Yamnaya-related admixture in Bronze Age northern Iberia

The question of when ancient steppe or Yamnaya-related ancestry first entered Iberia is crucial to the Proto-Indo-European (PIE) homeland debate.

If the steppe or Kurgan PIE hypothesis is correct, then we'd expect this to have happened during the Bronze Age rather than, say, the Medieval Period with the migrations into Iberia of Northern Europeans likely rich in Yamnaya-related admixture like the Visigoths. That's because Indo-European languages are attested in Iberia as early as the Iron Age.

And indeed, the earliest Iberian sample in my dataset to show Yamnaya-related ancestry is Iberia_BA ATP9 from Gunther et al. 2015, dated to 3,700–3,568 C14 cal yBP or the Middle Bronze Age. This has not been reported before, but I'm certain that my finding will be confirmed sooner or later in scientific literature.

Let's start with a basic Principal Component Analysis (PCA) featuring ATP9 alongside a wide range of modern-day and ancient samples from West Eurasia and South Central Asia.

Clearly, ATP9 is shifted east, closer to Yamnaya, relative to the earlier Iberia Chalcolithic (Iberia_ChL) group, and almost clusters with Basques, who are known to harbor significant Yamnaya-related ancestry (see here). I can use formal statistics as well as models based on formal statistics to investigate this in more detail.

Mbuti Yamnaya_Samara Iberia_ChL Iberia_BA D 0.0031 Z 0.859
Mbuti Yamnaya_Samara Iberia_ChL Basque_French D 0.0086 Z 5.035
Mbuti Yamnaya_Samara Basque_French Iberia_BA D -0.0044 Z -1.316

Surprisingly, based on those D-stats ATP9 doesn't appear to share more drift with Yamnaya Samara relative to Iberia_ChL (Z<3). But I suspect this might be due to inflated hunter-gatherer ancestry in Iberia_ChL, so let's try something a little different.

Western_HG Yamnaya_Samara Iberia_ChL Iberia_BA D 0.0188 Z 4.987
Western_HG Yamnaya_Samara Iberia_ChL Basque_French D 0.024 Z 13.163
Western_HG Yamnaya_Samara Basque_French Iberia_BA D -0.0063 Z -1.768

OK, that's basically in line with the PCA above, and I can cement this finding with the qpAdm algorithm. Note the nice chunk of Early Bronze Age steppe (Steppe_EBA) ancestry in ATP9.

Outgroups
AG3-MA1
Chukchi
Dusun
Igorot
Iran_Neolithic
Karitiana
Kosipe
Kostenki14
Lebbo
Levant_Neolithic
Mbuti
Satsurblia
Ust_Ishim
Villabruna

Iberia_BA ATP9
Caucasus_HG 0.038±0.063
Lengyel_LN 0.683±0.066
Steppe_EBA 0.177±0.087
Western_HG 0.102±0.044
chisq 5.216 tail_prob 0.876272

Spanish
Caucasus_HG 0.014±0.028
Lengyel_LN 0.607±0.028
Nganasan 0.011±0.016
Onge 0.013±0.022
Steppe_EBA 0.273±0.043
Western_HG 0.059±0.020
Yoruba 0.021±0.006
chisq 1.605 tail_prob 0.978452

Basque_French
Lengyel_LN 0.590±0.027
Nganasan 0.009±0.016
Onge 0.015±0.022
Steppe_EBA 0.285±0.031
Western_HG 0.096±0.019
Yoruba 0.006±0.006
chisq 3.485 tail_prob 0.900346

Of course, Basques are not Indo-Europeans, so the fact that ATP9 has some Yamnaya-related ancestry doesn't necessarily mean she was an Indo-European. However, it's not unreasonable to assume that the ancestors of Basques incurred gene flow from early Indo-Europeans moving into the Iberian Peninsula, and this probably explains their relatively high level of Yamnaya-related ancestry. So ATP9 may well have spoken an Indo-European language, and if not, then like Basques she probably has Indo-European ancestry

See also...

qpAdm tour of Europe: Mesolithic to Neolithic transition

First look at Latvian and Ukrainian ancient genomes

Below are three plots featuring ancient genomes from the recent Jones et al. paper on the Neolithic transition in the East Baltic and Ukraine. The relevant data is available here, and compatible with my Days of High Adventure, Basal-rich K7 and Global 10 analyses, respectively.

See anything interesting? Feel free to share it in the comments. Please note, however, that I can't guarantee that the results will make perfect sense for all of these samples, most of which have mean genome-wide coverage of less than 1x.

Citation...

Jones at al., The Neolithic Transition in the Baltic Was Not Driven by Admixture with Early European Farmers, Current Biology, Published Online: February 02, 2017, DOI: http://dx.doi.org/10.1016/j.cub.2016.12.060

See also...

No game changer

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...

So how many of you really read the preprints at bioRxiv?

There's a new preprint at bioRxiv about the spread of the plague across much of Eurasia via the expansions of Early Bronze Age steppe pastoralists. It's been up for a few days now. Judging by the number of tweets on the preprint, a lot of people have read it. Or have they?

The manuscript contains a glaring error, a couple times over, in which the authors mix up the Afanasievo Culture with the Andronovo Culture. That's OK, this is why we have preprints and bioRxiv. I just found it somewhat amusing to see one lonely voice pointing this out under the rash of tweets recommending the paper.

Update 20/12/2016: A corrected version of the preprint has just been posted at bioRxiv. See here.

