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Sunday, December 27, 2015

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!

Thursday, December 17, 2015

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.

Saturday, December 12, 2015

The Scythian


It's time to have a look at the Scythian steppe warrior from the Mathieson et al. dataset. This is the first Scythian individual to be genotyped.

He comes from the eastern end of the Pontic-Caspian steppe, is dated to 380-200 calBCE, and belongs to Y-chromosome haplogroup R1a, which is the dominant Y-haplogroup in Scythian and related remains tested to date.

His genome-wide data puts him closest to Northeast and Northwest Europeans from among present-day populations, rather than West and South Asians, who should, in theory, carry significant Scythian ancestry. We can probably put this down to the complex ancestry of West and South Asians.

Moreover, he can be modeled as a mixture of the Middle Bronze Age Potapovka people of the Pontic-Caspian steppe and present-day Nganasans of Siberia. This gels rather nicely with archaeological evidence, which suggests that Scythians were the descendants of Bronze Age Eastern European migrants to South Siberia, who expanded west across the Eurasian steppe during the Iron Age and eventually ended up back in Europe.

Identical-by-State (IBS) similarity

Lithuanian 0.645247
Estonian 0.645233
Latvian 0.645024
Russian_Kostroma 0.644946
Irish 0.644902
Orcadian 0.644792
Norwegian 0.644754
Belorussian 0.644727
Swedish 0.644667
Polish 0.644664
Austrian 0.644639
Danish 0.644587
English_Cornwall 0.644556
Belgian 0.644552
Scottish_Argyll 0.644548

Full output available here

Outgroup f3 shared drift statistics

Estonian 0.313726
Latvian 0.313664
Lithuanian 0.313574
Russian_Orel 0.313346
Finnish_Southwest 0.312997
Orcadian 0.312768
Norwegian 0.312768
Belorussian 0.312676
Russian_Kostroma 0.312669
Swedish 0.312608
Karelian 0.312567
Polish 0.31243
Irish 0.312281
Polish_Estonian 0.312156
Finnish 0.312102

Full output available here

qpAdm mixture model

Scythian_IA
Potapovka 0.913
Nganasan 0.087
chisq 5.815 tail prob 0.213365

Full output available here
Citation...

Mathieson et al., Genome-wide patterns of selection in 230 ancient Eurasians, Nature, Published online 23 November, 2015doi:10.1038/nature16152. Genotype dataset available here.

See also...

Cimmerians, Scythians and Sarmatians came from...

Genetic origins and legacy of the Scythians and Sarmatians

Wednesday, December 9, 2015

Mixed marriages on the early Eneolithic steppe


It looks like the Sredny Stog culture was the early vector for the spread of both Anatolian Neolithic and Caucasus hunter-gatherer (CHG) admixture onto the steppe, from the west and east, respectively:

These data testify the assumption about the existence of mixed Tripolye-Sredniy Stog marriages, because Tripolye population represented the Mediterranean anthropological type according to the not numerous Tripolye burials (Потехина 1999, c.154). It is interesting, that the massive Protoeuropoid type was typical for the oldest and the most eastern monuments of Sredniy Stog, while mesomorphic Mediterranean type was typical for the Igren cemetery, which was one of the youngest monuments related to the second and third periods of the Sredniy Stog culture and synchronous to the Tripolye B I and B I-II.

...

Appearance of pottery with pearls at the settlements of the third period of Sredniy Stog culture and glossy ceramics without ornamentation in the eastern variant sites, as well as the group of vessels with the steppe traces at the Svobodnoe settlement, allow me to assume the existence of mixed marriages between the Sredniy Stog and Northern Caucasus population.

Source: Early Eneolithic in the Pontic Steppes, book by Nadezhda Sergeenva Kotova, available at Academia.edu here.

See also...

The beast among Y-haplogroups

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

Who's your (proto) daddy Western Europeans?

Thursday, November 26, 2015

The Khvalynsk men


This is where the three Samara Eneolithic or Khvalynsk samples from the recent Mathieson et al. paper plot on my Principal Component Analysis (PCA) of ancient West Eurasia. They're labeled as Steppe_CA (steppe Copper Age). I've also marked them with their Y-chromosome haplogroups.


