name: Svensson, Erik I
last_name: Svensson
- first_name: Martyna
full_name: Zwoinska, Martyna
last_name: Zwoinska
- first_name: Ludovic
full_name: Dutoit, Ludovic
last_name: Dutoit
- first_name: Filip
full_name: Ruzicka, Filip
id: 347955dd-57b0-11ee-9095-c28bdd368f4b
last_name: Ruzicka
citation:
ama: Connallon T, Czuppon P, Olito C, et al. Predicting the prevalence of genetic
trade-offs among adaptive substitutions. Evolution. 2025;79(7):1243-1255.
doi:10.1093/evolut/qpaf061
apa: Connallon, T., Czuppon, P., Olito, C., Goedert, D., Kokko, H., Nava-Bolaños,
A., … Ruzicka, F. (2025). Predicting the prevalence of genetic trade-offs among
adaptive substitutions. Evolution. Oxford University Press. https://doi.org/10.1093/evolut/qpaf061
chicago: Connallon, Tim, Peter Czuppon, Colin Olito, Debora Goedert, Hanna Kokko,
Angela Nava-Bolaños, Sofie Nilén, et al. “Predicting the Prevalence of Genetic
Trade-Offs among Adaptive Substitutions.” Evolution. Oxford University
Press, 2025. https://doi.org/10.1093/evolut/qpaf061.
ieee: T. Connallon et al., “Predicting the prevalence of genetic trade-offs
among adaptive substitutions,” Evolution, vol. 79, no. 7. Oxford University
Press, pp. 1243–1255, 2025.
ista: Connallon T, Czuppon P, Olito C, Goedert D, Kokko H, Nava-Bolaños A, Nilén
S, Svensson EI, Zwoinska M, Dutoit L, Ruzicka F. 2025. Predicting the prevalence
of genetic trade-offs among adaptive substitutions. Evolution. 79(7), 1243–1255.
mla: Connallon, Tim, et al. “Predicting the Prevalence of Genetic Trade-Offs among
Adaptive Substitutions.” Evolution, vol. 79, no. 7, Oxford University Press,
2025, pp. 1243–55, doi:10.1093/evolut/qpaf061.
short: T. Connallon, P. Czuppon, C. Olito, D. Goedert, H. Kokko, A. Nava-Bolaños,
S. Nilén, E.I. Svensson, M. Zwoinska, L. Dutoit, F. Ruzicka, Evolution 79 (2025)
1243–1255.
date_created: 2025-07-21T07:57:28Z
date_published: 2025-07-01T00:00:00Z
date_updated: 2025-09-30T14:06:38Z
day: '01'
ddc:
- '570'
department:
- _id: BeVi
doi: 10.1093/evolut/qpaf061
ec_funded: 1
external_id:
isi:
- '001477180800001'
file:
- access_level: open_access
checksum: 68c4c996d0e8c9ee3d4fb61bca75b31a
content_type: application/pdf
creator: dernst
date_created: 2025-07-22T10:04:57Z
date_updated: 2025-07-22T10:04:57Z
file_id: '20068'
file_name: 2025_Evolution_Connallon.pdf
file_size: 8150623
relation: main_file
success: 1
file_date_updated: 2025-07-22T10:04:57Z
has_accepted_license: '1'
intvolume: ' 79'
isi: 1
issue: '7'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: 1243-1255
project:
- _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c
call_identifier: H2020
grant_number: '101034413'
name: 'IST-BRIDGE: International postdoctoral program'
publication: Evolution
publication_identifier:
eissn:
- 1558-5646
issn:
- 0014-3820
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
status: public
title: Predicting the prevalence of genetic trade-offs among adaptive substitutions
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 79
year: '2025'
...
---
OA_place: publisher
OA_type: hybrid
PlanS_conform: '1'
_id: '20182'
abstract:
- lang: eng
text: Sex chromosomes have evolved many times throughout the tree of life, and understanding
what has shaped their unusual morphological, sequence, and regulatory features
has been a long-standing goal. Most early insights into insect sex chromosome
biology came from a few model species, such as the fruit fly Drosophila melanogaster,
which limited broad-scale evolutionary inferences. More recently, extensive comparative
genomics studies have uncovered several unexpected patterns, which we highlight
in this review. First, we describe the conservation of the ancestral X chromosome
over 450 million years but also its recurrent turnover (i.e. its reversal to an
autosome when a new X chromosome arose) in at least one order. We then summarize
classical and more recent findings on how insects modulate the expression of X-linked
genes following the degradation of the Y chromosome and how the diverse mechanisms
of dosage compensation identified may elucidate important principles of sex chromosome
regulatory evolution.
acknowledgement: This work was supported by an Austrian Research Fund (FWF) grant
to B.V. (PAT 8748323) and by the Louisiana Board of Regents Research Competitiveness
Subprogram (LEQSF(2025-28)-RD-A-20) to MAT.
article_number: '101411'
article_processing_charge: Yes (via OA deal)
article_type: review
author:
- first_name: Melissa A
full_name: Toups, Melissa A
id: 4E099E4E-F248-11E8-B48F-1D18A9856A87
last_name: Toups
orcid: 0000-0002-9752-7380
- first_name: Beatriz
full_name: Vicoso, Beatriz
id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
last_name: Vicoso
orcid: 0000-0002-4579-8306
citation:
ama: 'Toups MA, Vicoso B. Insect sex chromosome evolution: Conservation, turnover,
and mechanisms of dosage compensation. Current Opinion in Insect Science.
2025;72. doi:10.1016/j.cois.2025.101411'
apa: 'Toups, M. A., & Vicoso, B. (2025). Insect sex chromosome evolution: Conservation,
turnover, and mechanisms of dosage compensation. Current Opinion in Insect
Science. Elsevier. https://doi.org/10.1016/j.cois.2025.101411'
chicago: 'Toups, Melissa A, and Beatriz Vicoso. “Insect Sex Chromosome Evolution:
Conservation, Turnover, and Mechanisms of Dosage Compensation.” Current Opinion
in Insect Science. Elsevier, 2025. https://doi.org/10.1016/j.cois.2025.101411.'
ieee: 'M. A. Toups and B. Vicoso, “Insect sex chromosome evolution: Conservation,
turnover, and mechanisms of dosage compensation,” Current Opinion in Insect
Science, vol. 72. Elsevier, 2025.'
ista: 'Toups MA, Vicoso B. 2025. Insect sex chromosome evolution: Conservation,
turnover, and mechanisms of dosage compensation. Current Opinion in Insect Science.
72, 101411.'
mla: 'Toups, Melissa A., and Beatriz Vicoso. “Insect Sex Chromosome Evolution: Conservation,
Turnover, and Mechanisms of Dosage Compensation.” Current Opinion in Insect
Science, vol. 72, 101411, Elsevier, 2025, doi:10.1016/j.cois.2025.101411.'
short: M.A. Toups, B. Vicoso, Current Opinion in Insect Science 72 (2025).
corr_author: '1'
date_created: 2025-08-17T22:01:35Z
date_published: 2025-12-01T00:00:00Z
date_updated: 2025-12-30T13:14:38Z
day: '01'
ddc:
- '570'
department:
- _id: BeVi
doi: 10.1016/j.cois.2025.101411
external_id:
isi:
- '001582424100001'
file:
- access_level: open_access
checksum: 262640abc34277686b56eb60102976f6
content_type: application/pdf
creator: dernst
date_created: 2025-12-30T13:14:20Z
date_updated: 2025-12-30T13:14:20Z
file_id: '20917'
file_name: 2025_CurrOpinionInsectScience_Toups.pdf
file_size: 897079
relation: main_file
success: 1
file_date_updated: 2025-12-30T13:14:20Z
has_accepted_license: '1'
intvolume: ' 72'
isi: 1
language:
- iso: eng
month: '12'
oa: 1
oa_version: Published Version
project:
- _id: 8ed82125-16d5-11f0-9cad-fbcae312235b
grant_number: PAT 8748323
name: Sex chromosomes in evolution and development
publication: Current Opinion in Insect Science
publication_identifier:
eissn:
- 2214-5753
issn:
- 2214-5745
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Insect sex chromosome evolution: Conservation, turnover, and mechanisms of
dosage compensation'
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: 72
year: '2025'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
PlanS_conform: '1'
_id: '20223'
abstract:
- lang: eng
text: The first influential hypothesis for sex chromosome evolution was proposed
in 1914 by H. J. Muller, who argued that once recombination was suppressed between
the X and Y chromosomes, Y-linked genes become “sheltered” from selection, leading
to accumulation of recessive loss-of-function (LOF) mutations and decay of Y-linked
genes. The hypothesis fell out of favor in the 1970s because early mathematical
models failed to support it and data on the dominance of lethal mutations were
viewed as incompatible with the hypothesis. We reevaluate the main arguments against
Muller's hypothesis and find that they do not conclusively exclude a role for
sheltering in sex chromosome evolution. By relaxing restrictive assumptions of
earlier models, we show that sheltering promotes fixation of LOF mutations with
sexually dimorphic fitness effects, resulting in decay of X-linked genes that
are exclusively expressed by males and Y-linked genes that are primarily, though
not necessarily exclusively, expressed by females. We further show that drift
and other processes contributing to Y degeneration (i.e. selective interference
and regulatory evolution) expand conditions of Y-linked gene loss by sheltering.
