Caucasus and Swiss hunter-gatherer genomes

I know I'm late for the party but better late than never, right?

A recent study sequenced three hunter-gatherer genomes from Georgia and one from Switzerland, expanding our understanding of the pre-Neolithic genetic landscape of West Eurasia.

Eppie R. Jones et al., Upper Palaeolithic genomes reveal deep roots of modern Eurasians. Nature Communications 2015. Open access → LINK [doi:10.1038/ncomms9912]

Abstract

We extend the scope of European palaeogenomics by sequencing the genomes of Late Upper Palaeolithic (13,300 years old, 1.4-fold coverage) and Mesolithic (9,700 years old, 15.4-fold) males from western Georgia in the Caucasus and a Late Upper Palaeolithic (13,700 years old, 9.5-fold) male from Switzerland. While we detect Late Palaeolithic–Mesolithic genomic continuity in both regions, we find that Caucasus hunter-gatherers (CHG) belong to a distinct ancient clade that split from western hunter-gatherers ~45 kya, shortly after the expansion of anatomically modern humans into Europe and from the ancestors of Neolithic farmers ~25 kya, around the Last Glacial Maximum. CHG genomes significantly contributed to the Yamnaya steppe herders who migrated into Europe ~3,000 BC, supporting a formative Caucasus influence on this important Early Bronze age culture. CHG left their imprint on modern populations from the Caucasus and also central and south Asia possibly marking the arrival of Indo-Aryan languages.

Figure 1: Genetic structure of ancient Europe.

 (a). Principal component analysis. Ancient data from Bichon, Kotias and Satsurblia genomes were projected¹¹ onto the first two principal components defined by selected Eurasians from the Human Origins data set¹. The percentage of variance explained by each component accompanies the titles of the axes. For context we included data from published Eurasian ancient genomes sampled from the Late Pleistocene and Holocene where at least 200 000 SNPs were called^{1, 2, 3, 4, 5, 6, 7, 9} (Supplementary Table 1). Among ancients, the early farmer and western hunter-gatherer (including Bichon) clusters are clearly identifiable, and the influence of ancient north Eurasians is discernible in the separation of eastern hunter-gatherers and the Upper Palaeolithic Siberian sample MA1. The two Caucasus hunter-gatherers occupy a distinct region of the plot suggesting a Eurasian lineage distinct from previously described ancestral components. The Yamnaya are located in an intermediate position between CHG and EHG. (b). ADMIXTURE ancestry components¹² for ancient genomes (K=17) showing a CHG component (Kotias, Satsurblia) which also segregates in in the Yamnaya and later European populations.

The Swiss one (Bichon, Jura) is maybe less of a novelty, roughly falling within the already known parameters for Western European hunter-gatherers of Magdalenian tradition (WHG in the jargon) but the three samples from the Caucasus (CHG) are really a much needed new data-point, different from everything else that what we knew and surprisingly close to modern Caucasus populations. 

They are however very distant from all other known ancient West Eurasian samples. Fig. 2 shows an estimated divergence with early Neolithic Europeans (EEF, Stuttgart) dating from before the Last Glacial Maximum, to 24,000 years ago. The divergence of this composite West Asian macro-population (EEF's Paleoeuropean admixture is accounted for separately) with the pre-Neolithic Europeans seems to be of c. 46,000 years, what is consistent with early Upper Paleolithic (the large error margin allows for a secondary Gravettian genesis contact anyhow). On the other hand the divergence between Bichon and Lochsbour seems to fit with the Magdalenian time-frame as one would expect.

CHG are surprisingly close to modern Caucasus population, particularly to Georgians. CHG also appear to be an excellent candidate population for the formation of the early Indoeuropean Yamna people, which fit best as a mix of CHG and EHG (Eastern European hunter-gatherers). 

Figure 4: The relationship of Caucasus hunter-gatherers to modern populations.

a). Genomic affinity of modern populations¹ to Kotias, quantified by the outgroup f₃-statistics of the form f₃(Kotias, modern population; Yoruba). Kotias shares the most genetic drift with populations from the Caucasus with high values also found for northern Europe and central Asia. (b). Sources of admixture into modern populations: semicircles indicate those that provide the most negative outgroup f₃ statistic for that population. Populations for which a significantly negative statistic could not be determined are marked in white. Populations for which the ancient Caucasus genomes are best ancestral approximations include those of the Southern Caucasus and interestingly, South and Central Asia. Western Europe tends to be a mix of early farmers and western/eastern hunter-gatherers while Middle Eastern genomes are described as a mix of early farmers and Africans.

