The genetic makings of South Asia – IVC as Proto-Dravidian

south-asian-language-families

Review (behind paywall) The genetic makings of South Asia, by Metspalu, Monda, and Chaubey, Current Opinion in Genetics & Development (2018) 53:128-133.

Interesting excerpts (emphasis mine):

(…) the spread of agriculture in Europe was a result of the demic diffusion of early Anatolian farmers, it was discovered that the spread of agriculture to South Asia was mediated by a genetically completely different farmer population in the Zagros mountains in contemporary Iran (IF). The ANI-ASI cline itself was interpreted as a mixture of three components genetically related to Iranian agriculturalists, Onge and Early and Middle Bronze Age Steppe populations (Steppe_EMBA).

The first ever autosomal aDNA from South Asia comes from Northern Pakistan (Swat Valley, early Iron Age). This study presented altogether 362 aDNA samples from the broad South and Central Asia and contributes substantially to our understanding of the evolutionary past of South and Central Asia. The study redefines the three genetic strata that form the basis of the Indian Cline. The Indus Periphery (IP) component is composed of (varying proportions of): first, IF, second, Ancient Ancestral South Asians (AASI), which represents an ancient branch of human genetic variation in Asia arising from a population split contemporaneous with the splits of East Asian, Onge and Australian Aboriginal ancestors and third, West_Siberian Hunter gatherers (WS_HG).

The authors argue that IP could have formed the genetic base of the Indus Valley Civilization (IVC). Upon the collapse of the IVC IP contributes to the formation of both ASI and ANI. ASI is formed as IP admixes further with AASI. ANI in turn forms when IP admixes with the incoming Middle and Late Bronze Age Steppe (Steppe_MLBA) component, (rather than the Steppe_EMBA groups suggested earlier)

ane-whg-ehg-chg-wshg-steppe
A sketch of the peopling history of South Asia. Depicting the full complexity of available reconstructions is not attempted. Placing of population labels does not indicate precise geographic location or range of the population in question. Rather we aim to highlight the essentials of the recent advancements in the field. We divide the scenario into three time horizons: Panels (a) before 10 000 BCE (pre agriculture era.); (b) 10 000 BCE to 3000 BCE (agriculture era) and (c) 3000 BCE to prehistoric era/modern era. (iron age).

Dating of the arrival of the Austro-Asiatic speakers in South Asia-based on Y chromosome haplogroup O2a1-M95 expansion estimates yielded dates between 3000 and 2000 BCE [30]. However, admixture LD decay-based approach on genome-wide data suggests the admixture between South Asian and incoming Austro-Asiatic speakers occurred slightly later between 1800 and 0 BCE (Tätte et al. submitted). It is interesting that while the mtDNA variants of the Mundas are completely South Asian, the Y chromosome variation is dominated at >60% by haplogroup O2a which is phylogeographically nested in East Asian-specific paternal lineages.

In India, the speakers of Tibeto-Burman (TB) languages live in the Seven Sisters States in Northeast India and in the very north of the country. Genetically they show a clear East Asian origin and around 20% of subsequent admixture with South Asians within the last 1000 years.The genetic flavour of East Asia in TB is different from that in Munda speakers as the best surrogates for the East Asian admixing component are contemporary Han Chinese.

I found the simplistic migration maps especially interesting to illustrate ancient population movements. The emergence of EHG is supposed to involve a WHG:ANE cline, though, and this isn’t clear from the map. Also, there is new information on what may be at the origin of WHG and Anatolian hunter-gatherers.

From the recent Reich’s session on South Asia at ISBA 8:

ani-asi-steppe-cline
– Tale of three clines, with clear indication that “Indus Periphery” samples drawn from an already-cosmopolitan and heterogeneous world of variable ASI & Iranian ancestry. (I know how some people like to pore over these pictures – so note red dots = just dummy data for illustration.)
– Some more certainty about primary window of steppe ancestry injection into S. Asia: 2000-1500 BC
Alexander M. Kim

Featured image: map of South Asian languages from http://llmap.org.

Related

Early Iranian steppe nomadic pastoralists also show Y-DNA bottlenecks and R1b-L23

New paper (behind paywall) Ancient genomes suggest the eastern Pontic-Caspian steppe as the source of western Iron Age nomads, by Krzewińska et al. Science (2018) 4(10):eaat4457.

Interesting excerpts (emphasis mine, some links to images and tables deleted for clarity):

Late Bronze Age (LBA) Srubnaya-Alakulskaya individuals carried mtDNA haplogroups associated with Europeans or West Eurasians (17) including H, J1, K1, T2, U2, U4, and U5 (table S3). In contrast, the Iron Age nomads (Cimmerians, Scythians, and Sarmatians) additionally carried mtDNA haplogroups associated with Central Asia and the Far East (A, C, D, and M). The absence of East Asian mitochondrial lineages in the more eastern and older Srubnaya-Alakulskaya population suggests that the appearance of East Asian haplogroups in the steppe populations might be associated with the Iron Age nomads, starting with the Cimmerians.

scythian-cimmerian-sarmatian-y-dna-mtdna

#UPDATE (5 OCT 2018): Some Y-SNP calls have been published in a Molgen thread, with:

  • Srubna samples have possibly two R1a-Z280, three R1a-Z93.
  • Cimmerians may not have R1b: cim357 is reported as R1a.
  • Some Scythians have low coverage to the point where it is difficult to assign even a reliable haplogroup (they report hg I2 for scy301, or E for scy197, probably based on some shared SNPs?), but those which can be reliably assigned seem R1b-Z2103 [hence probably the use of question marks and asterisks in the table, and the assumption of the paper that all Scythians are R1b-L23]:
    • The most recent subclade is found in scy305: R1b-Z2103>Z2106 (Z2106+, Y12538/Z8131+)
    • scy304: R1b-Z2103 (M12149/Y4371/Z8128+).
    • scy009: R1b-P312>U152>L2 (P312+, U152?, L2+)?
  • Sarmatians are apparently all R1a-Z93 (including tem002 and tem003);
  • You can read here the Excel file with (some probably as speculative as the paper’s own) results.

    About the PCA

    1. Srubnaya-Alakulskaya individuals exhibited genetic affinity to northern and northeastern present-day Europeans, and these results were also consistent with outgroup f3 statistics.
    2. The Cimmerian individuals, representing the time period of transition from Bronze to Iron Age, were not homogeneous regarding their genetic similarities to present-day populations according to the PCA. F3 statistics confirmed the heterogeneity of these individuals in comparison with present-day populations
    3. The Scythians reported in this study, from the core Scythian territory in the North Pontic steppe, showed high intragroup diversity. In the PCA, they are positioned as four visually distinct groups compared to the gradient of present-day populations:
      1. A group of three individuals (scy009, scy010, and scy303) showed genetic affinity to north European populations (…).
      2. A group of four individuals (scy192, scy197, scy300, and scy305) showed genetic similarities to southern European populations (…).
      3. A group of three individuals (scy006, scy011, and scy193) located between the genetic variation of Mordovians and populations of the North Caucasus (…). In addition, one Srubnaya-Alakulskaya individual (kzb004), the most recent Cimmerian (cim357), and all Sarmatians fell within this cluster. In contrast to the Scythians, and despite being from opposite ends of the Pontic-Caspian steppe, the five Sarmatians grouped close together in this cluster.
      4. A group of three Scythians (scy301, scy304, and scy311) formed a discrete group between the SC and SE and had genetic affinities to present-day Bulgarian, Greek, Croatian, and Turkish populations (…).
      5. Finally, one individual from a Scythian cultural context (scy332) is positioned outside of the modern West Eurasian genetic variation (Fig. 1C) but shared genetic drift with East Asian populations.
    scythian-cimmerian-pca
    Radiocarbon ages and geographical locations of the ancient samples used in this study. Figure panels presented (Left) Bar plot visualizing approximate timeline of presented and previously published individuals. (Right) Principal component analysis (PCA) plot visualizing 35 Bronze Age and Iron Age individuals presented in this study and in published ancient individuals (table S5) in relation to modern reference panel from the Human Origins data set (41).

    Cimmerians

    The presence of an SA component (as well as finding of metals imported from Tien Shan Mountains in Muradym 8) could therefore reflect a connection to the complex networks of the nomadic transmigration patterns characteristic of seasonal steppe population movements. These movements, although dictated by the needs of the nomads and their animals, shaped the economic and social networks linking the outskirts of the steppe and facilitated the flow of goods between settled, semi-nomadic, and nomadic peoples. In contrast, all Cimmerians carried the Siberian genetic component. Both the PCA and f4 statistics supported their closer affinities to the Bronze Age western Siberian populations (including Karasuk) than to Srubnaya. It is noteworthy that the oldest of the Cimmerians studied here (cim357) carried almost equal proportions of Asian and West Eurasian components, resembling the Pazyryks, Aldy-Bel, and Iron Age individuals from Russia and Kazakhstan (12). The second oldest Cimmerian (cim358) was also the only one with both uniparental markers pointing toward East Asia. The Q1* Y chromosome sublineage of Q-M242 is widespread among Asians and Native Americans and is thought to have originated in the Altai Mountains (24)

    Scythians

    In contrast to the eastern steppe Scythians (Pazyryks and Aldy-Bel) that were closely related to Yamnaya, the western North Pontic Scythians were instead more closely related to individuals from Afanasievo and Andronovo groups. Some of the Scythians of the western Pontic-Caspian steppe lacked the SA and the East Eurasian components altogether and instead were more similar to a Montenegro Iron Age individual (3), possibly indicating assimilation of the earlier local groups by the Scythians.

    Toward the end of the Scythian period (fourth century CE), a possible direct influx from the southern Ural steppe zone took place, as indicated by scy332. However, it is possible that this individual might have originated in a different nomadic group despite being found in a Scythian cultural context.

    scythian-alakul-variation
    Genetic diversity and ancestral components of Srubnaya-Alakulskaya population.(here called “Srubnaya”): (Left) Mean f3 statistics for Srubnaya and other Bronze Age populations. Srubnaya group was color-coded the same as with PCA. (Right) Pairwise mismatch estimates for Bronze Age populations.

    Comments

    I am surprised to find this new R1b-L23-based bottleneck in Eastern Iranian expansions so late, but admittedly – based on data from later times in the Pontic-Caspian steppe near the Caucasus – it was always a possibility. The fact that pockets of R1b-L23 lineages remained somehow ‘hidden’ in early Indo-Iranian communities was clear already since Narasimhan et al. (2018), as I predicted could happen, and is compatible with the limited archaeological data on Sintashta-Potapovka populations outside fortified settlements. I already said that Corded Ware was out of Indo-European migrations then, this further supports it.

    Even with all these data coming just from a north-west Pontic steppe region (west of the Dnieper), these ‘Cimmerians’ – or rather the ‘Proto-Scythian’ nomadic cultures appearing before ca. 800 BC in the Pontic-Caspian steppes – are shown to be probably formed by diverse peoples from Central Asia who brought about the first waves of Siberian ancestry (and Asian lineages) seen in the western steppes. You can read about a Cimmerian-related culture, Anonino, key for the evolution of Finno-Permic peoples.

    Also interesting about the Y-DNA bottleneck seen here is the rejection of the supposed continuous western expansions of R1a-Z645 subclades with steppe tribes since the Bronze Age, and thus a clearest link of the Hungarian Árpád dynasty (of R1a-Z2123 lineage) to either the early Srubna-related expansions or – much more likely – to the actual expansions of Hungarian tribes near the Urals in historic times.

    NOTE. I will add the information of this paper to the upcoming post on Ugric and Samoyedic expansions, and the late introduction of Siberian ancestry to these peoples.

