All Ancient DNA Dataset

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    • #27555
      Carlos Quiles
      Keymaster

      Announcements of changes to the compiled dataset of Y-DNA and mtDNA data for reported ancient samples, including analyses of BAM files, nomenclature, culture labelling, etc.

      Official site for different formats is at

      Ancient Y-DNA and mtDNA

      For direct download of the latest version published use https://haplogroup.info/

      • This topic was modified 8 months, 3 weeks ago by Carlos Quiles. Reason: sticky, not supersticky
      • This topic was modified 8 months, 3 weeks ago by Carlos Quiles.
    • #27627
      Carlos Quiles
      Keymaster

      Files updated to v. 1.89, including newly reported samples from Sardinia and the Mediterranean, as well as some not so recent ones I had missed – Mazovian prince, Early Poles – and some updated SNPs of samples from different published papers.

    • #27825
      Carlos Quiles
      Keymaster

      I have updated the file with SNP inferences of samples from Sirak et al. (2019).

      Two very interesting new ones from Late Trypillia and Italy MBA!

      I had to delete update dates and start anew, because the previous ones were all messed up, probably due to messing around with different formats (Excel, CSV, txt).

    • #27888
      Carlos Quiles
      Keymaster

      These are some curiously similar SNP inferences around Lake Baikal, apparently N1a1*(xN1a1a), but nevertheless with multiple positives for N1a-L1026 equivalents, showing that this specific lineage (whichever it was) was widespread on both sides of the lake during the Neolithic.

      I14460 Eneolithic Russia (Fofonovo)

      DA345 Ust’-Ida LN

      For some reason, this last one didn’t make its way into YFull.

      EDIT: According to Pribislav, they are N1a-pre-B187, from Y24317, a rare sister clade of N1a-708. ISOGG 2019 is really far behind new SNPs compared to FTDNA and YFull, and the current nomenclature doesn’t make much sense…

      • This reply was modified 7 months, 3 weeks ago by Carlos Quiles. Reason: Pribislav SNP calls for Fofonovo and DA345
    • #27889
      Carlos Quiles
      Keymaster

      The SNP calls for Villabruna show it is negative for V2219 and L389 subclades (although the L389 level is not covered). I’d say it was more likely of a basal subclade that hasn’t survived to this day.

      Villabruna Palaeolithic Epigravettian

      The question is thus if the associated Epigravettian WHG expansion in Western Europe consisted mainly of this subclade, and V2219-associated peoples expanded in a different (later?) wave into SE Europe, or if it was a common L754-rich migration of which we can only see the effects after regional bottlenecks.

      Sadly, Iboussieres31-2 has a too small coverage to help support any option.

       

    • #27936
      Carlos Quiles
      Keymaster

      I have updated the dataset, including reported Neanderthal and Denisovan Y-DNA (ISOGG only).

      I have also checked out some of the samples of hg. T. I can’t find Genetiker’s reported SNP for the Varna individual. The best I can do (like the original paper) is CT+.

      It’s quite interesting that the R1a-Z93 from the Balkans shows SNP calls similar to the Glăvăneştii one, suggesting that it is an R1a-Z93* sample more closely related to Late Trypillian groups, and thus a potential resurgence event more than a Srubnaya-related migration:

      https://docs.google.com/spreadsheets/d/1qUPG0M6auVIwD79cdXifoCB_LFqkzf2acrcprwh8Hfk/edit?usp=sharing

      I have also updated all maps of Y-DNA.

    • #27943
      Carlos Quiles
      Keymaster

      Updated with Sicilian Epigravettian, Mesolithic, and Early Neolithic samples from van de Loosdrecht et al. bioRxiv (2020).

    • #27974
      Carlos Quiles
      Keymaster

      Version 1.89.13:

      1. I have tested all Baltic Neolithic samples reported as R1b-L754 or P297: all have enough coverage to show they are of basal subclades P297* (xM73, xM269).

      2. I also tried using Skoglund et al. (2014) PMDtools with different thresholds to improve damaged samples:

      Unsuccessful with the Balkan Chalcolithic outlier from Smyadovo: all positive SNPs except BT are excluded, so we are stuck with the more risky: P-, but R+, R1b+, R1b-M269+ results. For some reason (maybe a specific threshold??) the authors assumed that the R-P280 call was acceptable, though.

