Assessing SNP-markers to study population mixing and ecological adaptation in Baltic cod.
Journal
PloS one
ISSN: 1932-6203
Titre abrégé: PLoS One
Pays: United States
ID NLM: 101285081
Informations de publication
Date de publication:
2019
2019
Historique:
received:
28
03
2019
accepted:
27
05
2019
entrez:
21
6
2019
pubmed:
21
6
2019
medline:
15
2
2020
Statut:
epublish
Résumé
Atlantic cod (Gadus morhua) is a species of great ecological and economical importance in the Baltic Sea. Here, two genetically differentiated stocks, the western and the eastern Baltic cod, display substantial mechanical mixing, hampering our understanding of cod ecology and impeding stock assessments and management. Based on whole-genome re-sequencing data from reference samples obtained from the study area, we designed two different panels of Single Nucleotide Polymorphisms markers (SNPs), which take into account the exceptional genome architecture of cod. A minimum panel of 20 diagnostic SNPs and an extended panel (20 diagnostic and 18 biologically informative SNPs, 38 in total) were developed and validated to distinguish unambiguously between the western and the eastern Baltic cod stocks and to enable studies of local adaptation to the specific environment in the Baltic Sea, respectively. We tested both panels on cod sampled from the southern Baltic Sea (n = 603) caught in 2015 and 2016. Genotyping results showed that catches from the mixing zone in the Arkona Sea, were composed of similar proportions of individuals of the western and the eastern stock. Catches from adjacent areas to the east, the Bornholm Basin and Gdańsk Deep, were exclusively composed of eastern Baltic cod, whereas catches from adjacent western areas (Belt Sea and Öresund) were composed of western Baltic cod. Interestingly, the two Baltic cod stocks showed strong genetic differences at loci associated with life-history trait candidate genes, highlighting the species' potential for ecological adaptation even at small geographical scales. The minimum and the extended panel of SNP markers presented in this study provide powerful tools for future applications in research and fisheries management to further illuminate the mixing dynamics of cod in the Baltic Sea and to better understand Baltic cod ecology.
Identifiants
pubmed: 31220098
doi: 10.1371/journal.pone.0218127
pii: PONE-D-19-08856
pmc: PMC6586271
doi:
Substances chimiques
Genetic Markers
0
Banques de données
figshare
['10.6084/m9.figshare.7907333']
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
e0218127Déclaration de conflit d'intérêts
The authors have declared that no competing interests exist.
Références
Genome Biol Evol. 2016 Apr 11;8(4):1012-22
pubmed: 26983822
Hereditas. 1965;54(1):19-48
pubmed: 5896612
Mol Ecol Resour. 2012 Nov;12(6):1158-60
pubmed: 22883857
Mol Ecol. 2016 May;25(10):2130-43
pubmed: 26923504
Mol Ecol. 2017 Sep;26(17):4452-4466
pubmed: 28626905
Mol Ecol Resour. 2010 Jul;10(4):701-10
pubmed: 21565075
Heredity (Edinb). 2017 Dec;119(6):418-428
pubmed: 28930288
BMC Genomics. 2017 Jan 18;18(1):95
pubmed: 28100185
R Soc Open Sci. 2016 Jan 13;3(1):150338
pubmed: 26909164
Forensic Sci Int Genet. 2015 Sep;18:152-9
pubmed: 25795277
Sci Adv. 2018 May 09;4(5):eaar8195
pubmed: 29750199
BMC Genet. 2009 Sep 03;10:51
pubmed: 19728884
Proc Natl Acad Sci U S A. 1973 Dec;70(12):3321-3
pubmed: 4519626
Ecol Evol. 2014 Nov;4(22):4399-428
pubmed: 25540699
Nat Commun. 2012 May 22;3:851
pubmed: 22617291
Mol Ecol. 2013 Oct;22(20):5098-111
pubmed: 23998762
Mol Ecol. 2019 Mar;28(6):1394-1411
pubmed: 30633410
Evolution. 1989 Jan;43(1):223-225
pubmed: 28568501
Mar Genomics. 2015 Feb;19:17-22
pubmed: 24910372
Proc Biol Sci. 2009 Mar 7;276(1658):833-41
pubmed: 19033139
Mar Pollut Bull. 2008;57(6-12):287-94
pubmed: 18508091
Sci Rep. 2016 Mar 17;6:23246
pubmed: 26983361
Genetika. 2013 Sep;49(9):1079-87
pubmed: 25486775
PLoS Genet. 2006 Dec;2(12):e190
pubmed: 17194218
Bioinformatics. 2010 Feb 1;26(3):419-20
pubmed: 20080509
Proc Natl Acad Sci U S A. 2014 Apr 15;111(15):5628-33
pubmed: 24706804
Mol Ecol. 2003 Jun;12(6):1497-508
pubmed: 12755878
Genome Biol Evol. 2015 May 20;7(6):1644-63
pubmed: 25994933
Genetics. 2000 Jun;155(2):945-59
pubmed: 10835412
Evolution. 1984 Nov;38(6):1358-1370
pubmed: 28563791
Evol Appl. 2019 Jan 20;12(4):830-844
pubmed: 30976313
Sci Rep. 2016 Aug 08;6:31235
pubmed: 27499266
Trends Ecol Evol. 2005 Mar;20(3):136-42
pubmed: 16701357
Bioinformatics. 2007 Jul 15;23(14):1801-6
pubmed: 17485429