    A few interesting lessons to be learned:

    • Remember the fantasy story about that supposed steppe nomadic pastoralist society sharing different Y-DNA lineages? You know, that Yamna culture expanding with R1b from Khvalynsk-Repin into the whole Pontic-Caspian steppes and beyond, developing R1b-dominated Afanasevo, Bell Beaker, and Poltavka, but suddenly appearing (in the middle of those expansions through the steppes) as a different culture, Corded Ware, to the north (in the east-central European forest zone) and dominated by R1a? Well, it hasn’t happened with any other steppe migration, so…maybe Proto-Indo-Europeans were that kind of especially friendly language-teaching neighbours?
    • Remember that ‘pure-R1a’ Indo-Slavonic society emerged from Sintashta ca. 2100 BC? (or even Graeco-Aryan??) Hmmmm… Another good fantasy story that didn’t happen; just like a central-east European Bronze Age Balto-Slavic R1a continuity didn’t happen, either. So, given that cultures from around Estonia are those showing the closest thing to R1a continuity in Europe until the Iron Age, I assume we have to get ready for the Gulf of Finland Balto-Slavic soon.
    • Remember that ‘pure-R1a’ expansion of Indo-Europeans based on the Tarim Basin samples? This paper means ipso facto an end to the Tarim Basin – Tocharian artificial controversy. The Pre-Tocharian expansion is represented by Afanasevo, and whether or not (Andronovo-related) groups of R1a-Z645 lineages replaced part or eventually all of its population before, during, or after the Tocharian expansion into the Tarim Basin, this does not change the origin of the language split and expansion from Yamna to Central Asia; just like this paper does not change the fact that these steppe groups were Proto-Iranian (Srubna) and Eastern Iranian (Scythian) speakers, regardless of their dominant haplogroup.
    • And, best of all, remember the Copenhagen group’s recent R1a-based “Indo-Germanic” dialect revival vs. the R1b-Tocharo-Italo-Celtic? Yep, they made that proposal, in 2018, based on the obvious Yamna—R1b-L23 association, and the desire to support Kristiansen’s model of Corded Ware – Indo-European expansion. Pepperidge Farm remembers. This new data on Early Iranians means another big NO to that imaginary R1a-based PIE society. But good try to go back to Gimbutas’ times, though.
    olander-classificatoin
    Olander’s (2018) tree of Indo-European languages. Presented at Languages and migrations in pre-historic Europe (7-12 Aug 2018)

    Do you smell that fresher air? It’s the Central and East European post-Communist populist and ethnonationalist bullshit (viz. pure blond R1a-based Pan-Nordicism / pro-Russian Pan-Slavism / Pan-Eurasianism, as well as Pan-Turanism and similar crap from the 19th century) going down the toilet with each new paper.

    #EDIT (5 OCT 2018): It seems I was too quick to rant about the consequences of the paper without taking into account the complexity of the data presented. Not the first time this impulsivity happens, I guess it depends on my mood and on the time I have to write a post on the specific work day…

    While the data on Srubna, Cimmerians, and Sarmatians shows clearer Y-DNA bottlenecks (of R1a-Z645 subclades) with the new data, the Scythian samples remain controversial, because of the many doubts about the haplogroups (although the most certain cases are R1b-Z2103), their actual date, and cultural attribution. However, I doubt they belong to other peoples, given the expansionist trends of steppe nomads before, during, and after Scythians (as shown in statistical analyses), so most likely they are Scythian or ‘Para-Scythian’ nomadic groups that probably came from the east, whether or not they incorporated Balkan populations. This is further supported by the remaining R1b-P312 and R1b-Z2103 populations in and around the modern Eurasian steppe region.

    scythian-peoples-balkans
    Early Iron Age cultures of the Carpathian basin ca. 7-6th century BC, including steppe groups Basarabi and Scythians. Ďurkovič et al. (2018).

    You can find an interesting and detailed take on the data published (in Russian) at Vol-Vlad’s LiveJournal (you can read an automatic translation from Google). I think that post is maybe too detailed in debunking all information associated to the supposed Scythians – to the point where just a single sample seems to be an actual Scythian (?!) -, but is nevertheless interesting to read the potential pitfalls of the study.

    Related

    Corded Ware—Uralic (I): Differences and similarities with Yamna

    indo-european-uralic-migrations-corded-ware

    I was reading The Bronze Age Landscape in the Russian Steppes: The Samara Valley Project (2016), and I was really surprised to find the following excerpt by David W. Anthony:

    The Samara Valley links the central steppes with the western steppes and is a north-south ecotone between the pastoral steppes to the south and the forest-steppe zone to the north [see figure below]. The economic contrast between pastoral steppe subsistence, with its associated social organizations, and forest-zone hunting and fishing economies probably explains the shifting but persistent linguistic border between forest-zone Uralic languages to the north (today largely displaced by Russian) and a sequence of steppe languages to the south, recently Turkic, before that Iranian, and before that probably an eastern dialect of Proto-Indo-European (Anthony 2007). The Samara Valley represents several kinds of borders, linguistic, cultural, and ecological, and it is centrally located in the Eurasian steppes, making it a critical place to examine the development of Eurasian steppe pastoralism.

    uralic-languages-forest-zone-volga
    Language map of the middle Volga-Ural region. After “Geographical Distribution of the Uralic Languages” by Finno-Ugrian Society, Helsinki, 1993.

    Khokhlov (translated by Anthony) further insists on the racial and ethnic divide between both populations, Abashevo to the north, and Poltavka to the south, during the formation of the Abashevo – Sintashta-Potapovka community that gave rise to Proto-Indo-Iranians:

    Among all cranial series in the Volga-Ural region, the Potapovka population represents the clearest example of race mixing and probably ethnic mixing as well. The cultural advancements seen in this period might perhaps have been the result of the mixing of heterogeneous groups. Such a craniometric observation is to some extent consistent with the view of some archaeologists that the Sintashta monuments represent a combination of various cultures (principally Abashevo and Poltavka, but with other influences) and therefore do not correspond to the basic concept of an archaeological culture (Kuzmina 2003:76). Under this option, the Potapovka-Sintashta burial rite may be considered, first, a combination of traits to guarantee the afterlife of a selected part of a heterogeneous population. Second, it reflected a kind of social “caste” rather than a single population. In our view, the decisive element in shaping the ethnic structure of the Potapovka-Sintashta monuments was their extensive mobility over a fairly large geographic area. They obtained knowledge of various cultures from the populations with whom they interacted.

    steppe-lmba-sintashta-potapovka-filatovka
    Late Middle Bronze Age cultures with the Proto-Indo-Iranian Sintashta-Potapovka-Filatovka group (shaded). After Anthony (2007 Figure 15.5), from Anthony (2016).

    Interesting is also this excerpt about the predominant population in the Abashevo – Sintashta-Potapovka admixture (which supports what Chetan said recently, although this does not seemed backed by Y-DNA haplogroups found in the richest burials), coupled with the sign of incoming “Uraloid” peoples from the east, found in both Sintashta and eastern Abashevo:

    The socially dominant anthropological component was Europeoid, possibly the descendants of Yamnaya. The association of craniofacial types with archaeological cultures in this period is difficult, primarily because of the small amount of published anthropological material of the cultures of steppe and forest belt (Balanbash, Vol’sko-Lbishche) and the eastern and southern steppes (Botai-Tersek). The crania associated with late MBA western Abashevo groups in the Don-Volga forest zone were different from eastern Abashevo in the Urals, where the expression of the Old Uraloid craniological complex was increased. Old Uraloid is found also on a single skull of Vol’sko-Lbishche culture (Tamar Utkul VII, Kurgan 4). Potentially related variants, including Mongoloid features, could be found among the Seima-Turbino tribes of the forest-steppe zone, who mixed with Sintashta and Abashevo. In the Sintashta Bulanova cemetery from the western Urals, some individuals were buried with implements of Seima-Turbino type (Khalyapin 2001; Khokhlov 2009; Khokhlov and Kitov 2009). Previously, similarities were noted between some individual skulls from Potapovka I and burials of the much older Botai culture in northern Kazakhstan (Khokhlov 2000a). Botai-Tersek is, in fact, a growing contender for the source of some “eastern” cranial features.

    khvalynsk-yamna-srubna-facial-reconstruction
    Facial reconstructions based on skulls from (a) Khvalynsk II Grave 24, a young adult male; (b) Poludin Grave 6, Yamnaya culture, a mature male (both by A. I. Nechvaloda); and (c) Luzanovsky cemetery, Srubnaya culture (by L. T. Yablonsky). In Khokhlov (2016).

    The wave of peoples associated with “eastern” features can be seen in genetics in the Sintashta outliers from Narasimhan et al. (2018), and it probably will be eventually seen in Abashevo, too. These may be related to the Seima-Turbino international network – but most likely it is directly connected to Sintashta through the starting Andronovo and Seima-Turbino horizons, by admixing of prospective groups and small-scale back-migrations.

    Corded Ware – Yamna similarities?

    So, if peoples of north-eastern Europe have been assumed for a long time to be Uralic speakers, what is happening with the Corded Ware = IE obsession? Is it Gimbutas’ ghost possessing old archaeologists? Probably not.

    It is about certain cultural similarities evident at first sight, which have been traditionally interpreted as a sign of cultural diffusion or migration. Not dissimilar to the many Bell Beaker models available, where each archaeologist is pushing certain differences, mixing what seemed reasonable, what still might seem reasonable, and what certainly isn’t anymore after the latest ancient DNA data.

    kurgan-expansion
    “European dialect” expansion of Proto-Indo-European according to Gimbutas (1963)

    The initial models of Gimbutas, Kristiansen, or Anthony – which are known to many today – were enunciated in the infancy of archaeological studies in the regions, during and just after the fall of the USSR, and before many radiocarbon dates that we have today were published (with radiocarbon dating being still today in need of refinement), so it is only logical that gross mistakes were made.

    We have similar gross mistakes related to the origins of Bell Beakers, and studying them was certainly easier than studying eastern data.

    • Gimbutas believed – based mainly on Kurgan-like burials – that Bell Beaker formed from a combination of Yamna settlers with the Vučedol culture, so she was not that far from the truth.
    • The expansion of Corded Ware from peoples of the North Pontic forest-steppe area, proposed by Gimbutas and later supported also by Kristiansen (1989) as the main Indo-European expansion – , is probably also right about the approximate origins of the culture. Only its ‘Indo-European’ nature is in question, given the differences with Khvalynsk and Yamna evolution.
    • Anthony only claimed that Yamna migrants settled in the Balkans and along the Danube into the Hungarian steppes. He never said that Corded Ware was a Yamna offshoot until after the first genetic papers of 2015 (read about his newest proposal). He initially claimed that only certain neighbouring Corded Ware groups “adopted” Indo-European (through cultural diffusion) because of ‘patron-client’ relationships, and was never preoccupied with the fate of Corded Ware and related cultures in the east European forest zone and Finland.

    So none of them was really that far from the true picture; we might say a lot people are more way off the real picture today than the picture these three researchers helped create in the 1990s and 2000s. Genetics is just putting the last nail in the coffin of Corded Ware as a Yamna offshoot, instead of – as we believed in the 2000s – to Vučedol and Bell Beaker.

    So let’s revise some of these traditional links between Corded Ware and Yamna with today’s data:

    Archaeology

    Even more than genetics – at least until we have an adequate regional and temporary sampling – , archaeological findings lead what we have to know about both cultures.

    It is essential to remember that Corded Ware, starting ca. 3000/2900 BC in east-central Europe, has been proposed to be derived from Early Yamna, which appeared suddenly in the Pontic-Caspian steppes ca. 3300 BC (probably from the late Repin expansion), and expanded to the west ca. 3000.

    Early Yamna is in turn identified as the expanding Late Proto-Indo-European community, which has been confirmed with the recent data on Afanasevo, Bell Beaker, and Sintashta-Potapovka and derived cultures.

    The question at hand, therefore, is if Corded Ware can be considered an offshoot of the Late PIE community, and thus whether the CWC ethnolinguistic community – proven in genetics to be quite homogeneous – spoke a Late PIE dialect, or if – alternatively – it is derived from other neighbouring cultures of the North Pontic region.

