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

MPS-Authors
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Rohrlach,  Adam Ben
Archaeogenetics, Max Planck Institute for the Science of Human History, Max Planck Society;

/persons/resource/persons222931

Papac,  Luka
Archaeogenetics, Max Planck Institute for the Science of Human History, Max Planck Society;

/persons/resource/persons242932

Childebayeva,  Ainash
Archaeogenetics, Max Planck Institute for the Science of Human History, Max Planck Society;

/persons/resource/persons247987

Rivollat,  Maite
Archaeogenetics, Max Planck Institute for the Science of Human History, Max Planck Society;

/persons/resource/persons231928

Villalba-Mouco,  Vanessa
Archaeogenetics, Max Planck Institute for the Science of Human History, Max Planck Society;

/persons/resource/persons239489

Neumann,  Gunnar U.
Archaeogenetics, Max Planck Institute for the Science of Human History, Max Planck Society;

/persons/resource/persons247910

Penske,  Sandra Ellen
Archaeogenetics, Max Planck Institute for the Science of Human History, Max Planck Society;

/persons/resource/persons222963

Skourtanioti,  Eirini
Archaeogenetics, Max Planck Institute for the Science of Human History, Max Planck Society;

/persons/resource/persons221869

Loosdrecht,  Marieke Sophia van de
Archaeogenetics, Max Planck Institute for the Science of Human History, Max Planck Society;

/persons/resource/persons207359

Stockhammer,  Philipp W.
Archaeogenetics, Max Planck Institute for the Science of Human History, Max Planck Society;
MHAAM, Max Planck Institute for the Science of Human History, Max Planck Society;

/persons/resource/persons188736

Posth,  Cosimo
Archaeogenetics, Max Planck Institute for the Science of Human History, Max Planck Society;

/persons/resource/persons72801

Krause,  Johannes
Archaeogenetics, Max Planck Institute for the Science of Human History, Max Planck Society;
MHAAM, Max Planck Institute for the Science of Human History, Max Planck Society;

/persons/resource/persons179620

Herbig,  Alexander
Archaeogenetics, Max Planck Institute for the Science of Human History, Max Planck Society;

/persons/resource/persons186115

Haak,  Wolfgang
Archaeogenetics, Max Planck Institute for the Science of Human History, Max Planck Society;

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Citation

Rohrlach, A. B., Papac, L., Childebayeva, A., Rivollat, M., Villalba-Mouco, V., Neumann, G. U., et al. (2021). Using Y-chromosome capture enrichment to resolve haplogroup H2 shows new evidence for a two-Path Neolithic expansion to Western Europe. bioRxiv, 431761. doi:10.1101/2021.02.19.431761.


Cite as: https://hdl.handle.net/21.11116/0000-0008-0F45-B
Abstract
Uniparentally-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 arrays such as the 1240K, 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 1240K capture, YMCA significantly improves the coverage and number of sites hit 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.Competing Interest StatementThe authors have declared no competing interest.