      Successful with the Samara HG sample: a low threshold (=0.1) confirms one R1b-M73-equivalent SNP, with two negative R1b-M269-equivalent reads, so the most plausible haplogroup seems to be M73, until proven otherwise.

      3. I added samples from Egypt, including two newly reported from the Kurchatov Institute (no clear date or location), also the dubious R1b-M269 from the KV 55 coffin and the mtDNA of Djehutynakht in Loreille et al. (2018).

    • #28188
      Carlos Quiles
      Keymaster

      Changes into version 1.89.16 include:

      1. Addition of mtDNA from Ancient mitogenomes show plateau populations from last 5200 years partially contributed to present-day Tibetans, by Ding et al. Proc R Soc B (2020).

      2. Review of SNP inferences of Bronze Age R1b-Z2103 samples, including negative SNPs.

      Now using Yleaf v. 2.2, but I didn’t see any marked differences with previous inferences made with Yleaf v.2.

    • #28724
      Carlos Quiles
      Keymaster

      Updated to version 1.90, including the recent East Asian samples from Wang et al. (2020) and Jeong et al. (2020).

      In version 1.90.1 I added changes proposed by Kovalev to culture and group classification of samples from Jeong et al. (2020).

      I have left the samples labelled as C2a… according to what I could find in Japanese pages, which suggest they belong to ISOGG 2019 C2b, even though no recent ISOGG nomenclature included them in the past 5 years… These include C2a1a1, C2a1a2, but particularly C2a1a3, whose corresponding C2b1a3?? I couldn’t find anywhere.

       

       

    • #29041
      Carlos Quiles
      Keymaster

      Updated version 1.90.4 with new mtDNA reported in Evaluation of DNA conservation in Nile-Saharan environment, Missiminia, in Nubia: Tracking maternal lineage of “X-Group”, by Yahia Mehdi Seddik Cherifi, Selma Amrani.

    • #29159
      Carlos Quiles
      Keymaster

      Updated version 1.90.5, including corrections to I1 subclades (in my file) posted on YFull Facebook Group by Simon Hedley.

      Included two mtDNA reported by Rogers et al. from WSU Human Biology Open Access preprints at https://digitalcommons.wayne.edu/humbiol_preprints/160

    • #29160
      Carlos Quiles
      Keymaster

      Version 1.90.6, updated with reports from Simon Hedley’s great Haplogroup I1 Ancient DNA Samples Google Map.

      He includes very detailed BAM analyses of ancient I1 samples reported to date.

    • #29327
      Carlos Quiles
      Keymaster

      Version 1.90.8 includes minor updates and mtDNA from the study Mitochondrial genomes from Bronze Age Poland reveal genetic continuity from the Late Neolithic and additional genetic affinities with the steppe populations, by Juras et al. J. Phys. Anthropol. (2020)

    • #29599
      Carlos Quiles
      Keymaster

      Updated to version 1.90.15 (to keep my personal update numbers), including the recent Linderholm et al. (2020) and Furtwängler et al. (2020), as well as mtDNA of Hanging Coffin samples from Zhang et al. (2020).

    • #29795
      Carlos Quiles
      Keymaster

      Uploaded version 1.91, including – among other minor changes – updates to SNP inferences by amateurs, report on Egyptian mummies, the new Béla III Y-chromosome report, and the latest Nakatsuka et al. (2020) about the evolution of Andean populations.

    • #29856
      Carlos Quiles
      Keymaster

      Updated from version 1.91.9 to version 1.91.12, including the new Baikal samples from Yu et al. Cell (2020) and the Maros samples from Zegarac et al. bioRxiv (2020), as well as the few reported Trentino samples in Graeffen’s thesis (2020), the few mtDNA from East Asian genomes, or the few Inner Mongolia samples from Li et al. Phys. Anthr. (2020), which updates their previous Li et al. (2017) report.

    • #30280
      Carlos Quiles
      Keymaster

      Updated to version 1.92 with all recently published papers, including Lake Baikal, East Asia, SE Asia, Caribbean (x2), Middle East (x2), France (x2), or the new Pitted Ware samples of BAC influence.

      Update to version 1.93 with automated SNP calls from genotypes shared by Kolgeh (as suggested in comments).

