Yamnaya replaced Europeans, but admixed heavily as they spread to Asia

narasimhan-spread-yamnaya-ancestry

Recent papers The formation of human populations in South and Central Asia, by Narasimhan, Patterson et al. Science (2019) and An Ancient Harappan Genome Lacks Ancestry from Steppe Pastoralists or Iranian Farmers, by Shinde et al. Cell (2019).

NOTE. For direct access to Narasimhan, Patterson et al. (2019), visit this link courtesy of the first author and the Reich Lab.

I am currently not on holidays anymore, and the information in the paper is huge, with many complex issues raised by the new samples and analyses rather than solved, so I will stick to the Indo-European question, especially to some details that have changed since the publication of the preprint. For a summary of its previous findings, see the book series A Song of Sheep and Horses, in particular the sections from A Clash of Chiefs where I discuss languages and regions related to Central and South Asia.

I have updated the maps of the Preshistory Atlas, and included the most recently reported mtDNA and Y-DNA subclades. I will try to update the Eurasian PCA and related graphics, too.

NOTE. Many subclades from this paper have been reported by Kolgeh (download), Pribislav and Principe at Anthrogenica on this thread. I have checked some out for comparison, but even if it contradicted their analyses mine would be the wrong ones. I will upload my spreadsheets and link to them from this page whenever I find the time.

caucasus-cline-narasimhan
Ancestry clines (1) before and (2) after the advent of farming. Colour modified from the original to emphasize the CHG cline: notice the apparent relevance of forest-steppe groups in the formation of this CHG mating network from which Pre-Yamnaya peoples emerged.

Indo-Europeans

I think the Narasimhan, Patterson et al. (2019) paper is well-balanced, and unexpectedly centered – as it should – on the spread of Yamnaya-related ancestry (now Western_Steppe_EMBA) as the marker of Proto-Indo-European migrations, which stretched ca. 3000 BC “from Hungary in the west to the Altai mountains in the east”, spreading later Indo-European dialects after admixing with local groups, from the Atlantic to South Asia.

I. Afanasievo

I.1. East or West PIE?

I expected Afanasievo to show (1) R1b-L23(xZ2103, xL51) and (2) R1b-L51 lineages, apart from (3) the known R1b-Z2103 ones, pointing thus to an ancestral PIE community before the typical Yamnaya bottlenecks, and with R1b-L51 supporting a connection with North-West Indo-European. The presence of some samples of hg. Q pointed in this direction, too.

However, Afanasievo samples show overwhelmingly R1b-Z2103 subclades (all except for those with low coverage), all apparently under R1b-Z2108 (formed ca. 3500 BC, TMRCA ca. 3500 BC), like most samples from East Yamnaya.

This necessarily shifts the split and spread of R1b-L23 lineages to Khvalynsk/early Repin-related expansions, in line with what TMRCA suggested, and what advances by Anthony (2019) and Khokhlov (2018) on future samples from the Reich Lab suggest.

Given the almost indistinguishable ancestry between Afanasievo and Early Yamnaya, there seems to be as of yet little potential information to support in population genomics that Pre-Tocharians were more closely related to North-West Indo-Europeans than to Graeco-Aryans, as it is proposed in linguistics based on the few shared traits between them, and the lack of innovations proper of the Graeco-Aryan community.

NOTE. A new issue of Wekʷos contains an abstract from a relevant paper by Blažek on vocabulary for ‘word’, including the common NWIE *wrdʰo-/wordʰo-, but also a new (for me, at least) Northern Indo-European one: *rēki-/*rēkoi̯-, shared by Slavic and Tocharian.

The fact that bottlenecks happened around the time of the late Repin expansion suggests that we might be able to see different clans based on the predominant lineages developing around the Don-Volga area in the 4th millennium BC. The finding of Pre-R1b-L51 in Lopatino (see below), and of a Catacomb sample of hg. R1b-Z2103(Z2105-) in the North Caucasus steppe near Novoaleksandrovskij also support a star-like phylogeny of R1b-L23 stemming from the Don-Volga area.

NOTE. Interestingly, a dismissal of a common trunk between Tocharian and North-West Indo-European would mean that shared similarities between such disparate groups could be traced back to a Common Late PIE trunk, and not to a shared (western) Repin community. For an example of such a ‘pure’ East-West dialectal division, see the diagram of Adams & Mallory (2007) at the end of the post. It would thus mean a fatal blow to Kortlandt’s Indo-Slavonic group among other hypothetical groupings (remade versions of the ancient Centum-Satem division), as well as to certain assumptions about laryngeal survival or tritectalism that usually accompany them. Still, I don’t think this is the case, so the question will remain a linguistic one, and maybe some similarities will be found with enough number of samples that differentiate Northern Indo-Europeans from the East Yamna/Catacomb-Poltavka-Balkan_EBA group.

afanasievo-y-dna
Y-chromosome haplogroups of Afanasievo samples and neighbouring groups. See full maps.

I.2. Expansion or resurgence of hg. Q1b?

Haplogroup Q1b-Y6802(xY6798) seems to be the main lineage that expanded with Afanasievo, or resurged in their territory. It’s difficult to tell, because the three available samples are family, and belong to a later period.

NOTE. I have finally put some order to the chaos of Q1a vs. Q1b subclades in my spreadsheet and in the maps. The change of ISOGG 2016 to 2017 has caused that many samples reported as of Q1 subclades from papers prepared during the 2017-2018 period, and which did not provide specific SNP calls, were impossible to define with certainty. By checking some of them I could determine the specific standard used.

In favour of the presence of this haplogroup in the Pre-Yamnaya community are:

  • The statement by Anthony (2019) that Q1a [hence maybe Q1b in the new ISOGG nomenclature] represented a significant minority among an R1b-rich community.
  • The sample found in a Sintastha WSHG outlier (see below), of hg. Q1b-Y6798, and the sample from Lola, of hg. Q1b-L717, are thus from other lineage(s) separated thousands of years from the Afanasievo subclade, but might be related to the Khvalynsk expansion, like R1b-V1636 and R1b-M269 are.

These are the data that suggest multiple resurgence events in Afanasievo, rather than expanding Q1b lineages with late Repin:

  • Overwhelming presence of R1b in early Yamnaya and Afanasievo samples; one Q1(xQ1b) sample reported in Khvalynsk.
  • The three Q1b samples appear only later, although wide CI for radiocarbon dates, different sites, and indistinguishable ancestry may preclude a proper interpretation of the only available family.
    • Nevertheless, ancestry seems unimportant in the case of Afanasievo, since the same ancestry is found up to the Iron Age in a community of varied haplogroups.
  • Another sample of hg. Q1b-Y6802(xY6798) is found in Aigyrzhal_BA (ca. 2120 BC), with Central_Steppe_EMBA (WSHG-related) ancestry; however, this clade formed and expanded ca. 14000 BC.
  • The whole Altai – Baikal area seems to be a Q1b-L54 hotspot, although admittedly many subclades separated very early from each other, so they might be found throughout North Eurasia during the Neolithic.
  • One Afanasievo sample is reported as of hg. C in Shin (2017), and the same haplogroup is reported by Hollard (2014) for the only available sample of early Chemurchek to date, from Kulala ula, North Altai (ca. 2400 BC).
afanasievo-chemurchek-y-dna
Y-chromosome haplogroups of late Afanasievo – early Chemurchek samples and neighbouring groups. See full maps.