    NOTE. The interpretation of an Indo-Slavonic group represented by a previous branching off of the group is untenable with today’s data, since Indo-Slavonic – for those who support it – would itself be a branch of Graeco-Aryan, and Palaeo-Balkan languages expanded most likely with West Yamna (i.e. R1b-L23, mainly R1b-Z2103) to the south.

    The convoluted alternative explanation would be that Corded Ware represents an earlier, Middle PIE branch (somehow carrying R1a??) which influences expanding Late PIE dialects; this has been recently supported by Kortlandt, although this simplistic picture also fails to explain the Uralic problem.

    Kurgans: The Yamna tradition was inherited from late Repin, in turn inherited from Khvalynsk-Novodanilovka proto-Kurgans. As for the CWC tradition, it is unclear if the tumuli were built as a tradition inherited from North and West Pontic cultures (in turn inherited or copied from Khvalynsk-Novodanilovka), such as late Trypillia, late Kvityana, late Dereivka, late Sredni Stog; or if they were built because of the spread of the ‘Transformation of Europe’, set in motion by the Early Yamna expansion ca. 3300-3000 BC (as found in east-central European cultures like Coţofeni, Lizevile, Șoimuș, or the Adriatic Vučedol). My guess is that it inherits an older tradition than Yamna, with an origin in east-central Europe, because of the mound-building distribution in the North Pontic area before the Yamna expansion, but we may never really know.

    pit-graves-central-europe-cwc
    Distribution of Pit-Grave burials west of the Black Sea likely dating to the 2nd half of the IVth millennium BC (triangles: side-crouched burials; filled circles: supine extended burials; open circles: suspected). Frînculeasa, Preda, and Heyd (2015)

    Burial rite: Yamna features (with regional differences) single burials with body on its back, flexed upright knees, poor grave goods, common orientation east-west (heads to the west) inherited from Repin, in turn inherited from Khvalynsk-Novodanilovka. CWC tradition – partially connected to Złota and surrounding east-central European territories (in turn from the Khvalynsk-Novodanilovka expansion) – features single graves, body in fetal position, strict gender differentiation – men on the right, women on the left -, looking to the south, graves with standardized assemblages (objects representing affirmation of battle, hunting, and feasting). The burial rites clearly represent different ideologies.

    pit-grave-burial-schemes
    Left: Pit-Grave burial types expanded with Khvalynsk-Novodanilovka. Right: Pit-Grave burial types associated with the Yamna expansion and influence. Frînculeasa, Preda, and Heyd (2015)

    Corded decoration: Corded ware decoration appears in the Balkans during the 5th millennium, and represents a simple technique whereby a cord is twisted, or wrapped around a stick, and then pressed directly onto the fresh surface of a vessel leaving a characteristic decoration. It appears in many groups of the 5th and 4th millennium BC, but it was Globular Amphorae the culture which popularized the drinking vessels and their corded ornamentation. It appears thus in some regional groups of Yamna, but it becomes the standard pottery only in Corded Ware (especially with the A-horizon), which shows continuity with GAC pottery.

    corded-ware-first-horizon
    Origins of the first Corded Ware horizon (5th millennium BC) after the Khvalynsk-Novodanilovka expansion. Corded Ware (circles) and horse-head scepters (rectangles) and other steppe elements (triangles). Image from Bulatović (2014).

    Economy: Yamna expands from Repin (and Repin from Khvalynsk-Novodanilovka) as a nomadic or semi-nomadic purely pastoralist society (with occasional gathering of wild seeds), which naturally thrives in the grasslands of the Pontic-Caspian, lower Danube and Hungarian steppes. Corded Ware shows agropastoralism (as late Eneolithic forest-steppe and steppe groups of eastern Europe, such as late Trypillian, TRB, and GAC groups), inhabits territories north of the loess line, with heavy reliance of hunter-gathering depending on the specific region.

    Cattle herding: Interestingly, both west Yamna and Corded Ware show more reliance on cattle herding than other pastoralist groups, which – contrasted with the previous Eneolithic herding traditions of the Pontic-Caspian steppe, where sheep-goats predominate – make them look alike. However, the cattle-herding economy of Yamna is essential for its development from late Repin and its expansion through the steppes (over western territories practising more hunter-gathering and sheep-goat herding economy), and it does not reach equally the Volga-Ural region, whose groups keep some of the old subsistence economy (read more about the late Repin expansion). Corded Ware, on the other hand, inherits its economic strategy from east European groups like TRB, GAC, and especially late Trypillian communities, showing a predominance of cattle herding within an agropastoral community in the forest-steppe and forest zones of Volhynia, Podolia, and surrounding forest-steppe and forest regions.

    yamna-scheme
    Scheme of interlinked socio-economic-ideological innovations forming the Yamnaya. Frînculeasa, Preda, and Heyd (2015)

    Horse riding: Horse riding and horse transport is proven in Yamna (and succeeding Bell Beaker and Sintashta), assumed for late Repin (essential for cattle herding in the seas of grasslands that are the steppes, without nearby water sources), quite likely during the Khvalynsk expansion (read more here), and potentially also for Samara, where the predominant horse symbolism of early Khvalynsk starts. Corded Ware – like the north Pontic forest-steppe and forest areas during the Eneolithic – , on the other hand, does not show a strong reliance on horse riding. The high mobility and short-term settlements characteristic of Corded Ware, that are often associated with horse riding by association with Yamna, may or may not be correct, but there is no need for horses to explain their herding economy or their mobility, and the north-eastern European areas – the one which survived after Bell Beaker expansion – did certainly not rely on horses as an essential part of their economy.

    NOTE: I cannot think of more supposed similarities right now. If you have more ideas, please share in the comments and I will add them here.

    Genetic similarities

    EHG: This is the clearest link between both communities. We thought it was related to the expansion of ANE-related ancestry to the west into WHG territory, but now it seems that it will be rather WHG expanding into ANE territory from the Pontic-Caspian region to the east (read more on recent Caucasus Neolithic, on , and on Caucasus HG).

    NOTE. Given how much each paper changes what we know about the Palaeolithic, the origin and expansion of the (always developing) known ancestral components and specific subclades (see below) is not clear at all.

    CHG: This is the key link between both cultures, which will delimit their interaction in terms of time and space. CHG is intermediate between EHG and Iran N (ca. 8000 BC). The ancestry is thus linked to the Caucasus south of the steppe before the emergence of North Pontic (western) and Don-Volga-Ural (eastern) communities during the Mesolithic. The real question is: when we have more samples from the steppe and the Caucasus during the Neolithic, how many CHG groups are we going to find? Will the new specific ancestral components (say CHG1, CHG2, CHG3, etc.) found in Yamna (from Khvalynsk, in the east) and Corded Ware (probably from the North Pontic forest-steppe) be the same? My guess is, most likely not, unless they are mediated by the Khvalynsk-Novodanilovka expansion (read more on CHG in the Caucasus).

    yamnaya-chg-ancestry
    Formation of Yamna and CHG contribution, in Damgaard et al. (Science 2018). A 10-leaf model based on combining the models in Fig. S16 and Fig. S19 and re-estimating the model parameters.

    WHG/EEF: This is the obvious major difference – known today – in the formation of both communities in the steppe, and shows the different contacts that both groups had at least since the Eneolithic, i.e. since the expansion of Repin with its renewed Y-DNA bottleneck, and probably since before the early Khvalynsk expansion (read more on Yamna-Corded Ware differences contrasting with Yamna-Afanasevo, Yamna-Bell Beaker, and Yamna-Sintashta similarities).

    NOTE 1. Some similarities between groups can be seen depending on the sampled region; e.g. Baltic groups show more similarities with southern Pontic-Caspian steppe populations, probably due to exogamy.

    yamna-corded-ware-diff-qpgraph
    Tested qpGraph model in Tambets et al. (2018). The qpGraph model fitting the data for the tested populations. “Colour codes for the terminal nodes: pink—modern populations (‘Population X’ refers to test population) and yellow—ancient populations (aDNA samples and their pools). Nodes coloured other than pink or yellow are hypothetical intermediate populations. We putatively named nodes which we used as admixture sources using the main recipient among known populations. The colours of intermediate nodes on the qpGraph model match those on the admixture proportions panel.”

    NOTE 2. We have this information on the differences in “steppe ancestry” between Yamna and Corded Ware, compared to previous studies, because now we have more samples of neighbouring, roughly contemporaneous Eneolithic groups, to analyse the real admixture processes. This kind of fine scale studies is what is going to show more and more differences between Khvalynsk-Yamna and Sredni Stog-Corded Ware as more data pours in. The evolution of both communities in archaeology and in PCA (see below) is probably witness to those differences yet to be published.

    R1: Even though some people try very hard to think in terms of “R1” vs. (Caucasus) J or G or any other upper clade, this is plainly wrong. It is possible, given what we know now, that Q1a2-M242 expanded ANE ancestry to the west ca. 13000 BC, while R1b-P279 expanded WHG ancestry to the east with the expansion of post-Swiderian cultures, creating EHG as a WHG:ANE cline. The role of R1a-M459 is unknown, but it might be related to any of these migrations, or others (plural) along northern Eurasia (read more on the expansion of R1b-P279, on Palaeolithic Q1a2, and on R1a-M417).

    NOTE. I am inclined to believe in a speculative Mesolithic-Early Neolithic community involving Eurasiatic movements accross North Eurasia, and Indo-Uralic movements in its western part, with the last intense early Uralic-PIE contacts represented by the forming west (Mariupol culture) and east (Don-Volga-Ural cultures, including Samara) communities developing side by side. Before their known Eneolithic expansions, no large-scale Y-DNA bottleneck is going to be seen in the Pontic-Caspian steppe, with different (especially R1a and R1b subclades) mixed among them, as shown in North Pontic Neolithic, Samara HG, and Khvalynsk samples.

    PCA-trypillia-greece-neolithic-outlier-anatolian
    Image modified from Wang et al. (2018). Samples projected in PCA of 84 modern-day West Eurasian populations (open symbols). Previously known clusters have been marked and referenced. Marked and labelled are the Balkan samples referenced in this text An EHG and a Caucasus ‘clouds’ have been drawn, leaving Pontic-Caspian steppe and derived groups between them. See the original file here.

    Corded Ware and ‘steppe ancestry’

    If we take a look at the evolution of Corded Ware cultures, the expansion of Bell Beakers – dominated over most previous European cultures from west to east Europe – influenced the development of the whole European Bronze Age, up to Mierzanowice and Trzciniec in the east.

    The only relevant unscathed CWC-derived groups, after the expansion of Sintashta-Potapovka as the Srubna-Andronovo horizon in the Eurasian steppes, were those of the north-eastern European forest zone: between Belarus to the west, Finland to the north, the Urals to the east, and the forest-steppe region to the south. That is, precisely the region supposed to represent Uralic speakers during the Bronze Age.

    This inconsistency of steppe ancestry and its relation with Uralic (and Balto-Slavic) peoples was observed shortly after the publication of the first famous 2015 papers by Paul Heggarty, of the Max-Planck Institute for Evolutionary Anthropology (read more):

    Haak et al. (2015) make much of the high Yamnaya ancestry scores for (only some!) Indo-European languages. What they do not mention is that those same results also include speakers of other languages among those with the highest of all scores for Yamnaya ancestry. Only these are languages of the Uralic family, not Indo-European at all; and their Yamnaya-ancestry signals are far higher than in many branches of Indo-European in (southern) Europe. Estonian ranks very high, while speakers of the very closely related Finnish are curiously not shown, and nor are the Saami. Hungarian is relevant less directly since this language arrived only c. 900 AD, but also high.

    uralic-steppe-ancestry

    These data imply that Uralic-speakers too would have been part of the Yamnaya > Corded Ware movement, which was thus not exclusively Indo-European in any case. And as well as the genetics, the geography, chronology and language contact evidence also all fit with a Yamnaya > Corded Ware movement including Uralic as well as Balto-Slavic.

