Who's your (proto) daddy Western Europeans?

Considering the increasingly large numbers of paleogenomic samples being released online nowadays, it's no longer practical for me to try to highlight most archaeological cultures and even genetic clusters in my Principal Component Analyses (PCA) of the ancient world. Thus, from now on, I'll be focusing attention in such PCA on the main population shifts that have led to the formation of the modern-day West Eurasian gene pool and genetic substructures, like on the PCA plot below, which includes the new Lipson et al. 2017 data (available at the Reich Lab here).

The relevant PCA datasheet can be gotten here. By grouping several hundred ancient samples into just nine clusters, I'm attempting to highlight four key processes and resulting genetic shifts in Europe, the Near East and Central Asia:

- European forger populations mixing with genetically much more southern early farmers of Near Eastern origin, mostly during the Neolithic, bringing about the total disintegration of the Europe to Siberia Hunter-Gatherer cline

- "Old Europeans" being overrun and largely absorbed by Y-haplogroup R1-rich Kurgan pastoralists from the Pontic-Caspian steppe during the Eneolithic and Bronze Age, leading to the formation of at least one major new cline from the Bronze Age steppe into post-Kurgan expansion Europe

- the ancient Near East "imploding" or becoming significantly more compact in terms of genetic structure, likely due to a variety of major population expansions from the chalcolithic onwards from the eastern and western parts of the Fertile Crescent, as well as probably the Caucasus and Europe (note how the post-Neolithic western Asian cluster stretches out towards Europe)

- fully nomadic and very wide ranging pastoral and warrior cultures dominating the entire Eurasian steppe during the Iron Age, leading to the emergence of progressively more East Asian-admixed populations from west to east across the Eurasian steppe

An interesting outcome of the denser sampling from space and time in West Eurasia is that Y-haplogroup R1b, once so elusive in the ancient DNA record, is now popping up all over the place. The new Lipson et al. dataset, for instance, includes two R1b "Old Europeans" from Blatterhole in Germany dated to the Middle Neolithic. Below is the same PCA as above except with all of the ancients belonging to R1b marked with an X. The two Blatterhole samples are sitting in the largely empty space between the European/Siberian Hunter-Gatherer cline and most of the "Old Europe" cluster. The relevant PCA datasheet is available here.

So it may seem that we're back to square one in the long running effort to pinpoint the origin of Y-haplogroup R1b-L51, which encompasses almost 100% of modern-day Western European R1b lineages, and thus probably ranks as Europe's most common Y-haplogroup. But at this stage I'd say no, because R1b-L51 is a subclade of R1b-M269, of which the oldest sample comes from the Bronze Age steppe. In fact, as can be seen in the above PCA, this sample is sitting in exactly the right spot to be one of those pastoralists who overran "Old Europe", or at least a very close relative thereof.

Or am I wrong? Feel free to let me know in the comments.

I didn't bother creating a similar plot of ancient samples belonging to Y-haplogroup R1a, because, unlike R1b, this marker is still non-existent in samples from outside of Eastern Europe and Siberia dating to before the late Neolithic. And I doubt that this is simply due to a lack of the right ancient material. Moreover, the recent discovery of Y-haplogroup R1a-M417, which encompasses almost 100% of all modern-day R1a lineages on the planet, in a North Pontic steppe sample belonging to the Eneolithic Sredny Stog culture means that it's game over for the naysayers as far as the steppe origin of most modern-day R1a lineages is concerned (see here and here).

In other words, if you're still hoping to see R1a, and especially R1a-M417, pop up in non-steppe derived ancient individuals in, say, such far away places as South Asia, then you'll probably be waiting forever.

For the linguistic implications of all of this, see...

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

Update 15/11/2017: After a couple of days of messing around with the Lipson et al. dataset, I'm certain that Late Copper Age sample Protoboleraz_LCA I2788 shows significant steppe-related admixture. This is the only sample from Lipson et al. with such an obvious signal of steppe-related input that had enough data to be analyzed individually by me with PCA and D-stats.

For the time being, amongst the best proxies for this signal appear to be Yamnaya_Samara and Samara_Eneolithic. But it's likely that the real source of the admixture is yet to enter the ancient DNA record, or at least my dataset. When it does, it'll probably be an Eneolithic pastoralist population from the North Pontic steppe.

Yamnaya_Samara also gives the best statistical fit as the single source population in qpAdm (see here). It's an important result, because it suggests that steppe peoples very similar to Yamnaya were already expanding on and out of the steppe as far back as ~3500 BCE, and perhaps a few hundred years earlier.