I.3. Agricultural substrate

Evidence of continuous contacts of Central_Steppe_MLBA populations with BMAC from ca. 2100 BC on – visible in the appearance of Steppe ancestry among BMAC samples and BMAC ancestry among Steppe pastoralists – supports the close interaction between Indo-Iranian pastoralists and BMAC agriculturalists as the origin of the Asian agricultural substrate found in Proto-Indo-Iranian, hence likely related to the language of the Oxus Civilization.

Similar to the European agricultural substrate adopted by West Yamnaya settlers (both NWIE and Palaeo-Balkan speakers), Tocharian shows a few substrate terms in common with Indo-Iranian, which can be explained by contacts in different dialectal stages through phonetic reconstruction alone.

The recent Hermes et al. (2019) supports the early integration of pastoralism and millet cultivation in Central Asia (ca. 2700 BC or earlier), with the spread of agriculture to the north – through the Inner Asian Mountain Corridor – being thus unrelated to the Indo-Iranian expansions, which might support independent loans.

However, compared to the huge number of parallel shared loans between NWIE and Palaeo-Balkan languages in the European substratum, Indo-Iranians seem to have been the first borrowers of vocabulary from Asian agriculturalists, while Proto-Tocharian shows just one certain related word, with phonetic similarities that warrant an adoption from late Indo-Iranian dialects.

chemurchek-sintashta-bmac
Y-chromosome haplogroups of Sintashta, Central Asia, and neighbouring groups in the Early Bronze Age. See full maps.

The finding of hg. (pre-)R1b-PH155 in a BMAC sample from Dzharkutan (to the west of Xinjiang) together with hg. R1b in a sample from Central Mongolia previously reported by Shin (2017) support the widespread presence of this lineage to the east and west of Xinjiang, which means it might have become incorporated to Indo-Iranian migrants into the Xiaohe horizon, to the Afanasievo-Chemurchek-derived groups, or the later from the former. In other words, the Island Biogeography Theory with its explanation of founder effects might be, after all, applicable to the whole Xinjiang area, not only during the Chemurchek – Tianshan-Beilu – Xiaohe interaction.

Of course, there is no need for too complicated models of haplogroup resurgence events in Central and South Asia, seeing how the total amount of hg. R1a-L657 (today prevalent among Indo-Aryan speakers from South Asia) among ancient Western/Central_Steppe_MLBA-related samples amounts to a total of 0, and that many different lineages survived in the region. Similar cases of haplogroup resurgence and Y-DNA bottleneck events are also found in the Central and Eastern Mediterranean, and in North-Eastern Europe. From the paper:

[It] could reflect stronger ecological or cultural barriers to the spread of people in South Asia than in Europe, allowing the previously established groups more time to adapt and mix with incoming groups. A second difference is the smaller proportion of Steppe pastoralist– related ancestry in South Asia compared with Europe, its later arrival by ~500 to 1000 years, and a lower (albeit still significant) male sex bias in the admixture (…).

Y-chromosome haplogroups of samples from the Srubna-Andronovo and Andronovo-related horizon, Xiaohe, late BMAC, and neighbouring groups. See full maps.

II. R1b-Beakers replaced R1a-CWC peoples

II.1. R1a-M417-rich Corded Ware

Newly reported Corded Ware samples from Radovesice show hg. R1a-M417, at least some of them xZ645, ‘archaic’ lineages shared with the early Bergrheinfeld sample (ca. 2650 BC) and with the coeval Esperstedt family, hence supporting that it eventually became the typical Western Corded Ware lineage(s), probably dominating over the so-called A-horizon and the Single Grave culture in particular. On the other hand, R1a-Z645 was typical of bottlenecks among expanding Eastern Corded Ware groups.

Interestingly, it is supported once again that known bottlenecks under hg. R1a-M417 happened during the Corded Ware expansion, evidenced also by the remarkable high variability of male lineages among early Corded Ware samples. Similarly, these Corded Ware samples from Bohemia form part of the typical ‘Central European’ cluster in the PCA, which excludes once again not only the ‘official’ Espersted outlier I1540, but also the known outlier with Yamnaya ancestry.

NOTE. The fact that Esperstedt is closely related geographically and in terms of ancestry to later Únětice samples further complicates the assumption that Únětice is a mixture of Bell Beakers and Corded Ware, being rather an admixture of incoming Bell Beakers with post-Yamnaya vanguard settlers who admixed with Corded Ware (see more on the expansion of Yamnaya ancestry). In other words, Únětice is rather an admixture of Yamnaya+EEF with Yamnaya+(CWC+EEF).

Y-chromosome haplogroups of samples from Catacomb, Poltavka, Balkan EBA, and Bell Beaker, as well as neighbouring groups. See full maps.

On Ukraine_Eneolithic I6561

If the bottlenecks are as straightforward as they appear, with a star-like phylogeny of R1a-M417 starting with the Pre-Corded Ware expansion, then what is happening with the Alexandria sample, so precisely radiocarbon dated to ca. 4045-3974 BC? The reported hg. R1a-M417 was fully compatible, while R1a-Z645 could be compatible with its date, but the few positive SNPs I got in my analysis point indeed to a potential subclade of R1a-Z94, and I trust more experienced hobbyists in this ‘art’ of ascertaining the SNPs of ancient samples, and they report hg. R1a-Z93 (Z95+, Y26+, Y2-).

Seeing how Y-DNA bottlenecks worked in Yamnaya-Afanasievo and in Corded Ware and related groups, and if this sample really is so deep within R1a-Z93 in a region that should be more strongly affected by the known Neolithic Y-chromosome bottlenecks and forest-steppe ecotone, someone from the lab responsible for this sample should check its date once again, before more people keep chasing their tails with an individual that (based on its derived SNPs’ TMRCA) might actually be dated to the Bronze Age, where it could make much more sense in terms of ancestry and position in the PCA.

EDIT (14 SEP 2019): … and with the fact that he is the first individual to show the genetic adaptation for lactase persistence (I3910-T), which is only found later among Bell Beakers, and much later in Sintashta and related Steppe_MLBA peoples (see comments below).

This is also evidenced by the other Ukraine_Eneolithic (likely a late Yamnaya) sample of hg. R1b-Z2103 from Dereivka (ca. 2800 BC) and who – despite being in a similar territory 1,000 years later – shows a wholly diluted Yamnaya ancestry under typically European HG ancestry, even more so than other late Sredni Stog samples from Dereivka of ca. 3600-3400 BC, suggesting a decrease in Steppe ancestry rather than an increase – which is supposedly what should be expected based on the ancestry from Alexandria…

Like the reported Chalcolithic individual of Hajji Firuz who showed an apparently incompatible subclade and Yamnaya ancestry at least some 1,000 years before it should, and turned out to be from the Iron Age (see below), this may be another case of wrong radiocarbon dating.

