Differentiation and diffusion in Palaeolithic Siberia
Based on the phylogenetic analyses and the current distributions of relative sub-lineages, we propose that the prehistoric population differentiation in Siberia after the LGM (post-LGM) provided the genetic basis for the emergence of the Paleo-Indian, American aborigine, population. According to the phylogenetic tree of Y-chromosome haplogroup C2-M217 (Fig. 2 and Figure S1), eight sub-lineages emerged in a short period between 15.3 kya and 14.3 kya (Table S5). Within these sub-lineages, haplogroups C2-M48, C2-F1918, and C2- F1756 are predominant paternal lineages in modern Altaic-speaking populations [46, 51, 52]. Samples of haplogroups C2-F8535 and C2-P53.1 were found in two Turkic- and Mongolic-speaking minorities in China (Table S1). Both archeological and genetic data suggest that Altaic-speaking populations are results of population expansion in the past several thousand years in the Altai Mountain, Mongolia Plateau, and Amur River region [51–54].
By contrast, three other sub-lineages, C2-B79, C2-B77, and C2-P39, appear only in Koryaks and Native Americans [16, 35]. The latitude of the Altai Mountain, the Mongolia Plateau, and Amur River region are much lower than that of Beringia, where the ancestors of Native Americans finally separated from their close relatives in Siberia. Therefore, the phylogeographic patterns of sub-lineages of C2-M217 in this study reveal a major splitting event between populations in a lower latitude region of Siberia and ancestors of Koryaks and Native Americans during the post-LGM period.
The sub-lineages of the Y-chromosome Q-M242 haplogroup were found in populations throughout the Eurasia continent. According to available data, the Q1-L804 lineage is exclusively found in Northwest Europe, while Q1-M120 is primarily restricted to East Asia . Additionally, the lineage Q1-L330 is the predominant paternal lineage in Altai, Tuva, and Kets in South Siberia [34–36, 55]. A number of Q1-M242 samples have also been found in ancient remains from South Siberia and adjacent regions [56, 57]. Other sub-lineages of Q-M242 are scattered widely in different geographic regions of Eurasia, including Q1-L275, Q1-M25, and Q1-Y2659 [14, 35, 37, 58]. Additionally, the Y-chromosome of a 6000–5100 BCE sample (I4550) from Zvejnieki, Latvia has been identified as Q1-L56 . These findings suggest that the sub-lineages of Q-M242 started to diffuse throughout Eurasia in a very ancient period.
Emergence of Paleo-Indian populations
The revised phylogenetic tree of Y-chromosome haplogroup Q-M242 in this study provides clues regarding the origin of Native American lineages Q1-M3 and Q1-Z780 (Fig. 3). According to our estimates, haplogroup Q1-L54 expanded rapidly between 17.2 kya and 15.0 kya and finally gave rise to two major founding paternal lineages of Native American populations, known as Q1-Z780 and Q1-M3. Ancient DNA studies indicate that the early population in South Siberia, represented by MA1 genomes, had a genetic influence on both modern western European and Native American populations . Therefore, we conclude that the accumulated diversity of sub-lineages of Q-M242 before 15.3 kya resulted from the in situ differentiation of Q-M242 in Central Eurasia and South Siberia since the Paleolithic Age, and the appearance of the Paleo-Indian population is part of the great human diffusion throughout the Eurasia after the Last Glacial Maximum.
The Southern Caucasus PIE homeland
The origin of Q-M242 in Zvejnieki, like those of Lola (Q1a2-M25) and Steppe Maykop (Q1a2-M25) from Wang et al. (2018) are therefore most likely migrations throughout North Eurasia dated to the Palaeolithic.
NOTE. In fact, the position of this early Khvalynsk sample in the PCA is near the Steppe Eneolithic cluster, in turn near ANE (with the Lola sample Q1a2-M25, circle in dark blue/violet above), and Steppe Maykop (which includes the other Q1a2-M25 sample).
It is often assumed that these populations absorbed in the Pontic-Caspian steppe were dominated by haplogroup J, due to the oldest representatives of CHG ancestry (Kotias Klde and Satsurblia).
However, it would not be surprising now to find out that (one or more of) these “CHG/ANE-rich” groups from the steppe (possibly the Kairshak culture in the North Caspian region) were in fact dominated by Q1-M25 subclades.
If this is the case, I don’t know where the proponents of the (south of the) Caucasus homeland will retreat to.
In recent decades, evidence has accumulated for comparable enclosures of later dates, including the Early Bronze Age Únětice Culture between 2200 and 1600 BC, and thus into the chronological and cultural context of the Nebra sky disc. Based on the analysis of one of these enclosure sites, recently excavated at Pömmelte on the flood plain of the Elbe River near Magdeburg, Saxony-Anhalt, and dating to the late third millennium BC
The main occupation began at 2321–2211 cal BC, with the stratigraphically earliest features containing exclusively Bell Beaker finds. Bell Beaker ceramics continue after 2204–2154 cal BC (boundary occupation I/II), although they were probably undecorated, but are now complemented by Únětice Culture (and other Early Bronze Age) types. At this time, with features common to both cultures predominate. Only contexts dating to the late main occupation phase (late phase II) and thereafter contained exclusively Únětice Culture finds. Evidently, the bearers of the Bell Beaker Culture were the original builders of the enclosure. During a second phase of use, Final Neolithic and Early Bronze Age cultures coexisted and intermingled. The material remains, however, should not be taken as evidence for successive groups of differing archaeological cultures, but as witnesses to a cultural transition from the Bell Beaker Culture to the Únětice Culture (Spatzier 2015). The main occupation ended 2086–2021 cal BC with the deconstruction of the enclosure; Bell Beaker finds are now absent. Finally, a few features (among them one shaft) and radiocarbon dates attest the sporadic re-use of the site in a phase of abandonment/re-use that ended 1636– 1488 cal BC.
How the above-ground structures possibly influenced perception may reveal another layer of meaning that highlights social functions related to ritual. While zone I was disconnected from the surroundings by a ‘semi-translucent’ post-built border, zones II/III were separated from the outside world by a wooden wall (i.e. the palisade), and zone III probably separated individuals from the crowd gathered in zone II. Accessing the interior or centre therefore meant passing through transitional zones, to first be secluded and then segregated. Exiting the structure meant re-integration and re-connection. The experience possibly induced when entering and leaving the monument reflects the three stages of ‘rites of passage’ described by van Gennep (1909): separation, liminality and incorporation. The enclosure’s outer zone(s) represents the pre- and post-liminal phase; the central area, the liminal phase. Seclusion and liminality in the interior promoted a sense of togetherness, which can be linked to Turner’s “communitas” (1969: 132–33). We might therefore see monuments such as the Pömmelte enclosure as important communal structures for social regulation and the formation of identity.
(…) The long-term stability of these connotations must be emphasised. As with the tradition of making depositions, these meanings were valid from the start of the occupation — c. 2300 BC — until at least the early period following the deconstruction event, c. 2050 BC. While the spatial organisation and the solar alignment of the main entrances were maintained throughout the main occupation, stone axes and ‘formal’ graves indicate the continuation of the spatial concepts described above until the twentieth to nineteenth centuries BC.
