Spatially Explicit Analysis of Genome-Wide SNPs Detects Subtle Population Structure in a Mobile Marine Mammal, the Harbor Porpoise
Publication Date
October 26, 2016
Journal
PLOS ONE
Authors
Ljerka Lah, Daronja Trense, Harald Benke, Per Berggren, et al
Volume
11
Issue
10
Pages
e0162792
DOI
https://dx.plos.org/10.1371/journal.pone.0162792
Publisher URL
http://journals.plos.org/plosone/article?id=10.1371%2Fjournal.pone.0162792
Scopus
84992630108
Mendeley
http://www.mendeley.com/research/spatially-explicit-analysis-genomewide-snps-detects-subtle-population-structure-mobile-marine-mammal
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Mendeley | Further Information

{"title"=>"Spatially explicit analysis of genome-wide SNPs detects subtle population structure in a mobile marine mammal, the harbor porpoise", "type"=>"journal", "authors"=>[{"first_name"=>"Ljerka", "last_name"=>"Lah", "scopus_author_id"=>"23667818000"}, {"first_name"=>"Daronja", "last_name"=>"Trense", "scopus_author_id"=>"57191738566"}, {"first_name"=>"Harald", "last_name"=>"Benke", "scopus_author_id"=>"6603146641"}, {"first_name"=>"Per", "last_name"=>"Berggren", "scopus_author_id"=>"35423285400"}, {"first_name"=>"Porvaldur", "last_name"=>"Gunnlaugsson", "scopus_author_id"=>"57191726143"}, {"first_name"=>"Christina", "last_name"=>"Lockyer", "scopus_author_id"=>"7004477797"}, {"first_name"=>"Ayakaö", "last_name"=>"Öztürk", "scopus_author_id"=>"7103003514"}, {"first_name"=>"Bayramö", "last_name"=>"Öztürk", "scopus_author_id"=>"7006498430"}, {"first_name"=>"Iwona", "last_name"=>"Pawliczka", "scopus_author_id"=>"35424600300"}, {"first_name"=>"Anna", "last_name"=>"Roos", "scopus_author_id"=>"7102533477"}, {"first_name"=>"Ursula", "last_name"=>"Siebert", "scopus_author_id"=>"7004796609"}, {"first_name"=>"Krzysztof Skó", "last_name"=>"Ra", "scopus_author_id"=>"57191728091"}, {"first_name"=>"Gísli", "last_name"=>"Víkingsson", "scopus_author_id"=>"6507637711"}, {"first_name"=>"Ralph", "last_name"=>"Tiedemann", "scopus_author_id"=>"57201455802"}], "year"=>2016, "source"=>"PLoS ONE", "identifiers"=>{"scopus"=>"2-s2.0-84992630108", "sgr"=>"84992630108", "doi"=>"10.1371/journal.pone.0162792", "pui"=>"612916954", "pmid"=>"27783621", "isbn"=>"1932-6203 (Electronic)\r1932-6203 (Linking)", "issn"=>"19326203"}, "id"=>"4f633d36-1bd7-3598-9d95-f5a3a01a80eb", "abstract"=>"RESEARCHARTICLE Spatially Explicit Analysis of Genome-Wide SNPs Detects Subtle Population Structure in a Mobile Marine Mammal, the Harbor Porpoise Ljerka Lah1, Daronja Trense1, Harald Benke2, Per Berggren3, Þorvaldur Gunnlaugsson4, Christina Lockyer5, AyakaO ¨ ztu ¨rk6, BayramO ¨rk6, Iwona Pawliczka7, Anna Roos8, ¨ ztu Ursula Siebert9, Krzysztof Sko ´ra7†, Gı´sli Vı´kingsson4, Ralph Tiedemann1* 1 Unit of Evolutionary Biology/Systematic Zoology, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany, 2 Deutsches Meeresmuseum, Stralsund, Germany, 3 Dove Marine Laboratory, School of Marine Science and Technology, Newcastle University, Cullercoats, North Shields, United Kingdom, 4 Marine Research Institute, Reykjavı ´k, Iceland, 5 North Atlantic Marine Mammal Commission, Tromsø, Norway, 6 Marine Biology Department, Faculty of Fisheries, Istanbul University, Istanbul, Turkey, 7 Hel Marine Station, University of Gdansk, Hel, Poland, 8 Swedish Museum of Natural History, Stockholm, Sweden, 9 Institute for Terrestrial and Aquatic Wildlife Research (ITAW), University of Veterinary Medicine Hannover Foundation, Bu ¨sum, Germany † Deceased. * tiedeman@uni-potsdam.de Abstract The population structure of the highly mobile marine mammal, the harbor porpoise (Pho- coena 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 con- nected 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. Weused 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 sep- aration 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 distinc- tion 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 impor- tant for conservation management of this endangered cetacean in threatened habitats, par- ticularly 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.", "link"=>"http://www.mendeley.com/research/spatially-explicit-analysis-genomewide-snps-detects-subtle-population-structure-mobile-marine-mammal", "reader_count"=>42, "reader_count_by_academic_status"=>{"Student > Doctoral Student"=>6, "Researcher"=>10, "Student > Ph. D. Student"=>11, "Student > Postgraduate"=>1, "Student > Master"=>10, "Student > Bachelor"=>2, "Lecturer"=>1, "Professor"=>1}, "reader_count_by_user_role"=>{"Student > Doctoral Student"=>6, "Researcher"=>10, "Student > Ph. D. Student"=>11, "Student > Postgraduate"=>1, "Student > Master"=>10, "Student > Bachelor"=>2, "Lecturer"=>1, "Professor"=>1}, "reader_count_by_subject_area"=>{"Environmental Science"=>6, "Biochemistry, Genetics and Molecular Biology"=>11, "Agricultural and Biological Sciences"=>23, "Arts and Humanities"=>1, "Earth and Planetary Sciences"=>1}, "reader_count_by_subdiscipline"=>{"Earth and Planetary Sciences"=>{"Earth and Planetary Sciences"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>23}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>11}, "Environmental Science"=>{"Environmental Science"=>6}, "Arts and Humanities"=>{"Arts and Humanities"=>1}}, "group_count"=>0}

Scopus | Further Information

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