      More recent versions (1.93.x) include mainly corrections to (exact and/or randomized) location of samples for the new Web App GIS Map (read more about it here).

      ArcGIS Web App

    • #30352
      Carlos Quiles
      Keymaster

      Version 2.0x includes new columns for:

      • FTDNA haplotree
      • YFull mtree
      • Responsible for mtDNA SNP calls and the SNP calls published by them.
      • Lactase Persistence – now separated from “other”, more focused on diseases.

      The most interesting part is the correction of nomenclature and hyperlinks, so that the file may be accurately used for mtDNA phylogeography.

      Newly reported samples – or recently found by me – have also been added.

      The new standard versions don’t have fields specific for GIS maps.

      Announcement is here.

    • #30358
      Carlos Quiles
      Keymaster

      Updated to version 2.01.7 with data from the new Cassidy et al. (2020) mostly updating data from her 2017 thesis.

      Also added skin – hair – eye color data thanks to their assessments, even though they are limited to early available (and more ‘western’) samples.

    • #30513
      Carlos Quiles
      Keymaster

      Updated to version 2.01.14. I spent hours reviewing SNP calls for I2 subclades and adding positive, negative, and dubious SNPs. It was very interesting, but also very frustrating when I realized after spending so many hours during the weekend that I couldn’t find what I was looking for: a clear patrilineal connection between all Megalithic groups.

      This post shows the result of that work:

      Demic vs. cultural diffusion and patrilineal Megalithic societies

    • #30560
      Carlos Quiles
      Keymaster

      Updated to version 2.01.19, including negative SNPs for R, R1, R1a (up to Z283 and part of Z93), and some N1c and R1b.

      I have also added a link to SNP calls from YLeaf v.2/v.2.2 in the haplogroup inference section of the website.

    • #30720
      Carlos Quiles
      Keymaster

      Updated to version 2.01.23, including the data published in Saag et al. (2020).

      I have also added Y-DNA SNP calls for FASTQ data of Narasimhan et al. (2020) in the haplogroup inference section. For reference of individual files, check ENA project PRJEB32466.

    • #30724
      Carlos Quiles
      Keymaster

      Updated to version 2.01.24, including mtDNA data from Umbri published in Modi et al. Scientific Reports (2020).

      Given the recently published data from Norht-Eastern Europe and the Cis-Baikal Neolithic and EBA, I’ve also decided to change the symbol of the questionable Chalcolithic N-TAT from Chekunova (2014), as well as  the two Baikalic Neolithic R1a-M198 from Moussa (2016), to an “Unknown” instead of N1c and R1a, respectively. I am not ready to strike them out yet. I still hope they will retest, retrace, or recheck those samples and/or perform radiocarbon dates in the near future.

    • #30725
      Carlos Quiles
      Keymaster

      Updated to version 2.01.26, including update of Early Hungarians from Determination of the phylogenetic origins of the Árpád Dynasty based on Y chromosome sequencing of Béla the Third, by Nagy et al. Eur J Hum Genet (2020).

      Also included in Google Drive Y-DNA SNP calls from Yu et al. (2020).

    • #31004
      Carlos Quiles
      Keymaster

      Updated to version 2.01.35, including reported Initial Jōmon mtDNA from Mizuno et al. (2020), and YFull inferences of Béla the Third and the other published ancient individuals.

    • #31292
      Carlos Quiles
      Keymaster

      Updated to version 2.02.01, including recently reported samples from the Tollense Valley.

      Updated to version 2.02.07, including Xiongnu samples and updates based on STRs (mainly to R1a-Z2125) of previously reported R1a samples.

      Also included are two updated mtDNA subclades from mitogenomes published in Furtwängler et al. (2020).

    • #31316
      Carlos Quiles
      Keymaster

      Updated to version 2.02.07, including samples from A Paleogenomic Reconstruction of the Deep Population History of the Andes, by Nakatsuka, Lazaridis, et al. Cell (2020).

    • #31425
      Carlos Quiles
      Keymaster

      Updated to version 2.02.17, including new inferences from FTDNA (e.g. the Villanovan sample from Civitavecchia) and the Tagliente2 sample.

    • #31461
      Carlos Quiles
      Keymaster

      Updated to version 2.02.24, including samples and mtDNA reported in Harney, Cheronet et al. bioRxiv (2020).

