The Bacho Kiro surprise (Hajdinjak et al. 2021)

Over at Nature at this LINK. The paper focuses on Neanderthal ancestry in Initial Upper Paleolithic (IUP) humans from what is now Bulgaria. But, to me, much more interesting is the claim by its authors that present-day East Asians harbor ancient European, or, at least, European-related ancestry. From the paper, emphasis is mine:

When we explored models of population history that are compatible with the observations above using admixture graphs [28], we found that the IUP Bacho Kiro Cave individuals were related to populations that contributed ancestry to the Tianyuan individual in China as well as, to a lesser extent, to the GoyetQ116-1 and Ust’Ishim individuals (all |Z| < 3; Fig. 2d, Supplementary Information 6). This resolves the previously unclear relationship between the GoyetQ116-1 and Tianyuan individuals [13] without the need for gene flow between these two geographically distant individuals.

...

In conclusion, the Bacho Kiro Cave genomes show that several distinct modern human populations existed during the early Upper Palaeolithic in Eurasia. Some of these populations, represented by the Oase1 and Ust’Ishim individuals, show no detectable affinities to later populations, whereas groups related to the IUP Bacho Kiro Cave individuals contributed to later populations with Asian ancestry as well as some western Eurasian humans such as the GoyetQ116-1 individual in Belgium. This is consistent with the fact that IUP archaeological assemblages are found from central and eastern Europe to present-day Mongolia [5,15,16] (Fig. 1), and a putative IUP dispersal that reached from eastern Europe to East Asia. Eventually populations related to the IUP Bacho Kiro Cave individuals disappeared in western Eurasia without leaving a detectable genetic contribution to later populations, as indicated by the fact that later individuals, including BK1653 at Bacho Kiro Cave, were closer to present-day European populations than to present-day Asian populations [29,30].

Hajdinjak, M., Mafessoni, F., Skov, L. et al. Initial Upper Palaeolithic humans in Europe had recent Neanderthal ancestry. Nature 592, 253–257 (2021). https://doi.org/10.1038/s41586-021-03335-3

See also...

Ust'-Ishim belongs to K-M526

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

Ancient ancestry proportions in present-day Europeans (to be continued)

This year has already been massive in all sorts of ways, including for new data and software releases. So I'm thinking it might be time to update many of the analyses that were featured at this blog a while ago.

Let's start with the classic hunter vs farmer vs herder mixture model for present-day European populations. The rules of the game are as follows:

- run the latest version of qpAdm using qpfstats output

- use transversion sites and 1240K capture data

- pick a set of diverse and chronologically sound outgroups

- for a model to be successful the p-value must reach 0.01

- tweak the left pops in models that are clearly underperforming

- follow high end scientific literature, logic and common sense

Obviously, the reason that I decided to limit my analysis to markers from transversion sites is to mitigate problems associated with modeling the ancestry of modern, high quality samples with relatively low quality ancients. One of these problems appears to be qpAdm assigning faux East Asian/Siberian admixture to present-day Europeans (for instance, see figure 4 here).

My starting reference populations and outgroups are listed below. In qpAdm terminology the former are known as the "left pops", while the latter as the "right pops". Most of these samples are freely available at the David Reich Lab website here.

left pops:

HUN_Koros_N_HG
TUR_Barcin_N
UKR_Yamnaya

right pops:

CMR_Shum_Laka_8000BP
MAR_Taforalt
Levant_Natufian
IRN_Ganj_Dareh_N
Levant_PPNB
CZE_Vestonice16
BEL_GoyetQ116-1
Iberia_ElMiron
RUS_Karelia_HG
RUS_West_Siberia_HG
MNG_North_N
RUS_Ust_Kyakhta

As you can see, I picked a wide variety of right pops. But I chose most of them specifically to be able to differentiate the three streams of ancestry - from ancient hunters, farmers and herders - that are the focus of my analysis. I also intentionally avoided using samples in the right pops that may have experienced gene flow, including cryptic gene flow, from the populations in the left pops.

I somewhat speculatively earmarked HUN_Koros_N_HG, from the Early Neolithic Carpathian Basin, and UKR_Yamnaya, from the Early Bronze Age North Pontic steppe in what is now Ukraine, to represent the hunter-gatherer and pastoralist streams of ancestry, respectively.