    Both papers fail to address properly the question of the Uralic languages. And this despite — or because? — the only Uralic speakers they report rank so high among modern populations with Yamnaya ancestry. Their linguistic ancestors also have a good claim to have been involved in the Corded Ware and Yamnaya cultures, and of course the other members of the Uralic family are scattered across European Russia up to the Urals.

    NOTE. Although the author was trying to support the Anatolian hypothesis – proper of glottochronological studies often published from the Max Planck Institute – , the question remains equally valid: “if Proto-Indo-European expands with Corded Ware and steppe ancestry, what is happening with Uralic peoples?”

    For my part, I claimed in my draft that ancestral components were not the only relevant data to take into account, and that Y-DNA haplogroups R1a and R1b (appearing separately in CWC and Yamna-Bell Beaker-Afanasevo), together with their calculated timeframes of formation – and therefore likely expansion – did not fit with the archaeological and linguistic description of the spread of Proto-Indo-European and its dialects.

    In fact, it seemed that only one haplogroup (R1b-M269) was constantly and consistenly associated with the proposed routes of Late PIE dialectal expansions – like Anthony’s second (Afanasevo) and third (Lower Danube, Balkan) waves. What genetics shows fits seamlessly with Mallory’s association of the North-West Indo-European expansion with Bell Beakers (read here how archaeologists were right).

    balanovksy-yamnaya-ancestry
    Map of the much beloved steppe (or “Yamnaya”) ancestry in modern populations, by Balanovsky. Modified from Klejn (2017).

    More precise inconsistencies were observed after the publication of Olalde et al. (2017) and Mathieson et al. (2017), by Volker Heyd in Kossinna’s smile (2017). Letting aside the many details enumerated (you can read a summary in my latest draft), this interesting excerpt is from the conclusion:

    NOTE. An open access ealier draft version of the paper is offered for download by the author.

    Simple solutions to complex problems are never the best choice, even when favoured by politicians and the media. Kossinna also offered a simple solution to a complex prehistoric problem, and failed therein. Prehistoric archaeology has been aware of this for a century, and has responded by becoming more differentiated and nuanced, working anthropologically, scientifically and across disciplines (cf. Müller 2013; Kristiansen 2014), and rejecting monocausal explanations. The two aDNA papers in Nature, powerful and promising as they are for our future understanding, also offer rather straightforward messages, heavily pulled by culture-history and the equation of people with culture. This admittedly is due partly to the restrictions of the medium that conveys them (and despite the often relevant additional detail given as supplementary information, which is unfortunately not always given full consideration).

    While I have no doubt that both papers are essentially right, they do not reflect the complexity of the past. It is here that archaeology and archaeologists contributing to aDNA studies find their role; rather than simply handing over samples and advising on chronology, and instead of letting the geneticists determine the agenda and set the messages, we should teach them about complexity in past human actions and interactions. If accepted, this could be the beginning of a marriage made in heaven, with the blessing smile of Gustaf Kossinna, and no doubt Vere Gordon Childe, were they still alive, in a reconciliation of twentieth- and twenty-first-century approaches. For us as archaeologists, it could also be the starting point for the next level of a new archaeology.

    heyd-yamnaya-expansion
    Main distribution of Yamnaya kurgans in the Pontic-Caspian steppe of modern day Russia, Ukraine, and Kazakhstan, and its western branch in modern south-east European countries of Romania, Bulgaria, Serbia, and Hungary, with numbers of excavated kurgans and graves given. Picture: Volker Heyd (2018).

    The question was made painfully clear with the publication of Olalde et al. (2018) & Mathieson et al. (2018), where the real route of Yamna expansion into Europe was now clearly set through the steppes into the Carpathian basin, later expanded as Bell Beakers.

    This has been further confirmed in more recent papers, such as Narasimhan et al. (2018), Damgaard et al. (2018), or Wang et al. (2018), among others.

    However, the discussion is still dominated by political agendas based on prevalent Y-DNA haplogroups in modern countries and ethnic groups.

    Related

    Haplogroup R1a and CWC ancestry predominate in Fennic, Ugric, and Samoyedic groups

    uralic-languages

    Open access Genes reveal traces of common recent demographic history for most of the Uralic-speaking populations, by Tambets et al. Genome Biology (2018).

    Interesting excerpts (emphasis mine):

    Methods

    A total of 286 samples of Uralic-speaking individuals, of those 121 genotyped in this study, were analysed in the context of 1514 Eurasian samples (including 14 samples published for the first time) based on whole genome single nucleotide polymorphisms (SNPs) (Additional file 1: Table S1). All these samples, together with the larger sample set of Uralic speakers, were characterized for mtDNA and chrY markers.

    The question as which material cultures may have co-spread together with proto-Uralic and Uralic languages depends on the time estimates of the splits in the Uralic language tree. Deeper age estimates (6,000 BP) of the Uralic language tree suggest a connection between the spread of FU languages from the Volga River basin towards the Baltic Sea either with the expansion of the Neolithic culture of Combed Ware, e.g. [6, 7, 17, 26] or with the Neolithic Volosovo culture [7]. Younger age estimates support a link between the westward dispersion of Proto-Finno-Saamic and eastward dispersion of Proto-Samoyedic with a BA Sejma-Turbino (ST) cultural complex [14, 18, 27, 28] that mediated the diffusion of specific metal tools and weapons from the Altai Mountains over the Urals to Northern Europe or with the Netted Ware culture [23], which succeeded Volosovo culture in the west. It has been suggested that Proto-Uralic may have even served as the lingua franca of the merchants involved in the ST phenomenon [18]. All these scenarios imply that material culture of the Baltic Sea area in Europe was influenced by cultures spreading westward from the periphery of Europe and/or Siberia. Whether these dispersals involved the spread of both languages and people remains so far largely unknown.

    The population structure of Uralic speakers

    To contextualize the autosomal genetic diversity of Uralic speakers among other Eurasian populations (Additional file 1: Table S1), we first ran the principal component (PC) analysis (Fig. 2a, Additional file 3: Figure S1). The first two PCs (Fig. 2a, Additional file 3: Figure S1A) sketch the geography of the Eurasian populations along the East-West and North-South axes, respectively. The Uralic speakers, along with other populations speaking Slavic and Turkic languages, are scattered along the first PC axis in agreement with their geographic distribution (Figs. 1 and 2a) suggesting that geography is the main predictor of genetic affinity among the groups in the given area. Secondly, in support of this, we find that FST-distances between populations (Additional file 3: Figure S2) decay in correlation with geographical distance (Pearson’s r = 0.77, p < 0.0001). On the UPGMA tree based on these FST-distances (Fig. 2b), the Uralic speakers cluster into several different groups close to their geographic neighbours.

    uralic-pca
    Principal component analysis (PCA) and genetic distances of Uralic-speaking populations. a PCA (PC1 vs PC2) of the Uralic-speaking populations.

    We next used ADMIXTURE [48], which presents the individuals as composed of inferred genetic components in proportions that maximize Hardy-Weinberg and linkage equilibrium in the overall sample (see the ‘Methods’ section for choice of presented K). Overall, and specifically at lower values of K, the genetic makeup of Uralic speakers resembles that of their geographic neighbours. The Saami and (a subset of) the Mansi serve as exceptions to that pattern being more similar to geographically more distant populations (Fig. 3a, Additional file 3: S3). However, starting from K = 9, ADMIXTURE identifies a genetic component (k9, magenta in Fig. 3a, Additional file 3: S3), which is predominantly, although not exclusively, found in Uralic speakers. This component is also well visible on K = 10, which has the best cross-validation index among all tests (Additional file 3: S3B). The spatial distribution of this component (Fig. 3b) shows a frequency peak among Ob-Ugric and Samoyed speakers as well as among neighbouring Kets (Fig. 3a). The proportion of k9 decreases rapidly from West Siberia towards east, south and west, constituting on average 40% of the genetic ancestry of FU speakers in Volga-Ural region (VUR) and 20% in their Turkic-speaking neighbours (Bashkirs, Tatars, Chuvashes; Fig. 3a). The proportion of this component among the Saami in Northern Scandinavia is again similar to that of the VUR FU speakers, which is exceptional in the geographic context. It is also notable that North Russians, sampled from near the White Sea, differ from other Russians by sporting higher proportions of k9 (10–15%), which is similar to the values we observe in their Finnic-speaking neighbours. Notably, Estonians and Hungarians, who are geographically the westernmost Uralic speakers, virtually lack the k9 cluster membership.

    siberian-ancestry
    Population structure of Uralic-speaking populations inferred from ADMIXTURE analysis on autosomal SNPs in Eurasian context. a Individual ancestry estimates for populations of interest for selected number of assumed ancestral populations (K3, K6, K9, K11). Ancestry components discussed in a main text (k2, k3, k5, k6, k9, k11) are indicated and have the same colours throughout. The names of the Uralic-speaking populations are indicated with blue (Finno-Ugric) or orange (Samoyedic). The full bar plot is presented in Additional file 3: Figure S3. b Frequency map of component k9

    We also tested the different demographic histories of female and male lineages by comparing outgroup f3 results for autosomal and X chromosome (chrX) data for pairs of populations (Estonians, Udmurts or Khanty vs others) with high versus low probability to share their patrilineal ancestry in chrY hg N (see the ‘Methods’ section, Additional file 3: Figure S13). We found a minor but significant excess of autosomal affinity relative to chrX for pairs of populations that showed a higher than 10% chance of two randomly sampled males across the two groups sharing their chrY ancestry in hg N3-M178, compared to pairs of populations where such probability is lower than 5% (Additional file 3: Figure S13).

    In sum, these results suggest that most of the Uralic speakers may indeed share some level of genetic continuity via k9, which, however, also extends to the geographically close Turkic speakers.

    uralic-modern-europe

    Identity-by-descent

    We found that it is the admixture with the Siberians that makes the Western Uralic speakers different from the tested European populations (Additional file 3: Figure S4A-F, H, J, L). Differentiating between Estonians and Finns, the Siberians share more derived alleles with Finns, while the geographic neighbours of Estonians (and Finns) share more alleles with Estonians (Additional file 3: Figure S4M). Importantly, Estonians do not share more derived alleles with other Finnic, Saami, VUR FU or Ob-Ugric-speaking populations than Latvians (Additional file 3: Figure S4O). The difference between Estonians and Latvians is instead manifested through significantly higher levels of shared drift between Estonians and Siberians on the one hand and Latvians and their immediate geographic neighbours on the other hand. None of the Uralic speakers, including linguistically close Khanty and Mansi, show significantly closer affinities to the Hungarians than any non-FU population from NE Europe (Additional file 3: Figure S4R).

    ibd-uralic-genetics
    Share of ~ 1–2 cM identity-by-descent (IBD) segments within and between regional groups of Uralic speakers. For each Uralic-speaking population representing lines in this matrix, we performed permutation test to estimate if it shows higher IBD segment sharing with other population (listed in columns) as compared to their geographic control group. Empty rectangles indicate no excess IBD sharing, rectangles filled in blue indicate comparisons when statistically significant excess IBD sharing was detected between one Uralic-speaking population with another Uralic-speaking population (listed in columns), rectangles filled in green mark the comparisons when a Uralic-speaking population shows excess IBD sharing with a non-Uralic-speaking population. For each tested Uralic speaker (matrix rows) populations in the control group that were used to generate permuted samples are indicated using small circles. For example, the rectangle filled in blue for Vepsians and Komis (A) implies that the Uralic-speaking Vepsians share more IBD segments with the Uralic-speaking Komis than the geographic control group for Vepsians, i.e. populations indicated with small circles (Central and North Russians, Swedes, Latvians and Lithuanians). The rectangle filled in green for Vepsians and Dolgans shows that the Uralic-speaking Vepsians share more IBD segments with the non-Uralic-speaking Dolgans than the geographic control group

    Time of Siberian admixture

    The time depth of the Globetrotter (Fig. 5b) inferred admixture events is relatively recent—500–1900 AD (see also complementary ALDER results, in Additional file 13: Table S12 and Additional file 3: Figure S7)—and agrees broadly with the results reported in Busby et al. [55]. A more detailed examination of the ALDER dates, however, reveals an interesting pattern. The admixture events detected in the Baltic Sea region and VUR Uralic speakers are the oldest (800–900 AD or older) followed by those in VUR Turkic speakers (∼1200–1300 AD), while the admixture dates for most of the Siberian populations (>1500 AD) are the most recent (Additional file 3: Figure S7). The West Eurasian influx into West Siberia seen in modern genomes was thus very recent, while the East Eurasian influx into NE Europe seems to have taken place within the first millennium AD (Fig. 5b, Additional file 3: Figure S7).

