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 on their dataset. 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 run 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 samples (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 sample set, but even labels them with the word "Poland". The relevant PCA datasheet can be gotten here.

But, 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

Viking invasion at bioRxiv

A new preprint featuring hundreds of Viking Age genomes has appeared at bioRxiv [LINK]. Titled Population genomics of the Viking world, it looks like a solid effort overall, although I'm skeptical about its conclusions. I might elaborate on that in the comments below, but I'll have a lot more to say on the topic if and when I get to check out the ancient genomes with my own tools. Details about the new samples, including their Y-chromosome haplogroup assignments, are available here. Below is the abstract, emphasis is mine:

The Viking maritime expansion from Scandinavia (Denmark, Norway, and Sweden) marks one of the swiftest and most far-flung cultural transformations in global history. During this time (c. 750 to 1050 CE), the Vikings reached most of western Eurasia, Greenland, and North America, and left a cultural legacy that persists till today. To understand the genetic structure and influence of the Viking expansion, we sequenced the genomes of 442 ancient humans from across Europe and Greenland ranging from the Bronze Age (c. 2400 BC) to the early Modern period (c. 1600 CE), with particular emphasis on the Viking Age. We find that the period preceding the Viking Age was accompanied by foreign gene flow into Scandinavia from the south and east: spreading from Denmark and eastern Sweden to the rest of Scandinavia. Despite the close linguistic similarities of modern Scandinavian languages, we observe genetic structure within Scandinavia, suggesting that regional population differences were already present 1,000 years ago. We find evidence for a majority of Danish Viking presence in England, Swedish Viking presence in the Baltic, and Norwegian Viking presence in Ireland, Iceland, and Greenland. Additionally, we see substantial foreign European ancestry entering Scandinavia during the Viking Age. We also find that several of the members of the only archaeologically well-attested Viking expedition were close family members. By comparing Viking Scandinavian genomes with present-day Scandinavian genomes, we find that pigmentation-associated loci have undergone strong population differentiation during the last millennia. Finally, we are able to trace the allele frequency dynamics of positively selected loci with unprecedented detail, including the lactase persistence allele and various alleles associated with the immune response. We conclude that the Viking diaspora was characterized by substantial foreign engagement: distinct Viking populations influenced the genomic makeup of different regions of Europe, while Scandinavia also experienced increased contact with the rest of the continent.

Margaryan et al., Population genomics of the Viking world, bioRxiv, posted July 17, 2019, doi: https://doi.org/10.1101/703405

See also...

They came, they saw, and they mixed

Who were the people of the Nordic Bronze Age?

Asiatic East Germanics

Modern-day Poles vs Bronze Age peoples of the East Baltic

Below are three of my staple Principal Component Analyses (PCA) featuring Baltic Bronze Age (Baltic_BA) samples from the recent Mittnik et al. 2018 paper (open access here). On each of the plots I've also highlighted modern-day Balts and Poles. The latter two PCA also include most of the other ancients from the said paper (listed here). They're not highlighted, but all of the relevant datasheets are available here, here and here, and easy to plot with the Past software.

No doubt, these Bronze Age peoples of the East Baltic, and in particular the four individuals from Turlojiske, Lithuania, are very closely related to modern-day Balts and northern Slavs. They may well be our ancestors, or at least close relatives thereof. This is argued and demonstrated well enough by Mittnik et al., and it clearly shows in my PCA, especially the first one, which is designed to focus on entho-linguistic-specific genetic drift in Northern Europe.

Nevertheless, overall, they do clearly show a higher cut of indigenous European Hunter-Gatherer ancestry relative to modern-day Northeast Europeans (note how in the second PCA the Baltic_BA samples pull towards the European Hunter-Gatherers compared to Balts and especially Poles). I'm not exactly sure what the explanation is for this yet. Indeed, there might be several different explanations. But generally speaking, it's probably in large part the result of post-Bronze Age gene flow into the Baltic region from Central Europe.

