title: Conservation genomics of anadromous Atlantic salmon across its North American range: outlier loci identify the same patterns of population structure as neutral loci.
abstract: Anadromous Atlantic salmon (Salmo salar) is a species of major conservation and management concern in North America, where population abundance has been declining over the past 30 years. Effective conservation actions require the delineation of conservation units to appropriately reflect the spatial scale of intraspecific variation and local adaptation. Towards this goal, we used the most comprehensive genetic and genomic database for Atlantic salmon to date, covering the entire North American range of the species. The database included microsatellite data from 9142 individuals from 149 sampling locations and data from a medium-density SNP array providing genotypes for >3000 SNPs for 50 sampling locations. We used neutral and putatively selected loci to integrate adaptive information in the definition of conservation units. Bayesian clustering with the microsatellite data set and with neutral SNPs identified regional groupings largely consistent with previously published regional assessments. The use of outlier SNPs did not result in major differences in the regional groupings, suggesting that neutral markers can reflect the geographic scale of local adaptation despite not being under selection. We also performed assignment tests to compare power obtained from microsatellites, neutral SNPs and outlier SNPs. Using SNP data substantially improved power compared to microsatellites, and an assignment success of 97% to the population of origin and of 100% to the region of origin was achieved when all SNP loci were used. Using outlier SNPs only resulted in minor improvements to assignment success to the population of origin but improved regional assignment. We discuss the implications of these new genetic resources for the conservation and management of Atlantic salmon in North America.
authors.affiliation: Institut de Biologie Intégrative et des Systèmes, Université Laval, 1030 Avenue de la Médecine, Québec, Québec, G1V 0A6, Canada.
authors.forename: Jean-Sébastien
authors.initials: JS
authors.lastname: Moore
authors.forename: Vincent
authors.initials: V
authors.lastname: Bourret
authors.forename: Mélanie
authors.initials: M
authors.lastname: Dionne
authors.forename: Ian
authors.initials: I
authors.lastname: Bradbury
authors.forename: Patrick
authors.initials: P
authors.lastname: O'Reilly
authors.forename: Matthew
authors.initials: M
authors.lastname: Kent
authors.forename: Gérald
authors.initials: G
authors.lastname: Chaput
authors.forename: Louis
authors.initials: L
authors.lastname: Bernatchez
mesh_terms: D000818:Animals; D001499:Bayes Theorem; D016000:Cluster Analysis; D003247:Conservation of Natural Resources; D030541:Databases, Genetic; D005828:Genetics, Population; D023281:Genomics; D005838:Genotype; D018895:Microsatellite Repeats; D009656:North America; D020641:Polymorphism, Single Nucleotide; D020317:Salmo salar / Q000235:genetics*; D017422:Sequence Analysis, DNA
keywords: SNP array; assignment tests; fishery; hierarchical population structure; local adaptation; microsatellites; single nucleotide polymorphisms