    Affinities of the Uralic speakers with ancient Eurasians

    We next calculated outgroup f3-statistics [48] to estimate the extent of shared genetic drift between modern and ancient Eurasians (Additional file 14: Table S13, Additional file 3: Figures S8-S9). Consistent with previous reports [45, 50], we find that the NE European populations including the Uralic speakers share more drift with any European Mesolithic hunter-gatherer group than Central or Western Europeans (Additional file 3: Figure S9A-C). Contrasting the genetic contribution of western hunter-gatherers (WHG) and eastern hunter-gatherers (EHG), we find that VUR Uralic speakers and the Saami share more drift with EHG. Conversely, WHG shares more drift with the Finnic and West European populations (Additional file 3: Figure S9A). Interestingly, we see a similar pattern of excess of shared drift between VUR and EHG if we substitute WHG with the aDNA sample from the Yamnaya culture (Additional file 3: Figure S9D). As reported before [2, 45], the genetic contribution of European early farmers decreases along an axis from Southern Europe towards the Ural Mountains (Fig. 6, Additional file 3: Figure S9E-F).

    yamna-cwc-qpgraph-admixture-uralic
    Proportions of ancestral components in studied European and Siberian populations and the tested qpGraph model. a The qpGraph model fitting the data for the tested populations. Colour codes for the terminal nodes: pink—modern populations (‘Population X’ refers to test population) and yellow—ancient populations (aDNA samples and their pools). Nodes coloured other than pink or yellow are hypothetical intermediate populations. We putatively named nodes which we used as admixture sources using the main recipient among known populations. The colours of intermediate nodes on the qpGraph model match those on the admixture proportions panel. b Admixture proportions (%) of ancestral components. We calculated the admixture proportions summing up the relative shares of a set of intermediate populations to explain the full spectrum of admixture components in the test population. We further did the same for the intermediate node CWC’ and present the proportions of the mixing three components in the stacked column bar of CWC’. Colour codes for ancestral components are as follows: dark green—Western hunter gatherer (WHG’); light green—Eastern hunter gatherer (EHG’); grey—European early farmer (LBK’); dark blue—carriers of Corded Ware culture (CWC’); and dark grey—Siberian. CWC’ consists of three sub-components: blue—Caucasian hunter-gatherer in Yamnaya (CHGinY’); light blue—Eastern hunter-gatherer in Yamnaya (EHGinY’); and light grey—Neolithic Levant (NeolL’)

    We then used the qpGraph software [48] to test alternative demographic scenarios by trying to fit the genetic diversity observed in a range of the extant Finno-Ugric populations through a model involving the four basic European ancestral components: WHG, EHG, early farmers (LBK), steppe people of Yamnaya/Corded Ware culture (CWC) and a Siberian component (Fig. 6, Additional file 3: Figure S10). We chose the modern Nganasans to serve as a proxy for the latter component because we see least evidence for Western Eurasian admixture (Additional file 3: Figure S3) among them. We also tested the Khantys for that proxy but the model did not fit (yielding f2-statistics, Z-score > 3). The only Uralic-speaking population that did not fit into the tested model with five ancestral components were Hungarians. The qpGraph estimates of the contributions from the Siberian component show that it is the main ancestry component in the West Siberian Uralic speakers and constitutes up to one third of the genomes of modern VUR and the Saami (Fig. 6). It drops, however, to less than 10% in most of NE Europe, to 5% in Estonians and close to zero in Latvians and Lithuanians.

    Discussion

    uralic-groups-haplogroup-r1a
    Additional file 6: Table S5. Y chromosome haplogroup frequencies in Eurasia. Modified by me: in bold haplogroup N1c and R1a from Uralic-speaking populations, with those in red showing where R1a is the major haplogroup. Observe that all Uralic subgroups – Finno-Permic, Ugric, and Samoyedic – have some populations with a majority of R1a lineages.

    One of the notable observations that stands out in the fineSTRUCTURE analysis is that neither Hungarians nor Estonians or Mordovians form genetic clusters with other Uralic speakers but instead do so with a broad spectrum of geographically adjacent samples. Despite the documented history of the migration of Magyars [63] and their linguistic affinity to Khantys and Mansis, who today live east of the Ural Mountains, there is nothing in the present-day gene pool of the sampled Hungarians that we could tie specifically to other Uralic speakers.

    Perhaps even more surprisingly, we found that Estonians, who show close affinities in IBD analysis to neighbouring Finnic speakers and Saami, do not share an excess of IBD segments with the VUR or Siberian Uralic speakers. This is eIn this context, it is important to remind that the limited (5%, Fig. 6) East Eurasian impact in the autosomal gene pool of modern Estonians contrasts with the fact that more than 30% of Estonian (but not Hungarian) men carry chrY N3 that has an East Eurasian origin and is very frequent among NE European Uralic speakers [36]. However, the spread of chrY hg N3 is not language group specific as it shows similar frequencies in Baltic-speaking Latvians and Lithuanians, and in North Russians, who in all our analyses are very similar to Finnic-speakers. The latter, however, are believed to have either significantly admixed with their Uralic-speaking neighbours or have undergone a language shift from Uralic to Indo-European [38].ven more striking considering that the immediate neighbours—Finns, Vepsians and Karelians—do.

    With some exceptions such as Estonians, Hungarians and Mordovians, both IBD sharing and Globetrotter results suggest that there are detectable inter-regional haplotype sharing ties between Uralic speakers from West Siberia and VUR, and between NE European Uralic speakers and VUR. In other words, there is a fragmented pattern of haplotype sharing between populations but no unifying signal of sharing that unite all the studied Uralic speakers.

    Comments

    The paper is obviously trying to find a “N1c/Siberian ancestry = Uralic” link, but it shows (as previous papers using ancient DNA) that this identification is impossible, because it is not possible to identify “N1c=Siberian ancestry”, “N1c=Uralic”, or “Siberian ancestry = Uralic”. In fact, the arrival of N subclades and Siberian ancestry are late, both events (probably multiple stepped events) are unrelated to each other, and represent east-west demic diffusion waves (as well as founder effects) that probably coincide in part with the Scythian and Turkic (or associated) expansions, i.e. too late for any model of Proto-Uralic or Proto-Finno-Ugric expansion.

    On the other hand, it shows interesting data regarding ancestry of populations that show increased Siberian influence, such as those easternmost groups admixed with Yeniseian-like populations (Samoyedic), those showing strong founder effects (Finnic), or those isolated in the Circum-Artic region with neighbouring Siberian peoples in Kola (Saami). All in all, Hungarians, Estonians and Mordovians seem to show the original situation better than the other groups, which is also reflected in part in Y-DNA, conserved as a majority of R1a lineages precisely in these groups. Just another reminder that CWC-related ancestry is found in every single Uralic group, and that it represents the main ancestral component in all non-Samoyedic groups.

    estonians-hungarians-mordvinian
    Selection of the PCA, with the group of Estonians, Mordovians, and Hungarians selected.

    The qpGraph shows the ancestor of Yamna (likely Khvalynsk) and Corded Ware stemming as different populations from a common (likely Neolithic) node – whose difference is based on the proportion of Anatolian-related ancestry – , that is, probably before the Indo-Hittite expansion; and ends with CWC groups forming the base for all Uralic peoples. Below is a detail of the qpGraph on the left, and my old guess (2017) on the right, for comparison:

    yamna-corded-ware-qpgraph

    #EDIT (22 sep 2018): I enjoyed re-reading it, and found this particular paragraph funny:

    Despite the documented history of the migration of Magyars [63] and their linguistic affinity to Khantys and Mansis, who today live east of the Ural Mountains, there is nothing in the present-day gene pool of the sampled Hungarians that we could tie specifically to other Uralic speakers.

    They are so obsessed with finding a link to Siberian ancestry and N1c, and so convinced of Kristiansen’s idea of CWC=Indo-European, that they forgot to examine their own data from a critical point of view, and see the clear link between all Uralic peoples with Corded Ware ancestry and R1a-Z645 subclades… Here is a reminder about Hungarians and R1a-Z282, and about the expansion of R1a-Z645 with Uralic peoples.

    Related

    Palaeolithic Caucasus samples reveal the most important component of West Eurasians

    dzudzuana-ancestry-europe

    Preprint Paleolithic DNA from the Caucasus reveals core of West Eurasian ancestry, by Lazaridis et al. bioRxiv (2018).

    Interesting excerpts:

    We analyzed teeth from two individuals 63 recovered from Dzudzuana Cave, Southern Caucasus, from an archaeological layer previously dated to ~27-24kya (…). Both individuals had mitochondrial DNA sequences (U6 and N) that are consistent with deriving from lineages that are rare in the Caucasus or Europe today. The two individuals were genetically similar to each other, consistent with belonging to the same population and we thus analyze them jointly.

    (…) our results prove that the European affinity of Neolithic Anatolians does not necessarily reflect any admixture into the Near East from Europe, as an Anatolian Neolithic-like population already existed in parts of the Near East by ~26kya. Furthermore, Dzudzuana shares more alleles with Villabruna-cluster groups than with other ESHG (Extended Data Fig. 5b), suggesting that this European affinity was specifically related to the Villabruna cluster, and indicating that the Villabruna affinity of PGNE populations from Anatolia and the Levant is not the result of a migration into the Near East from Europe. Rather, ancestry deeply related to the Villabruna cluster was present not only in Gravettian and Magdalenian-era Europeans but also in the populations of the Caucasus, by ~26kya. Neolithic Anatolians, while forming a clade with Dzudzuana with respect to ESHG, share more alleles with all other PGNE (Extended Data Fig. 5d), suggesting that PGNE share at least partially common descent to the exclusion of the much older samples from Dzudzuana.

    dzudzuana-anatolia-pca
    Ancient West Eurasian population structure. PCA of key ancient West Eurasians, including additional populations (shown with grey shells), in the space of outgroup f4-statistics (Methods).

    Our co-modeling of Epipaleolithic Natufians and Ibero-Maurusians from Taforalt confirms that the Taforalt population was mixed, but instead of specifying gene flow from the ancestors of Natufians into the ancestors of Taforalt as originally reported, we infer gene flow in the reverse direction (into Natufians). The Neolithic population from Morocco, closely related to Taforalt is also consistent with being descended from the source of this gene flow, and appears to have no admixture from the Levantine Neolithic (Supplementary Information 166 section 3). If our model is correct, Epipaleolithic Natufians trace part of their ancestry to North Africa, consistent with morphological and archaeological studies that indicate a spread of morphological features and artifacts from North Africa into the Near East. Such a scenario would also explain the presence of Y-chromosome haplogroup E in the Natufians and Levantine farmers, a common link between the Levant and Africa.

    (…) we cannot reject the hypothesis that Dzudzuana and the much later Neolithic Anatolians form a clade with respect to ESHG (P=0.286), consistent with the latter being a population largely descended from Dzudzuana-like pre-Neolithic populations whose geographical extent spanned both Anatolia and the Caucasus. Dzudzuana itself can be modeled as a 2-way mixture of Villabruna-related ancestry and a Basal Eurasian lineage.