See also...

Migration of the Bell Beakers—but not from Iberia (Olalde et al. 2018)

Genetic and linguistic structure across space and time in Northern Europe

I feel that I need to do a double take, and demonstrate more obviously why my new PCA, the one that I introduced in the recent Tollense Valley warrior blog post (see here), should prove very useful for analyzing both genetic and ethnolinguistic links in Northern Europe between modern-day populations and ancient samples, particularly those from late prehistory to early history, which is when the main ethnolinguistic groups that today dominate Northern Europe formed. Judging by some of the reactions in the comments, not everyone was convinced, so let's try this again.

Below is a new version of the said PCA that focuses on several ancient individuals who, based on their archaeological contexts, should show strong genetic affinities to modern-day speakers of Celtic, Germanic and Slavic languages in Northern Europe. These are three Iron Age samples from what is now England, one Iron Age sample from what is now Sweden, and two Medieval samples from what is now Bohemia, Czech Republic, respectively. The relevant datasheet is available here.

And clearly these ancients do show the expected genetic affinities considering where they cluster relative to modern-day Northern Europeans in the two most significant dimensions of genetic variation. Moreover, despite the fact that the Anglo-Saxon and English Iron Age samples were all excavated from sites in eastern England, the Anglo-Saxons cluster between the English Iron Age individuals and the singleton Scandinavian Iron Age sample. This of course makes perfect sense, considering that the Anglo-Saxons were Germanic speakers with recent ancestry from very near to Scandinavia.

So everything seems in good order, and for now it's very difficult for me to consider that those Tollense Valley warriors who cluster alongside modern-day Slavic speakers on my PCA are not ethnolinguistically closer to them than to Celtic and Germanic speakers.

On the other hand, my standard PCA of West Eurasian genetic variation does a comparatively lousy job at matching ethnolinguistic origins with genetic structure, at least in Northern Europe. Note below, for instance, that the same Celtic and Germanic samples from England and Scandinavia form a tight cluster between the two Slavs from Bohemia. Hence, based on this PCA it would be very difficult, perhaps impossible, to correctly predict the ethnolinguistic ties of these ancients just by looking where they cluster relative to modern-day Germanics, Slavs and so on. Right click and open in a new tab to enlarge to the max.

But this is not surprising, because this PCA is based on a wider, more diverse range of populations, and so rather than being dominated by relatively recent, ethnolinguistic-specific genetic drift within Northern Europe, it's much more reflective of deeper, more basic genetic relationships across West Eurasia.

See also...

Tollense Valley Bronze Age warriors were very close relatives of modern-day Slavs

Ancient genomes from NE Europe suggest in tandem spread of Siberian admixture and Uralic languages into the region >3,500 ya

Tollense Valley Bronze Age warriors were very close relatives of modern-day Slavs

This is strongly suggested by the Principal Component Analysis (PCA) below, which shows that many of the Tollense Valley warriors (Welzin_BA) cluster in the Slavic-specific part of the plot. The relevant datasheet is available here.

I designed this PCA with the sole purpose of using Balto-Slavic-specific genetic drift to differentiate Slavs from Germans, except of course those Germans with a lot of Slavic ancestry, who are usually from eastern Germany and Austria. Admittedly, these Welzin_BA samples are preliminary low quality versions, but I can assure you, people who don't harbor significant Slavic ancestry never cluster in this part of the plot.

The only other ancient samples that cluster in the Slavic zone are, as expected, an early Slav from Bohemia and, interestingly, a Bronze Age individual from what is now Hungary. But we've already seen strong genetic, and indeed genealogical, links between another Hungarian Bronze Age genome and present-day Slavs (see figure 3 here).

So what's going on? Did the proto-Slavs come into existence during the Bronze Age, as opposed to the more generally accepted early Medieval Period? And did they expand from what is now Hungary? Or did they migrate there from the Baltic region? Thanks to Matt in the comments for the table below.

See also...

Genetic and linguistic structure across space and time in Northern Europe

Hilariously wrong

From a recent paper at Forensic Science International:

The most commonly found haplogroups [among Lithuanians] are R1a and N, hence it can be argued that Lithuanians originate from Pakistan/Northwest India and East China/Taiwan.

Jankauskiene et al., Population data and forensic genetic evaluation with the YfilerTM Plus PCR Amplification kit in the Lithuanian population, Forensic Science International, DOI: http://dx.doi.org/10.1016/j.fsigss.2017.10.009

For a reality check see here...

