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Thread: Y haplogroup H2 evidence for a two-Path Neolithic expansion to Western Europe

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    Y haplogroup H2 evidence for a two-Path Neolithic expansion to Western Europe

    Using Y-chromosome capture enrichment to resolve haplogroup H2 shows new evidence for a two-Path Neolithic expansion to Western Europe
    Adam Benjamin Rohrlach, Luka Papac, Ainash Childebayeva, Maite Rivollat, Vanessa Villalba-Mouco, Gunnar U Neumann, Sandra Penske, Eirini B Skourtanioti, Marieke van de Loosdrecht, Murat Akar, Kamen Boyadzhiev, Yavor Boyadzhiev, Marie-France Deguilloux, Miroslav Dobes, Yilmaz S Erdal, Michal Ernee, Marcella Frangipane, Miroslaw Furmanek, Susanne Friederich, Emmanuel Ghesquiere, Agata Haluszko, Svend Hansen, Mario Kuessner, Marcello Mannino, Rana Oezbal, Sabine Reinhold, Stephane Rottier, Domingo Carlos Salazar-Garcia, Jorge Soler Diaz, Philipp W Stockhammer, Consuelo Roca de Togores Munoz, K. Aslıhan Yener, Cosimo Posth, Johannes Krause, Alexander Herbig, Wolfgang Haak

    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.

    ...

    "We curated a data set of 46 previously published individuals (45 ancient and 1 modern), and 49 newly YMCA-sequenced individuals (all ancient)."

    Unfortunately, the paper didn't provide the ENA number:
    "Data generated for this study can be found at the European Nucleotide Archive under the study
    accession number XXXXXXXXX."

    The H2 (H-P96) tree at yfull . --- thanks Megalophias!
    Last edited by pmokeefe; 02-20-2021 at 01:04 PM.
    YFull: YF14620 (Dante Labs 2018)

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    Good stuff. Seems like there are two major subclades of H2: H2d and H2m. The former contains a mix of ISOGG H2, H2a, H2a and H2c1a and the latter a mix of ISOGG H2, H2a1 and H2b1. That's a pretty big rewriting of the structure.

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    Hoping to see more published samples get the same treatment. The 32k Y-variants targeted by 1240k are grossly insufficient for dealing with Y-haplogroups whose distribution in modern populations is negligible - like H2.

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    Quote Originally Posted by pmokeefe View Post
    The H2 tree in yfull is currently empty https://www.yfull.com/arch-3.10/tree/H2/
    Well that's the May 2015 tree you are looking at, the present one is much better.

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    Is it possible to see all haplogroup assignment anywhere? I checked the Supplement table, there are all the samples with the mtDNA assignments, but not the final Y haplogroups.
    There is only a graph about new H2 branches found.

    Haplogroup H2.jpg

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    A very important finding is the unpublished data they have shared. This probably means there is some study is going to be published, does anyone know when?

    The result of the Shulaveri Shomu culture individual ARO008 with H2* is quite interesting. Earlier someone on this forum shared this lecture: https://www.youtube.com/watch?v=60qB5dkFf74. Maybe ARO008 is part of this new population which migrated from the South and Southwest into the Caucasus during the Early Neolithic period. H2* was also found among an individual of the PPNB period of the Southern Levant.

    Also, there are many other H2 data from unpublished studies in the supplementary file. And the results of the Leubingen archaeological site is also included.

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    Yes, they have new high-coverage YMCA samples from Bronze Age Leubingen, Germany.
    https://en.wikipedia.org/wiki/Leubingen_tumulus

    Y Haplogroup
    R1b - LEU001.A0101
    T1a - LEU002.A0101
    G2a - LEU003.A0101
    I2a1 - LEU005.A0101
    R1b - LEU007.A0101
    R1a - LEU011.A0101
    R1b - LEU012.A0101
    H2 - LEU019.A0101
    R1b - LEU024.A0101
    R1a - LEU027.A0101
    R1a - LEU033.A0101
    R1b - LEU041.A0101
    R1a - LEU047.A0101
    R1b - LEU060.A0101
    I2a2 - LEU061.A0101
    R1b - LEU062.A0101
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    Quote Originally Posted by RCO View Post
    Yes, they have new high-coverage YMCA samples from Bronze Age Leubingen, Germany.
    https://en.wikipedia.org/wiki/Leubingen_tumulus

    Y Haplogroup
    R1b - LEU001.A0101
    T1a - LEU002.A0101
    G2a - LEU003.A0101
    I2a1 - LEU005.A0101
    R1b - LEU007.A0101
    R1a - LEU011.A0101
    R1b - LEU012.A0101
    H2 - LEU019.A0101
    R1b - LEU024.A0101
    R1a - LEU027.A0101
    R1a - LEU033.A0101
    R1b - LEU041.A0101
    R1a - LEU047.A0101
    R1b - LEU060.A0101
    I2a2 - LEU061.A0101
    R1b - LEU062.A0101
    According to several reports online, there is only one individual in the Leubingen tumulus? Is there any paper giving archaeological information on all of the individuals?

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    What I can find is there was a male around 50yrs of age found, with a younger male lain across his body. The younger persons remains were missed during the first excavation. The mound was later used as a later medieval burial ground.
    Last edited by Paul333; 02-20-2021 at 03:42 PM.

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    Quote Originally Posted by RCO View Post
    Yes, they have new high-coverage YMCA samples from Bronze Age Leubingen, Germany.
    https://en.wikipedia.org/wiki/Leubingen_tumulus

    Y Haplogroup
    R1b - LEU001.A0101
    T1a - LEU002.A0101
    G2a - LEU003.A0101
    I2a1 - LEU005.A0101
    R1b - LEU007.A0101
    R1a - LEU011.A0101
    R1b - LEU012.A0101
    H2 - LEU019.A0101
    R1b - LEU024.A0101
    R1a - LEU027.A0101
    R1a - LEU033.A0101
    R1b - LEU041.A0101
    R1a - LEU047.A0101
    R1b - LEU060.A0101
    I2a2 - LEU061.A0101
    R1b - LEU062.A0101
    Is there any information about their deeper subclades?

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