These layers of meaning mirror parallel concepts of space including, although not necessarily restricted to, the formation of group identities (see Hansen & Meyer 2013: 5). They can perhaps be better understood as a ‘cosmological geography’ manifested in the symbolism of superimposed levels of conceptual ideas related to space and to certain cardinal points (Figure 8). This idea is closely related to Eliade’s (1959: 29–36) understanding of “organized — hence comicized — territory”, that is territory consecrated to provide orientation within the homogeneity of the chaotic ‘outside world’, and the equivalence of spatial consecration and cosmogony. Put differently, the Pömmelte enclosure can be interpreted as a man-made metaphor and an icon of the cosmos, reflecting the Weltanschauung (a comprehensive conception of the world) of the people who built and used it. By bringing together Eliade and Rappaport’s ideas of meaningfulness in relation to religious experience (Rappaport 1999: 391–95), it may be argued that Pömmelte was a place intended to induce oneness with the cosmos. In combining multiple layers that symbolically represent different aspects of life (first-ordermeaning), the enclosure became an icon metaphorically representing the world (second-order-meaning). As this icon was the place to reaffirm life symbolism ritually, through their actions, people perhaps experienced a sense of rootedness in, or unity with, the cosmos (highest-order-meaning). Although we can only speculate about the perceptions of ancient people, such a theory aiming to describe general principles of religious experience can provide insight.
The circular enclosure of Pömmelte is the first Central European monumental complex of primarily sacred importance that has been excavated and studied in detail. It reveals aspects of society and belief during the transition from the Final Neolithic to the Early Bronze Age, in the second half of the third millennium BC. Furthermore, it offers details of ritual behaviour and the way that people organised their landscape. A sacred interior was separated from the profane environment, and served as a venue for rites that secured the continuity of the social, spiritual and cosmic order. Ancestor worship formed another integral part of this: a mound-covered burial hut and a square-shaped ditch sanctuary (located, respectively, within and near the enclosure’s south-eastern sector; cf. Figure 2)—dating to 2880–2580 cal BC and attributed to the Corded Ware Culture (Spatzier 2017a: 235–44)—suggest that this site was deliberately chosen. With construction of the ring sanctuary, this place gained an immense expansion in meaning—comparable to Stonehenge. Through architectural transformation, both of these sites developed into sanctuaries with increasingly complex religious functions, including in relation to the cult of the dead. The cosmological and social functions, and the powerful symbolism of the Nebra sky disc and hoard (Meller 2010: 59–70), are reflected in Pömmelte’s monumental architecture.
All of these features—along with Pömmelte’s dating, function and complex ring structure—are well documented for British henge monuments (Harding 2003; Gibson 2005). The continuous use of circular enclosures in Central Europe from around 3000– 1500 BC remains to be confirmed, but strong evidence indicates usage spanning from the fifth to the first millennia BC (Spatzier 2017a: 273–96). From 2500 BC onwards, examples in Central Europe, Iberia and Bulgaria (Bertemes 2002; Escudero Carrillo et al. 2017) suggest a Europe-wide concept of sanctuary. This indicates that in extensive communication networks at the beginning of bronze metallurgy (Bertemes 2016), intellectual and religious contents circulated alongside raw materials. The henge monuments of the British Isles are generally considered to represent a uniquely British phenomenon, unrelated to Continental Europe; this position should now be reconsidered. The uniqueness of Stonehenge lies, strictly speaking, with its monumental megalithic architecture.
The Classical Bell Beaker heritage
No serious scholar can argue at this point against the male-biased East Bell Beaker migrations that expanded the European languages related to Late Proto-Indo-European-speaking Yamna (see David Reich’s comments), and thus most likely North-West Indo-European – the ancestor of Italo-Celtic, Germanic, and Balto-Slavic, apart from Pre-Celtic IE in the British Isles, Lusitano-Galician in Iberia, or Messapic in Italy (see here a full account).
With language, these migrants (several ten thousands) brought their particular Weltanschauung to all of Western, Central, and Northern Europe. Their admixture precisely in Hungary shows that they had close interactions with non-Indo-European peoples (genetically related to the Globular Amphorae culture), something that we knew from the dozens of non-Indo-European words reconstructed exclusively for North-West Indo-European, apart from the few reconstructed non-Indo-European words that NWIE shares with Palaeo-Balkan languages, which point to earlier loans from their ancestors, Yamna settlers migrating along the lower Danube.
It is not difficult to imagine that the initial East Bell Beaker group shared a newly developed common cosmological point of view that clashed with other neighbouring Yamna-related worldviews (e.g. in Balkan EBA cultures) after the cultural ties with Yamna were broken. Interesting in this respect is for example their developed (in mythology as in the new North-West Indo-European concept) *Perkwūnos, the weather god – probably remade (in language as in concept) from a Yamna minor god also behind Old Indian parjányas, the rain god – as one of the main gods from the new Pantheon, distinct from *Dyēus patēr, the almighty father sky god. In support of this, the word *meldh-n- ‘lightning’, behind the name of the mythological hammer of the weather god (cf. Old Norse Mjǫllnir or Latvian Milna), was also a newly coined North-West Indo-European term, although the myth of the hero slaying the dragon with the magical object is older.
Circular enclosures are known in Europe since the Neolithic. Also, the site selected for the Pömmelte enclosure had been used to bury Corded Ware individuals some centuries before its construction, and Corded Ware symbolism (stone axe vs. quern) is seen in the use given by Bell Beakers and later Únětice at this place. All this and other regional similarities between Bell Beakers and different local cultures (see here an example of Iberian Bell Beakers) points to syncretism of the different Bell Beaker groups with preceding cultures in the occupied regions. After all, their genealogical ancestors included also those of their maternal side, and not all encountered males disappeared, as is clearly seen in the resurge of previous paternal lineages in Central-East Europe and in Scandinavia. The admixture of Bell Beakers with previous groups (especially those of similar steppe-related ancestry from Corded Ware) needs more complex analyses to clarify potential early dialectal expansions (read what Iosif Lazaridis has to say).
The popular “big and early” expansions
These syncretic trends gave rise to distinct regional cultures, and eventually different local groups rose to power in the new cultural regions and ousted the old structures. Social norms, hierarchy, and pantheons were remade. Events like this must have been repeated again and again in Bronze and Iron Age Europe, and in many cases it was marked by a difference in the prevailing archaeological culture attested, and probably accompanied by certain population replacements that will be seen with more samples and studies of fine-scale population structure.
Some of these cultural changes, marked by evident haplogroup or admixture replacement, are defined as a ‘resurge’ of ancestry linked to previous populations, although that is obviously not equivalent to a resurge of a previous cultural group, because they usually represent just a successful local group of the same supraregional culture with a distinct admixture and/or haplogroup (see e.g. resurge of R1a-Z645 in Central-East European Bronze Age). Social, religious, or ethnic concepts may have changed in each of these episodes, along with the new prestige dialect.
This must have happened then many times during the hundreds (or thousands in some cases) of years until the first attestation of a precise ancient language and culture (read e.g. about one of the latest branches to be attested, Balto-Slavic). Ancient language contacts, like substrates or toponymy, can only rarely be detected after so many changes, so their absence (or the lack of proper studies on them) is usually not relevant – and certainly not an argument – in scholarly discussions. Their presence, on the other hand, is a proof of such contacts.
We have dozens of papers supporting Uralic dialectal substrate influence on Pre-Germanic, Proto-Balto-Slavic, and Pre- and Proto-Indo-Iranian (and even Proto-Celtic), as well as superstrate influence of Palaeo-Germanic (i.e. from Pre- to Proto-Germanic) and Proto-Balto-Slavic into Proto-Finno-Saamic, much stronger than the Indo-Iranian adstrate influence on Finno-Ugric (see the relative importance of each influence) which locates all these languages and their evolution to the north and west of the steppe (with Proto-Permic already separated, in North-East Europe, as is Proto-Ugric further east near the Urals), probably around the Baltic and Scandinavia after the expansion of Bell Beakers. These connections have been known in linguistics for decades.
