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Monday, June 29, 2015

K8 results for selected Allentoft et al. genomes


Running the ancient genomes from Allentoft et al. in ADMIXTURE is proving a challenge. The reasons for this are covered in the paper; see section 6.2 in the supp info. Fortunately, I managed to obtain robust outcomes using my K8 model for ten samples representing almost all of the main ancient groups studied by the authors.

The spreadsheet with the results is here. Below you can see a Principal Component Analysis (PCA) produced with the data. Click on the image to go to my drive, where you can download a high quality copy.



Some of the outcomes might look unusual, but as I say, they are solid. I double checked each one with an unsupervised ADMIXTURE test and genotype-based PCA. For instance, the genotype-based PCA featuring RISE247 and RISE479, respectively, look like this:



Citation...

Allentoft et al., Bronze Age population dynamics, selection, and the formation of Eurasian genetic structure, Nature 522, 167–172 (11 June 2015) doi:10.1038/nature14507

See also...

Bell Beaker, Corded Ware, EHG and Yamnaya genomes in the fateful triangle

Sunday, June 28, 2015

R1b from Vučedol period Hungary


Via the Bell Beaker Blogger:

It is noteworthy that the R1b occurred first after the Middle Chalcolithic in Transdanubia. (Late Chalcolithic has not been not examined yet, and so a hiatus remains between the Middle Chalcolithic and the Early Bronze Age data.) The two R1b samples are dated to the Vučedol period (~2,870-2,580 cal BC) and to the Gáta/Wieslburg culture (~1,950- 1,760 cal BC). R1b is the most frequent haplogroup in today’s Europe, with a frequency peak in Western Europe (Balaresque et al., 2010). From prehistoric context, this haplogroup is known from the Late Neolithic Central Germany (Bell Beaker culture, Lee et al., 2012). The theory that R1b reached Central Europe (and possibly the Carpathian Basin as well) with the Bell Beaker migration, starting from southwestern Europe (Brandt et al., 2014) seems to be collapsing, as R1b (M269) has recently been found in Yamnaya (3,300-2,700 cal BC) population on the Russian steppe as well (Haak et al., 2015).

The other Vučedol period sample belongs to I2a2. Also worth noting is the J2 from the Late Neolithic Sopot/Lengyel remains.


Source: Szecsenyi-Nagy, Anna (2015) Molecular genetic investigation of the Neolithic population history in the western Carpathian Basin, Dissertation

Friday, June 26, 2015

Genetic substructures among Late Neolithic/Bronze Age Scandinavians


I may have discovered an interesting pattern in the Allentoft et al. data. It seems that during the Late Neolithic/Bronze Age, Scandinavia was populated by two somewhat different populations; one characterized by Y-Chromosome haplogroup R1b and a genome-wide genetic structure typical of present-day Northwestern Europeans, and another by Y-Chromosome haplogroup R1a and a relatively more eastern genome-wide genetic profile.

Below are two Principal Component Analyses (PCA), both featuring ancient Swedish genomes classified as part of the Late Neolithic Battle-Axe archeological culture. However, the first sample clusters near present-day Norwegians and belongs to Y-haplogroup R1b-U106, which is nowadays typically known as a Germanic paternal marker. On the other hand, the second sample clusters among present-day Russians and Mordovians, from all the way near the Volga, and belongs to Y-haplogroup R1a-Z645, which very likely expanded from Eastern Europe during the Late Neolithic.




Here's another example of basically the same thing, but this time with two ancient genomes from Denmark. If you're having trouble finding the ancient samples, download the PDF files and type their IDs in the PDF search field.



Coincidence? Probably not, but we obviously need more samples to confirm these results and establish that there is indeed a pattern.

Citation...

Allentoft et al., Bronze Age population dynamics, selection, and the formation of Eurasian genetic structure, Nature 522, 167–172 (11 June 2015) doi:10.1038/nature14507

Monday, June 22, 2015

First look at an ancient genome from Neolithic Anatolia


Felix at GGT is in the process of uploading the genomes from the recent Pinhasi et al. paper. The file for the early Neolithic sample from Barcin, Turkey, is basically ready. I analyzed it with my K8 model and got these results (click on the image to enlarge).


I was only able to use a couple hundred SNPs for the test, so the outcome can't be taken too seriously. But it does make sense. The lack of Ancient North Eurasian (ANE) ancestry isn't surprising, because it mirrors the results of early European farmers we've seen to date.

Moreover, the relatively high level of Western European Hunter-Gatherer (WHG) ancestry, or at least something very similar, is also in line with expectations, considering that the sample was dug up in far western Anatolia, almost on the European border.

I also ran an Identical-by-State (IBS) affinity test using the Human Origins dataset and around 1800 SNPs. The results broadly back up the K8 analysis, with southern Europeans topping the list.


Citation...

Pinhasi R, Fernandes D, Sirak K, Novak M, Connell S, Alpaslan-Roodenberg S, et al. (2015) Optimal Ancient DNA Yields from the Inner Ear Part of the Human Petrous Bone. PLoS ONE 10(6): e0129102. doi:10.1371/journal.pone.0129102

See also...

The Near East ain't what it used to be

Oase 1: An early modern human from Romania with a recent Neanderthal ancestor


The Y-chromosome belongs to macrohaplogroup F and the mtDNA to macrohaplogroup N. For details see the supp info PDF here. The full paper is freely available here.

Abstract: Neanderthals are thought to have disappeared in Europe approximately 39,000–41,000 years ago but they have contributed 1–3% of the DNA of present-day people in Eurasia1. Here we analyse DNA from a 37,000–42,000-year-old2 modern human from Peştera cu Oase, Romania. Although the specimen contains small amounts of human DNA, we use an enrichment strategy to isolate sites that are informative about its relationship to Neanderthals and present-day humans. We find that on the order of 6–9% of the genome of the Oase individual is derived from Neanderthals, more than any other modern human sequenced to date. Three chromosomal segments of Neanderthal ancestry are over 50 centimorgans in size, indicating that this individual had a Neanderthal ancestor as recently as four to six generations back. However, the Oase individual does not share more alleles with later Europeans than with East Asians, suggesting that the Oase population did not contribute substantially to later humans in Europe.

Qiaomei Fu et al., An early modern human from Romania with a recent Neanderthal ancestor, Nature (2015) doi:10.1038/nature14558