See also...

Early Baltic Corded Ware form a genetic clade with Yamnaya, but...

The genetic history of Northern Europe (or rather the South Baltic)

Genetic and linguistic structure across space and time in Northern Europe

Polish aDNA PCA

Below is a Principal Component Analysis (PCA) that I put together for an upcoming presentation on Polish ancient DNA (aDNA). The five RISE samples are from Allentoft et al. 2015, including RISE569, the early Slavic genome from the Czech Republic, which was initially wrongly labeled as that of a Czech Bell Beaker (see here). PL_N17 is an Early Bronze Age (EBA) sample from Gustorzyn, Northern Poland (see here).

I also organized f3 outgroup statistics of the form f3(European_pop,Test,Yoruba) for each of these samples to compare their genetic affinities to present-day European populations. Although f3 outgroup statistics aren't as sensitive as haplotype tests, I think these results look interesting and useful, with both PL_N17 and RISE569 seemingly showing strong links to modern-day West Slavs. The full output is available in a zip file here.

Poland_EBA PL_N17
Lithuanian 0.175778
Ukrainian_West 0.174866
Sorb 0.174334
Estonian 0.174313
Icelandic 0.17397
Irish 0.173863
Polish_West 0.173743
Polish_East 0.173549
Czech 0.173545
Norwegian 0.173533

Early Slav RISE569
Sorb 0.169171
Lithuanian 0.168945
Estonian 0.168819
Polish_West 0.168267
Polish_East 0.168143
Irish 0.168092
Czech 0.167941
Norwegian 0.167787
Icelandic 0.167696
Finnish 0.167685

See also...

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

Globular Amphora people were starkly different from Yamnaya people

The figure below is from the recent Mathieson et al. 2017 preprint; slightly edited to highlight the results of nine Globular Amphora Culture (GAC) samples from two burial sites in what are now Poland and Ukraine.

Despite living in East Central Europe at about the same time as the nearby Yamnaya people of the Pontic-Caspian Steppe, these GAC individuals show practically zero Yamnaya-related or steppe ancestry (note the almost total absence of the orange "Yamnaya" component in the Globular_Amphora results in the ADMIXTURE bar graph). Instead, they're very similar to Chalcolithic and Middle Neolithic Central and Western Europeans, with whom they overlap in the Principal Component Analysis (PCA).

During the tail end of the GAC period, East Central Europe was suddenly dominated by a new archaeological complex called the Corded Ware Culture (CWC). Although most CWC individuals sampled to date show minor GAC-related ancestry, they're overwhelmingly Yamnaya-like, which suggests that by and large the CWC population has its origins on the Pontic-Caspian Steppe. In fact, some of the earliest CWC examples from the Baltic States, such as Latvia_LN in the ADMIXTURE bar graph, are basically identical to Yamnaya people.

It was suggested not long ago that the presence of Yamnaya-related ancestry in modern-day Europeans could be mostly explained by the so called Isolation-by-Distance phenomenon (see here). But as I said at the time, this was a major faux pas, and thanks to these GAC samples I now have direct evidence from ancient DNA to back me up. So forget the idea of anything resembling a gentle cline in Yamnaya-like ancestry east to west across Europe before proto-CWC and Yamnaya exploded from the steppes.

By the way, in that critique I said that it's not possible to recapitulate ancient populations with ADMIXTURE components. I stand by that statement, although as we can see in Mathieson et al. 2017, it is possible to get close at times with enough of the right ancient samples; close enough to make some general observations anyway.

Interestingly, on the PCA plot, the European Bronze Age cluster is more or less half way between GAC and Latvia_LN. This is also where modern-day Poles and Ukrainians cluster on such plots when they're not significantly skewed by projection bias or shrinkage. Thus, I do wonder if the Slavs of East Central Europe are essentially a 50/50 mixture of early CWC and late GAC? I'll try and test this when the Mathieson et al. 2017 dataset goes online.