Individual 10433, belonging to Y-chromosome haplogroup R1a, is almost a pure Eastern European Hunter-Gatherer, which is perhaps surprising, considering he was buried with copper artifacts. On the other hand, sample 10434, the one belonging to haplogroup Q1a, and positioned further east than the other two, appears to have been whacked over the head a few times and simply thrown into a ditch.

The PCA also has most of the other samples featured in Mathieson et al., including Neolithic Anatolians (labeled Anatolia_N), as well as extra samples from Allentoft et al. and Jones et al.

See also...

The Khvalynsk men #2

Monday, November 16, 2015

CHG and the Indo-European question


The recent Jones et al. palaeogenomics paper focusing on Caucasus hunter-gatherers (CHG) has this to say about the Indo-European and Indo-Aryan expansions:

CHG left their imprint on modern populations from the Caucasus and also central and south Asia possibly marking the arrival of Indo-Aryan languages.

...

It has been proposed that modern Indians are a mixture of two ancestral components, an Ancestral North Indian component related to modern West Eurasians and an Ancestral South Indian component related more distantly to the Onge [25]; here Kotias proves the majority best surrogate for the former [28,29] (Supplementary Table 10). It is estimated that this admixture in the ancestors of Indian populations occurred relatively recently, 1,900–4,200 years BP, and is possibly linked with migrations introducing Indo-European languages and Vedic religion to the region (28).

...

Finally, we found that CHG ancestry was also carried east to become a major contributor to the Ancestral North Indian component found in the Indian subcontinent. Exactly when the eastwards movement occurred is unknown, but it likely included migration around the same time as their contribution to the western European gene pool and may be linked with the spread of Indo-European languages. However, earlier movements associated with other developments such as that of cereal farming and herding are also plausible.

To their credit, in that last quote the authors leave open the possibility that CHG arrived in South Asia in multiple waves and with a variety of groups, including Neolithic farmers. Nevertheless, I'd say their comments are still confusing and perhaps also incredibly naive, because essentially they appear to be hoping that in CHG they've identified the Proto-Indo-European and Proto-Indo-Aryan genetic component.

Indeed, a lot of people actually believe that the overwhelming part of the West Eurasian admixture in South Asia should be attributed to the Indo-Aryans. But that's just stupid.

After all, many Dravidian groups that in all likelihood never spoke Indo-Aryan languages carry significant ratios of West Eurasian ancestry. Some of this influence can be explained by admixture with Indo-Aryans, but uniparental markers suggest that much of it was brought from West Asia by the Proto-Dravidians (see here).

Below is the aforementioned Supplementary Table 10. Note that two of the Indian populations that are best modeled with D-stats as mixtures of Kotias (one of the two CHG genomes) and Onge are Dravidian speakers (Mala and Vishwabrahmin or Viskwakarma, a Malayali community). Another three are Indo-Aryans (GujaratiC, GujaratiD and Lodhi), but with high levels of Ancestral South Indian (ASI) admixture, which suggests their ancestors might have been language shifters.

On the other hand, the three populations that are best modeled as Afanasievo (a pastoralist group from the Early Bronze Age steppe) and Onge are all Indo-Aryans (GujaratiA, GujaratiB and Tiwari).




But like I say, South Asia is a complex melting pot of Indo-Aryans, Dravidians, and several other linguistic groups, so a more comprehensive analysis than a comparison of a few D-stats is needed to unravel the origins of its people in a meaningful way.

By the way, Jones et al. also argue that CHG is basically an offshoot of the so called Basal Eurasian clade, which was first described in Lazaridis et al. 2014. I'm highly skeptical of this claim, and I might check it out after I get my hands on the CHG genomes.

Citation...

Jones, E. R. et al. Upper palaeolithic genomes reveal deep roots of modern eurasians. Nat. Commun. 6:8912 doi: 10.1038/ncomms9912 (2015).

See also...

The "fourth strand" of European ancestry came from the Caucasus

The "fourth strand" of European ancestry came from the Caucasus


From a news feature about a forthcoming palaeogenomics paper:

"The question of where the Yamnaya come from has been something of a mystery up to now," said one of the lead senior authors Dr Andrea Manica, from Cambridge's Department of Zoology.