Apart from some early 20th century scholars, only a minority of Indo-Europeanists support nowadays an Indo-European (i.e. centum) substrate for Balto-Slavic, to keep alive an Indo-Slavonic group based on a hypothetical 19th century Satem group; so e.g. Holzer with his Temematic, and Kortlandt supporting him, also with some supposed Indo-European substrate with heavy non-Indo-European influence for Germanic and Balto-Slavic, that now (thanks mainly to the views of the Copenhagen group) have been linked to the Corded Ware culture, as it has become clear even to them that Bell Beakers expanded North-West Indo-European.
For their part, only a minority among Uralicists, such as Kuz’mina, Parpola or Häkkinen, believe in an ‘eastern’ origin of Uralic languages, around the Southern Urals. Genomic finds – like their peers – are clearly not supporting their views. But even if we accept this hypothesis, there is little space beyond Abashevo and related East Corded Ware cultures after the recent papers on Corded Ware and Fennoscandian samples. And yet here we are:
substitutes arrows for Kron-like colors (where danger red = Indo-European) with the same end result of many other late 20th century whole-Europe Kurgan maps, linking Sredni Stog and Corded Ware with Yamna, but obviating the precise origin of Corded Ware peoples (is it Sredni Stog, or is it that immutable Middle Dnieper group? is it West Yamna, or Yamna Hungary? is it wool, or is it wheels?);
relegates Uralic speakers to a tiny corner, a ‘Volosovo’ cultural region, thus near Khvalynsk/Yamna (but not too much), that miraculously survives surrounded by all-early-splitting, all-Northern Eneolithic Indo-Europeans, thus considering Uralic languages irrelevant not only to locate the PIE Urheimat, but also to locate their own homeland; also, cultures identified in color with Uralic speakers expand until the Iron Age with enough care not to even touch in the map one of the known R1a samples published to date (because, for some people, apparently R1a must be Indo-European); and of course N1c or Siberian ancestry are irrelevant, too;
and adds findings of wheels and wool probably in support of some new ideas based on yet another correlation = causation argument (that I cannot then properly criticize without access to its reasoning beyond cute SmartArt-like symbols) similar to their model – already becoming a classic example of wrong use of statistical methods – based on the infamously named Yamnaya ancestral component™, which is obviously still used here, too.
The end result is thus similar to any other simplistic 1990s Gimbutas (or rather the recently radicalized IE Sredni Stog -> Corded Ware -> BBC version by the Danish workgroup) + 2000s R1a-map + 2010s Yamnaya ancestry™; but, hard to believe, it is published in mid-2018. A lot of hours of senseless effort, because after its publication it becomes ipso facto outdated.
For comparison of Yamna and Bell Beaker expansions, here is a recent simplistic, static (and yet more accurate) pair of maps, from the Reich Lab:
If the Copenhagen group keeps on pushing Gimbutas’ long ago outdated IE Sredni Stog -> Corded Ware theory as modified by Kristiansen, with their recently invented Corded Ware -> Bell Beaker model in genetics, at some point they are bound to clash with the Reich-Jena team, which seems to have less attachment to the classic Kurgan model and the wrong interpretations of the 2015 papers, and that would be something to behold. Because, as Cersei would say: “When you play the game of thrones, you win or you die. There is no middle ground.” And when you play the game of credibility, after so many, so wrong publications, well…
NOTE. I have been working on a similar GIS tool for quite some time, using my own maps and compiled genetic data, which I currently only use for my 2018 revision of the Indo-European demic diffusion model. Maybe within some weeks or months I will be able to publish the maps properly, after the revised papers. It’s a pitty that so much work on GIS and analysis with genetic data and cultural regions has to be duplicated, but I intend to keep some decent neutrality in my revised cultural maps, and this seems impossible at this point with some workgroups who have put all their eggs in one broken basket…
The Merovingian period in Northeast France (developing from 440/450 to 700/710 CE; Legoux et al., 2004) represents [a case of multiple burial], where a large majority of the types of deposits encountered consists of individual burials. In this context, whereas hundreds of individual burials are known, the syntheses recently conducted have enabled the inventory of only six multiple burials (Lefebvre and Lafosse, 2016). These observations naturally raised questions about the exceptional circumstances that led the members of the community to set up such unusual burials. The archaeological site of Hérange, excavated in 2014 (Lorraine, Grand Est region; Fig. S1), holds a key position in the debate surrounding the interpretation of multiple burials during the Merovingian period since it contains one of these rare multiple burials: burial 41, which was dated through archaeological material to the period 530–640 CE.
(…) The biological analysis of the human remains recovered in the second burial (“burial 41”) enabled the demonstration of the combined presence of a woman of approximately 40 years old (A) and three immature individuals, including a 4–5-year-old child (B), a 14–16-year-old teenager (C) and a 2,5–3-month-old infant (D) (Lefebvre and Lafosse, 2016) (Fig. 1). Since rare multiple burials described for the Merovingian period in Northeast France mainly contained two or rarely three deceased, the discovery of a burial grouping four individuals reinforced its exceptional nature. (…) Intriguingly, great care was observed in the treatment of the dead, as illustrated through a special arrangement of the deceased in the grave (Fig. 1). Indeed, the woman A occupied a central position in the grave, with her left arm covering part of the body of child D, her right arm covering the torso of child B and her right hand covering the legs of children B and C. Several arguments, such as the close contact or the imbrication of the bones of individuals A, B and C, have attested to the simultaneity of their deposits in the burial (Lefebvre and Lafosse, 2016).
Interestingly, studies have demonstrated an important chronological homogeneity for the rare multiple burials discovered for the Merovingian period in the Lorraine region (Lefebvre and Lafosse, 2016). The collected data support the existence of an epiphenomenon arisen around the middle of the Merovingian period and that may have linked the multiple burials to (i) a funerary “fashion trend” for a special group of the community, (ii) an increase in cases of violence or (iii) an epidemic crisis linked to infectious disease. In other Lorraine sites, none of the available indices permitted the specification of the cause of death for the individuals recovered in these specific burials. The deceased could well have died of natural causes, violent acts or infectious diseases that had left no visible evidence on the skeletal.
The aDNA analyses conducted on the four individuals discovered in the exceptional multiple burial 41 from Hérange (Lorraine) have demonstrated strong biological links between three individuals. Notably, we could propose that the woman A was the mother of the two immatures B and D deposited just besides her whereas she was not genetically closely related to the teenager C deposited along her legs. Consequently, we propose that the special arrangement of the deceased in the grave clearly reflected the degree of biological links between the deposited individuals. In Hérange, the bereaved were well aware of kinship among the deceased, wanted to express this close linkage through their relative location within the burial, and intentionally arranged body positions consequently. In conclusion, the collected archaeological, archaeo-anthropological and genetic data suggest that the special setup of the multiple burial 41 in the Hérange necropolis and the great care in the treatment of the dead, could be explained by the contemporaneous death of the four related individuals. Data gathered for other archaeological sites from the region or in Germany suggested an epidemic crisis (plague epidemic?) during the middle of the Merovingian period that may explain the contemporaneous death of related individuals living in close contact and easily sharing pathogens.
Reported mtDNA haplogroups include U* for samples A, B, and D, and H for sample C.
Interesting is this apparently newly reported information including a female sample from the Ikawazu Jōmon of Japan ca. 570 BC (emphasis mine):
The two oldest samples — Hòabìnhians from Pha Faen, Laos [La368; 7950 with 7795 calendar years before the present (cal B.P.)] and Gua Cha, Malaysia (Ma911; 4415 to 4160 cal B.P.)—henceforth labeled “group 1,” cluster most closely with present-day Önge from the Andaman Islands and away from other East Asian and Southeast-Asian populations (Fig. 2), a pattern that differentiates them from all other ancient samples. We used ADMIXTURE (14) and fastNGSadmix (15) to model ancient genomes as mixtures of latent ancestry components (11). Group 1 individuals differ from the other Southeast Asian ancient samples in containing components shared with the supposed descendants of the Hòabìnhians: the Önge and the Jehai (Peninsular Malaysia), along with groups from India and Papua New Guinea.
