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).

PPNB ancient mtDNA and its legacy

There are several interesting studies in my "to do" list and I will be commenting them in the following days (I am quite busy these weeks and therefore I concentrate my efforts on weekends).

In this entry we have a rather interesting analysis of ancient mtDNA from the Pre-Pottery Neolithic B of Syria (NE and South) and its legacy on modern populations of West Asia and SE Europe, as well as on ancient European Neolithic ones.

Eva Fernández et al., Ancient DNA Analysis of 8000 B.C. Near Eastern Farmers Supports an Early Neolithic Pioneer Maritime Colonization of Mainland Europe through Cyprus and the Aegean Islands. PLoS Genetics 2014. Open access → LINK [doi:10.1371/journal.pgen.1004401]

I understand that the sequences are not really new but that they were first discussed in Fernández 2005 (thesis in Spanish) and 2008. What is new is the comparison with ancient and modern populations in search of their possible legacy.

Early PPNB (from CONTEXT C14 database)

In spite of the relevance of this analysis, it must be cautioned that the Tell Ramad and Tell Halula sites may not be fully representative of the actual genetic diversity of PPNB as a whole, a cultural area that spanned all the Levant, from the Kurdish mountains to the Sinai and Cyprus.

If, as the authors argue and I have already suggested in relation to the NE African affinities of European Neolithic ancestry, the arrival of Neolithic to Thessaly happened via a coastal route, inland PPNB sites may well not be as informative as Palestinian or Cypriot ones.

But this is what we have for now, so let's see what these ancient Syrian farmers tell us, while we await further Neolithic sequences from potentially more relevant sites.

Table 1. Mitochondrial DNA typing of 15 Near Eastern PPNB skeletons.

40% of the sequences belong to haplogroup K, a U8-derived lineage unknown in Europe before the Neolithic. Most of the other lineages (40%) belong to R0 but half of them belong to R0(xHV), extremely rare in Europe (common in Arabia instead) and the H sequences cannot be identified either with anything common nowadays. The remaining 20% of lineages (U*, N* and L3*) are not too helpful either.

So when the authors compare them with modern and ancient populations most of the affinity corresponds to a single basal haplotype of K (16224C,16311C) as described in supplementary table 5.

Figure 2. Contour map displaying the percentage of individuals of the database carrying PPNB haplotypes.
Only populations with clear geographic distribution were included. Gradients indicate the degree of similarity between PPNB and modern populations (dark: high; clear: small).

The SE European and West Asian populations with the greatest legacy of this haplotype are: the Csángó of Moldavia (22%), Cypriots (13%), Ashkenazi Jews (11%), Crimean Tatars (10%) and Georgians (9%). Cardium Pottery farmers from Catalonia (23%) and a pooled Central European Danubian Neolithic sample (10%) also score high for this lineage.

Some other PPNB matrilineages also show some lesser modern prevalence:

• 16223T (L3) → Qatar, Yemen (not necessarily the same L3(xM,N) lineage, it must be said)
• 16224C,16311C,16366T (K) → Druze
• 16256T (H) → Bedouin

The other haplotypes have not been detected in modern nor European Neolithic populations.

The obvious conclusion is that only the 16224C+16311C K haplotype was, of all the Euphrates PPNB lineages active in the Neolithic European founder effect. This haplotype was present only in 1/15 individuals from the Euphrates PPNB, so rather marginal over there, although a close relative found today among the Druze was more common (3/15).

Another conclusion is that the Csángó probably have a quite direct line of ancestry to the early European farmers, shedding some light on the origin of this mysterious population at risk of extinction.

The coastal route to Thessaly proposed here makes all sense to me because, on one side, early Anatolian Neolithic cultures do not seem to have any obvious cultural affinity with the first European Neolithic of Sesklo (Painted Pottery) and Otzaki (Cardium Pottery), and, on the other side, there is clear evidence of some NE African genetic legacy mediated by Palestine: Y-DNA E1b-V13 naturally but also the "Basal Eurasian" speculation of Lazaridis that ended up being revealed as Dinka affinity in fig. S7 of Skoglund & Malström.