The actual contribution of sheltering to sex chromosome evolution hinges upon
the distribution of dominance and sex-specific fitness effects of LOF mutations,
which we discuss.
acknowledged_ssus:
- _id: ScienComp
acknowledgement: We thank Filip Ruzicka, Colin Olito, Akane Uesugi, Melissa Toups,
Daniel Jeffries, the Associate Editor, and anonymous reviewers, for comments and
suggestions on earlier versions of the paper. We are particularly grateful to Deborah
Charlesworth and Brian Charlesworth for extensive comments on two different drafts
of the manuscript. We also thank Aneil Agrawal and Thomas Lenormand for email correspondence
about the data on dominance and ways to interpret it. Technical support was provided
by ISTA Scientific Computing Unit.
article_number: msaf177
article_processing_charge: Yes
article_type: original
author:
- first_name: Andrea
full_name: Mrnjavac, Andrea
id: 353FAC84-AE61-11E9-8BFC-00D3E5697425
last_name: Mrnjavac
- first_name: Beatriz
full_name: Vicoso, Beatriz
id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
last_name: Vicoso
orcid: 0000-0002-4579-8306
- first_name: Tim
full_name: Connallon, Tim
last_name: Connallon
citation:
ama: Mrnjavac A, Vicoso B, Connallon T. An extension of Muller’s sheltering hypothesis
for the evolution of sex chromosome gene content. Molecular Biology and Evolution.
2025;42(8). doi:10.1093/molbev/msaf177
apa: Mrnjavac, A., Vicoso, B., & Connallon, T. (2025). An extension of Muller’s
sheltering hypothesis for the evolution of sex chromosome gene content. Molecular
Biology and Evolution. Oxford University Press. https://doi.org/10.1093/molbev/msaf177
chicago: Mrnjavac, Andrea, Beatriz Vicoso, and Tim Connallon. “An Extension of Muller’s
Sheltering Hypothesis for the Evolution of Sex Chromosome Gene Content.” Molecular
Biology and Evolution. Oxford University Press, 2025. https://doi.org/10.1093/molbev/msaf177.
ieee: A. Mrnjavac, B. Vicoso, and T. Connallon, “An extension of Muller’s sheltering
hypothesis for the evolution of sex chromosome gene content,” Molecular Biology
and Evolution, vol. 42, no. 8. Oxford University Press, 2025.
ista: Mrnjavac A, Vicoso B, Connallon T. 2025. An extension of Muller’s sheltering
hypothesis for the evolution of sex chromosome gene content. Molecular Biology
and Evolution. 42(8), msaf177.
mla: Mrnjavac, Andrea, et al. “An Extension of Muller’s Sheltering Hypothesis for
the Evolution of Sex Chromosome Gene Content.” Molecular Biology and Evolution,
vol. 42, no. 8, msaf177, Oxford University Press, 2025, doi:10.1093/molbev/msaf177.
short: A. Mrnjavac, B. Vicoso, T. Connallon, Molecular Biology and Evolution 42
(2025).
date_created: 2025-08-24T22:01:31Z
date_published: 2025-08-01T00:00:00Z
date_updated: 2025-09-30T14:25:57Z
day: '01'
ddc:
- '570'
department:
- _id: BeVi
doi: 10.1093/molbev/msaf177
external_id:
isi:
- '001547617100001'
pmid:
- '40713898'
file:
- access_level: open_access
checksum: f40abffa56cb1e9ff65800f2a7d7b39a
content_type: application/pdf
creator: dernst
date_created: 2025-09-02T07:47:32Z
date_updated: 2025-09-02T07:47:32Z
file_id: '20274'
file_name: 2025_MolecularBioEvolution_Mrnjavac.pdf
file_size: 1239841
relation: main_file
success: 1
file_date_updated: 2025-09-02T07:47:32Z
has_accepted_license: '1'
intvolume: ' 42'
isi: 1
issue: '8'
language:
- iso: eng
month: '08'
oa: 1
oa_version: Published Version
pmid: 1
publication: Molecular Biology and Evolution
publication_identifier:
eissn:
- 1537-1719
issn:
- 0737-4038
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
related_material:
link:
- relation: software
url: https://git.ista.ac.at/bvicoso/xydegenerate
scopus_import: '1'
status: public
title: An extension of Muller's sheltering hypothesis for the evolution of sex chromosome
gene content
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 42
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_place: publisher
OA_type: hybrid
PlanS_conform: '1'
_id: '20404'
abstract:
- lang: eng
text: Collagens are fundamental components of extracellular matrices, requiring
precise intracellular post-translational modifications for proper function. Among
the modifications, prolyl 4-hydroxylation is critical to stabilise the collagen
triple helix. In humans, this reaction is mediated by collagen prolyl 4-hydroxylases
(P4Hs). While humans possess three genes encoding these enzymes (P4H⍺s), Drosophila
melanogaster harbour at least 26 candidates for collagen P4H⍺s despite its simple
genome, and it is poorly understood which of them are actually working on collagen
in the fly. In this study, we addressed this question by carrying out thorough
bioinformatic and biochemical analyses. We demonstrate that among the 26 potential
collagen P4H⍺s, PH4⍺EFB shares the highest homology with vertebrate collagen P4H⍺s.
Furthermore, while collagen P4Hs and their substrates must exist in the same cells,
our transcriptomic analyses at the tissue and single cell levels showed a global
co-expression of PH4⍺EFB but not the other P4H⍺-related genes with the collagen
IV genes. Moreover, expression of PH4⍺EFB during embryogenesis was found to precede
that of collagen IV, presumably enabling efficient collagen modification by PH4⍺EFB.
Finally, biochemical assays confirm that PH4⍺EFB binds collagen, supporting its
direct role in collagen IV modification. Collectively, we identify PH4⍺EFB as
the primary and potentially constitutive prolyl 4-hydroxylase responsible for
collagen IV biosynthesis in Drosophila. Our findings highlight the remarkably
simple nature of Drosophila collagen IV biosynthesis, which may serve as a blueprint
for defining the minimal requirements for collagen engineering.
acknowledgement: "This project was supported by the All May See Foundation 7031,182
to YI, the Louisiana Board of Regents Support Fund: Research Competitiveness Subprogram
to MAT, Austrian science fund (FWF) as part of the SFB Meiosis consortium FWF SFB
F88-10 to Beatriz Vicoso (supported ME), American Heart Association 16POST2726018
and American Cancer Society 132,123-PF-18–025–01-CSM postdoctoral fellowships to
ALZ, National Institutes of Health R01 GM136961 and R35 GM148485 to SH-B, and the
Academy of Medical Sciences/the Wellcome Trust/ the Government Department of Business,
Energy and Industrial Strategy/the British Heart Foundation/Diabetes UK Springboard
Award SBF008\\1115 to YM. \r\nComputational analyses of single-nucleus transcriptome
data were performed on the high performance computer (HPC) at Bournemouth University,
the HPC at Institute of Science and Technology Austria, and the high-performance
computational resources provided by the Louisiana Optical Network Infrastructure
(http://www.loni.org). The authors are grateful to the researchers who published
the transcriptome datasets [48,49,52,55] that became the essential bases for this
study, to FlyBase for curating the datasets in an easily accessible format, and
the Drosophila Genomics Resource Center (DGRC), supported by NIH grant 2P40OD010949,
for providing the D17 cell line used in this research. The authors thank Kristian
Koski (University of Oulu, Finland) for crucial advice on the domain structure of
collagen P4H⍺s, and Ryusuke Niwa and Ryo Hoshino (University of Tsukuba, Japan)
for helpful discussions on SP."