Reference...

Mathieson et al., The Genomic History Of Southeastern Europe, bioRxiv, Posted May 9, 2017, doi: https://doi.org/10.1101/135616

See also...

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

Poles in the new Human Origins dataset

Harvard's Human Origins dataset is being updated with 238 new samples, including 23 from Poland (15 from Poznan in western Poland and 8 from Lublin in eastern Poland). It should be available for download soon at the Reich Lab website here, although many of the new samples will only be accessible to people who sign a waiver. Below is a Principal Component Analysis (PCA) from Lazaridis et al. 2016 featuring the new samples. Interestingly, most of the Poles, probably those from Poznan, cluster with Sorbs from eastern Germany.

Citation...

Lazaridis et al., The genetic structure of the world's first farmers, bioRxiv preprint, posted June 16, 2016, doi: https://dx.doi.org/10.1101/059311

Around 65% LN/EBA European ancestry in the Hindu Kush (?)

One of the toughest nuts to crack in population genetics has proved to be the story of the people of the Hindu Kush. However, using TreeMix and ancient genomes from the recent Allentoft et al. and Haak et al. papers, I'm seeing most of the Kalash and Pathan individuals from the HGDP modeled as ~65% Late Neolithic/Early Bronze Age (LN/EBA) European and ~35% Central Asian. This, to me at least, makes a lot of sense. For instance:

The Kalash and Pathan samples that can't be modeled in this way, at least with the reference populations that I'm using, are fitted within a framework that closely resembles the old two-way Ancestral South Indian/Ancestral North Indian model (ASI/ANI). They usually score ~12% admixture from the branch leading to the Dai of southern China, which is obviously the proxy for ASI.

Both of these models are correct; they just show the same thing in different ways. So if we mesh them together the Kalash and Pathans come out ~65% LNE/EBA European (which includes substantial Caucasus or Caucasus-related ancestry), ~12% ASI, and ~23% something as yet undefined.

If I had to guess, I'd say the mystery ~23% was Neolithic admixture from what is now Iran. But ancient DNA has thrown plenty of curve balls at us already, so that's a low confidence prediction, even though it does make good sense.

It's also interesting to see the migration edges running from the Ulchi of east Siberia to the LN/EBA Europeans. This might be a signal of minor Eastern non-African (ENA), in other words East Eurasian, admixture. Then again, it might just be the algorithm trying to compensate for something, like excess Eastern Hunter-Gatherer (EHG) ancestry.

The full output from my analysis can be downloaded here. The reference samples and markers are listed here and here.

See also...

The Poltavka outlier

The real thing

The enigma of the Kalash

Badasses of the Bronze Age: Analysis of Andronovo, Battle-Axe, Corded Ware and Sintashta genomes - part one

From the Eneolithic to the Late Bronze Age vast areas of Eurasia were inhabited by a series of highly mobile and innovative groups that mostly relied on pastoralism for subsistence and, judging by their warlike grave goods, didn't mind a bit of biffo.

In Europe, where they first appeared, their archeological remains are generally classified as part of the Corded Ware Culture (or its Battle-Axe and Single Grave offshoots), and in Asia, where they expanded rapidly from the Trans-Urals to the Pamirs and south Siberia, as part of the Sintashta, Petrovka and Andronovo cultures.

It's likely that these groups had a profound impact on the Bronze Age world, including on Mycenaean Greece and Hittite Anatolia. The Sintashta Culture, for instance, is credited with the development of the spoked-wheel chariot, which became widely used in warfare all the way from Egypt to China.

Unfortunately, a lot of nonsense has been written on this topic in the past. In my view, one of the most sensible and up do date sources currently online is the thesis The Origin and Spread of the War Chariot by Elias Manuel Morgado Pinheiro.