I find notable that the CHG component (do not confuse with the African one of similar color) is still apparent in the Indian subcontinent, something that was already detected in other analyses. The CHG component seems to be the core of the so called "ancient North Indian" (ANI) component, also known as "Gedrosian" or "Caucaso-Baloch". What they call in the above analysis "South Asian" would be approximately the also known as "ancient South Indian" (ASI) component, which is presumably pre-Neolithic. 

"Farmer" means European Early Farmer (EEF) and already implies some Paleolithic European admixture, until we have some Levant and Mesopotamian genuine first Neolithic samples, we should not assume that all the Fertile Crescent Neolithic people were just like that, although some may have been close. In fact, I tend to think that the CHG or a similar "highlander" component was probably important in the Zagros Neolithic and consequently in the Mesopotamian and Iranian one, reaching eventually to South Asia. See here for more details on how the Neolithic expansion in Europe and India were largely parallel but not identical at all in source populations. 

To illustrate this early Neolithic complexity, still apparent to some extent in West Asian genetics and, as I just said, in European and South Asian ones, the following archaeo-cultural map should help:

Source: Eleni Asouti 2006 (red color annotation is mine)

I strongly recommend to read the full source study, because it is very informative about what were some of our ancestors¹ doing when farming and herding were being developed in West Asia, but the map above alone gives a very good glimpse of the ethno-cultural complexity of these ancient West Asian populations. 

My understading is that the mainline (Thessalian or Aegean) European Neolithic founders must have originated within the PPNA/B complex, although uncertain about which specific culture within it (most likely not Harifian because that one is surely at the origin of Semitic languages but almost any other one would do, notably those close to the Mediterranean coast: Sultanian, Aswadian and Mureybetian). Instead the populations affecting Eastern European, Mesopotamian-Iranian (Sumer and Elam) and Indian Neolithic are most probably rather linked to what is here called as M'lafatian or Zagros Neolithic, which in turn were most likely linked one way or the other to Caucasus hunter-gatherers and in general to the "highlander" West Asian element apparent in other studies in contrast to a more EEF-like "lowlander" one. 

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¹ Sure: I'm thinking mostly of Euro-Mediterranean and Central-South Asian peoples but even if you are East Asian or Tropical African it's still very probable that some random ancestor comes from this crucial paleo-historical knot (or almost from anywhere else: admixture never ends and we are all related, even if thinly, within the last millennium or so).

Echoes from the past (Sep 16)

A. sediba

Is Australopithecus sediba in fact Homo sediba? Both brain and hand (but also pelvis and ankle) make, in the opinion of some researchers, this australopithecine the best candidate for ancestor of our own principal ancestor: Homo erectus. Science Daily has a whole series on this theory and the facts that back it: 1, 2, 3 and 4 articles. Also at PhysOrg and some of the original papers at Science (pay per view of course): 1, 2, 3, 4, 5. 


More on the Southern Iberian Neolithic idols (in Spanish but with many nice photos) at Neolítico de la Península Ibérica.


The oldest 'pub' of Scotland? Chalcolithic or Neolithic (c. 4600 years ago) building at Jarlshof (Shetland) was at least a beer brewery and bakery. It is possible that the site was also used as tavern of some sort ··> Daily Record.

The Jarlshof brewery

Reproduction with Neanderthals was rare ··> France24 (and, update!, a criticism by John Hawks).


Ötzi, the Chalcolithic herder from La Lagozza culture, was also Y-DNA G2a according to a video reported by Dienekes. This is the second time that G2a (a relatively small haplogroup today of quite clear West Asian origins) has been reported in post-Cardial Neolithic peoples in Mediterranean Europe. Earlier this year it was reported in the majority of a related population of Occitania (SE French state), together with some I2a. It is notable that both populations were culturally related, not just because of their shared Cardium Pottery roots, but also because of the Chassey-La Lagozza cultural fusion, which I'd dare suggest as precursor of the historical Ligures.