That's because I expected HUN_Koros_N_HG to be the best proxy for the hunter-gatherer ancestry that was initially absorbed by the early farmers who fanned out from the Aegean region across much of the European continent, and of course it made sense to choose a steppe pastoralist population that was located close to Central Europe where such groups first made the biggest impact outside of the steppe.

Interestingly, HUN_Koros_N_HG and UKR_Yamnaya did prove to be among most effective choices for the types of ancestries that they represented. For instance, UKR_Yamnaya generally produced much stronger statistical fits than a very similar set of Yamnaya samples from the Caspian steppe (more precisely, from the Samara region in Russia). However, this might well be an artifact, due to very specific characteristics of these few ancient individuals. Larger sample sets would be welcome, especially from Yamnaya sites in Ukraine.

Below, dear audience, is a spreadsheet featuring the preliminary results. Click on the image to view and/or download the spreadsheet. The general rule is that the higher the tail prob, or p-value, the more likely it is that the ancestry proportions are close to the truth (a tail prob of well below 0.05 is usually a strong indication that something isn't right). For a detailed look at each of the qpAdm runs, feel free to consult the zip file here.

Note, however, that many of the European groups in my burgeoning genotype dataset are yet to make an appearance in the spreadsheet. That's because their models with the standard left pops showed p-values well under 0.01, which essentially meant that they failed, and I'm still trying to make them work.

But round one has certainly revealed some fascinating stuff. For instance, except for Hungarians and Estonians, none of the Uralic-speaking groups can be modeled successfully in the standard three-way model.

However, I managed to significantly improve the statistical fits in their models by adding a Siberian population, RUS_Baikal_BA, to the left pops. This is unlikely to be a coincidence, because the Proto-Uralic homeland was almost certainly located in or very near Siberia. Iain Mathieson please take note.

Saami
HUN_Koros_N_HG 0.134±0.043
RUS_Baikal_BA 0.270±0.015
TUR_Barcin_N 0.081±0.026
UKR_Yamnaya 0.515±0.058

chisq 19.865

tail prob 0.0108571

Full output

See also...

Yamnaya-related ancestry proportions in present-day Poles

Don't believe everything you read in peer reviewed papers

Case in point, here's a quote from a recent paper at the Journal of Human Genetics (emphasis is mine):

The Mordovian and Csango samples have a moderate to slight orientation toward the Central-Asian and Siberian Turkic groups. This could suggest the more significant East Eurasian or Turkic ancestry of these populations, which should be further investigated. German samples are inhomogeneous, and some of the German samples also show this tendency, which can be the result of the recent 20th century Turkish immigration into Germany [42].

Nope, these German samples don't show anything even remotely resembling recent Turkish ancestry. The authors of the paper, Ádám, V., Bánfai, Z., Maász, A. et al., should've been able to figure this out, even with the standard analyses that they ran. Failing that, the peer reviewers at the Journal of Human Genetics should've noticed that the authors were confused.

Moreover, if the authors and peer reviewers actually bothered to take a closer look at metadata for these samples, which were sourced from the Estonian Biocentre, they'd see that they're not even from Germany. In fact, they represent self-reported ethnic Germans from Russia.

My own quick and dirty analysis of these individuals suggests that many of them harbor East Slavic and/or Volga Finnic ancestries. Indeed, only some of them can pass genetically for run of the mill Germans from Germany. The Principal Component Analysis (PCA) below is self-explanatory. It was plotted with the Vahaduo Custom PCA tools freely available here. The relevant PCA datasheet can be gotten here.

That's not to say, of course, that some Germans don't have recent Turkish ancestry, because an increasing number of Germans nowadays do, nor that people with German heritage in Russia shouldn't identify as Germans, because that's entirely their choice.

This blog post isn't about what it takes to be German, and this is not something that I ever want to discuss for obvious reasons. The point I'm making here is that the authors and peer reviewers of the said paper at the Journal of Human Genetics were sloppy and half-arsed in their approach. And, sadly, this isn't an isolated case in peer reviewed scientific literature dealing with human population genetics.

I feel that the Estonian Biocentre is also partly to blame for this cock up, due to its somewhat peculiar sampling and labelling strategies. For instance, its scientists rely solely on self-reported identity to establish the ethnic origins of their samples, and they apparently never remove genetic outliers from their datasets or even try to identify them.

