Restriction-site associated DNA sequencing (RAD-seq) and related methods are revolutionizing the field of population genomics in non-model 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.
Bibliographical noteKAUST Repository Item: Exported on 2020-10-01
Acknowledgements: We wish to thank Iñigo Krug, Inma Martín, Naiara Serrano and Iñaki Rico (AZTI), Eneko Bachiller (IMR) and Craig T. Michel (KAUST) for technical assistance and five anonymous reviewers and the editor for useful comments on the manuscript. We are also grateful to Marianna Giannoulaki (Hellenic Centre for Marine Research, Greece), Valentina Tirelli (Istituto Nazionale Di Oceanografia E Geofisica Sperimentale, Italy), Encarnación Garcia Rodríguez (IEO, Murcia, Spain) and François Grégoire (Fisheries and Oceans Canada) for sharing samples. This project was supported by the Department of Agriculture, Fisheries and Food of the Basque Country and the General Secretary of Fisheries of the Spanish Government. This manuscript is contribution 758 from the Marine Research Division of AZTI.
ASJC Scopus subject areas
- Ecology, Evolution, Behavior and Systematics