"We can now answer that as we've found that their genetic make-up is a mix of Eastern European hunter-gatherers and a population from this pocket of Caucasus hunter-gatherers who weathered much of the last Ice Age in apparent isolation. This Caucasus pocket is the fourth major strand of ancient European ancestry, one that we were unaware of until now," he said

Read more at: 'Fourth strand' of European ancestry originated with hunter-gatherers isolated by Ice Age

Update: the paper is now out and open access at Nature Communications.

The two ancient Georgian genomes belong to Y-chromosome haplogroup J. So it looks like I was right when I said that this type of ancestry mostly entered the European steppe from the Caucasus via female mediated gene flow during the Bronze Age (see here and here).

However, one of the Eastern European Hunter-Gatherers (EHG) from Mathieson et al. 2015 also belonged to haplogroup J. This suggests that there was intermittent gene flow, including some paternal gene flow, between the Caucasus and the steppe well before the Bronze Age.

Nevertheless, it's now even more difficult to accept that Y-haplogroup R1 and the Proto-Indo-Europeans might have originated south of the steppe. Clearly, R1 appears to be a steppe marker from way back, and I seriously doubt that Indo-European languages were introduced into highly patriarchal steppe societies by female migrants from the Caucasus.


Image credit: Nature Communications, dx.doi.org/10.1038/ncomms9912

Thursday, October 29, 2015

Mitochondrial DNA from Maykop + Wolfgang Haak on Near Eastern-related ancestry in Yamnaya


From page 166 of a report posted recently at Academia.edu:

Majkop verfügen sowohl über eine «paläolithische» Haplogruppe (U8) als auch über «neolithische» Haplogruppen: V (Недолужко u. a. 2014), T2, N1. Bei einem Objekt aus einem Grab bei der Staniza Novosvobodnaja fanden wir auch die Haplogruppe М52. Die gewonnenen Daten sprechen für eine (auf dem Niveau der mitochondrialen DNA) mögliche genetische Gemeinschaft der archäologischen Kulturen von Majkop und Novosvobodnaja.

The presence of Indian-specific mtDNA haplogroup M52 is surprising. Maykop territory was located just south of the steppe, but M52 isn't found in any of the Bronze and Iron Age samples from the steppe tested to date.

Here's the comment from Haak, from an abstract titled The role of the Caucasus in the formation of the Eurasia's genetic makeup: Insights and questions from ancient DNA research.

Recent genetic research on autosomal and uniparentally-inherited markers has shown a remarkable genetic uniformity of Caucasian populations despite the region’s notable linguistic and cultural diversity. When compared to neighbouring regions, the smooth genetic transition from the Near/Middle East to the Caucasus is in stark contrast to the marked differences to populations from the East European steppes. Flanked by the Black and the Caspian Seas, it remains unclear to what extent the Caucasus served as a corridor and whether and if so when ancient migrations had affected and shaped the region’s genetic profile. Ancient DNA research on Mesolithic, Neolithic and Bronze Age individuals from Western Eurasia have recently thrown fresh light on the Caucasus as region, which appears to have played a critical role in the formation of the genetic ancestry of the Yamnaya people, Bronze Age pastoralist of the east European steppes. The Yamnaya carry strong signals of eastern hunter-gatherer (EHG) ancestry and ancient Near Eastern ancestry that is different from the one that giving rise to early European farmers. While modern-day Armenians are the best proxy for the putative source population of the EHG dilution in the steppes, it is highly likely that prehistoric cultural groups from the Caucasus will provide a much better temporal and contextual fit.

Actually, I'd say western Georgians are the best proxy for the putative source population of the EHG dilution in the steppes. See here...

Yamnaya's exotic ancestry: The Kartvelian connection

See also...

Steppe Maykop: a buffer zone?

Genetic borders are usually linguistic borders too

On the genetic prehistory of the Greater Caucasus (Wang et al. 2018 preprint)

Thursday, October 22, 2015

Plague germs may have facilitated Bronze Age expansions from the steppe


Update 07/12/2018: Europe's ancient proto-cities may have been ravaged by the plague

...

