---
_id: '14812'
abstract:
- lang: eng
text: This repository contains the code and VCF files needed to conduct the analyses
in our MS. Each folder contains a readMe document explaining the nature of each
file and dataset and the results and analyses that they relate to. The same anlaysis
code (but not VCF files) is also available at https://github.com/seanstankowski/Littorina_reproductive_mode
article_processing_charge: No
author:
- first_name: Sean
full_name: Stankowski, Sean
id: 43161670-5719-11EA-8025-FABC3DDC885E
last_name: Stankowski
citation:
ama: 'Stankowski S. Data and code for: The genetic architecture of a recent transition
to live-bearing in marine snails. 2023. doi:10.5281/ZENODO.8318995'
apa: 'Stankowski, S. (2023). Data and code for: The genetic architecture of a recent
transition to live-bearing in marine snails. Zenodo. https://doi.org/10.5281/ZENODO.8318995'
chicago: 'Stankowski, Sean. “Data and Code for: The Genetic Architecture of a Recent
Transition to Live-Bearing in Marine Snails.” Zenodo, 2023. https://doi.org/10.5281/ZENODO.8318995.'
ieee: 'S. Stankowski, “Data and code for: The genetic architecture of a recent transition
to live-bearing in marine snails.” Zenodo, 2023.'
ista: 'Stankowski S. 2023. Data and code for: The genetic architecture of a recent
transition to live-bearing in marine snails, Zenodo, 10.5281/ZENODO.8318995.'
mla: 'Stankowski, Sean. Data and Code for: The Genetic Architecture of a Recent
Transition to Live-Bearing in Marine Snails. Zenodo, 2023, doi:10.5281/ZENODO.8318995.'
short: S. Stankowski, (2023).
contributor:
- first_name: Zusanna
last_name: Zagrodzka
- first_name: Martin
last_name: Garlovsky
- first_name: Arka
id: 6AAB2240-CA9A-11E9-9C1A-D9D1E5697425
last_name: Pal
orcid: 0000-0002-4530-8469
- first_name: Daria
id: 428A94B0-F248-11E8-B48F-1D18A9856A87
last_name: Shipilina
orcid: 0000-0002-1145-9226
- first_name: Diego Fernando
id: ae681a14-dc74-11ea-a0a7-c6ef18161701
last_name: Garcia Castillo
- first_name: Hila
id: d6ab5470-2fb3-11ed-8633-986a9b84edac
last_name: Lifchitz
- first_name: Alan
last_name: Le Moan
- first_name: Erica
last_name: Leder
- first_name: James
last_name: Reeve
- first_name: Kerstin
last_name: Johannesson
- first_name: Anja M
id: 3C147470-F248-11E8-B48F-1D18A9856A87
last_name: Westram
orcid: 0000-0003-1050-4969
- first_name: Roger
last_name: Butlin
date_created: 2024-01-16T10:23:01Z
date_published: 2023-09-05T00:00:00Z
date_updated: 2024-03-05T09:35:25Z
day: '05'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.5281/ZENODO.8318995
has_accepted_license: '1'
license: https://creativecommons.org/licenses/by/4.0/
main_file_link:
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url: https://doi.org/10.5281/zenodo.8318995
month: '09'
oa: 1
oa_version: Published Version
publisher: Zenodo
related_material:
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status: public
status: public
title: 'Data and code for: The genetic architecture of a recent transition to live-bearing
in marine snails'
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image: /images/cc_by.png
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type: research_data_reference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '12800'
abstract:
- lang: eng
text: 'The evolutionary processes that brought about today’s plethora of living
species and the many billions more ancient ones all underlie biology. Evolutionary
pathways are neither directed nor deterministic, but rather an interplay between
selection, migration, mutation, genetic drift and other environmental factors.
Hybrid zones, as natural crossing experiments, offer a great opportunity to use
cline analysis to deduce different evolutionary processes - for example, selection
strength. Theoretical cline models, largely assuming uniform distribution of individuals,
often lack the capability of incorporating population structure. Since in reality
organisms mostly live in patchy distributions and their dispersal is hardly ever
Gaussian, it is necessary to unravel the effect of these different elements of
population structure on cline parameters and shape. In this thesis, I develop
a simulation inspired by the A. majus hybrid zone of a single selected locus under
frequency dependent selection. This simulation enables us to untangle the effects
of different elements of population structure as for example a low-density center
and long-range dispersal. This thesis is therefore a first step towards theoretically
untangling the effects of different elements of population structure on cline
parameters and shape. '
alternative_title:
- ISTA Master's Thesis
article_processing_charge: No
author:
- first_name: Mara
full_name: Julseth, Mara
id: 1cf464b2-dc7d-11ea-9b2f-f9b1aa9417d1
last_name: Julseth
citation:
ama: Julseth M. The effect of local population structure on genetic variation at
selected loci in the A. majus hybrid zone. 2023. doi:10.15479/at:ista:12800
apa: Julseth, M. (2023). The effect of local population structure on genetic
variation at selected loci in the A. majus hybrid zone. Institute of Science
and Technology Austria. https://doi.org/10.15479/at:ista:12800
chicago: Julseth, Mara. “The Effect of Local Population Structure on Genetic Variation
at Selected Loci in the A. Majus Hybrid Zone.” Institute of Science and Technology
Austria, 2023. https://doi.org/10.15479/at:ista:12800.
ieee: M. Julseth, “The effect of local population structure on genetic variation
at selected loci in the A. majus hybrid zone,” Institute of Science and Technology
Austria, 2023.
ista: Julseth M. 2023. The effect of local population structure on genetic variation
at selected loci in the A. majus hybrid zone. Institute of Science and Technology
Austria.
