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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Online Access: | https://hdl.handle.net/20.500.12627/119164 https://doi.org/10.1371/journal.pone.0162792 |
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ftistanbuluniv:oai:http://acikerisim.istanbul.edu.tr:20.500.12627/119164 2023-05-15T17:35:26+02:00 Spatially Explicit Analysis of Genome-Wide SNPs Detects Subtle Population Structure in a Mobile Marine Mammal, the Harbor Porpoise BENKE, Harald LAH, Ljerka BERGGREN, Per TRENSE, Daronja GUNNLAUGSSON, Porvaldur LOCKYER, Christina PAWLICZKA, Iwona ROOS, Anna Siebert, Ursula SKORA, Krzysztof VIKINGSSON, Gisli TIEDEMANN, Ralph Ozturk, Ayaka Ozturk, Bayram University of Potsdam , , 27595 2016 https://hdl.handle.net/20.500.12627/119164 https://doi.org/10.1371/journal.pone.0162792 eng eng PLOS ONE LAH L., TRENSE D., BENKE H., BERGGREN P., GUNNLAUGSSON P., LOCKYER C., Ozturk A., Ozturk B., PAWLICZKA I., ROOS A., et al., "Spatially Explicit Analysis of Genome-Wide SNPs Detects Subtle Population Structure in a Mobile Marine Mammal, the Harbor Porpoise", PLOS ONE, cilt.11, 2016 1932-6203 av_b2e8e678-eef0-4652-92dd-e1a701d2346f vv_1032021 http://hdl.handle.net/20.500.12627/119164 https://doi.org/10.1371/journal.pone.0162792 11 10 Temel Bilimler ÇOK DİSİPLİNLİ BİLİMLER Doğa Bilimleri Genel Temel Bilimler (SCI) Makale 2016 ftistanbuluniv https://doi.org/20.500.12627/119164 https://doi.org/10.1371/journal.pone.0162792 2022-08-10T13:32:07Z 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 polymor-phisms (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 İstanbul Üniversitesi Açık Erişim Sistemi PLOS ONE 11 10 e0162792 |
institution |
Open Polar |
collection |
İstanbul Üniversitesi Açık Erişim Sistemi |
op_collection_id |
ftistanbuluniv |
language |
English |
topic |
Temel Bilimler ÇOK DİSİPLİNLİ BİLİMLER Doğa Bilimleri Genel Temel Bilimler (SCI) |
spellingShingle |
Temel Bilimler ÇOK DİSİPLİNLİ BİLİMLER Doğa Bilimleri Genel Temel Bilimler (SCI) BENKE, Harald LAH, Ljerka BERGGREN, Per TRENSE, Daronja GUNNLAUGSSON, Porvaldur LOCKYER, Christina PAWLICZKA, Iwona ROOS, Anna Siebert, Ursula SKORA, Krzysztof VIKINGSSON, Gisli TIEDEMANN, Ralph Ozturk, Ayaka Ozturk, Bayram Spatially Explicit Analysis of Genome-Wide SNPs Detects Subtle Population Structure in a Mobile Marine Mammal, the Harbor Porpoise |
topic_facet |
Temel Bilimler ÇOK DİSİPLİNLİ BİLİMLER Doğa Bilimleri Genel Temel Bilimler (SCI) |
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 polymor-phisms (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. |
author2 |
University of Potsdam , , 27595 |
format |
Article in Journal/Newspaper |
author |
BENKE, Harald LAH, Ljerka BERGGREN, Per TRENSE, Daronja GUNNLAUGSSON, Porvaldur LOCKYER, Christina PAWLICZKA, Iwona ROOS, Anna Siebert, Ursula SKORA, Krzysztof VIKINGSSON, Gisli TIEDEMANN, Ralph Ozturk, Ayaka Ozturk, Bayram |
author_facet |
BENKE, Harald LAH, Ljerka BERGGREN, Per TRENSE, Daronja GUNNLAUGSSON, Porvaldur LOCKYER, Christina PAWLICZKA, Iwona ROOS, Anna Siebert, Ursula SKORA, Krzysztof VIKINGSSON, Gisli TIEDEMANN, Ralph Ozturk, Ayaka Ozturk, Bayram |
author_sort |
BENKE, Harald |
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 |
publishDate |
2016 |
url |
https://hdl.handle.net/20.500.12627/119164 https://doi.org/10.1371/journal.pone.0162792 |
genre |
North Atlantic Phocoena phocoena |
genre_facet |
North Atlantic Phocoena phocoena |
op_relation |
PLOS ONE LAH L., TRENSE D., BENKE H., BERGGREN P., GUNNLAUGSSON P., LOCKYER C., Ozturk A., Ozturk B., PAWLICZKA I., ROOS A., et al., "Spatially Explicit Analysis of Genome-Wide SNPs Detects Subtle Population Structure in a Mobile Marine Mammal, the Harbor Porpoise", PLOS ONE, cilt.11, 2016 1932-6203 av_b2e8e678-eef0-4652-92dd-e1a701d2346f vv_1032021 http://hdl.handle.net/20.500.12627/119164 https://doi.org/10.1371/journal.pone.0162792 11 10 |
op_doi |
https://doi.org/20.500.12627/119164 https://doi.org/10.1371/journal.pone.0162792 |
container_title |
PLOS ONE |
container_volume |
11 |
container_issue |
10 |
container_start_page |
e0162792 |
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1766134606661156864 |