Open access at Cell:

Summary: The bacteria Yersinia pestis is the etiological agent of plague and has caused human pandemics with millions of deaths in historic times. How and when it originated remains contentious. Here, we report the oldest direct evidence of Yersinia pestis identified by ancient DNA in human teeth from Asia and Europe dating from 2,800 to 5,000 years ago. By sequencing the genomes, we find that these ancient plague strains are basal to all known Yersinia pestis. We find the origins of the Yersinia pestis lineage to be at least two times older than previous estimates. We also identify a temporal sequence of genetic changes that lead to increased virulence and the emergence of the bubonic plague. Our results show that plague infection was endemic in the human populations of Eurasia at least 3,000 years before any historical recordings of pandemics.


Rasmussen et al., Early Divergent Strains of Yersinia pestis in Eurasia 5,000 Years Ago, Cell, Volume 163, Issue 3, p571–582, 22 October 2015, DOI: https://dx.doi.org/10.1016/j.cell.2015.10.009

Also, some juicy quotes at ScienceDaily:

Study co-author Dr Marta Mirazón-Lahr, from Cambridge's Leverhulme Centre for Human Evolutionary Studies (LCHES), points out that a study earlier this year from Willerslev's Copenhagen group showed the Bronze Age to be a highly active migratory period, which could have led to the spread of pneumonic plague.

"The Bronze Age was a period of major metal weapon production, and it is thought increased warfare, which is compatible with emerging evidence of large population movements at the time. If pneumonic plague was carried as part of these migrations, it would have had devastating effects on small groups they encountered," she said.

"Well-documented cases have shown the pneumonic plague's chain of infection can go from a single hunter or herder to ravaging an entire community in two to three days."

University of Cambridge. "Plague in humans 'twice as old' but didn't begin as flea-borne, ancient DNA reveals." ScienceDaily, 22 October 2015. www.sciencedaily.com/releases/2015/10/151022124532.htm.

Friday, October 16, 2015

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.

Tuesday, October 13, 2015

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

Saturday, October 10, 2015

Eight thousand years of natural selection in Europe - take 2


Open access at bioRxiv [LINK]. Lots of new samples in this updated version. The Principal Component Analysis (PCA) below from the paper appears to be affected by projection bias or shrinkage, but it's more or less correct. Can't wait to get my hands on the genotype data.

Abstract: The arrival of farming in Europe around 8,500 years ago necessitated adaptation to new environments, pathogens, diets, and social organizations. While indirect evidence of adaptation can be detected in patterns of genetic variation in present-day people, ancient DNA makes it possible to witness selection directly by analyzing samples from populations before, during and after adaptation events. Here we report the first genome-wide scan for selection using ancient DNA, capitalizing on the largest genome-wide dataset yet assembled: 230 West Eurasians dating to between 6500 and 1000 BCE, including 163 with newly reported data. The new samples include the first genome-wide data from the Anatolian Neolithic culture, who we show were members of the population that was the source of Europe's first farmers, and whose genetic material we extracted by focusing on the DNA-rich petrous bone. We identify genome-wide significant signatures of selection at loci associated with diet, pigmentation and immunity, and two independent episodes of selection on height.



Mathieson et al., Eight thousand years of natural selection in Europe, bioRxiv revised preprint, posted October 10, 2015, doi: https://dx.doi.org/10.1101/016477

See also...

Lactase persistence and ancient DNA

Sunday, October 4, 2015

Yamnaya's exotic ancestry: The Kartvelian connection


I've made a discovery. The Near Eastern-related ancestors of the Yamnaya steppe pastoralists were also the ancestors of present-day Georgian Mingrelians, or their very close relatives, and in all likelihood speakers of Kartvelian, which has a long history in the Caucasus. Here's a nice map from Wikipedia and a pic of some Mingrelians. Check out the impressive headware.



TreeMix is very specific and precise about this. In my analyses, based on a couple of different methods, the Mingrelians are the only population chosen as a source for the Near Eastern-related ancestry in the Yamnaya.

Keep in mind, this is an unsupervised test and the algorithm has an infinite number of choices, because migration edges can run from any part of the tree, and yet it chooses the Mingrelians. By the way, if anyone's wondering, I did also try the Bronze Age Armenians, to no avail.



This outcome is also more or less reproducible with more complex topologies that include samples from Central Asia. In the graph below the Georgian Mingrelians form a clade with the Near Eastern-related ancestry of the Yamnaya. It'd be interesting to see if other Georgian groups, like the Svans, do even better, if that's actually possible, but they're not available at the moment.