mla: Julseth, Mara. The Effect of Local Population Structure on Genetic Variation
at Selected Loci in the A. Majus Hybrid Zone. Institute of Science and Technology
Austria, 2023, doi:10.15479/at:ista:12800.
short: M. Julseth, The Effect of Local Population Structure on Genetic Variation
at Selected Loci in the A. Majus Hybrid Zone, Institute of Science and Technology
Austria, 2023.
date_created: 2023-04-04T18:57:11Z
date_published: 2023-04-05T00:00:00Z
date_updated: 2023-06-02T22:30:05Z
day: '05'
ddc:
- '576'
degree_awarded: MS
department:
- _id: GradSch
- _id: NiBa
doi: 10.15479/at:ista:12800
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file_size: 52795
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date_created: 2023-04-06T06:11:27Z
date_updated: 2023-06-02T22:30:04Z
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date_created: 2023-04-06T08:26:37Z
date_updated: 2023-06-02T22:30:04Z
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file_name: ThesisMaraJulseth_04_23.pdf
file_size: 1741364
relation: main_file
file_date_updated: 2023-06-02T22:30:04Z
has_accepted_license: '1'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: '21'
publication_identifier:
issn:
- 2791-4585
publication_status: published
publisher: Institute of Science and Technology Austria
status: public
supervisor:
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
title: The effect of local population structure on genetic variation at selected loci
in the A. majus hybrid zone
type: dissertation
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2023'
...
---
_id: '11702'
abstract:
- lang: eng
text: When Mendel’s work was rediscovered in 1900, and extended to establish classical
genetics, it was initially seen in opposition to Darwin’s theory of evolution
by natural selection on continuous variation, as represented by the biometric
research program that was the foundation of quantitative genetics. As Fisher,
Haldane, and Wright established a century ago, Mendelian inheritance is exactly
what is needed for natural selection to work efficiently. Yet, the synthesis remains
unfinished. We do not understand why sexual reproduction and a fair meiosis predominate
in eukaryotes, or how far these are responsible for their diversity and complexity.
Moreover, although quantitative geneticists have long known that adaptive variation
is highly polygenic, and that this is essential for efficient selection, this
is only now becoming appreciated by molecular biologists—and we still do not have
a good framework for understanding polygenic variation or diffuse function.
acknowledgement: I thank Laura Hayward, Jitka Polechova, and Anja Westram for discussions
and comments.
article_number: e2122147119
article_processing_charge: No
article_type: original
author:
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: Barton NH. The “New Synthesis.” Proceedings of the National Academy of Sciences
of the United States of America. 2022;119(30). doi:10.1073/pnas.2122147119
apa: Barton, N. H. (2022). The “New Synthesis.” Proceedings of the National Academy
of Sciences of the United States of America. Proceedings of the National Academy
of Sciences. https://doi.org/10.1073/pnas.2122147119
chicago: Barton, Nicholas H. “The ‘New Synthesis.’” Proceedings of the National
Academy of Sciences of the United States of America. Proceedings of the National
Academy of Sciences, 2022. https://doi.org/10.1073/pnas.2122147119.
ieee: N. H. Barton, “The ‘New Synthesis,’” Proceedings of the National Academy
of Sciences of the United States of America, vol. 119, no. 30. Proceedings
of the National Academy of Sciences, 2022.
ista: Barton NH. 2022. The ‘New Synthesis’. Proceedings of the National Academy
of Sciences of the United States of America. 119(30), e2122147119.
mla: Barton, Nicholas H. “The ‘New Synthesis.’” Proceedings of the National Academy
of Sciences of the United States of America, vol. 119, no. 30, e2122147119,
Proceedings of the National Academy of Sciences, 2022, doi:10.1073/pnas.2122147119.
short: N.H. Barton, Proceedings of the National Academy of Sciences of the United
States of America 119 (2022).
date_created: 2022-07-31T22:01:47Z
date_published: 2022-07-18T00:00:00Z
date_updated: 2022-08-01T11:00:25Z
day: '18'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1073/pnas.2122147119
external_id:
pmid:
- '35858408'
file:
- access_level: open_access
checksum: 06c866196a8957f0c37b8a121771c885
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creator: dernst
date_created: 2022-08-01T10:58:28Z
date_updated: 2022-08-01T10:58:28Z
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file_name: 2022_PNAS_Barton.pdf
file_size: 848511
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- iso: eng
month: '07'
oa: 1
oa_version: Published Version
pmid: 1
publication: Proceedings of the National Academy of Sciences of the United States
of America
publication_identifier:
eissn:
- 1091-6490
issn:
- 0027-8424
publication_status: published
publisher: Proceedings of the National Academy of Sciences
quality_controlled: '1'
scopus_import: '1'
status: public
title: The "New Synthesis"
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short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 119
year: '2022'
...
---
_id: '11128'
abstract:
- lang: eng
text: "Although we often see studies focusing on simple or even discrete traits
in studies of colouration,\r\nthe variation of “appearance” phenotypes found in
nature is often more complex, continuous\r\nand high-dimensional. Therefore, we
developed automated methods suitable for large datasets\r\nof genomes and images,
striving to account for their complex nature, while minimising human\r\nbias.
We used these methods on a dataset of more than 20, 000 plant SNP genomes and\r\ncorresponding
fower images from a hybrid zone of two subspecies of Antirrhinum majus with\r\ndistinctly
coloured fowers to improve our understanding of the genetic nature of the fower\r\ncolour
in our study system.\r\nFirstly, we use the advantage of large numbers of genotyped
plants to estimate the haplotypes in\r\nthe main fower colour regulating region.
