Dear David, Nick, Iosif...let's set the record straight

Almost a decade ago scientists at the David Reich Lab extracted DNA from the remains of three men from the Khvalynsk II cemetery at the northern end of the Pontic-Caspian (PC) steppe.

These Eneolithic Eastern Europeans showed significant genetic heterogeneity, with highly variable levels of Eastern Hunter-Gatherer (EHG) and Near Eastern-related ancestry components.

As a result, the people at the David Reich Lab concluded that the Eneolithic populations of the PC steppe formed from a relatively recent admixture between local hunter-gatherers and Near Eastern migrants.

Unfortunately, this view has since become the consensus among scientists working with ancient DNA.

I say unfortunately because there's a more straightforward and indeed obvious explanation for the genetic heterogeneity among the samples from Khvalynsk II. It's also the only correct explanation, and it doesn't involve any recent gene flow from the Near East.

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

- EHG is best represented by samples from Karelia and Lebyazhinka, which are modern-day Russian localities in the forest zone and on the border between the steppe and the forest-steppe, respectively

- Khvalynsk II is also located on the boundary between the steppe and the forest-steppe, and very far from the Near East

- so the genetic structure of the people buried at Khvalynsk II does represent an admixture event

- however, this admixture event simply involved an EHG population from the forest-steppe and a very distantly Near Eastern-related group native to the steppe (that is, two different Eastern European populations).

I've written this blog post because I think David Reich, Nick Patterson, Iosif Lazaridis and colleagues should finally admit that they didn't quite get this right. And it'd be nice if they could put out a paper sometime soon in which they set the record straight.

See also...

Dear Iosif #2

In my last blog post I made a mistake in my interpretation of this quote from Lazaridis, Alpaslan-Roodenberg et al., because it confused the crap out of me:

However, the complete lack of association of R-haplogroup descendants and EHG ancestry in either Armenia or Iran is consistent with either a massive dilution of EHG ancestry in these populations resulting in the dissociation of Y-chromosome lineages from autosomal ancestry over time, or with a scenario in which R-M269 was not associated with substantial EHG ancestry to begin with.

I thought they meant that they couldn't find any Eastern European hunter-gatherer (EHG) ancestry in samples from Armenia or Iran bearing Y-chromosome R1b-M269.

Of course, they did find EHG ancestry in these individuals, it's just that they couldn't establish an association specifically between this type of ancestry and Y-haplogroup R1b.

That is, males with Y-haplogroup R1b in Armenia, Iran and everywhere else generally show about the same level of EHG ancestry as their ethnic kin with other Y-haplogroups.

But so what? Why mention this when discussing the origins of R1b-M269, when it has absolutely no value in this context?

Y-haplogroups aren't linked directly to autosomal DNA, and Lazaridis, Alpaslan-Roodenberg et al. are obviously aware of this (hence their point about the potential massive dilution of EHG ancestry).

In regards to the origins of R1b-M269, and the provenance of West Asian R1b-M269, the really powerful observation is that R1b-M269 shows up rather late and suddenly in the West Asian ancient DNA record along with EHG and steppe ancestry.

That, and the fact that Eastern Europe is an ancient R1b hotbed (while West Asia a desert), means there's virtually no chance that R1b-M269 is native to West Asia. In other words, there was no R1b-M269 in West Asia until the steppe people brought it there from north of the Caucasus.

See also...

Dear Iosif...

Dear Iosif #3

But Iosif, what about the Phrygians?

Dear Iosif, about that ~2%

Dear Iosif...Yamnaya

Fully automated graph exploration

Scientists at Broad MIT are working on a new feature-packed and "lightning fast" version of Admixtools that runs in R. It's already available via this link...

uqrmaie1.github.io/admixtools

I don't have access to a Linux machine right now, but since this thing runs in R then it also runs in Windows, and I do have a Windows computer here.

One of the most interesting and useful features in the new R package is arguably the find_graphs function, which automatically searches for admixture graphs that reflect the observed f-statistics. That is, once the user chooses the samples and settings, find_graphs runs an unsupervised admixture graph analysis.

Here are a couple of graphs that I knocked out with find_graphs in about five minutes each. The commands and settings that I used are listed in a text file here.

The two topologies above were among the most commonly seen in a series of about 50 runs with the same sample set. A couple of basic inferences based on the output:

- RUS_Progress-Vonyuchka_En harbors GEO_Kotias-Satsurblia_HG-related ancestry, not IRN_Ganj_Dareh_N-related ancestry

- IRN_Ganj_Dareh_N and TKM_Geoksyur_En form a clade to the exclusion of GEO_Kotias-Satsurblia_HG.

The results are certainly in line with those from other types of analyses that I've done on this blog (for instance, see here and here).

