Interesting excerpts (only introduction and conclusions, emphasis mine):
Archaeological setting at the site of Maidanetske, Ukraine
From ca. 4800 to 3350 BCE, Trypillia settlements were widespread over parts of eastern Romania, Moldova and Ukraine (Menotti and Korvin-Piotrovskiy, 2012; Müller et al., 2016; Videiko, 2004). Maidanetske (Fig. 1B) is one of the so-called “mega-sites” which developed during ca. 3900–3400 BCE in central Ukraine, in the Uman region (Cherkasy district) (Müller and Videiko, 2016; Müller et al., 2017). In this region, nine of these “mega-sites” have been found. Mega-sites are characterized by a regular plan with concentric rings of houses around a large empty central space, additional quartiers, with radial and peripheral track ways (Fig. 1B). The three mega-sites Maidanetske, Taljanky and Dobrovody, lay ca. 15 km apart from each other (Fig. 1A); other mega-sites are located within a 50 km radius around Maidanetske. Archaeologically, these mega-sites consist of the remains of buildings most of them burnt, although a minority of unburnt buildings is known of as well (Burdo and Videiko, 2016; Müller and Videiko, 2016; Ohlrau, 2015). Most of these buildings have a standardized regular size (average 6×12 m) and architecture including domestic installations and a standardized assemblage of artifacts. At Maidanetske beside normal sized houses there are few larger rectangular buildings that are located regularly along the main pathways. Further archaeological contexts include pits, pottery kilns, and peripheral ditches. A huge variety of mostly painted pottery (including many with figurative animal and plant motives), some flint artifacts, rare copper objects, querns, adzes and a broad range of anthropomorphic and zoomorphic figurines are attested within houses and mega-structures. In terms of organic remains, animal bones are fairly common, while botanical macro-remains appear to be scarce and poorly preserved (Kirleis and Dal Corso, 2016; Pashkevich and Videjko, 2006).
Environmental setting at Maidanetske
The Trypillia sites in central Ukraine, including Maidanetske, are located in a semi-arid forest-steppe ecozone, a mosaic-like ecosystem stretched between the dry steppe grasslands in the south and temperate woodland biomes in the north (Fig. 1A). In this transitional zone the natural vegetation is supposed to be patchy and sensitive to climate and topography (Feurdean et al., 2015; Molnàr et al., 2012; Walter, 1974). Since most of the accessible plateaus are converted to agricultural land and the scarce broadleaf woodlands are managed, the natural landscape heterogeneity is difficult to trace within the current landscape (Kuzemko et al., 2014). Besides agricultural fields and villages, narrow river valleys incised into the loess plateaus are present, with riparian vegetation and artificial lakes. This western Pontic area has a humid continental climate with wet winters and warm summers (Köppen and Geiger, 1939), which corresponds to a semi-arid 0.2–0.5 aridity index value according to UNEP (1997). Nevertheless, the reconstruction of past climatic as well as environmental conditions is not straightforward, since undisturbed archives for pollen analysis are lacking in the region and published climatic reconstructions combine evidences from peripheral areas (Gerasimenko, 1997; Harper, 2017; Kirleis and Dreibrodt, 2016). In the Transylvanian forest-steppe region, palynological investigations suggest that dry grasslands have expanded since the end of the 4th millennium BCE, fostered by Bronze Age forest clearance, while before this the area was largely forested (Feurdean et al., 2015). In the Hungarian forest-steppe, the mixed oak forest on Loess almost disappeared by the end of the 18th century AD, hampered by factors such as fragmentation, slow regeneration, spread of invasive species and lowering of the water table due to increased aridity (Molnàr et al., 2012). It is clear that forest-steppe environments are very sensitive to aridity and land use practices. To understand whether similar landscape change can have occurred in central Ukraine already at the time of Chalcolithic mega-sites, an understanding of the extent of crop growing and deforestation is crucial.
The site of Maidanetske is situated on a plateau covered by Loess deposited during the Last Glaciation. This plateau is dissected by valleys of different sizes with perennial rivers present within the large valleys. One of these rivers passes the site in a distance of less than 500 m. The soils that are present nowadays are Chernozems. They show dark greyish-brown A-horizons of thicknesses between 30 and 50 cm and a texture dominated by silt. Numerous filled crotowinas indicate an intensive bioturbation during the formation of these soils. The Chernozems cover the archaeological record. The variations in thickness of the A-horizon are probably reflecting post-depositional soil erosion processes. Buried soils discovered at lower slope positions below colluvial layers show properties of Cambisols, thus pointing towards a forested past of the surrounding landscape (Kirleis and Dreibrodt, 2016).