NOTE. It would be interesting, if this turns out to be another Hajji Firuz-like error, to check how well different ancestry models worked in whose hands exactly, and if anyone actually pointed out that this sample was derived, and not ancestral, to many different samples that were used in combination with it. It would also be a great control to check if those still supporting a Sredni Stog origin for PIE would shift their preference even more to the north or west, depending on where the first “true” R1a-M417 samples popped up. Such a finding now could be thus a great tool to discover whether haplogroup-based bias plays a role in ancestry magic as related to the Indo-European question, i.e. if it really is about “pure statistics”, or there is something else to it…

II.1. R1b-L51-rich Bell Beakers

The overwhelming majority of R1b-L51 lineages in Radovesice during the Bell Beaker period, just after the sampled Corded Ware individuals from the same site, further strengthen the hypothesis of an almost full replacement of R1a-M417 lineages from Central Europe up to southern Scandinavia after the arrival of Bell Beakers.

Yet another R1b-L151* sample has popped up in Central Europe, in the individual classified as Bilina_BA (ca. 2200-800 BC), which clusters with Bell Beakers from Bohemia, with the outlier from Turlojiškė, and with Early Slavs, suggesting once again that a group of central-east European Beakers represented the Pre-Proto-Balto-Slavic community before their spread and admixture events to the east.

The available ancient distribution of R1b-L51*, R1b-L52* or R1b-L151* is getting thus closer to the most likely origin of R1b-L51 in the expansion of East Bell Beakers, who trace their paternal ancestors to Yamnaya settlers from the Carpathian Basin:

NOTE. Some of these are from other sources, and some are samples I have checked in a hurry, so I may have missed some derived SNPs. If you send me a corrected SNP call to dismiss one of these, or more ‘archaic’ samples, I’ll correct the map accordingly. See also maps of modern distributionof R1b-M269 subclades.

r1b-l51-ancient-europe
Distribution of ‘archaic’ R1b-L51 subclades in ancient samples, overlaid over a map of Yamnaya and Bell Beaker migrations. In blue, Yamnaya Pre-L51 from Lopatino (not shown) and R1b-L52* from BBC Augsburg. In violet, R1b-L51 (xP312,xU106) from BBC Prague and Poland. In maroon, hg. R1b-L151* from BBC Hungary, BA Bohemia, and (not shown) a potential sample from BBC at Mondelange, which is certainly xU106, maybe xP312. Interestingly, the earliest sample of hg. R1b-U106 (a lineage more proper of northern Europe) has been found in a Bell Beaker from Radovesice (ca. 2350 BC), between two of these ‘archaic’ R1b-L51 samples; and a sample possibly of hg. R1b-ZZ11+ (ancestral to DF27 and U152) was found in a Bell Beaker from Quedlinburg, Germany (ca. 2290 BC), to the north-west of Bohemia. The oldest R1b-U152 are logically from Central Europe, too.

III. Proto-Indo-Iranian

Before the emergence of Proto-Indo-Iranian, it seems that Pre-Proto-Indo-Iranian-speaking Poltavka groups were subjected to pressure from Central_Steppe_EMBA-related peoples coming from the (south-?)east, such as those found sampled from Mereke_BA. Their ‘kurgan’ culture was dated correctly to approximately the same date as Poltavka materials, but their ancestry and hg. N2(pre-N2a) – also found in a previous sample from Botai – point to their intrusive nature, and thus to difficulties in the Pre-Proto-Indo-Iranian community to keep control over the previous East Yamnaya territory in the Don-Volga-Ural steppes.

We know that the region does not show genetic continuity with a previous period (or was not under this ‘eastern’ pressure) because of an Eastern Yamnaya sample from the same site (ca. 3100 BC) showing typical Yamnaya ancestry. Before Yamnaya, it is likely that Pre-Yamnaya ancestry formed through admixture of EHG-like Khvalynsk with a North Caspian steppe population similar to the Steppe_Eneolithic samples from the North Caucasus Piedmont (see Anthony 2019), so we can also rule out some intermittent presence of a Botai/Kelteminar-like population in the region during the Khvalynsk period.

It is very likely, then, that this competition for the same territory – coupled with the known harsher climate of the late 3rd millennium BC – led Poltavka herders to their known joint venture with Abashevo chiefs in the formation of the Sintashta-Potapovka-Filatovka community of fortified settlements. Supporting these intense contacts of Poltavka herders with Central Asian populations, late ‘outliers’ from the Volga-Ural region show admixture with typical Central_Steppe_MLBA populations: one in Potapovka (ca. 2220 BC), of hg. R1b-Z2103; and four in the Sintashta_MLBA_o1 cluster (ca. 2050-1650 BC), with two samples of hg. R1b-L23 (one R1b-Z2109), one Q1b-L56(xL53), one Q1b-Y6798.

central-steppe-pastoralists
Outlier analysis reveals ancient contacts between sites. We plot the average of principal component 1 (x axis) and principal component 2 (y axis) for the West Eurasian and All Eurasian PCA plots (…). In the Middle to Late Bronze Age Steppe, we observe, in addition to the Western_Steppe_MLBA and Central_Steppe_MLBA clusters (indistinguishable in this projection), outliers admixed with other ancestries. The BMAC-related admixture in Kazakhstan documents northward gene flow onto the Steppe and confirms the Inner Asian Mountain Corridor as a conduit for movement of people.

Similar to how the Sintashta_MLBA_o2 cluster shows an admixture with central steppe populations and hg. R1a-Z645, the WSHG ancestry in those outliers from the o1 cluster of typically (or potentially) Yamnaya lineages show that Poltavka-like herders survived well after centuries of Abashevo-Poltavka coexistence and admixture events, supporting the formation of a Proto-Indo-Iranian community from the local language as pronounced by the incomers, who dominated as elites over the fortified settlements.

The Proto-Indo-Iranian community likely formed thus in situ in the Don-Volga-Ural region, from the admixture of locals of Yamnaya ancestry with incomers of Corded Ware ancestry – represented by the ca. 67% Yamnaya-like ancestry and ca. 33% ancestry from the European cline. Their community formed thus ca. 1,000 years later than the expansion of Late PIE ca. 3500 BC, and expanded (some 500 years after that) a full-fledged Proto-Indo-Iranian language with the Srubna-Andronovo horizon, further admixing with ca. 9% of Central_Steppe_EMBA (WSHG-related) ancestry in their migration through Central Asia, as reported in the paper.

IV. Armenian

The sample from Hajji Firuz, of hg. R1b-Z2103 (xPF331), has been – as expected – re-dated to the Iron Age (ca. 1193-1019 BC), hence it may offer – together with the samples from the Levant and their Aegean-like ancestry rapidly diluted among local populations – yet another proof of how the Late Bronze Age upheaval in Europe was the cause of the Armenian migration to the Armenoid homeland, where they thrived under the strong influence from Hurro-Urartian.

middle-east-armenia-y-dna
Y-chromosome haplogroups of the Middle East and neighbouring groups during the Late Bronze Age / Iron Age. See full maps.

Indus Valley Civilization and Dravidian

A surprise came from the analysis reported by Shinde et al. (2019) of an Iran_N-related IVC ancestry which may have split earlier than 10000 BC from a source common to Iran hunter-gatherers of the Belt Cave.

For the controversial Elamo-Dravidian hypothesis of the Muscovite school, this difference in ancestry between both groups (IVC and Iran Neolithic) seems to be a death blow, if population genomics was even needed for that. Nevertheless, I guess that a full rejection of a recent connection will come down to more recent and subtle population movements in the area.

