R1a-Z280 from Early Bronze Age Northern Poland

PL_N17, an Early Bronze Age genome from Gustorzyn, Northern Poland, recently uploaded to the European Nucleotide Archive (ENA) under accession number SAMN04633627, belongs to Y-chromosome haplogroup R1a-Z280.

R1a-Z280 today shows very high frequencies (>50%) and relatively high SNP diversity in Northern Poland. This is a strong argument for genetic continuity in Northern Poland since the Early Bronze Age.

The analysis was run by Vladimir Tagankin from YFull, who, I'm told, is also pretty sure that PL_N17 falls under SNP R-S24902.

Interestingly, R-S24902 is an extremely rare marker that currently appears to be most common in Northwestern Europe. But I'd say that there are two very good reasons for this: 1) most Y-chromosomes tested at this sort of level are from Northwestern Europe and 2) today Northwestern Europe shows higher genetic diversity than Eastern Europe. So I expect this pattern to be repeated for many other high resolution ancient Y-chromosome samples from Central and Eastern Europe.

Update 19/06/2017: Here's a Principal Component Analysis (PCA) featuring PL_N17 alongside several other ancient samples from Poland and the Czech Republic.

See also...

R1a1a from an Early Bronze Age warrior grave in Poland

Testing for genetic continuity in Poland from the Bronze Age to the present

qpAdm tour of Europe: Mesolithic to Neolithic transition

For a while now I've been trying to work out a way to model present-day Europeans with qpAdm as a mixture of Neolithic and Mesolithic populations. It hasn't been easy, because often what works for some Europeans doesn't work for others. But I've finally figured it out.

The trick is to account for Siberian, East Asian and Sub-Saharan ancestry, by including the Nganasan from Siberia, Onge from the Andaman Islands, and Yoruba from West Africa, respectively, as reference pops.

Below is the spreadsheet with the results and outgroups. Judging by the chisq and tail prob, most of the fits aren't spectacular, but as far as I can tell, they work.

Moreover, in the entire analysis not a single standard error reached 2%. Based on my experience with qpAdm, that's a remarkable thing for such a complex analysis, and I think it suggests that the reference populations are relevant.

Interestingly, while, as expected, the Nganasan-related admixture peaks in far Northern Europe, the Onge-related ancestry is, perhaps surprisingly, most pronounced in Southern Europe. Any ideas why? My thoughts on that here.

Update 014/01/2017: If you guys want to reproduce my analysis, but you don't have the same dataset, which is more than likely, you should be able to get very similar results using the full Human Origins dataset. Try these reference pops and outgroups.

pleft
Barcin_Neolithic
Caucasus_HG (Kotias)
Eastern_HG (Karelia_HG x2, Samara_HG)
Nganasan
Onge
Western_HG (Hungary_HG, Iberia_HG, Loschbour)
Yoruba (from the HGDP)

pright
AG3-MA1
Chukchi
Han
Karitiana
Kostenki14
Levant_Neolithic
Mbuti (Mbuti.DG x3 from Fu et al.)
Papuan
Satsurblia
Ust_Ishim
Villabruna

If you're seeing "infeasible", then remove the redundant reference population that might be causing problems, usually Yoruba or Nganasan, and run again.

If it's still not working, then maybe your dataset is just too different in some way, perhaps with not enough markers (there should be around 200K SNPs available for these runs).

See also...

Ancient ancestry proportions in present-day Europeans

The puzzle of the early Corded Ware grave

In a recent paper and talk, archaeologist Kristian Kristiansen mentions a very early Corded Ware (CW) burial in Tiefbrunn, Germany; one of a few that contain a hammer-headed bone pin, like those found in Yamnaya and Catacomb graves on the steppe, particularly in the North Caucasus region.

Sr isotope ratios suggest that the older man was non-local, while the young man and the child may be locals. The skulls of all three individuals exhibited signs of severe trauma and they had probably suffered violent deaths.

...

The grave goods consisted of only a flint blade and a hammer-headed bone pin, laid down beside the older male. Such pins are rare in the CW of Central Europe, but common in the Pontic Steppe region where they occur in a variety of forms until they disappear around 2600 BC [38].

All three individuals from this grave had their genomes sequenced as part of The Rise project and were labeled RISE434, RISE435 and RISE436. This is how they cluster in my Principal Component Analysis (PCA) of ancient West Eurasia.

As far as I can tell, based on the Sr isotope ratios from Sjögren K-G, Price TD, Kristiansen K 2016, RISE436 is the older man with the pin and RISE434 the young man (see here).

But if so, what is the likely non-local RISE436 doing as the most western of the Corded Ware samples sequenced to date? And why are the potentially local RISE434 and RISE435 so much more Yamnaya-like than him?

My interpretation of these results is that RISE436 was the descendant of a proto-Corded Ware male migrant from the steppe, and that his mother may have been of pre-Corded Ware farmer stock from Central or East-Central Europe. Note that this individual belongs to the Eastern European Y-chromosome haplogroup R1a, Western European (?) mitochondrial haplogroup U5b1c2, and on the plot above clusters almost exactly half-way between Yamnaya and early European farmers (Europe_EN and Europe_MN).

On the other hand, the young man and infant may derive from a more fully developed Corded Ware community in Central Europe, largely made up of second and third generation migrants from the steppe.

Any other ideas?

Citations...

Sjögren K-G, Price TD, Kristiansen K (2016) Diet and Mobility in the Corded Ware of Central Europe. PLoS ONE 11(5): e0155083. doi:10.1371/journal.pone.0155083

Allentoft et al., Population genomics of Bronze Age Eurasia, Nature 522, 167–172 (11 June 2015) doi:10.1038/nature14507

The Metal Age invader that never was #2

I just figured out how the Metal Age invader that never was came about. Take a look at this slide from an FTDNA presentation by Dr. Michael Hammer.

Hammer's taken the ADMIXTURE analysis from Lazaridis et al. 2013 and labeled the clusters according to what he thinks they represent. FTDNA then basically copied the analysis and the cluster labels for their "Ancient Origins" test.

But those clusters do not represent what Hammer thinks they do, in other words ancient populations like Western Hunter-Gatherers (WHG) or Ancient North Eurasians (ANE). Ancient ancestry proportions are listed in other parts of the Lazaridis et al. paper, like table S.14.10.

Moreover, Hammer appears to be under the impression that the Metal Age invader (that never was) came from Asia, and today it is the Kalasha people of the Hindu Kush who carry the highest ancestry proportion from this ancient population (that, of course, never actually was).

First of all, the Bronze Age Yamnaya pastoralists and related groups (i.e. the real Metal Age invaders) expanded both into Europe and Asia from the Pontic-Caspian Steppe. Obviously, the Pontic-Caspian Steppe is located in what is now known as Eastern Europe, not Asia.

Secondly, the Kalasha people carry about the same amount of Yamnaya-related ancestry as present-day Northern and Eastern Europeans, not three or four times as much, which, as per the figure above, is what Hammer seems to think.

Formal stats-based Yamnaya-related (or Steppe_EMBA) ancestry proportions for Europeans are listed in Haak et al. 2015 and for South Asians, including the Kalasha, in Lazaridis et al. 2016. See below.

See also...

Who's your (proto) daddy Western Europeans?

Late PIE ground zero now obvious; location of PIE homeland still uncertain, but...