At the site of Maidanetske, the phytolith record from different contexts including multiple houses, was studied, which confirmed cereal cultivation as part of the subsistence economy of the site. Furthermore, phytoliths gave information about wild grasses, whereas dicotyledonous material was scarce. For the house structures cereal byproducts, chaff and straw were identified as material selected for tempering daub for the wall construction. Ash layers in a pit filled with house remains show similar pattern. Daub fragments and pit filling are the most promising archives for further phytolith work on cereals at Trypillia sites. The sediment inside four burnt houses and the areas outside two houses, where also grinding stones were sampled, showed little presence of the remains of final cereal processing, suggesting that either the surfaces were cleaned and the chaff was collected after dehusking, or the cereal processing activity took place somewhere else. Specific archaeological contexts, such as vessels and grinding stones, did not differ much from the control samples from archaeological sediment nearby, suggesting disturbance of the record.(…)
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.
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.
In 1898, two megalithic tombs containing graves of a local social elite dated to the Early Bronze Age were discovered by N. I. Veselovsky near the village of Tsarskaya (modern Novosvobodnaya, Republic of Adygeya) (Fig. 1 (a)) (Baye 1900, 43–59; IAC 1901, 33–8; Sagona 2018, 281–97).
Radiocarbon dates place both tombs within the Novosvobodnaya phase of the Maykop culture, between c. 3200 and 2900 BC (Trifonov et al. 2017). Along with the human remains (one adult individual was interred in each dolmen), the tombs yielded rich funerary offerings, including artefacts made of gold, silver and semi-precious stones. (…) This paper presents results of a technical analysis of just one type of artefact, from kurgan 2 at Tsarskaya: thin-walled jointless beads made from gold.
Ever since M. I. Rostovtzeff noted a stylistic similarity between Maykop art and Sumerian art (Rostovtzeff 1920) and M. V. Andreeva described this phenomenon within a broad cultural and chronological context (Andreeva 1977), new archaeological studies have only extended this picture of a vast cultural province that appeared between the Caucasus and the northern fringe of Western Asia (Trifonov 1987). The discovery of the Leyla-Tepe culture (Narimanov 1987) and Maykop-type kurgans in Azerbaijan (Lyonnet et al. 2008) and adjacent Iran (Muscarella 1969, 1971, 2003; Trifonov 2000) has confirmed the spatial and temporal unity of this phenomenon as a precondition for free circulation of cultural patterns and technical innovations across vast areas of the Caucasus and Western Asia. Jewellery made of gemstones and precious metals, primarily gold, was probably one such innovation.
Attempts to demarcate the historical region where the Maykop culture emerged and developed have emphasized the role of Upper Mesopotamia in the development of the Sumerian civilization and the definition of a northern centre of urbanization, independent from the centres of the south (Rothman 2002; Oats et al. 2007). The turn of the fourth millennium BC saw the development of various cultural traditions in south-east Anatolia, north-east Syria and north-west Iran; on the northern fringe, these traditions manifested themselves through the Maykop culture. Perhaps it is no coincidence that the first high-status burials containing gold and gemstone jewellery (including carnelian, turquoise and lapis lazuli) appear in these northern, rather than southern, centres in the first quarter of 4000 BC (e.g., Tepe Gawra, graves 109, 110) (Piasnall 2002). With regard to funeral rites and stylistic characteristics of jewellery pieces, these graves have many parallels with early Maykop burials (Munchaev 1975, 329; Trifonov 1987, 20).
It still remains unclear if the goldsmiths of Upper Mesopotamia mastered the technique of making thin-walled jointless beads. The gold beads from Tepe Gawra are described as spherical or ball-shaped, but their maximum diameter (5–8mm) always exceeds the length of the bore (3–4mm) (Tobler 1950, 89, 199, pl. LV, a). On the whole, these measurements are consistent with the proportions and sizes of some Maykop beads.(…)
It is quite possible that a distinctive technique of making thin-walled jointless beads from gold was a regional technological development of Maykop culture goldsmiths, within a wider tradition of Near East metalwork, as a type of production regulated by ritual beliefs (Gell 1992; Benzel 2013).
