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

2021Journal article Open access
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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.authorFarajzadeh, Leila
dc.contributor.authorBendixen, Christian
dc.contributor.authorCăuia, Eliza
dc.contributor.authorCharrière, Jean Daniel
dc.contributor.authorCoffey, Mary F.
dc.contributor.authorCosta, Cecilia
dc.contributor.authorDall'Olio, Raffaele
dc.contributor.authorDe la Rúa, Pilar
dc.contributor.authorDražić, Marica Maja
dc.contributor.authorFilipi, Janja
dc.contributor.authorGalea, Thomas
dc.contributor.authorGolubovski, Miroljub
dc.contributor.authorGregorc, Aleš
dc.contributor.authorGrigoryan, Karina
dc.contributor.authorHatjina, Fani
dc.contributor.authorIlyasov, Rustem
dc.contributor.authorIvanova, Evgeniya Neshova
dc.contributor.authorJanashia, Irakli
dc.contributor.authorKandemir, Irfan
dc.contributor.authorKaratasou, Aikaterini
dc.contributor.authorKekecoglu, Meral
dc.contributor.authorKezic, Nikola
dc.contributor.authorMatray, Enikö Sz
dc.contributor.authorMifsud, David
dc.contributor.authorMoosbeckhofer, Rudolf
dc.contributor.authorNikolenko, Alexei G.
dc.contributor.authorPapachristoforou, Alexandros
dc.contributor.authorPetrov, Plamen
dc.contributor.authorPinto, M. Alice
dc.contributor.authorPoskryakov, Aleksandr V.
dc.contributor.authorSharipov, Aglyam Y.
dc.contributor.authorSiceanu, Adrian
dc.contributor.authorSoysal, M. Ihsan
dc.contributor.authorUzunov, Aleksandar
dc.contributor.authorZammit Mangion, Marion
dc.contributor.authorVingborg, Rikke
dc.contributor.authorBouga, Maria
dc.contributor.authorKryger, Per
dc.contributor.authorMeixner, Marina D.
dc.contributor.authorEstonba, Andone
dc.date.accessioned2018-02-19T10:00:00Z
dc.date.accessioned2021-11-22T10:27:17Z
dc.date.available2018-01-19T10:00:00Z
dc.date.available2021-11-22T10:27:17Z
dc.date.issued2021
dc.description.abstractWith 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 FST) 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_EN
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.
dc.description.versioninfo:eu-repo/semantics/publishedVersionen_EN
dc.identifier.citationMomeni, Jamal; Parejo, Melanie; Nielsen, Rasmus O.; Langa, Jorge; Montes, Iratxe; Papoutsis, Laetitia; Farajzadeh, Leila; Bendixen, Christian; Căuia, Eliza; Charrière, Jean Daniel; Coffey, Mary F.; Costa, Cecilia; Dall’Olio, Raffaele; De la Rúa, Pilar; Drazic, M. Maja; Filipi, Janja; Galea, Thomas; Golubovski, Miroljub; Gregorc, Ales; Grigoryan, Karina; Hatjina, Fani; Ilyasov, Rustem; Ivanova, Evgeniya; Janashia, Irakli; Kandemir, Irfan; Karatasou, Aikaterini; Kekecoglu, Meral; Kezic, Nikola; Matray, Enikö Sz; Mifsud, David; Moosbeckhofer, Rudolf; Nikolenko, Alexei G.; Papachristoforou, Alexandros; Petrov, Plamen; Pinto, M. Alice; Poskryakov, Aleksandr V.; Sharipov, Aglyam Y.; Siceanu, Adrian; Soysal, M. Ihsan; Uzunov, Aleksandar; Zammit-Mangion, Marion; Vingborg, Rikke; Bouga, Maria; Kryger, Per; Meixner, Marina D.; Estonba, Andone (2021). Authoritative subspecies diagnosis tool for European honey bees based on ancestry informative SNPs. BMC Genomics. ISSN . 22:1, p.en_EN
dc.identifier.doi10.1186/s12864-021-07379-7en_EN
dc.identifier.urihttp://hdl.handle.net/10198/24226
dc.language.isoeng
dc.peerreviewedyesen_EN
dc.relation2013.1.3–02
dc.subjectApis mellifera, European subspeciesen_EN
dc.subjectBiodiversityen_EN
dc.subjectConservationen_EN
dc.subjectMachine learningen_EN
dc.subjectPredictionen_EN
dc.titleAuthoritative subspecies diagnosis tool for European honey bees based on ancestry informative SNPsen_EN
dc.typejournal article
dspace.entity.typePublication
person.familyNamePinto
person.givenNameM. Alice
person.identifier.ciencia-idF814-A1D0-8318
person.identifier.orcid0000-0001-9663-8399
person.identifier.scopus-author-id8085507800
rcaap.rightsopenAccessen_EN
rcaap.typearticleen_EN
relation.isAuthorOfPublication0667fe04-7078-483d-9198-56d167b19bc5
relation.isAuthorOfPublication.latestForDiscovery0667fe04-7078-483d-9198-56d167b19bc5

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