I actually came up with basically the same result earlier this year using qpAdm (see here). But at the time I was skeptical of its usefulness because qpAdm only offers a supervised test, so picking Georgians as a reference population and getting a good statistical fit doesn't mean as much as a reproducible unsupervised migration edge.

Now, judging by their ADMIXTURE results, these Georgian Mingrelians do carry some Early European farmer-related ancestry, which is missing in the Yamnaya (see here). Therefore, it's likely that ancient samples from the west or northwest Caucasus will prove to be even better proxies for the Near Eastern-related ancestry in the Yamnaya.

The samples used to produce the above TreeMix graphs are listed here. They're sourced from the Allentoft et al., Haak et al., and Lazaridis et al. datasets. I limited the markers to ~65K transversion (high confidence) SNPs that overlap between these datasets.

Updates...

Caucasus hunter-gatherers (CHG) and the Indo-European question

'Fourth strand' of European ancestry originated with (Caucasus) hunter-gatherers isolated by Ice Age

Mixed marriages on the early Eneolithic steppe

Saturday, October 3, 2015

Linguistics, Archeology and Genetics (L-A-G) Conference abstracts


The Max Planck Institute is holding a conference in a few days dedicated to the latest developments in the search for the Indo-European homeland.

Linguistics, Archeology and Genetics: Integrating new evidence for the origin and spread of Indo-European languages

A draft book of presentation abstracts is available here. This one from Danish linguist Guus Kroonen looks very promising.

Pre-Indo-European speech carrying a Neolithic signature emanating from the Aegean

Guus Kroonen, Institute for Nordic Studies and Linguistics, Copenhagen University, Copenhagen

When different Indo-European speaking groups settled Europe, they did not arrive in terra nullius. Both from the perspective of the Anatolian hypothesis and the Steppe hypothesis the carriers of Indo-European speech likely encountered existing populations that spoke dissimilar, unrelated languages. Relatively little is known about the Pre-Indo-European linguistic landscape of Europe, as the Indo-Europeanization of the continent caused a largely unrecorded, massive linguistic extinction event. However, when the different Indo-European groups entered Europe, they incorporated lexical material from Europe’s original languages into their own vocabularies. By integrating these “natural samples” of Pre-Indo-European speech, the original European linguistic and cultural landscape can partly be reconstructed and matched against the Anatolia and the Steppe hypotheses. My results reveal that Pre-Indo-European speech contains a clear Neolithic signature emanating from the Aegean, and thus patterns with the prehistoric migration of Europe’s first farming populations. These results also imply that Indo-European speech came to Europe following a later migration wave, and therefore favor the Steppe Hypothesis as a likely scenario for the spread of the Proto-Indo-Europeans.

Also, we've known for a while now that the good people at Broad MIT/Harvard have analyzed remains from Neolithic Anatolia, but it's nice to see this framed in the context of the Indo-European homeland debate.

Close genetic relationship of Neolithic Anatolians to early European farmers

Iosif Lazaridis et al.

We study 1.2 million genome-wide single nucleotide polymorphisms on a sample of 26 Neolithic individuals (~6,300 years BCE) from northwestern Anatolia. Our analysis reveals a homogeneous population that was genetically similar to early farmers from Europe (FST=0.004±0.0003 and frequency of 60% of Y-chromosome haplogroup G2a). We model Early Neolithic farmers from central Europe and Iberia as a genetic mixture of ~90% Anatolians and ~10% European hunter-gatherers, suggesting little influence by Mesolithic Europeans prior to the dispersal of European farmers into the interior of the continent. Neolithic Anatolians differ from all present-day populations of western Asia, suggesting genetic changes have occurred in parts of this region since the Neolithic period. We suggest that the language spoken by the homogeneous Anatolian-European Neolithic farmers is unlikely to have been the same as that spoken by the Yamnaya steppe pastoralists whose ancestry was derived from eastern Europe and a different population from the Caucasus/Near East [Haak et al. 2015], and discuss implications for alternative models of Indo-European dispersals.

Indeed, my view is that the implications of this data for the Anatolian hypothesis are fatal (see here). It might also have dire implications for the Armenian Plateau hypothesis, although for the time being this hypothesis limps on.