These deep-rooted Near East traditions of ritualization of the production and use of jewellery pieces made of gold, silver and gemstones in the Maykop culture, on the one hand, maintained familiar canons of ritual behaviour and, on the other, made perception of sophisticated symbolism of gemstones more difficult for neighbouring cultures with different living standards, levels of social development and value systems to understand. The jewellery traditions of the Maykop culture had no successors in the Caucasus or the adjacent steppes. In the third millennium BC, the goldsmiths of Europe and Asia had to reinvent the technique of making thin-walled jointless gold beads from scratch (Born et al. 2009).
Related excerpts, about the climate of an adjacent region of the Caucasus before, during, and after the Maykop culture:
The 7th millennium BC featured a warm and arid climate, so that time corresponds to the steppe landscapes in the final stage of the Mesolithic. It is likely that the formation of a producing economy in the mountainous zone of Dagestan gradually emerged against this background. In the Neolithic period, the area remained almost treeless, as it was still warm and quite dry. However, archaeological data indicates that long-term settlements with well-developed farming spread in the mountainous zone around 6200-5500 BC.
The beginning of increasing humidity and the appearance of deciduous forests corresponds to the early Chalcolithic period of the Eastern Caucasus. It is the most poorly studied period in the history of this region. Covering a time span of 2000 years, this period was the least saturated by archaeological sites. At the start of this period, only the stands of herdsman in the mountain zone are known, dating to the second half of the 6th millennium BC (Gadgiev, 1991). It is still not clear whether the mountains were not settled in such a favorable climatic stage. The uncertainty may be due to the fact that people have chosen other ecological niches, or it could be we simply do not have data due to the insufficient archaeological survey of the territory. It is surprising that the turn to drier climate and the reduction of deciduous forests in the inner mountainous part of Dagestan, the large, long-term settlements like Ginchi emerge with pronounced specialization in agriculture (Fig. 7 panel (2)) (Gadgiev, 1991).
After the dry climate, simultaneously with cooling, the subsequent spread of pine forests coincides with the beginning of expansion of Kura-Araxes culture from the territory of Georgia through Chechnya to the mountainous Dagestan. Debates on the impact of past climate on Kura-Araxes societies in Transcaucasus have a long history (for the comprehensive review see, for example, Connor and Kvavadze, 2014 and references therein). In general, it is clear that after 3000 BC, forest cover in most areas of the Kura-Araxes region in the Transcaucasia reached its maximum extent in the Holocene (Connor and Kvavadze, 2014). However, at the same time lakes in Central Anatolia began to dry out and Caspian Sea levels fell (Roberts et al. 2011; Leroy et al. 2013), and arid conditions were identified in mountainous Dagestan in the 4th millennium. Clearly the regional moisture balance shifted in the Eastern Caucasus only in the late 4th to early 3rd millennium BC (this study). The only available radiocarbon dating of Dagestan confirms that the agricultural settlements of the Early Bronze Age appear not in the middle of the 4th millennium BC, but in the early 3rd millennium BC; that is not earlier than the stage of increasing moistening and the appearance of pine forests.
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.
The Turganik settlement in the Orenburg Region constitutes part of the so-called Ivanovo microregion of cultural heritage monuments, along with the Mesolithic Starotokskaya site; an Ivanovskoye multi-layered settlement (Neolithic, Eneolithic [or Chalcolithic], Late Bronze Age); Toksky I and Toksky II settlements attributed to the Late Bronze Age (the Timber-Grave archaeological culture); an Ivanovsky ground burial dated to the Eneolithic; and the Ivanovsky kurgan cemetery of the Early Iron Age (Fig. 1).
The ancient settlements are located at the Turganik River mouth, where the river joins the Tok River (the Samara River drainage basin). The Turganik River enters an old channel of the Tok which continues to flow due to that fact. Both valleys are wide and dissected by multiple river channels. The floodplain landscapes are mostly wet meadows with rich herb and grass vegetation, pastures, and hay fields. On both sides of the Turganik River, and farther along the right side of the Tok valley there are flat-topped elevations, with occasional forests (Chibilev, 1996). The Turganik settlement was positioned on a slightly elevated surface at the confluence of the Turganik and Tok rivers, on the right side of the valley. The settlement was inhabited in the Eneolithic and the Late Bronze Age, the fifth to fourth millennia BC.
