Złota a GAC-CWC transitional group…but not the origin of Corded Ware peoples

koszyce-gac-zlota-cwc

Open access Unraveling ancestry, kinship, and violence in a Late Neolithic mass grave, by Schroeder et al. PNAS (2019).

Interesting excerpts of the paper and supplementary materials, about the Złota group variant of Globular Amphora (emphasis mine):

A special case is the so-called Złota group, which emerged around 2,900 BCE in the northern part of the Małopolska Upland and existed until 2,600-2,500 BCE. Originally defined as a separate archaeological “culture” (15), this group is mainly defined by the rather local introduction of a distinct form of burial in the area mentioned. Distinct Złota settlements have not yet been identified. Nonetheless, because of the character of its burial practices and material culture, which both retain many elements of the GAC and yet point forward to the Corded Ware tradition, and because of its geographical location, the Złota group has attracted significant archaeological attention (15, 16).

The Złota group buried their dead in a new, distinct type of funerary structure; so-called niche graves (also called catacomb graves). These structures featured an entrance shaft or pit and, below that, a more or less extensive niche, sometimes connected to the entrance area by a narrow corridor. Local limestone was used to seal off the entrance shaft and to pave the floor of the niche, on which the dead were usually placed along with grave goods. This specific and relatively sophisticated form of burial probably reflects contacts between the northern Małopolska Upland and the steppe and forest-steppe communities further to the east, who also buried their dead in a form of catacomb graves. Individual cases of the use of ochre and of deformation of skulls in Złota burials provide further indications of such a connection (15). At the same time, the Złota niche grave practice also retains central elements of the GAC funerary tradition, such as the frequent practice of multiple burials in one grave, often entailing redeposition and violation of the anatomical order of corpses, and thus differs from the catacomb grave customs found on the steppes which are strongly dominated by single graves. Nonetheless, at Złota group cemeteries single burial graves appear, and even in multiple burial graves the identity of each individual is increasingly emphasized, e.g. by careful deposition of the body and through the personal nature of grave goods (16).

globular-amphorae-corded-ware-zlota-amphorae
Correspondence analysis of amphorae from the Złota-graveyards reveals that there is no typological break between Globular Amphorae and Corded Ware Amphorae, including ‘Strichbündelamphorae’ (after Furholt 2008)

Just like its burial practices, the material culture and grave goods of the Złota group combine elements of the GAC, such as amber ornaments and central parts of the ceramic inventory, with elements also found in the Corded Ware tradition, such as copper ornaments, stone shaft-hole axes, bone and shell ornaments, and other stylistic features of the ceramic inventory. In particular, Złota group ceramic styles have been seen as a clear transitional phenomenon between classical GAC styles and the subsequent Corded Ware ceramics, probably playing a key role in the development of the typical cord decoration patterns that came to define the latter (17).

As briefly summarized above, the Złota group displays a distinct funerary tradition and combination of material culture traits, which give the clear impression of a cultural “transitional situation”. While the group also appears to have had long-distance contacts directed elsewhere (e.g. to Baden communities to the south), it is the combination of Globular Amphora traits, on the one hand, and traits found among late Yamnaya or Catacomb Grave groups to the east as well as the closely related Corded Ware groups that emerged around 2,800 BCE, on the other hand, that is such a striking feature of the Złota group and which makes it interesting when attempting to understand cultural and demographic dynamics in Central and Eastern Europe during the early 3rd millennium BCE.

catacomb-grave-ksiaznice
Catacomb grave no. 2a/06 from Książnice, Złota culture (acc. to Wilk 2013). Image from Włodarczak (2017)

Książnice (site 2, grave 3ZC), Świętokrzyskie province. This burial, a so-called niche grave of the Złota type (with a vertical entrance shaft and perpendicularly situated niche), was excavated in 2006 and contained the remains of 8 individuals, osteologically identified as three adult females and five children, positioned on limestone pavement in the niche part of the grave. Radiocarbon dating of the human remains indicates that the grave dates to 2900-2630 BCE, 95.4% probability (Dataset S1). The grave had an oval entrance shaft with a diameter of 60 cm and depth of 130 cm; the depth of the niche reached to 170 cm (both measured from the modern surface), and it also contained a few animal bones, a few flint artefacts and four ceramic vessels typical of the Złota group. Książnice is located in the western part of the Małopolska Upland, which only has a few Złota group sites but a stronger presence of other, contemporary groups (including variants of the Baden culture).

