Spatially Explicit Analysis of Genome-Wide SNPs Detects Subtle Population Structure in a Mobile Marine Mammal, the Harbor Porpoise.
The population structure of the highly mobile marine mammal, the harbor porpoise (Phocoena phocoena), in the Atlantic shelf waters follows a pattern of significant isolation-by-distance. The population structure of harbor porpoises from the Baltic Sea, which is connected with the North Sea through a...
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ftdoajarticles:oai:doaj.org/article:bcfcc5ee0fbc4a42a1848be9b2ca6709 2023-05-15T17:35:14+02:00 Spatially Explicit Analysis of Genome-Wide SNPs Detects Subtle Population Structure in a Mobile Marine Mammal, the Harbor Porpoise. Ljerka Lah Daronja Trense Harald Benke Per Berggren Þorvaldur Gunnlaugsson Christina Lockyer Ayaka Öztürk Bayram Öztürk Iwona Pawliczka Anna Roos Ursula Siebert Krzysztof Skóra Gísli Víkingsson Ralph Tiedemann 2016-01-01T00:00:00Z https://doi.org/10.1371/journal.pone.0162792 https://doaj.org/article/bcfcc5ee0fbc4a42a1848be9b2ca6709 EN eng Public Library of Science (PLoS) http://europepmc.org/articles/PMC5082642?pdf=render https://doaj.org/toc/1932-6203 1932-6203 doi:10.1371/journal.pone.0162792 https://doaj.org/article/bcfcc5ee0fbc4a42a1848be9b2ca6709 PLoS ONE, Vol 11, Iss 10, p e0162792 (2016) Medicine R Science Q article 2016 ftdoajarticles https://doi.org/10.1371/journal.pone.0162792 2022-12-31T03:34:58Z The population structure of the highly mobile marine mammal, the harbor porpoise (Phocoena phocoena), in the Atlantic shelf waters follows a pattern of significant isolation-by-distance. The population structure of harbor porpoises from the Baltic Sea, which is connected with the North Sea through a series of basins separated by shallow underwater ridges, however, is more complex. Here, we investigated the population differentiation of harbor porpoises in European Seas with a special focus on the Baltic Sea and adjacent waters, 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 same set of individuals. Spatial principal components analysis (sPCA), and Bayesian clustering on a subset of SNPs suggest three main groupings at the level of all studied regions: the Black Sea, the North Atlantic, and the Baltic Sea. Furthermore, we observed a distinct separation of the North Sea harbor porpoises from the Baltic Sea populations, and identified splits between porpoise populations within the Baltic Sea. We observed a notable distinction between the Belt Sea and the Inner Baltic Sea sub-regions. Improved delineation of harbor porpoise population assignments for the Baltic based on genomic evidence is important for conservation management of this endangered cetacean in threatened habitats, particularly in the Baltic Sea proper. In addition, we show that SNPs outperform microsatellite markers and demonstrate the utility of RAD-tags from a relatively small, opportunistically sampled cetacean sample set for population diversity and divergence analysis. Article in Journal/Newspaper North Atlantic Phocoena phocoena Directory of Open Access Journals: DOAJ Articles PLOS ONE 11 10 e0162792 |
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Directory of Open Access Journals: DOAJ Articles |
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language |
English |
topic |
Medicine R Science Q |
spellingShingle |
Medicine R Science Q Ljerka Lah Daronja Trense Harald Benke Per Berggren Þorvaldur Gunnlaugsson Christina Lockyer Ayaka Öztürk Bayram Öztürk Iwona Pawliczka Anna Roos Ursula Siebert Krzysztof Skóra Gísli Víkingsson Ralph Tiedemann Spatially Explicit Analysis of Genome-Wide SNPs Detects Subtle Population Structure in a Mobile Marine Mammal, the Harbor Porpoise. |
topic_facet |
Medicine R Science Q |
description |
