Next year the Armenian Plateau hypothesis will collapse

It's been a great year for population genetics and paleogenomics, and also for this blog. I ran a lot of analyses in 2015 and managed to make a few discoveries that were subsequently confirmed, or at least, backed up by academia. For instance:

- first to show with ancient genomes that the Anglo-Saxons made a significant genetic impact on England. See here. Eventually confirmed here.

- first to show that the southern admixture in the Yamnaya pastoralists of the Early Bronze Age steppe was Georgian-related rather than Armenian-related. See here. Confirmed here.

- first to show that Anatolian Neolithic farmers were very similar to European Neolithic farmers, and lacked Ancient North Eurasian (ANE) ancestry. See here. Confirmed here.

- first to show using ancient DNA and formal statistics that South Asia experienced massive gene flow originating in Late Neolithic/Bronze Age Europe. See here. Backed up with my help here.

The fact that Caucasus hunter-gatherers (CHG) like Kotias are essentially an ideal fit for the southern ancestry in the Yamnaya is a big problem for the Armenian Plateau Indo-European homeland hypothesis. This TreeMix graph shows why.

Basically, it looks like the Kotias-related ancestry in the Yamnaya came from the North Caucasus, rather than any place closer to the Near East than Georgia. Unless, of course, the southern Caucasus was populated by unadmixed CHG right until the 4th Millennium BC, when the hypothetical Proto-Indo-Europeans from the Armenian Plateau set off on their journey to Northern Europe around the Caspian Sea. But let's be honest, that's extremely unlikely.

Indeed, I expect that next year we'll see the first Neolithic and Copper Age samples from Armenia and/or surrounds, and even though they will be in large part CHG, they'll be nowhere near unadmixed. This will essentially kill the Armenian Plateau hypothesis, and thus leave the Kurgan or steppe hypothesis as the only plausible choice.

In any case, 2016 will probably be the year when ancient DNA helps to settle the Indo-European homeland question once and for all. So get ready for more ancient DNA from the steppe, but also, among others, from Mesolithic and Neolithic Iran, Mycenaean Greece and the Maikop Culture of the North Caucasus. I'm also pretty sure that the Varna man with the golden codpiece will make an appearance in a paper about Neolithic and Copper Age Bulgaria. Bring it on!

At least three genetically distinct Indo-European migrations into South Asia

First came the Indo-Aryans, probably in a couple of waves. Historical linguistics and archeology tell us that they originated on the Trans-Urals steppe in the Sintashta-Andronovo horizon, and pushed south around 2,000 BC to establish themselves as the ruling elite over Central Asian agriculturalists, who were probably in large part of West Asian origin.

There are multiple lines of genetic evidence suggesting that this is indeed what happened, which I discussed in detail in several earlier blog posts, like here.

But arguably the easiest way to show it is with D-stats of the form D(Indo-Aryan,Southeast_Asian; X,Outgroup), where the Indo-Aryans are the Kalash, a population isolate from the Hindu Kush with a relatively low level of extra-West Eurasian admixture and speaking an archaic form of Indo-Aryan. The Southeast Asians are the Dai from southern China, one of the best proxies for the South and East Asian admixture in the Kalash, while X represents a wide variety of present-day and ancient populations in my dataset. The top five D-stats, each based on well over 500K SNPs, are listed below:

Kalash Dai Kotias Ju_hoan_North 0.0684 22.704
Kalash Dai Sintashta Ju_hoan_North 0.0632 25.036
Kalash Dai Georgian Ju_hoan_North 0.0625 30.991
Kalash Dai Afanasievo Ju_hoan_North 0.0612 24.496
Kalash Dai Yamnaya_Samara Ju_hoan_North 0.0611 27.97

Really cool results. Obviously, Kotias is the recently published Caucasus hunter-gatherer (CHG) genome. The Kalash appear to carry the highest level of Kotias-related ancestry among present-day populations, which they probably acquired from both the Central Asian agriculturists and Indo-Aryan invaders. At the same time, however, Georgians show the highest affinity to Kotias because they harbor less extra-West Eurasian admixture.

After the Indo-Aryans came the Iranians, in all likelihood also from the steppe. They were either an offshoot of Sintashta-Andronovo or the more westerly Srubnaya Culture. I'd say the D-stats below, of the form D(Eastern_Iranian,Southeast_Asian)(X,Outgroup), are inconclusive, because the differences are small, and the outcome possibly affected by the methodology and/or sampling bias.

Tajik_Shugnan Dai Sintashta Ju_hoan_North 0.0716 26.427
Tajik_Shugnan Dai Poltavka Ju_hoan_North 0.0695 25.234
Tajik_Shugnan Dai Afanasievo Ju_hoan_North 0.0691 24.703
Tajik_Shugnan Dai Srubnaya Ju_hoan_North 0.069 28.266
Tajik_Shugnan Dai Corded_Ware_Germany Ju_hoan_North 0.0684 27.328

But again, the top five results make a lot of sense in the context of historical linguistics and archeology. By the way, Tajik Shugnans are a population isolate in the Pamir Mountains, like the Kalash with low level extra-West Eurasian admixture, and thus likely to be among the best available reference groups for early Eastern Iranians.

