Cargando…
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...
Autores principales: | , , , , , , , , , , , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Public Library of Science
2016
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5082642/ https://www.ncbi.nlm.nih.gov/pubmed/27783621 http://dx.doi.org/10.1371/journal.pone.0162792 |
_version_ | 1782463102379360256 |
---|---|
author | Lah, Ljerka Trense, Daronja Benke, Harald Berggren, Per Gunnlaugsson, Þorvaldur Lockyer, Christina Öztürk, Ayaka Öztürk, Bayram Pawliczka, Iwona Roos, Anna Siebert, Ursula Skóra, Krzysztof Víkingsson, Gísli Tiedemann, Ralph |
author_facet | Lah, Ljerka Trense, Daronja Benke, Harald Berggren, Per Gunnlaugsson, Þorvaldur Lockyer, Christina Öztürk, Ayaka Öztürk, Bayram Pawliczka, Iwona Roos, Anna Siebert, Ursula Skóra, Krzysztof Víkingsson, Gísli Tiedemann, Ralph |
author_sort | Lah, Ljerka |
collection | PubMed |
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 | Online Article Text |
id | pubmed-5082642 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2016 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-50826422016-11-04 Spatially Explicit Analysis of Genome-Wide SNPs Detects Subtle Population Structure in a Mobile Marine Mammal, the Harbor Porpoise Lah, Ljerka Trense, Daronja Benke, Harald Berggren, Per Gunnlaugsson, Þorvaldur Lockyer, Christina Öztürk, Ayaka Öztürk, Bayram Pawliczka, Iwona Roos, Anna Siebert, Ursula Skóra, Krzysztof Víkingsson, Gísli Tiedemann, Ralph PLoS One Research Article 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. Public Library of Science 2016-10-26 /pmc/articles/PMC5082642/ /pubmed/27783621 http://dx.doi.org/10.1371/journal.pone.0162792 Text en © 2016 Lah et al http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. |
spellingShingle | Research Article Lah, Ljerka Trense, Daronja Benke, Harald Berggren, Per Gunnlaugsson, Þorvaldur Lockyer, Christina Öztürk, Ayaka Öztürk, Bayram Pawliczka, Iwona Roos, Anna Siebert, Ursula Skóra, Krzysztof Víkingsson, Gísli Tiedemann, Ralph Spatially Explicit Analysis of Genome-Wide SNPs Detects Subtle Population Structure in a Mobile Marine Mammal, the Harbor Porpoise |
title | 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_short | 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 |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5082642/ https://www.ncbi.nlm.nih.gov/pubmed/27783621 http://dx.doi.org/10.1371/journal.pone.0162792 |
work_keys_str_mv | AT lahljerka spatiallyexplicitanalysisofgenomewidesnpsdetectssubtlepopulationstructureinamobilemarinemammaltheharborporpoise AT trensedaronja spatiallyexplicitanalysisofgenomewidesnpsdetectssubtlepopulationstructureinamobilemarinemammaltheharborporpoise AT benkeharald spatiallyexplicitanalysisofgenomewidesnpsdetectssubtlepopulationstructureinamobilemarinemammaltheharborporpoise AT berggrenper spatiallyexplicitanalysisofgenomewidesnpsdetectssubtlepopulationstructureinamobilemarinemammaltheharborporpoise AT gunnlaugssonþorvaldur spatiallyexplicitanalysisofgenomewidesnpsdetectssubtlepopulationstructureinamobilemarinemammaltheharborporpoise AT lockyerchristina spatiallyexplicitanalysisofgenomewidesnpsdetectssubtlepopulationstructureinamobilemarinemammaltheharborporpoise AT ozturkayaka spatiallyexplicitanalysisofgenomewidesnpsdetectssubtlepopulationstructureinamobilemarinemammaltheharborporpoise AT ozturkbayram spatiallyexplicitanalysisofgenomewidesnpsdetectssubtlepopulationstructureinamobilemarinemammaltheharborporpoise AT pawliczkaiwona spatiallyexplicitanalysisofgenomewidesnpsdetectssubtlepopulationstructureinamobilemarinemammaltheharborporpoise AT roosanna spatiallyexplicitanalysisofgenomewidesnpsdetectssubtlepopulationstructureinamobilemarinemammaltheharborporpoise AT siebertursula spatiallyexplicitanalysisofgenomewidesnpsdetectssubtlepopulationstructureinamobilemarinemammaltheharborporpoise AT skorakrzysztof spatiallyexplicitanalysisofgenomewidesnpsdetectssubtlepopulationstructureinamobilemarinemammaltheharborporpoise AT vikingssongisli spatiallyexplicitanalysisofgenomewidesnpsdetectssubtlepopulationstructureinamobilemarinemammaltheharborporpoise AT tiedemannralph spatiallyexplicitanalysisofgenomewidesnpsdetectssubtlepopulationstructureinamobilemarinemammaltheharborporpoise |