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Yoshihiro
full_name: Ishikawa, Yoshihiro
last_name: Ishikawa
- first_name: Melissa A
full_name: Toups, Melissa A
id: 4E099E4E-F248-11E8-B48F-1D18A9856A87
last_name: Toups
orcid: 0000-0002-9752-7380
- first_name: Marwan N
full_name: Elkrewi, Marwan N
id: 0B46FACA-A8E1-11E9-9BD3-79D1E5697425
last_name: Elkrewi
orcid: 0000-0002-5328-7231
- first_name: Allison L.
full_name: Zajac, Allison L.
last_name: Zajac
- first_name: Sally
full_name: Horne-Badovinac, Sally
last_name: Horne-Badovinac
- first_name: Yutaka
full_name: Matsubayashi, Yutaka
last_name: Matsubayashi
citation:
ama: Ishikawa Y, Toups MA, Elkrewi MN, Zajac AL, Horne-Badovinac S, Matsubayashi
Y. Evidence for the major role of PH4⍺EFB in the prolyl 4-hydroxylation of Drosophila
collagen IV. Matrix Biology. 2025;141(11):101-113. doi:10.1016/j.matbio.2025.09.002
apa: Ishikawa, Y., Toups, M. A., Elkrewi, M. N., Zajac, A. L., Horne-Badovinac,
S., & Matsubayashi, Y. (2025). Evidence for the major role of PH4⍺EFB in the
prolyl 4-hydroxylation of Drosophila collagen IV. Matrix Biology. Springer
Nature. https://doi.org/10.1016/j.matbio.2025.09.002
chicago: Ishikawa, Yoshihiro, Melissa A Toups, Marwan N Elkrewi, Allison L. Zajac,
Sally Horne-Badovinac, and Yutaka Matsubayashi. “Evidence for the Major Role of
PH4⍺EFB in the Prolyl 4-Hydroxylation of Drosophila Collagen IV.” Matrix Biology.
Springer Nature, 2025. https://doi.org/10.1016/j.matbio.2025.09.002.
ieee: Y. Ishikawa, M. A. Toups, M. N. Elkrewi, A. L. Zajac, S. Horne-Badovinac,
and Y. Matsubayashi, “Evidence for the major role of PH4⍺EFB in the prolyl 4-hydroxylation
of Drosophila collagen IV,” Matrix Biology, vol. 141, no. 11. Springer
Nature, pp. 101–113, 2025.
ista: Ishikawa Y, Toups MA, Elkrewi MN, Zajac AL, Horne-Badovinac S, Matsubayashi
Y. 2025. Evidence for the major role of PH4⍺EFB in the prolyl 4-hydroxylation
of Drosophila collagen IV. Matrix Biology. 141(11), 101–113.
mla: Ishikawa, Yoshihiro, et al. “Evidence for the Major Role of PH4⍺EFB in the
Prolyl 4-Hydroxylation of Drosophila Collagen IV.” Matrix Biology, vol.
141, no. 11, Springer Nature, 2025, pp. 101–13, doi:10.1016/j.matbio.2025.09.002.
short: Y. Ishikawa, M.A. Toups, M.N. Elkrewi, A.L. Zajac, S. Horne-Badovinac, Y.
Matsubayashi, Matrix Biology 141 (2025) 101–113.
date_created: 2025-09-28T22:01:26Z
date_published: 2025-11-01T00:00:00Z
date_updated: 2026-01-05T13:09:08Z
day: '01'
ddc:
- '570'
department:
- _id: BeVi
doi: 10.1016/j.matbio.2025.09.002
external_id:
isi:
- '001583892100002'
pmid:
- '40946811'
file:
- access_level: open_access
checksum: 764257db41865d19daec1935788f72d7
content_type: application/pdf
creator: dernst
date_created: 2026-01-05T13:09:01Z
date_updated: 2026-01-05T13:09:01Z
file_id: '20948'
file_name: 2025_MatrixBiology_Ishikawa.pdf
file_size: 5844254
relation: main_file
success: 1
file_date_updated: 2026-01-05T13:09:01Z
has_accepted_license: '1'
intvolume: ' 141'
isi: 1
issue: '11'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
page: 101-113
pmid: 1
project:
- _id: 34ae1506-11ca-11ed-8bc3-c14f4c474396
grant_number: F8810
name: The highjacking of meiosis for asexual reproduction
publication: Matrix Biology
publication_identifier:
eissn:
- 1569-1802
issn:
- 0945-053X
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Evidence for the major role of PH4⍺EFB in the prolyl 4-hydroxylation of Drosophila
collagen IV
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: 141
year: '2025'
...
---
OA_place: publisher
OA_type: hybrid
PlanS_conform: '1'
_id: '20655'
abstract:
- lang: eng
text: Traits that affect organismal fitness are often highly genetically variable.
This genetic variation is vital for populations to adapt to their environments,
but it is also surprising given that nature – after all – ‘selects’ the best genotypes
at the expense of those that fall short. Explaining the extensive genetic variation
of fitness‐related traits is thus a longstanding puzzle in evolutionary biology,
with cascading implications for ecology, conservation, and human health. Balancing
selection – an umbrella term for scenarios in which natural selection maintains
genetic variation – is a century‐old explanation to resolve this puzzle that has
gained recent momentum from genome‐scale methods for detecting it. Yet evaluating
whether balancing selection can, in fact, resolve the puzzle is challenging, given
the logistical constraints of distinguishing balancing selection from alternative
hypotheses and the daunting collection of theoretical models that formally underpin
this debate. Here, we track the development of balancing selection theory over
the last century and provide an accessible review of this rich collection of models.
We first outline the range of biological scenarios that can generate balancing
selection. We then examine how fundamental features of genetic systems – non‐random
mating between individuals, ploidy levels, genetic drift, linkage, and genetic
architectures of traits – have been progressively incorporated into the theory.
We end by linking these theoretical predictions to ongoing empirical efforts to
understand the evolutionary processes that explain genetic variation.
acknowledgement: 'We thank Brian Charlesworth, Deborah Charlesworth, and Sally Otto
for extensive comments and suggestions. We also thank Göran Arnqvist, Adam Eyre-Walker,
Philip Hedrick, Jitka Polechová, and Henrique Teotónio for further helpful comments
on the manuscript. This work was supported by a H2020 Marie Skłodowska-Curie COFUND
Action fellowship (#101034413, to F. R.), the Birgitta Sintring Foundation (#S2024-0007,
to M. K. Z.), the Research Council of Norway (302619, to D. G.), the Alexander von
Humboldt Foundation (to H. K.), the Swiss National Science Foundation (#211549,
to X. L. R.), the Swedish Research Council (#2022-03603, to CO; #2020-03123, to
E. I. S.) and the European Research Council (ERC-2023-STG-#101117517, to C. O.).
We are particularly grateful to the European Society for Evolutionary Biology for
funding a Special Topics Network workshop (to T. C., H. K., E. I. S.), from which
this review began. Open Access funding provided by Institute of Science and Technology
Austria/KEMÖ.'
article_number: brv.70103
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Filip
full_name: Ruzicka, Filip
id: 347955dd-57b0-11ee-9095-c28bdd368f4b
last_name: Ruzicka
- first_name: Martyna K.
full_name: Zwoinska, Martyna K.
last_name: Zwoinska
- first_name: Debora
full_name: Goedert, Debora
last_name: Goedert
- first_name: Hanna
full_name: Kokko, Hanna
last_name: Kokko
- first_name: Xiang‐Yi
full_name: Li Richter, Xiang‐Yi
last_name: Li Richter
- first_name: Iain R.
full_name: Moodie, Iain R.
last_name: Moodie
- first_name: Sofie
full_name: Nilén, Sofie
last_name: Nilén
- first_name: Colin
full_name: Olito, Colin
last_name: Olito
- first_name: Erik I.
full_name: Svensson, Erik I.