Unfortunately, I fear that this relaxed approach will eventually lead to basic errors and even unusual conclusions in a number of so called peer reviewed papers.

I first raised this issue with the Estonian Biocentre about five years ago, when I noticed that some of the supposedly Polish individuals in its dataset were genetically more similar to various groups from northern Russia than to Poles from Poland. These individuals also showed significant Siberian ancestry, which was very unusual indeed. Where the hell did the Estonian Biocentre find Poles who resembled people from near the Arctic Circle, you might ask? Apparently in Estonia.

OK, I can imagine that sampling ethnic Poles from Estonia may have been easier for the Estonian Biocentre than sampling Poles from Poland. And Estonian Poles certainly make for interesting and useful data points. However, as you can see in the PCA below, some of these individuals (labeled Polish_Estonia by me) aren't representative of the native Polish population, and yet the Estonian Biocentre not only lumps them with their Poles from Poland, but even labels them with the word "Poland". The relevant PCA datasheet can be gotten here.

However, based on my communications with some of the scientists at the Estonian Biocentre, including head honcho Mait Mestpalu, it seems that nothing will ever change there in regards to this issue. Who knows, perhaps some day we'll see a paper based on Estonian Biocentre data in the Journal of Human Genetics claiming that Poles originated near the Arctic Circle? I wouldn't be shocked if that actually happened.

Citation...

Ádám, V., Bánfai, Z., Maász, A. et al. Investigating the genetic characteristics of the Csangos, a traditionally Hungarian speaking ethnic group residing in Romania. J Hum Genet (2020). https://doi.org/10.1038/s10038-020-0799-6

See also...

Like three peas in a pod

Interesting times ahead

The map below made a big impression on me. Can't wait to see all of these ancient samples online. More details here.

See also...

Is Yamnaya overrated?

Y-haplogroup R1a and mental health

Getting the most out of the Global25

Evidence of European ancestry in the Philistines

The abstract below has just appeared at the European Nucleotide Archive (see here), so I'm guessing that the relevant paper and accompanying ancient genome-wide data will be published within weeks if not days. Emphasis is mine:

The ancient Mediterranean port-city of Ashkelon, identified as “Philistine” during the Iron Age, underwent a dramatic cultural change between the Late Bronze- and the early Iron- Age. It has been long debated whether this change was driven by a substantial movement of people, possibly linked to a larger migration of the so-called “Sea Peoples”. Here, we report genome-wide data of ten Bronze- and Iron- Age individuals from Ashkelon. We find that the early Iron Age population was genetically distinct due to a European related admixture. Interestingly, this genetic signal is no longer detectible in the later Iron Age population. Our results support that a migration event occurred during the Bronze- to Iron- Age transition in Ashkelon but did not leave a long-lasting genetic signature.

Update 4/7/2019: The paper is now available at Science Advances [LINK]. One of the Ashkelon ancients, who also shows a relatively high level of European ancestry, belongs to Y-Chromosome haplogroup R1 (probably R1b-M269). I've updated my Global25 datasheets with the new samples. Look for the Levant_ISR_Ashkelon prefix. Same links as always...

Global25 datasheet ancient scaled

Global25 pop averages ancient scaled

Global25 datasheet ancient

Global25 pop averages ancient

This is how they cluster in my Principal Component Analysis (PCA) of ancient West Eurasian genetic variation. The relevant datasheet is available here. Based on these results, it's tempting to think that the European ancestry in the Philistines may have been of Greek provenance. But keep in mind that this is just a two dimensional view and a simplification of reality. I'll have more to say about the ancestry of these individuals and the origins of the Philistines in future blog posts.

See also...

Five foot Philistines

How did steppe ancestry spread into the Biblical-era Levant?

Blast from the past: Matters of basic geography

I'm re-posting this article from 2017 for the benefit of some Science News journalists, who are apparently having major problems dealing with basic geography. That's because they think that the Yamnaya culture was located in Asia rather than Eastern Europe. Take my advice and don't read Science News whatever you do. It might rot your brain.

...


