Multiple SNP markers reveal fine-scale population and deep phylogeographic structure in European anchovy (Engraulis encrasicolus L.).

Handle URI:
http://hdl.handle.net/10754/323578
Title:
Multiple SNP markers reveal fine-scale population and deep phylogeographic structure in European anchovy (Engraulis encrasicolus L.).
Authors:
Zarraonaindia, Iratxe; Iriondo, Mikel; Albaina, Aitor; Pardo, Miguel Angel; Manzano, Carmen; Grant, W Stewart; Irigoien, Xabier ( 0000-0002-5411-6741 ) ; Estonba, Andone
Abstract:
Geographic surveys of allozymes, microsatellites, nuclear DNA (nDNA) and mitochondrial DNA (mtDNA) have detected several genetic subdivisions among European anchovy populations. However, these studies have been limited in their power to detect some aspects of population structure by the use of a single or a few molecular markers, or by limited geographic sampling. We use a multi-marker approach, 47 nDNA and 15 mtDNA single nucleotide polymorphisms (SNPs), to analyze 626 European anchovies from the whole range of the species to resolve shallow and deep levels of population structure. Nuclear SNPs define 10 genetic entities within two larger genetically distinctive groups associated with oceanic variables and different life-history traits. MtDNA SNPs define two deep phylogroups that reflect ancient dispersals and colonizations. These markers define two ecological groups. One major group of Iberian-Atlantic populations is associated with upwelling areas on narrow continental shelves and includes populations spawning and overwintering in coastal areas. A second major group includes northern populations in the North East (NE) Atlantic (including the Bay of Biscay) and the Mediterranean and is associated with wide continental shelves with local larval retention currents. This group tends to spawn and overwinter in oceanic areas. These two groups encompass ten populations that differ from previously defined management stocks in the Alboran Sea, Iberian-Atlantic and Bay of Biscay regions. In addition, a new North Sea-English Channel stock is defined. SNPs indicate that some populations in the Bay of Biscay are genetically closer to North Western (NW) Mediterranean populations than to other populations in the NE Atlantic, likely due to colonizations of the Bay of Biscay and NW Mediterranean by migrants from a common ancestral population. Northern NE Atlantic populations were subsequently established by migrants from the Bay of Biscay. Populations along the Iberian-Atlantic coast appear to have been founded by secondary waves of migrants from a southern refuge.
KAUST Department:
Biological and Environmental Sciences and Engineering (BESE) Division; Red Sea Research Center (RSRC)
Citation:
Zarraonaindia I, Iriondo M, Albaina A, Pardo MA, Manzano C, et al. (2012) Multiple SNP Markers Reveal Fine-Scale Population and Deep Phylogeographic Structure in European Anchovy (Engraulis encrasicolus L.). PLoS ONE 7: e42201. doi:10.1371/journal.pone.0042201.
Publisher:
Public Library of Science (PLoS)
Journal:
PLoS ONE
Issue Date:
30-Jul-2012
DOI:
10.1371/journal.pone.0042201
PubMed ID:
22860082
PubMed Central ID:
PMC3408476
Type:
Article
ISSN:
1932-6203
Sponsors:
This work was supported by a research grant to IZ from the Education, Universities and Investigation Department of the Basque Government, by the European Commission (FACTS, FP7-KBBE-2009-3, grant agreement 244966) and two funded projects from the Ministry of Science and Innovation of Spain (RTA2006-00068-C02-02) and the Agriculture and Fisheries Department of the Basque Government (ECOANCHOA). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Additional Links:
http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0042201; http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3408476/
Appears in Collections:
Articles; Red Sea Research Center (RSRC); Biological and Environmental Sciences and Engineering (BESE) Division

