Genetic diversity, demographic history and neo-sex chromosomes in the Critically Endangered Raso lark
Small effective population sizes could expose island species to inbreeding and loss of genetic variation. Here, we investigate factors shaping genetic diversity in the Raso lark, which has been restricted to a single islet for approximately 500 years, with a population size of a few hundred. We asse...
Published in: | Proceedings of the Royal Society B: Biological Sciences |
---|---|
Main Authors: | , , , , , , |
Other Authors: | , , , |
Format: | Article in Journal/Newspaper |
Language: | English |
Published: |
The Royal Society
2020
|
Subjects: | |
Online Access: | http://dx.doi.org/10.1098/rspb.2019.2613 https://royalsocietypublishing.org/doi/pdf/10.1098/rspb.2019.2613 https://royalsocietypublishing.org/doi/full-xml/10.1098/rspb.2019.2613 |
id |
crroyalsociety:10.1098/rspb.2019.2613 |
---|---|
record_format |
openpolar |
spelling |
crroyalsociety:10.1098/rspb.2019.2613 2024-09-09T19:39:28+00:00 Genetic diversity, demographic history and neo-sex chromosomes in the Critically Endangered Raso lark Dierickx, Elisa G. Sin, Simon Yung Wa van Veelen, H. Pieter J. Brooke, M. de L. Liu, Yang Edwards, Scott V. Martin, Simon H. Royal Society Vocatio Trinity College, University of Cambridge St John's College, University of Cambridge 2020 http://dx.doi.org/10.1098/rspb.2019.2613 https://royalsocietypublishing.org/doi/pdf/10.1098/rspb.2019.2613 https://royalsocietypublishing.org/doi/full-xml/10.1098/rspb.2019.2613 en eng The Royal Society https://royalsociety.org/journals/ethics-policies/data-sharing-mining/ Proceedings of the Royal Society B: Biological Sciences volume 287, issue 1922, page 20192613 ISSN 0962-8452 1471-2954 journal-article 2020 crroyalsociety https://doi.org/10.1098/rspb.2019.2613 2024-08-12T04:27:37Z Small effective population sizes could expose island species to inbreeding and loss of genetic variation. Here, we investigate factors shaping genetic diversity in the Raso lark, which has been restricted to a single islet for approximately 500 years, with a population size of a few hundred. We assembled a reference genome for the related Eurasian skylark and then assessed diversity and demographic history using RAD-seq data (75 samples from Raso larks and two related mainland species). We first identify broad tracts of suppressed recombination in females, indicating enlarged neo-sex chromosomes. We then show that genetic diversity across autosomes in the Raso lark is lower than in its mainland relatives, but inconsistent with long-term persistence at its current population size. Finally, we find that genetic signatures of the recent population contraction are overshadowed by an ancient expansion and persistence of a very large population until the human settlement of Cape Verde. Our findings show how genome-wide approaches to study endangered species can help avoid confounding effects of genome architecture on diversity estimates, and how present-day diversity can be shaped by ancient demographic events. Article in Journal/Newspaper Eurasian Skylark The Royal Society Proceedings of the Royal Society B: Biological Sciences 287 1922 20192613 |
institution |
Open Polar |
collection |
The Royal Society |
op_collection_id |
crroyalsociety |
language |
English |
description |
Small effective population sizes could expose island species to inbreeding and loss of genetic variation. Here, we investigate factors shaping genetic diversity in the Raso lark, which has been restricted to a single islet for approximately 500 years, with a population size of a few hundred. We assembled a reference genome for the related Eurasian skylark and then assessed diversity and demographic history using RAD-seq data (75 samples from Raso larks and two related mainland species). We first identify broad tracts of suppressed recombination in females, indicating enlarged neo-sex chromosomes. We then show that genetic diversity across autosomes in the Raso lark is lower than in its mainland relatives, but inconsistent with long-term persistence at its current population size. Finally, we find that genetic signatures of the recent population contraction are overshadowed by an ancient expansion and persistence of a very large population until the human settlement of Cape Verde. Our findings show how genome-wide approaches to study endangered species can help avoid confounding effects of genome architecture on diversity estimates, and how present-day diversity can be shaped by ancient demographic events. |
author2 |
Royal Society Vocatio Trinity College, University of Cambridge St John's College, University of Cambridge |
format |
Article in Journal/Newspaper |
author |
Dierickx, Elisa G. Sin, Simon Yung Wa van Veelen, H. Pieter J. Brooke, M. de L. Liu, Yang Edwards, Scott V. Martin, Simon H. |
spellingShingle |
Dierickx, Elisa G. Sin, Simon Yung Wa van Veelen, H. Pieter J. Brooke, M. de L. Liu, Yang Edwards, Scott V. Martin, Simon H. Genetic diversity, demographic history and neo-sex chromosomes in the Critically Endangered Raso lark |
author_facet |
Dierickx, Elisa G. Sin, Simon Yung Wa van Veelen, H. Pieter J. Brooke, M. de L. Liu, Yang Edwards, Scott V. Martin, Simon H. |
author_sort |
Dierickx, Elisa G. |
title |
Genetic diversity, demographic history and neo-sex chromosomes in the Critically Endangered Raso lark |
title_short |
Genetic diversity, demographic history and neo-sex chromosomes in the Critically Endangered Raso lark |
title_full |
Genetic diversity, demographic history and neo-sex chromosomes in the Critically Endangered Raso lark |
title_fullStr |
Genetic diversity, demographic history and neo-sex chromosomes in the Critically Endangered Raso lark |
title_full_unstemmed |
Genetic diversity, demographic history and neo-sex chromosomes in the Critically Endangered Raso lark |
title_sort |
genetic diversity, demographic history and neo-sex chromosomes in the critically endangered raso lark |
publisher |
The Royal Society |
publishDate |
2020 |
url |
http://dx.doi.org/10.1098/rspb.2019.2613 https://royalsocietypublishing.org/doi/pdf/10.1098/rspb.2019.2613 https://royalsocietypublishing.org/doi/full-xml/10.1098/rspb.2019.2613 |
genre |
Eurasian Skylark |
genre_facet |
Eurasian Skylark |
op_source |
Proceedings of the Royal Society B: Biological Sciences volume 287, issue 1922, page 20192613 ISSN 0962-8452 1471-2954 |
op_rights |
https://royalsociety.org/journals/ethics-policies/data-sharing-mining/ |
op_doi |
https://doi.org/10.1098/rspb.2019.2613 |
container_title |
Proceedings of the Royal Society B: Biological Sciences |
container_volume |
287 |
container_issue |
1922 |
container_start_page |
20192613 |
_version_ |
1809908600712200192 |