We study colour- and geography-related characteristics\r\nof the estimated haplotypes
and how they connect to their relatedness. We show discrepancies\r\nfrom the expected
fower colour distributions given the genotype and identify particular\r\nhaplotypes
leading to unexpected phenotypes. We also confrm a signifcant defcit of the\r\ndouble
recessive recombinant and quite surprisingly, we show that haplotypes of the most\r\nfrequent
parental type are much less variable than others.\r\nSecondly, we introduce our
pipeline capable of processing tens of thousands of full fower\r\nimages without
human interaction and summarising each image into a set of informative scores.\r\nWe
show the compatibility of these machine-measured fower colour scores with the
previously\r\nused manual scores and study impact of external efect on the resulting
scores. Finally, we use\r\nthe machine-measured fower colour scores to ft and
examine a phenotype cline across the\r\nhybrid zone in Planoles using full fower
images as opposed to discrete, manual scores and\r\ncompare it with the genotypic
cline."
acknowledged_ssus:
- _id: ScienComp
- _id: Bio
alternative_title:
- ISTA Thesis
article_processing_charge: No
author:
- first_name: Lenka
full_name: Matejovicova, Lenka
id: 2DFDEC72-F248-11E8-B48F-1D18A9856A87
last_name: Matejovicova
citation:
ama: Matejovicova L. Genetic basis of flower colour as a model for adaptive evolution.
2022. doi:10.15479/at:ista:11128
apa: Matejovicova, L. (2022). Genetic basis of flower colour as a model for adaptive
evolution. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:11128
chicago: Matejovicova, Lenka. “Genetic Basis of Flower Colour as a Model for Adaptive
Evolution.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:11128.
ieee: L. Matejovicova, “Genetic basis of flower colour as a model for adaptive evolution,”
Institute of Science and Technology Austria, 2022.
ista: Matejovicova L. 2022. Genetic basis of flower colour as a model for adaptive
evolution. Institute of Science and Technology Austria.
mla: Matejovicova, Lenka. Genetic Basis of Flower Colour as a Model for Adaptive
Evolution. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:11128.
short: L. Matejovicova, Genetic Basis of Flower Colour as a Model for Adaptive Evolution,
Institute of Science and Technology Austria, 2022.
date_created: 2022-04-07T08:19:54Z
date_published: 2022-04-06T00:00:00Z
date_updated: 2023-06-23T06:26:41Z
day: '06'
ddc:
- '576'
- '582'
degree_awarded: PhD
department:
- _id: GradSch
- _id: NiBa
doi: 10.15479/at:ista:11128
file:
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checksum: e9609bc4e8f8e20146fc1125fd4f1bf7
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creator: cchlebak
date_created: 2022-04-07T08:11:34Z
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file_size: 23036766
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has_accepted_license: '1'
language:
- iso: eng
month: '04'
oa: 1
oa_version: Published Version
page: '112'
publication_identifier:
isbn:
- 978-3-99078-016-9
issn:
- 2663-337X
publication_status: published
publisher: Institute of Science and Technology Austria
status: public
supervisor:
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
title: Genetic basis of flower colour as a model for adaptive evolution
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: dissertation
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2022'
...
---
_id: '10604'
abstract:
- lang: eng
text: Maternally inherited Wolbachia transinfections are being introduced into natural
mosquito populations to reduce the transmission of dengue, Zika, and other arboviruses.
Wolbachia-induced cytoplasmic incompatibility provides a frequency-dependent reproductive
advantage to infected females that can spread transinfections within and among
populations. However, because transinfections generally reduce host fitness, they
tend to spread within populations only after their frequency exceeds a critical
threshold. This produces bistability with stable equilibrium frequencies at both
0 and 1, analogous to the bistability produced by underdominance between alleles
or karyotypes and by population dynamics under Allee effects. Here, we analyze
how stochastic frequency variation produced by finite population size can facilitate
the local spread of variants with bistable dynamics into areas where invasion
is unexpected from deterministic models. Our exemplar is the establishment of
wMel Wolbachia in the Aedes aegypti population of Pyramid Estates (PE), a small
community in far north Queensland, Australia. In 2011, wMel was stably introduced
into Gordonvale, separated from PE by barriers to A. aegypti dispersal. After
nearly 6 years during which wMel was observed only at low frequencies in PE, corresponding
to an apparent equilibrium between immigration and selection, wMel rose to fixation
by 2018. Using analytic approximations and statistical analyses, we demonstrate
that the observed fixation of wMel at PE is consistent with both stochastic transition
past an unstable threshold frequency and deterministic transformation produced
by steady immigration at a rate just above the threshold required for deterministic
invasion. The indeterminacy results from a delicate balance of parameters needed
to produce the delayed transition observed. Our analyses suggest that once Wolbachia
transinfections are established locally through systematic introductions, stochastic
“threshold crossing” is likely to only minimally enhance spatial spread, providing
a local ratchet that slightly—but systematically—aids area-wide transformation
of disease-vector populations in heterogeneous landscapes.
acknowledgement: We thank S. O'Neill, C. Simmons, and the World Mosquito Project for
providing access to unpublished data. S. Ritchie provided valuable insights into
Aedes aegypti biology and the literature describing A. aegypti populations near
Cairns. We thank B. Cooper for help with the figures and D. Shropshire, S. O'Neill,
S. Ritchie, A. Hoffmann, B. Cooper, and members of the Cooper lab for comments on
an earlier draft. Comments from three reviewers greatly improved our presentation.
article_processing_charge: No
article_type: original
author:
- first_name: Michael
full_name: Turelli, Michael
last_name: Turelli
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: Turelli M, Barton NH. Why did the Wolbachia transinfection cross the road?
Drift, deterministic dynamics, and disease control. Evolution Letters.