    In qpAdm modeling, a deeply divergent hunter-gatherer lineage that contributed in relatively unmixed form to the much later hunter-gatherers of the Villabruna cluster is specified as contributing to earlier hunter-gatherer groups (Gravettian Vestonice16: 35.7±11.3% and Magdalenian ElMiron: 60.6±11.3%) and to populations of the Caucasus (Dzudzuana: 199 72.5±3.7%, virtually identical to that inferred using ADMIXTUREGRAPH). In Europe, descendants of this lineage admixed with pre-existing hunter-gatherers related to Sunghir3 from Russia for the Gravettians and GoyetQ116-1 from Belgium for the Magdalenians, while in the Near East it did so with Basal Eurasians. Later Europeans prior to the arrival of agriculture were the product of re-settlement of this lineage after ~15kya in mainland Europe, while in eastern Europe they admixed with Siberian hunter-gatherers forming the WHG-ANE cline of ancestry [See PCA above]. In the Near East, the Dzudzuana-related population admixed with North African-related ancestry in the Levant and with Siberian hunter-gatherer and eastern non-African-related ancestry in Iran and the Caucasus. Thus, the highly differentiated populations at the dawn of the Neolithic were primarily descended from Villabruna Cluster and Dzudzuana-related ancestors, with varying degrees of additional input related to both North Africa and Ancient North/East Eurasia whose proximate sources may be clarified by future sampling of geographically and temporally intermediate populations.

    qpgraph-dzudzuana
    An admixture graph model of Paleolithic West Eurasians. An automatically generated admixture graph models fits populations (worst Z-score of the difference between estimated and fitted f-statistics is 2.7) or populations (also including South_Africa_HG, worst Z-score is 3.5). This is a simplified model assuming binary admixture events and is not a unique solution (Supplementary Information section 2). Sampled populations are shown with ovals and select labeled internal nodes with rectangles.

    Interesting excerpts from the supplementary materials:

    From our analysis of Supplementary Information section 3, we showed that these sources are indeed complex, and only one of these (WHG, represented by Villabruna) appears to be a contributor to all the remaining sources. This should not be understood as showing that hunter-gatherers from mainland Europe migrated to the rest of West Eurasia, but rather that the fairly homogeneous post-15kya population of mainland Europe labeled WHG appear to represent a deep strain of ancestry that seems to have contributed to West Eurasians from the Gravettian era down to the Neolithic period.

    Villabruna is representative of the WHG group. We also include ElMiron, the best sample from the Magdalenian era as we noticed that within the WHG group there were individuals that could not be modeled as a simple clade with Villabruna but also had some ElMiron-related ancestry. Ddudzuana is representative of the Ice Age Caucasus population, differentiated from Villabruna by Basal Eurasian ancestry. AG3 represents ANE/Upper Paleolithic Siberian ancestry, sampled from the vicinity of Lake Baikal, while Russia_Baikal_EN related to eastern Eurasians and represents a later layer of ancestry from the same region of Siberia as AG3 Finally, Mbuti are a deeply diverged African population that is used here to represent deep strains of ancestry (including Basal Eurasian) prior to the differentiation between West Eurasians and eastern non-Africans that are otherwise not accounted for by the remaining five sources. Collectively, we refer to this as ‘Basal’ or ‘Deep’ ancestry, which should be understood as referring potentially to both Basal Eurasian and African ancestry.

    It has been suggested that there is an Anatolia Neolithic-related affinity in hunter-gatherers from the Iron Gates. Our analysis confirms this by showing that this population has Dzudzuana-related ancestry as do many hunter-gatherer populations from southeastern Europe, eastern Europe and Scandinavia. These populations cannot be modeled as a simple mixture of Villabruna and AG3 but require extra Dzudzuana-related ancestry even in the conservative estimates, with a positive admixture proportion inferred for several more in the speculative ones. Thus, the distinction between European hunter-gatherers and Near Eastern populations may have been gradual in pre-Neolithic times; samples from the Aegean (intermediate between those from the Balkans and Anatolia) may reveal how gradual the transition between Dzudzuana-like Neolithic Anatolians and mostly Villabruna-like hunter-gatherers was in southeastern Europe.

    ancient-modern-european-admixture
    Modified image (cut, with important samples marked). Modeling present-day and ancient West-Eurasians. Mixture proportions computed with qpAdm (Supplementary Information section 4). The proportion of ‘Mbuti’ ancestry represents the total of ‘Deep’ ancestry from lineages that split prior to the 365 split of Ust’Ishim, Tianyuan, and West Eurasians and can include both ‘Basal Eurasian’ and other (e.g., Sub-Saharan African) ancestry. (a) ‘Conservative’ estimates. Each population 367 cannot be modeled with fewer admixture events than shown.

    Villabruna: This type of ancestry differentiates between present-day Europeans and non-Europeans within West Eurasia, attaining a maximum of ~20% in the Baltic in accordance with previous observations and with the finding of a later persistence of significant hunter-gatherer ancestry in the region. Its proportion drops to ~0% throughout the Near East. Interestingly, a hint of such ancestry is also inferred in all North African populations west of Libya in the speculative proportions, consistent with an archaeogenetic inference of gene flow from Iberia to North Africa during the Late Neolithic.

    ElMiron: This type of ancestry is absent in present-day West Eurasians. This may be because most of the Villabruna-related ancestry in Europeans traces to WHG populations that lacked it (since ElMiron-related ancestry is quite variable within European hunter-gatherers). However, ElMiron ancestry makes up only a minority component of all WHG populations sampled to date and WHG-related ancestry is a minority component of present-day Europeans. Thus, our failure to detect it in present day people may be simply be too little of it to detect with our methods.

    Dzudzuana: Our analysis identifies Dzudzuana-related ancestry as the most important component of West Eurasians and the one that is found across West Eurasian-North African populations at ~46-88% levels. Thus, Dzudzuana-related ancestry can be viewed as the common core of the ancestry of West Eurasian-North African populations. Its distribution reaches its minima in northern Europe and appears to be complementary to that of Villabruna, being most strongly represented in North Africa, the Near East (including the Caucasus) and Mediterranean Europe. Our results here are expected from those of Supplementary Information section 3 in which we modeled ancient Near Eastern/North African populations (the principal ancestors of present-day people from the same regions) as deriving much of their ancestry from a Dzudzuana-related source. Migrations from the Near East/Caucasus associated with the spread of the Neolithic, but also the formation of steppe population introduced most of the Dzudzuana-related ancestry present in Europe, although (as we have seen above) some such ancestry was already present in some pre-agricultural hunter-gatherers in Europe.

    AG3: Ancestry related to the AG3 sample from Siberia has a northern distribution, being strongly represented in both central-northern Europe and the north Caucasus.

    Russia_Baikal_EN: Ancestry related to hunter-gatherers from Lake Baikal in Siberia (postdating AG3) appears to have affected primarily northeastern European populations which have been previously identified as having East Eurasian ancestry; some such ancestry is also identified for a Turkish population from Balıkesir, likely reflecting the Central Asian ancestry of Turkic speakers which has been recently confirmed directly in an Ottoman sample from Anatolia.

    Some comments

    So, to try and sum up:

    • Dzudzuana shares ancestry with ‘Common West Eurasian’ (CWE). the ancestor cluster of Villabruna.
    • Dzudzuana diverges from CWE because of a Basal Eurasian ancestry contribution [which supports that Basal Eurasian ancestry was a deep Middle Eastern lineage].
    • Dzudzuana is closest to Anatolia Neolithic, and close to Gravettian.
    palaeolithic-gravettian-villabruna
    Palaeolithic migrations and clusters in Europe. See more maps.

    Chronologically:

    1. Aurignacian: First West Eurasians arrive ca. 36,000 BP, Goyet cluster expands probably with C1a2 lineages.
    2. After that, the early or ‘unmixed’ Villabruna cluster (‘hidden’ somewhere probably east of Europe, either North Eurasia or South Eurasia), lineages unknown (possibly IJ), contributes to:
      1. Gravettian (ca. 30,000 BP): Věstonice cluster expands, probably with IJ lineages.
      2. A (hidden) ‘Common West Eurasian’ population.
      3. In turn:

        • Dzudzuana ca. 26,000 BP derived from Common West Eurasian (curiously, haplogroup G seems to split in today’s subclades ca. 26,000 BP).
        • During the Gravettian (ca. 26,000 BP), an Anatolian Neolithic-like population exists already in the Near East. Both Věstonice and this Anatolian HG are close to Dzudzuana; in turn, Dzudzuana from CWE.

      4. Magdalenian (ca. 20,000 BP): El Mirón cluster expands, probably with more specific I lineages.
    3. Bølling-Allerød warming period (ca. 14,000 BP): ‘late’ Villabruna cluster or WHG (=CWE with greater affinity to Near Eastern populations) expands, probably spreading with R1b in mainland Europe and to the east (admixing with Siberian HG), creating the WHG — ANE ancestry cline, as reflected in Iron Gates HG, Baltic HG, etc.

    [Here we have the possible “bidirectional gene flow between populations ancestral to Southeastern Europeans of the early Holocene and Anatolians of the late glacial or a dispersal of Southeastern Europeans into the Near East” inferred from Anatolian hunter-gatherers]

    palaeolithic-gravettian-magdalenian-migrations
    The Gravettian (30,000 to 20,000 years) is drawn in black and white; the subsequent Magdalenian (17,000 to 10,000 years) and Hamburgian (13,000-11,750 years) are in light blue and red. It is not known whether the spread of the Gravettian was a result of diffusion of people or cultures. This figure illustrates the possible monocentric origins of the Gravettian, in which the Gravettian is hypothesized to have its origin in the Middle Danube Basin, first spreading west (solid lines) and later spreading east and southeast (dashed lines). This scenario is largely based on the chronology of sites. Thus far, genome-wide data has been collected from only three of the ten< Gravettian regions indicated on the map. These regions are northern Austria (1 sample), the Czech Republic (6), southern Italy (3) and Belgium (3), indicating that they all share a genomic ancestry. However, it is unknown whether samples from the remaining regions also share a close genomic ancestry. Some skeletal remains associated with the Gravettian that could be investigated paleogenomically are from Sungir (Russia); Laghar Velho (central Portugal); Cussac Cave; Les Garennes, near Vilhonneur; and Level 2 at Abri Pataud116 (western France). Light blue and light red regions represent the approximate distributions of the Magdalenian Culture and the Hamburgian Culture (13,000-11,750 years). Figure adapted from Kozłowski. Image from Harris (2017)

    The paper talks about possibilities for Common West Eurasian:

    1. Migration from mainland Europe to Near East or vice versa (not very likely);
    2. Migration from a geographically intermediate Ice Age refugium in southeast Europe, Anatolia, or the circum-Pontic region that explain post-glacial affinity of post-glacial Levantine and Anatolian populations.

    It also re-states what was known:

    • EHG (ca. 8,000 BP) = between WHG — ANE (ca. 24,000 BP).
    • CHG (ca. 10,000 BP) = between EHG — Iran N.

    I would say that the distinct CHG vs. Dzudzuana ancestry puts CHG probably to the south, within the Iranian Plateau, during the Gravettian, expanding probably later.

    Also important, Ancestral North African probably accompanied by haplogroup E. Early expansion of North Africans into the Near East further confirms the impossibility of Afroasiatic (much younger) to be associated with these expansions, and confirms that the still unclear Green Sahara migrations are the key.

    Related

    Scythians in Ukraine, Natufian and sub-Saharan ancestry in North Africa (ISBA 8, 21st Sep)

    jena-isba8

    Interesting information from ISBA 8 sesions today, as seen on Twitter (see programme in PDF, and sessions from the 19th and the 20th september).

    Official abstracts are listed first (emphasis mine), then reports and images and/or link to tweets. Here is the list for quick access:

    Scythian population genetics and settlement patterns

    Genetic continuity in the western Eurasian Steppe broken not due to Scythian dominance, but rather at the transition to the Chernyakhov culture (Ostrogoths), by Järve et al.

