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Title: Population structure of Atlantic mackerel inferred from RAD-seq-derived SNP markers: effects of sequence clustering parameters and hierarchical SNP selection
Authors: Rodriguez-Ezpeleta, Naiara; Bradbury, Ian R.; Mendibil, Inaki; Cotano, Unai; Irigoien, Xabier; Alvarez, Paula
Citation: MOLECULAR ECOLOGY RESOURCES, 2016, 16, 991-1001
Abstract: 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 (SNPs) 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 SNPs 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.
Keywords: Atlantic mackerel; population structure; RAD-seq; read merging parameters; SNP; Stacks; SCOMBER-SCOMBRUS; TOOL SET; DE-NOVO; GENOMICS; CONSERVATION; MARINE; DIFFERENTIATION; DISCOVERY; GENETICS; FISHES
Issue Date: 2016
Type: Article
Language: English
DOI: 10.1111/1755-0998.12518
ISSN: 1755-098X
E-ISSN: 1755-0998
Funder: Department of Agriculture, Fisheries and Food of the Basque Country
General Secretary of Fisheries of the Spanish Government
Appears in Publication types:Artículos científicos

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