2022;6(1):92-105. doi:10.1002/evl3.270
apa: Turelli, M., & Barton, N. H. (2022). Why did the Wolbachia transinfection
cross the road? Drift, deterministic dynamics, and disease control. Evolution
Letters. Wiley. https://doi.org/10.1002/evl3.270
chicago: Turelli, Michael, and Nicholas H Barton. “Why Did the Wolbachia Transinfection
Cross the Road? Drift, Deterministic Dynamics, and Disease Control.” Evolution
Letters. Wiley, 2022. https://doi.org/10.1002/evl3.270.
ieee: M. Turelli and N. H. Barton, “Why did the Wolbachia transinfection cross the
road? Drift, deterministic dynamics, and disease control,” Evolution Letters,
vol. 6, no. 1. Wiley, pp. 92–105, 2022.
ista: Turelli M, Barton NH. 2022. Why did the Wolbachia transinfection cross the
road? Drift, deterministic dynamics, and disease control. Evolution Letters. 6(1),
92–105.
mla: Turelli, Michael, and Nicholas H. Barton. “Why Did the Wolbachia Transinfection
Cross the Road? Drift, Deterministic Dynamics, and Disease Control.” Evolution
Letters, vol. 6, no. 1, Wiley, 2022, pp. 92–105, doi:10.1002/evl3.270.
short: M. Turelli, N.H. Barton, Evolution Letters 6 (2022) 92–105.
date_created: 2022-01-09T09:45:17Z
date_published: 2022-02-01T00:00:00Z
date_updated: 2023-08-02T13:50:09Z
day: '01'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.1002/evl3.270
external_id:
isi:
- '000754412600008'
file:
- access_level: open_access
checksum: 7e9a37e3b65b480cd7014a6a4a7e460a
content_type: application/pdf
creator: dernst
date_created: 2022-07-29T06:59:10Z
date_updated: 2022-07-29T06:59:10Z
file_id: '11689'
file_name: 2022_EvolutionLetters_Turelli.pdf
file_size: 2435185
relation: main_file
success: 1
file_date_updated: 2022-07-29T06:59:10Z
has_accepted_license: '1'
intvolume: ' 6'
isi: 1
issue: '1'
keyword:
- genetics
- ecology
- evolution
- behavior and systematics
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
page: 92-105
publication: Evolution Letters
publication_identifier:
eissn:
- 2056-3744
publication_status: published
publisher: Wiley
quality_controlled: '1'
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relation: research_data
status: public
status: public
title: Why did the Wolbachia transinfection cross the road? Drift, deterministic dynamics,
and disease control
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 6
year: '2022'
...
---
_id: '11686'
abstract:
- lang: eng
text: Maternally inherited Wolbachia transinfections are being introduced into natural
mosquito populations to reduce the transmission of dengue, Zika and other arboviruses.
Wolbachia-induced cytoplasmic incompatibility provides a frequency-dependent reproductive
advantage to infected females that can spread transinfections within and among
populations. However, because transinfections generally reduce host fitness, they
tend to spread within populations only after their frequency exceeds a critical
threshold. This produces bistability with stable equilibrium frequencies at both
0 and 1, analogous to the bistability produced by underdominance between alleles
or karyotypes and by population dynamics under Allee effects. Here, we analyze
how stochastic frequency variation produced by finite population size can facilitate
the local spread of variants with bistable dynamics into areas where invasion
is unexpected from deterministic models. Our exemplar is the establishment of
wMel Wolbachia in the Aedes aegypti population of Pyramid Estates (PE), a small
community in far north Queensland, Australia. In 2011, wMel was stably introduced
into Gordonvale, separated from PE by barriers to Ae. aegypti dispersal. After
nearly six years during which wMel was observed only at low frequencies in PE,
corresponding to an apparent equilibrium between immigration and selection, wMel
rose to fixation by 2018. Using analytic approximations and statistical analyses,
we demonstrate that the observed fixation of wMel at PE is consistent with both
stochastic transition past an unstable threshold frequency and deterministic transformation
produced by steady immigration at a rate just above the threshold required for
deterministic invasion. The indeterminacy results from a delicate balance of parameters
needed to produce the delayed transition observed. Our analyses suggest that once
Wolbachia transinfections are established locally through systematic introductions,
stochastic “threshold crossing” is likely to only minimally enhance spatial spread,
providing a local ratchet that slightly – but systematically – aids area-wide
transformation of disease-vector populations in heterogeneous landscapes.
acknowledgement: 'Bill and Melinda Gates Foundation, Award: OPP1180815'
article_processing_charge: No
author:
- first_name: Michael
full_name: Turelli, Michael
last_name: Turelli
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: 'Turelli M, Barton NH. Wolbachia frequency data from: Why did the Wolbachia
transinfection cross the road? Drift, deterministic dynamics and disease control.
2022. doi:10.25338/B81931'
apa: 'Turelli, M., & Barton, N. H. (2022). Wolbachia frequency data from: Why
did the Wolbachia transinfection cross the road? Drift, deterministic dynamics
and disease control. Dryad. https://doi.org/10.25338/B81931'
chicago: 'Turelli, Michael, and Nicholas H Barton. “Wolbachia Frequency Data from:
Why Did the Wolbachia Transinfection Cross the Road? Drift, Deterministic Dynamics
and Disease Control.” Dryad, 2022. https://doi.org/10.25338/B81931.'
ieee: 'M. Turelli and N. H. Barton, “Wolbachia frequency data from: Why did the
Wolbachia transinfection cross the road? Drift, deterministic dynamics and disease
control.” Dryad, 2022.'
ista: 'Turelli M, Barton NH. 2022. Wolbachia frequency data from: Why did the Wolbachia
transinfection cross the road? Drift, deterministic dynamics and disease control,
Dryad, 10.25338/B81931.'