last_name: Svensson
- first_name: Peter
full_name: Czuppon, Peter
last_name: Czuppon
- first_name: Tim
full_name: Connallon, Tim
last_name: Connallon
citation:
ama: Ruzicka F, Zwoinska MK, Goedert D, et al. A century of theories of balancing
selection. Biological Reviews. 2025. doi:10.1111/brv.70103
apa: Ruzicka, F., Zwoinska, M. K., Goedert, D., Kokko, H., Li Richter, X., Moodie,
I. R., … Connallon, T. (2025). A century of theories of balancing selection. Biological
Reviews. Wiley. https://doi.org/10.1111/brv.70103
chicago: Ruzicka, Filip, Martyna K. Zwoinska, Debora Goedert, Hanna Kokko, Xiang‐Yi
Li Richter, Iain R. Moodie, Sofie Nilén, et al. “A Century of Theories of Balancing
Selection.” Biological Reviews. Wiley, 2025. https://doi.org/10.1111/brv.70103.
ieee: F. Ruzicka et al., “A century of theories of balancing selection,”
Biological Reviews. Wiley, 2025.
ista: Ruzicka F, Zwoinska MK, Goedert D, Kokko H, Li Richter X, Moodie IR, Nilén
S, Olito C, Svensson EI, Czuppon P, Connallon T. 2025. A century of theories of
balancing selection. Biological Reviews., brv. 70103.
mla: Ruzicka, Filip, et al. “A Century of Theories of Balancing Selection.” Biological
Reviews, brv. 70103, Wiley, 2025, doi:10.1111/brv.70103.
short: F. Ruzicka, M.K. Zwoinska, D. Goedert, H. Kokko, X. Li Richter, I.R. Moodie,
S. Nilén, C. Olito, E.I. Svensson, P. Czuppon, T. Connallon, Biological Reviews
(2025).
corr_author: '1'
date_created: 2025-11-19T09:43:50Z
date_published: 2025-11-14T00:00:00Z
date_updated: 2025-12-01T15:28:22Z
day: '14'
ddc:
- '570'
department:
- _id: BeVi
doi: 10.1111/brv.70103
ec_funded: 1
external_id:
isi:
- '001614285900001'
pmid:
- '41235821 '
has_accepted_license: '1'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1111/brv.70103
month: '11'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c
call_identifier: H2020
grant_number: '101034413'
name: 'IST-BRIDGE: International postdoctoral program'
publication: Biological Reviews
publication_identifier:
eissn:
- 1469-185X
issn:
- 1464-7931
publication_status: epub_ahead
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: A century of theories of balancing selection
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: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2025'
...
---
_id: '20780'
abstract:
- lang: eng
text: Sex-chromosome systems are highly variable across animals, but how they transition
from one to another is not well understood. Diptera have undergone multiple sex-chromosome
turnovers and expansions while maintaining their general chromosomal content,
which makes them an ideal clade to study such transitions. We analysed more than
100 dipteran whole-genome assemblies and identified 4 new lineages that underwent
sex-chromosome turnover (in addition to the 5 previously reported). We find the
majority of turnovers happened in the group Schizophora, which tend to have fewer
genes on the F element (the chromosome homologous to the ancestral insect X chromosome)
than lower dipterans, a factor previously hypothesized to facilitate turnover.
Most derived X chromosomes have higher GC content than autosomes, consistent with
a high prevalence of male-achiasmy in Diptera. In addition, an excess of gene
movement out of the X is detected for most of these new X chromosomes, and many
of these moved genes have high testis expression in Drosophila, suggesting that
out-of-X gene movement contributes to the long-term demasculinization of X chromosomes.
acknowledged_ssus:
- _id: ScienComp
article_processing_charge: No
author:
- first_name: Lorena Alexandra
full_name: Layana Franco, Lorena Alexandra
id: 02814589-eb8f-11eb-b029-a70074f3f18f
last_name: Layana Franco
orcid: 0000-0002-1253-6297
- first_name: Melissa A
full_name: Toups, Melissa A
id: 4E099E4E-F248-11E8-B48F-1D18A9856A87
last_name: Toups
orcid: 0000-0002-9752-7380
- first_name: Beatriz
full_name: Vicoso, Beatriz
id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
last_name: Vicoso
orcid: 0000-0002-4579-8306
citation:
ama: Layana Franco LA, Toups MA, Vicoso B. Causes and consequences of sex-chromosome
turnovers in Diptera. 2025. doi:10.15479/AT-ISTA-20780
apa: Layana Franco, L. A., Toups, M. A., & Vicoso, B. (2025). Causes and consequences
of sex-chromosome turnovers in Diptera. Institute of Science and Technology Austria.
https://doi.org/10.15479/AT-ISTA-20780
chicago: Layana Franco, Lorena Alexandra, Melissa A Toups, and Beatriz Vicoso. “Causes
and Consequences of Sex-Chromosome Turnovers in Diptera.” Institute of Science
and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-20780.
ieee: L. A. Layana Franco, M. A. Toups, and B. Vicoso, “Causes and consequences
of sex-chromosome turnovers in Diptera.” Institute of Science and Technology Austria,
2025.
ista: Layana Franco LA, Toups MA, Vicoso B. 2025. Causes and consequences of sex-chromosome
turnovers in Diptera, Institute of Science and Technology Austria, 10.15479/AT-ISTA-20780.
mla: Layana Franco, Lorena Alexandra, et al. Causes and Consequences of Sex-Chromosome
Turnovers in Diptera. Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-20780.
short: L.A. Layana Franco, M.A. Toups, B. Vicoso, (2025).
corr_author: '1'
date_created: 2025-12-10T23:40:14Z
date_published: 2025-12-01T00:00:00Z
date_updated: 2025-12-15T11:13:32Z
department:
- _id: BeVi
doi: 10.15479/AT-ISTA-20780
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file_size: 1204
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success: 1
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has_accepted_license: '1'
keyword:
- Schizophora
- sex chromosomes
- sex-chromosome turnover
- Diptera
- genomic features
- out-of-X movement.
month: '12'
oa: 1
oa_version: None
publisher: Institute of Science and Technology Austria
status: public
title: Causes and consequences of sex-chromosome turnovers in Diptera
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: 68b8ca59-c5b3-11ee-8790-cd641c68093d
year: '2025'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
PlanS_conform: '1'
_id: '20796'
abstract:
- lang: eng
text: Rapid prophase chromosome movements ensure faithful alignment of the parental
homologous chromosomes and successful synapsis formation during meiosis. These
movements are driven by cytoplasmic forces transmitted to the nuclear periphery,
where chromosome ends are attached through transmembrane proteins. During many
developmental stages a specific genome architecture with chromatin nuclear periphery
contacts mediates specific gene expression. Whether chromatin is removed from
the nuclear periphery as a consequence of chromosome motions or by a specific
mechanism is not fully understood. Here, we identify a mechanism to remove chromatin
from the nuclear periphery through vaccinia related kinase (VRK-1)–dependent phosphorylation
of Barrier to Autointegration Factor 1 (BAF-1) in Caenorhabditis elegans early
prophase of meiosis. Interfering with chromatin removal delays chromosome pairing,
impairs synapsis, produces oocytes with abnormal chromosomes and elevated apoptosis.
Long read sequencing reveals deletions and duplications in offspring lacking VRK-1
underscoring the importance of the BAF-1–VRK-1 module in preserving genome stability
in gametes during rapid chromosome movements.
acknowledgement: We are grateful to Monique Zetka, Nicola Silva, and Yumi Kim, Needhi
Bhalla, George Krohne and Rueyling Lin for providing reagents; Scott Kennedy for
sharing the multiplexed FISH library; and members of the Max Perutz Labs’ BioOptics
facility (Irmgard Fischer, Josef Gotzmann, Thomas Peterbauer, Clara Bodner, and
Nick Wedige) for training and support in image acquisition. We also thank the members
of the NGS facility at the Vienna Biocenter. This work was funded by the Austrian
Science Fund (FWF) SFB projects F 8805-B (VJ), https://doi.org/10.55776/F88, F 8809-B
(ITB), and F8810-B (BV). We are also grateful to members of the V. Jantsch laboratory
for helpful discussions. Some strains were provided by the Caenorhabditis Genetics
Center, which is funded by the National Institutes of Health Office of Research
Infrastructure Programs (P40OD010440).