The steppe north of the Black Sea in Ukraine has basically always been considered a part of Europe, and just over 100 years ago some guy with a map decided that the steppe between the eastern coast of the Black Sea in Russia and the Ural River in western Kazakhstan should also be Europe.

So nowadays, right or wrong, it's generally accepted that the entire steppe region west of the Ural River, known as the Pontic-Caspian steppe, is in Eastern Europe. Here's a map courtesy of Wikipedia showing how the official boundary between Eastern Europe and Asia has shifted since the 18th century.

But this decision wasn't entirely arbitrary, because the current boundary between Eastern Europe and Asia by and large follows several major geographic barriers, including the Caucasus Mountains, the Caspian Sea and the Ural Mountains. It'd be hard to argue that these barriers haven't had a profound impact across the ages on the character of Europe and its people, and this has probably been known for well over a couple hundred years.

For instance, if we're to trust the most common interpretations of the works of ancient geographers like Hecataeus and Herodotus, then their worlds in some important ways resembled the typical Principal Component Analysis (PCA) of West Eurasian genetic variation. And it seems that they had a pretty good idea where both the strong continental boundaries and fuzzy areas were located.

Below, on the geographic map inspired by Herodotus, Europa or Europe is delineated from much of Asia by the Black Sea, the Caucasus Mountains and the Caspian Sea, while on the genetic map, most European and Asian populations form two, more or less parallel, clusters fairly cleanly separated by empty space (this was first noted in Lazaridis et al. 2013). Indeed, this empty space is the work of the Black Sea, the Caucasus Mountains and the Caspian Sea acting as rather effective barriers to gene flow between Eastern Europe and Asia (see Yunusbayev et al. 2012).

However, on the genetic map, the Iranic Scythians of the Asian steppes straddle my somewhat arbitrary red line separating Europa and Asia, and this is echoed on the Herodotus map by Iranic and related peoples like the Massagetae and Issedones, who inhabit the seemingly undefined part of the world between Europa and Asia east of the Caspian Sea (Mare Caspium).

Nothing really ground breaking, but pretty cool stuff.

On a related note, I've seen the term "mainland Europe" used recently in at least one of the big ancient DNA papers to describe the part of Europe west of the Pontic-Caspian steppe. It seems that the authors wanted to underline the fairly stark genetic difference that existed between most of Europe and the steppe just prior to the expansion of Yamnaya and related steppe herder groups that initiated the formation of the present-day European gene pool.

I can see why they did this, but to my mind they got things backwards. That's because the term mainland implies the opposite of island and/or peninsula, and of course the part of Europe west of the Pontic-Caspian steppe is a relatively narrow strip of land surrounded by water, so it's a peninsula. Let's visualize these two models on a map of Europe courtesy of Wikipedia:

I understand that my model might result in heart palpitations for some readers, especially those from Western Europe, who generally see their part of Europe as core Europe, but I feel that it makes good sense from a purely geographic POV.

See also...

Max Planck scientists: on a mission against geography

Genetic borders are usually linguistic borders too

Matters of geography

The steppe north of the Black Sea in Ukraine has basically always been considered a part of Europe, and just over 100 years ago some guy with a map decided that the steppe between the eastern coast of the Black Sea in Russia and the Ural River in western Kazakhstan should also be Europe.

So nowadays, right or wrong, it's generally accepted that the entire steppe region west of the Ural River, known as the Pontic-Caspian steppe, is in Eastern Europe. Here's a map courtesy of Wikipedia showing how the official boundary between Eastern Europe and Asia has shifted since the 18th century.

But this decision wasn't entirely arbitrary, because the current boundary between Eastern Europe and Asia by and large follows several major geographic barriers, including the Caucasus Mountains, the Caspian Sea and the Ural Mountains. It'd be hard to argue that these barriers haven't had a profound impact across the ages on the character of Europe and its people, and this has probably been known for well over a couple hundred years.

For instance, if we're to trust the most common interpretations of the works of ancient geographers like Hecataeus and Herodotus, then their worlds in some important ways resembled the typical Principal Component Analysis (PCA) of West Eurasian genetic variation. And it seems that they had a pretty good idea where both the strong continental boundaries and fuzzy areas were located.