mla: 'Turelli, Michael, and Nicholas H. Barton. Wolbachia Frequency Data from:
Why Did the Wolbachia Transinfection Cross the Road? Drift, Deterministic Dynamics
and Disease Control. Dryad, 2022, doi:10.25338/B81931.'
short: M. Turelli, N.H. Barton, (2022).
date_created: 2022-07-29T06:45:41Z
date_published: 2022-01-06T00:00:00Z
date_updated: 2023-08-02T13:50:08Z
day: '06'
ddc:
- '570'
department:
- _id: NiBa
doi: 10.25338/B81931
keyword:
- Biological sciences
license: https://creativecommons.org/publicdomain/zero/1.0/
main_file_link:
- open_access: '1'
url: https://doi.org/10.25338/B81931
month: '01'
oa: 1
oa_version: Published Version
publisher: Dryad
related_material:
record:
- id: '10604'
relation: used_in_publication
status: public
status: public
title: 'Wolbachia frequency data from: Why did the Wolbachia transinfection cross
the road? Drift, deterministic dynamics and disease control'
tmp:
image: /images/cc_0.png
legal_code_url: https://creativecommons.org/publicdomain/zero/1.0/legalcode
name: Creative Commons Public Domain Dedication (CC0 1.0)
short: CC0 (1.0)
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2022'
...
---
_id: '10736'
abstract:
- lang: eng
text: Predicting function from sequence is a central problem of biology. Currently,
this is possible only locally in a narrow mutational neighborhood around a wildtype
sequence rather than globally from any sequence. Using random mutant libraries,
we developed a biophysical model that accounts for multiple features of σ70 binding
bacterial promoters to predict constitutive gene expression levels from any sequence.
We experimentally and theoretically estimated that 10–20% of random sequences
lead to expression and ~80% of non-expressing sequences are one mutation away
from a functional promoter. The potential for generating expression from random
sequences is so pervasive that selection acts against σ70-RNA polymerase binding
sites even within inter-genic, promoter-containing regions. This pervasiveness
of σ70-binding sites implies that emergence of promoters is not the limiting step
in gene regulatory evolution. Ultimately, the inclusion of novel features of promoter
function into a mechanistic model enabled not only more accurate predictions of
gene expression levels, but also identified that promoters evolve more rapidly
than previously thought.
acknowledgement: 'We thank Hande Acar, Nicholas H Barton, Rok Grah, Tiago Paixao,
Maros Pleska, Anna Staron, and Murat Tugrul for insightful comments and input on
the manuscript. This work was supported by: Sir Henry Dale Fellowship jointly funded
by the Wellcome Trust and the Royal Society (grant number 216779/Z/19/Z) to ML;
IPC Grant from IST Austria to ML and SS; European Research Council Funding Programme
7 (2007–2013, grant agreement number 648440) to JPB.'
article_number: e64543
article_processing_charge: No
article_type: original
author:
- first_name: Mato
full_name: Lagator, Mato
id: 345D25EC-F248-11E8-B48F-1D18A9856A87
last_name: Lagator
- first_name: Srdjan
full_name: Sarikas, Srdjan
id: 35F0286E-F248-11E8-B48F-1D18A9856A87
last_name: Sarikas
- first_name: Magdalena
full_name: Steinrueck, Magdalena
last_name: Steinrueck
- first_name: David
full_name: Toledo-Aparicio, David
last_name: Toledo-Aparicio
- first_name: Jonathan P
full_name: Bollback, Jonathan P
id: 2C6FA9CC-F248-11E8-B48F-1D18A9856A87
last_name: Bollback
orcid: 0000-0002-4624-4612
- first_name: Calin C
full_name: Guet, Calin C
id: 47F8433E-F248-11E8-B48F-1D18A9856A87
last_name: Guet
orcid: 0000-0001-6220-2052
- first_name: Gašper
full_name: Tkačik, Gašper
id: 3D494DCA-F248-11E8-B48F-1D18A9856A87
last_name: Tkačik
orcid: 0000-0002-6699-1455
citation:
ama: Lagator M, Sarikas S, Steinrueck M, et al. Predicting bacterial promoter function
and evolution from random sequences. eLife. 2022;11. doi:10.7554/eLife.64543
apa: Lagator, M., Sarikas, S., Steinrueck, M., Toledo-Aparicio, D., Bollback, J.
P., Guet, C. C., & Tkačik, G. (2022). Predicting bacterial promoter function
and evolution from random sequences. ELife. eLife Sciences Publications.
https://doi.org/10.7554/eLife.64543
chicago: Lagator, Mato, Srdjan Sarikas, Magdalena Steinrueck, David Toledo-Aparicio,
Jonathan P Bollback, Calin C Guet, and Gašper Tkačik. “Predicting Bacterial Promoter
Function and Evolution from Random Sequences.” ELife. eLife Sciences Publications,
2022. https://doi.org/10.7554/eLife.64543.
ieee: M. Lagator et al., “Predicting bacterial promoter function and evolution
from random sequences,” eLife, vol. 11. eLife Sciences Publications, 2022.
ista: Lagator M, Sarikas S, Steinrueck M, Toledo-Aparicio D, Bollback JP, Guet CC,
Tkačik G. 2022. Predicting bacterial promoter function and evolution from random
sequences. eLife. 11, e64543.
mla: Lagator, Mato, et al. “Predicting Bacterial Promoter Function and Evolution
from Random Sequences.” ELife, vol. 11, e64543, eLife Sciences Publications,
2022, doi:10.7554/eLife.64543.
short: M. Lagator, S. Sarikas, M. Steinrueck, D. Toledo-Aparicio, J.P. Bollback,
C.C. Guet, G. Tkačik, ELife 11 (2022).