EDIT (12 SEP): Apparently, Iosif Lazaridis is not so sure about this deep splitting of ‘lineages’ as shown in the paper, so we may be talking about different contributions of AME+ANE/ENA, which means the Elamo-Dravidian game is afoot; at least in genomics:

I shared the idea that the Indus Valley Civilization was linked to the Proto-Dravidian community, so I’m inclined to support this statement by Narasimhan, Patterson, et al. (2019), even if based only on modern samples and a few ancient ones:

The strong correlation between ASI ancestry and present-day Dravidian languages suggests that the ASI, which we have shown formed as groups with ancestry typical of the Indus Periphery Cline moved south and east after the decline of the IVC to mix with groups with more AASI ancestry, most likely spoke an early Dravidian language.

india-steppe-indus-valley-andamanese-ancestry
Natural neighbour interpolation of qpAdm results – Maximum A Posteriori Estimate from the Hierarchical Model (estimates used in the Narasimhan, Patterson et al. 2019 figures) for Central_Steppe_MLBA-related (left), Indus_Periphery_West-related (center) and Andamanese_Hunter-Gatherer-related ancestry (right) among sampled modern Indian populations. In blue, peoples of IE language; in red, Dravidian; in pink, Tibeto-Burman; in black, unclassified. See full image.

I am wary of this sort of simplistic correlation with modern speakers, because we have seen what happened with the wrong assumptions about modern Balto-Slavic and Finno-Ugric speakers and their genetic profile (see e.g. here or here). In fact, I just can’t differentiate as well as those with deep knowledge in South Asian history the social stratification of the different tribal groups – with their endogamous rules under the varna and jati systems – in the ancestry maps of modern India. The pattern of ancestry and language distribution combined with the findings of ancient populations seem in principle straightforward, though.

Conclusion

The message to take home from Shinde et al. (2019) is that genomic data is fully at odds with the Anatolian homeland hypothesis – including the latest model by Heggarty (2014)* – whose relevance is still overvalued today, probably due in part to the shift of OIT proponents to more reasonable Out-of-Iran models, apparently more fashionable as a vector of Indo-Aryan languages than Eurasian steppe pastoralists?
*The authors listed this model erroneously as Heggarty (2019).

The paper seems to play with the occasional reference to Corded Ware as a vector of expansion of Indo-European languages, even after accepting the role of Yamnaya as the most evident population expanding Late PIE to western Europe – and the different ancestry that spread with Indo-Iranian to South Asia 1,000 years later. However, the most cringe-worthy aspect is the sole citation of the debunked, pseudoscientific glottochronological method used by Ringe, Warnow, and Taylor (2002) to support the so-called “steppe homeland”, a paper and dialectal scheme which keeps being referenced in papers of the Reich Lab, probably as a consequence of its use in Anthony (2007).

On the other hand, these are the equivalent simplistic comments in Narasimhan, Patterson et al. (2019):

The Steppe ancestry in South Asia has the same profile as that in Bronze Age Eastern Europe, tracking a movement of people that affected both regions and that likely spread the unique features shared between Indo-Iranian and Balto-Slavic languages. (…), which despite their vast geographic separation share the “satem” innovation and “ruki” sound laws.

mallory-adams-tree
Indo-European dialectal relationships, from Mallory and Adams (2006).

The only academic closely related to linguistics from the list of authors, as far as I know, is James P. Mallory, who has supported a North-West Indo-European dialect (including Balto-Slavic) for a long time – recently associating its expansion with Bell Beakers – opposed thus to a Graeco-Aryan group which shared certain innovations, “Satemization” not being one of them. Not that anyone needs to be a linguist to dismiss any similarities between Balto-Slavic and Indo-Iranian beyond this phonetic trend, mind you.

Even Anthony (2019) supports now R1b-rich Pre-Yamnaya and Yamnaya communities from the Don-Volga region expanding Middle and Late Proto-Indo-European dialects.

So how does the underlying Corded Ware ancestry of eastern Europe (where Pre-Balto-Slavs eventually spread to from Bell Beaker-derived groups) and of the highly admixed (“cosmopolitan”, according to the authors) Sintashta-Potapovka-Filatovka in the east relate to the similar-but-different phonetic trends of two unrelated IE dialects?

If only there was a language substrate that could (as Shinde et al. put it) “elegantly” explain this similar phonetic evolution, solving at the same time the question of the expansion of Uralic languages and their strong linguistic contacts with steppe peoples. Say, Eneolithic populations of mainly hunter-fisher-gatherers from the North Pontic forest-steppes with a stronger connection to metalworking

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

    Munda admixture happened probably during the ANI-ASI mixture

    language-tree-munda

    Preprint The genetic legacy of continental scale admixture in Indian Austroasiatic speakers, by Tätte et al. bioRxiv (2018).

    Interesting excerpts:

    Studies analysing mtDNA and Y chromosome markers have revealed a sex-specific admixture pattern of admixture of Southeast and South Asian ancestry components for Munda speakers. While close to 100% of mtDNA lineages present in Mundas match those in other Indian populations, around 65% of their paternal genetic heritage is more closely related to Southeast Asian than South Asian variation. Such a contrasting distribution of maternal and paternal lineages among the Munda speakers is a classic example of ‘father tongue hypothesis’. However, the temporality of this expansion is contentious. Based on Y-STR data the coalescent time of Indian O2a-M95 haplogroup was estimated to be >10 KYA. Recently, the reconstructed phylogeny of 8.8 Mb region of Y chromosome data showed that Indian O2a-M95 lineages coalesce within a clade nested within East/Southeast Asian within the last ~5-7 KYA. This date estimate sets the upper boundary for the main episode of gene flow of Y chromosomes from Southeast Asia to India.

    munda-pca
    Supplementary Figure S4. First two components of principal component analysis (PCA). Individuals and population medians (circles) are marked with abbreviations from population names. Different colours represent populations from different geographic areas and/or linguistic groups as shown on the legend on the right. For the full names of populations see Supplementary Table S1. PCA was performed using software EIGENSOFT 6.1.42 on the whole filtered dataset (1072 individuals), previously LD pruned as described in the title of Supplementary Figure S1. The first two principal components describe 5.13% and 2.57% of total variance.

    Admixture proportions suggest a novel scenario

    Regardless of which West Asian population we used, we found that Munda speakers can be described on average as a mixture of ~19% Southeast Asian, 15% West Asian and 66% Onge (South Asian) components. Alternatively, the West and South Asian components of Munda could be modelled using a single South Asian population (Paniya), accounting on average to 77% of the Munda genome. When rescaling the West and South Asian (Onge) components to 1 to explore the Munda genetic composition prior to the introduction of the Southeast Asian component, we note that the West Asian component is lower (~19%) in Munda compared to Paniya (27%) (Supplementary Table S4: *Average_Lao=0). Consistently with qpGraph analyses in Narasimhan et al. (2018), this may point to an initial admixture of a Southeast Asian substrate with a South Asian substrate free of any West Asian component, followed by the encounter of the resulting admixed population with a Paniya-like population. Such a scenario would imply an inverse relationship between the Southeast and West Asian relative proportions in Munda or, in other words, the increase of Southeast Asian component should cause a greater reduction of the West Asian compared to the reduction in the South Asian component in Munda.

    admixture-munda-india
    The distribution of genetic components (K=13) based on the global ADMIXTURE analysis (Supplementary Figure S1, S2, S3) for a subset of populations on a map of South and Southeast Asia. The circular legend in the bottom left corner shows the ancestral components corresponding to the colours on pie charts. The sector sizes correspond to population median.

