Population structure of Atlantic Mackerel inferred from RAD-seq derived SNP markers: effects of sequence clustering parameters and hierarchical SNP selection

Handle URI:
http://hdl.handle.net/10754/601319
Title:
Population structure of Atlantic Mackerel inferred from RAD-seq derived SNP markers: effects of sequence clustering parameters and hierarchical SNP selection
Authors:
Rodríguez-Ezpeleta, Naiara; Bradbury, Ian R.; Mendibil, Iñaki; Álvarez, Paula; Cotano, Unai; Irigoien, Xabier ( 0000-0002-5411-6741 )
Abstract:
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.
KAUST Department:
Red Sea Research Center (RSRC)
Citation:
Population structure of Atlantic Mackerel inferred from RAD-seq derived SNP markers: effects of sequence clustering parameters and hierarchical SNP selection 2016:n/a Molecular Ecology Resources
Publisher:
Wiley-Blackwell
Journal:
Molecular Ecology Resources
Issue Date:
3-Mar-2016
DOI:
10.1111/1755-0998.12518
Type:
Article
ISSN:
1755098X
Sponsors:
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.
Additional Links:
http://doi.wiley.com/10.1111/1755-0998.12518
Appears in Collections:
Articles; Red Sea Research Center (RSRC)

Full metadata record

DC FieldValue Language
dc.contributor.authorRodríguez-Ezpeleta, Naiaraen
dc.contributor.authorBradbury, Ian R.en
dc.contributor.authorMendibil, Iñakien
dc.contributor.authorÁlvarez, Paulaen
dc.contributor.authorCotano, Unaien
dc.contributor.authorIrigoien, Xabieren
dc.date.accessioned2016-03-13T13:58:16Zen
dc.date.available2016-03-13T13:58:16Zen
dc.date.issued2016-03-03en
dc.identifier.citationPopulation structure of Atlantic Mackerel inferred from RAD-seq derived SNP markers: effects of sequence clustering parameters and hierarchical SNP selection 2016:n/a Molecular Ecology Resourcesen
dc.identifier.issn1755098Xen
dc.identifier.doi10.1111/1755-0998.12518en
dc.identifier.urihttp://hdl.handle.net/10754/601319en
dc.description.abstractRestriction-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.en
dc.description.sponsorshipWe 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.en
dc.language.isoenen
dc.publisherWiley-Blackwellen
dc.relation.urlhttp://doi.wiley.com/10.1111/1755-0998.12518en
dc.rightsThis is the peer reviewed version of the following article: Rodríguez‐Ezpeleta, N., Bradbury, I.R., Mendibil, I., Álvarez, P., Cotano, U. and Irigoien, X., 2016. Population structure of Atlantic Mackerel inferred from RAD‐seq derived SNP markers: effects of sequence clustering parameters and hierarchical SNP selection. Molecular Ecology Resources., which has been published in final form at http://doi.wiley.com/10.1111/1755-0998.12518. This article may be used for non-commercial purposes in accordance With Wiley Terms and Conditions for self-archiving.en
dc.subjectRAD-seqen
dc.subjectSNPen
dc.subjectStacksen
dc.subjectread merging parametersen
dc.subjectpopulation structureen
dc.subjectAtlantic mackerelen
dc.titlePopulation structure of Atlantic Mackerel inferred from RAD-seq derived SNP markers: effects of sequence clustering parameters and hierarchical SNP selectionen
dc.typeArticleen
dc.contributor.departmentRed Sea Research Center (RSRC)en
dc.identifier.journalMolecular Ecology Resourcesen
dc.eprint.versionPost-printen
dc.contributor.institutionAZTI; Marine Research Division; Sukarrieta Bizkaia Spainen
dc.contributor.institutionDepartment of Fisheries and Oceans; St. John's; Newfoundland Canadaen
dc.contributor.affiliationKing Abdullah University of Science and Technology (KAUST)en
kaust.authorIrigoien, Xabieren
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