date_created: 2022-02-06T23:01:32Z
date_published: 2022-01-26T00:00:00Z
date_updated: 2023-08-02T14:09:02Z
day: '26'
ddc:
- '576'
department:
- _id: CaGu
- _id: GaTk
- _id: NiBa
doi: 10.7554/eLife.64543
ec_funded: 1
external_id:
isi:
- '000751104400001'
pmid:
- '35080492'
file:
- access_level: open_access
checksum: decdcdf600ff51e9a9703b49ca114170
content_type: application/pdf
creator: cchlebak
date_created: 2022-02-07T07:14:09Z
date_updated: 2022-02-07T07:14:09Z
file_id: '10739'
file_name: 2022_ELife_Lagator.pdf
file_size: 5604343
relation: main_file
success: 1
file_date_updated: 2022-02-07T07:14:09Z
has_accepted_license: '1'
intvolume: ' 11'
isi: 1
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: 2578D616-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '648440'
name: Selective Barriers to Horizontal Gene Transfer
publication: eLife
publication_identifier:
eissn:
- 2050-084X
publication_status: published
publisher: eLife Sciences Publications
quality_controlled: '1'
scopus_import: '1'
status: public
title: Predicting bacterial promoter function and evolution from random sequences
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 11
year: '2022'
...
---
_id: '11334'
abstract:
- lang: eng
text: Hybridization is a common evolutionary process with multiple possible outcomes.
In vertebrates, interspecific hybridization has repeatedly generated parthenogenetic
hybrid species. However, it is unknown whether the generation of parthenogenetic
hybrids is a rare outcome of frequent hybridization between sexual species within
a genus or the typical outcome of rare hybridization events. Darevskia is a genus
of rock lizards with both hybrid parthenogenetic and sexual species. Using capture
sequencing, we estimate phylogenetic relationships and gene flow among the sexual
species, to determine how introgressive hybridization relates to the origins of
parthenogenetic hybrids. We find evidence for widespread hybridization with gene
flow, both between recently diverged species and deep branches. Surprisingly,
we find no signal of gene flow between parental species of the parthenogenetic
hybrids, suggesting that the parental pairs were either reproductively or geographically
isolated early in their divergence. The generation of parthenogenetic hybrids
in Darevskia is, then, a rare outcome of the total occurrence of hybridization
within the genus, but the typical outcome when specific species pairs hybridize.
Our results question the conventional view that parthenogenetic lineages are generated
by hybridization in a window of divergence. Instead, they suggest that some lineages
possess specific properties that underpin successful parthenogenetic reproduction.
acknowledgement: "The authors thank A. van der Meijden and F. Ahmadzadeh for providing
specimens and tissue samples, and A. Vardanyan, C. Corti, F. Jorge, and S. Drovetski
for support during field work. The authors also thank S. Qiu for assistance with
python scripting, S. Rocha for her support in BEAST analysis, and B. Wielstra for
his comments on\r\na previous version of the manuscript. SF was funded by FCT grant
SFRH/BD/81483/2011 (a PhD individual grant). AMW was funded by the European Union’s
Horizon 2020 research and innovation programme under Marie Skłodowska-Curie grant
agreement no. 797747. TS acknowledges funding from the Swiss National Science Foundation
(grants\r\nPP00P3_170627 and 31003A_182495). The work was carried out under financial
support of the projects “Preserving Armenian biodiversity: Joint Portuguese – Armenian
program for training in modern conservation biology” of Gulbenkian Foundation (Portugal)
and PTDC/BIABEC/101256/2008 of Fundação para a Ciência e a Tecnologia (FCT, Portugal)."
article_processing_charge: No
article_type: original
author:
- first_name: Susana
full_name: Freitas, Susana
last_name: Freitas
- first_name: Anja M
full_name: Westram, Anja M
id: 3C147470-F248-11E8-B48F-1D18A9856A87
last_name: Westram
orcid: 0000-0003-1050-4969
- first_name: Tanja
full_name: Schwander, Tanja
last_name: Schwander
- first_name: Marine
full_name: Arakelyan, Marine
last_name: Arakelyan
- first_name: Çetin
full_name: Ilgaz, Çetin
last_name: Ilgaz
- first_name: Yusuf
full_name: Kumlutas, Yusuf
last_name: Kumlutas
- first_name: David James
full_name: Harris, David James
last_name: Harris
- first_name: Miguel A.
full_name: Carretero, Miguel A.
last_name: Carretero
- first_name: Roger K.
full_name: Butlin, Roger K.
last_name: Butlin
citation:
ama: 'Freitas S, Westram AM, Schwander T, et al. Parthenogenesis in Darevskia lizards:
A rare outcome of common hybridization, not a common outcome of rare hybridization.
Evolution. 2022;76(5):899-914. doi:10.1111/evo.14462'
apa: 'Freitas, S., Westram, A. M., Schwander, T., Arakelyan, M., Ilgaz, Ç., Kumlutas,
Y., … Butlin, R. K. (2022). Parthenogenesis in Darevskia lizards: A rare outcome
of common hybridization, not a common outcome of rare hybridization. Evolution.
Wiley. https://doi.org/10.1111/evo.14462'
chicago: 'Freitas, Susana, Anja M Westram, Tanja Schwander, Marine Arakelyan, Çetin
Ilgaz, Yusuf Kumlutas, David James Harris, Miguel A. Carretero, and Roger K. Butlin.