We also find a distinctive relationship between the group 1 samples and the Ikawazu Jōmon of Japan (IK002). Outgroup f3 statistics (11, 16) show that group 1 shares the most genetic drift with all ancient mainland samples and Jōmon (fig. S12 and table S4). All other ancient genomes share more drift with present-day East Asian and Southeast Asian populations than with Jōmon (figs. S13 to S19 and tables S4 to S11). This is apparent in the fastNGSadmix analysis when assuming six ancestral components (K = 6) (fig. S11), where the Jōmon sample contains East Asian components and components found in group 1. To detect populations with genetic affinities to Jōmon, relative to present-day Japanese, we computed D statistics of the form D(Japanese, Jōmon; X, Mbuti), setting X to be different presentday and ancient Southeast Asian individuals (table S22). The strongest signal is seen when X=Ma911 and La368 (group 1 individuals), showing a marginally nonsignificant affinity to Jōmon (11). This signal is not observed with X = Papuans or Önge, suggesting that the Jōmon and Hòabìnhians may share group 1 ancestry (11).
(…) Finally, the Jōmon individual is best-modeled as a mix between a population related to group 1/Önge and a population related to East Asians (Amis), whereas present-day Japanese can be modeled as a mixture of Jōmon and an additional East Asian component (Fig. 3 and fig. S29)
Interesting in relation to the oral communication of the SMBE O-03-OS02 Whole genome analysis of the Jomon remain reveals deep lineage of East Eurasian populations by Gakuuhari et al.:
Post late-Paleolithic hunter-gatherers lived throughout the Japanese archipelago, Jomonese, are thought to be a key to understanding the peopling history in East Asia. Here, we report a whole genome sequence (x1.85) of 2,500-year old female excavated from the Ikawazu shell-mound, unearthed typical remains of Jomon culture. The whole genome data places the Jomon as a lineage basal to contemporary and ancient populations of the eastern part of Eurasian continent, and supports the closest relationship with the modern Hokkaido Ainu. The results of ADMIXTURE show the Jomon ancestry is prevalent in present-day Nivkh, Ulchi, and people in the main-island Japan. By including the Jomon genome into phylogenetic trees, ancient lineages of the Kusunda and the Sherpa/Tibetan, early splitting from the rest of East Asian populations, is emerged. Thus, the Jomon genome gives a new insight in East Asian expansion. The Ikawazu shell-mound site locates on 34,38,43 north latitude, and 137,8, 52 east longitude in the central main-island of the Japanese archipelago, corresponding to a warm and humid monsoon region, which has been thought to be almost impossible to maintain sufficient ancient DNA for genome analysis. Our achievement opens up new possibilities for such geographical regions.
Thus, our data favor a process of Near Eastern animal domestication that is dispersed in space and time, rather than radiating from a central core (3, 11). This resonates with archaeozoological evidence for disparate early management strategies from early Anatolian, Iranian, and Levantine Neolithic sites (12, 13). Interestingly, our finding of divergent goat genomes within the Neolithic echoes genetic investigation of early farmers. Northwestern Anatolian and Iranian human Neolithic genomes are also divergent (14–16), which suggests the sharing of techniques rather than large-scale migrations of populations across Southwest Asia in the period of early domestication. Several crop plants also show evidence of parallel domestication processes in the region (17).
PCA affinity (Fig. 2), supported by qpGraph and outgroup f3 analyses, suggests that modern European goats derive from a source close to the western Neolithic; Far Eastern goats derive from early eastern Neolithic domesticates; and African goats have a contribution from the Levant, but in this case with considerable admixture from the other sources (figs. S11, S16, and S17 and tables S26 and 27). The latter may be in part a result of admixture that is discernible in the same analyses extended to ancient genomes within the Fertile Crescent after the Neolithic (figs. S18 and S19 and tables S20, S27, and S31) when the spread of metallurgy and other developments likely resulted in an expansion of inter-regional trade networks and livestock movement.
Our results imply a domestication process carried out by humans in dispersed, divergent, but communicating communities across the Fertile Crescent who selected animals in early millennia, including for pigmentation, the most visible of domestic traits.
About two months ago I stumbled upon a gem in archaeological studies related to Proto-Indo-Europeans, the book О скипетрах, о лошадях, о войне: этюды в защиту миграционной концепции М.Гимбутас (On sceptres, on horses, on war: Studies in defence of M. Gimbutas’ migration concepts), 2007, by V. A. Dergachev, from the Institute of Cultural Heritage of the Moldavian Republic.
Dergachev’s work dedicates 488 pages to a very specific Final Neolithic-Eneolithic period in the Pontic-Caspian steppe, and the most relevant parts of the book concern the nature and expansion of horses and horse domestication, horse-head scepters, and other horse-related symbology – arguably the most relevant cultural signs associated with Proto-Indo-European speakers in this period.
I haven’t had enough time to read the whole book, but I have read with interest certain important chapters.
The genetic and chronological relationship of horse-head pommel-scepters is classified with incredible detail, to the extent that one could divide subregions among those cultures using them.
Simplified conclusions of this section include (emphasis mine):
The [horse-head pommel-]scepters arose originally in the depth of the Khvalynsk culture. Following the now well-known finds, they are definitely related to those of the Middle Volga group.
In their next modifications, these scepters continued to evolve and develop into the area of the Khvalynsk culture in its latest stages, and possibly later.
Simultaneously, with the same modifications, these scepters “are introduced” into common usage in the Novodanilovka culture, which in its spread by one wing was in contact and interspersed immediately with the area of Khvalynsk remains; and on the other hand, far in the south – in the Pre-Kuban and Ciscaucasian regions – within the range of the Domaikopska culture; and in the west – in the Carpathian – Post-Kuban – with the areas of early agricultural cultures Cucuteni A – Trypillia B1, Gumelnița-Karanovo VI.
The simultaneous presence in the areas of the Ciscaucasian, Carpatho-Danubian, and especially Novodinilovka cultures, whose carriers continue the Khvalynian traditions of making stone scepters, and the scepters themselves (in their non-functional implication in the local cultural environment), all definitely allow us to view these findings as imported Novodanilovka objects.
Cultural relevance of scepters
The text goes on to make an international comparison of scepters and their relevance as a cultural phenomenon, with its strong symbolic functions as divine object, its use in times of peace, in times of war, and in a system of ritual power.
Especially interesting is the section dedicated to Agamemnon’s scepter in the Iliad, one of the oldest Indo-European epics. Here is an excerpt from Illiad II.100-110 (see here the Greek version) with the scepter’s human and divine genealogy:
Then among them lord Agamemnon uprose, bearing in his hands the sceptre which Hephaestus had wrought with toil. Hephaestus gave it to king Zeus, son of Cronos, and Zeus gave it to the messenger Argeïphontes; and Hermes, the lord, gave it to Pelops, driver of horses, and Pelops in turn gave it to Atreus, shepherd of the host; and Atreus at his death left it to Thyestes, rich in flocks, and Thyestes again left it to Agamemnon to bear, that so he might be lord of many isles and of all Argos.
About the horse
His studies on horse remains show an interesting, detailed quantitative and statistical approach to the importance and (cultural and chronological) origin of horses (and likely horse domestication) in each culture.