    • #31470
      Carlos Quiles
      Keymaster

      Updated to version 2.02.30, including data recently shared by Svetoslav Stamov from the upcoming Reich Lab paper on SE Europe.

    • #31514
      Carlos Quiles
      Keymaster

      Updated to version 2.02.33 with some updated Y-SNP calls from the FTDNA team.

    • #31541
      Carlos Quiles
      Keymaster

      Updated to version 2.03.01:

      • Completed update of references, including short name, full citation, DOI and (whenever available) accession codes.
      • Updated subclades from the Mokrin necropolis and the Tollense valley.
      • Some more old papers on ancient samples includes: mainly mtDNA, mostly from the Americas.

      Also updated with these changes are the local files and the ArcGIS maps.

    • #31683
      Carlos Quiles
      Keymaster

      Updated to version 2.03.25, including

      • Complete update of mtDNA hyperlinks for FTDNA and YFull.
      • The latest reported samples.
      • Updated new YFull SNP calls for ancient samples.
      • This reply was modified 2 months, 1 week ago by Carlos Quiles. Reason: Update
    • #32225
      Carlos Quiles
      Keymaster

      Updated to version 2.04, today subversion 08, including:

      • All Viking data from FTDNA and some new samples. See the full report here.
      • New additions to the YFull tree.
      • Minor additions to mtDNA data, e.g. Iberia Neolithic from Gomes et al. (2020) and very recent (historical) samples from Tierra del Fuego.
    • #32347
      Carlos Quiles
      Keymaster

      Version 2.04.10 with new/updated samples from Ning et al. bioRxiv (2020).

    • #32627
      Carlos Quiles
      Keymaster

      Updated to version 2.04.24 with new/updated data (among others) from:

      Due to the increasingly tedious loading of files for some old computers, there is now a new “native” Google Sheet format in the Google Drive folder, recommended for easy reading and for searching online.

      • This reply was modified 1 month ago by Carlos Quiles.
    • #33473
      Carlos Quiles
      Keymaster

      Updated to version 2.04.37 with updated samples from:

      • Specific subclades for ancient samples within the N2 branch (added from v. 2.04.32 on) thanks to Uros Uzelac from FTDNA N-P189.2 Group.
      • Specific subclades for ancient (mainly I2) samples from Ireland and Megalithic Europe, thanks to the FTDNA team (see full report in Roberta Estes’ blog), and some new or updated subclades for some of the same samples from YFull.
    • #33926
      Carlos Quiles
      Keymaster

      Updated to version 2.04.42, with updates of FTDNA, YFull, and N2 by Uros Uzelac.

      Also, an interesting new branch reported by FTDNA for Funadomari5, a Late Jomon individual: D1a-CTS1824, forming a clade with NA19004 (Tokio, Japan), from 1000 Genomes. Equivalent to ISOGG 2019-2020 D1a2a2*, YFull D-Z1516*.

    • #34291
      Carlos Quiles
      Keymaster

      Updated to version 2.04.50 with very interesting updates to the I Haplogroup Tree from FTDNA. Information by Göran Runfeldt:

      ftdna-i-haplotree

      I-L758 (pre-I-M170):

      • KremsWA3 – Austria – Gravettian 31,250-30,690 calBP (Fu et al. 2016)
      • Krems1-1/I2483 – Monozygotic twin from Austria – Gravettian 31,000 cal BP (Teschler-Nicola et al. 2020)
      • Krems1-2/I2484 – Monozygotic twin from Austria – Gravettian 31,000 cal BP (Teschler-Nicola et al. 2020)

      I-Z2699 (pre-I1-M253):

      • SF11 – Stora Förvar, Sweden – Mesolithic 9,023-8,760 cal BP (Günther et al. 2018)
      • BAL051 – Balma Guilanyà, Spain – Late Upper Paleolithic/Azilian 13,380–12,660 cal BP/12,830–10,990 cal BP (Villalba-Mouco 2019 et al. 2019)
      • Carl/I10899 – Cueva de la Carigüela, Piñar, Granada, Andalusia, Spain – 9700–5500 BCE (Olalde et al. 2019)
    • #34321
      Carlos Quiles
      Keymaster

      Updated to version 2.04.53, including new data from (and updates to previously reported) early farmers of Anatolia, South-East and Central Europe, from Marchi et al. bioRxiv (2020).

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