article_number: '10446'
article_processing_charge: Yes
article_type: original
author:
- first_name: Dimitra
full_name: Paouneskou, Dimitra
last_name: Paouneskou
- first_name: Antoine
full_name: Baudrimont, Antoine
last_name: Baudrimont
- first_name: Réka K
full_name: Kelemen, Réka K
id: 48D3F8DE-F248-11E8-B48F-1D18A9856A87
last_name: Kelemen
orcid: 0000-0002-8489-9281
- first_name: Marwan N
full_name: Elkrewi, Marwan N
id: 0B46FACA-A8E1-11E9-9BD3-79D1E5697425
last_name: Elkrewi
orcid: 0000-0002-5328-7231
- first_name: Angela
full_name: Graf, Angela
last_name: Graf
- first_name: Shehab
full_name: Moukbel Ali Aldawla, Shehab
last_name: Moukbel Ali Aldawla
- first_name: Claudia
full_name: Kölbl, Claudia
last_name: Kölbl
- first_name: Irene
full_name: Tiemann-Boege, Irene
last_name: Tiemann-Boege
- first_name: Beatriz
full_name: Vicoso, Beatriz
id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
last_name: Vicoso
orcid: 0000-0002-4579-8306
- first_name: Verena
full_name: Jantsch, Verena
last_name: Jantsch
citation:
ama: Paouneskou D, Baudrimont A, Kelemen RK, et al. BAF-1–VRK-1 mediated release
of meiotic chromosomes from the nuclear periphery is important for genome integrity.
Nature Communications. 2025;16. doi:10.1038/s41467-025-65420-9
apa: Paouneskou, D., Baudrimont, A., Kelemen, R. K., Elkrewi, M. N., Graf, A., Moukbel
Ali Aldawla, S., … Jantsch, V. (2025). BAF-1–VRK-1 mediated release of meiotic
chromosomes from the nuclear periphery is important for genome integrity. Nature
Communications. Springer Nature. https://doi.org/10.1038/s41467-025-65420-9
chicago: Paouneskou, Dimitra, Antoine Baudrimont, Réka K Kelemen, Marwan N Elkrewi,
Angela Graf, Shehab Moukbel Ali Aldawla, Claudia Kölbl, Irene Tiemann-Boege, Beatriz
Vicoso, and Verena Jantsch. “BAF-1–VRK-1 Mediated Release of Meiotic Chromosomes
from the Nuclear Periphery Is Important for Genome Integrity.” Nature Communications.
Springer Nature, 2025. https://doi.org/10.1038/s41467-025-65420-9.
ieee: D. Paouneskou et al., “BAF-1–VRK-1 mediated release of meiotic chromosomes
from the nuclear periphery is important for genome integrity,” Nature Communications,
vol. 16. Springer Nature, 2025.
ista: Paouneskou D, Baudrimont A, Kelemen RK, Elkrewi MN, Graf A, Moukbel Ali Aldawla
S, Kölbl C, Tiemann-Boege I, Vicoso B, Jantsch V. 2025. BAF-1–VRK-1 mediated release
of meiotic chromosomes from the nuclear periphery is important for genome integrity.
Nature Communications. 16, 10446.
mla: Paouneskou, Dimitra, et al. “BAF-1–VRK-1 Mediated Release of Meiotic Chromosomes
from the Nuclear Periphery Is Important for Genome Integrity.” Nature Communications,
vol. 16, 10446, Springer Nature, 2025, doi:10.1038/s41467-025-65420-9.
short: D. Paouneskou, A. Baudrimont, R.K. Kelemen, M.N. Elkrewi, A. Graf, S. Moukbel
Ali Aldawla, C. Kölbl, I. Tiemann-Boege, B. Vicoso, V. Jantsch, Nature Communications
16 (2025).
date_created: 2025-12-11T10:45:06Z
date_published: 2025-11-25T00:00:00Z
date_updated: 2025-12-15T09:28:37Z
day: '25'
ddc:
- '570'
department:
- _id: BeVi
doi: 10.1038/s41467-025-65420-9
external_id:
pmid:
- '41290579'
file:
- access_level: open_access
checksum: a952f7ea050242b79008540de49a0e61
content_type: application/pdf
creator: dernst
date_created: 2025-12-15T09:25:51Z
date_updated: 2025-12-15T09:25:51Z
file_id: '20823'
file_name: 2025_NatureComm_Paouneskou.pdf
file_size: 8096309
relation: main_file
success: 1
file_date_updated: 2025-12-15T09:25:51Z
has_accepted_license: '1'
intvolume: ' 16'
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 34ae1506-11ca-11ed-8bc3-c14f4c474396
grant_number: F8810
name: The highjacking of meiosis for asexual reproduction
publication: Nature Communications
publication_identifier:
eissn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: BAF-1–VRK-1 mediated release of meiotic chromosomes from the nuclear periphery
is important for genome integrity
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: 16
year: '2025'
...
---
OA_place: publisher
OA_type: gold
_id: '19370'
abstract:
- lang: eng
text: Sex-linked and autosomal loci experience different selective pressures and
evolutionary dynamics. X (or Z) chromosomes are often hemizygous in males (or
females), as Y (or W) chromosomes often degenerate. Such hemizygous regions can
be under greater efficacy of selection, as recessive mutations are immediately
exposed to selection in the heterogametic sex leading to faster adaptation and
faster divergence on the X chromosome (the so-called Faster-X or Faster-Z effect).
However, in young nonrecombining regions, Y/W chromosomes often have many functional
genes, and many X/Z-linked loci are therefore diploid. The sheltering of recessive
mutations on the X/Z by the Y/W homolog is expected to drive slower adaptation
for diploid X/Z loci, i.e. a reduction in the efficacy of selection. While the
Faster-X effect has been studied extensively, much less is known empirically about
the evolutionary dynamics of diploid X or Z chromosomes. Here, we took advantage
of published population genomic data in the female-heterogametic human parasite
Schistosoma japonicum to characterize the gene content and diversity levels of
the diploid and hemizygous regions of the Z chromosome. We used different metrics
of selective pressures acting on genes to test for differences in the efficacy
of selection in hemizygous and diploid Z regions, relative to autosomes. We found
consistent patterns suggesting reduced Ne, and reduced efficacy of purifying selection,
on both hemizygous and diploid Z regions. Moreover, relaxed selection was particularly
pronounced for female-biased genes on the diploid Z, as predicted by recent theoretical
work.
acknowledgement: The authors would like to thank three anonymous reviewers for comments
and suggestions. We are also grateful to Christelle Fraïsse, Marwan Elkrewi, and
Filip Ruzicka for the help in this project.
article_number: evaf021
article_processing_charge: Yes
article_type: original
author:
- first_name: Andrea
full_name: Mrnjavac, Andrea
id: 353FAC84-AE61-11E9-8BFC-00D3E5697425
last_name: Mrnjavac
- first_name: Beatriz
full_name: Vicoso, Beatriz
id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
last_name: Vicoso
orcid: 0000-0002-4579-8306
citation:
ama: Mrnjavac A, Vicoso B. Reduced efficacy of selection on a young Z chromosome
region of schistosoma japonicum. Genome Biology and Evolution. 2025;17(2).
doi:10.1093/gbe/evaf021
apa: Mrnjavac, A., & Vicoso, B. (2025). Reduced efficacy of selection on a young
Z chromosome region of schistosoma japonicum. Genome Biology and Evolution.
Oxford University Press. https://doi.org/10.1093/gbe/evaf021
chicago: Mrnjavac, Andrea, and Beatriz Vicoso. “Reduced Efficacy of Selection on
a Young Z Chromosome Region of Schistosoma Japonicum.” Genome Biology and Evolution.