Full metadata record

DC FieldValue Language
dc.contributor.authorZarraonaindia, Iratxeen
dc.contributor.authorIriondo, Mikelen
dc.contributor.authorAlbaina, Aitoren
dc.contributor.authorPardo, Miguel Angelen
dc.contributor.authorManzano, Carmenen
dc.contributor.authorGrant, W Stewarten
dc.contributor.authorIrigoien, Xabieren
dc.contributor.authorEstonba, Andoneen
dc.date.accessioned2014-07-22T10:47:01Z-
dc.date.available2014-07-22T10:47:01Z-
dc.date.issued2012-07-30en
dc.identifier.citationZarraonaindia I, Iriondo M, Albaina A, Pardo MA, Manzano C, et al. (2012) Multiple SNP Markers Reveal Fine-Scale Population and Deep Phylogeographic Structure in European Anchovy (Engraulis encrasicolus L.). PLoS ONE 7: e42201. doi:10.1371/journal.pone.0042201.en
dc.identifier.issn1932-6203en
dc.identifier.pmid22860082en
dc.identifier.doi10.1371/journal.pone.0042201en
dc.identifier.urihttp://hdl.handle.net/10754/323578en
dc.description.abstractGeographic surveys of allozymes, microsatellites, nuclear DNA (nDNA) and mitochondrial DNA (mtDNA) have detected several genetic subdivisions among European anchovy populations. However, these studies have been limited in their power to detect some aspects of population structure by the use of a single or a few molecular markers, or by limited geographic sampling. We use a multi-marker approach, 47 nDNA and 15 mtDNA single nucleotide polymorphisms (SNPs), to analyze 626 European anchovies from the whole range of the species to resolve shallow and deep levels of population structure. Nuclear SNPs define 10 genetic entities within two larger genetically distinctive groups associated with oceanic variables and different life-history traits. MtDNA SNPs define two deep phylogroups that reflect ancient dispersals and colonizations. These markers define two ecological groups. One major group of Iberian-Atlantic populations is associated with upwelling areas on narrow continental shelves and includes populations spawning and overwintering in coastal areas. A second major group includes northern populations in the North East (NE) Atlantic (including the Bay of Biscay) and the Mediterranean and is associated with wide continental shelves with local larval retention currents. This group tends to spawn and overwinter in oceanic areas. These two groups encompass ten populations that differ from previously defined management stocks in the Alboran Sea, Iberian-Atlantic and Bay of Biscay regions. In addition, a new North Sea-English Channel stock is defined. SNPs indicate that some populations in the Bay of Biscay are genetically closer to North Western (NW) Mediterranean populations than to other populations in the NE Atlantic, likely due to colonizations of the Bay of Biscay and NW Mediterranean by migrants from a common ancestral population. Northern NE Atlantic populations were subsequently established by migrants from the Bay of Biscay. Populations along the Iberian-Atlantic coast appear to have been founded by secondary waves of migrants from a southern refuge.en
dc.description.sponsorshipThis work was supported by a research grant to IZ from the Education, Universities and Investigation Department of the Basque Government, by the European Commission (FACTS, FP7-KBBE-2009-3, grant agreement 244966) and two funded projects from the Ministry of Science and Innovation of Spain (RTA2006-00068-C02-02) and the Agriculture and Fisheries Department of the Basque Government (ECOANCHOA). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.en
dc.language.isoenen
dc.publisherPublic Library of Science (PLoS)en
dc.relation.urlhttp://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0042201en
dc.relation.urlhttp://www.ncbi.nlm.nih.gov/pmc/articles/PMC3408476/en
dc.rightsArchived with thanks to PloS oneen
dc.subject.meshAnimalsen
dc.subject.meshCell Nucleusen
dc.subject.meshDNA, Mitochondrialen
dc.subject.meshFishesen
dc.subject.meshGenetic Markersen
dc.subject.meshPhylogenyen
dc.subject.meshPolymorphism, Single Nucleotideen
dc.subject.meshAnimalsen
dc.subject.meshCell Nucleusen
dc.subject.meshDNA, Mitochondrialen
dc.subject.meshFishesen
dc.subject.meshGenetic Markersen
dc.subject.meshPhylogenyen
dc.subject.meshPolymorphism, Single Nucleotideen
dc.titleMultiple SNP markers reveal fine-scale population and deep phylogeographic structure in European anchovy (Engraulis encrasicolus L.).en
dc.typeArticleen
dc.contributor.departmentBiological and Environmental Sciences and Engineering (BESE) Divisionen
dc.contributor.departmentRed Sea Research Center (RSRC)en
dc.identifier.journalPLoS ONEen
dc.identifier.pmcidPMC3408476en
dc.eprint.versionPublisher's Version/PDFen
dc.contributor.institutionLaboratory of Genetics, Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Sarriena auzoa z/g, Leioa (Bizkaia), Spain.en
dc.contributor.affiliationKing Abdullah University of Science and Technology (KAUST)en
kaust.authorIrigoien, Xabieren
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