Results and discussion
Pollen assemblages of the Atlantic optimum ~ 5500 yr BP indicate some increase in moisture supply and related afforestation of the floodplain (Lavrushin and Spiridonova, 1995). As follows from our data, the site was abandoned at that time and the no-longer-functioning cultural layer VI was gradually buried under deposits of frequent floods. According to the 14C ages obtained on archeological materials, the age of layer VI (or the second stage of the Eneolithic epoch on the Turganik settlement) may be dated to 4237–3790 cal yr BC, that is, somewhat earlier than the Holocene optimum suggested by palynologists.
Layer V shows another interval marked by increasing climate aridity and the dominance of grass steppes. As stated by the above-cited authors, the climate at the time that layer V was functioning was even dryer than during the formation of layer VI. That is confirmed by our data on the layer V composition, was formed during early Pit-Grave culture (the Early Bronze Age), in the range from 3800–3360 BC, according to the dates obtained on archeological materials (Morgunova et al., 2016b). As follows from the above, the maximum of aridity coincided with the Atlantic optimum.
It follows from the above that the Atlantic period of the Holocene was mostly characterized by arid environments; the peak of aridity fell on the early Bronze Age, the time of the early (Repino) stage of the Yamnaya culture in the Cis-Ural steppes. The Subboreal and Subatlantic periods were relatively colder and more humid, though short episodes of aridity could occur and some of them happened to be recorded in the sequence under study.
The reconstructed history of the climate changes in the Cis-Ural steppes during three intervals of the Holocene is in a good agreement with the results obtained in other regions. According to Alexandrovskiy (1996, 2000; Alexandrovskiy et al., 1999, 2004), the Atlantic period was the most arid one in the south of Russia, the subsequent intervals being comparatively wetter and colder. The extreme aridity was recorded on the Ukraine territory at the final Atlantic period, a few less arid chrono-intervals having been identified over the entire period (Kotova, 2009).
There are, however, other schemes of climate fluctuations in the central part of the Russian steppe zone; a few of them consider the Atlantic period to be humid, or even the most humid, as compared with the second half of the Holocene (Ivanov, 1992; Demkin, 1997). Also acceptable is a scenario of climatic fluctuations occurring at different times in different regions (Chendev et al., 2010). Further investigations and accumulation of empirical data would help to gain a better insight into the problem.
The ancient people inhabited the place from 5000 to 4000 BC (actually throughout the Atlantic period), when the place was not subjected to flooding. At the time of human habitation, the climate was mostly arid. Paleosols of that time are attributable to the Kastanozems (Endosalic Protosodic). They developed under grass (or herb and grass) steppes. The peak of aridity falls on the final Atlantic period. At the end of Eneolithic epoch (the fifth millennium BC) and in the Early Bronze Age (the fourth millennium BC) there were short-term but violent floods, which forced people to leave the habitable place.
During the Subboreal and Subatlantic periods of the Holocene, the climate became more humid, the floods became regular, the vegetation was dominated by meadow forbs and herbs growing on meadow-chernozem soils (Luvic Chernozem [Stagnic]), and the settlement was completely abandoned. In general, the studied sedimentary record at the Turganik archeological site reveals traceable climate change towards lower temperatures and increasing humidity in the second part of the Holocene, with occasional episodes of aridity that did not affect the general trend.
The central East European plains are famous for their Epigravettian sites that date to around 15–12 14C ka BP (ca. 18.2–13.8 cal ka BP) and display impressive large structures made from the bones of woolly mammoth (Mammuthus primigenius; e.g., Gladkih et al., 1984; Soffer, 1985; Hoffecker, 2002). The origin of the large accumulations of mammoth remains is still a matter of debate, with the main hypotheses being the collection of natural occurrences versus active hunting (e.g., Soffer, 1985; Haynes 1989; Svoboda et al., 2005). In favor of this second scenario, studies of the mammoth remains of Yudinovo (Germonpré et al., 2008) concluded that the mammoths were hunted and, at Mezhyrich, mammoths were obtained by combined procurement via collection of carcasses and active hunting (Péan, 2015). Hunting practices were observed in older sites of the Gravettian culture in the Dnieper and Desna valleys (Demay et al., 2016).
Between ca. 22 and 12 14C ka BP (ca. 26.2–13.8 ka cal BP), the Dnieper and Desna basins correspond to the southern part of the geographical distribution of the woolly mammoth (Markova et al., 2013; Kahlke, 2014). Over time their distribution shifted northwards, while the density of the mammoth population decreased (Markova et al., 2013). According to Markova et al. (2013), the combined effect of gradual warming and growing human pressure is most likely to have had a negative impact on the mammoths, resulting in their local extinction in the Russian and Ukrainian plains around 14–12 14C kaBP (ca. 17.0–13.8 ka cal BP; Stuart et al., 2005).