Interestingly, based on that list the Shugnans look more European than the Kalash. In large part this might be a reflection of the sharp rise in the level of European-specific Western hunter-gatherer (WHG) admixture on the steppe during the Middle Bronze Age, probably caused by population movements originating at the western edge of the steppe and/or in East Central Europe.

As far as I can tell, the fact that the Shugnans and Kalash have around the same level of extra-West Eurasian admixture means that I can try to hone in on the differences between their steppe-derived ancestry with D-stats of the form D(Kalash,Tajik_Shugnan)(Kotias,X). The top result seems to confirm my hunch, because Loschbour is, of course, a Western hunter-gatherer.

Loschbour 0.0149 3.874
Basque_Spanish 0.0113 4.232
Anatolia_Neolithic 0.0112 4.257
Karelia_HG 0.0105 3.005
Poltavka 0.01 3.539
Corded_Ware_Germany 0.0099 3.734
Afanasievo 0.0094 3.213
Srubnaya 0.0094 3.538
Yamnaya_Kalmykia 0.0091 3.362
Albanian 0.0088 3.419
Altai_IA 0.0088 3.087
Sintashta 0.0088 3.146
Greek 0.0076 3.094

Full output available here

More recently, during historic times, large parts of northern South Asia were settled by the Balochi, a Western Iranian people from the South Caspian region, whose ancestors were probably Indo-Europeanized a couple millennia earlier by Proto-Iranians from the steppe moving west across the Iranian Plateau. D-stats comparing the Balochi to the Kalash and Shugnans, respectively, clearly reflect the Near Eastern origins of the Balochi.

BedouinB 0.0104 6.151
Anatolia_Neolithic 0.0094 5.495
Druze 0.0084 5.228
Cypriot 0.0082 4.839
Syrian 0.0079 4.714
Armenian 0.0063 3.935
Satsurblia 0.0059 2.472
Georgian 0.0055 3.443
Iranian 0.0055 3.345
Abkhasian 0.0053 3.279
Greek 0.0052 3.166

...

Okunevo -0.0081 -3.552
Karelia_HG -0.0104 -4.666

Full output available here

Satsurblia 0.007 2.078
BedouinB 0.0051 2.277
...

Basque_Spanish -0.0073 -3.156
Mezhovskaya -0.0085 -3.045
Altai_IA -0.0092 -3.677
Scythian_IA -0.0092 -3.108
Yamnaya_Samara -0.0095 -4.092
Karitiana -0.0098 -3.501
Karasuk -0.0099 -4.322
Andronovo -0.01 -4.09
Sintashta -0.01 -3.951
Corded_Ware_Germany -0.0102 -4.34
Srubnaya -0.0106 -4.605
Yamnaya_Kalmykia -0.011 -4.511
MA1 -0.0118 -3.691
Okunevo -0.0122 -3.783
Poltavka -0.0125 -5.043
Afanasievo -0.0136 -5.235
Loschbour -0.0148 -4.201
Karelia_HG -0.0208 -6.537

Full output available here

In this analysis I used ancient samples from the recently published Jones et al. and Mathieson et al. studies, available on request from the authors and at the Reich lab website here, respectively. The present-day samples are from the Human Origins dataset, also available at the Reich lab website.

Basques are not simply a fusion of Iberian hunter-gatherers and early farmers

I thought I'd revisit the issue of Basque origins with my new Principal Component Analysis (PCA) of West Eurasian genetic variation. The useful thing about this PCA is that it gets around two problems that routinely affect PCA featuring ancient samples: projection bias, otherwise known as shrinkage, and exaggerated outcomes for individuals with high counts of homozygous genotypes.

A couple of recent papers argued that Basques were the direct descendants of local hunter-gatherers and early Neolithic farmers who arrived in Iberia from the eastern Mediterranean. This is probably correct for the most part, but it doesn't tell the whole story.

On the PCA above, Basques are quite distinct from Early Neolithic, Middle Neolithic and Copper Age Iberians (marked Iberia_EN, Iberia_MN and Iberia_CA, respectively), because they are significantly more eastern. In fact, they cluster with the only Bronze Age Iberian on the plot (Iberia_BA), which is the same individual that I found to harbor steppe-related ancestry (see here).

Thus, the story told by the PCA is that Basques are the progeny of Bronze Age Iberians, who, unlike their Copper Age predecessors, experienced a pulse of steppe-related admixture from the east.

Formal statistics back this up. For instance, here's a quote from the recently revised Mathieson et al. preprint:

However, the statistic f4(Basque, Iberia_Chalcolithic; Yamnaya_Samara,Chimp)=0.00168 is significantly positive (Z=8.1), as is the statistic f4(Spanish, Iberia_Chalcolithic; Yamnaya_Samara, Chimp)= 0.00092 (Z=4.6). This indicates that steppe ancestry occurs in present-day southwestern European populations, and that even the Basques cannot be considered as mixtures of early farmers and hunter-gatherers without it (4).