    The long-held archaeological view sees the Early Iron Age nomadic Scythians expanding west from their Altai region homeland across the Eurasian Steppe until they reached the Ponto-Caspian region north of the Black and Caspian Seas by around 2,900 BP1. However, the migration theory has not found support from ancient DNA evidence, and it is still unclear how much of the Scythian dominance in the Eurasian Steppe was due to movements of people and how much reflected cultural diffusion and elite dominance. We present new whole-genome results of 31 ancient Western and Eastern Scythians as well as samples pre- and postdating them that allow us to set the Scythians in a temporal context by comparing the Western Scythians to samples before and after within the Ponto-Caspian region. We detect no significant contribution of the Scythians to the Early Iron Age Ponto-Caspian gene pool, inferring instead a genetic continuity in the western Eurasian Steppe that persisted from at least 4,800–4,400 cal BP to 2,700–2,100 cal BP (based on our radiocarbon dated samples), i.e. from the Yamnaya through the Scythian period.

    However, the transition from the Scythian to the Chernyakhov culture between 2,100 and 1,700 cal BP does mark a shift in the Ponto-Caspian genetic landscape, with various analyses showing that Chernyakhov culture samples share more drift and derived alleles with Bronze/Iron Age and modern Europeans, while the Scythians position outside modern European variation. Our results agree well with the Ostrogothic origins of the Chernyakhov culture and support the hypothesis that the Scythian dominance was cultural rather than achieved through population replacement.

    Detail of the slide with admixture of Scythian groups in Ukraine:

    scythians-admixture

    Interesting to read in combination with yesterday’s re-evaluation of Scythian mobility and settlement patterns in the west (showing adaptation to the different regional cultures), The Steppe was Sown – multi-isotopic research changes our understandings of Scythian diet and mobility, by Ventresca Miller et al.

    Nomadic pastoralists conventionally known as the Scythians occupied the Pontic steppe during the Iron Age, c. 700-200 BC, a period of unprecedented pan-regional interaction. Popular science accounts of the Scythians promote narratives of roving bands of nomadic warriors traversing the steppe from the Altai Mountains to the Black Sea coastline. The quantity and scale of mobility in the region is usually emphasized based on the wide distribution of material culture and the characterization of Iron Age subsistence economies in the Pontic steppe and forest-steppe as mobile pastoralism. Yet, there remains a lack of systematic, direct analysis of the mobility of individuals and their animals. Here, we present a multi-isotopic analysis of humans from Iron Age Scythian sites in Ukraine. Mobility and dietary intake were documented through strontium, carbon and oxygen isotope analyses of tooth enamel. Our results provide direct evidence for mobility among populations in the steppe and forest-steppe zones, demonstrating a range of localized mobility strategies. However, we found that very few individuals came from outside of the broader vicinity of each site, often staying within a 90 km radius. Dietary intake varied at the intrasite level and was based in agro-pastoralism.

    While terrestrial protein did form a portion of the diet for some individuals, there were also high levels of a 13C-enriched food source among many individuals, which has been interpreted as millet consumption. Individuals exhibiting 87Sr/86Sr ratios that fell outside the local range were more likely to have lower rates of millet consumption than those that fell within the local range. This suggests that individuals moving to the site later in life had different economic pursuits and consumed less millet. There is also strong evidence that children and infants moved at the pan-regional scale. Contrary to the popular narrative, the majority of Scythians engaged in localized mobility as part of agricultural lifeways while pan-regional movements included family groups.

    North-Africans show ancestry from the ancient Near East and sub-Saharan Africa

    Pleistocene North Africans show dual genetic ancestry from the ancient Near East and sub-Saharan Africa, by van de Loosdrecht et al.

    North Africa, connecting sub-Saharan Africa and Eurasia, is important for understanding human history. However, the genetic history of modern humans in this region is largely unknown before the introduction of agriculture. After the Last Glacial Maximum modern humans, associated with the Iberomaurusian culture, inhabited a wide area spanning from Morocco to Libya. The Iberomaurusian is part of the early Later Stone Age and characterized by a distinct microlithic bladelet technology, complex hunter-gathering and tooth evulsion.

    Here we present genomic data from seven individuals, directly dated to ~15,000-year-ago, from Grotte des Pigeons, Taforalt in Morocco. Uni-parental marker analyses show mitochondrial haplogroup U6a for six individuals and M1b for one individual, and Y-chromosome haplogroup E-M78 (E1b1b1a1) for males. We find a strong genetic affinity of the Taforalt individuals with ancient Near Easterners, best represented by ~12,000 year old Levantine Natufians, that made the transition from complex hunter-gathering to more sedentary food production. This suggests that genetic connections between Africa and the Near East predate the introduction of agriculture in North Africa by several millennia. Notably, we do not find evidence for gene flow from Paleolithic Europeans into the ~15,000 year old North Africans as previously suggested based on archaeological similarities. Finally, the Taforalt individuals derive one third of their ancestry from sub-Saharan Africans, best approximated by a mixture of genetic components preserved in present-day West Africans (Yoruba, Mende) and Africans from Tanzania (Hadza). In contrast, modern North Africans have a much smaller sub-Saharan African component with no apparent link to Hadza. Our results provide the earliest direct evidence for genetic interactions between modern humans across Africa and Eurasia.

    A detail of the cultures involved in these population movements:

    north-africa-natufian-saharan

    So, most likely, Natufian-related ancestry – as sub-Saharan ancestry – not related to the Afroasiatic expansion.

    NOTE. This now probably outdated already by the new preprint on Dzudzuana samples, from the Caucasus.

    Impact of colonization in north-eastern Siberia

    Exploring the genomic impact of colonization in north-eastern Siberia by Seguin-Orlando et al.

    Yakutia is the coldest region in the northern hemisphere, with winter record temperatures below minus 70°C. The ability of Yakut people to adapt both culturally and biologically to extremely cold temperatures has been key to their subsistence. They are believed to descend from an ancestral population, which left its original homeland in the Lake Baykal area following the Mongol expansion between the 13th and 15th centuries AD. They originally developed a semi-nomadic lifestyle, based on horse and cattle breeding, providing transportation, primary clothing material, meat, and milk. The early colonization by Russians in the first half of the 17th century AD, and their further expansion, have massively impacted indigenous populations. It led not only to massive epidemiological outbreaks, but also to an important dietary shift increasingly relying on carbohydrate-rich resources, and a profound lifestyle transition with the gradual conversion from Shamanism to Christianity and the establishment of new marriage customs. Leveraging an exceptional archaeological collection of more than a hundred of bodies excavated by MAFSO (Mission Archéologique Française en Sibérie Orientale) over the last 15 years and naturally kept frozen by the extreme cold temperatures of Yakutia, we have started to characterize the (epi)genome of indigenous individuals who lived from the 16th to the 20th century AD. Current data include the genome sequence of approximately 50 individuals that lived prior to and after Russian contact, at a coverage from 2 to 40 fold. Combined with data from archaeology and physical anthropology, as well as microbial DNA preserved in the specimens, our unique dataset is aimed at assessing the biological consequences of the social and biological changes undergone by the Yakut people following their neolithisation by Russian colons.

    Also interesting to read Balanovsky’s session, and a previous paper on the expansion of Yakuts.

    The Iron Age expansion of Southern Siberian groups and ancestry with Scythians

    iron_age-sarmatians

    Maternal genetic features of the Iron Age Tagar population from Southern Siberia (1st millennium BC), by Pilipenko et al. (2018).

    Interesting excerpts (emphasis mine):

    The positions of non-Tagar Iron Age groups in the MDS plot were correlated with their geographic position within the Eurasian steppe belt and with frequencies of Western and Eastern Eurasian mtDNA lineages in their gene pools. Series from chronological Tagar stages (similar to the overall Tagar series) were located within the genetic variability (in terms of mtDNA) of Scythian World nomadic groups (Figs 5 and 6; S4 and S6 Tables). Specifically, the Early Tagar series was more similar to western nomads (North Pontic Scythians), while the Middle Tagar was more similar to the Southern Siberian populations of the Scythian period. The Late Tagar group (Tes`culture) belonging to the Early Xiongnu period had the “western-most” location on the MDS plot with the maximal genetic difference from Xiongnu and other eastern nomadic groups (but see Discussion concerning the low sample size for the Tes`series).

    In a comparison of our Tagar series with modern populations in Eurasia, we detected similarity between the Tagar group and some modern Turkic-speaking populations (with the exception of the Indo-Iranian Tajik population) (Fig 7; S2 Table). Among the modern Turkic-speaking groups, populations from the western part of the Eurasian steppe belt, such as Bashkirs from the Volga-Ural region and Siberian Tatars from the West Siberian forest-steppe zone, were more similar to the Tagar group than modern Turkic-speaking populations of the Altay-Sayan mountain system (including the Khakassians from the Minusinsk basin) (Fig 7).

    tagar-archaeology
    Location of Tagar archaeological sites from which samples for this study were obtained. Burial grounds: 1—Novaya Chernaya-1; 2—Podgornoe Ozero, Barsuchiha-1, Barsuchiha-6, Barsuchiha-7; 3—Perevozinskiy; 4—Ulug-Kyuzyur, Kichik-Kyuzyur, Sovetskaya Khakassiya; 5—Tepsey-3, Tepsey-8, Tepsey-9; 6—Dolgiy Kurgan. https://doi.org/10.1371/journal.pone.0204062.g001

    Mitochondrial DNA diversity and genetic relationships of the Tagar population

    Our results are not inconsistent with the assumption of a probable role of gene flow due to the migration from Western Eurasia to the Minusinsk basin in the Bronze Age in the formation of the genetic composition of the Tagar population. Particularly, we detected many mtDNA lineages/clusters with probable West Eurasian origin that were dominant in modern populations of different parts of Europe, Caucasus, and the Near East (such as K and HV6) in our Tagar series based on a phylogeographic analysis.

    We detected relatively low genetic distances between our Tagar population and two Bronze Age populations from the Minusinsk basin—the Okunevo culture population (pre-Andronovo Bronze Age) and Andronovo culture population, followed by Afanasievo population from the Minusinsk Basin and Middle Bronze Age population from the Mongolian Altai Mountains (the region adjacent to the Minusinsk basin) (Figs 3 and 6; S3 and S5 Tables). Among West Eurasian part of our Tagar series we also observed haplogroups/sub-haplogroups and haplotypes shared with Early and Middle Bronze Age populations from Minusinsk Basin and western part of Eurasian steppe belt (Fig 4; S5 Table). Thus, our results suggested a potentially significant role of the genetic components, introduced by migrants from Western Eurasia during the Bronze Age, in the formation of the genetic composition of the Tagar population. It is necessary to note the relatively small size of available mtDNA samples from the Bronze Age populations of Minusinsk basin; accordingly, additional mtDNA data for these populations are required to further confirm our inference.

    tagar-mtdna-tree
    Phylogenetic tree of mtDNA lineages from the Tagar population. Color coding of the Tagar stages: orange—the Early Tagar stage; blue—the Middle Tagar Stage; green—the Late Tagar stage. Color of haplogroup labels: yellow—for Western Eurasian haplogroups; red—for Eastern Eurasian haplogroups. https://doi.org/10.1371/journal.pone.0204062.g002

    Another substantial part of the mtDNA pool of the Tagar and other eastern populations of the Scythian World is typical of populations in Southern Siberia and adjacent regions of Central Asia (autochthonous Central Asian mtDNA clusters). Most of these components belong to the East Eurasian cluster of mtDNA haplogroups. Moreover, the role of each of these components in the formation of the genetic composition of subsequent (to the present) populations in South Siberia and Central Asia could be very different. In this regard, cluster C4a2a (and its subcluster C4a2a1), and haplogroup A8 are of particular interest.