Feel free to post and discuss your favorite abstracts in the comments below. If anyone reading is going to this thing, I'd love to hear more about the Y-haplogroups of the Anatolian farmers.

Friday, October 2, 2015

Essential reading: Paleoecology, Subsistence, and 14C Chronology of the Eurasian Caspian Steppe


To help things run more smoothly in the comments, I urge everyone taking part in the debates here about the colonization of the Eurasian steppe and the Indo-European homeland question to read carefully the following three papers. They're all open access:

1) Paleoecology, Subsistence, and 14C Chronology of the Eurasian Caspian Steppe Bronze Age

2) The Steppe and the Caucasus During the Bronze Age Mutual Relationships and Mutual Enrichments

3) New Radiocarbon Dates and a Review of the Chronology of Prehistoric Populations from the Minusinsk Basin, Southern Siberia, Russia

In particular, please note the latest calibrated radiocarbon-based dates of the main archaeological cultures being discussed:

- Khvalynsk, Eneolithic, 4300–3800 cal BC

- Steppe Maikop, Early Bronze Age, 3800–3000 cal BC

- Yamnaya, Early Bronze Age, 3000–2450 cal BC

- Afanasievo, Early Bronze Age, 2900-2500 cal BC

- Early Catacomb, Early Bronze Age, 2600–2350 cal BC

Of course, Yamnaya are in large part of Eastern European hunter-gatherer (EHG) origin but with roughly 50% of Near Eastern-related ancestry from an unknown population (Haak et al. 2015). Paper #2 linked to above provides tentative isotopic evidence that the latter might be the Steppe Maikop people or their descendants (see paragraph 4 on page 58).

However, the Khvalynsk population from the Samara region harbors around 25% of the same or very similar Near Eastern-related ancestry (unpublished data courtesy of David Anthony). And, as per the dates above, Khvalynsk existed before Steppe Maikop.

Thus, although the increase of the Near Eastern-related ancestry on the steppe from the Khvalynsk to the Yamnaya periods can be tentatively attributed to Maikop influence, this cannot be the initial source of this type of ancestry on the steppe.

Moreover, dates older than 3,000 cal BC for Afanasievo appear to be spurious (see paper #3 above). If so, what this means is that Afanasievo is around the same age as Yamnaya, or perhaps a little younger, and thus the generally accepted hypothesis that Afanasievo derives from Yamnaya or pre-Yamnaya looks safe.

Now, it's especially important that everyone concerned is aware of the key climatic shifts on the steppe, because climatic changes are often invoked as likely causes of major population movements within and out of the steppe. So I'm re-posting here Table 1 from paper #1 (click to enlarge).


I'll update this post as new information comes in, which will hopefully be very soon. There are signals that something big is on the way from the Reich Lab pertaining to the Indo-European homeland debate (for instance, see here).

See also...

Near Eastern admixture in Yamnaya: a couple of graphs + some ideas

Thursday, October 1, 2015

Near Eastern admixture in Yamnaya: a couple of graphs + some ideas


Update 05/10/2015: Yamnaya's exotic ancestry: The Kartvelian connection

...

The Afanasievo and Yamnaya samples published to date are remarkably homogeneous. Hopefully the bar graphs below, based on a couple of my recent ADMIXTURE runs, illustrate this well enough.

The Near Eastern-related ancestry proportions among the Yamnaya individuals do appear to rise steadily from early Yamnaya to late Yamnaya/early Catacomb. But the ancestral components remain the same, and if the increase in the Near Eastern-related admixture is real, the process is very subtle.

What this suggests to me is that groups of a southern provenance - in all likelihood Neolithic farmers seeking new land - arrived somewhere on the Pontic-Caspian steppe very early, perhaps even during the Early Neolithic, to eventually blend with local foragers. That's because the basic Yamnaya genotype had to have existed before the Yamnaya or pre-Yamnaya ancestors of the Afanasievo nomads set off on their 2000 km trek to the Minusinsk Basin in South Siberia, probably around 3,300 BC.