“Parthenogenesis in Darevskia Lizards: A Rare Outcome of Common Hybridization,
Not a Common Outcome of Rare Hybridization.” Evolution. Wiley, 2022. https://doi.org/10.1111/evo.14462.'
ieee: 'S. Freitas et al., “Parthenogenesis in Darevskia lizards: A rare outcome
of common hybridization, not a common outcome of rare hybridization,” Evolution,
vol. 76, no. 5. Wiley, pp. 899–914, 2022.'
ista: 'Freitas S, Westram AM, Schwander T, Arakelyan M, Ilgaz Ç, Kumlutas Y, Harris
DJ, Carretero MA, Butlin RK. 2022. Parthenogenesis in Darevskia lizards: A rare
outcome of common hybridization, not a common outcome of rare hybridization. Evolution.
76(5), 899–914.'
mla: 'Freitas, Susana, et al. “Parthenogenesis in Darevskia Lizards: A Rare Outcome
of Common Hybridization, Not a Common Outcome of Rare Hybridization.” Evolution,
vol. 76, no. 5, Wiley, 2022, pp. 899–914, doi:10.1111/evo.14462.'
short: S. Freitas, A.M. Westram, T. Schwander, M. Arakelyan, Ç. Ilgaz, Y. Kumlutas,
D.J. Harris, M.A. Carretero, R.K. Butlin, Evolution 76 (2022) 899–914.
date_created: 2022-04-24T22:01:44Z
date_published: 2022-05-01T00:00:00Z
date_updated: 2023-08-03T07:00:28Z
day: '01'
ddc:
- '570'
department:
- _id: NiBa
- _id: BeVi
doi: 10.1111/evo.14462
ec_funded: 1
external_id:
isi:
- '000781632500001'
pmid:
- '35323995'
file:
- access_level: open_access
checksum: c27c025ae9afcf6c804d46a909775ee5
content_type: application/pdf
creator: dernst
date_created: 2022-08-05T06:19:28Z
date_updated: 2022-08-05T06:19:28Z
file_id: '11729'
file_name: 2022_Evolution_Freitas.pdf
file_size: 2855214
relation: main_file
success: 1
file_date_updated: 2022-08-05T06:19:28Z
has_accepted_license: '1'
intvolume: ' 76'
isi: 1
issue: '5'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc/4.0/
month: '05'
oa: 1
oa_version: Published Version
page: 899-914
pmid: 1
project:
- _id: 265B41B8-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '797747'
name: Theoretical and empirical approaches to understanding Parallel Adaptation
publication: Evolution
publication_identifier:
eissn:
- 1558-5646
issn:
- 0014-3820
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Parthenogenesis in Darevskia lizards: A rare outcome of common hybridization,
not a common outcome of rare hybridization'
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 76
year: '2022'
...
---
_id: '11447'
abstract:
- lang: eng
text: Empirical essays of fitness landscapes suggest that they may be rugged, that
is having multiple fitness peaks. Such fitness landscapes, those that have multiple
peaks, necessarily have special local structures, called reciprocal sign epistasis
(Poelwijk et al. in J Theor Biol 272:141–144, 2011). Here, we investigate the
quantitative relationship between the number of fitness peaks and the number of
reciprocal sign epistatic interactions. Previously, it has been shown (Poelwijk
et al. in J Theor Biol 272:141–144, 2011) that pairwise reciprocal sign epistasis
is a necessary but not sufficient condition for the existence of multiple peaks.
Applying discrete Morse theory, which to our knowledge has never been used in
this context, we extend this result by giving the minimal number of reciprocal
sign epistatic interactions required to create a given number of peaks.
acknowledgement: We are grateful to Herbert Edelsbrunner and Jeferson Zapata for helpful
discussions. Open access funding provided by Austrian Science Fund (FWF). Partially
supported by the ERC Consolidator (771209–CharFL) and the FWF Austrian Science Fund
(I5127-B) grants to FAK.
article_number: '74'
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Raimundo J
full_name: Saona Urmeneta, Raimundo J
id: BD1DF4C4-D767-11E9-B658-BC13E6697425
last_name: Saona Urmeneta
orcid: 0000-0001-5103-038X
- first_name: Fyodor
full_name: Kondrashov, Fyodor
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Kseniia
full_name: Khudiakova, Kseniia
id: 4E6DC800-AE37-11E9-AC72-31CAE5697425
last_name: Khudiakova
orcid: 0000-0002-6246-1465
citation:
ama: Saona Urmeneta RJ, Kondrashov F, Khudiakova K. Relation between the number
of peaks and the number of reciprocal sign epistatic interactions. Bulletin
of Mathematical Biology. 2022;84(8). doi:10.1007/s11538-022-01029-z
apa: Saona Urmeneta, R. J., Kondrashov, F., & Khudiakova, K. (2022). Relation
between the number of peaks and the number of reciprocal sign epistatic interactions.
Bulletin of Mathematical Biology. Springer Nature. https://doi.org/10.1007/s11538-022-01029-z
chicago: Saona Urmeneta, Raimundo J, Fyodor Kondrashov, and Kseniia Khudiakova.
“Relation between the Number of Peaks and the Number of Reciprocal Sign Epistatic
Interactions.” Bulletin of Mathematical Biology. Springer Nature, 2022.
https://doi.org/10.1007/s11538-022-01029-z.
ieee: R. J. Saona Urmeneta, F. Kondrashov, and K. Khudiakova, “Relation between
the number of peaks and the number of reciprocal sign epistatic interactions,”
Bulletin of Mathematical Biology, vol. 84, no. 8. Springer Nature, 2022.
ista: Saona Urmeneta RJ, Kondrashov F, Khudiakova K. 2022. Relation between the
number of peaks and the number of reciprocal sign epistatic interactions. Bulletin
of Mathematical Biology. 84(8), 74.
mla: Saona Urmeneta, Raimundo J., et al. “Relation between the Number of Peaks and
the Number of Reciprocal Sign Epistatic Interactions.” Bulletin of Mathematical
Biology, vol. 84, no. 8, 74, Springer Nature, 2022, doi:10.1007/s11538-022-01029-z.