Although the part on horse remains is probably a bit outdated today, after many recent studies of Eneolithic steppe sites (see here one example), it still shows the relative distribution of horse bone remains among different steppe cultures, which is probably similar to what could be reported today:
Even more interesting is the relationship of the distribution of horse remains with archaeological complexes and horse-related symbols. Some excerpts from the conclusions of this section:
Accounting and analysis of archeo-zoological and archaeological data proper for a horse for a vast area from the Tisza and the Middle Danube to the Caucasus and the Urals (which includes the main cultures of the western agricultural, Caucasian, and Eastern European cultural zones) clearly points to the eastern cultural zone as a zone of the originally the most important social significance of a horse as the only possible zone of the earliest domestication, horseback riding and all-round use of a horse. In relation to the eastern, the western land – the ancient Carpatho-Danubian or the Caucasian cultural zones – are secondary and subordinate to the first on the phenomenon under consideration.
The first quantitative leap in the manifestation of the remnants of a horse, marking itself and the first qualitative changes in the social status of this animal, is due mainly to the Middle Volga culture of the developed Neolithic of the Middle Volga region (in part, the Southwest Urals), which, accordingly, determine the cultural context, time and geographic region – or, the initial, single and main epicenter of the process of taming and domestication of a horse.
On the one hand, the subsequent substantial increase in the number of horse remnants, and, on the other, the wide inclusion of the horse in cults, rituals, funerary rituals (horse pendants, ornamented metacarpus, horse bones, sacrificial altars) in the Samara culture of the Early Eneolithic of the same region definitely indicates the continuing increase in the social significance of this species of animal, which was most likely expressed in the final design of a specialized horse breeding culture and, accordingly, in a wide range of applications using a horse for riding. At the same time, we can observe the beginning of the transfer of the already domesticated horse from the original historical and geographic epicenter to other cultures of the eastern cultural zone and, in part, the cultures closest to the periphery of this zone, into the western agricultural zone (Bolgrad-Aldeni P, Pre-CuCuteni-Trypillya A) .
Middle Eneolithic – early stages. One of the leading places in the remnants of the horse is in the Middle Volga region, the Khvalynsk culture. Genetically related to the Samara, the Khvalynsk I culture preserves the traditions of the ritual, cultural meaning, the treatment of the image of a horse in funerals (altars, horse bones, funerary rituals). But, At the same time, it is in this precise culture that the image of the horse, included in the social symbolism (horse-head pommel-scepter), for the first time it acquires a special, maximum social significance. That is why the appearance and subsequent widespread distribution of the social symbols in Novodanilovka-type objects can definitely be considered as another qualitative leap in the social significance of a horse – its use for military purposes for close and distant expeditions. And such an interpretation is fully confirmed from the analysis of Novodanilovka-type objects, which is the subject of discussion.
Judging by the osteological data and the typological evolution of the horse-head scepters, the Khvalynian culture and remains of the Novodanilovka type are already associated with the relatively widespread and intensive findings of domesticated horses in various areas of the eastern cultural zone (semi-desert regions of the Lower Volga and the Caspian region – Khvalynsk culture, forest-steppe and steppe from the Volga to the Dnieper – Sredni Stog, Repin cultures), and the western – agricultural (Gumelnitsa, Cucuteni A-Tripolye Bl), and the Caucasus (Pre-Maykop) zones, where, however, the horse played a very modest role.
From the functional point of view, according to the sum of the data, there is no reason to doubt that in the eastern zone the horse is already present in the Late Neolithic period. Since its domestication and the emergence of a specialized horse breeding, it has been also widely used for meat, milk and dairy products (including the traditional hippace tradition of the later Scythians), and since the beginning of the early Eneolithic for transport and for riding purposes. Another thing is the horse as a means of war, a means of distant travel and expansion. The beginning of the use of a horse for these purposes, in the opinion of the author, is determined by the appearance of social symbolism in the form of horse-head scepters, and is most fully reflected in the memories of the Khvalynsk culture and, in particular, the Novodanilovka type. Concerning western or Caucasian cultural zones related to Khvalynsk, the horse is thought to have been linked to the eastern region, used mainly for riding, as a means of transport and for communication, which, however, does not exclude its use for meat.
These are the main conclusions-interpretations, suggesting the analysis and archaeological and other sources containing information about the horse. And as for our pommel-scepters, then, as can be seen from these sources, the main thing is that the culture of the Middle Volga region, according to all the data, definitely accumulates in itself the longest traditions associated with the gradual increase of social significance of the horse. And if so, this circumstance motivates the possibility or necessity of appearing in the environment of the bearers of this culture of unique signs-symbols that carry within themselves or reflect the image of this animal as an extremely significant social reality. The revealed and characterized quality, as a matter of fact, fill or open by themselves the hypothetical elements we have previously identified, the meanings of that particularity, folded in the social sign-symbol, in our case – the horse-head-shaped scepter.
The relevance of Dergachev’s work
As you certainly know by now if you are a usual reader of this blog, there were two other seminal publications that same year correcting and expanding Gimbutas’ model:
Each one of these works taken independently (especially the books) may give a different version of Proto-Indo-European migrations; Anthony and Dergachev are heirs of Gimbutas’ simplistic kurgan-based model, and of other previous, now rejected ideas, and they reflect them whenever they don’t deal with first-hand investigation (and even sometimes when interpreting their own data). Taken together – and especially in combination with recent genetic studies – , though, they describe a clearer, solider model of how Proto-Indo-Europeans developed and expanded.
Anthony’s publication overshadowed the importance of Dergachev’s work for the English-speaking world – and by extension for the rest of us. However, V. A. Dergachev’s updated study of his previous work on steppe cultures shows the right, thorough, and diligent way of describing the expansion of early Khvalynsk-Novodanilovka chieftains with the horse and horse symbolism into the Caucasus and the Lower Danube (like the seminal work of Harrison & Heyd 2007 described the expansion of Yamna settlers with East Bell Beakers, culturally opposed to Corded Ware and to the Proto-Beakers). On the other hand, Anthony’s broad-brush, superficial description of thousands of years of potential Indo-European-speaking peoples gave a migration picture that – although generally right (like radiocarbon-based Iberian origin of the Bell Beaker culture was right) – was bound to be wrong in some essential details, as we are seeing in archaeology and genetics.
NOTE. As I have said before, Anthony’s interpretations of Sredni Stog culture representing a sort of ‘peasants’ under the rule of Novodanilovka chiefs was based on old theories of Telegin, who changed his mind – as did the rest of the Russian school well before the publication of Dergachev’s book, considering both as distinct cultural phenomena. Anthony selected the old interpretation, not to follow a Gimbutas / Kristiansen model of Sredni Stog being Indo-European and expanding with GAC into Corded Ware (because, for him, Corded Ware peoples were originally non-Indo-European speakers): he seems to have done it to prove that Proto-Anatolian traveled indeed through the North Pontic area, i.e. to avoid the regional ‘gap’ in the maps, if you like. Then with the expansion of Repin over the area, Sredni Stog peoples would have been absorbed. With genetic investigation, as we know, and with this kind of detailed archaeological studies, the traditional preference for “large and early” IE territories – proper of the mid-20th century – are no longer necessary.
We already had in 2016 a Samara hunter-gatherer sample dated ca. 5600 BC, representative of EHG ancestry, of haplogroup R1b1a. We also had three early Khvalynsk samples from Samara Eneolithic dated ca. 4600 BC, with a drift towards (what we believe now is) a population from the Caucasus, showing haplogroups Q1a, R1a1(xM198), and R1b1a, the last one described in its paper as from a high-status burial, similar to high-status individuals buried under kurgans in later Yamna graves (of R1b-L23 lineages), and therefore likely a founder of an elite group of patrilineally-related families, while the R1a1 sample showed scarce decoration, and does not belong to the M417 lineage expanded later in Sredni Stog or Corded Ware.