No doubt, the mixing didn't stop after the initial farmer/forger admixture event, and this is probably why the Near Eastern-related ancestry proportions rise gradually throughout the Yamnaya period. Indeed, considering the high mobility of Bronze Age steppe pastoralists, it's likely that long distance trade, alliances and marriages resulted in the genetic homogenization of vast stretches of Eastern Europe during their reign.


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.

Thursday, September 17, 2015

Uralic 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 Uralics. 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

Sunday, September 13, 2015

ASHG 2015 abstracts


The abstract search is here. Feel free to post your picks in the comments. Lots of detail in this one, which is very much appreciated.

It has hitherto been difficult to obtain genome-wide data from the Near East. By targeting the inner ear region of the petrous bone for extraction [Pinhasi et al., PLoS One 2015] and using a genome-wide capture technology [Haak et al., Nature, 2015] we achieved unprecedented success in obtaining genome-wide data on more than 1.2 million single nucleotide polymorphism targets from 34 Neolithic individuals from Northwestern Anatolia (~6,300 years BCE), including 18 at greater than 1× coverage. Our analysis reveals a homogeneous population that is genetically a plausible source for the first farmers of Europe in the sense of (i) having a high frequency of Y-chromosome haplogroup G2a, and (ii) low Fst distances from early farmers of Germany (0.004 ± 0.0004) and Spain (0.014 ± 0.0009). Model-free principal components and model-based admixture analyses confirm a strong genetic relationship between Anatolian and European farmers. We model early European farmers as mixtures of Neolithic Anatolians and Mesolithic European hunter-gatherers, revealing very limited admixture with indigenous hunter-gatherers during the initial spread of Neolithic farmers into Europe. Our results therefore provide an overwhelming support to the migration of Near Eastern/Anatolian farmers into southeast and Central Europe around 7,000-6,500 BCE [Ammerman & Cavalli Sforza, 1984, Pinhasi et al., PLoS Biology, 2005]. Our results also show differences between early Anatolians and all present-day populations from the Near East, Anatolia, and Caucasus, showing that the early Anatolian farmers, just as their European relatives, were later demographically replaced to a substantial degree.

I. Lazaridis, D. Fernandes, N. Rohland, S. Mallick, K. Stewardson, S. Alpaslan, N. Patterson, R. Pinhasi, D. Reich, Genome-wide data on 34 ancient Anatolians identifies the founding population of the European Neolithic. ASHG 2015 abstract. Talk to be held on October 9.

See also...

The ancient DNA case against the Anatolian hypothesis

Monday, September 7, 2015

Copper & Bronze Age genomes from northern Spain


Update: the paper is now available and open access here.

See also: Yamnaya-related admixture in Bronze Age northern Iberia

...

A paper titled "Ancient genomes link early farmers from Atapuerca in Spain to modern-day Basques", by Günther et al., will appear shortly in PNAS early edition. Here's the press release from Uppsala University.

An international team led by researchers at Uppsala University reports a surprising discovery from the genomes of eight Iberian Stone-Age farmer remains. The analyses revealed that early Iberian farmers are the closest ancestors to modern-day Basques, in contrast previous hypotheses that linked Basques to earlier pre-farming groups.

The team could also demonstrate that farming was brought to Iberia by the same/similar groups that migrated to northern and central Europe and that the incoming farmers admixed with local, Iberian hunter-gather groups, a process that continued for at least 2 millennia.

The study is published today, ahead of print, in the leading scientific journal Proceedings of the National Academy of Sciences of the USA, PNAS.

Most of the previous studies about the transition from small and mobile hunter-gatherer groups to larger and sedentary farming populations have focused on central and northern Europe, however much less in known about how this major event unfolded in Iberia. This time, the research team investigated eight individuals associated with archaeological remains from farming cultures in the El Portalón cave from the well-known Anthropological site Atapuerca in northern Spain.

“The El Portalon cave is a fantastic site with amazing preservation of artefact material,” says Dr. Cristina Valdiosera of Uppsala University and La Trobe University, one of the lead authors.

“Every year we find human and animal bones and artifacts, including stone tools, ceramics, bone artefacts and metal objects, it is like a detailed book of the last 10,000 years, providing a wonderful understanding of this period. The preservation of organic remains is great and this has enabled us to study the genetic material complementing the archaeology,” Dr. Cristina Valdiosera continues.

