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Runs of homozygosity reveal past bottlenecks and contemporary inbreeding across diverging island populations of a bird
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  • Claudia Martin,
  • Eleanor Sheppard,
  • Juan Carlos Illera,
  • Alexander Suh,
  • Krystyna Nadachowska-Brzyska,
  • Lewis Spurgin,
  • David Richardson
Claudia Martin
University of East Anglia

Corresponding Author:[email protected]

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Eleanor Sheppard
University of East Anglia
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Juan Carlos Illera
University of Oviedo
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Alexander Suh
University of East Anglia
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Krystyna Nadachowska-Brzyska
Jagiellonian University in Krakow
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Lewis Spurgin
University of East Anglia
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David Richardson
University of East Anglia
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Genomes retain evidence of the demographic history and evolutionary forces that have shaped populations. Across island systems, contemporary patterns of genetic diversity reflect complex population demography, including colonisation events, bottlenecks, gene flow and genetic drift. Here, we investigate whether island founder events have prolonged effects on genome-wide diversity and runs of homozygosity (ROH) distributions, using whole genome resequencing from six populations across three archipelagos of Berthelot’s pipit (Anthus berthelotii) - a passerine which has undergone island speciation relatively recently. Pairwise sequential Markovian coalescent (PSMC) analyses estimated divergence from its sister species approximately two million years ago. Results indicate that all Berthelot’s pipit populations had shared ancestry until approximately 50,000 years ago, when the Madeiran archipelago populations were founded, while the Selvagens were colonised within the last 8,000 years. We identify extensive long ROH (>1 Mb) in genomes in the most recently colonised populations of Madeira and Selvagens which have experienced sequential island founder events and population crashes. Population expansion within the last 100 years may have eroded long ROH in the Madeiran archipelago, resulting in a prevalence of short ROH (<1 Mb). Extensive long and short ROH in the Selvagens reflects strong recent inbreeding, small contemporary effective population size and past bottleneck effects, with as much as 37.7% of the autosomes comprised of ROH >250 kb in length. These findings highlight the importance of demographic history, as well as selection and genetic drift, in shaping contemporary patterns of genomic diversity across diverging populations.
27 Sep 2022Submitted to Molecular Ecology
29 Sep 2022Submission Checks Completed
29 Sep 2022Assigned to Editor
13 Oct 2022Reviewer(s) Assigned
18 Nov 2022Review(s) Completed, Editorial Evaluation Pending
22 Nov 2022Editorial Decision: Revise Minor
11 Jan 2023Review(s) Completed, Editorial Evaluation Pending
11 Jan 20231st Revision Received
20 Jan 2023Editorial Decision: Accept