Discussion and conclusion
Humans could have taken advantage of the mammoth vulnerability, as reflected by lower δ15N values, to access animals that died naturally, collect bones, and hunt the most fragile individuals. This, with the possible assistance of domesticated dogs as hunting partners, could have countered a possible return to more suitable conditions for mammoth (Sablin and Khlopachev, 2002; Shipman, 2015). Our results confirm at least that mammoth specimens from Mezhyrich, Buzhanka 2, and, to a lesser extent, Eliseevichi were part of late mammoth populations surviving in sub-optimal conditions. They were thus most likely vulnerable to any pressure from environmental and/or human origin. Detecting further such cases among the late surviving mammoth populations using stable isotopic tracking may be a way to test if mammoth populations still had an optimal ecology or were metastable and, therefore, vulnerable to extinction. For instance, the insular Holocene population of mammoth on Saint Paul Island exhibited low and variable δ15N values, indicating suboptimal ecological conditions preceding their final disappearance (Graham et al., 2016).
The results of δ34S analyses showed no differences among mammoth according to the site but possibly a forage range partitioning between mammoth and coexisting large ungulates. Thus, variability in the mobility pattern for the mammoth between the high and low δ15N groups, such as migratory versus sedentary individuals, is not supported so far. We consider that rapid environmental modifications over time, probably not detectable through radiocarbon dating, can be a valid alternative explanation. Combined with direct competition with other large herbivores, such as the horse, and hunting of the most vulnerable individuals, the loss of their optimal habitat was likely to be the driving factor behind the local extinction of the mammoth in the central East European plains.
Interesting excerpts (modified for clarity, emphasis mine):
Canid mitochondrial phylogenies show that dogs and wolves are not reciprocally monophyletic. The mitochondrial tree contains four deeply rooted clades encompassing dogs and many grey wolf groups. These four clades form the basis of dog mitochondrial haplogroup assignment, known as haplogroups A-D. The time of the most recent common ancestor (TMRCA) of haplogroups A-D significantly predates estimates for domestication based on archeological and genetic evidence. Instead, these clades may represent variation present among the founding population of the dog lineage or the results of wolf introgressions into dog populations. The relative frequencies of mitochondria haplogroups are not stable over time, with changes reflecting processes such as drift, migration, and population growth. Although the mitochondria A and B haplogroups are most common in contemporary European dogs, surveys of ancient samples indicate that the majority of ancient European dogs carried the C or D mitochondrial haplotype. This apparent turnover in mitochondrial haplogroups may reflect the migration of a distinct dog population into Europe over the past 15,000 years.
Using the variation discovered from sequence data, we applied a Bayesian MCMC approach to estimate TMRCAs for each haplotype group. Our estimated Y-chromosome mutation rate (3.07 × 10− 10 substitutions per site per year, relaxed clock model) falls within the range of a previous estimate by Ding et al. who used a similar calibration and estimate 1.35 × 10− 10– 4.31 × 10− 10 substitutions per site per year. The TMRCAs we estimated are substantially older than mitochondria phylogenies calibrated with tip dates of ancient samples, which report clade-specific TMRCAs < 25,000 years ago. We note that our Y-chromosome TMRCA estimates are extremely sensitive to our assumptions about the age of the root of the tree and should be interpreted with caution due to the uncertainty in this single calibration point. However, the relative ages of the branches and the chronological order of haplogroup divergences are more robust than the absolute estimated dates.
In general, the relationships between Y-chromosome haplogroups and autosomal ancestry we report are very similar to the relationships described in Shannon et al. As noted earlier, our dataset includes a subset of wolves with Y-chromosomes assigned to a dog Y-haplogroup. However, ADMIXTURE analysis does not indicate substantial recent dog ancestry in these samples, suggesting that their placement on the Y-chromosome phylogeny reflects variation in Y-chromosome haplotypes that was present in the ancestral population and therefore predates the domestication process or is the result of ancient introgression events whose signature of autosomal ancestry has been diluted.