Below, on the geographic map inspired by Herodotus, Europa or Europe is delineated from much of Asia by the Black Sea, the Caucasus Mountains and the Caspian Sea, while on the genetic map, most European and Asian populations form two, more or less parallel, clusters fairly cleanly separated by empty space (this was first noted in Lazaridis et al. 2013). Indeed, this empty space is the work of the Black Sea, the Caucasus Mountains and the Caspian Sea acting as rather effective barriers to gene flow between Eastern Europe and Asia (see Yunusbayev et al. 2012).

However, on the genetic map, the Iranic Scythians of the Asian steppes straddle my somewhat arbitrary red line separating Europa and Asia, and this is echoed on the Herodotus map by Iranic and related peoples like the Massagetae and Issedones, who inhabit the seemingly undefined part of the world between Europa and Asia east of the Caspian Sea (Mare Caspium).

Nothing really ground breaking, but pretty cool stuff.

On a related note, I've seen the term "mainland Europe" used recently in at least one of the big ancient DNA papers to describe the part of Europe west of the Pontic-Caspian steppe. It seems that the authors wanted to underline the fairly stark genetic difference that existed between most of Europe and the steppe just prior to the expansion of Yamnaya and related steppe herder groups that initiated the formation of the present-day European gene pool.

I can see why they did this, but to my mind they got things backwards. That's because the term mainland implies the opposite of island and/or peninsula, and of course the part of Europe west of the Pontic-Caspian steppe is a relatively narrow strip of land surrounded by water, so it's a peninsula. Let's visualize these two models on a map of Europe courtesy of Wikipedia:

I understand that my model might result in heart palpitations for some readers, especially those from Western Europe, who generally see their part of Europe as core Europe, but I feel that it makes good sense from a purely geographic POV.

See also...

Max Planck scientists: on a mission against geography

Genetic borders are usually linguistic borders too

Recent gene flow from Africa and the Near East into Europe

A new paper at PNAS by Botigué et al. takes a close look at African and Near Eastern admixture in Europe:

Human genetic diversity in southern Europe is higher than in other regions of the continent. This difference has been attributed to postglacial expansions, the demic diffusion of agriculture from the Near East, and gene flow from Africa. Using SNP data from 2,099 individuals in 43 populations, we show that estimates of recent shared ancestry between Europe and Africa are substantially increased when gene flow from North Africans, rather than Sub-Saharan Africans, is considered. The gradient of North African ancestry accounts for previous observations of low levels of sharing with Sub-Saharan Africa and is independent of recent gene flow from the Near East. The source of genetic diversity in southern Europe has important biomedical implications; we find that most disease risk alleles from genome-wide association studies follow expected patterns of divergence between Europe and North Africa, with the principal exception of multiple sclerosis.

The term "recent" is used throughout the paper to describe the IBD results, but as far as I can see there's no mention of any dates. Based on the data in the very thorough Ralph and Coop European IBD study (see here), I'd say that segments of over 1.5cM represent gene flow from well within the past 5,000 years. If this assumption is correct, then the results certainly make a lot of sense. That's because there were well documented historical events that could account for the main outcomes in the figure below: a) low level IBD sharing between Sub-Saharan Africa and much of Southern Europe; b) inflated IBD sharing between North Africa and Southwestern Europe; and c) inflated IBD sharing between Southeastern Europe and the Near East.

I probably don't need to discus in detail what these events might have been. Suffice it to say that the Mediterranean Basin has seen several major empires which facilitated regular population movements between Southern Europe, North Africa and the Near East. This process included the slave trade, which was one of the main economic activities in the region for a couple thousand years.

It's important to note, however, that fastIBD doesn't specify the direction of gene flow. In other words, shared IBD segments can be the result of our ancestors either receiving or giving admixture, or gene flow from a third party. But as Botigué et al. point out, the North African samples which show the highest IBD sharing with Iberians are also those with the lowest European ancestry proportions in the ADMIXTURE analysis (see below). Therefore, it's unlikely that this shared IBD is of European origin in any significant degree.

Key: Canis - Canary Islands; And - Andalusia; Gal - Galicia; Bas - Basques; Spa - Spain; Por - Portugal; Fra - France; Ita - Italy; Tsi - Tuscany; Gre - Greece ; ItaJ - Italian Jews; AshJ - Ashkenazi Jews; Qat - Qatar; NMor - North Morocco; SMor - South Morocco; OccS - Saharawi; Alg - Algeria; Tun - Tunisia; Lib - Libya; Egy - Egypt; Yri - Yoruba from Nigeria; Mkk - Maasai from Kenya.