Update 05/01/21: Robert Maier, one of the creators of Admixtools2, has left this message in the comments below.

I'm glad to see that there is so much interest in Admixtools2! I very much appreciate any comments and suggestions on how to improve it and how to make it more user friendly.

Because it's still under active development, some things are likely to change in the future. For example, there is a faster successor to "find_graphs", called "find_graphs2", but in the future they will probably be merged into one.

I'm in David Reich’s group at Harvard and Broad and we are hoping to publish a paper describing Admixtools2 where we illustrate its value by using it to test how robust several previously published results are by exploring a large number of alternative models for each of them. If any of you use Admixtools2 to find graphs that are significantly better fits than published graphs and are also historically plausible - or if you find families of graphs that are equally good fits to the published ones but provide qualitatively different conclusions about population relationships - please contact us. That would be a meaningful contribution to the paper we write about this and we’d be open to including someone as a co-author based on identifying case studies like this.

Yamnaya-related ancestry proportions in present-day Poles

Modeling ancient ancestry proportions in present-day Europeans with the qpAdm software is now a lot more difficult. The reasons for this are updates to qpAdm as well as the availabiity of more useuful outgroups or right pops.

This isn't necessarily a bad thing, because users are forced to work harder to find successful models, which is likely to lead to some interesting discoveries. But it can be very frustrating.

I don't think that settling for poor statistical fits or using a small number of outrgoups are acceptable short cuts. Perhaps sequencing modern-day samples in exactly the same way as the ancient samples, and thus increasing the compatability between them, might help?

Limiting qpAdm runs to higher quality SNPs from transversion sites does help, but perhaps largely because of the significant reduction in markers?

In any case, I've now given up on running such analyses, at least until I see some serious pointers on the topic from Harvard's qpAdm experts. But before I put this project to bed for the time being, I'd like to share some new results for Poles from eastern and western Poland, respectively.

right pops:

CMR_Shum_Laka_8000BP
MAR_Taforalt
IRN_Ganj_Dareh_N
Levant_PPNB
GEO_CHG
TUR_Barcin_N
RUS_Piedmont_En
SRB_Iron_Gates_HG
WHG
RUS_Karelia_HG
MNG_North_N
RUS_Ust_Kyakhta

left pops:

Polish_East
CWC_Baltic_early 0.572±0.024
SWE_TRB 0.428±0.024
chisq 11.776
tail prob 0.300296
Full output

Polish_West
CWC_Baltic_early 0.587±0.021
SWE_TRB 0.413±0.021
chisq 11.165
tail prob 0.34478
Full output

Even using transversion sites, this is one of the very few combinations of ancient reference samples that works for the Poles with these right pops. That is, the combination of early Corded Ware samples from the East Baltic (CWC_Baltic_early) and Funnel Beaker samples from Scandinavia (SWE_TRB). The former are obviously the proxy here for Yamnaya-related ancestry.

Adding any sort of hunter-gatherer population to this model doesn't help or even makes things worse (for instance, see here and here). It is possible to add Baltic hunter-gatherers to a similar model after dropping CWC_Baltic_early in favor of closely related samples from the Early to Middle Bronze Age Pontic-Caspian steppe. Note, however, that the statistical fits are somewhat poorer.

Polish_East
Baltic_LTU_Narva 0.032±0.014
PC_steppe_EMBA 0.483±0.019
SWE_TRB 0.485±0.019
chisq 17.143
tail prob 0.0465198
Full output

Polish_West
Baltic_LTU_Narva 0.031±0.011
PC_steppe_EMBA 0.491±0.015
SWE_TRB 0.477±0.016
chisq 22.444
tail prob 0.00757421
Full output

Interestingly, but not surprisingly, the ancestry of many present-day Northwestern European populations can be modeled in basically the same way. That's because ancient ancestry proportions are more closely correlated with latitude than longitude across much of the European continent.

English_Kent
CWC_Baltic_early 0.527±0.024
SWE_TRB 0.473±0.024
chisq 13.042
tail prob 0.221357
Full output

Icelandic
CWC_Baltic_early 0.586±0.023
SWE_TRB 0.414±0.023
chisq 16.517
tail prob 0.085751
Full output

Scottish
CWC_Baltic_early 0.583±0.021
SWE_TRB 0.417±0.021
chisq 12.144
tail prob 0.275536
Full output

A zip file with the qpAdm output from this analysis and a list of the most relevant ancients is available here. I might try to run a few more populations over the next few days, but probably only from the northern half of Europe, so please check the zip file in a week or so to see what else is in there.

If anyone wants to challenge my results, note that these and very similar samples are freely available to the public via Harvard University here and here.