The key question now is who brought the steppe-related ancestry to Basque country. Were they Indo-Europeans or speakers of Proto-Basque? Also, did they actually come from the steppe, or somewhere nearby, like the Carpathian Basin?

The reason I mention the Carpathian Basin is because, as per the PCA, Basques more or less cluster between Copper Age Iberians and some of the Bronze Age Hungarians (marked Hungary_BA). But this is just one possibility, and I'm not sure at this stage how plausible it looks with, say, formal statistics.

In this analysis I used samples from the Allentoft et al., Gunther et al., Haak et al. and Lazaridis et al. datasets, all of which are publicly available. The latter two are found at the Reich Lab site here. If you're confused by some of the acronyms in the PCA key, see here.

New PCA format

From now on, every time a new dataset of ancient West Eurasian samples is made available online, I'll run it in a Principal Component Analysis (PCA) like this:

Please note that the plots above include the majority of recently published ancient samples, and yet they are not affected by projection bias, otherwise known as shrinkage. If you're confused by some of the acronyms in the PCA key, see here.

See also...

Basques are not simply a fusion of Iberian hunter-gatherers and early farmers

Uralian genes

Below is a graph based on a couple of D-statistics. Note that out of the five Uralic-speaking groups, only Hungarians remain under the upward-sloping red line, clustering among Indo-European-speakers. On the other hand, the Indo-European-speaking Russians from Kargopol cluster with Uralic speakers. However, Russia is a complex affair in this context, because much of the north and east of European Russia was Uralic-speaking until very recently. The relevant D-stats are available here.

See also...

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

A multidimensional approach

This is arguably the most interesting Principal Component Analysis (PCA) I've run to date. Note that overall the ancient steppe genomes appear to be the crucial link in the Indo-European chain, basically bridging the gap between European and South Asian Indo-European-speakers. A plot with all of the samples labeled individually can be downloaded here. If you have any questions about the methodology, just ask in the comments.

In this analysis I used samples from the Allentoft et al., Haak et al. and Lazaridis et al. datasets, all of which are publicly available. The latter two are found at the Reich Lab site here.

See also...

No significant genetic substructures within (eastern) Yamnaya

Children of the Divine Twins

The Trundholm sun chariot was found in a peat bog on the island of Zealand, Denmark, in 1902. It's thought to be an Indo-European religious artefact dating back to the Nordic Bronze Age; a representation of a horse pulling the sun and perhaps also the moon in a spoked wheel chariot. So one way or another it appears to be a reference to the Divine Twins mythos.

The Divine Twins are a key part of Indo-European religion, and they appear in the Rigveda, the most archaic of the Indo-Aryan Vedic texts.

However, because the concept includes the spoked wheel chariot, it probably can't be much older than 2,000 BC. That's because the invention of the spoked wheel chariot is more often than not credited to the Sintashta Culture of the Trans-Urals, which is dated to 2100-1800 BC.

Considering these cultural and technological ties between Bronze Age Scandinavia and South Asia, it's an interesting question whether there were also strong genetic links between these two outposts of the early Indo-European world.

Unfortunately, we don't yet have any ancient genomes from South Asia to compare to the Late Neolithic/Bronze Age (LN/BA) Nordic genomes published recently with Allentoft et al. 2015. However, we do have the Kalash.

The Kalash people of the Hindu Kush are Indo-Aryans, but they're also an extreme cultural and genetic isolate. It's likely that they haven't mixed very much with any of their neighbors since the Bronze Age. About half of them also practice a unique Vedic religion that celebrates the sun and moon (see section 1.5.4. "Creation myths" in Witzel 2002).

In the TreeMix analysis below I used three random Kalash individuals from the Human Origins dataset (HGDP00311, HGDP00313 and HGDP00315). I didn't run the whole set of 18 because they seem to create a genetic monolith that is impossible to break down and analyze correctly with TreeMix.

Note that after their Central Asian admixture is accounted for with a migration edge of 33%, the Kalash sit on what seems to be an early Indo-European branch that also includes the LN/BA Scandinavians. The full output from this analysis is available for download here.

I also employed the qpAdm software to model all of the Kalash from the Human Origins as a mixture of LN/BA Scandinavians, various ancient and present-day West Asians and Dai from south China. The ancestry proportions are listed at the bottom of the sheets. To check the success of the models consult the chisq, tail prob and standard (std.) errors.

Nordic LN-BA/Armenia BA/Dai

Nordic LN-BA/Iranian/Dai

Nordic LN-BA/Iranian Jew/Dai

Nordic LN-BA/Georgian/Dai

Now, qpAdm is easy to run but very difficult to use correctly. However, even when fumbling around like a drunk with this software, it's easy to pick up some useful hints. Clearly, even if the ancestry proportions are way off, the Kalash show stronger affinity to the ancient Scandinavians than to West Asians. Also, the models more or less reflect the TreeMix analysis above.

Thus, the answer to my question is a resounding yes; there were indeed strong genetic ties between Scandinavia and South Asia during the Bronze Age.

