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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
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 cel...
Autores principales: | , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Nature Publishing Group UK
2021
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8298398/ https://www.ncbi.nlm.nih.gov/pubmed/34294811 http://dx.doi.org/10.1038/s41598-021-94491-z |
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author | Rohrlach, Adam B. Papac, Luka Childebayeva, Ainash Rivollat, Maïté Villalba-Mouco, Vanessa Neumann, Gunnar U. Penske, Sandra Skourtanioti, Eirini van de Loosdrecht, Marieke Akar, Murat Boyadzhiev, Kamen Boyadzhiev, Yavor Deguilloux, Marie-France Dobeš, Miroslav Erdal, Yilmaz S. Ernée, Michal Frangipane, Marcella Furmanek, Mirosław Friederich, Susanne Ghesquière, Emmanuel Hałuszko, Agata Hansen, Svend Küßner, Mario Mannino, Marcello Özbal, Rana Reinhold, Sabine Rottier, Stéphane Salazar-García, Domingo Carlos Diaz, Jorge Soler Stockhammer, Philipp W. de Togores Muñoz, Consuelo Roca Yener, K. Aslihan Posth, Cosimo Krause, Johannes Herbig, Alexander Haak, Wolfgang |
author_facet | Rohrlach, Adam B. Papac, Luka Childebayeva, Ainash Rivollat, Maïté Villalba-Mouco, Vanessa Neumann, Gunnar U. Penske, Sandra Skourtanioti, Eirini van de Loosdrecht, Marieke Akar, Murat Boyadzhiev, Kamen Boyadzhiev, Yavor Deguilloux, Marie-France Dobeš, Miroslav Erdal, Yilmaz S. Ernée, Michal Frangipane, Marcella Furmanek, Mirosław Friederich, Susanne Ghesquière, Emmanuel Hałuszko, Agata Hansen, Svend Küßner, Mario Mannino, Marcello Özbal, Rana Reinhold, Sabine Rottier, Stéphane Salazar-García, Domingo Carlos Diaz, Jorge Soler Stockhammer, Philipp W. de Togores Muñoz, Consuelo Roca Yener, K. Aslihan Posth, Cosimo Krause, Johannes Herbig, Alexander Haak, Wolfgang |
author_sort | Rohrlach, Adam B. |
collection | PubMed |
description | 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 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. |
format | Online Article Text |
id | pubmed-8298398 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | Nature Publishing Group UK |
record_format | MEDLINE/PubMed |
spelling | pubmed-82983982021-07-23 Using Y-chromosome capture enrichment to resolve haplogroup H2 shows new evidence for a two-path Neolithic expansion to Western Europe Rohrlach, Adam B. Papac, Luka Childebayeva, Ainash Rivollat, Maïté Villalba-Mouco, Vanessa Neumann, Gunnar U. Penske, Sandra Skourtanioti, Eirini van de Loosdrecht, Marieke Akar, Murat Boyadzhiev, Kamen Boyadzhiev, Yavor Deguilloux, Marie-France Dobeš, Miroslav Erdal, Yilmaz S. Ernée, Michal Frangipane, Marcella Furmanek, Mirosław Friederich, Susanne Ghesquière, Emmanuel Hałuszko, Agata Hansen, Svend Küßner, Mario Mannino, Marcello Özbal, Rana Reinhold, Sabine Rottier, Stéphane Salazar-García, Domingo Carlos Diaz, Jorge Soler Stockhammer, Philipp W. de Togores Muñoz, Consuelo Roca Yener, K. Aslihan Posth, Cosimo Krause, Johannes Herbig, Alexander Haak, Wolfgang Sci Rep Article 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 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. Nature Publishing Group UK 2021-07-22 /pmc/articles/PMC8298398/ /pubmed/34294811 http://dx.doi.org/10.1038/s41598-021-94491-z Text en © The Author(s) 2021 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . |
spellingShingle | Article Rohrlach, Adam B. Papac, Luka Childebayeva, Ainash Rivollat, Maïté Villalba-Mouco, Vanessa Neumann, Gunnar U. Penske, Sandra Skourtanioti, Eirini van de Loosdrecht, Marieke Akar, Murat Boyadzhiev, Kamen Boyadzhiev, Yavor Deguilloux, Marie-France Dobeš, Miroslav Erdal, Yilmaz S. Ernée, Michal Frangipane, Marcella Furmanek, Mirosław Friederich, Susanne Ghesquière, Emmanuel Hałuszko, Agata Hansen, Svend Küßner, Mario Mannino, Marcello Özbal, Rana Reinhold, Sabine Rottier, Stéphane Salazar-García, Domingo Carlos Diaz, Jorge Soler Stockhammer, Philipp W. de Togores Muñoz, Consuelo Roca Yener, K. Aslihan Posth, Cosimo Krause, Johannes Herbig, Alexander Haak, Wolfgang Using Y-chromosome capture enrichment to resolve haplogroup H2 shows new evidence for a two-path Neolithic expansion to Western Europe |
title | Using Y-chromosome capture enrichment to resolve haplogroup H2 shows new evidence for a two-path Neolithic expansion to Western Europe |
title_full | Using Y-chromosome capture enrichment to resolve haplogroup H2 shows new evidence for a two-path Neolithic expansion to Western Europe |
title_fullStr | Using Y-chromosome capture enrichment to resolve haplogroup H2 shows new evidence for a two-path Neolithic expansion to Western Europe |
title_full_unstemmed | Using Y-chromosome capture enrichment to resolve haplogroup H2 shows new evidence for a two-path Neolithic expansion to Western Europe |
title_short | Using Y-chromosome capture enrichment to resolve haplogroup H2 shows new evidence for a two-path Neolithic expansion to Western Europe |
title_sort | using y-chromosome capture enrichment to resolve haplogroup h2 shows new evidence for a two-path neolithic expansion to western europe |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8298398/ https://www.ncbi.nlm.nih.gov/pubmed/34294811 http://dx.doi.org/10.1038/s41598-021-94491-z |
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