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Spatially Explicit Analysis of Genome-Wide SNPs Detects Subtle Population Structure in a Mobile Marine Mammal, the Harbor Porpoise

Lookup NU author(s): Professor Per Berggren



This work is licensed under a Creative Commons Attribution 4.0 International License (CC BY 4.0).


The population structure of the highly mobile marine mammal, the harbor porpoise (Phocoenaphocoena), in the Atlantic shelf waters follows a pattern of significant isolation-bydistance.The population structure of harbor porpoises from the Baltic Sea, which is connectedwith the North Sea through a series of basins separated by shallow underwaterridges, however, is more complex. Here, we investigated the population differentiation ofharbor porpoises in European Seas with a special focus on the Baltic Sea and adjacentwaters, using a population genomics approach. We used 2872 single nucleotide polymorphisms(SNPs), derived from double digest restriction-site associated DNA sequencing(ddRAD-seq), as well as 13 microsatellite loci and mitochondrial haplotypes for the sameset of individuals. Spatial principal components analysis (sPCA), and Bayesian clusteringon a subset of SNPs suggest three main groupings at the level of all studied regions: theBlack Sea, the North Atlantic, and the Baltic Sea. Furthermore, we observed a distinct separationof the North Sea harbor porpoises from the Baltic Sea populations, and identifiedsplits between porpoise populations within the Baltic Sea. We observed a notable distinctionbetween the Belt Sea and the Inner Baltic Sea sub-regions. Improved delineation ofharbor porpoise population assignments for the Baltic based on genomic evidence is importantfor conservation management of this endangered cetacean in threatened habitats, particularlyin the Baltic Sea proper. In addition, we show that SNPs outperform microsatellitemarkers and demonstrate the utility of RAD-tags from a relatively small, opportunisticallysampled cetacean sample set for population diversity and divergence analysis.

Publication metadata

Author(s): Lah L, Trense D, Benke H, Berggren P, Gunnlaugsson T, Lockyer C, Özturk A, Özturk B, Pawliczka I, Roos A, Siebert U, Skóra K, Vikingsson G, Tiedemann R

Publication type: Article

Publication status: Published

Journal: PLoS One

Year: 2016

Volume: 11

Issue: 10

Pages: e0162792

Online publication date: 26/10/2016

Acceptance date: 29/08/2016

Date deposited: 28/10/2016

ISSN (electronic): 1932-6203

Publisher: Public Library of Science


DOI: 10.1371/journal.pone.0162792


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