From these individuals who lived 3,500-5,500 years ago, the authors generated the first genome-wide sequence data from Iberian ancient farmers and observed that these share a similar story to those of central and northern Europe. That is, they originate from a southern wave of expansion, and also admixed with local hunter-gatherer populations and spread agricultural practices through population expansions. The authors noticed that although they share these similarities with other European farmers, this early Iberian population has its own particularities.

“We show that the hunter-gatherer genetic component increases with time during several millennia, which means that later farmers were genetically more similar to hunter-gatherers than their forefathers who brought farming to Europe,” says Dr. Torsten Günther of Uppsala University and one of the lead authors.

“We also see that different farmers mixed with different hunter-gatherer groups across Europe, for example, Iberian farmers mixed with Iberian hunter-gatherers and Scandinavian farmers mixed with Scandinavian hunter-gatherers.” Dr. Cristina Valdiosera adds.

The study also reports that compared to all modern Spanish populations, the El Portalón individuals are genetically most similar to modern-day Basques. Basques have so far – based on their distinct culture, non-indo-European language, but also genetic make-up – been thought of as a population with a long continuity in the area, probably since more than 10,000 years ago.

“Our results show that the Basques trace their ancestry to early farming groups from Iberia, which contradicts previous views of them being a remnant population that trace their ancestry to Mesolithic hunter-gatherer groups,” says Prof. Mattias Jakobsson of Uppsala University, who headed the study.

“The difference between Basques and other Iberian groups is these latter ones show distinct features of admixture from the east and from north Africa.” he continues.

These findings shed light into the demographic processes taking place in Europe and Iberia during the last 5,000 years which highlights the unique opportunities gained from the collaborative work of archaeologists, anthropologists and geneticists in the analysis of ancient DNA.

“One of the great things about working with ancient DNA is that the data obtained is like opening a time capsule. Seeing the similarities between modern Basques and these early farmers directly tells us that Basques remained relatively isolated for the last 5,000 years but not much longer,” says Dr. Torsten Günther.

Source: Ancient genomes link early farmers to Basques

Wednesday, September 2, 2015

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

Saturday, August 29, 2015

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

Monday, August 24, 2015

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

Wednesday, August 19, 2015

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

Tuesday, August 18, 2015

Warfare and torture in the last years of the LBK


More than half of the 26 victims of an apparent ambush on a Linear Pottery (LBK) village in Neolithic Germany had their legs broken. The archaeologists studying the site think it was either torture or ritual mutilation. Also note the lack of young women in the death pit. They were probably kidnapped. The paper is behind a pay wall, but there's a news feature on the findings here.

Abstract: Conflict and warfare are central but also disputed themes in discussions about the European Neolithic. Although a few recent population studies provide broad overviews, only a very limited number of currently known key sites provide precise insights into moments of extreme and mass violence and their impact on Neolithic societies. The massacre sites of Talheim, Germany, and Asparn/Schletz, Austria, have long been the focal points around which hypotheses concerning a final lethal crisis of the first Central European farmers of the Early Neolithic Linearbandkeramik Culture (LBK) have concentrated. With the recently examined LBK mass grave site of Schöneck-Kilianstädten, Germany, we present new conclusive and indisputable evidence for another massacre, adding new data to the discussion of LBK violence patterns. At least 26 individuals were violently killed by blunt force and arrow injuries before being deposited in a commingled mass grave. Although the absence and possible abduction of younger females has been suggested for other sites previously, a new violence-related pattern was identified here: the intentional and systematic breaking of lower limbs. The abundance of the identified perimortem fractures clearly indicates torture and/or mutilation of the victims. The new evidence presented here for unequivocal lethal violence on a large scale is put into perspective for the Early Neolithic of Central Europe and, in conjunction with previous results, indicates that massacres of entire communities were not isolated occurrences but rather were frequent features of the last phases of the LBK.

Meyer et al., The massacre mass grave of Schöneck-Kilianstädten reveals new insights into collective violence in Early Neolithic Central Europe, Published online before print August 17, 2015, doi: 10.1073/pnas.1504365112

Sunday, August 16, 2015

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.

Thursday, August 13, 2015

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

Tuesday, August 11, 2015

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

Sunday, August 9, 2015

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

Wednesday, July 29, 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