The population structure of the highly mobile marine mammal, the harbor porpoise (Phocoena phocoena), in the Atlantic shelf waters follows a pattern of significant isolation-by-distance. The population structure of harbor porpoises from the Baltic Sea, which is connected with the North Sea through a series of basins separated by shallow underwater ridges, however, is more complex. Here, we investigated the population differentiation of harbor porpoises in European Seas with a special focus on the Baltic Sea and adjacent waters, 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 same set of individuals. Spatial principal components analysis (sPCA), and Bayesian clustering on a subset of SNPs suggest three main groupings at the level of all studied regions: the Black Sea, the North Atlantic, and the Baltic Sea. Furthermore, we observed a distinct separation of the North Sea harbor porpoises from the Baltic Sea populations, and identified splits between porpoise populations within the Baltic Sea. We observed a notable distinction between the Belt Sea and the Inner Baltic Sea sub-regions. Improved delineation of harbor porpoise population assignments for the Baltic based on genomic evidence is important for conservation management of this endangered cetacean in threatened habitats, particularly in the Baltic Sea proper. In addition, we show that SNPs outperform microsatellite markers and demonstrate the utility of RAD-tags from a relatively small, opportunistically sampled cetacean sample set for population diversity and divergence analysis. |
format |
Article in Journal/Newspaper |
author |
Ljerka Lah Daronja Trense Harald Benke Per Berggren Þorvaldur Gunnlaugsson Christina Lockyer Ayaka Öztürk Bayram Öztürk Iwona Pawliczka Anna Roos Ursula Siebert Krzysztof Skóra Gísli Víkingsson Ralph Tiedemann |
author_facet |
Ljerka Lah Daronja Trense Harald Benke Per Berggren Þorvaldur Gunnlaugsson Christina Lockyer Ayaka Öztürk Bayram Öztürk Iwona Pawliczka Anna Roos Ursula Siebert Krzysztof Skóra Gísli Víkingsson Ralph Tiedemann |
author_sort |
Ljerka Lah |
title |
Spatially Explicit Analysis of Genome-Wide SNPs Detects Subtle Population Structure in a Mobile Marine Mammal, the Harbor Porpoise. |
title_short |
Spatially Explicit Analysis of Genome-Wide SNPs Detects Subtle Population Structure in a Mobile Marine Mammal, the Harbor Porpoise. |
title_full |
Spatially Explicit Analysis of Genome-Wide SNPs Detects Subtle Population Structure in a Mobile Marine Mammal, the Harbor Porpoise. |
title_fullStr |
Spatially Explicit Analysis of Genome-Wide SNPs Detects Subtle Population Structure in a Mobile Marine Mammal, the Harbor Porpoise. |
title_full_unstemmed |
Spatially Explicit Analysis of Genome-Wide SNPs Detects Subtle Population Structure in a Mobile Marine Mammal, the Harbor Porpoise. |
title_sort |
spatially explicit analysis of genome-wide snps detects subtle population structure in a mobile marine mammal, the harbor porpoise. |
publisher |
Public Library of Science (PLoS) |
publishDate |
2016 |
url |
https://doi.org/10.1371/journal.pone.0162792 https://doaj.org/article/bcfcc5ee0fbc4a42a1848be9b2ca6709 |
genre |
North Atlantic Phocoena phocoena |
genre_facet |
North Atlantic Phocoena phocoena |
op_source |
PLoS ONE, Vol 11, Iss 10, p e0162792 (2016) |
op_relation |
http://europepmc.org/articles/PMC5082642?pdf=render https://doaj.org/toc/1932-6203 1932-6203 doi:10.1371/journal.pone.0162792 https://doaj.org/article/bcfcc5ee0fbc4a42a1848be9b2ca6709 |
op_doi |
https://doi.org/10.1371/journal.pone.0162792 |
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PLOS ONE |
container_volume |
11 |
container_issue |
10 |
container_start_page |
e0162792 |
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1766134328115331072 |