Authoritative subspecies diagnosis tool for European honey bees based on ancestry informative SNPs

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dc.authoridCosta, Cecilia/0000-0001-9985-2729
dc.authoridMeixner, Marina/0000-0002-7785-4894
dc.authoridDe la Rua, Pilar/0000-0002-0058-1402
dc.authoridIlyasov, Rustem A./0000-0003-2445-4739
dc.authoridCauia, Eliza/0000-0002-4476-4411
dc.authoridKryger, Per/0000-0001-5306-3230
dc.authoridLanga, Jorge/0000-0001-5137-8204
dc.authorwosidCosta, Cecilia/AAY-6405-2021
dc.authorwosidMeixner, Marina/ABD-6400-2021
dc.authorwosidDe la Rua, Pilar/A-4578-2009
dc.authorwosidIlyasov, Rustem A./O-2665-2014
dc.authorwosidCauia, Eliza/ABD-8134-2021
dc.authorwosidKryger, Per/H-4600-2019
dc.contributor.authorMomeni, Jamal
dc.contributor.authorParejo, Melanie
dc.contributor.authorNielsen, Rasmus O.
dc.contributor.authorLanga, Jorge
dc.contributor.authorMontes, Iratxe
dc.contributor.authorPapoutsis, Laetitia
dc.contributor.authorCosta, Cecilia
dc.date.accessioned2021-12-01T18:51:16Z
dc.date.available2021-12-01T18:51:16Z
dc.date.issued2021
dc.department[Belirlenecek]en_US
dc.description.abstractBackground With numerous endemic subspecies representing four of its five evolutionary lineages, Europe holds a large fraction of Apis mellifera genetic diversity. This diversity and the natural distribution range have been altered by anthropogenic factors. The conservation of this natural heritage relies on the availability of accurate tools for subspecies diagnosis. Based on pool-sequence data from 2145 worker bees representing 22 populations sampled across Europe, we employed two highly discriminative approaches (PCA and F-ST) to select the most informative SNPs for ancestry inference. Results Using a supervised machine learning (ML) approach and a set of 3896 genotyped individuals, we could show that the 4094 selected single nucleotide polymorphisms (SNPs) provide an accurate prediction of ancestry inference in European honey bees. The best ML model was Linear Support Vector Classifier (Linear SVC) which correctly assigned most individuals to one of the 14 subspecies or different genetic origins with a mean accuracy of 96.2% +/- 0.8 SD. A total of 3.8% of test individuals were misclassified, most probably due to limited differentiation between the subspecies caused by close geographical proximity, or human interference of genetic integrity of reference subspecies, or a combination thereof. Conclusions The diagnostic tool presented here will contribute to a sustainable conservation and support breeding activities in order to preserve the genetic heritage of European honey bees.en_US
dc.description.sponsorshipEuropean CommissionEuropean CommissionEuropean Commission Joint Research Centre [2013.1.3-02, 613960]; Basque GovernmentBasque Government [IT1233-19]en_US
dc.description.sponsorshipThe SmartBees project was funded by the European Commission under its FP7 KBBE programme (2013.1.3-02, SmartBees Grant Agreement number 613960) https://ec.europa.eu/research/fp7.MP was supported by a Basque Government grant (IT1233-19). The funders provided the financial support to the research, but had no role in the design of the study, analysis, interpretations of data and in writing the manuscript.en_US
dc.identifier.doi10.1186/s12864-021-07379-7
dc.identifier.issn1471-2164
dc.identifier.issue1en_US
dc.identifier.pmid33535965en_US
dc.identifier.scopus2-s2.0-85100413967en_US
dc.identifier.scopusqualityQ1en_US
dc.identifier.urihttps://doi.org/10.1186/s12864-021-07379-7
dc.identifier.urihttps://hdl.handle.net/20.500.12684/10988
dc.identifier.volume22en_US
dc.identifier.wosWOS:000614429400001en_US
dc.identifier.wosqualityQ2en_US
dc.indekslendigikaynakWeb of Scienceen_US
dc.indekslendigikaynakPubMeden_US
dc.indekslendigikaynakScopusen_US
dc.language.isoenen_US
dc.publisherBmcen_US
dc.relation.ispartofBmc Genomicsen_US
dc.relation.publicationcategoryMakale - Uluslararası Hakemli Dergi - Kurum Öğretim Elemanıen_US
dc.rightsinfo:eu-repo/semantics/openAccessen_US
dc.subjectApis melliferaen_US
dc.subjectEuropean subspeciesen_US
dc.subjectConservationen_US
dc.subjectMachine learningen_US
dc.subjectPredictionen_US
dc.subjectBiodiversityen_US
dc.titleAuthoritative subspecies diagnosis tool for European honey bees based on ancestry informative SNPsen_US
dc.typeArticleen_US

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