    Genetic features of successive Tagar groups

    We compared successive Tagar groups (Early, Middle, and Late Tagar) with each other and with other Iron Age nomadic populations to evaluate changes in the mtDNA pool structure. Despite the genetic similarity between the Early and Middle Tagar series and Scythian World nomadic groups (Figs 5 and 6; S4 and S6 Tables), there were some peculiarities. For example, the Early Tagar series was more similar to North Pontic Classic Scythians, while the Middle Tagar samples were more similar to the Southern Siberian populations of the Scythian period (i.e., completely synchronous populations of regions neighboring the Minusinsk basin, such as the Pazyryk population from the Altay Mountains and Aldy-Bel population from Tuva).

    We observed differences in the mtDNA pool structure between the Early and the Middle chronological stages of the Tagar culture population, as evidenced by the change in the ratio of Western to Eastern Eurasian mtDNA components. The contribution of Eastern Eurasian lineages increased from about one-third (34.8%) in the Early Tagar group to almost one-half (45.8%) in the Middle Tagar group.

    tagar-mtdna-fst
    Results of multidimensional scaling based on matrix of Slatkin population differentiation (FST) according to frequencies of mtDNA haplogroup in Tagar populations and modern populations of Eurasia. Populations: Tagar (red pentagon) (this study); Mongolian-speaking populations: Khamnigans (Buryat Republic, Russia) [43]; Barghuts (Inner Mongolia, China) [44]; Buryats (Buryat Republic, Southern Siberia, Russia) [43]; Mongols (Mongolia) [45]. Turkic-speaking populations: Tuvinians (Tuva Republic, Russia) [43]; Tofalars (Irkutsk region, Russia) [46]; Altai-Kizhi ((Altai Republic, Russia) [43, 47]; Telenghits (Altai Republic, Russia) [43,47]; Tubalars (Altai Republic) [48]; Shors (Kemerovo region, Russia) [43, 47]; Khakassians (Khakassian Rupublic, Russia) [43, 46]; Altaian Kazakhs (Altai Republic) [49]; Kazakhs (Kazakhstan, Uzbekistan) [50, 51]; Kirghiz (Kyrgyzstan) [50, 51]; Uighurs (Kazakhstan and Xinjiang) [50, 52]; Siberian Tatars (Tyumen and Omsk regions, Russia) [53]; Tatars (Volga-Ural rigion, Russia) [54]; Bashkirs (Volga-Ural region, Russia) [55]; Uzbeks (Uzbekistan) [51, 56]; Turkmens (Turkmenistan) [51, 56]; Nogays [57]; Turkeys [58]; other populations: Evenks [43, 46]; Ulchi [59]; Koreans (South Korea) [43]; Han Chinese [60]; Zhuang (Guangxi, China) [61]; Tadjiks (Tadjikistan) [43, 51]; Iranians [60]; Russians [62]. https://doi.org/10.1371/journal.pone.0204062.g007

    At the level of mtDNA haplogroups, we detected a decrease in the diversity of phylogenetic clusters during the transition from the Early Tagar to the Middle Tagar. This decline in diversity equally affected the West Eurasian and East Eurasian components of the Tagar mtDNA pool. It should be noted that this decrease can be partially explained by the smaller number of Middle Tagar than Early Tagar samples. Under a simple binomial approximation the mtDNA clusters, observed at frequencies of 6.3% and 11.7%, could be lost by chance in our Early (N = 46) and Middle (N = 24) Tagar samples, respectively. However, the simultaneous lack of several such clusters, with a total frequency in the gene pool of the Early group of 34.8%, is unlikely.

    The observed reduction in the genetic distance between the Middle Tagar population and other Scythian-like populations of Southern Siberia(Fig 5; S4 Table), in our opinion, is primarily associated with an increase in the role of East Eurasian mtDNA lineages in the gene pool (up to nearly half of the gene pool) and a substantial increase in the joint frequency of haplogroups C and D (from 8.7% in the Early Tagar series to 37.5% in the Middle Tagar series). These features are characteristic of many ancient and modern populations of Southern Siberia and adjacent regions of Central Asia, including the Pazyryk population of the Altai Mountains. We did not obtain strong evidence for an intensification of genetic contact between the population of the Minusinsk basin and the Altai Mountains in the Middle Tagar period compared with the Early Tagar period. Although, several archaeologists have found evidence for the intensification of contact at the level of material culture, namely, a cultural influence of the population of the Altai Mountains (represented by the Pazyryk population) on the population of the Minusinsk basin (the Saragash Tagar group) [6, 71, 72].

    Another important issue is the change in the genetic structure of the Tagar population during the transition from the Middle (Saragash) to the Late (Tes`) stage. The Late Tagar stage refers to the Xiongnu period. Many archaeologists suggest that the formation of the Tes`stage involved the direct cultural influence of the Xiongnu and/or related groups of nomads from more eastern regions of Central Asia [71, 73]. Some archaeologists have even suggested renaming the Tes`stage in the Tes`culture [71], emphasizing the role of new eastern cultural elements. If this influence also existed at the genetic level, then we would expect to observe new genetic elements in the Tes`gene pool, particularly those of East Eurasian origin.

    Siberian ancestry

    Just a reminder of the recent session in ISBA 8 on expanding Scythians (and also Mongolians and Turks) spreading Siberian ancestry, usually (wrongly) identified as “Uralic-Yeniseian” based on modern populations (similar to how steppe ancestry is wrongly identified as “Indo-European”), see the following graphic including the Tagar population:

    siberian-genetic-component-chronology
    Very important observation with implication of population turnover is that pre-Turkic Inner Eurasian populations’ Siberian ancestry appears predominantly “Uralic-Yeniseian” in contrast to later dominance of “Tungusic-Mongolic” sort (which does sporadically occur earlier). Alexander M. Kim

    And also the poster by Alexander M. Kim et al. Yeniseian hypotheses in light of genome-wide ancient DNA from historical Siberia:

    The relevance of ancient DNA data to debates in historical linguistics is an emphatic strand in much recent work on the archaeogenetics of Eurasia, where the discussion has focused heavily on Indo-European (Haak et al. 2015; Narasimhan et al. 2018; de Barros Damgaard et al. 2018a,b). We present new genome-wide ancient DNA data from a historical Siberian individual in relation to Yeniseian, an isolated language “microfamily” (Vajda 2014) that nonetheless sits at the center of numerous controversial proposals in historical linguistics and cultural interaction. Yeniseian’s sole surviving representative is Ket, a critically endangered language fluently spoken by only a few dozen individuals near the Middle Yenisei River of Central Siberia.

    In strong contrast to the present-day picture, river names and argued substrate influences and loanwords in languages outside the current range of Yeniseian, as well as direct records from the Russian colonial period, indicate that speakers of extinct Yeniseian languages had a formerly much broader presence in the taiga of Central Siberia as well as further south in the mountainous Altai-Sayan region – and perhaps even further afield in Inner Asia (Vajda 2010; Gorbachov 2017; Blažek 2016). The consilience of these proposals with genetic data is not straightforward (Flegontov et al. 2015, 2017) and faces a major obstacle in the lack of genetic information from verifiable speakers of Yeniseian languages other than the Kets, who have had complex ongoing interactions with speakers of non-Yeniseian languages such as the Samoyedic Selkups. We attempt to remedy this with new historical Siberian aDNA data, orienting our search for common denominators and systematic difference in a broader landscape of concordance, discordance, and uncertainty at the interface of diachronic linguistics and genetics.

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    Mitogenomes suggest rapid expansion of domesticated horse before 3500 BC

    Open access Origin and spread of Thoroughbred racehorses inferred from complete mitochondrial genome sequences: Phylogenomic and Bayesian coalescent perspectives, by Yoon et al. PLOS One (2018).

    Abstract (emphasis mine)

    The Thoroughbred horse breed was developed primarily for racing, and has a significant contribution to the qualitative improvement of many other horse breeds. Despite the importance of Thoroughbred racehorses in historical, cultural, and economical viewpoints, there was no temporal and spatial dynamics of them using the mitogenome sequences. To explore this topic, the complete mitochondrial genome sequences of 14 Thoroughbreds and two Przewalski’s horses were determined. These sequences were analyzed together along with 151 previously published horse mitochondrial genomes from a range of breeds across the globe using a Bayesian coalescent approach as well as Bayesian inference and maximum likelihood methods. The racing horses were revealed to have multiple maternal origins and to be closely related to horses from one Asian, two Middle Eastern, and five European breeds. Thoroughbred horse breed was not directly related to the Przewalski’s horse which has been regarded as the closest taxon to the all domestic horses and the only true wild horse species left in the world. Our phylogenomic analyses also supported that there was no apparent correlation between geographic origin or breed and the evolution of global horses. The most recent common ancestor of the Thoroughbreds lived approximately 8,100–111,500 years ago, which was significantly younger than the most recent common ancestor of modern horses (0.7286 My). Bayesian skyline plot revealed that the population expansion of modern horses, including Thoroughbreds, occurred approximately 5,500–11,000 years ago, which coincide with the start of domestication. This is the first phylogenomic study on the Thoroughbred racehorse in association with its spatio-temporal dynamics. The database and genetic history information of Thoroughbred mitogenomes obtained from the present study provide useful information for future horse improvement projects, as well as for the study of horse genomics, conservation, and in association with its geographical distribution.

    horse-domestication
    Bayesian skyline plot (BSP) based on mitochondrial genome sequences from 167 modern horses.
    The dark line in the BSP represents the estimated effective population size through time. The green area represents the 95% highest posterior density confidence intervals for this estimate.

    Interesting excerpts:

    We carried out a Bayesian coalescent approach using extended mitochondrial genome sequences from 167 horses in order to further assess the timescale of horse domestication. Here, we first calculated the time of the most recent common ancestor of Thoroughbred horses. Our analysis revealed the age of the most recent common ancestor of the racing horse to be around 8,100–111,500 years old. This estimate is much younger than that of the most recent common ancestor of the global horses, which has been estimated at 0.7286 Mys old.

    phylogenetic-tree-horses
    Bayesian maximum clade credibility phylogenomic tree on the ground of the mitochondrial genome sequences of 167 modern horses.
    The data set (16,432 base pairs) was also analyzed phylogenetically using Bayesian inference (BI) and maximum likelihood (ML) methods which showed the same topologies. 95% Highest Posterior Density of node heights are shown by blue bars. Groups are marked by a “G”. Numbers at the nodes represent (left to right): posterior probabilities (≥0.80) for the BI tree and bootstrap values (≥70%) for the ML tree. The racing horses were revealed to have multiple maternal origins and to be closely related to horses from one Asian, two Middle Eastern, and five European breeds. Results of phylogenomic analyses also uncovered no apparent association between geographic origin or breed and heterogeneity of global horses. The most recent common ancestor of the Thoroughbreds lived approximately 8,100–111,500 years ago, which was significantly younger than the most recent common ancestor of modern horses (0.7286 My).

    On the domestication time of modern horses, there have been several publications derived from both archaeological [49–51] and molecular [11–12, 23, 48] evidences. D’Andrade [49] reported that the origin of domestic horses was around 4,000 years ago. Ludwig et al. [50] stated the domestication time to be about 5,000 years ago, while Anthony [51] noted that horse rearing by humans may have occurred approximately 6,000 years ago. Subsequently, on the basis of mitochondrial genome sequences, Lippold et al. [11] and Achilli et al. [12] postulated domestication time to be about 6,000–8,000 and 6,000–7,000 years ago, respectively. Warmuth [48] dated domestication time to 5,500 years ago based on autosomal genotype data, while Orlando et al. [23] claimed that Przewalski’s and domestic horse populations diverged 38,000–72,000 years ago based on analysis of genome sequences. In contrast to the previous hypothesized date of horse domestication, the results of our Bayesian skyline plot (BSP) analysis depict a rapid expansion of the horse population approximately 5,500–11,000 years ago, which coincides with the start of domestication.

    It seems that we will not have an update on horse aDNA from the ISBA 8, so we will have to make do with this for the moment.

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