Indeed, the obvious awesomeness of these ancient people has stirred much controversy about their origins and legacy. The academic consensus is that they were closely related, and that at least some of their ancestors were early Indo-Europeans from Eneolithic Eastern Europe. But a few archeologists have argued that the Corded Ware Culture was native to Central Europe, and others that the Sintashta population arrived in the Trans-Urals from Iran or even Syria.

Moreover, linguists generally consider the Sintashta/Andronovo people as the most likely candidates for the Proto-Indo-Iranians, and thus the precursors of the Indo-Aryans. But this is contested by many Indologists, who prefer to see the deepest roots of the Indo-Iranians closer to India and often oppose the idea of an Aryan conquest of South Asia during the Bronze Age.

In the near future, probably within the next couple of years, ancient genomics will leave very little room for debate in these matters and the arguments will cease, at least in mainstream academia.

But we already have a reasonable collection of ancient DNA from the relevant archeological cultures. Does it back the general consensus? Let's take a look, starting with the Y-chromosome data sorted by culture. The bracketed numbers are the sample sources, which are listed at the bottom of the post.

Corded Ware, Germany, Individuals 2,3,4 [1], R1a
Corded Ware, Germany, I0104 [3], R1a
Corded Ware, Germany, RISE434 [4], R1a
Corded Ware, Germany, RISE436 [4], R1a
Corded Ware, Poland, RISE1 [4], R1b?
Corded Ware, Germany, RISE446 [4], R1a
Corded Ware, Poland, RISE431 [4], R1a

Single Grave?, Denmark, RISE61 [4], R1a

Battle-Axe, Sweden, RISE94 [4], R1a
Battle-Axe?, Sweden, RISE98 [4], R1b

Sintashta, Trans-Urals, Russia, RISE386 [4], R1a
Sintashta, Trans-Urals, Russia, RISE392 [4], R1a

Andronovo, South Siberia, Russia, S07 [2], C
Andronovo, South Siberia, Russia, S10 [2], R1a
Andronovo, South Siberia, Russia, S16 [2], R1a
Andronovo, Altai region, Russia, RISE512 [4], R1a

Fascinating stuff. Keep in mind also that at higher resolution, most, if not all, of these R1a lineages are actually R1a1a1, which is estimated to be only around 5,000-6,000 years old based on full Y-Chromosome sequences. In other words, these groups were certainly closely related, and in large part the descendants of a patriarch who lived no earlier than the Middle or even Late Neolithic.

Now, based on that list it might seem as if both R1a and Corded Ware were indeed native to North-Central Europe. But this is not so.

R1a appears to be an Eastern Hunter-Gatherer (EHG) marker that in all likelihood failed to penetrate west of present-day Ukraine until the Late Neolithic, because it's missing in all the relevant samples before this period. So it probably first arrived in Central Europe with the Corded Ware people. We know that the Corded Ware people were foreign to Central Europe because their genome-wide genetic structure is starkly different from that of the Middle Neolithic farmers who lived there before them.

This is easy to demonstrate. The Principal Component Analyses (PCA) below show where two ancient samples cluster alongside a variety of present-day West Eurasians from the Human Origins dataset [3]. Note that Esperstedt_MN, a Middle Neolithic sample from a Baalberge Group burial in east-central Germany [3], looks more at home in Sardinia than Central Europe. On the other hand, the Corded Ware sample [4], also from east-central Germany, is sitting at the other end of the plot, among groups from the Volga-Ural region.

I'll throw in a few more PCA featuring Corded Ware, Battle-Axe, Sintashta and Andronovo genomes that offered enough data to be placed on the plots with a high degree of accuracy [4]. Note that the only clear outlier is RISE512, an Andronovo sample with an inflated level of East Eurasian admixture. If you're having trouble finding the ancient samples, download the PDF files and use the PDF search field.