Using sequencing data, we find that the estimated TMRCA of dog Y haplogroups predates dog domestication. We further reveal the placement of several wolf Y-chromosomes within deep branches of dog haplogroup clades. Using an expanded set of mutations diagnostic for each haplogroup, we find that distinct Y haplogroups were present in Europe during the Neolithic and that CTC, a ~ 4700 year old ancient dog from Germany has a Y-chromosome that shares diagnostic alleles with wolves found in India.
While Proto-Indo-European- and Proto-Uralic-speakers had a close relationship with dogs (revealed in their reconstructed language and attributed archaeological cultures), I think it will be very difficult to ascertain any population movement based on them, unless there is a clear, well-established archaeological relationship between a specific culture and dog-breeding.
NOTE. I think one of the important changes in this version compared to the preprint is the addition of the recent Iberomaurusian samples.
Abstract (emphasis mine):
The extent to which prehistoric migrations of farmers influenced the genetic pool of western North Africans remains unclear. Archaeological evidence suggests that the Neolithization process may have happened through the adoption of innovations by local Epipaleolithic communities or by demic diffusion from the Eastern Mediterranean shores or Iberia. Here, we present an analysis of individuals’ genome sequences from Early and Late Neolithic sites in Morocco and from Early Neolithic individuals from southern Iberia. We show that Early Neolithic Moroccans (∼5,000 BCE) are similar to Later Stone Age individuals from the same region and possess an endemic element retained in present-day Maghrebi populations, confirming a long-term genetic continuity in the region. This scenario is consistent with Early Neolithic traditions in North Africa deriving from Epipaleolithic communities that adopted certain agricultural techniques from neighboring populations. Among Eurasian ancient populations, Early Neolithic Moroccans are distantly related to Levantine Natufian hunter-gatherers (∼9,000 BCE) and Pre-Pottery Neolithic farmers (∼6,500 BCE). Late Neolithic (∼3,000 BCE) Moroccans, in contrast, share an Iberian component, supporting theories of trans-Gibraltar gene flow and indicating that Neolithization of North Africa involved both the movement of ideas and people. Lastly, the southern Iberian Early Neolithic samples share the same genetic composition as the Cardial Mediterranean Neolithic culture that reached Iberia ∼5,500 BCE. The cultural and genetic similarities between Iberian and North African Neolithic traditions further reinforce the model of an Iberian migration into the Maghreb.
FST and outgroup-f3 distances indicate a high similarity between IAM and Taforalt. As observed for IAM, most Taforalt sample ancestry derives from Epipaleolithic populations from the Levant. However, van de Loosdrecht et al. (17) also reported that one third of Taforalt ancestry was of sub-Saharan African origin. To confirm whether IAM individuals show a sub-Saharan African component, we calculated f4(chimpanzee, African population; Natufian, IAM) in such a way that a positive result for f4 would indicate that IAM is composed both of Levantine and African ancestries. Consistent with the results observed for Taforalt, f4 values are significantly positive for West African populations, with the highest value observed for Gambian and Mandenka (Fig. 3 and SI Appendix, Supplementary Note 10). Together, these results indicate the presence of the same ancestral components in ∼15,000-y old and ∼7,000-y-old populations from Morocco, strongly suggesting a temporal continuity between Later Stone Age and Early Neolithic populations in the Maghreb. However, it is important to take into account that the number of ancient genomes available for comparison is still low and future sampling can provide further refinement in the evolutionary history of North Africa.
Genetic analyses have revealed that the population history of modern North Africans is quite complex (11). Based on our aDNA analysis, we identify an Early Neolithic Moroccan component that is (i) restricted to North Africa in present-day populations (11); (ii) the sole ancestry in IAM samples; and (iii) similar to the one observed in Later Stone Age samples from Morocco (17). We conclude that this component, distantly related to that of Epipaleolithic communities from the Levant, represents the autochthonous Maghrebi ancestry associated with Berber populations. Our data suggests that human populations were isolated in the Maghreb since Upper Paleolithic times. Our hypothesis is in agreement with archaeological research pointing to the first stage of the Neolithic expansion in Morocco as the result of a local population that adopted some technological innovations, such as pottery production or farming, from neighboring areas.