There's also a PCA in the supplementary PDF which further underlines that most of the IBD sharing between Europe and North Africa, as well as Qatar, is not of European origin, because it creates significant substructures within the European sample.

Unfortunately the Qataris are the only Near Eastern sample used in the study. Then again, if I was to pick a single ethnic group to represent the Near East in an IBD study like this, then Qataris would probably be near the top of the list. That's because they've been affected by population movements from other parts of the Arabian Peninsula and also Persia, but at the same time never experienced significant gene flow from Europe. More information about the genome-wide genetic ancestry of Qataris is available in this recent open-access paper by Omberg et al.

Botigué et al. also make some interesting comments about Jewish genetic ancestry in Europe. The quote below comes from the supplementary PDF.

Another possible hypothesis to explain the increased diversity in southern Europe is that an influx of Jewish ancestry had a heterogeneous effect on genetic diversity in Europe. However, in most European populations here, virtually no Jewish ancestry was detected. On average, 1% of Jewish ancestry is found in Tuscan HapMap population and Italian Swiss, as well as Greeks and Cypriots. This may reflect the higher sharing with Near Eastern populations in the Italian peninsula and southeastern Europe (Fig. 2C) or low levels of gene flow with the early Italian Jewish communities (6). Estimates from the IBD analysis are in agreement with ADMIXTURE estimates that the amount of sharing between these populations is extremely low (SI Appendix, Table S3). Specifically, results of IBD sharing between southwestern Europe and North Africa are two orders of magnitude greater than those found between the same region and Jews, the average WEA for southern Europe and North Africa is 203, while for southwestern Europe and European Jews is 1.3.

Reference...

LR Botigué*, BM Henn*, S Gravel, BK Maples, CR Gignoux, E Corona, G Atzmon, E Burns, H Ostrer, C Flores, J Bertranpetit, D Comas, CD Bustamante, Gene flow from North Africa contributes to differential human genetic diversity in Southern Europe, PNAS, published online before print June 3, 2013, doi: 10.1073/pnas.1306223110

So who's the most (indigenous) European of us all?

Basically, the first map below reveals the answer. It shows the spread of a European specific cluster from a global-wide ADMIXTURE analysis at K=8 (eight ancestral populations assumed), which I call "North European". Thus, genetically, the most European populations are found around the Baltic Sea, and in particular in the East Baltic region. In my genome collection, samples from Lithuania clearly and consistently score the highest percentages in ADMIXTURE clusters specific to Europe. However, I suspect that if I had Latvians with no known foreign ancestry going back more than four generations, they'd come out the "most European". Hopefully we can test that in the near future.

Below are the fifteen Eurogenes sample sets that scored the highest levels of membership in the North European cluster. The list only includes groups with five or more individuals present in the analysis, so some populations, like Estonians or Danes, weren't included, even though they easily made the cut. The spreadsheet with all the results from this run can be seen here. A table of Fst (genetic) distances between the eight clusters is available here.

Lithuanians 77%
Finns 74%
Belorussians 70%
Swedes 69%
Norwegians 68%
Kargopol Russians 68%
Russians 68%
Poles 68%
Erzya 66%
Ukrainians 66%
Moksha 66%
Orcadians 63%
HapMap Utah Americans (CEU) 63%
Irish 63%
British 62%

So why did I pick the results from K=8, and not some other K, like 2, 10, or 25? Well, it's not possible to evaluate who is more European without a European-specific cluster (ie. modal in Europeans, with a low frequency outside of Europe). Provided that a decent number and range of global and West Eurasian samples are used in the analysis, such clusters begin appearing at around K=5 or K=6, and start breaking up into local clusters from about K=9. I found that runs below K=8 produced European clusters that spilled too generously outside of the borders of Europe. On the other hand, runs above K=8 produced European clusters that weren't representative of enough European groups (ie. too localized). But the European cluster from K=8 was pretty much perfect, and I think that's obvious from the map. In fact, I can hardly believe how well it fits the modern geographic concept of Europe - north of the Mediterranean and west of the Urals. Amazing stuff.