Update 22/08/2020: From Nick Patterson (Broad) in the comments:

My general advice for qpAdm is 1) Work on the right hand set. Don't include irrelevant population (except for one population as an outgroup); picking the best RHS can dramatically reduce s. errors on the admixture weights. 2) If qpAdm gives a very low p-value try and understand why, sometimes it is telling you that the target is not a mixture of the sources but sometimes the assumptions are violated, for example recent gene-flow from left pops -> right.

See also...

Ancient ancestry proportions in present-day Europeans

Villabruna people existed in Europe at least 17,000 years ago (Bortolini et al. 2020 preprint)

Over at bioRxiv at this LINK. So, like I said here a few years back, there was no migration into Europe from the Near East ~14,00 years ago. I don't think there was even such a migration ~17,000 years ago. My view is that the so called Villabruna cluster formed somewhere in Europe at least 20,000 years ago. Below is the Bortolini et al. abstract, emphasis is mine:

The end of the Last Glacial Maximum (LGM) in Europe (~16.5 ka ago) set in motion major changes in human culture and population structure. In Southern Europe, Early Epigravettian material culture was replaced by Late Epigravettian art and technology about 18-17 ka ago at the beginning of southern Alpine deglaciation, although available genetic evidence from individuals who lived ~14 ka ago opened up questions on the impact of migrations on this cultural transition only after that date. Here we generate new genomic data from a human mandible uncovered at the Late Epigravettian site of Riparo Tagliente (Veneto, Italy), that we directly dated to 16,980-16,510 cal BP (2σ). This individual, affected by a low-prevalence dental pathology named focal osseous dysplasia, attests that the very emergence of Late Epigravettian material culture in Italy was already associated with migration and genetic replacement of the Gravettian-related ancestry. In doing so, we push back by at least 3,000 years the date of the diffusion in Southern Europe of a genetic component linked to Balkan/Anatolian refugia, previously believed to have spread during the later Bolling/Allerod warming event (~14 ka ago). Our results suggest that demic diffusion from a genetically diverse population may have substantially contributed to cultural changes in LGM and post-LGM Southern Europe, independently from abrupt shifts to warmer and more favourable conditions.

Bortolini et al., Early Alpine human occupation backdates westward human migration in Late Glacial Europe, bioRxiv, posted August 10, 2020, doi: https://doi.org/10.1101/2020.08.10.241430

See also...

Villabruna cluster =/= Near Eastern migrants

The great and the good

Here's a quote from a new paper on the impact of genetics, and especially ancient DNA, on archeology and linguistics co-authored by archeologist James Mallory and geneticist Oleg Balanovsky:

Just as the genetic evidence for a steppe homeland appeared to weaken a popular theory (among archaeologists more than linguists) that the Indo-European languages spread from an Anatolian homeland with the spread of farming and the AF genetic signature, a new complication arose: the steppe signal that is found from Ireland to the Yenisei comprises an admixture of EHG and CHG. Such an admixture would appear to involve two deep sources that should have developed separately over the course of thousands of years; in short, there is no reason to believe that the two components spoke closely related languages or even belonged to the same language families. Such a model suggested that Proto-Indo-European may have originated out of the merger of two very different language families, a theory that had once had been suggested by several linguists but had never attained anything remotely resembling consensus [62]. If one does not accept an “admixture language” then the natural question remains: did Proto-Indo-European evolve out of language spoken by EHG or out of language spoken by CHG? So genetics has pushed the current homeland debate into several camps: those who seek the homeland either in the southern Caucasus or Iran (CHG) and those who locate it in the steppelands north of the Caucasus and Caspian Sea (EHG). DOI: https://doi.org/10.1134/S1022795419120081

Make no mistake, this is, in common parlance, total horsehit. That's because:

- if we go back far enough, every goddamn human population that ever existed is a mixture of genetically highly diverged earlier populations, but this obviously doesn't mean that all languages are creoles

- in fact, the so called CHG/EHG mixture that Balanovsky and Mallory are talking about was already present on the Pontic-Caspian steppe around 4,300 BCE, and probably much earlier, so it's likely that it first emerged there before the existence of anything even resembling an Indo-European language

- come to think of it, I'm not aware of any tradition in historical linguistics that requires language families to be directly traced back to specific Mesolithic hunter-gatherer populations. So, with all due respect to Mallory and Balanovsky, it looks like they pulled that theory out of their hats.

The impression that I've been getting for a while now is that the great and the good at various major academic institutions are having a rather difficult time interpreting the ancient DNA data relevant to the Indo-European homeland debate. Why? I don't have a clue. Someone should e-mail them and ask. Feel free to let me know what they say in the comments below.

See also...

A final note for the year

A note on Steppe Maykop

Did South Caspian hunter-fishers really migrate to Eastern Europe?