    Dating the admixture event

    In this study, we have replicated a result previously reported in Chaubey et al. (2011)7 that the Mundas lack one ancestral component (k2) that is characteristic to Indian Indo-European and Dravidian speaking populations. If this component came to India through one of the Indo-Aryan migrations then it would be fair to presume that the Munda admixture happened before this component reached India or at least before it spread all over the country. However, the admixture time computed here, falls in the exact same timeframe as the ANI-ASI mixture has been estimated to have happened in India through which the k2 component probably spread. Therefore, we propose that if the Munda admixture happened at the same time, it is possible for it to have happened in the eastern part of the country, east of Bangladesh, and later when populations from East Asia moved to the area, the Mundas migrated towards central India. Such a scenario, which may be further clarified by ancient DNA analyses, seems to be further supported by the fact that Mundas harbor a smaller fraction of West Asian ancestry compared to contemporary Paniya (Supplementary Table S4) and cannot therefore be seen as a simple admixture product of Southern Indian populations with incoming Southeast Asian ancestries.

    namazga-expansion-south-asia
    Image from Damgaard et al. (2018). A summary of the four qpAdm models fitted for South Asian populations. For each modern South Asian population. we fit different models with qpAdm to explain their ancestry composition using ancient groups and present the f irst model that we could not reject in the following priority order: 1. Namazga_CA + Onge, 2. Namazga_CA + Onge + Late Bronze Age Steppe, 3. Namazga_CA + Onge + Xiongnu_lA (East Asian proxy). and 4. Turkmenistan_lA + Xiongnu_lA. Xiongnu_lA were used here to represent East Asian ancestry. We observe that while South Asian Dravidian speakers can be modeled as a mixture of Onge and Namazga_CA. an additional source related to Late Bronze Age steppe groups is required for IE speakers. In Tibeto-Burman and Austro-Asiatic speakers. an East Asian rather than a Steppe_MLBA source is required

    Linguistics and genome-wide data

    (…) by and large, the linguistic classification justifies itself but Kharia and Juang do not fit in this simplification perfectly.

    Once again, with the current level of detail in genetic studies, there is often no clear dialectal division possible for certain groups without fine-scale population studies, and the help from linguistics and archaeology.

    Featured image from open access paper by Chaubey et al. (2011).

    Related

    Modelling of prehistoric dispersal of rice varieties in India point to a north-western origin

    rice-dispersal

    New paper (behind paywall), A tale of two rice varieties: Modelling the prehistoric dispersals of japonica and proto-indica rices, by Silva et al., The Holocene (2018).

    Interesting excerpts (emphasis mine):

    Materials

    Our empirical evidence comes from the Rice Archaeological Database (RAD). The first version of this database was used for a synthesis of rice dispersal by Fuller et al. (2010), a slightly expanded dataset (version 1.1) was used to model the dispersal of rice, land area under wet rice cultivation and associated methane emissions from 5000–1000 BP (Fuller et al., 2011). The present dataset (version 2) was used in a previous analysis of the origins of rice domestication (Silva et al., 2015). The database records sites and chronological phases within sites where rice has been reported, including whether rice was identified from plant macroremains, phytoliths or impressions in ceramics. Ages are recorded as the start and end date of each phase, and a median age of the phase is then used for analysis. Dating is based on radiocarbon evidence (…)

    Modelling framework

    Our approach expands on previous efforts to model the geographical origins, and subsequent spread, of japonica rice (Silva et al., 2015). The methodology is based on the explicit modelling of dispersal hypotheses using the Fast Marching algorithm, which computes the cost-distance of an expanding front at each point of a discrete lattice or raster from the source(s) of diffusion (Sethian, 1996; Silva and Steele, 2012, 2014). Sites in the RAD database are then queried for their cost-distance, the distance from the source(s) of dispersal along the cost-surface that represents the hypothesis being modelled (see Connolly and Lake, 2006; Douglas, 1994; Silva et al., 2015; Silva and Steele, 2014 for more on this approach) and, together with the site’s dating, used for regression analysis. (…)

    india-japonica-rice
    Predicted arrival times of the non-shattering rice variety (japonica or the hybrid indica) across southern Asia based on best-fitting model H2. Included are also sites with known presence of non-shattering spikelet bases (see text).

    Model and results

    The ‘Inner Asia Mountain Corridor’ hypothesis (H2) therefore predicts japonica rice to arrive first in northwest India via a route that starts in the Yellow river valley, travels west via the well-known Hexi corridor, then just south of the Inner Asian Mountains and thence to India.

    The results also show that the addition of the Inner Asia Mountain Corridor significantly improves the model’s fit to the data, particularly model H2 where rice is introduced to the Indian subcontinent exclusively via a trade route that circumvents the Tibetan plateau. This agrees with independent archaeological evidence that sees millets spread westwards along this corridor perhaps as early as 3000 BC (e.g. Boivin et al., 2012; Kohler-Schneider and Canepelle, 2009; Rassamakin, 1999) and certainly by 2500–2000 BC (Frachetti et al., 2010; Spengler 2015; Stevens et al., 2016), that is, in the same time frame as that predicted for rice in model H2. The arrival of western livestock (sheep, cattle) into central China, 2500–2000 BC (Fuller et al., 2011; Yuan and Campbell, 2009), and wheat, ca. 2000 BC (Betts et al., 2014; Flad et al., 2010; Stevens et al., 2016; Zhao, 2015), add evidence for the role of the Inner Asia Mountain Corridor for domesticated species dispersal in this period.

    Conclusion

    Through a combination of explicit spatial modelling and simulation, we have demonstrated the high likelihood that dispersal of rice via traders in Central Asia introduced japonica rice into South Asia. Only slightly less likely is a combination of introduction via two routes including a Central Asia to Pakistan/northwestern India route as well as introduction to northeastern India directly from China/Myanmar. However, there is a very low probability that current archaeological evidence for rice fits with a single introduction of japonica into India via the northeast. We have also simulated the minimum amount of archaeobotanical sampling from the Neolithic (to Bronze Age) period in the regions of northeastern India and Myanmar that will be necessary to strengthen support for the combined introduction (model H3) or a single Central Asian introduction (model H2).

    Related

    “Steppe people seem not to have penetrated South Asia”

    indo-iranian-sintashta-uralic-migrations

    Open access structured abstract for The first horse herders and the impact of early Bronze Age steppe expansions into Asia from Damgaard et al. Science (2018) 360(6396):eaar7711.

    Abstract (emphasis mine):

    The Eurasian steppes reach from the Ukraine in Europe to Mongolia and China. Over the past 5000 years, these flat grasslands were thought to be the route for the ebb and flow of migrant humans, their horses, and their languages. de Barros Damgaard et al. probed whole-genome sequences from the remains of 74 individuals found across this region. Although there is evidence for migration into Europe from the steppes, the details of human movements are complex and involve independent acquisitions of horse cultures. Furthermore, it appears that the Indo-European Hittite language derived from Anatolia, not the steppes. The steppe people seem not to have penetrated South Asia. Genetic evidence indicates an independent history involving western Eurasian admixture into ancient South Asian peoples.