There are two other clusters that show up across Europe in non-trivial amounts - Mediterranean and Caucasus (see maps below). These can also be thought of as native European clusters, since they've been on the continent for thousands of years. However, their peak frequencies are found in West Asia, so they're not particularly useful signals of European-specific ancestry.

So what do these three clusters show exactly? They represent certain allele frequencies in modern populations, and in fact, these can change fairly rapidly due to admixture, selection, and genetic drift. So claiming that such clusters represent pure ancient populations is unlikely to be true in most cases, if ever. However, I don't think there's anything wrong in saying that, when robust enough, they can be thought of as signals of ancestry from relatively distinct ancestral groups.

Indeed, anyone who's read up on the prehistory of Europe, knows that there are three general Neolithic archeological waves to consider when trying to untangle the story of the peopling of Europe. These are Mediterranean Neolithic, Anatolian Neolithic and Forest Neolithic (for example, see here).

Mediterranean Neolithic refers to a series of migrations from West Asia via the Mediterranean and its coasts. The areas most profoundly affected by these movements include the islands of Sardinia and Corsica, and the Southwest European mainland. Anatolian Neolithic describes migrations into Europe from modern day Turkey, mostly into the Balkans, but also as far as Germany and France. At the moment, Forest Neolithic of Northeastern Europe is something of a mystery. However, the general opinion is that it was largely the result of native Mesolithic hunter-gatherers adopting agriculture.

Obviously, it's very difficult to dismiss the correlations between these three broad archeological groups and the European and two European/West Asian clusters produced in my K=8 ADMIXTURE analysis. Is it a coincidence that the Mediterranean cluster today peaks in Sardinia, which has been largely shielded from foreign admixture since the Neolithic, and today forms a very distinct Southern European isolate? Why does the North European cluster show the highest peaks in classic Forest Neolithic territory? And why does the Caucasus cluster radiate in Europe from the southeast, which is where Anatolian farmers had the greatest impact? These can't all be coincidences, and I'm willing to bet that none of them are. I'm convinced that the three clusters from my K=8 run are strong signals from the Neolithic, and the North European cluster also from the Mesolithic.

Eventually, these issues will be settled with ancient DNA data, in a much more comprehensive way than ever possible using modern genomes. We've already seen some preliminary results, mostly from Mesolithic, Neolithic and Bronze Age sites around Europe, so perhaps it's useful to ask whether my ADMIXTURE analysis and commentary here mirror these early findings? I think they do. For instance, here's an interesting conclusion regarding the East Baltic area from a study on ancient Scandinavian mtDNA by Malmström et al.

Through analysis of DNA extracted from ancient Scandinavian human remains, we show that people of the Pitted Ware culture were not the direct ancestors of modern Scandinavians (including the Saami people of northern Scandinavia) but are more closely related to contemporary populations of the eastern Baltic region. Our findings support hypotheses arising from archaeological analyses that propose a Neolithic or post-Neolithic population replacement in Scandinavia [7]. Furthermore, our data are consistent with the view that the eastern Baltic represents a genetic refugia for some of the European hunter-gatherer populations.

I suppose there will be people wondering why I didn't take Sub-Saharan African, East Asian, and South Asian admixtures into account in my analysis. The reason is that I wasn't looking at which group was most West Eurasian, or Caucasoid. Based on everything I've seen to date, in my own work as well as elsewhere, the most West Eurasian group would probably be the French Basques from the HGDP. However, the differences between them, and certain groups from Northeastern Europe, like Northern Poles and Lithuanians, really wouldn't be that great anyway. I might do a write up about that at some point.


Credits...

- Maps by Eurogenes project member FR7

- Additional stats by Eurogenes project member DESEUK1


References...

Helena Malmström et al., Ancient DNA Reveals Lack of Continuity between Neolithic Hunter-Gatherers and Contemporary Scandinavians, Current Biology, 24 September 2009, doi:10.1016/j.cub.2009.09.017

Noreen von Cramon-Taubadel and Ron Pinhasi, Craniometric data support a mosaic model of demic and cultural Neolithic diffusion to outlying regions of Europe, Proc. R. Soc. B published online 23 February 2011, doi: 10.1098/rspb.2010.2678