In 2017 we knew of the Ukraine_Eneolithic sample I6561, from Alexandria, of a precise subclade (L657) of haplogroup R1a-Z93, dated ca. 4000 BC, and likely from the Sredni Stog (or maybe Kvitjana) culture. This sample alone makes it quite likely that the expansion of R1a-Z645 subclades happened earlier than expected, and that it was associated with movements along forest-steppe cultures, most likely along the Upper Dniester or Dnieper-Dniester corridor up to the Forest Zone.
We have now confirmation that Khvalynsk samples from the Yekaterinovka Cape settlement ca. 4250-4000 BC were reported by a genetic lab (to the archaeological team responsible) as being of R1b-L23 subclades, although the precise clades (reported as P312 and U106) are possibly not accurate.
NOTE. Curiously enough, and quite revealing for the close relationship of scepters to the ritual source of power for Khvalynsk chieftains (political and/or religious leaders), the scepter found in the elite burial 45 of the Ekaterinovka cape (a riverine settlement) shows a unique zoomorphic carving, possibly resembling a toothed fish or reptile, rather than the most common horse-related motifs of the time.
With Wang et al. (2018), a real game-changer in the Khvalynsk – Sredni Stog (and also in the Yamna/Bell Beaker – Corded Ware) opposition, we also know that two Steppe Eneolithic samples from the Northern Caucasus Piedmont, dated ca. 4300-4100 BC, show haplogroup R1b1. Although its direct connection to the expansion of early Khvalynsk with horse-related symbolism is not clear from the archaeological information shared (none), this is what the paper has to say about them:
The two distinct clusters are already visible in the oldest individuals of our temporal transect, dated to the Eneolithic period (~6300-6100 yBP/4300-4100 calBCE). Three individuals from the sites of Progress 2 and Vonjuchka 1 in the North Caucasus piedmont steppe (‘Eneolithic steppe’), which harbor Eastern and Caucasian hunter-gatherer related ancestry (EHG and CHG, respectively), are genetically very similar to Eneolithic individuals from Khalynsk II and the Samara region19, 27. This extends the cline of dilution of EHG ancestry via CHG/Iranian-like ancestry to sites immediately north of the Caucasus foothills.
In contrast, the oldest individuals from the northern mountain flank itself, which are three first degree-related individuals from the Unakozovskaya cave associated with the Darkveti-Meshoko Eneolithic culture (analysis label ‘Eneolithic Caucasus’) show mixed ancestry mostly derived from sources related to the Anatolian Neolithic (orange) and CHG/Iran Neolithic (green) in the ADMIXTURE plot (Fig. 2C). While similar ancestry profiles have been reported for Anatolian and Armenian Chalcolithic and Bronze Age individuals20, 23, this result suggests the presence of the mixed Anatolian/Iranian/CHG related ancestry north of the Great Caucasus Range as early as ~6500 years ago.
During the late 5th millennium BC, cultural groups of the Eneolithic occupied the northern circumpontic area and the areas between the North Caucasus and the Lower Volga. For the first time, individual inhumations were placed below low burial mounds (Rassamakin, 2011). During the 4th millennium BC, the area split into two cultural spheres. In the northern steppe area communities continued with the burial practice of crouched inhumations below low mounds, with this culturally transforming into the early Pit Grave culture. In contrast, in the Caucasian foothill zone and the neighbouring steppe, the Majkop-Novosvobodnaya culture emerged (Kohl and Trifonov, 2014). Similarly, during the 3rd millennium BC, two cultural spheres influenced the area: The North Caucasian Culture dominated the Caucasian foothills for the next five centuries, while in the steppe area between the Lower Don and the Caucasus, regional groups of the Catacomb Culture existed side-by-side.
Burials of the Eneolithic epoch (late 5th millennium BC)
The oldest group of individuals with trepanations are found in the North Caucasian variant of the late circumpontic Eneolithic and date to the last third of the 5th millennium BC (Korenevsky, 2012). Burials of this epoch are inhumations in shallow pits, chiefly without burial goods, but covered with large quantities of red ochre. Of special interest is a collective burial of seven individuals from VP 1/12, who were interred together in a secondary burial ritual. The sites of Tuzluki, Mukhin, Voinuchka, Progress, and Sengileevskii all belong to this period.
Without the datasets to test different models, you can only imagine what is happening with the processed, secondary data we have. The position of Eneolithic Steppe cluster in the PCA (probably Khvalynsk-related peoples already influenced by the absorbed, previous Caucasus population), as well as other potential Caucasus groups intermediate between Steppe Maykop and Caucasus Maykop (as suggested by other ancient and modern Caucasus samples), may indicate that Yamna is between Khvalynsk and such intermediate Caucasus populations (as the source of the additional CHG-related ancestry) and – as the paper itself states – that it also received additional EEF contribution, probably from the western cultures absorbed during these Khvalynsk-Novodanilovka migrations (or later during Khvalynsk/Repin migrations).
Also interpreted in light of these early Khvalynsk-Novodanilovka migrations of horse riding chieftains (and their close contacts with the Caucasus), you can clearly see where the similar CHG-like contribution to Ukraine Eneolithic and other North Pontic forest-steppe cultures (which later contributed to Proto-Corded Ware peoples) must have come from. The simplistically reported proportions of EHG:CHG:EEF ancestry might be similar in many of these groups, but the precise origin and evolution of such ancestral components is certainly not the same: statistical methods will eventually show this, when (and if) we have many more samples, but for the moment Y-DNA is the most obvious indicator of such differences.
What lies between the formation of that early Eneolithic cultural-historical community, and what we see in archaeology and genetics in Middle and Late Eneolithic steppe cultures, is the radical differentiation of western (Ukraine Eneolithic, mainly forest-steppe) and eastern (Samara and Khvalynsk/Repin, mainly steppe) cultures and peoples, i.e. precisely the period of differentiation of an eastern, Proto-Indo-Hittite-speaking early Khvalynsk community (that expanded with the horse and horse-related symbols) from a western, probably Early Proto-Uralic speaking community of the North Pontic forest-steppe cultural area.
NOTE. I am not against a Neolithic ‘steppe’ language. But this steppe language was spoken before and/or during the first Neolithisation wave, and should be associated with Indo-Uralic. If there was no Indo-Uralic language, then some communities would have developed Early Proto-Indo-European and Early Proto-Uralic side by side, in close contact to allow for dozens of loanwords or wanderwords to be dated to this period (where, simplistically, PIH *H corresponds to EPU *k, with some exceptions).
The convergence that we see in PCA and Admixture of Yamna and the earliest Baltic LN / Corded Ware ‘outlier’ samples (if not directly related exogamy of some Baltic LN/CWC groups with Yamna migrants, e.g. those along the Prut), must be traced back to the period of genetic drift that began precisely with these Khvalynsk-Novodanilovka expansions, also closely associated with populations of the Caucasus, thus bringing North Pontic forest-steppe cultures (probably behind Proto-Corded Ware peoples) nearer to Khvalynsk, and both by extension to Yamna.
Steppe Eneolithic peoples were thus no different to other previous and posterior expanding groups, and ancestry is going to be similar for people living in neighbouring regions, so Y-DNA will remain the essential tool to distinguish different peoples (see here a summary of Proto-Indo-Europeans expanding R1b-L23).
We are nevertheless still seeing “R1b zombies” (a quite appropriate name I read on Anthrogenica) still arguing for a Western European origin of R1b-L23 based on EEF-like ancestry and few steppe-related contribution found in Iberian Bell Beakers (read what David Reich has to say on this question); and “OIT zombies” still arguing for IVC representing Proto-Indo-European, based on Iran_N ancestry and the minimal steppe ancestry-related impact on certain ancient Asian cultures, now partly helped by “Caucasus homeland zombies” with the new PIE=CHG model; apart from many other pet theory zombies rising occasionally from their graves here and there. Let’s hope that this virus of the undead theories does not spread too strongly to the R1a-Indo-European association, when the official data on Khvalynsk, West Yamna, and Yamna Hungary come out and show that they were dominated by R1b-L23 lineages.