By 3,000 BCE, a continuity in the Neolithic spread brought Mediterranean-like ancestry to the Maghreb, most likely from Iberia. Other archaeological remains, such as African elephant ivory and ostrich eggs found in Iberian sites, confirm the existence of contacts and exchange networks through both sides of the Gibraltar strait at this time. Our analyses strongly support that at least some of the European ancestry observed today in North Africa is related to prehistoric migrations, and local Berber populations were already admixed with Europeans before the Roman conquest. Furthermore, additional European/ Iberian ancestry could have reached the Maghreb after KEB people; this scenario is supported by the presence of Iberian-like Bell-Beaker pottery in more recent stratigraphic layers of IAM and KEB caves. Future paleogenomic efforts in North Africa will further disentangle the complex history of migrations that forged the ancestry of the admixed populations we observe today.
Also, from the main author’s Twitter account:
I just realized that the paragraph with information on data availability is missing! Sequence data in the European Nucleotide Archive (PRJEB22699). Consensus mtDNA sequences are available at the National Center of Biotechnology Information (Accession Numbers MF991431-MF991448).
I find it hard to believe that this genetic continuity from Upper Palaeolithic to Late Neolithic could be representative of an autochthonous development of Afroasiatic. An important population movement – likely more than one – must be found in ancient DNA influencing North-Central and North-East Africa, probably during the time of the Green Sahara corridor.
The retrieval of ancient DNA from osteological material provides direct evidence of human genetic diversity in the past. Ancient DNA samples are often used to investigate whether there was population continuity in the settlement history of an area. Methods based on the serial coalescent algorithm have been developed to test whether the population continuity hypothesis can be statistically rejected by analysing DNA samples from the same region but of different ages. Rejection of this hypothesis is indicative of a large genetic shift, possibly due to immigration occurring between two sampling times. However, this approach is only able to reject a model of full continuity model (a total absence of genetic input from outside), but admixture between local and immigrant populations may lead to partial continuity. We have recently developed a method to test for population continuity that explicitly considers the spatial and temporal dynamics of populations. Here we extended this approach to estimate the proportion of genetic continuity between two populations, by using ancient genetic samples. We applied our original approach to the question of the Neolithic transition in Central Europe. Our results confirmed the rejection of full continuity, but our approach represents an important step forward by estimating the relative contribution of immigrant farmers and of local hunter‐gatherers to the final Central European Neolithic genetic pool. Furthermore, we show that a substantial proportion of genes brought by the farmers in this region were assimilated from other hunter‐gatherer populations along the way from Anatolia, which was not detectable by previous continuity tests. Our approach is also able to jointly estimate demographic parameters, as we show here by finding both low density and low migration rate for pre‐Neolithic hunter‐gatherers. It provides a useful tool for the analysis of the numerous aDNA datasets that are currently being produced for many different species.
Our results are in general accordance with two distinct ancestry components that have previously been detected at the continental scale by Lazaridis, Patterson et al. (2014): the “early European farmer” (EEF), which corresponds here to the NFA from Anatolia (zone C in Figure 3), and the “West European hunter-gatherer” (WHG), which corresponds here to the PHG from zones A and B in Figure 3. Notably, the contribution of an Ancient North Eurasians (ANE) component is not included in our model as we did not consider potential post-Neolithic immigration waves, which could have contributed to the modern European genetic pool, such as the wave that came from the Pontic steppes and was associated with the Yamnaya culture (Haak, Lazaridis et al. 2015). Without considering the ANE ancestry component, our estimate of the autosomal genetic contribution of Early farmers to the gene pool of Central European populations (25%) tends to be lower than the EEF ancestry estimated in most modern Western European populations, but is of the same order than the estimations in modern Estonians and in the ancient Late Neolithic genome “Karsdorf” from Germany (Lazaridis, Patterson et al. 2014, Haak, Lazaridis et al. 2015). Note that the contribution of hunter-gatherers to Neolithic communities appears to be variable in different regions of Europe (Skoglund, Malmstrom et al. 2012, Brandt, Haak et al. 2013, Lazaridis, Patterson et al. 2014), while we computed an average value for Central Europe. Moreover, we computed the ancestry of the two groups at the end of the Neolithic period while previous studies estimated it in modern times. Finally, previous studies used molecular information to directly estimate admixture proportions, while we use molecular information to estimate the model parameters and, then, we computed the expected genetic contributions of both groups using the best parameters, without using molecular information during this second step. Model assumptions may thus influence the inferences on the relative genetic contribution of both groups. In particular, we made the assumption of a uniform expansion of NFA with constant and similar assimilation of PHG over the whole continent but spatio-temporally heterogeneous environment, variable assimilation rate and long distance dispersal may have played an important role. The effects of those factors should be investigated in future studies.