Oxford University Press, 2025. https://doi.org/10.1093/gbe/evaf021.
ieee: A. Mrnjavac and B. Vicoso, “Reduced efficacy of selection on a young Z chromosome
region of schistosoma japonicum,” Genome Biology and Evolution, vol. 17,
no. 2. Oxford University Press, 2025.
ista: Mrnjavac A, Vicoso B. 2025. Reduced efficacy of selection on a young Z chromosome
region of schistosoma japonicum. Genome Biology and Evolution. 17(2), evaf021.
mla: Mrnjavac, Andrea, and Beatriz Vicoso. “Reduced Efficacy of Selection on a Young
Z Chromosome Region of Schistosoma Japonicum.” Genome Biology and Evolution,
vol. 17, no. 2, evaf021, Oxford University Press, 2025, doi:10.1093/gbe/evaf021.
short: A. Mrnjavac, B. Vicoso, Genome Biology and Evolution 17 (2025).
corr_author: '1'
date_created: 2025-03-09T23:01:27Z
date_published: 2025-02-01T00:00:00Z
date_updated: 2025-09-30T10:49:17Z
day: '01'
ddc:
- '570'
department:
- _id: BeVi
doi: 10.1093/gbe/evaf021
external_id:
isi:
- '001423671400001'
pmid:
- '39913672'
file:
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checksum: e3aa993e3d6dad10cb806c243fa57408
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creator: dernst
date_created: 2025-03-10T08:25:59Z
date_updated: 2025-03-10T08:25:59Z
file_id: '19378'
file_name: 2025_GBE_Mrnjavac.pdf
file_size: 768371
relation: main_file
success: 1
file_date_updated: 2025-03-10T08:25:59Z
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intvolume: ' 17'
isi: 1
issue: '2'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
pmid: 1
publication: Genome Biology and Evolution
publication_identifier:
eissn:
- 1759-6653
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
related_material:
link:
- relation: software
url: https://git.ista.ac.at/amrnjava/schistosomes_slower_z
record:
- id: '18549'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: Reduced efficacy of selection on a young Z chromosome region of schistosoma
japonicum
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 17
year: '2025'
...
---
DOAJ_listed: '1'
OA_place: publisher
OA_type: gold
_id: '19735'
abstract:
- lang: eng
text: The males and females of the brine shrimp Artemia franciscana are highly dimorphic,
and this dimorphism is associated with substantial sex-biased gene expression
in heads and gonads. How these sex-specific patterns of expression are regulated
at the molecular level is unknown. A. franciscana also has differentiated ZW sex
chromosomes, with complete dosage compensation, but the molecular mechanism through
which compensation is achieved is unknown. Here, we conducted CUT&TAG assays targeting
7 post-translational histone modifications (H3K27me3, H3K9me2, H3K9me3, H3K36me3,
H3K27ac, H3K4me3, and H4K16ac) in heads and gonads of A. franciscana, allowing
us to divide the genome into 12 chromatin states. We further defined functional
chromatin signatures for all genes, which were correlated with transcript level
abundances. Differences in the occupancy of the profiled epigenetic marks between
sexes were associated with differential gene expression between males and females.
Finally, we found a significant enrichment of the permissive H4K16ac histone mark
in the Z-specific region in both tissues of females but not males, supporting
the role of this histone mark in mediating dosage compensation of the Z chromosome.
acknowledged_ssus:
- _id: ScienComp
acknowledgement: We thank the Vicoso lab for their help in maintaining Artemia and
for their valuable feedback and suggestions. We thank Marwan Elkrewi for his useful
technical advice and discussions. We are also grateful to the Scientific Unit at
ISTA Austria for computational resources and assistance. This work was supported
by Austrian science fund (FWF) grants PAT8748323 and SFB F88-10 (as part of the
SFB Meiosis consortium https://sfbmeiosis.org) to BV and Swedish Research Council
(Vetenskapsrådet, grant number 2020-06424) to MSTA.
article_number: msaf085
article_processing_charge: Yes
article_type: original
author:
- first_name: Vincent K
full_name: Bett, Vincent K
id: 57854184-AAE0-11E9-8D04-98D6E5697425
last_name: Bett
- first_name: Minerva S
full_name: Trejo Arellano, Minerva S
id: 2b681148-eed5-11eb-b81b-ae229e8620f8
last_name: Trejo Arellano
orcid: 0000-0002-1982-3475
- first_name: Beatriz
full_name: Vicoso, Beatriz
id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
last_name: Vicoso
orcid: 0000-0002-4579-8306
citation:
ama: Bett VK, Trejo Arellano MS, Vicoso B. Chromatin landscape is associated with
sex-biased expression and Drosophila-like dosage compensation of the Z chromosome
in Artemia franciscana. Molecular Biology and Evolution. 2025;42(5). doi:10.1093/molbev/msaf085
apa: Bett, V. K., Trejo Arellano, M. S., & Vicoso, B. (2025). Chromatin landscape
is associated with sex-biased expression and Drosophila-like dosage compensation
of the Z chromosome in Artemia franciscana. Molecular Biology and Evolution.
Oxford University Press. https://doi.org/10.1093/molbev/msaf085
chicago: Bett, Vincent K, Minerva S Trejo Arellano, and Beatriz Vicoso. “Chromatin
Landscape Is Associated with Sex-Biased Expression and Drosophila-like Dosage
Compensation of the Z Chromosome in Artemia Franciscana.” Molecular Biology
and Evolution. Oxford University Press, 2025. https://doi.org/10.1093/molbev/msaf085.
ieee: V. K. Bett, M. S. Trejo Arellano, and B. Vicoso, “Chromatin landscape is associated
with sex-biased expression and Drosophila-like dosage compensation of the Z chromosome
in Artemia franciscana,” Molecular Biology and Evolution, vol. 42, no.
5. Oxford University Press, 2025.
ista: Bett VK, Trejo Arellano MS, Vicoso B. 2025. Chromatin landscape is associated
with sex-biased expression and Drosophila-like dosage compensation of the Z chromosome
in Artemia franciscana. Molecular Biology and Evolution. 42(5), msaf085.
mla: Bett, Vincent K., et al. “Chromatin Landscape Is Associated with Sex-Biased
Expression and Drosophila-like Dosage Compensation of the Z Chromosome in Artemia
Franciscana.” Molecular Biology and Evolution, vol. 42, no. 5, msaf085,
Oxford University Press, 2025, doi:10.1093/molbev/msaf085.
short: V.K. Bett, M.S. Trejo Arellano, B. Vicoso, Molecular Biology and Evolution
42 (2025).
corr_author: '1'
date_created: 2025-05-25T22:16:56Z
date_published: 2025-05-01T00:00:00Z
date_updated: 2026-04-07T12:28:15Z
day: '01'
ddc:
- '570'
department:
- _id: BeVi
- _id: DaZi
doi: 10.1093/molbev/msaf085
external_id:
isi:
- '001483460200001'
pmid:
- '40202086'
file:
- access_level: open_access
checksum: 6c14b03f94b4aadf8869be2c4366d077
content_type: application/pdf
creator: dernst
date_created: 2025-05-28T09:34:36Z
date_updated: 2025-05-28T09:34:36Z
file_id: '19756'
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file_size: 1282772
relation: main_file
success: 1
file_date_updated: 2025-05-28T09:34:36Z
has_accepted_license: '1'
intvolume: ' 42'
isi: 1
issue: '5'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 8ed82125-16d5-11f0-9cad-fbcae312235b
grant_number: PAT 8748323
name: Sex chromosomes in evolution and development
- _id: 34ae1506-11ca-11ed-8bc3-c14f4c474396
grant_number: F8810
name: The highjacking of meiosis for asexual reproduction
publication: Molecular Biology and Evolution
publication_identifier:
eissn:
- 1537-1719
issn:
- 0737-4038
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
related_material:
link:
- relation: software
url: https://github.com/vkb25/Chromatin-landscape-in-Artemia-franciscana.git
record:
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relation: dissertation_contains
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relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: Chromatin landscape is associated with sex-biased expression and Drosophila-like
dosage compensation of the Z chromosome in Artemia franciscana
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 42
year: '2025'
...
---
OA_place: publisher
_id: '20449'
acknowledged_ssus:
- _id: ScienComp
acknowledgement: "This work was supported by the Austrian Science Fund (FWF) through
grants PAT8748323\r\nand SFB F88-10 awarded to Professor Beatriz Vicoso."