    INTRODUCTION
    According to the commonly accepted “steppe hypothesis,” the initial spread of Indo-European (IE) languages into both Europe and Asia took place with migrations of Early Bronze Age Yamnaya pastoralists from the Pontic-Caspian steppe. This is believed to have been enabled by horse domestication, which revolutionized transport and warfare. Although in Europe there is much support for the steppe hypothesis, the impact of Early Bronze Age Western steppe pastoralists in Asia, including Anatolia and South Asia, remains less well understood, with limited archaeological evidence for their presence. Furthermore, the earliest secure evidence of horse husbandry comes from the Botai culture of Central Asia, whereas direct evidence for Yamnaya equestrianism remains elusive.

    RATIONALE
    We investigated the genetic impact of Early Bronze Age migrations into Asia and interpret our findings in relation to the steppe hypothesis and early spread of IE languages. We generated whole-genome shotgun sequence data (~1 to 25 X average coverage) for 74 ancient individuals from Inner Asia and Anatolia, as well as 41 high-coverage present-day genomes from 17 Central Asian ethnicities.

    damgaard-south-asia
    Model-based admixture proportions for selected ancient and present-day individuals, assuming K = 6, shown with their corresponding geographical locations. Ancient groups are represented by larger admixture plots, with those sequenced in the present work surrounded by black borders and others used for providing context with blue borders. Present-day South Asian groups are represented by smaller admixture plots with dark red borders.

    RESULTS
    We show that the population at Botai associated with the earliest evidence for horse husbandry derived from an ancient hunter-gatherer ancestry previously seen in the Upper Paleolithic Mal’ta (MA1) and was deeply diverged from the Western steppe pastoralists. They form part of a previously undescribed west-to-east cline of Holocene prehistoric steppe genetic ancestry in which Botai, Central Asians, and Baikal groups can be modeled with different amounts of Eastern hunter-gatherer (EHG) and Ancient East Asian genetic ancestry represented by Baikal_EN.

    In Anatolia, Bronze Age samples, including from Hittite speaking settlements associated with the first written evidence of IE languages, show genetic continuity with preceding Anatolian Copper Age (CA) samples and have substantial Caucasian hunter-gatherer (CHG)–related ancestry but no evidence of direct steppe admixture.

    In South Asia, we identified at least two distinct waves of admixture from the west, the first occurring from a source related to the Copper Age Namazga farming culture from the southern edge of the steppe, who exhibit both the Iranian and the EHG components found in many contemporary Pakistani and Indian groups from across the subcontinent. The second came from Late Bronze Age steppe sources, with a genetic impact that is more localized in the north and west.

    CONCLUSION
    Our findings reveal that the early spread of Yamnaya Bronze Age pastoralists had limited genetic impact in Anatolia as well as Central and South Asia. As such, the Asian story of Early Bronze Age expansions differs from that of Europe. Intriguingly, we find that direct descendants of Upper Paleolithic hunter-gatherers of Central Asia, now extinct as a separate lineage, survived well into the Bronze Age. These groups likely engaged in early horse domestication as a prey-route transition from hunting to herding, as otherwise seen for reindeer. Our findings further suggest that West Eurasian ancestry entered South Asia before and after, rather than during, the initial expansion of western steppe pastoralists, with the later event consistent with a Late Bronze Age entry of IE languages into South Asia. Finally, the lack of steppe ancestry in samples from Anatolia indicates that the spread of the earliest branch of IE languages into that region was not associated with a major population migration from the steppe.

    I think the wording of the abstract is weird, but consequent with their samples and results, so probably just clickbait / citebait for Indian journalists and social networks, or maybe a new attempt to ‘show respect for the sensibilities of Indians’ related to the artificially magnified “AIT vs. OIT” controversy, that is only present in India.

    However, everything is possible, since it is brought to you by the same Danish group who proposed the Yamnaya ancestral component™, the CHG = Indo-European (and simultaneously EHG in Maykop = Anatolian??), and now also the CWC/R1a = Indo-European & Volosovo = Uralic

    Here is the reaction of Narasimhan: Narasimhan has deleted the Tweet, it basically questioned the sentence that steppe people did not penetrate South Asia.

    Related

    Origin of horse domestication likely on the North Caspian steppes

    Open access Late Quaternary horses in Eurasia in the face of climate and vegetation change, by Leonardi et al. Science Advances (2008) 4(7):eaar5589.

    Interesting excerpts (emphasis mine):

    Here, we compiled an extensive continental-scale database, consisting of 3070 radiocarbon dates associated to horse paleontological and archeological finds across the whole of Eurasia, that has been analyzed in association with coarse-scale paleoclimatic reconstructions. We further collected the number of identified specimens (NISP) frequency data for horses versus other ungulates in 1120 archeological layers in Europe (…) This ma.ssive amount of data allowed us to track,with unprecedented details, how the geographic distribution of the species changed through time

    Geographic range through time

    For most analyses, the data have been divided into climatic periods: pre-LGM(older than 27 ka B.P.), LGM(27 to 18 ka B.P.), Late Glacial (18 to 11.7 ka B.P.), Preboreal (11.7 to 10.6 ka B.P.), Boreal (10.6 to 9.1 ka B.P.), Early Atlantic (9.1 to 7.5 ka B.P.), Late Atlantic (7.5 to 5.5 ka B.P.), and Recent (younger than 5.5 ka B.P.) (Fig. 1, A and B). The spatial and temporal distribution of horse remains compiled in our database reveals a strong imbalance in Eurasia (Fig. 1, A and B).

    We found a common trend in both regions for a high number of occurrences at the end of the Pleistocene (with a decrease during the LGM, only visible in Europe), followed by a drastic reduction in the Early and Middle Holocene, and a relative increase toward more recent times. These included both the Early Atlantic in Europe, which started ~9.1 ka B.P., and the time range after 5.5 ka B.P. for Asia. The horse fossil record appears ubiquitous throughout Europe in the Late Pleistocene, while in the Early and Middle Holocene the finds are concentrated in central-western Europe and Iberia. From 7.5 ka B.P., the number of finds increases markedly, and the geographical distribution extends toward the east and southeast.

    horse-distribution-climate
    Horse occurrences through time. (A) Horse occurrences through time. Histograms showing the number of horse observations in Europe (left panel) and Asia (right panel) for each time bin (top) and for climatic period (bottom). Only time bins with more than 10 observations (black horizontal line) have been considered for the SDM analyses. From 22 ka B.P. backward (gray vertical line), time bins cover 2 ka following the available paleoclimatic reconstructions. The central map shows the boundaries considered while defining European and Asian regions, with the black line representing the Urals. The zoomed area shows the geographical resolution of the climatic reconstructions, with each pixel representing a grid cell. (B) Geographic distribution of horse occurrences. Maps showing horse occurrences for each climatic period in Europe (left) and Asia (right).

    Different Asian and European niches

    This analysis revealed that, in both continents, horses occupied only a portion of the climatic space available. The range covered by random locations shows that the paleoecological conditions present in Europe were only a subset of those found in Asia. However, European horses occupied a much wider climatic space than in Asia, with only limited overlap between the two ranges.