The Metal Age invader that never was

FTDNA has launched a new "Ancient Origins" analysis, and I've been asked a few times now what I think of the "Metal Age invader" component in this test. Essentially, I share the view of one of the commentators in the comments here.

FTDNA now models Europeans as a mix of hunter-gatherers (Loschbour, La Brana 1 and Motala), early European farmers (Stuttgart, Iceman, LBK) and so called "Metal Age invaders" which are based on Corded Ware and Yamnaya samples - so the latter is what we more typically call "steppe admixture". (Plus they add non-European admixture in case someone has it very evidently.) This model looks crude for our present-day standards, and their results look very different from what I've seen here in Davidski's analyses or in other ancient-DNA calculators on Gedmatch, as their inferred proportions of steppe admixture are much lower, about half of that inferred by others. And moreover to me it looks completely wrong that FTDNA suggests that I (1/4 Italian, strong southwest European component) have more Metal Age invader admixture than my fully East Prussian grandmother.

Indeed, any Early Bronze Age Steppe-inspired component should peak at 40-50% amongst Northern and Eastern Euros. This apparently doesn't. Why? No idea.

I know better than almost anyone else that there's no such thing as a perfect ancestry test, and FTDNA has every right to offer an experimental analysis to its clients, so let's leave it at that. But if you want to see what an ADMIXTURE test with a half-decent Yamnaya component looks like, then check out my attempt HERE. These are graphs from the linked blog entry showing inferred levels of Yamnaya-related ancestry proportions for Europeans and West Asians.

See also...

Massive migration from the steppe is a source for Indo-European languages in Europe (Haak et al. 2015 preprint).

Wolfgang Haak et al., Massive migration from the steppe is a source for Indo-European languages in Europe, bioRxiv, Posted February 10, 2015, doi: http://dx.doi.org/10.1101/013433

See also...

The Metal Age invader that never was #2

Who's your (proto) daddy Western Europeans?

Big deal of 2016: the territory of present-day Iran cannot be the Indo-European homeland

It's been a pretty big year. Not as big as many of us had hoped for, but there's still a few more weeks till 2017, so who knows what will happen?

In any case, for me 2016 will be the year in which we finally saw hard data - courtesy of Lazaridis et al. and Broushaki at al. - that crossed off the territory of present-day Iran from the list of potential Proto-Indo-European (PIE) homelands.

Now, it's true, Lazaridis et al. and Broushaki et al. were somewhat vague in what their data meant in this context, and indeed, both sets of authors left open the possibility that what is now Iran might prove to be the PIE homeland. However, their data left no doubt: look elsewhere for the PIE Urheimat.

Why? Here it is, in point form, as simply as I can put it:

- the Mesolithic and Neolithic peoples of the Zagros range and South Caspian region were highly distinct both in terms of genome-wide genetic structure and uniparental markers, and clearly only contributed meaningful gene flow to South Asia, not to Europe or Anatolia

- after the descendants of Neolithic farmers from the Zagros range, or at least their very close relatives, migrated to South Asia, the territory of present-day Iran, as per the data in Lazaridis et al. and Broushaki et al., saw waves of migrations from the west and north that dramatically shifted the population structure of the region, bringing it closer in this respect to the Levant and Europe

- most of the Neolithic samples from Iran in Lazaridis et al. and Broushaki et al. came from near the proto-Elamite homeland in the Kor River basin in central Fars, which strongly suggests that their close relatives who streamed into South Asia were not Indo-Europeans, but rather speakers of languages closely related to Elamite

- even though Lazaridis et al. successfully modeled Early/Middle Bronze Age steppe populations, including Yamnaya, as largely of Iran Chalcolithic origin, this appeared to be a coincidence, because the Chalcolithic samples from Iran showed fairly typical South Caspian uniparental markers, such as Y-chromosome haplogroups J and G1 and mitochondrial (mtDNA) haplogroup U7, which are conspicuous by their absence from an exceptionally wide range of Bronze Age steppe samples.

I do realize that many readers won't accept these arguments for emotional reasons, because the PIE homeland debate is an emotional one for a lot of people. Nevertheless, if you decide to argue with me in the comments, make sure you have a coherent argument.

Actually, the territory of present-day Iran has never been a serious contender in the PIE homeland debate. This is something that many Iranian scholars will freely admit.

Not only was central Fars the proto-Elamite homeland, but much of what is now western Iran was the stomping ground of the Hurrians. The Indo-Europeans, in the form of Indo-Iranians such as the Medes, only got there late in the game, in all likelihood from the Eurasian steppes.

But a lot of newbies to the PIE debate don't know this, or they don't want to know it. I guess to them Iran makes sense because it's in between Europe and South Asia? Or maybe it's the fact that the word Iran is kind of similar to the word Aryan? No idea, really, but like I say, it's now all over.

See also...

A homeland, but not the homeland

Zarathushtra and his steppe posse

The story of mtDNA haplogroup U7

Days of high adventure

I've redesigned and streamlined my Principal Component Analysis (PCA) plot of West Eurasia in anticipation of the arrival of many more ancient samples. Rumor has it we'll not only get stuff from the Balkans, but also finally from the steppes north of the Black Sea and South Asia.

I'd say my new plot does a better job of highlighting relationships between the different prehistoric groups and population shifts across space and time. The datasheet is available here.

It should be pretty clear from this plot how the modern-day European gene pool came about. So I don't expect any major surprises when the new samples come in. Nevertheless, the wait is killing me, and many others I'm sure.

Update 13/11/2017: A year on, I've acquired many new samples and, as a result, streamlined the PCA some more, see...

Who's your (proto) daddy Western Europeans?