Y-DNA of 129 high quality shotgun ancient samples

ftdna-shotgun-samples-map

The Reich Lab has recently pre-published high quality shotgun sequencing data from 216 ancient individuals within the framework of the Allen Ancient Genome Diversity Project / John Templeton Ancient DNA Atlas. Metadata for the 216 genomes are available here.

Their median coverage is 4.9x, and among them there are 50 high coverage genomes (17-36x), but there are also samples with a coverage similar to the previously published ones.

The FamilyTreeDNA Haplotree team formed by phylogeneticist Michael Sager and Göran Runfeldt from the R&D team has analyzed all 129 males for Y-SNP calls, using – and updating with them – … Read the rest “Y-DNA of 129 high quality shotgun ancient samples”

Iron Age nomads of West Siberia of hg. Q1b, R1a, and basal N1a-L1026

scythian-iron-age-sakas-ancient-dna

Open access Ancient genomic time transect from the Central Asian Steppe unravels the history of the Scythians, by Gnecchi-Ruscone et al. Sci Adv. 7 (13) eabe4414.

Interesting excerpts (emphasis mine):

From an archaeological perspective, the earliest IA burials associated with nomad-warrior cultures were identified in the eastern fringes of the Kazakh Steppe, in Tuva and the Altai region (ninth century BCE).

Following this early evidence, the Tasmola culture in central and north Kazakhstan is among the earliest major IA nomad warrior cultures emerging (eighth to sixth century BCE).

iron-age-scythians-sarmatians

These earlier groups were followed by the iconic Saka cultures located

Read the rest “Iron Age nomads of West Siberia of hg. Q1b, R1a, and basal N1a-L1026”

Another “Pre-Yamnaya” sample from the Northern Caucasus?

wang-caucasus-maykop

I have updated the Ancient DNA Dataset, including a lot of new information from – among other sources – the latest version of Reich Lab curated Dataset, now renamed Allen Ancient DNA Resource (AADR). This includes new columns:

  1. Object-ID: I am now using whenever possible the Master-ID; Version-ID for a quick identification of the ‘best’ sample to include in SmartPCA or ADMIXTURE runs; and Index as a key with a unique reference number for each sample. That should make for enough stable references for any external tool to use the data.
  2. mtDNA: Added mtDNA coverage
Read the rest “Another “Pre-Yamnaya” sample from the Northern Caucasus?”

IBD sharing between Corded Ware and Yamnaya-related populations

yamnaya-corded-ware

Oral communication Ancient DNA and the New Science of the Human Past by David Reich (March 3, 2021).

I noticed this interesting slide called “Caught red-handed”, at approximately 45m 17s, where David Reich asserts that sampled Corded Ware populations had many “close cousins” with Yamnaya-related populations “within generations”. The method could also be used, always according to Reich, to identify “who the Yamnaya mixed with to form groups like Corded Ware”.

NOTE. Notice also the the number of new sampled individuals from Khvalynsk, Ekaterinovka, and new Yamnaya groups from Chelyabinsk, Urals, Volga, Don, Moldova, and Romania.

This represents the … Read the rest “IBD sharing between Corded Ware and Yamnaya-related populations”

Germanic runes in the Prague-Type Pottery culture

slavic-prague-type-pottery-culture

Recent paper (behind paywall) Runes from Lány (Czech Republic) – The oldest inscription among Slavs. A new standard for multidisciplinary analysis of runic bones by Macháček et al. J. Archaeol Sci (2021).

Interesting excerpts (emphasis mine):

To date no archaeological find is generally accepted as evidence for a direct contact between Germanic tribes and Early Slavs in Central Europe (Brather, 2004). Here we report a novel archaeological find in support of a direct contact: a rune-inscribed fragment of a bone from the late 6th century found in a Slavic settlement. Runes are an alphabetic script, called fuþark,

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The importance of archaeology before population genomics

early-mesolithic-scandinavia

Recent paper First encounters in the north: cultural diversity and gene flow in Early Mesolithic Scandinavia, by Manninen et al. Antiquity (2021).

The authors criticize the model laid out in Günther et al. (2018), whereby the origin of the previously defined Mesolithic Scandinavian hunter-gatherer genetic group (SHG) was defined as an admixture between genetically defined WHG and EHG populations that migrated into Scandinavia from two separate Ice Age refugia: the south (WHG) and north (EHG). This dualistic model was further associated with two specific lithic blade technologies present in Early Mesolithic Scandinavia (Sørensen et al. 2013), as summarized … Read the rest “The importance of archaeology before population genomics”

Proto-Indo-Europeans: A family business

khvalynsk-yamnaya-y-dna-bottleneck

I have been updating the Ancient DNA Dataset with date estimates published in the recent preprint by Sedig, Olalde, Patterson & Reich bioRxiv (2020), and it had a reference to some interesting new samples from Khvalynsk, showing tight family connections.

Information below is taken from the preprint and from the latest version of the Reich Lab’s Allen Ancient DNA Resource (AADR). Information about the three published Khvalynsk samples is taken from Mathieson et al. Nature (2015) supplementary materials, and each ID features a different font color in the text below for clarity’s sake.

Khvalynsk Family A

I0434, … Read the rest “Proto-Indo-Europeans: A family business”

R1b in Eastern Arabia Late Neolithic / Bronze Age

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A reader asked my opinion about my reported R1b subclade of one low quality sample from Ra’s Al-Ḥamrāʾ 5 necropolis, Muscat (Oman), published (without Y-DNA) in Harney et al. (2020). For those interested, here are the relevant calls, with information on the graves taken from Salvatori (2007):

I11919_I11920_I11921: Grave 221 (ca. 3700-3200 BC), mtDNA H2a2a1, Y-DNA R1bL754 (xPH155; xL389P297M269; xPF6323PF6292).
* The samples show a straightforward path (but full of deamination question marks): CT (with 1 ancestral call M5813 1x C-A) -PP295M45P284P226 -KM526YSC0000186 Read the rest “R1b in Eastern Arabia Late Neolithic / Bronze Age”

The Last of the Single Gravers

the-last-of-the-mohicans

The BAM files from Egfjord et al. (2021) are out, and Y-SNPs of two-year-old Nordic MN_LN/LN migrant Gjerrild 5 (ca. 2284-2035 calBC) were accurately reported, which means that the sample will need to be labelled R1b>L754>L389>(pre-?)V1636, since one derived read Y125110+ (A->G) in this and one ancestral in a Progress2 sample, PG2001, cannot be used to infer anything certain.

NOTE. It has one derived read (A-T) for FT3897 at the R1b>L754>L389>V1636>Y83069 level, but the other 8 SNPs ancestral, which is not really helpful to define a potential pre-Y83069 branch, given the doubts above. A possible relative could Read the rest “The Last of the Single Gravers”