This theory can only be strongly confirmed if Palestinian and Cypriot ancient DNA is sequenced and fits well in it. Similarly ancient Balcanic DNA would be most interesting to have as well for a more direct reference. But, in any case, the theory seems at the very least plausible and supported by some important evidence.

My hypothetical reconstruction of a plausible coastal route of Neolithic towards Thessaly (dashed red line)
on a base map of Middle PPNB from the CONTEXT database.

It is also important to notice that the Syrian PPNB sequences are different from the modern mtDNA pool of West Asia, dominated by lineages like J, T1 and U3. This suggests that, at the very least in this region of the Syrian Euphrates, there have been important demographic changes since Neolithic, something confirmed by data from the same are but of later dates (which anyhow is not yet modern either). 

Fernández et al. discuss this issue in some detail:

Our PPNB population includes a high percentage (80%) of lineages with a Palaeolithic coalescence age (K, R0 and U*) and differs from the current populations from the same area, which exhibit a high frequency of mitochondrial haplogroups J, T1 and U3 (Table S7). The latter have been traditionally linked with the Neolithic expansion due to their younger coalescence age, diversity and geographic distribution [11], [12], [49]. In addition to the PPNB population, haplogroup T1 is also absent in other Early Neolithic populations analyzed so far [17], [22], [26], [30]. Haplogroup U3 has been found only in one LBK individual and it has been suggested that it could have been already part of the pre-Neolithic Central European mitochondrial background [19].

Haplogroup J is present in moderate frequencies in Central European LBK-AVK populations (11.75%) and it has been proposed as part of the Central European “mitochondrial Neolithic package” [19]. However, it has also been described in one late hunter-gatherer specimen of Germany, raising the possibility of a pre-Neolithic origin [23]. Haplogroup J is present in low frequency (4%) in Cardial/Epicardial Neolithic samples of North Eastern Spain [27], [28], [31]. Absence of Mesolithic samples from the same region prevents making any inference about its emergence during the Mesolithic or the Neolithic. However, its absence in the PPNB genetic background reinforces the first hypothesis.

These findings suggest that (1) late Neolithic or post-Neolithic demographic processes rather than the original Neolithic expansion might have been responsible for the current distribution of mitochondrial haplogroups J, T1 and U3 in Europe and the Near East and (2) lineages with Late Paleolithic coalescent times might have played an important role in the Neolithic expansive process. The first suggestion alerts against the use of modern Near Eastern populations as representative of the genetic stock of the first Neolithic farmers while the second will be explored in depth in the following section.

From the viewpoint of material Prehistory, it is of course correct, that PPNB was overwhelmed by later cultural processes, which may have implied demic expansions and replacements of some sort, even if many of them seem to originate within West Asia.

First of all, there is the Halafian cultural expansion, originating in Upper Mesopotamia; then we also have to consider the Semitic cultural and linguistic expansion, originating in Palestine; finally we have to consider the Indoeuropean waves: first the Anatolian group (Hittites, etc.) via the Caucasus, later the Balcanic group of Phrygians (and probably Armenians as derived branch) and finally the Iranian one from Central Asia. Even within the Semitic expansion there were probably several waves as well. All together must have significantly reshuffled the genetic landscape of the region. 

But unless we get more ancient West Asian DNA it will be most difficult to discern clearly how all that played out. After all the Syrian Euphrates can be exceptional in many aspects, being right in the middle of all: a true pivot of the Fertile Crescent, subject to pressure from all directions. 

Stoning at Dmanisi

H. georgicus

Lots of cobbles have been found in a gully near Dmanisi, Georgia, the oldest known site of Homo erectus (or habilis or georgicus) in Eurasia. The cobbles could not have arrived there naturally and are not found in other areas of the site (Olduwayan style tools have been found instead). 

The researchers suspect that the abundance of cobbles in the gully was caused because it was a pass our ancient relatives used to attack carnivores, by stoning them, and rob them their prey. The unusually high frequencies of carnivore bones in the site would seem to support this kind of strategy and ratify our earliest relatives as active scavengers who could rob their prey to other predators by using the skills nature gave them: sociality, intelligence and two free hands. 

Full story at The Great Beyond (found at Archaeology in Europe).