See also...

The Poltavka outlier

The mystery of the Sintashta people

The real thing

Pre- and Post-Kurgan Europe

The Principal Component Analysis (PCA) below is based on four sets of D-statistics. The second image shows what they are and how they affect the components. The datasheet is available here. If you don't know what EHG, SHG and WHG stand for, see here.

Note that the post-Kurgan Europeans are shifted east, towards the Bronze Age steppe groups (most of which are in fact classified as Kurgan cultures), relative to the pre-Kurgan Europeans. Coincidence? Certainly not. Interestingly, the West Asians show a similar shift to the east, although it's not yet clear who caused it and when.

In this analysis I used samples from the Allentoft et al., Haak et al. and Lazaridis et al. datasets, all of which are publicly available. The latter two are found at the Reich Lab site here.

Update 12/09/2015: Matt posted these graphs in the comments. The first graph shows Yamnaya-related ancestry proportions for a series of points along the Yamnaya-Middle Neolithic continuum, which can be used to estimate Yamnaya-related admixture in samples that cluster near these points.

See also...

Smarter than the average bear

Smarter than the average bear

Using a few ancient hunter-gatherer sequences, formal statistics, and enough present-day samples, I can predict with basically 100% accuracy whether an ethnic group is of European or extra-European origin. Actually, there's probably an infinite number of ways of doing the same thing nowadays, but I thought this was an effective way of visualizing it. The datasheet can be downloaded here.

I also tried to analyze the Indo-European expansion in a similar way. The results are a lot less obvious, and there are a number of reasons for this. One of the main factors, I'd say, is that languages can be learned or imposed very quickly, and this happened often during historic times, well after the Proto-Indo-European dispersals.

For instance, Sardinians spoke Paleo-Sardinian or Nuragic languages until they adopted Indo-European speech, in the form of Latin, from the Romans (see page 118 here). Indeed, it's highly unlikely that any Proto-Indo-Europeans ever stepped foot on Sardinia. The relevant datasheet is here.

In this analysis I used samples from the Allentoft et al., Haak et al. and Lazaridis et al. datasets, all of which are publicly available. The latter two are found at the Reich Lab site here.

See also...

Pre and Post-Kurgan Europe

No significant genetic substructures within (eastern) Yamnaya

It's interesting and perhaps important that there's practically no difference between the two sets of Yamnaya samples published to date, despite the fact that they're from regions separated by ~1,000 kilometers. Yamnaya_Rise is from between the Black and Caspian seas, while Yamnaya_Haak from just north of the Caspian.

Note the lack of significant Z scores (around 3 or more) in these D-stats. Although the almost significant Z score with Loschbour, a Mesolithic Western Hunter-Gatherer (WHG) from Luxembourg, does look somewhat curious.

It's difficult to know what all of this means exactly without seeing any ancient samples from archaeological cultures that preceded Yamnaya on the Pontic-Caspian Steppe. However, it could mean that the Yamnaya nomads arrived north of the Caspian from the south, which is also what preliminary Y-chromosome data is hinting at (see here).

Yamnaya was succeeded northeast of the Caspian by its offshoot, the Poltavka Culture, which in turn was replaced by the Sintashta Culture. The most widely accepted theory, based on archaeological data, is that Sintashta formed from a chain of cultures derived from the late Corded Ware horizon of East-Central Europe. This is backed up by the D-stats below, which suggest some western admixture in Sintashta that is missing in Yamnaya.

In this analysis I used samples from the Allentoft et al. (Rise Project), Haak et al. and Lazaridis et al. datasets, all of which are publicly available. The latter two are found at the Reich Lab site here.

See also...

A multidimensional approach

D(Outgroup, PopTest) (Pop1, Pop2)

I ran these tests using 65-112K transversion sites, so the results should be very solid. The spreadsheet is here. My impression is that MA1-related (ANE?) ancestry was present in South Central Asia before R1a-Z93 steppe people moved into the area during the Bronze Age. Any thoughts?

All of the samples are from the recent Allentoft et al. and Haak et al. papers, available on request from the authors and here, respectively.

Kets are rich in Ancient North Eurasian (ANE) ancestry

There's an interesting and very thorough preprint at bioRxiv looking at the genomic structure of Kets, the last nomadic hunter-gatherers of Siberia. From the paper:

Based on all analyses, we can tentatively model Kets as a two-way mixture of East Asians and ANE. Therefore, ANE ancestry in Kets can be estimated using various f4-ratios from 27% to 62% (depending on the dataset and reference populations), vs. 2% in Nganasans, 30 ‒ 39% in Karitiana, and 23 ‒ 28% in Mayans (Suppl. file S7, see details in Suppl. Information Section 8). Integrating data by different methods, we conservatively estimate that Kets have the highest degree of ANE ancestry among all investigated modern Eurasian populations west of Chukotka and Kamchatka. We speculate that ANE ancestry in Kets was acquired in the Altai region, where the Bronze Age Okunevo culture was located, with a surprisingly close genetic proximity to Mal'ta. Later, Yeniseian-speaking people occupied this region until the 16th-18th centuries. We suggest that Mal'ta ancestry was later introduced into Uralic-speaking Selkups, starting to mix with Kets extensively in the 17-18th centuries.