R1a: The beast among Y-haplogroups

Finngolians #2

The mad scientists are at it again. The quote below is from an American Society of Human Genetics (ASHG) talk abstract. For the whole thing see here. Now, as I've pointed out on this blog before, Finns do not have Buryat or Mongolian ancestry, or anything even closely related dating to the Middle Ages. What they do have is some sort of Siberian admixture, which has been poorly characterized to date, but is probably associated with archaeologically attested population movements across northern Eurasia during the metal ages.

We identified significant gene flow from the Buryats to the Finnish which was predicted to be occurred in 1,228 (±87) year. Moreover, 13.38% of Buryat admixture was predicted in the Finnish genome.

This sort of nonsense should never be let through peer review anywhere. It makes the ASHG and indeed population genetics look like a total joke. In fact, imagine if such sloppy inferences from population genetics are allowed to influence medical genetics work. Someone might eventually get hurt.

See also...

Finngolians #1

R1a and R1b from an early Mongolian tomb

The beast among Y-haplogroups

A lot has been written about Y-haplogroup R1a over the years. Sadly, most of it was wrong, such as its posited Pleistocene origin in the Indian subcontinent and subsequent migration to Europe.

In all likelihood, R1a was born somewhere in North Eurasia. More importantly, its R1a-M417 subclade, which encompasses almost 100% of modern-day R1a lineages, no doubt came into existence somewhere on the Pontic-Caspian (or Western) steppe in what is now Ukraine and southern Russia just 7,000-6,000 years ago.

And within a couple of thousand years it expanded in almost all directions, probably on the back of the early Indo-European dispersals (see here), to cover a massive range from Scandinavia to South Asia. It is the beast among Y-haplogroups.

The most common subclade of R1a-M417 in South Asia today is R1a-Z93, and, realistically, it couldn't have arrived there earlier than about 2,000BC. So much for the Pleistocene.

See also...

Y-haplogroup R1a and mental health

The Poltavka outlier

Yamnaya isn't from Iran just like R1a isn't from India

Ancient genomes from Neolithic North Africa (Fregel et al. 2017 preprint)

Over at bioRxiv at this LINK. The paper includes three ancient North African Y-haplogroup results: two instances of E-M35 from the Early Neolithic (5300-4800 BCE) and a singleton T-M184 from the Late Neolithic (3780-3650 BCE). Emphasis is mine:

Abstract: One of the greatest transitions in the human story was the change from hunter-gatherer to farmer. How farming traditions expanded from their birthplace in the Fertile Crescent has always been a matter of contention. Two models were proposed, one involving the movement of people and the other based on the transmission of ideas. Over the last decade, paleogenomics has been instrumental in settling long-disputed archaeological questions, including those surrounding the Neolithic revolution. Compared to the extensive genetic work done on Europe and the Near East, the Neolithic transition in North Africa, including the Maghreb, remains largely uncharacterized. Archaeological evidence suggests this process may have happened through an in situ development from Epipaleolithic communities, or by demic diffusion from the Eastern Mediterranean shores or Iberia. In fact, Neolithic pottery in North Africa strongly resembles that of European cultures like Cardial and Andalusian Early Neolithic, the southern-most early farmer culture from Iberia. Here, we present the first analysis of individuals' genome sequences from early and late Neolithic sites in Morocco, as well as Andalusian Early Neolithic individuals. We show that Early Neolithic Moroccans are distinct from any other reported ancient individuals and possess an endemic element retained in present-day Maghrebi populations, indicating long-term genetic continuity in the region. Among ancient populations, early Neolithic Moroccans share affinities with Levantine Natufian hunter-gatherers (~9,000 BCE) and Pre-Pottery Neolithic farmers (~6,500 BCE). Late Neolithic (~3,000 BCE) Moroccan remains, in comparison, share an Iberian component of a prominent European-wide demic expansion, supporting theories of trans-Gibraltar gene flow. Finally, the Andalusian Early Neolithic samples share the same genetic composition as the Cardial Mediterranean Neolithic culture that reached Iberia ~5,500 BCE. The cultural and genetic similarities of the Iberian Neolithic cultures with that of North African Neolithic sites further reinforce the model of an Iberian intrusion into the Maghreb.

Fregel et al., Neolithization of North Africa involved the migration of people from both the Levant and Europe, bioRxiv, Posted September 21, 2017, doi: https://doi.org/10.1101/191569

Ancient IBD/cM matrix analysis offer

I've had a few requests from personal genomics customers to stick their files into an Identity-by-Descent/cM matrix like the one at the link below. Also please check out the accompanying comments thread for ideas of what can be done with the output.