Corded_Ware_RISE00_Estonia

Corded_Ware_RISE431_Poland

Battle-Axe_RISE94_Sweden

Battle-Axe_RISE98_Sweden

Single_Grave_RISE61_Denmark

Sintashta_RISE386_Russia

Sintashta_RISE392_Russia

Sintashta_RISE394_Russia

Sintashta_RISE395_Russia

Andronovo_RISE500_Russia

Andronovo_RISE503_Russia

Andronovo_RISE505_Russia

Andronovo_RISE512_Russia

However, the meat and potatoes of ancient genomics are formal statistics. So in part 2 of this series I'll explore the genetic ancestry and legacy of the so called badasses of the Bronze Age using the ADMIXTOOLS software package.

Update 28/04/2016: I'm gearing up to finally write the second part of the Badasses of the Bronze Age. But before I do that, I need to update the first part, because I now have two more sets of ancient samples that can be described as truly badass in the context of this series: Potapovka and Srubnaya.

Incredibly, seven out of the eight Potapovka and Srubnaya males belong to R1a. One of the Potapovka individuals turned out P1, but that was only because of a lack of data, otherwise, in all likelihood, he'd also belong to R1a.

Potapovka, Samara, Russia, I0419 [5], R1a

Srubnaya, Samara, Russia, I0232 [5], R1a
Srubnaya, Samara, Russia, I0360 [5], R1a
Srubnaya, Samara, Russia, I0361 [5], R1a
Srubnaya, Samara, Russia, I0423 [5], R1a
Srubnaya, Samara, Russia, I0424 [5], R1a
Srubnaya, Samara, Russia, I0430 [5], R1a

Also, I recently changed the way I run PCA. Indeed, I can now accurately plot samples on a typical genetic map of West Eurasia with as little as 15K SNPs. So instead of a few plots featuring the best Potapovka and Srubnaya sequences separately, here's a plot with all of the badasses together.

Update 22/09/2017: Unfortunately, I won't be able to finish this series anytime soon. Things are moving very quickly, but the full picture won't be known to us for a while yet. Some recent developments are covered at my other blog under these links...

R1a-M417 from Eneolithic Ukraine!!!11

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

Citations...

1. Haak et al., Ancient DNA, Strontium isotopes, and osteological analyses shed light on social and kinship organization of the Later Stone Age, PNAS, Published online before print November 17, 2008, doi:10.1073/pnas.0807592105

2. Keyser et al., Ancient DNA provides new insights into the history of south Siberian Kurgan people, Human Genetics, Saturday, May 16, 2009, doi: 10.1007/s00439-009-0683-0

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

4. Allentoft et al., Bronze Age population dynamics, selection, and the formation of Eurasian genetic structure, Nature 522, 167–172 (11 June 2015) doi:10.1038/nature14507

5. Mathieson et al., Genome-wide patterns of selection in 230 ancient Eurasians, Nature, 528, 499–503 (24 December 2015), doi:10.1038/nature16152

R1a1a from an Early Bronze Age warrior grave in Poland

Ancient DNA tests on a skeleton from an Early Bronze Age "warrior" grave near Hrubieszow, southeastern Poland, have revealed that the remains belong to Y-haplogroup R1a1a [source].

Mitochondrial sequences were also obtained from seven other samples from the same burial site, and assigned to mt-haplogroups H1a, H1b (two), H2a (two), H6 and U5b1.

R1a1a is by far the most frequent Y-haplogroup in Poland today, and its presence in the remains from a high-status burial might be a clue as to how it became so common in East-Central Europe.

Interestingly, the site is classified as part of the Strzyżow Culture, which is considered by Polish archaeologists to be the result of contacts between local communities in southeastern Poland and Kurgan newcomers from the North Pontic steppe.

All of the other ancient R1a1a samples reported to date from Central Europe are also younger than the Middle Neolithic and from presumably steppe-derived Indo-European archeological cultures:

- Late Neolithic, Eulau, Germany, Corded Ware Culture, three related samples

- Late Neolithic, Esperstedt, Gemany, Corded Ware Culture, one sample

- Late Bronze Age, Halberstadt, Germany, Urnfield Culture (?), one sample

- Late Bronze Age, Lichtenstein Cave, Germany, Urnfield Culture, two samples

More info about the Bronze Age Pole, including photos of a facial reconstruction, can be found here and here (in Polish).

