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Evolutionary history and seascape genomics of Harbour porpoises (Phocoena phocoena) across environmental gradients in the North Atlantic and adjacent waters
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  • Enrique Celemín,
  • Marijke Autenrieth,
  • Anna Roos,
  • Iwona Pawliczka,
  • María Quintela,
  • Ulf Lindstrøm,
  • Harald Benke,
  • Ursula Siebert,
  • Christina Lockyer,
  • Per Berggren,
  • Ayaka Öztürk,
  • Bayram Öztürk,
  • Véronique Lesage,
  • Ralph Tiedemann
Enrique Celemín
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Marijke Autenrieth
Universitat Potsdam
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Iwona Pawliczka
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María Quintela
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Ulf Lindstrøm
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Harald Benke
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Ursula Siebert
University of Veterinary Medicine Hannover, Institute for Terrestrial and Aquatic Wildlife Research
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Christina Lockyer
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Per Berggren
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Ayaka Öztürk
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Bayram Öztürk
Faculty of Fisheries, Istanbul University
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Véronique Lesage
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Ralph Tiedemann

Corresponding Author:[email protected]

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The Harbour porpoise (Phocoena phocoena) is a highly mobile cetacean species which primarily occurs in coastal and shelf waters across the Northern hemisphere. It inhabits heterogeneous seascapes that vary broadly in salinity and temperature. Here we produced 74 whole genomes at intermediate coverage to study Harbour porpoise’s evolutionary history and investigate the role of local adaptation in the diversification into subspecies and populations. We identified ~6 million high quality SNPs sampled at 8 localities across the North Atlantic and adjacent waters, which we used for population structure, demographic, and genotype-environment association analyses. Our results support a genetic differentiation between three subspecies, and three distinct populations within the subspecies P.p. phocoena: Atlantic, Belt Sea and Proper Baltic Sea. Effective population size and Tajima’s D levels suggest a population contraction in both Black Sea and Iberian porpoises while a population expansion in the P.p. phocoena populations. Phylogenetic trees indicate a post-glacial colonization of Harbour porpoises from a southern refugium. Genotype-environment association analysis identified salinity as a major driver in genomic variation and we identified candidate genes putatively underlying adaptation to different salinity levels. Our study highlights the value of whole genome resequencing to unravel subtle population structure in highly mobile species and shows how strong environmental gradients and local adaptation may lead to population differentiation. The results have great conservation implications as we found major levels of inbreeding and low genetic diversity in the endangered Black Sea subspecies and identified the critically endangered Proper Baltic Sea porpoises as a separate population.
25 Nov 2022Submitted to Molecular Ecology Resources
16 Dec 2022Submission Checks Completed
16 Dec 2022Assigned to Editor
16 Dec 2022Review(s) Completed, Editorial Evaluation Pending
21 Dec 2022Reviewer(s) Assigned
14 Mar 2023Editorial Decision: Revise Minor
18 Apr 20231st Revision Received
19 Apr 2023Assigned to Editor
19 Apr 2023Submission Checks Completed
19 Apr 2023Review(s) Completed, Editorial Evaluation Pending
04 May 2023Reviewer(s) Assigned
12 Jun 2023Editorial Decision: Revise Minor
06 Jul 20232nd Revision Received
07 Jul 2023Submission Checks Completed
07 Jul 2023Assigned to Editor
07 Jul 2023Review(s) Completed, Editorial Evaluation Pending
07 Aug 2023Editorial Decision: Revise Minor
09 Aug 20233rd Revision Received
10 Aug 2023Assigned to Editor
10 Aug 2023Submission Checks Completed
10 Aug 2023Review(s) Completed, Editorial Evaluation Pending
16 Aug 2023Editorial Decision: Accept