I'd say these findings make a lot of sense. Below is a spatial map put together by Sergey, based on my K8 model, showing the distribution of ANE across much of Eurasia. Note the ANE peak of around 28% among the Kets.

Citation...

Flegontov et al., Genomic study of the Ket: a Paleo-Eskimo-related ethnic group with significant ancient North Eurasian ancestry, bioRxiv, Posted August 13, 2015, doi: https://dx.doi.org/10.1101/024554

Finngolians

Of course, Mongolians never made it to Finland or even Northern Russia (Kargopol area) where these Russian samples are from. How did this crap get through peer review?

The proportions of admixture from ancestral EUR and EAS [European and East Eurasian, respectively] were estimated, and are shown in Table 2. CEU populations mostly originating from France and Germany had a small fraction (0.7 +/- 0.8%) of genetic material from EAS. People from Great Britain such as British (GBR) and Orcadian inherited 2.5%–3.8% from ancestral EAS. Finnish (FIN) and Russians inherited significantly more genetic material (>12%) from ancestral EAS, which is consistent with their historical record of admixture with Mongolian populations. Besides, Adygei from Caucasus inherited 3.2 +/- 1.0% from ancestral EAS.

Pengfei Qin et al., Quantitating and Dating Recent Gene Flow between European and East Asian Populations, Scientific Reports 5, 02 April 2015, Article number: 9500, doi:10.1038/srep09500

See also...

Finngolians #2

Comic relief

When, and how exactly, did ANI become ANE? I didn't get the memo.

The geographical distribution of the dark green component (ASI or Ancestral South Indian- unique to the subcontinent) was largely limited to the Indian subcontinent, and can be seen among all the populations of the subcontinent albeit in variable amount, whereas the second major component (light green: ANI or Ancestral North Indian (now ANE- Ancestral North Eurasian [76])) was shared with Central Asia, the Caucasus, Middle East and Europe (Fig 1c). The geographical origin of light green component (ANI or ANE) is so far unclear and more research is needed from unsampled area as well as from ancient DNA; however, the time of spread of this component from its origin place (either of any; the Caucasus, Near East, Indus Valley, or Central Asia) has happened more than 12.5 thousand years before [38], which is significantly earlier than the purported expansion of Dravidians and Aryans languages from outside the subcontinent. Notably, the Andaman Islanders are not the only population carrying the ASI component exclusively, as was suggested before [37]. Austroasiatic speakers (more precisely, the South Munda) of the subcontinent also seem to possess the ASI component in near unadulterated form (Fig 1c). More research with complete genome analysis would be required to clear the geographic center of the ANE component; however, it is evident from the present analysis that the dark green component (ASI) can be considered as a connecting thread for all the Indian populations (Fig 1c). Taken together, these results support the second hypothesis suggesting that all Indians, irrespective of their caste or tribal affiliations, share a common genetic ancestry, which is undoubtedly founded over the indigenous ASI component.

Citation: Chaubey G, Kadian A, Bala S, Rao VR (2015) Genetic Affinity of the Bhil, Kol and Gond Mentioned in Epic Ramayana. PLoS ONE 10(6): e0127655. doi:10.1371/journal.pone.0127655

Latvians: very similar to Lithuanians

The Estonian Biocentre has uploaded a new dataset from a forthcoming paper on the population structure of Slavs. It includes Latvians, Slovakians and Slovenians. Below is a Principal Component Analysis (PCA) featuring these individuals. Most of the other samples are from the Human Origins dataset.

Obviously, Latvians aren't Slavs; they're Balts just like Lithuanians. They're probably in this dataset because Balts are close neighbors and relatives of Slavs.

Note that these six Latvians are overall the most northerly group in this analysis, which suggests that they have the highest ratio of European hunter-gatherer ancestry. Nevertheless, they're obviously still very similar to Lithuanians and their Uralic neighbors to the north, the Estonians.

See also...

Finno-Ugric Poles in Kushniarevich et al. 2015

The ancient DNA case against the Anatolian hypothesis

In the debate over the location of the Proto-Indo-European urheimat, Colin Renfrew's Anatolian hypothesis is usually mentioned as the most viable alternative to the steppe or Kurgan hypothesis. But probably not for very much longer.

Below is a Principal Component Analysis (PCA) featuring extant Indo-European and non-Indo-European groups from West Eurasia, a couple of typical early Neolithic farmers from Central Europe, a typical Western Hunter-Gatherer, also from Central Europe, and the Iceman from the Copper Age Tyrolean Alps, again typical of his time and place.*

It's just a taste of the ancient genomic data we have available from prehistoric Europe, but it has almost everything that is pertinent to the issue at hand.