See also...

R1a-Z280 from Early Bronze Age Northern Poland

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

Eurogenes' North Euro clusters - phase 2, final results

This is a continuation of my ChromoPainter analysis of Europeans from north of the Pyrenees, Alps and Balkans (see here). To obtain the most accurate results possible on my laptop, I increased the burn-ins and iterations in fineSTRUCTURE to 500K each (5 hour run in all, which is all I'm willing to put this machine through). The end product looks very similar to my initial analysis, in which I explored the data at 200K burn-ins and iterations. What I think this shows is that the results are robust, and I doubt they'd change much even after a couple of days of running fineSTRUCTURE.

Indeed, as mentioned in my previous blog entry, this appears to be the most detailed and accurate cluster analysis of this part of Europe produced anywhere to date. There are 21 clusters in all, with at least 20 looking like strong signals of genetic substructures across North, West, Central and East Europe (see spreadsheet for individual classifications). They include:

pop0 - West Finnish1: This is a pair of reference individuals, most likely from Western Finland, judging by their PCA and ADMIXTURE results. They are either from the same community, or have a very similar mix of very specific ancestries.

pop1 - Erzya + Moksha: This includes all of the Erzya and Moksha in the project, plus a Russian with recent Erzya ancestry. It's closely related to ethnic Russian clusters that stretch from Northwest Russia to near the Volga, and also to the Estonian cluster.

pop2 - South/Central Finnish: This is the largest Finnish cluster, and that's probably more than just the result of sampling bias. I would say that the greater part of the Finnish population would belong to this type of cluster, which occupies regions of highest population density within the country.

pop3 - Fenno-Scandian: This cluster includes a Northern Swede, a Swede with probable recent Finnish ancestry, and Finns with probable recent Swedish influence. I have a feeling that Finland Swedes and Aland Islanders would also be placed here more often than not.

pop4 - Northwest Russian/Southeast Finnish: Although this cluster includes only two individuals, it's definitely much more than just the result of two relatively closely related samples being in the same run. I'd hazard a guess that Northwest Russians with, say, significant Ingrian ancestry, would land here, and so would Finns with recent Russian ancestry.

pop5 - West Finnish2: Based on PCA and ADMIXTURE results, most of these Finns likely come from Western Finland, probably from places like Southern Ostrobothnia. They possibly also have some Swedish influence.

pop6 - West German: This cluster is based on individuals from Western and Northwestern Germany. It also includes a Dutchman, Austrian and people of mixed origin, like a Dane with French and German ancestry, and Americans with British, German, Scandinavian and/or Polish ancestry. In other words, this is where Northwestern Europe meets Central Europe.

pop7 - Vologda Russian: Most of the Vologda Russians from the HGDP land here, so this appears to be a local cluster. Judging from its phylogeny, it looks like a mix of North Slavic, Baltic and Finnic influences.

pop8 - East Finnish: All the project and reference Finns with substantial ancestry from new settlement areas of Eastern Finland appear in this cluster. No wonder then, that this is the cluster with the highest chunk count in this analysis.

pop9 - Estonian: This is a mixed cluster, including individuals from Estonia, and, as far as I know, Russians with substantial ancestry from near Estonia. As mentioned above, it's closely related to the Erzya + Moksha, Northwest Russian and Vologda clusters. However, it's clearly much more western than any of these clusters (for instance, see the PCA below), which suggests Germanic influence in its makeup.

pop10 - Cornish: Almost all of my Cornish samples from the 1000 Genomes Project feature in this very local cluster, which shows the highest chunk count among the Western European samples. The overall results suggest a lack of outbreeding in recent times.