short: R.J. Saona Urmeneta, F. Kondrashov, K. Khudiakova, Bulletin of Mathematical
Biology 84 (2022).
date_created: 2022-06-17T16:16:15Z
date_published: 2022-06-17T00:00:00Z
date_updated: 2023-08-03T07:20:53Z
day: '17'
ddc:
- '510'
- '570'
department:
- _id: GradSch
- _id: NiBa
- _id: JaMa
doi: 10.1007/s11538-022-01029-z
ec_funded: 1
external_id:
isi:
- '000812509800001'
file:
- access_level: open_access
checksum: 05a1fe7d10914a00c2bca9b447993a65
content_type: application/pdf
creator: dernst
date_created: 2022-06-20T07:51:32Z
date_updated: 2022-06-20T07:51:32Z
file_id: '11455'
file_name: 2022_BulletinMathBiology_Saona.pdf
file_size: 463025
relation: main_file
success: 1
file_date_updated: 2022-06-20T07:51:32Z
has_accepted_license: '1'
intvolume: ' 84'
isi: 1
issue: '8'
keyword:
- Computational Theory and Mathematics
- General Agricultural and Biological Sciences
- Pharmacology
- General Environmental Science
- General Biochemistry
- Genetics and Molecular Biology
- General Mathematics
- Immunology
- General Neuroscience
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
project:
- _id: 26580278-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '771209'
name: Characterizing the fitness landscape on population and global scales
- _id: c098eddd-5a5b-11eb-8a69-abe27170a68f
grant_number: I05127
name: Evolutionary analysis of gene regulation
publication: Bulletin of Mathematical Biology
publication_identifier:
eissn:
- 1522-9602
issn:
- 0092-8240
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- relation: erratum
url: https://doi.org/10.1007/s11538-022-01118-z
scopus_import: '1'
status: public
title: Relation between the number of peaks and the number of reciprocal sign epistatic
interactions
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 84
year: '2022'
...
---
_id: '11546'
abstract:
- lang: eng
text: Local adaptation leads to differences between populations within a species.
In many systems, similar environmental contrasts occur repeatedly, sometimes driving
parallel phenotypic evolution. Understanding the genomic basis of local adaptation
and parallel evolution is a major goal of evolutionary genomics. It is now known
that by preventing the break-up of favourable combinations of alleles across multiple
loci, genetic architectures that reduce recombination, like chromosomal inversions,
can make an important contribution to local adaptation. However, little is known
about whether inversions also contribute disproportionately to parallel evolution.
Our aim here is to highlight this knowledge gap, to showcase existing studies,
and to illustrate the differences between genomic architectures with and without
inversions using simple models. We predict that by generating stronger effective
selection, inversions can sometimes speed up the parallel adaptive process or
enable parallel adaptation where it would be impossible otherwise, but this is
highly dependent on the spatial setting. We highlight that further empirical work
is needed, in particular to cover a broader taxonomic range and to understand
the relative importance of inversions compared to genomic regions without inversions.
acknowledgement: We thank the editor and two anonymous reviewers for their helpful
and interesting comments on this manuscript.
article_number: '20210203'
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Anja M
full_name: Westram, Anja M
id: 3C147470-F248-11E8-B48F-1D18A9856A87
last_name: Westram
orcid: 0000-0003-1050-4969
- first_name: Rui
full_name: Faria, Rui
last_name: Faria
- first_name: Kerstin
full_name: Johannesson, Kerstin
last_name: Johannesson
- first_name: Roger
full_name: Butlin, Roger
last_name: Butlin
- first_name: Nicholas H
full_name: Barton, Nicholas H
id: 4880FE40-F248-11E8-B48F-1D18A9856A87
last_name: Barton
orcid: 0000-0002-8548-5240
citation:
ama: 'Westram AM, Faria R, Johannesson K, Butlin R, Barton NH. Inversions and parallel
evolution. Philosophical Transactions of the Royal Society B: Biological Sciences.
2022;377(1856). doi:10.1098/rstb.2021.0203'
apa: 'Westram, A. M., Faria, R., Johannesson, K., Butlin, R., & Barton, N. H.
(2022). Inversions and parallel evolution. Philosophical Transactions of the
Royal Society B: Biological Sciences. Royal Society of London. https://doi.org/10.1098/rstb.2021.0203'
chicago: 'Westram, Anja M, Rui Faria, Kerstin Johannesson, Roger Butlin, and Nicholas
H Barton. “Inversions and Parallel Evolution.” Philosophical Transactions of
the Royal Society B: Biological Sciences. Royal Society of London, 2022. https://doi.org/10.1098/rstb.2021.0203.'
ieee: 'A. M. Westram, R. Faria, K. Johannesson, R. Butlin, and N. H. Barton, “Inversions
and parallel evolution,” Philosophical Transactions of the Royal Society B:
Biological Sciences, vol. 377, no. 1856. Royal Society of London, 2022.'
ista: 'Westram AM, Faria R, Johannesson K, Butlin R, Barton NH. 2022. Inversions
and parallel evolution. Philosophical Transactions of the Royal Society B: Biological
Sciences. 377(1856), 20210203.'
mla: 'Westram, Anja M., et al. “Inversions and Parallel Evolution.” Philosophical
Transactions of the Royal Society B: Biological Sciences, vol. 377, no. 1856,
20210203, Royal Society of London, 2022, doi:10.1098/rstb.2021.0203.'
short: 'A.M. Westram, R. Faria, K. Johannesson, R. Butlin, N.H. Barton, Philosophical
Transactions of the Royal Society B: Biological Sciences 377 (2022).'
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