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Vincent K
full_name: Bett, Vincent K
id: 57854184-AAE0-11E9-8D04-98D6E5697425
last_name: Bett
citation:
ama: Bett VK. Evolution and regulation of the Z chromosome. 2025. doi:10.15479/AT-ISTA-20449
apa: Bett, V. K. (2025). Evolution and regulation of the Z chromosome. Institute
of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-20449
chicago: Bett, Vincent K. “Evolution and Regulation of the Z Chromosome.” Institute
of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-20449.
ieee: V. K. Bett, “Evolution and regulation of the Z chromosome,” Institute of Science
and Technology Austria, 2025.
ista: Bett VK. 2025. Evolution and regulation of the Z chromosome. Institute of
Science and Technology Austria.
mla: Bett, Vincent K. Evolution and Regulation of the Z Chromosome. Institute
of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-20449.
short: V.K. Bett, Evolution and Regulation of the Z Chromosome, Institute of Science
and Technology Austria, 2025.
corr_author: '1'
date_created: 2025-10-11T08:18:51Z
date_published: 2025-10-10T00:00:00Z
date_updated: 2026-04-07T12:28:15Z
day: '10'
ddc:
- '576'
degree_awarded: PhD
department:
- _id: GradSch
- _id: BeVi
doi: 10.15479/AT-ISTA-20449
file:
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creator: vbett
date_created: 2025-10-20T13:32:29Z
date_updated: 2025-10-20T13:32:29Z
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language:
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month: '10'
oa_version: Published Version
page: '114'
project:
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grant_number: PAT 8748323
name: Sex chromosomes in evolution and development
- _id: 34ae1506-11ca-11ed-8bc3-c14f4c474396
grant_number: F8810
name: The highjacking of meiosis for asexual reproduction
publication_identifier:
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
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relation: part_of_dissertation
status: public
- id: '15009'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Beatriz
full_name: Vicoso, Beatriz
id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
last_name: Vicoso
orcid: 0000-0002-4579-8306
title: Evolution and regulation of the Z chromosome
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: dissertation
user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd
year: '2025'
...
---
OA_embargo: '12'
OA_place: publisher
_id: '19386'
abstract:
- lang: eng
text: "Crustaceans are a large group of arthropods with a great diversity of species
and\r\ndifferent types of sex determination systems and reproductive modes (Subramoniam,
2017).\r\nThis makes them a great model for exploring the evolution of sex chromosomes
and sexual\r\ndimorphism and investigating the evolutionary mechanisms driving
and maintaining the\r\ndiversity of reproductive systems. Within this taxon, Brine
shrimp of the genus Artemia, a\r\nbranchiopod crustacean, are well suited for
such explorations, as they have both highly\r\ndimorphic traits and closely related
sexual and asexual species. Although brine shrimp are\r\nknown to have ZW sex
chromosomes (Bowen, 1963; Parraguez et al., 2009), the sex\r\nchromosomes are
still not well characterized at the genomic level, the sex-determination gene\r\nis
unknown, and it is still unclear whether the same sex chromosomes as shared by
the\r\ndifferent species.\r\nThe first part of this thesis was to characterize
the Z and W chromosomes in Artemia\r\nusing an array of methods, from generating
multiple chromosome and contig level genome\r\nassemblies to identifying W-linked
scaffolds and transcripts in multiple species using k-mer\r\nbased approaches.\r\nThe
second part tackles the conservation of the cell type specific regulatory pathways\r\nin
the female reproductive system between Artemia and Drosophila, and the expression
of the\r\nZ-specific region throughout meiosis using single-nucleus RNA-seq data.
Our results show\r\nthat germline cells lack dosage compensation, with a subset
of cells showing evidence of\r\nextreme repression of the Z chromosome.\r\nWith
multiple sexual species and several asexual lineages of parthenogenetic females\r\nthat
produce rare males at low frequencies, Brine shrimp present the perfect opportunity
to\r\nexplore the transition to asexuality and shed light on the prerequisites
and repercussions of\r\nthe form of modified meiosis maintaining the asexual lineages.
The last chapter is an\r\ninvestigation of the molecular pathways involved in
asexual reproduction in Artemia using\r\nnewly generated single nucleus RNAseq
and WGS data and previously published data. "
acknowledged_ssus:
- _id: ScienComp
acknowledgement: My PhD work was funded by the Austrian science fund (FWF), as part
of the SFB Meiosis consortium (https://sfbmeiosis.org/, grant ID FWF SFB F88-10).
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Marwan N
full_name: Elkrewi, Marwan N
id: 0B46FACA-A8E1-11E9-9BD3-79D1E5697425
last_name: Elkrewi
orcid: 0000-0002-5328-7231
citation:
ama: Elkrewi MN. Evolution of sex chromosomes, sex determination and asexuality
in Artemia brine shrimp. 2025. doi:10.15479/AT-ISTA-19386
apa: Elkrewi, M. N. (2025). Evolution of sex chromosomes, sex determination and
asexuality in Artemia brine shrimp. Institute of Science and Technology Austria.
https://doi.org/10.15479/AT-ISTA-19386
chicago: Elkrewi, Marwan N. “Evolution of Sex Chromosomes, Sex Determination and
Asexuality in Artemia Brine Shrimp.” Institute of Science and Technology Austria,
2025. https://doi.org/10.15479/AT-ISTA-19386.
ieee: M. N. Elkrewi, “Evolution of sex chromosomes, sex determination and asexuality
in Artemia brine shrimp,” Institute of Science and Technology Austria, 2025.
ista: Elkrewi MN. 2025. Evolution of sex chromosomes, sex determination and asexuality
in Artemia brine shrimp. Institute of Science and Technology Austria.
mla: Elkrewi, Marwan N. Evolution of Sex Chromosomes, Sex Determination and Asexuality
in Artemia Brine Shrimp. Institute of Science and Technology Austria, 2025,
doi:10.15479/AT-ISTA-19386.
short: M.N. Elkrewi, Evolution of Sex Chromosomes, Sex Determination and Asexuality
in Artemia Brine Shrimp, Institute of Science and Technology Austria, 2025.
corr_author: '1'
date_created: 2025-03-11T12:54:31Z
date_published: 2025-03-14T00:00:00Z
date_updated: 2026-04-16T12:20:41Z
day: '14'
ddc:
- '570'
- '576'
degree_awarded: PhD
department:
- _id: GradSch
- _id: BeVi
doi: 10.15479/AT-ISTA-19386
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language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
page: '170'
project:
- _id: 34ae1506-11ca-11ed-8bc3-c14f4c474396
grant_number: F8810
name: The highjacking of meiosis for asexual reproduction
publication_identifier:
eissn:
- 2663-337X
isbn:
- '9783990780534'
publication_status: published
publisher: Institute of Science and Technology Austria
related_material:
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relation: part_of_dissertation
status: public
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relation: part_of_dissertation
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relation: part_of_dissertation
status: public
- id: '15009'
relation: part_of_dissertation
status: public
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relation: part_of_dissertation
status: public
- id: '17890'
relation: part_of_dissertation
status: public
status: public
supervisor:
- first_name: Beatriz
full_name: Vicoso, Beatriz
id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
last_name: Vicoso
orcid: 0000-0002-4579-8306
title: Evolution of sex chromosomes, sex determination and asexuality in Artemia brine
shrimp
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: dissertation
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2025'
...
---
_id: '14705'
abstract:
- lang: eng
text: Since the commercialization of brine shrimp (genus Artemia) in the 1950s,
this lineage, and in particular the model species Artemia franciscana, has been
the subject of extensive research. However, our understanding of the genetic mechanisms
underlying various aspects of their reproductive biology, including sex determination,
are still lacking. This is partly due to the scarcity of genomic resources for
Artemia species and crustaceans in general. Here, we present a chromosome-level
genome assembly of Artemia franciscana (Kellogg 1906), from the Great Salt Lake,
USA. The genome is 1GB, and the majority of the genome (81%) is scaffolded into
21 linkage groups using a previously published high-density linkage map. We performed
coverage and FST analyses using male and female genomic and transcriptomic reads
to quantify the extent of differentiation between the Z and W chromosomes. Additionally,
we quantified the expression levels in male and female heads and gonads and found
further evidence for dosage compensation in this species.
article_processing_charge: No
author:
- first_name: Marwan N
full_name: Elkrewi, Marwan N
id: 0B46FACA-A8E1-11E9-9BD3-79D1E5697425
last_name: Elkrewi
orcid: 0000-0002-5328-7231
citation:
ama: Elkrewi MN. Data from “Chromosome-level assembly of Artemia franciscana sheds
light on sex-chromosome differentiation.” 2024. doi:10.15479/AT:ISTA:14705
apa: Elkrewi, M. N. (2024). Data from “Chromosome-level assembly of Artemia franciscana
sheds light on sex-chromosome differentiation.” Institute of Science and Technology
Austria. https://doi.org/10.15479/AT:ISTA:14705
chicago: Elkrewi, Marwan N. “Data from ‘Chromosome-Level Assembly of Artemia Franciscana
Sheds Light on Sex-Chromosome Differentiation.’” Institute of Science and Technology
Austria, 2024. https://doi.org/10.15479/AT:ISTA:14705.