Still it is hard to explain the apparent high frequency of the lineage back then and the low one today (c. 5% on average across Europe). As for high tier exceptions, nowadays G (usually G2a in Europe) reaches 12% in mainland Italy,  14% in Sardinia (reaching as much as 21% in some locations), 12% in Corsica, 7% in Austrian Tyrol, up to 14% in some locations of Croatia, up to 11% in some locations of Greece, 13% in Moldova, 12% in Portugal and 8% in Spain. It may be a fluke that 2/3 known lineages from the Chassey-La Lagozza cultural complex are in this category (it is statistically quite reasonable) but we can't of course avoid rising an eyebrow.


Caucasian and European peoples are not really very much related. A new paper confirms that Caucasus peoples are on their own (maybe related to Anatolia, not sampled) within the West Eurasian macro-population, clustering better with West Asians than Europeans in any case, even North Caucasus populations like Chechens and such. The paper by B. Yunusbayev is also PPV, so I'll refer to Dienekes again, who includes nice, rather informative, graphs like this one:

Amber-trapped feathers show light on the evolution of birds and dinosaurs ··> BBC.


Astronomy and cosmology:

• Preferred direction of spacetime challenges the Cosmological Principle which claimed that everything was equally boring ··> PhysOrg.
• Fifty new exoplanets discovered in a row ··> BBC.
• Star rips exoplanet to shreds with X rays ··> Discovery News.

And soon to come in this blog (in separate articles to be written later):

• Is West African skull from Late Upper Paleolithic 'archaic' (meaning another species than Homo sapiens) ··> PLoS ONE.
• Gene influences behavior but... culture influences the gene that influences behavior ··> Not Exactly Rocket Science.

Grape domesticated West Asia

Kambiz mentions today this paper at Anthropology.net:

Sean Myles et al. Genetic structure and domestication history of the grape. PNAS, 2011. Open access.

Archaeological evidence suggests that grape domestication took place in the South Caucasus between the Caspian and Black Seas and that cultivated vinifera then spread south to the western side of the Fertile Crescent, the Jordan Valley, and Egypt by 5,000 y ago (1, 21). Our analyses of relatedness between vinifera and sylvestris populations are consistent with archaeological data and support a geographical origin of grape domestication in the Near East (Fig. 4 and Table 1).

He also mentions that the oldest known wine barrel is from Armenia. 

I understand that the data of fig. 4 suggest a domestication area between Turkey and Pakistan, with emphasis in the Caucasus region: Georgia, Azerbaijan and Daghestan specially. However Pakistani wild varieties cluster well also and I'd say it cannot be discarded that at least part of the development of this delicatessen crop happened maybe in the context of South Asian Neolithic.

Bronze Age culture discovered in the North Caucasus

The Telegraph reports (via AiE) that a previously unknown Bronze Age civilization has been discovered in the North Caucasus, after locating some 200 sites via air photography from the Soviet era. 

The Russo-German archaeological team found the sites all following a similar architectural plan, centered around an oval courtyard, and connected by roads. In some cases the foundations of the buildings retain up to a meter of their original height. 

The decorations and artifact styles are clearly related to the Kuban culture (axe at the left, from the Hermitage Museum), but this one is older by some 500 years, lasting from the 16th to the 13th century BCE. The sites are located rather high on the mountains, between 1400 and 2400 meters above sea level.

Approximate location of the findings

The sites stretch from the Kuban river to the west to the city of Nalchik by the East, in the autonomous republics of Karachay-Cherkessia and Kabardino-Balkaria. While Russian and Turkic languages are now spoken in the area also, a natural thought is to imagine the inhabitants of these settlements speaking NW Caucasian languages.

One detail I notice in the Wikipedia reference is that so far it was believed that the Kuban culture was derived from the, slightly older Colchian culture of Abkhazia and West Georgia, however this discovery would suggest that the opposite is true instead. This in turn may provide a frame for the migration of NW Caucasian towards the South (but notice the possible affinity with extinct Hattic), or alternatively for the arrival of Kartvelian languages maybe. It looks too recent anyhow to be related to the expansion of the Indoeuropean Hittites, which are known to have been in Anatolia since at least the 18th century BCE. This matter is admittedly complicated and surely warrants further debate in any case.


Update (Oct 13): Jean points me to this other small article at the Kyiv Post, which includes several images of the sites and the air photos that allowed their localization:

The phrasing of the relationship with the Kuban culture is significantly different (merging instead of precursor) and also the description of the area (eastern limit is said to be Kislovodsk instead of Nalchik), but I'd say that the Telegraph article seems better informed, even if it lacks images.