You don't need to be familiar with PCA methodology to be able to read the plot. Basically, it shows that the present-day European population structure is the result of two main events:

- the arrival of early farmers from Anatolia during the Neolithic transition, which eventually caused the extinction of people like the Western Hunter-Gatherer, who is the most obvious outlier on the plot

- the expansion of Kurgan groups such as the Yamnaya, which led to the formation of the Corded Ware horizon across much of Europe and shifted the genetic structure of almost all Europeans to the east, away from the Neolithic and Copper Age samples.

These were massive population turnovers, and, as a rule, massive population turnovers are accompanied by language change. So it's highly unlikely that any Europeans today are speaking languages derived from those of the Western Hunter-Gatherers or early Neolithic farmers of Central Europe (ie. according to Renfrew the ancestors of Celts, Germanics and other Indo-Europeans). Moreover, consider this:

- most present-day Indo-European speaking Europeans form an elongated cluster between the Neolithic farmers and the Corded Ware sample, pointing to the steppe-derived Corded Ware Culture as the proximate agent of the Indo-European expansion in much of Europe

- the only present-day Europeans who closely resemble Neolithic farmers are some Sardinians (the small Romance cluster just above the two Neolithic samples), but Sardinians spoke Paleo-Sardinian or Nuragic languages until they adopted Indo-European speech, in the form of Latin, from the Romans (see page 118 here).

Also, this isn't shown on the plot, but the dominant Y-chromosome haplogroup of early Neolithic farmers is G2a, which is a low frequency marker in Europe today. The two most common Y-chromosome haplogroups among present-day Europeans are R-M198 and R-M269, which are also typical of Corded Ware and Yamnaya males, respectively, and probably originally from the steppe.

So is there any way to rework the Anatolian hypothesis so that it can be salvaged? I doubt it. Even making the steppe a homeland for all of the main Indo-European branches apart from Anatolian and Armenian probably won't help.

It is true that the Yamnaya nomads carried Near Eastern-related ancestry which may represent Proto-Indo-European admixture from outside of the steppe. But there's no evidence that it came from Anatolia.

In fact, if Neolithic Anatolians were basically identical to early Neolithic European farmers, which seems to be the case (see here and here), then it's unlikely that it did, because the latter carried a peculiar genome-wide signal that is missing in Yamnaya genomes (orange cluster in the ADMIXTURE bar graph below).** Heck, even the early Corded Ware genomes from Germany barely show any of it.

I won't go into the linguistics arguments here why the Anatolian hypothesis is implausible. But it might be worth checking out a new book on the topic by linguists Asya Pereltsvaig and Martin W. Lewis: The Indo-European Controversy: Facts and Fallacies in Historical Linguistics. I haven't read it yet, so I welcome the opinions here of those who have. I did, however, read a lot of the online articles on which the book is based. As far as I know most of them are still available here and here.

*Another version of the same PCA, with the samples labeled individually, is available here. All possible combinations of dimensions 1 to 4 are shown here. The samples are listed here. All of the samples are from Haak et al. and Allentoft et al. The PCA was run using ~56K high confidence SNPs listed here.

The Corded Ware sample is a composite of Corded Ware sequences from Germany, Scandinavia, Estonia and Poland. The Yamnaya sample is a composite of Yamnaya sequences from the Kalmykia and Samara regions of Russia.

I chose to use these composites instead of individual sequences because I didn't want to run any samples with genotype rates of less than 98%.

** For a more detailed ADMIXTURE analysis comparing early Neolithic farmers to Yamnaya refer to Haak et al. Supplementary Information 6. Note the minimal sharing of components at the higher K between the early Neolithic farmers and Yamnaya, especially at K=16, which has the lowest median cross-validation (CV) error. This is in agreement with the PCA above.

See also...

Population genomics of Early Bronze Age Europe in three simple graphs

Global PCA of selected Late Neolithic/Bronze Age Eurasians

I was curious how the Bronze Age steppe and Corded Ware genomes from the Rise dataset would behave in Principal Component Analyses (PCA) alongside populations from across the globe. Ten genomes had enough high confidence (transversion) markers to be analyzed accurately in such a way. I also ran an Iron Age Swedish sample, just to see how it differed from the older genomes.

Click on the links to go to my drive to download the plots. If you're having trouble finding the ancient samples, type their IDs into the PDF search field and hit enter.

RISE509_Afanasievo
RISE509_Afanasievo
RISE509_Afanasievo

RISE511_Afanasievo
RISE511_Afanasievo
RISE511_Afanasievo

RISE500_Andronovo
RISE500_Andronovo
RISE500_Andronovo

RISE505_Andronovo
RISE505_Andronovo
RISE505_Andronovo

RISE00_Corded_Ware
RISE00_Corded_Ware
RISE00_Corded_Ware

RISE94_Corded_Ware
RISE94_Corded_Ware
RISE94_Corded_Ware

RISE493_Karasuk
RISE493_Karasuk
RISE493_Karasuk

RISE496_Karasuk
RISE496_Karasuk
RISE496_Karasuk

RISE548_Yamnaya
RISE548_Yamnaya
RISE548_Yamnaya

RISE552_Yamnaya
RISE552_Yamnaya
RISE552_Yamnaya

RISE174_Iron_Age_Scandinavia
RISE174_Iron_Age_Scandinavia
RISE174_Iron_Age_Scandinavia

I can't see any major surprises. But I do find it remarkable how very European the Andronovo individuals appear on these plots. Keep in mind that they're ~3,000-year-old samples from the Altai region of Russia. Their ancestors probably migrated there from the Trans-Urals steppe sometime during the Middle Bronze Age.