Because we need to explore in detail the continuation of Khvalynsk-related (potential Proto-Anatolian) cultures in the Lower Danube and the Balkans, e.g. from Cernavoda I to Cernavoda III, then maybe to Ezero, and then to Troy; as well as the specific areas of Late Indo-European expansions associated with Early Yamna settlers turning into Bell Beakers, Balkan EBA, and Steppe MLBA-associated cultures. There is a lot of work to do on proper definition of Bronze Age cultures and their potential dialects, as well as convergence and divergence trends, and not only of Indo-European, but also of Uralic-speaking communities derived from Corded Ware cultures.
If we let the narratives of the 2000s in Genetics (in combination with the 1960s in Archaeology) dominate the conversation, then a lot of time will be absurdly lost until reality imposes itself. And it will.
EDIT (2 JUL 2018): Some sentences corrected, and some information added to the original post.
Native Americans from the Amazon, Andes, and coastal geographic regions of South America have a rich cultural heritage but are genetically understudied, therefore leading to gaps in our knowledge of their genomic architecture and demographic history. In this study, we sequence 150 genomes to high coverage combined with an additional 130 genotype array samples from Native American and mestizo populations in Peru. The majority of our samples possess greater than 90% Native American ancestry, which makes this the most extensive Native American sequencing project to date. Demographic modeling reveals that the peopling of Peru began ∼12,000 y ago, consistent with the hypothesis of the rapid peopling of the Americas and Peruvian archeological data. We find that the Native American populations possess distinct ancestral divisions, whereas the mestizo groups were admixtures of multiple Native American communities that occurred before and during the Inca Empire and Spanish rule. In addition, the mestizo communities also show Spanish introgression largely following Peruvian Independence, nearly 300 y after Spain conquered Peru. Further, we estimate migration events between Peruvian populations from all three geographic regions with the majority of between-region migration moving from the high Andes to the low-altitude Amazon and coast. As such, we present a detailed model of the evolutionary dynamics which impacted the genomes of modern-day Peruvians and a Native American ancestry dataset that will serve as a beneficial resource to addressing the underrepresentation of Native American ancestry in sequencing studies.
The high frequency of Native American mitochondrial haplotypes suggests that European males were the primary source of European admixture with Native Americans, as previously found (23, 24, 41, 42). The only Peruvian populations that have a proportion of the Central American component are in the Amazon (Fig. 2A). This is supported by Homburger et al. (4), who also found Central American admixture in other Amazonian populations and could represent ancient shared ancestry or a recent migration between Central America and the Amazon.
Following the peopling of Peru, we find a complex history of admixture between Native American populations from multiple geographic regions (Figs. 2B and 3 A and C). This likely began before the Inca Empire due to Native American and mestizo groups sharing IBD segments that correspond to the time before the Inca Empire. However, the Inca Empire likely influenced this pattern due to their policy of forced migrations, known as “mitma” (mitmay in Quechua) (28, 31, 37), which moved large numbers of individuals to incorporate them into the Inca Empire. We can clearly see the influence of the Inca through IBD sharing where the center of dominance in Peru is in the Andes during the Inca Empire (Fig. 3C).
A similar policy of large-scale consolidation of multiple Native American populations was continued during Spanish rule through their program of reducciones, or reductions (31, 32), which is consistent with the hypothesis that the Inca and Spanish had a profound impact on Peruvian demography (25). The result of these movements of people created early New World cosmopolitan communities with genetic diversity from the Andes, Amazon, and coast regions as is evidenced by mestizo populations’ ancestry proportions (Fig. 3A). Following Peruvian independence, these cosmopolitan populations were those same ones that predominantly admixed with the Spanish (Fig. 3B). Therefore, this supports our model that the Inca Empire and Spanish colonial rule created these diverse populations as a result of admixture between multiple Native American ancestries, which would then go on to become the modern mestizo populations by admixing with the Spanish after Peruvian independence.
Further, it is interesting that this admixture began before the urbanization of Peru (26) because others suspected the urbanization process would greatly impact the ancestry patterns in these urban centers (25). (…)
The Middle Neolithic is known to mark the westward expansion of Comb Ware and related cultures in North-Eastern Europe.
Mathieson et al. (2017 and 2018) had this to say about the Middle Neolithic in the Baltic:
At Zvejnieki in Latvia, using 17 newly reported individuals and additional data for 5 previously reported34 individuals, we observe a transition in hunter-gatherer-related ancestry that is opposite to that seen in Ukraine. We find that Mesolithic and Early Neolithic individuals (labelled ‘Latvia_HG’) associated with the Kunda and Narva cultures have ancestry that is intermediate between WHG (approximately 70%) and EHG (approximately 30%), consistent with previous reports34–36(Supplementary Table 3). We also detect a shift in ancestry between Early Neolithic individuals and those associated with the Middle Neolithic Comb Ware complex (labelled ‘Latvia_MN’), who have more EHG-related ancestry; we estimate that the ancestry of Latvia_MN individuals comprises 65% EHG-related ancestry, but two of the four individuals appear to be 100% EHG in principal component space (Fig. 1b).
Other samples and errors on Y-SNP calls
The truth is, this is another sample (Latvia_MN_dup.I4627.SG) from the same individual ZVEJ26.
There is another sample used for the analysis of ZVEJ26, with the same data as in Mathieson et al. (2018), i.e. better coverage, and Y-DNA R1b1a1a(xR1b1a1a2).
Most samples in the tables from Wang et al. (2018) seem to be classified correctly, as in previous papers, but for:
Blätterhöhle Cave sample from Lipson et al. (2017), wrongly classified (again) as R1b1a1a2a1a2a1b2 (I am surprised no R1b-autochtonous-continuity-fan rushed to proclaim something based on this);
Mal’ta 1 sample from Raghavan et al. (2013) as R1b1a1a2;
Iron Gates HG, Schela Cladovey from Gonzalez Fortes (2017) as R1b1a1a2;
Oase1 from Fu (2015) as N1c1a;
samples from Skoglund et al. (2017) from Africa also wrongly classified as R1b1a1a2 and subclades.
It seems therefore that the poor coverage / SNPs hit on autosomes is the key common factor here for these Y-SNP calls, and so it is in the Zvejnieki MN1 duplicated sample. Anyway, if all Y-SNP calls come from the same software applied to all data, and this is going to be used in future papers, this seems to be a great improvement compared to Narasimhan et al. (2018)…
EDIT (25 JUN 2018): I have been reviewing some more papers apart from Mathieson et al. (2018) and Olalde et al. (2018) to compare the reported haplogroups, and there seems to be many potential errors (or updated data, difficult to say sometimes, especially when the newly reported haplogroup is just one or two subclades below the reported one in ‘old’ papers), not only those listed above.
The sample accession number in the European Nucleotide Archive (ENA) is SAMEA45565168 (Latvia_MN1/ZVEJ26) (see here), in case anyone used to this kind of analysis wishes to repeat the Y-SNP calls on both samples.
EDIT (25 JUN 2018): Added that it is another sample with lesser coverage from the same ZVEJ26 individual.
The main unequivocal conclusion after three decades of phylogeographic mtDNA studies is the African origin of all extant modern humans. In addition, a southern coastal route has been argued for to explain the Eurasian colonization of these African pioneers. Based on the age of macrohaplogroup L3, from which all maternal Eurasian and the majority of African lineages originated, the out-of-Africa event has been dated around 60-70 kya. On the opposite side, we have proposed a northern route through Central Asia across the Levant for that expansion and, consistent with the fossil record, we have dated it around 125 kya. To help bridge differences between the molecular and fossil record ages, in this article we assess the possibility that mtDNA macrohaplogroup L3 matured in Eurasia and returned to Africa as basal L3 lineages around 70 kya.