A Bronze Age dominion from the Atlantic to the Altai

I can do this for USD $15 per individual. The deadline for sending through the data files (which, in this run, can only be from 23andMe, Ancestry or FTDNA) is this time Tuesday.

I'll send out the results to each participant over e-mail. However, participants are encouraged to post their results in the comments thread below so that they can be discussed and analyzed further.

Update 20/09/2017: The analysis is underway. Please don't send any more data files. If there's enough interest, I'll do another run soon.

Update 22/09/2017: I've just sent out the results to the participants in the form of two text files titled "ancients_only" and "full_column". The former is a matrix of overall shared haplotype tracts in centimorgans (cM) that includes the user and 65 ancient genomes, and the latter a list of haplotype tracts, also in cM, shared between the user and well over 3000 public samples.

So what can we do with these files? For one, we can look at them, because simply eyeballing these sorts of stats can be very informative. Sorting the data in some way and calculating population averages might help with that.

The "ancients_only" file can be used for slightly more advanced analyses. For instance, below is a Neighbor joining graph produced with the Past 3 program (freely available here). I simply loaded my "ancients_only" file into Past 3, selected all of the columns and rows, and then did this: Multivariate > Clustering > Neighbor joining. Note that I cluster on the same branch as Slav_Bohemia, and this makes perfect sense considering my Polish ancestry. By the way, I dropped Oetzi from this run because he was behaving strangely, which is not unusual for low coverage genomes. Click on the image and open in a new tab for a better view.

Indeed, Past 3 can do a lot of interesting things with matrix files; anything from linear models to rotating three dimensional plots. If you'd like to repeat the linear models from my above linked to blog post, then choose the relevant two columns in your matrix and go Model > Generalized Linear Model. You should see something like this.

Moreover, a matrix with the 3000+ public samples can be gotten here and combined, in part or in whole, with your other files so that you can analyze yourself alongside a larger number of individuals.

So far so good for the Kurgan hypothesis

This is basically what I'm seeing in the ancient DNA published to date. Thus, the Kurgan hypothesis or steppe theory, which, of course, posits that the Proto-Indo-European homeland was on the Pontic-Caspian steppe, is looking really good at this stage. Indeed, unless there are some ancient DNA shocks on the way from, say, Anatolia or the Caucasus, that might buck the trend, then this one's in the bag.

See also...

"The Homeland: In the footprints of the early Indo-Europeans" time map

Genetic borders are usually linguistic borders too

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

A homeland, but not the homeland #2

The Out-of-India Theory (OIT) challenge: can we hear a viable argument for once?

A homeland, but not the homeland #2

Back in May, in a post titled A homeland but not the homeland, I said this:

It seems increasingly likely that ancient DNA has identified a massive expansion, or a series of expansions, from Mesopotamia and/or surrounds in basically all directions dating to the Chalcolithic (ChL) and Bronze Age (BA). This phenomenon is mainly characterized by the simultaneous spread of:

- Iran_ChL-related genome-wide ancestry

- Y-haplogroup J

- South Caspian-specific mitochondrial haplogroups such as R2 and U7

In the same post I also included a list of ancient populations that showed at least two of these characteristics. I can now add two more populations to this list: the Minoans and Mycenaeans.

- Anatolia_BA, Western Turkey, 2836-1800 calBCE (Lazaridis et al. 2017)

- Egyptian mummies, Middle Egypt, 776-2 calBCE (Schuenemann et al. 2017)

- Iran_ChL, Western Iran, 4839-3796 calBCE (Lazaridis et al. 2016)

- Levant_BA, Northwestern Jordan, 2489-1966 calBCE (Lazaridis et al. 2016)

- Minoans, Crete, Greece, 2900-1700 BCE (Lazaridis et al. 2017)

- Mycenaeans, Greece, 1700-1200 BCE (Lazaridis et al. 2017)

- Sidon_BA, Southern Lebanon, 1750-1600 BCE (Haber et al. 2017)

Out of all of these groups, only the Mycenaeans are generally accepted to have been speakers of an Indo-European language. However, they differ from the others in that they harbor minor but significant ancestry from a source, or multiple sources, closely related to Yamnaya, Sinatshta and other Bronze Age peoples of the Pontic-Caspian steppe.

Possible question for the discussion in the comments: what does this say about where the Mycenaeans got their Indo-European language? Also, who wants to bet that Bronze Age samples from the Indus Valley Civilization will too make it onto my list?

See also...

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