The Andronovo Culture was succeeded in the Altai region during the Late Bronze Age by the Karasuk Culture, which was probably a new composite of local and perhaps foreign groups. Interestingly, the Karasuk samples featured above are obviously of mixed European/East Asian origin.

Note also that the Afanasievo and Yammnaya individuals fall outside the range of present-day European variation in many of the dimensions, basically as if they were pulling towards the Karitiana Indians of the Amazon. No doubt, this is their excess ANE talking.

By the way, I recently ran some of the same samples in PCA limited to West Eurasian populations. You can see the results here.

The real thing

A couple of years ago Moorjani et al. concluded that present-day Georgians of the Transcaucasus were the best available proxy for the ancient West Eurasian population that mixed into the South Asian gene pool.

This was a solid statistical fit. And you can see on the TreeMix graph below, featuring a Georgian and a Kalash, why it worked so well.

But it was also a big fat coincidence, because check out what happens when I add another migration edge to the same graph.

Thus, the Indo-Iranian and hence Indo-European speaking Kalash no longer looks very similar to the Kartvelian speaking Georgian. In fact, he appears to be most closely related to the supposedly Indo-European speaking Afanasievo and Yamnaya nomads of the Early Bronze Age Eurasian steppe. The rest of his ancestry is probably best described as South Central Asian, which is an unknown quantity to me at this stage, but probably in large part of indigenous South Asian origin (see here).

I'm only able to show this thanks to the ancient samples that are on the tree, for which, as far as I know, there aren't any useful substitutes among present-day populations. Obviously, Moorjani et al. didn't have this luxury, so they ended up with a model that was statistically sound, but didn't make much sense otherwise, especially in terms of linguistics.

My TreeMix model is easily reproducible with most of the other South Asian samples from the Human Origins, and it gels nicely with uniparental marker data too. For instance, here's a close up from a similar graph featuring a Pathan, with a few extra details.

Yep, not only do Pathans cluster among these ancients of the Eurasian steppe, but most of them also carry the same Y-chromosome haplogroup: R1a-Z93, which is derived from R1a-M417, and in all likelihood first expanded in a big way with the Proto-Indo-Iranians of the Trans-Ural steppe.

By the way, the Human Origins has four different sets of Gujarati samples from Houston, USA, marked A, B, C and D, and each one shows a different level of ancient steppe admixture as inferred with my test. GujaratiA score around 50% while GujaratiD only 40%. Does anyone know why these Gujaratis were grouped in such a way? Was it based on genetic structure or caste origin?

Full output from the analysis above is available in a zip file here. The reference samples and markers are listed here and here. The ancient samples are from Allentoft et al. 2015 and Haak et al. 2015.

See also...

The Poltavka outlier

Iron Age and Anglo-Saxon genomes from eastern England (Schiffels et al. preprint)

I haven't read this properly yet, but the results appear to be very similar to those I obtained with some of the same ancient genomes (see here), which must be very heartening for the authors (j/k). By the way, it's interesting to note that the word Celtic doesn't appear anywhere in the paper. I wonder why?

British population history has been shaped by a series of immigrations and internal movements, including the early Anglo-Saxon migrations following the breakdown of the Roman administration after 410CE. It remains an open question how these events affected the genetic composition of the current British population. Here, we present whole-genome sequences generated from ten ancient individuals found in archaeological excavations close to Cambridge in the East of England, ranging from 2,300 until 1,200 years before present (Iron Age to Anglo-Saxon period). We use present-day genetic data to characterize the relationship of these ancient individuals to contemporary British and other European populations. By analyzing the distribution of shared rare variants across ancient and modern individuals, we find that today’s British are more similar to the Iron Age individuals than to most of the Anglo-Saxon individuals, and estimate that the contemporary East English population derives 30% of its ancestry from Anglo-Saxon migrations, with a lower fraction in Wales and Scotland. We gain further insight with a new method, rarecoal, which fits a demographic model to the distribution of shared rare variants across a large number of samples, enabling fine scale analysis of subtle genetic differences and yielding explicit estimates of population sizes and split times. Using rarecoal we find that the ancestors of the Anglo-Saxon samples are closest to modern Danish and Dutch populations, while the Iron Age samples share ancestors with multiple Northern European populations including Britain.

Schiffels et al., Iron Age and Anglo-Saxon genomes from East England reveal British migration history, bioRxiv, Posted July 17, 2015. doi: http://dx.doi.org/10.1101/022723

Population genomics of Early Bronze Age Europe in three simple graphs

Thanks to recent advances in ancient genomics there's very little doubt now that the Pontic-Caspian Steppe was the source of massive population movements deep into Europe during the Late Neolithic/Early Bronze Age.

