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 |
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2020
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Online Access: | https://hdl.handle.net/11370/af634268-d010-4a30-9338-81aee2fababc https://research.rug.nl/en/publications/af634268-d010-4a30-9338-81aee2fababc https://doi.org/10.1098/rspb.2019.2613 https://pure.rug.nl/ws/files/133209877/rspb.2019.2613.pdf |
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ftunigroningenpu:oai:pure.rug.nl:publications/af634268-d010-4a30-9338-81aee2fababc 2024-09-15T18:05:14+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. 2020-03-11 application/pdf https://hdl.handle.net/11370/af634268-d010-4a30-9338-81aee2fababc https://research.rug.nl/en/publications/af634268-d010-4a30-9338-81aee2fababc https://doi.org/10.1098/rspb.2019.2613 https://pure.rug.nl/ws/files/133209877/rspb.2019.2613.pdf eng eng https://research.rug.nl/en/publications/af634268-d010-4a30-9338-81aee2fababc info:eu-repo/semantics/openAccess Dierickx , E G , Sin , S Y W , van Veelen , H P J , Brooke , M D L , Liu , Y , Edwards , S V & Martin , S H 2020 , ' Genetic diversity, demographic history and neo-sex chromosomes in the critically endangered Raso lark ' , Proceedings of the Royal Society of London. Series B, Biological Sciences , vol. 287 , no. 1922 , 20192613 . https://doi.org/10.1098/rspb.2019.2613 recombination suppression Alauda conservation Cape Verde island endemic demography POPULATION-SIZE ALAUDA-RAZAE EXTINCTION EVOLUTION GENOMES RISK article 2020 ftunigroningenpu https://doi.org/10.1098/rspb.2019.2613 2024-06-24T16:11:05Z 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 University of Groningen research database Proceedings of the Royal Society B: Biological Sciences 287 1922 20192613 |
institution |
Open Polar |
collection |
University of Groningen research database |
op_collection_id |
ftunigroningenpu |
language |
English |
topic |
recombination suppression Alauda conservation Cape Verde island endemic demography POPULATION-SIZE ALAUDA-RAZAE EXTINCTION EVOLUTION GENOMES RISK |
spellingShingle |
recombination suppression Alauda conservation Cape Verde island endemic demography POPULATION-SIZE ALAUDA-RAZAE EXTINCTION EVOLUTION GENOMES RISK 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 |
topic_facet |
recombination suppression Alauda conservation Cape Verde island endemic demography POPULATION-SIZE ALAUDA-RAZAE EXTINCTION EVOLUTION GENOMES RISK |
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. |
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. |
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 |
publishDate |
2020 |
url |
https://hdl.handle.net/11370/af634268-d010-4a30-9338-81aee2fababc https://research.rug.nl/en/publications/af634268-d010-4a30-9338-81aee2fababc https://doi.org/10.1098/rspb.2019.2613 https://pure.rug.nl/ws/files/133209877/rspb.2019.2613.pdf |
genre |
Eurasian Skylark |
genre_facet |
Eurasian Skylark |
op_source |
Dierickx , E G , Sin , S Y W , van Veelen , H P J , Brooke , M D L , Liu , Y , Edwards , S V & Martin , S H 2020 , ' Genetic diversity, demographic history and neo-sex chromosomes in the critically endangered Raso lark ' , Proceedings of the Royal Society of London. Series B, Biological Sciences , vol. 287 , no. 1922 , 20192613 . https://doi.org/10.1098/rspb.2019.2613 |
op_relation |
https://research.rug.nl/en/publications/af634268-d010-4a30-9338-81aee2fababc |
op_rights |
info:eu-repo/semantics/openAccess |
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_ |
1810442811837775872 |