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Population structure of Atlantic mackerel inferred from RAD ‐seq‐derived SNP markers: effects of sequence clustering parameters and hierarchical SNP selection
Author(s) -
RodríguezEzpeleta Naiara,
Bradbury Ian R.,
Mendibil Iñaki,
Álvarez Paula,
Cotano Unai,
Irigoien Xabier
Publication year - 2016
Publication title -
molecular ecology resources
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 2.96
H-Index - 136
eISSN - 1755-0998
pISSN - 1755-098X
DOI - 10.1111/1755-0998.12518
Subject(s) - biology , population genomics , population , snp , genetics , locus (genetics) , single nucleotide polymorphism , genomics , computational biology , mackerel , evolutionary biology , genotype , genome , gene , fishery , fish <actinopterygii> , demography , sociology
Restriction‐site‐associated DNA sequencing ( RAD ‐seq) and related methods are revolutionizing the field of population genomics in nonmodel organisms as they allow generating an unprecedented number of single nucleotide polymorphisms ( SNP s) even when no genomic information is available. Yet, RAD ‐seq data analyses rely on assumptions on nature and number of nucleotide variants present in a single locus, the choice of which may lead to an under‐ or overestimated number of SNP s and/or to incorrectly called genotypes. Using the Atlantic mackerel ( Scomber scombrus L .) and a close relative, the Atlantic chub mackerel ( Scomber colias ), as case study, here we explore the sensitivity of population structure inferences to two crucial aspects in RAD ‐seq data analysis: the maximum number of mismatches allowed to merge reads into a locus and the relatedness of the individuals used for genotype calling and SNP selection. Our study resolves the population structure of the Atlantic mackerel, but, most importantly, provides insights into the effects of alternative RAD ‐seq data analysis strategies on population structure inferences that are directly applicable to other species.