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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

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.

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 Creators:
Rohrlach, Adam Ben1, Author              
Papac, Luka1, Author              
Childebayeva, Ainash1, Author              
Rivollat, Maite1, Author              
Villalba-Mouco, Vanessa1, Author              
Neumann, Gunnar U.1, Author              
Penske, Sandra Ellen1, Author              
Skourtanioti, Eirini1, Author              
Loosdrecht, Marieke Sophia van de1, Author              
Akar, Murat, Author
Boyadzhiev, Kamen, Author
Boyadzhiev, Yavor, Author
Deguilloux, Marie-France, Author
Dobeš, Miroslav, Author
Erdal, Yilmaz S., Author
Ernée, Michal, Author
Frangipane, Marcella, Author
Furmanek, Miroslaw, Author
Friederich, Susanne, Author
Ghesquière, Emmanuel, Author
Hałuszko, Agata, AuthorHansen, Svend, AuthorKüßner, Mario, AuthorMannino, Marcello, AuthorÖzbal, Rana, AuthorReinhold, Sabine, AuthorRottier, Stéphane, AuthorSalazar-García, Domingo Carlos, AuthorSoler Diaz, Jorge, AuthorStockhammer, Philipp W.1, 2, Author              Togores Muñoz, Togores Muñoz21,, AuthorAslihan Yener, K, AuthorPosth, Cosimo1, Author              Krause, Johannes1, 2, Author              Herbig, Alexander1, Author              Haak, Wolfgang1, Author               more..
Affiliations:
1Archaeogenetics, Max Planck Institute for the Science of Human History, Max Planck Society, ou_2074310              
2MHAAM, Max Planck Institute for the Science of Human History, Max Planck Society, ou_2541699              

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Free keywords: aDNA, Y Chromosome, target enrichment, Neolithic expansion, uniparentally inherited marker
 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.

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Language(s): eng - English
 Dates: 2021-02-19
 Publication Status: Published online
 Pages: 23
 Publishing info: -
 Table of Contents: Introduction
Results and Discussion
- Validating the performance of YMCA
- Application of YMCA to YHG H2 as a case study
- Identifying diagnostic SNPs for improved YHG H2 resolution
Discussion
Materials and Methods
- Data
- Contamination quality filtering
- Method of Y Haplogroup Assignment
- Comparing the Performance of our Y-capture Array
- Phylogenetic Tree Reconstruction
Data Availability
 Rev. Type: No review
 Identifiers: DOI: 10.1101/2021.02.19.431761
Other: shh2858
 Degree: -

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Title: bioRxiv
Source Genre: Journal
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Publ. Info: Cold Spring Harbor : Cold Spring Harbor Laboratory
Pages: - Volume / Issue: - Sequence Number: 431761 Start / End Page: - Identifier: URN: https://www.biorxiv.org/