Ancient phylogeography: spread of haplogroups R1b, R1a and N

haplogroups-r1a-r1b-q

The previous post showed the potential use of TreeToM to visualize ancient DNA samples in maps together with their Y-DNA phylogenetic trees. I have written Newick trees for Y-chromosome haplogroups R1b-L388 (encompassing R-V1636 and R-P297, which in turn split into R-M73 and R-M269), R1a, and N.

I have reviewed some of the BAM files from my previous bulk analyses with YLeaf v.2, to add information that I had not previously included in the All Ancient DNA Dataset, and which might be relevant to the proper depiction of phylogenetic trees; in particular, positive and negative SNPs potentially distinguishing archaicRead the rest “Ancient phylogeography: spread of haplogroups R1b, R1a and N”

The Lusatian culture, the most likely vector of Balto-Slavic expansions

early-bronze-age-languages-europe

New archaeological paper (behind paywall) New evidence on the southeast Baltic Late Bronze Age agrarian intensification and the earliest AMS dates of Lens culinaris and Vicia faba, by Minkevičius et al. Vegetation History and Archaeobotany (2019).

Interesting excerpts (emphasis mine):

Arrival of farming in the south-east Baltic

The current state of research reveals no firm evidence of crop cultivation in the region before the LBA (Piličiauskas et al. 2017b; Grikpėdis and Motuzaitė-Matuzevičiūtė 2018). Current archaeobotanical data firmly suggest the adoption of farming during the EBA to LBA transition. (…) By comparison, in other parts of N Europe subsistence economy

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Volosovo hunter-gatherers started to disappear earlier than previously believed

volosovo-corded-ware

Recent paper (behind paywall) Marmot incisors and bear tooth pendants in Volosovo hunter-gatherer burials. New radiocarbon and stable isotope data from the Sakhtysh complex, Upper-Volga region, by Macānea, Nordqvist, and Kostyleva, J. Archaeol. Sci. (2019) 26:101908.

Interesting excerpts (emphasis mine):

The Sakhtysh micro-region is located in the Volga-Oka interfluve, along the headwaters of the Koyka River in the Ivanovo Region, central European Russia (Fig. 1). The area has evidence of human habitation from the Early Mesolithic to the Iron Age, and includes altogether 11 long-term and seasonal settlements (Sakhtysh I–II, IIa, III–IV, VII–XI, XIV) and four artefact scatters (sites

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Genetic continuity among Uralic-speaking cultures in north-eastern Europe

east-europe-bronze-age

The recent study of Estonian Late Bronze Age/Iron Age samples has shown, as expected, large genetic continuity of Corded Ware populations in the East Baltic area, where West Uralic is known to have been spoken since at least the Early Bronze Age.

The most interesting news was that, unexpectedly for many, the impact of “Siberian ancestry” (whatever that actually means) was small, slow, and gradual, with slight increases found up to the Middle Ages, compatible with multiple contact events in north-eastern Europe. Haplogroup N became prevalent among Finnic populations only through late bottlenecks, as research of modern … Read the rest “Genetic continuity among Uralic-speaking cultures in north-eastern Europe”

R1a-Z280 and R1a-Z93 shared by ancient Finno-Ugric populations; N1c-Tat expanded with Micro-Altaic

Two important papers have appeared regarding the supposed link of Uralians with haplogroup N.

Avars of haplogroup N1c-Tat

Preprint Genetic insights into the social organisation of the Avar period elite in the 7th century AD Carpathian Basin, by Csáky et al. bioRxiv (2019).

Interesting excerpts (emphasis mine):

After 568 AD the Avars settled in the Carpathian Basin and founded the Avar Qaganate that was an important power in Central Europe until the 9th century. Part of the Avar society was probably of Asian origin, however the localisation of their homeland is hampered by the scarcity of historical and archaeological

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Aquitanians and Iberians of haplogroup R1b are exactly like Indo-Iranians and Balto-Slavs of haplogroup R1a

eba-indo-iranian-balto-slavs

The final paper on Indo-Iranian peoples, by Narasimhan and Patterson (see preprint), is soon to be published, according to the first author’s Twitter account.

One of the interesting details of the development of Bronze Age Iberian ethnolinguistic landscape was the making of Proto-Iberian and Proto-Basque communities, which we already knew were going to show R1b-P312 lineages, a haplogroup clearly associated during the Bell Beaker period with expanding North-West Indo-Europeans:

From the Bronze Age (~2200–900 BCE), we increase the available dataset from 7 to 60 individuals and show how ancestry from the Pontic-Caspian steppe (Steppe ancestry) appeared throughout Iberia

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ASoSaH Reread (II): Y-DNA haplogroups among Uralians (apart from R1a-M417)

corded-ware-yamna-ancestry

This is mainly a reread of from Book Two: A Game of Clans of the series A Song of Sheep and Horses: chapters iii.5. Early Indo-Europeans and Uralians, iv.3. Early Uralians, v.6. Late Uralians and vi.3. Disintegrating Uralians.

“Sredni Stog”

While the true source of R1a-M417 – the main haplogroup eventually associated with Corded Ware, and thus Uralic speakers – is still not known with precision, due to the lack of R1a-M198 in ancient samples, we already know that the Pontic-Caspian steppes were probably not it.

We have many samples from the north Pontic area since Read the rest “ASoSaH Reread (II): Y-DNA haplogroups among Uralians (apart from R1a-M417)”

Common pitfalls in human genomics and bioinformatics: ADMIXTURE, PCA, and the ‘Yamnaya’ ancestral component

invasion-from-the-steppe-yamnaya

Good timing for the publication of two interesting papers, that a lot of people should read very carefully:

ADMIXTURE

Open access A tutorial on how not to over-interpret STRUCTURE and ADMIXTURE bar plots, by Daniel J. Lawson, Lucy van Dorp & Daniel Falush, Nature Communications (2018).

Interesting excerpts (emphasis mine):

Experienced researchers, particularly those interested in population structure and historical inference, typically present STRUCTURE results alongside other methods that make different modelling assumptions. These include TreeMix, ADMIXTUREGRAPH, fineSTRUCTURE, GLOBETROTTER, f3 and D statistics, amongst many others. These models can be used both to probe whether assumptions of the model

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