ieee: M. N. Elkrewi, “Data from ‘Chromosome-level assembly of Artemia franciscana
sheds light on sex-chromosome differentiation.’” Institute of Science and Technology
Austria, 2024.
ista: Elkrewi MN. 2024. Data from ‘Chromosome-level assembly of Artemia franciscana
sheds light on sex-chromosome differentiation’, Institute of Science and Technology
Austria, 10.15479/AT:ISTA:14705.
mla: Elkrewi, Marwan N. Data from “Chromosome-Level Assembly of Artemia Franciscana
Sheds Light on Sex-Chromosome Differentiation.” Institute of Science and Technology
Austria, 2024, doi:10.15479/AT:ISTA:14705.
short: M.N. Elkrewi, (2024).
contributor:
- contributor_type: researcher
first_name: Vincent K
id: 57854184-AAE0-11E9-8D04-98D6E5697425
last_name: Bett
- contributor_type: project_member
first_name: Ariana
id: 2A0848E2-F248-11E8-B48F-1D18A9856A87
last_name: Macon
- contributor_type: supervisor
first_name: Beatriz
id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87
last_name: Vicoso
orcid: 0000-0002-4579-8306
- contributor_type: researcher
first_name: Marwan N
id: 0B46FACA-A8E1-11E9-9BD3-79D1E5697425
last_name: Elkrewi
orcid: 0000-0002-5328-7231
corr_author: '1'
date_created: 2023-12-22T13:40:48Z
date_published: 2024-01-02T00:00:00Z
date_updated: 2025-09-04T12:05:42Z
day: '02'
ddc:
- '576'
department:
- _id: GradSch
- _id: BeVi
doi: 10.15479/AT:ISTA:14705
file:
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checksum: bdaf1392867786634ec5466d528c36ca
content_type: text/plain
creator: melkrewi
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date_updated: 2023-12-22T13:54:21Z
file_id: '14707'
file_name: readme.txt.txt
file_size: 847
relation: main_file
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checksum: 973e1cbdab923a71709782177980829f
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creator: melkrewi
date_created: 2023-12-22T14:14:06Z
date_updated: 2023-12-22T14:14:06Z
file_id: '14708'
file_name: data_artemia_franciscana_genome.zip
file_size: 343632753
relation: main_file
success: 1
file_date_updated: 2023-12-22T14:14:06Z
has_accepted_license: '1'
keyword:
- sex chromosome evolution
- genome assembly
- dosage compensation
month: '01'
oa: 1
oa_version: Published Version
project:
- _id: 34ae1506-11ca-11ed-8bc3-c14f4c474396
grant_number: F8810
name: The highjacking of meiosis for asexual reproduction
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '15009'
relation: used_in_publication
status: public
status: public
title: Data from "Chromosome-level assembly of Artemia franciscana sheds light on
sex-chromosome differentiation"
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: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2024'
...
---
OA_place: publisher
OA_type: hybrid
_id: '18479'
abstract:
- lang: eng
text: The dominance of beneficial mutations is a key evolutionary parameter affecting
the rate and genetic basis of adaptation, yet it is notoriously difficult to estimate.
A leading method to infer it is to compare the relative rates of adaptive substitution
for X-linked and autosomal genes, which—according to a classic model by Charlesworth
et al. (1987)—is a simple function of the dominance of new beneficial mutations.
Recent evidence that rates of adaptive substitution are faster for X-linked genes
implies, accordingly, that beneficial mutations are usually recessive. However,
this conclusion is incompatible with leading theories of dominance, which predict
that beneficial mutations tend to be dominant or overdominant with respect to
fitness. To address this incompatibility, we use Fisher’s geometric model to predict
the distribution of fitness effects of new mutations and the relative rates of
positively selected substitution on the X and autosomes. Previous predictions
of faster-X theory emerge as a special case of our model in which the phenotypic
effects of mutations are small relative to the distance to the phenotypic optimum.
But as mutational effects become large relative to the optimum, we observe an
elevated tempo of positively selected substitutions on the X relative to the autosomes
across a broader range of dominance conditions, including those predicted by theories
of dominance. Our results imply that, contrary to previous models, dominant and
overdominant beneficial mutations can plausibly generate patterns of faster-X
adaptation. We discuss resulting implications for genomic studies of adaptation
and inferences of dominance.
acknowledgement: This work was supported by funds from the Australian Research Council
and The School of Biological Sciences at Monash University. F.R. was funded by a
H2020 Marie Skłodowska-Curie COFUND Action (No. 101034413). We thank three anonymous
reviewers for suggestions that substantially improved the paper and breadth of the
analysis.
article_number: e2406335121
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Yasmine
full_name: Mcdonough, Yasmine
last_name: Mcdonough
- first_name: Filip
full_name: Ruzicka, Filip
id: 347955dd-57b0-11ee-9095-c28bdd368f4b
last_name: Ruzicka
- first_name: Tim
full_name: Connallon, Tim
last_name: Connallon
citation:
ama: Mcdonough Y, Ruzicka F, Connallon T. Reconciling theories of dominance with
the relative rates of adaptive substitution on sex chromosomes and autosomes.
Proceedings of the National Academy of Sciences of the United States of America.
2024;121(44). doi:10.1073/pnas.2406335121
apa: Mcdonough, Y., Ruzicka, F., & Connallon, T. (2024). Reconciling theories
of dominance with the relative rates of adaptive substitution on sex chromosomes
and autosomes. Proceedings of the National Academy of Sciences of the United
States of America. National Academy of Sciences. https://doi.org/10.1073/pnas.2406335121
chicago: Mcdonough, Yasmine, Filip Ruzicka, and Tim Connallon. “Reconciling Theories
of Dominance with the Relative Rates of Adaptive Substitution on Sex Chromosomes
and Autosomes.” Proceedings of the National Academy of Sciences of the United
States of America. National Academy of Sciences, 2024. https://doi.org/10.1073/pnas.2406335121.
ieee: Y. Mcdonough, F. Ruzicka, and T. Connallon, “Reconciling theories of dominance
with the relative rates of adaptive substitution on sex chromosomes and autosomes,”
Proceedings of the National Academy of Sciences of the United States of America,
vol. 121, no. 44. National Academy of Sciences, 2024.
ista: Mcdonough Y, Ruzicka F, Connallon T. 2024. Reconciling theories of dominance
with the relative rates of adaptive substitution on sex chromosomes and autosomes.
Proceedings of the National Academy of Sciences of the United States of America.
121(44), e2406335121.
mla: Mcdonough, Yasmine, et al. “Reconciling Theories of Dominance with the Relative
Rates of Adaptive Substitution on Sex Chromosomes and Autosomes.” Proceedings
of the National Academy of Sciences of the United States of America, vol.
121, no. 44, e2406335121, National Academy of Sciences, 2024, doi:10.1073/pnas.2406335121.
short: Y. Mcdonough, F. Ruzicka, T. Connallon, Proceedings of the National Academy
of Sciences of the United States of America 121 (2024).
date_created: 2024-10-27T23:01:44Z
date_published: 2024-10-29T00:00:00Z
date_updated: 2025-09-08T14:31:58Z
day: '29'
ddc:
- '570'
department:
- _id: BeVi
doi: 10.1073/pnas.2406335121
ec_funded: 1
external_id:
isi:
- '001359216400017'
pmid:
- '39436652'
file:
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checksum: 73db3c87b35753e0f4324417f164a35e
content_type: application/pdf
creator: dernst
date_created: 2024-11-04T10:29:43Z
date_updated: 2024-11-04T10:29:43Z
file_id: '18501'
file_name: 2024_PNAS_McDonough.pdf
file_size: 1299095
relation: main_file
success: 1
file_date_updated: 2024-11-04T10:29:43Z
has_accepted_license: '1'
intvolume: ' 121'
isi: 1
issue: '44'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c
call_identifier: H2020
grant_number: '101034413'
name: 'IST-BRIDGE: International postdoctoral program'
publication: Proceedings of the National Academy of Sciences of the United States
of America
publication_identifier:
eissn:
- 1091-6490
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
scopus_import: '1'
status: public
title: Reconciling theories of dominance with the relative rates of adaptive substitution
on sex chromosomes and autosomes
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 121
year: '2024'
...