    Horses conquered temperate environments from a European source

    There is no evidence of climatic barriers between those two populations through time because the forecasts from Europe and Asia always overlap in central Eurasia, except 5 ka B.P. (figs. S3 and S4). An alternative explanation is the role of the Urals as a potential constraint for the dispersal of horses between Europe and north central Asia.

    climatic-suitability-horses
    Climatic suitability. (A) Cumulative climatic suitability for the past 44 ka based on simulation on the European (left), Eurasian (middle), and Asian (right) data sets. To correct for sampling bias in the Eurasian data set, for each time slice, all estimates and projections for Eurasia are performed considering 100 random resampling of European occurrences in the same number as Asian occurrences. The darker the colors, themore stable the climatic suitability for horses (climatic niche = p-Hor) through time. (B) Projection of climatic suitability across Eurasia in different climatic periods based on occurrences in Europe (left), Eurasia (middle), and Asia (right). Because of the scarcity of data available for Asia, no models for the Holocene have been possible for both Asia and Eurasia, with the exception of 5 and 3 ka B.P. (both included in the “Recent” period).

    Climatic and habitat association patterns for horses in Europe support increasing habitat fragmentation

    The decrease of horse remains in Europe is not characterized by a geographic reduction in the overall extent of the area occupied by the species but in a drop of frequencies in a geographic extent that does not vary much between the Late Glacial and the Early Atlantic (Figs. 1B and 4B). This pattern is more likely to result from habitat fragmentation than from a geographic shift in the climatic range suitable for the species, as observed for many animals during the LGM (23).

    In the whole period ranging from the Preboreal (11.7 to 10.6 ka B.P.) to the Late Atlantic (7.5 to 5.5 ka B.P.), the total amount of land space most and likely suitable to horses is wider than in the Late Glacial, and only between 8 to 7 ka ago the European range appears patchy and fragmented (Fig. 4C). When comparing each of four successive time bins during the Holocene (8, 7, 6, and 5 ka B.P., respectively) (Fig. 4E), the difference in successive p-Hor values in Europe shows that the suitability for the species in Iberia, northeastern France, Italy, the Balkans, and eastern Europe steadily increased, while in Central Europe strong differences can be observed between neighboring regions.

    horse-europe-asia
    Analyses of the European data set and biomefrequency. (A) Distribution through time of the frequency of horse remains in Europe calculated as NISP of horses versus other ungulates. (B) Density of horse remains through time in Europe, calculated as NISP of horses versus other ungulates. The numbers at the bottom of each bar represent the number of observations falling in each class, from 0 to >5%. (C) Climatic suitability for horses in Europe between 10 and 3 ka B.P. (D) Climatic suitability per time period. Percentage of land cells in Europe with a value of suitability for horses (p-Hor) > 0.5 and p-Hor > 0.8. (E) Holocene climatic amelioration. Difference in p-Hor in Europe comparing five successive time bins during the Holocene: 9, 8, 7, 6, and 5 ka B.P. Eachmap shows the difference in themore recent distribution compared to the previous one. (F) Environmental reconstructions in themacro area surrounding horse finds in Europe (left) and Asia (right) per climatic period. The lighter the color, the less forested is the region. The numbers at the bottom of the bars show the number of occurrences in closed environments over all the observations. The dotted line represents a frequency of 0.5.

    Taken at face value, this pattern would suggest that horses were not restricted to open environments but could equally well inhabit closed, forested environments, as previously suggested (18). However, as others recently emphasized (19), the faunal associations inHolocene sites from Europe suggest a different pattern. The PCAs based on faunal assemblages (figs. S1 and S2) separate on the second principal component sites characterized by ungulates associated to forested areas (red deer, wild boar, and roe deer) and all other animals, associated to semi-open and open environments, including horses for most records.

    Together, the contrast between the reconstructed microscale and macroscale vegetable coverage in Europe, the increase of horses in mainly forested macroregions, and the spatial pattern of extinction suggest that, from the beginning of the Holocene, the suitable environment became more and more patchy, with open areas increasingly fragmented by forests, where wild populations of horses could have survived in isolation until one or several waves of arrivals of domestic horses, leading to either local admixture or a full replacement of the preexisting local populations.

    Conclusion

    Our data show that, up to 5.5 ka ago, horse finds do not show association with species characteristic of forested areas such as wild boar and roe deer. We infer that the open and semi-open habitats occupied by horses on a narrow geographic scale appear less and less frequent at a macroenvironmental scale, supporting the possibility of increasing fragmentation of open habitats. This event is also likely to have led to an intensification of genetic isolation for the remaining horse populations, a pattern that still needs to be tested on genomic data.

    The suitability of both Iberia and eastern Europe appears constant throughout the entire post-LGM period, in line with these regions being hotspots of genetic diversity and, possibly, the refugia sources for the recolonization of the continent (11). While the Pontic-Caspian region appears not suitable for European horses around the time when horses where first domesticated some 5.5 ka ago (6), part of this region appears suitable for the Asian horses (with the Caspian Sea as the westernmost boundary). This may suggest that horse domestication started from a population background related to an Asian ancestry and that the further spread of the domesticated horses in Europe involved either adaptation to novel niches (possibly through selective breeding) or the application of domestication techniques to local horse populations pre-adapted to these environmental conditions. Testing this scenario will require mapping the genetic structure of the Eurasian horse population within the fifth to third millennium BCE.

    Some remarks

    Cultural-anthropological research and archaeological remains (see here), genetics (see here and here), and now also thorough palaeoclimatic and archaeological models point to the North Caspian region, settled by the Khvalynsk culture, as the most likely earliest origin of horse domestication. The paper also supports the favorable conditions of western Europe up to Iberia for the introduction of a horse-riding culture.

    I intended to write a post about the myth of Corded Ware horse riders, but for the moment I haven’t found the time. Not that Corded Ware pastoralists didn’t have horses, or could not ride them: they were a highly mobile culture of pastoralists stemming from eastern Poland / western Ukraine, so they must have known horses, like many other European cultures of the late 4th / early 3rd millennium influenced by expanding Yamna settlers. But it just cannot be said to have formed an essential part of their culture, as it was for Khvalynsk-Novodanilovka, and especially Yamna and later East Bell Beaker, Sintashta, etc.

    A mere look at these maps suffices to assess the limited role of the horse in north-eastern Europe, the only region where groups of late Corded Ware-derived cultures survived the expansion of Yamna, and especially East Bell Beakers after ca. 2500 BC, which transformed Western, Northern, and Central Europe, and even East Europe reaching the modern Baltic countries, Belarus, and Romania. Even Trzciniec was born out of the influence from expanding Bell Beakers into earlier Corded Ware territory, although the later (Iron Age) relevance of this culture was probably quite limited.

    As you can imagine, without horses and horse symbolism, horse riding, carts, and intensive cattle-breeding (associated with Yamna and the broad, east-central European grasslands typical of steppe regions), there can be no Proto-Indo-European, whose reconstructed vocabulary is particulary rich in horse-related words, and whose reconstructed culture, society, and religion cannot be understood without the domesticated horse. In forest regions to the north-east and eastern Europe, there was apparently little space for horses, but plenty of room for other ungulates and thus hunting, and indeed Uralic languages

    In the upcoming months we will see R1a-fans associating Proto-Indo-Europeans more and more with wool, and sheep, and corded ware, and forest regions, until the proposed homeland shifts to the Baltic and Finland, instead of dat boring horse-riding people of the steppes…No wait, it’s already happening.