The coalescence ages of all Eurasian (M,N) and African (L3 ) lineages, both around 71 kya, are not significantly different. The oldest M and N Eurasian clades are found in southeastern Asia instead near of Africa as expected by the southern route hypothesis. The split of the Y-chromosome composite DE haplogroup is very similar to the age of mtDNA L3. An Eurasian origin and back migration to Africa has been proposed for the African Y-chromosome haplogroup E. Inside Africa, frequency distributions of maternal L3 and paternal E lineages are positively correlated. This correlation is not fully explained by geographic or ethnic affinities. This correlation rather seems to be the result of a joint and global replacement of the old autochthonous male and female African lineages by the new Eurasian incomers.
These results are congruent with a model proposing an out-of-Africa migration into Asia, following a northern route, of early anatomically modern humans carrying pre-L3 mtDNA lineages around 125 kya, subsequent diversification of pre-L3 into the basal lineages of L3, a return to Africa of Eurasian fully modern humans around 70 kya carrying the basal L3 lineages and the subsequent diversification of Eurasian-remaining L3 lineages into the M and N lineages in the outside-of-Africa context, and a second Eurasian global expansion by 60 kya, most probably, out of southeast Asia. Climatic conditions and the presence of Neanderthals and other hominins might have played significant roles in these human movements. Moreover, recent studies based on ancient DNA and whole-genome sequencing are also compatible with this hypothesis.
You can also read the recent interesting open access review How did Homo sapiens evolve? by Julia Galway-Witham, Chris Stringer, Science (2018) 360:6395 1296-1298.
Archeological studies suggest that a subgroup of ancient populations of the Miaodigou culture (~ 6300–5500 BP) moved westward to the upper stream region of the Yellow River and created the Majiayao culture (~ 5400–4900 BP) (Liu et al. 2010), which was proposed to be the remains of direct ancestors of Tibeto-Burman populations (Sagart 2008). On the other hand, Han populations, the other major descendant group of the Yang-Shao culture (~ 7000–5500 BP), are composed of many other sub-lineages of Oα-F5 and extremely low frequencies of D-M174 (Additional files 1: Figure S1; Additional files 2: Table S1). Therefore, we propose that Oα-F5 may be one of the dominant paternal lineages in ancient populations of Yang-Shao culture and its successors.
In this study, we demonstrated that both sub-lineages of D-M174 and Oα-F5 are founding paternal lineages of modern Tibeto-Burman populations. The genetic patterns suggested that the ancestor group of modern Tibeto-Burman populations may be an admixture of two distinct ancient populations. One of them may be hunter–gatherer populations who survived on the plateau since the Paleolithic Age, represented by varied sub-lineages of sub-lineages of D-M174. The other one was comprised of farmers who migrated from the middle Yellow River basin, represented by sub-lineages of Oα-F5. In general, the genetic evidence in this study supports the conclusion that the appearance of the ancestor group of Tibeto-Burman populations was triggered by the Neolithic expansion from the upper-middle Yellow River basin and admixture with local populations on the Tibetan Plateau (Su et al. 2000).
Two neolithic expansion origins of Tibeto‑Burman populations
We also observed significant differences in the paternal gene pool of different subgroups of Tibeto-Burman populations. Haplogroup D-M174 contributed ~ 54% percent in a sampling of 2354 Tibetan males throughout the Tibetan Plateau (Qi et al. 2013). Previous studies have also found high frequencies of D-M174 in other populations on the Tibetan Plateau (Shi et al. 2008), including Sherpa (Lu et al. 2016) and Qiang (Wang et al. 2014). In contrast, haplogroup D-M174 is rare or absent from Tibeto-Burman populations from Northeast India and Burma (Shi et al. 2008). In populations of the Ngwi-Burmese language subgroup, the average frequencies of haplogroup D-M174 are ~ 5% (Dong et al. 2004; Peng et al. 2014). Furthermore, we found that lineage Oα1c1b-CTS5308 is mainly found in Tibeto-Burman populations from the Tibetan Plateau. In contrast, lineage Oα1c1a-Z25929 was found in Tibeto-Burman populations from Northeast India, Burma, and the Yunan and Hunan provinces of China (Additional files 1: Figure S1; Additional files 2: Table S1). In general, enrichment of lineage Oα1c1b- CTS5308 and high frequencies of D-M174 can be found in most Tibeto-Burman populations on the Tibetan Plateau and adjacent regions, whereas Tibeto-Burman populations from other regions tend to have lineage Oα1c1a-Z25929 and a little to no percentage of D-M174.
The inconsistent pattern we observed in the paternal gene pool of modern Tibeto-Burman populations suggested that there may be two distinct ancestor groups (Fig. 3). The proposed migration routes shown in Fig. 3 are somewhat different from those proposed by Su et al. (2000). According to our age estimation, most of the D1a2a-P47 samples belong to sub-lineage PH116, a young lineage that emerged ~ 2500 years ago (95% CI 1915–3188 years). On the other hand, continuous differentiation can be observed on a phylogenetic tree of lineages D1a1a1a1-PH4979 and D1a1a1a2-Z31591 since 6000 years ago. Therefore, we proposed that a group of ancient populations may have moved to the upper basin of the Yellow River and admixed intensively with local populations with high frequencies of haplogroup D-M174, including its sub-lineage D1a2a-P47 (Fig. 3). This ancestor group eventually gave birth to modern Tibeto-Burman populations on the Tibetan Plateau and adjacent regions. The other ancestor group moved toward the southwest and finally reached South East Asia (Burma and other locations) and the northeastern part of India (Fig. 3). This ancestor group may have had no or a minor admixture of D-M174 in their paternal gene pool.
Long‑term admixture before expansion to a high‑altitude region
It is interesting to investigate the time gap between the appearance of Neolithic cultures in the northeastern part of the Tibetan Plateau and the final phase of human expansion across the Tibetan Plateau. The Majiayao culture (~ 5400–4900 BP) is the earliest Neolithic culture in the northeastern part of the Tibetan Plateau (Liu et al. 2010). However, previous archeological study has suggested that the final phase of diffusion into the high-altitude area of the Tibetan Plateau occurred at approximately 3.6 kya (Chen et al. 2015). Our genetic evidence in this study is consistent with this scenario based on archeological evidence. Based on Y-chromosome analysis in this study, many unique lineages of Tibeto-Burman populations emerged between 6000 years ago and 2500 years ago (Additional files 3: Table S2). The most recent common age of D1a2-PH116, a sub-lineage that spread throughout the Tibetan Plateau, is only 2500 years ago.
We propose that there may be two important factors for the observed age gap. First, living in a high-altitude environment may require some crucial physical characteristics that were lacking from Neolithic immigrants from the middle Yellow River Basin. Intense genetic admixture with local people who had survived on the Tibetan Plateau since the Paleolithic Age may have actually guaranteed the expansion of humans across the Tibetan Plateau. Therefore, a long period of admixture, lasting from 5.4 to 3.6 kya, may be necessary for the appearance of a population with beneficial genetic variants that was genetically adapted to the high-altitude environment. Second, technological innovations, such as the domestication of wheat and highland barley (Chen et al. 2015), establishment of yak pastoralism (Rhode et al. 2007), and introduction of other culture elements in the Bronze Age (Ma et al. 2016), are also important factors that facilitated permanent settlements with large population sizes in the high-altitude area of the Tibetan Plateau.