But some people still don't get it, maybe because genomics isn't their thing? Others just refuse to get it probably because it's at odds with what they've been hoping to see.

To help the former, and piss off the latter some more, I've put together three simple TreeMix graphs featuring ancient samples from a wide range of European archeological cultures, along with a little bit of commentary. Enjoy.

Full output from the analysis above is available in a zip file here. The samples and markers are listed here and here. The ancient samples are from Allentoft et al. 2015 and Haak et al. 2015. The Sub-Saharan Africans are from the fully public Human Origins dataset available here.

ADMIXTURE analysis of Allentoft et al. and Haak et al. ancient genomes

I haven't had a chance to study the output in detail yet, and I don't know what the cross-validation errors are for each of these unsupervised runs, but I'd say they all look pretty good. A Principal Component Analysis (PCA) of some of the K=10 data, showing how present-day Armenians compare to two Bronze Age Armenians, can be seen here.

K=6 spreadsheet

K=7 spreadsheet

K=8 spreadsheet

K=9 spreadsheet

K=10 spreadsheet

I did attempt to go up to K=11, but the algorithm appeared to be struggling to find a solution, so I killed the run. I'll have another go when more samples come in.

By the way, the analysis is based on the Human Origins fully public dataset available at the Reich lab website here.

To reduce errors, I limited the markers to transversion SNPs, and only kept samples with minimum call rates of 20%. This left 113K SNPs and 101 ancient genomes; 47 from Allentoft et al., 36 from Haak et al., and 18 from other recent papers. I didn't thin the markers to correct for LD, because in my experience this often results in less accurate outcomes.

Genetic substructures among Late Neolithic/Bronze Age Scandinavians

I may have discovered an interesting pattern in the Allentoft et al. data. It seems that during the Late Neolithic/Bronze Age, Scandinavia was populated by two somewhat different populations; one characterized by Y-Chromosome haplogroup R1b and a genome-wide genetic structure typical of present-day Northwestern Europeans, and another by Y-Chromosome haplogroup R1a and a relatively more eastern genome-wide genetic profile.

Below are two Principal Component Analyses (PCA), both featuring ancient Swedish genomes classified as part of the Late Neolithic Battle-Axe archeological culture. However, the first sample clusters near present-day Norwegians and belongs to Y-haplogroup R1b-U106, which is nowadays typically known as a Germanic paternal marker. On the other hand, the second sample clusters among present-day Russians and Mordovians, from all the way near the Volga, and belongs to Y-haplogroup R1a-Z645, which very likely expanded from Eastern Europe during the Late Neolithic.

Here's another example of basically the same thing, but this time with two ancient genomes from Denmark. If you're having trouble finding the ancient samples, download the PDF files and type their IDs in the PDF search field.

Coincidence? Probably not, but we obviously need more samples to confirm these results and establish that there is indeed a pattern.

Citation...

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

First look at an ancient genome from Neolithic Anatolia

Felix at GGT is in the process of uploading the genomes from the recent Pinhasi et al. paper. The file for the early Neolithic sample from Barcin, Turkey, is basically ready. I analyzed it with my K8 model and got these results (click on the image to enlarge).

I was only able to use a couple hundred SNPs for the test, so the outcome can't be taken too seriously. But it does make sense. The lack of Ancient North Eurasian (ANE) ancestry isn't surprising, because it mirrors the results of early European farmers we've seen to date.

Moreover, the relatively high level of Western European Hunter-Gatherer (WHG) ancestry, or at least something very similar, is also in line with expectations, considering that the sample was dug up in far western Anatolia, almost on the European border.

I also ran an Identical-by-State (IBS) affinity test using the Human Origins dataset and around 1800 SNPs. The results broadly back up the K8 analysis, with southern Europeans topping the list.

Citation...

Pinhasi R, Fernandes D, Sirak K, Novak M, Connell S, Alpaslan-Roodenberg S, et al. (2015) Optimal Ancient DNA Yields from the Inner Ear Part of the Human Petrous Bone. PLoS ONE 10(6): e0129102. doi:10.1371/journal.pone.0129102

See also...

The Near East ain't what it used to be

Genetic substructures among Armenians from Armenia and Lebanon

The Armenian samples from the recent Haber et al. manuscript on the genetic history of Armenia are now freely available at the Wellcome Trust Sanger website here.

I ran an analysis of 127 of these Armenians using my K8 model, after removing a couple of the individuals from Chambarak with obvious European admixture, as well as a few other problem samples. The results are shown below, along with maps of the sampling locations (courtesy of Wikipedia).

It seems that, at least based on this dataset, Armenians are a fairly homogenous bunch of people. The two groups from east of Lake Sevan show slightly higher levels of ANE than most of the rest, but this is in line with geography, because they're located a little closer to the Northeast Caucasus, where ANE peaks in West Eurasia at almost 30%.

By the way, those of you having trouble with the acronyms in this and other recent blog posts, you'll find a list of often used Eurogenes acronyms here.

See also...

The Near East ain't what it used to be