    NOTE. Also open access is the recent Horse Y chromosome assembly displays unique evolutionary features and putative stallion fertility genes, by Janečka et al. Nature Communications (2018).

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    South-East Asia samples include shared ancestry with Jōmon

    pca-south-east-asia-jomon

    New paper (behind paywall) The prehistoric peopling of Southeast Asia, by McColl et al. (Science 2018) 361(6397):88-92 from a recent bioRxiv preprint.

    Interesting is this apparently newly reported information including a female sample from the Ikawazu Jōmon of Japan ca. 570 BC (emphasis mine):

    The two oldest samples — Hòabìnhians from Pha Faen, Laos [La368; 7950 with 7795 calendar years before the present (cal B.P.)] and Gua Cha, Malaysia (Ma911; 4415 to 4160 cal B.P.)—henceforth labeled “group 1,” cluster most closely with present-day Önge from the Andaman Islands and away from other East Asian and Southeast-Asian populations (Fig. 2), a pattern that differentiates them from all other ancient samples. We used ADMIXTURE (14) and fastNGSadmix (15) to model ancient genomes as mixtures of latent ancestry components (11). Group 1 individuals differ from the other Southeast Asian ancient samples in containing components shared with the supposed descendants of the Hòabìnhians: the Önge and the Jehai (Peninsular Malaysia), along with groups from India and Papua New Guinea.

    We also find a distinctive relationship between the group 1 samples and the Ikawazu Jōmon of Japan (IK002). Outgroup f3 statistics (11, 16) show that group 1 shares the most genetic drift with all ancient mainland samples and Jōmon (fig. S12 and table S4). All other ancient genomes share more drift with present-day East Asian and Southeast Asian populations than with Jōmon (figs. S13 to S19 and tables S4 to S11). This is apparent in the fastNGSadmix analysis when assuming six ancestral components (K = 6) (fig. S11), where the Jōmon sample contains East Asian components and components found in group 1. To detect populations with genetic affinities to Jōmon, relative to present-day Japanese, we computed D statistics of the form D(Japanese, Jōmon; X, Mbuti), setting X to be different presentday and ancient Southeast Asian individuals (table S22). The strongest signal is seen when X=Ma911 and La368 (group 1 individuals), showing a marginally nonsignificant affinity to Jōmon (11). This signal is not observed with X = Papuans or Önge, suggesting that the Jōmon and Hòabìnhians may share group 1 ancestry (11).

    jomon-japanese-migrations
    Model for plausible migration routes into SEA. This schematic is based on ancestry patterns observed in the ancient genomes. Because we do not have ancient samples to accurately resolve how the ancestors of Jōmon and Japanese populations entered the Japanese archipelago, these migrations are represented by dashed arrows. A mainland component in Indonesia is depicted by the dashed red-green line. Gr, group; Kra, Kradai.

    (…) Finally, the Jōmon individual is best-modeled as a mix between a population related to group 1/Önge and a population related to East Asians (Amis), whereas present-day Japanese can be modeled as a mixture of Jōmon and an additional East Asian component (Fig. 3 and fig. S29)

    Interesting in relation to the oral communication of the SMBE O-03-OS02 Whole genome analysis of the Jomon remain reveals deep lineage of East Eurasian populations by Gakuuhari et al.:

    Post late-Paleolithic hunter-gatherers lived throughout the Japanese archipelago, Jomonese, are thought to be a key to understanding the peopling history in East Asia. Here, we report a whole genome sequence (x1.85) of 2,500-year old female excavated from the Ikawazu shell-mound, unearthed typical remains of Jomon culture. The whole genome data places the Jomon as a lineage basal to contemporary and ancient populations of the eastern part of Eurasian continent, and supports the closest relationship with the modern Hokkaido Ainu. The results of ADMIXTURE show the Jomon ancestry is prevalent in present-day Nivkh, Ulchi, and people in the main-island Japan. By including the Jomon genome into phylogenetic trees, ancient lineages of the Kusunda and the Sherpa/Tibetan, early splitting from the rest of East Asian populations, is emerged. Thus, the Jomon genome gives a new insight in East Asian expansion. The Ikawazu shell-mound site locates on 34,38,43 north latitude, and 137,8, 52 east longitude in the central main-island of the Japanese archipelago, corresponding to a warm and humid monsoon region, which has been thought to be almost impossible to maintain sufficient ancient DNA for genome analysis. Our achievement opens up new possibilities for such geographical regions.

    Related

    Expansion of domesticated goat echoes expansion of early farmers

    goat-neolithic

    New paper (behind paywall) Ancient goat genomes reveal mosaic domestication in the Fertile Crescent, by Daly et al. Science (2018) 361(6397):85-88.

    Interesting excerpts (emphasis mine):

    Thus, our data favor a process of Near Eastern animal domestication that is dispersed in space and time, rather than radiating from a central core (3, 11). This resonates with archaeozoological evidence for disparate early management strategies from early Anatolian, Iranian, and Levantine Neolithic sites (12, 13). Interestingly, our finding of divergent goat genomes within the Neolithic echoes genetic investigation of early farmers. Northwestern Anatolian and Iranian human Neolithic genomes are also divergent (14–16), which suggests the sharing of techniques rather than large-scale migrations of populations across Southwest Asia in the period of early domestication. Several crop plants also show evidence of parallel domestication processes in the region (17).

    PCA affinity (Fig. 2), supported by qpGraph and outgroup f3 analyses, suggests that modern European goats derive from a source close to the western Neolithic; Far Eastern goats derive from early eastern Neolithic domesticates; and African goats have a contribution from the Levant, but in this case with considerable admixture from the other sources (figs. S11, S16, and S17 and tables S26 and 27). The latter may be in part a result of admixture that is discernible in the same analyses extended to ancient genomes within the Fertile Crescent after the Neolithic (figs. S18 and S19 and tables S20, S27, and S31) when the spread of metallurgy and other developments likely resulted in an expansion of inter-regional trade networks and livestock movement.

    goat-middle-east
    Maximumlikelihood phylogeny and geographical distributions of ancient mtDNA haplogroups. (A) A phylogeny placing ancient whole mtDNA sequences in the context of known haplogroups. Symbols denoting individuals are colored by clade membership; shape indicates archaeological period (see key). Unlabeled nodes are modern bezoar and outgroup sequence (Nubian ibex) added for reference.We define haplogroup T as the sister branch to the West Caucasian tur (9). (B and C) Geographical distributions of haplogroups show early highly structured diversity in the Neolithic period (B) followed by collapse of structure in succeeding periods (C).We delineate the tiled maps at 7250 to 6950 BP, a period >bracketing both our earliest Chalcolithic sequence (24, Mianroud) and latest Neolithic (6, Aşağı Pınar). Numbered archaeological sites also include Direkli Cave (8), Abu Ghosh (9), ‘Ain Ghazal (10), and Hovk-1 Cave (11) (table S1) (9).

    Our results imply a domestication process carried out by humans in dispersed, divergent, but communicating communities across the Fertile Crescent who selected animals in early millennia, including for pigmentation, the most visible of domestic traits.

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