Using Y-chromosome capture enrichment to resolve haplogroup H2 shows new evidence for a two-path Neolithic expansion to Western Europe

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dc.authoridRivollat, Maite/0000-0002-4011-2862
dc.authoridSkourtanioti, Eirini/0000-0003-2975-3869
dc.authoridChildebayeva, Ainash/0000-0002-3144-6481
dc.authoridHaluszko, Agata/0000-0001-8312-3222
dc.authoridrottier, stephane/0000-0002-1520-6648
dc.authoridOzbal, Rana/0000-0001-6765-2765
dc.authoridVillalba-Mouco, Vanessa/0000-0002-9357-5238
dc.contributor.authorRohrlach, Adam B.
dc.contributor.authorPapac, Luka
dc.contributor.authorChildebayeva, Ainash
dc.contributor.authorRivollat, Maite
dc.contributor.authorVillalba-Mouco, Vanessa
dc.contributor.authorNeumann, Gunnar U.
dc.contributor.authorPenske, Sandra
dc.date.accessioned2024-09-18T21:05:04Z
dc.date.available2024-09-18T21:05:04Z
dc.date.issued2021
dc.departmentHatay Mustafa Kemal Üniversitesien_US
dc.description.abstractUniparentally-inherited markers on mitochondrial DNA (mtDNA) and the non-recombining regions of the Y chromosome (NRY), have been used for the past 30 years to investigate the history of humans from a maternal and paternal perspective. Researchers have preferred mtDNA due to its abundance in the cells, and comparatively high substitution rate. Conversely, the NRY is less susceptible to back mutations and saturation, and is potentially more informative than mtDNA owing to its longer sequence length. However, due to comparatively poor NRY coverage via shotgun sequencing, and the relatively low and biased representation of Y-chromosome variants on capture assays such as the 1240 k, ancient DNA studies often fail to utilize the unique perspective that the NRY can yield. Here we introduce a new DNA enrichment assay, coined YMCA (Y-mappable capture assay), that targets the mappable regions of the NRY. We show that compared to low-coverage shotgun sequencing and 1240 k capture, YMCA significantly improves the mean coverage and number of sites covered on the NRY, increasing the number of Y-haplogroup informative SNPs, and allowing for the identification of previously undiscovered variants. To illustrate the power of YMCA, we show that the analysis of ancient Y-chromosome lineages can help to resolve Y-chromosomal haplogroups. As a case study, we focus on H2, a haplogroup associated with a critical event in European human history: the Neolithic transition. By disentangling the evolutionary history of this haplogroup, we further elucidate the two separate paths by which early farmers expanded from Anatolia and the Near East to western Europe.en_US
dc.description.sponsorshipMax Planck Society; French (ANR); German (DFG) Research Foundations under the INTERACT project [ANR17-FRAL-0010, DFG-HA-5407/4-1]; European Research Council (ERC) under the European Union [771234-PALEoRIDER]; Czech Academy of Sciences; Institute of Archaeology of the Czech Academy of Sciences, Prague [RVO 67985912]; Projekt DEALen_US
dc.description.sponsorshipOpen Access funding enabled and organized by Projekt DEAL. This study was funded by the Max Planck Society, the French (ANR) and German (DFG) Research Foundations under the INTERACT project (ANR17-FRAL-0010, DFG-HA-5407/4-1, 2018-2021) to M.R. and W.H., the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation program under Grant agreement no. 771234-PALEoRIDER to W.H., the award Praemium Academiae of the Czech Academy of Sciences to M.E. and the project RVO 67985912 of the Institute of Archaeology of the Czech Academy of Sciences, Prague to M.S.en_US
dc.identifier.doi10.1038/s41598-021-94491-z
dc.identifier.issn2045-2322
dc.identifier.issue1en_US
dc.identifier.pmid34294811en_US
dc.identifier.scopus2-s2.0-85111155721en_US
dc.identifier.scopusqualityQ1en_US
dc.identifier.urihttps://doi.org/10.1038/s41598-021-94491-z
dc.identifier.urihttps://hdl.handle.net/20.500.12483/13339
dc.identifier.volume11en_US
dc.identifier.wosWOS:000682802200038en_US
dc.identifier.wosqualityQ2en_US
dc.indekslendigikaynakWeb of Scienceen_US
dc.indekslendigikaynakScopusen_US
dc.indekslendigikaynakPubMeden_US
dc.language.isoenen_US
dc.publisherNature Portfolioen_US
dc.relation.ispartofScientific Reportsen_US
dc.relation.publicationcategoryMakale - Uluslararası Hakemli Dergi - Kurum Öğretim Elemanıen_US
dc.rightsinfo:eu-repo/semantics/openAccessen_US
dc.subjectMitochondrial-Dnaen_US
dc.subjectAncient Dnaen_US
dc.subjectGenomic Historyen_US
dc.subjectMutation-Rateen_US
dc.subjectDiversityen_US
dc.subjectSelectionen_US
dc.subjectSteppeen_US
dc.titleUsing Y-chromosome capture enrichment to resolve haplogroup H2 shows new evidence for a two-path Neolithic expansion to Western Europeen_US
dc.typeArticleen_US

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