title: Population structure of Atlantic mackerel inferred from RAD-seq-derived SNP markers: effects of sequence clustering parameters and hierarchical SNP selection.
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.
authors.affiliation: Marine Research Division, AZTI, Txatxarramend ugartea z/g, Sukarrieta 48395, Bizkaia, Spain.
authors.forename: Naiara
authors.initials: N
authors.lastname: Rodríguez-Ezpeleta
authors.affiliation: Department of Fisheries and Oceans, St. John's, NF A1C 5X1, Canada.
authors.forename: Ian R
authors.initials: IR
authors.lastname: Bradbury
authors.affiliation: Marine Research Division, AZTI, Txatxarramend ugartea z/g, Sukarrieta 48395, Bizkaia, Spain.
authors.forename: Iñaki
authors.initials: I
authors.lastname: Mendibil
authors.affiliation: Marine Research Division, AZTI, Txatxarramend ugartea z/g, Sukarrieta 48395, Bizkaia, Spain.
authors.forename: Paula
authors.initials: P
authors.lastname: Álvarez
authors.affiliation: Marine Research Division, AZTI, Txatxarramend ugartea z/g, Sukarrieta 48395, Bizkaia, Spain.
authors.forename: Unai
authors.initials: U
authors.lastname: Cotano
authors.affiliation: Red Sea Research Center, King Abdullah University of Technology, Thuwal 23955, Saudi Arabia.
authors.forename: Xabier
authors.initials: X
authors.lastname: Irigoien
mesh_terms: D000818:Animals; D016000:Cluster Analysis; D014644:Genetic Variation; D005838:Genotype; D060005:Genotyping Techniques / Q000379:methods*; D010473:Perciformes / Q000145:classification* / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide; D012680:Sensitivity and Specificity; D017422:Sequence Analysis, DNA / Q000379:methods*
keywords: Atlantic mackerel; RAD-seq; SNP; Stacks; population structure; read merging parameters