pop11 - French/Belgian: Interestingly, this cluster includes the bulk of the French samples, a French Canadian, and two Belgians. On the other hand, the most northerly French are placed in the more cosmopolitan Northwest European cluster (see below).

pop12 - Lithuanian: All of the more or less pure Lithuanians fall in this cluster. Those that don't are a reference sample from Behar et al. 2009, who always appears very Belorussian like in other analyses, and here sits in the East Slavic cluster, and a project member with recent German ancestry (LIT3). The Western European influence carried by the latter pushes him into the Polish/West Ukrainian cluster, despite not having any documented Polish or Ukrainian ancestry.

pop13 - Northwest Russian: This cluster appears to be made up of Russians who have more Finnic, and/or perhaps Eastern Baltic, ancestry than the individuals in the East Slavic cluster. In other words, it's more northerly, less westerly, and more closely related to the Finnic-speaking Erzya, Moksha and Estonians.

pop14 - Irish + West British: Most Irish individuals fall in this cluster, as well as British samples from Western Scotland and Wales. It's tempting to correlate this cluster with Celtic genetic ancestry in the Isles.

pop15 - South/West Scandinavian: This is basically a Norwegian and Southern Swedish cluster. It also features Swedes from other parts of the country who most likely have some German, Walloon and/or French influence.

pop16 - East German: This cluster includes individuals with significant or even overwhelming Germanic ancestry, but also with very clear Western Slavic input. One of the individuals here is of mixed Polish, German and Swedish ancestry, which pretty much sums up the character of this cluster in a modern context. The presence of two Hungarians from Behar et al. 2009. isn't surprising, because Hungary was settled by both Germanic and Western Slavic groups from the early Middle Ages until modern times.

pop17 - Northwest European: I had reasonable hopes of breaking up this large cluster into a couple of units at least. However, that did not happen, and I don't think it will unless I obtain more samples from the relevant areas of Europe, like Holland and specific parts of the UK. I think the main reason this cluster failed to budge was because of its cosmopolitan nature. In other words, the samples here include some of the most outbred in the analysis, and this, coupled with the fact that they carry very similar ancestral components, means that fineSTRUCTURE doesn't have anything to latch onto to create divisions.

pop18 - East Scandinavian: This could also be called a Swedish cluster. It's almost entirely made up of Swedes, usually from Eastern or Southeastern Sweden, and/or occasionally with recent Finnish influence.

pop19 - Polish/West Ukrainian: The vast majority of the Poles fall in this cluster, and about half of the Ukrainians from Yunusbayev et al. 2011. Most of these Ukrainians appear to be from the Lviv district in the west, and some might even have fairly recent Polish and/or German ancestry. In fact, I would say the latter is a good bet for UkrLv240Y, who shows large Western European segments on several chromosomes.

pop20 - East Slavic: All of the Belorussians cluster here, and so do Russians from near Belorussia and Ukraine, and almost half of the Ukrainians from Yunusbayev et al. 2011 (those who show more easterly genetic characteristics). An individual of mixed Polish and Lithuanian ancestry also makes an appearance here, suggesting that one of the main factors differentiating this cluster from the Polish/West Ukrainian group is a higher level of Baltic admixture in the former.

pop21 - East Central European: This cluster is based on most of the Hungarians in my dataset, but it also includes a number of Western and Southern Slavs, often with significant German ancestry. Not surprisingly, this cluster shows very high affinity with both the East German and Polish/West Ukrainian clusters.

Let's now move on to some graphics. Below, in order of appearance, are the following: raw data coancestry matrix, showing the placement of individual samples; aggregate coancestry matrix, showing the populations (or clusters) described above; pairwise coincidence matrix, which is useful for spotting very recent ancestral ties; a PCA plot of the 21 clusters. More detailed ChromoPainter/fineSTRUCTURE PCAs of Western Europe can be found at this link.





Finally, those of you who wish to run your own experiments with the ChromoPainter datasheets from this analysis can download them here. Please note, the sheets don't reveal any raw or traits/disease data.