- This topic has 40 replies, 1 voice, and was last updated 1 day, 16 hours ago by Carlos Quiles.
- March 2, 2020 at 11:50 am #27555Carlos QuilesKeymaster
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
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.
- March 4, 2020 at 10:08 am #27627Carlos QuilesKeymaster
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.
- March 7, 2020 at 9:33 pm #27825Carlos QuilesKeymaster
I have updated the file with SNP inferences of samples from Sirak et al. (2019).
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).
- March 8, 2020 at 6:29 pm #27888Carlos QuilesKeymaster
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.
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
- March 8, 2020 at 6:37 pm #27889Carlos QuilesKeymaster
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.
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.
- March 12, 2020 at 8:57 pm #27936Carlos QuilesKeymaster
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:
I have also updated all maps of Y-DNA.
- March 13, 2020 at 9:52 am #27943Carlos QuilesKeymaster
Updated with Sicilian Epigravettian, Mesolithic, and Early Neolithic samples from van de Loosdrecht et al. bioRxiv (2020).
- March 16, 2020 at 10:54 am #27974Carlos QuilesKeymaster
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).
- March 23, 2020 at 9:57 am #28188Carlos QuilesKeymaster
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.
- March 31, 2020 at 8:22 am #28724Carlos QuilesKeymaster
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.
- April 6, 2020 at 9:17 am #29041Carlos QuilesKeymaster
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.
- April 9, 2020 at 6:53 pm #29159Carlos QuilesKeymaster
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
- April 9, 2020 at 8:21 pm #29160Carlos QuilesKeymaster
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.
- April 17, 2020 at 10:53 am #29327Carlos QuilesKeymaster
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)
- April 22, 2020 at 10:53 am #29599
- May 8, 2020 at 10:38 am #29795
- May 21, 2020 at 12:50 pm #29856Carlos QuilesKeymaster
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.
- June 10, 2020 at 12:32 pm #30280Carlos QuilesKeymaster
Update to version 1.93 with automated SNP calls from genotypes shared by Kolgeh (as suggested in comments).
- June 17, 2020 at 12:23 pm #30352Carlos QuilesKeymaster
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.
- June 19, 2020 at 9:49 am #30358Carlos QuilesKeymaster
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.
- June 23, 2020 at 9:35 am #30513Carlos QuilesKeymaster
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:
- June 26, 2020 at 6:35 pm #30560
- July 5, 2020 at 2:08 pm #30720
- July 6, 2020 at 8:50 pm #30724Carlos QuilesKeymaster
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.
- July 7, 2020 at 10:14 pm #30725Carlos QuilesKeymaster
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).
- July 21, 2020 at 9:55 am #31004Carlos QuilesKeymaster
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.
- August 2, 2020 at 1:57 pm #31292Carlos QuilesKeymaster
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).
- August 4, 2020 at 6:12 pm #31316Carlos QuilesKeymaster
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).
- August 11, 2020 at 8:20 pm #31425
- August 20, 2020 at 9:06 am #31461Carlos QuilesKeymaster
Updated to version 2.02.24, including samples and mtDNA reported in Harney, Cheronet et al. bioRxiv (2020).
- August 24, 2020 at 4:53 pm #31470Carlos QuilesKeymaster
Updated to version 2.02.30, including data recently shared by Svetoslav Stamov from the upcoming Reich Lab paper on SE Europe.
- August 26, 2020 at 8:52 pm #31514Carlos QuilesKeymaster
Updated to version 2.02.33 with some updated Y-SNP calls from the FTDNA team.
- September 9, 2020 at 8:32 pm #31541Carlos QuilesKeymaster
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.
- September 15, 2020 at 10:45 am #31683Carlos QuilesKeymaster
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
- October 6, 2020 at 9:41 am #32225Carlos QuilesKeymaster
- October 13, 2020 at 12:28 pm #32347Carlos QuilesKeymaster
Version 2.04.10 with new/updated samples from Ning et al. bioRxiv (2020).
- October 21, 2020 at 12:51 pm #32627Carlos QuilesKeymaster
Updated to version 2.04.24 with new/updated data (among others) from:
- Longobards at Collegno and Szólád by FTDNA (including some updates to Z2123 samples with YLeaf).
- Updated SNPs from ancient samples in YFull’s YTree and MTree, now including specific Denisovan (DN) and Neanderthal (ND) clades.
- Ancient SE Asian samples from Guam in Pugach et al. bioRxiv (2020), and from Vanuatu in Lipson et al. Curr. Biol. (2020).
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.
- November 4, 2020 at 11:45 am #33473Carlos QuilesKeymaster
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.
- November 13, 2020 at 10:10 pm #33926Carlos QuilesKeymaster
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*.
- November 20, 2020 at 10:19 pm #34291Carlos QuilesKeymaster
Updated to version 2.04.50 with very interesting updates to the I Haplogroup Tree from FTDNA. Information by Göran Runfeldt:
- 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)
- 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)
- November 24, 2020 at 4:29 pm #34321Carlos QuilesKeymaster
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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