Wilczyce (site 90, grave 10), Świętokrzyskie province. A rescue excavation in 2001 uncovered a niche grave of the Złota type, which had a round entrance shaft measuring 90 cm in diameter. The grave was some 60-65 cm deep below the modern surface and the bottom of the niche was paved with thin limestone plates, on which remains of three individuals had been placed; two adults, one female and one male, and one child. Four ceramic vessels of Złota group type were deposited in the niche along with the bodies. Wilczyce is located in the Sandomierz Upland, an area with substantial presence of both the Globular Amphora culture and Złota group, as well as the Corded Ware culture from 2800 BCE.

zlota-gac-cwc
Genetic affinities of the Koszyce individuals and other GAC groups (here including Złota) analyzed in this study. (A) Principal component analysis of previously published and newly sequenced ancient individuals. Ancient genomes were projected onto modern reference populations, shown in gray. (B) Ancestry proportions based on supervised ADMIXTURE analysis (K = 3), specifying Western hunter-gatherers, Anatolian Neolithic farmers, and early Bronze Age steppe populations as ancestral source populations. LP, Late Paleolithic; M, Mesolithic; EN, Early Neolithic; MN, Middle Neolithic; LN, Late Neolithic; EBA, Early Bronze Age; PWC, Pitted Ware culture; TRB, Trichterbecherkultur/Funnelbeaker culture; LBK, Linearbandkeramik/Linear Pottery culture; GAC, Globular Amphora culture; Złota, Złota culture. Image modified to outline in red GAC and Złota groups.

To further investigate the ancestry of the Globular Amphora individuals, we performed a supervised ADMIXTURE (6) analysis, specifying typical western European hunter-gatherers (Loschbour), early Neolithic Anatolian farmers (Barcın), and early Bronze Age steppe populations (Yamnaya) as ancestral source populations (Fig. 2B). The results indicate that the Globular Amphora/Złota group individuals harbor ca. 30% western hunter-gatherer and 70% Neolithic farmer ancestry, but lack steppe ancestry. To formally test different admixture models and estimate mixture proportions, we then used qpAdm (7) and find that the Polish Globular Amphora/Złota group individuals can be modeled as a mix of western European hunter-gatherer (17%) and Anatolian Neolithic farmer (83%) ancestry (SI Appendix, Table S2), mirroring the results of previous studies.

zlota-steppe-ancestry-cwc
Table S2. qpADM results. The ancestry of most Globular Amphora/Złota group individuals
can be modelled as a two-way mixture of Mesolithic western hunter-gatherers (WHG), and early Anatolian Neolithic farmers (Barcın). The five individuals from Książnice (Złota group) show evidence for additional gene flow, most likely from an eastern source.

The lack of a direct genetic connection of Corded Ware peoples with the Złota group despite their common “steppe-like traits” – shared with Yamna – reveals, once more, how the few “Yamna-like” traits of Corded Ware do not support a direct connection with Indo-Europeans, and are the result of the expansion of the so-called steppe package all over Europe, and particularly among cultures closely related to the Khvalynsk expansion, and later under the influence of expanding Yamna peoples.

The results from Książnice may support that early Corded Ware peoples were in close contact with GAC peoples in Lesser Poland during the complex period of GAC-Trypillia-CWC interactions, and especially close to the Złota group at the beginning of the 3rd millennium BC. Nevertheless, patrilineal clans of Złota apparently correspond to Globular Amphorae populations, with the only male sample available yet being within haplogroup I2a-L801, prevalent in GAC.

NOTE. The ADMIXTURE of Złota samples in common with GAC samples (and in contrast with the shared Sredni Stog – Corded Ware “steppe ancestry”) makes the possibility of R1a-M417 popping up in the Złota group from now on highly unlikely. If it happened, that would complicate further the available picture of unusually diverse patrilineal clans found among Uralic speakers expanding with early Corded Ware groups, in contrast with the strict patrilineal and patrilocal culture of Indo-Europeans as found in Repin, Yamna and Bell Beakers.

Once again the traditional links between groups hypothesized by archaeologists – like Gimbutas and Kristiansen in this case – are wrong, as is the still fashionable trend in descriptive archaeology, of supporting 1) wide cultural relationships in spite of clear-cut inter-cultural differences (and intra-cultural uniformity kept over long distances by genetically-related groups), 2) peaceful interactions among groups based on few common traits, and 3) regional population continuities despite cultural change. These generalized ideas made some propose a steppe language shared between Pontic-Caspian groups, most of which have been proven to be radically different in culture and genetics.

gimbutas-kurgan-indo-european
The background shading indicates the tree migratory waves proposed by Marija Gimbutas, and personally checked by her in 1995. Image from Tassi et al. (2017).

Furthermore, paternal lines show once again marked bottlenecks in expanding Neolithic cultures, supporting their relevance to follow the ethnolinguistic identity of different cultural groups. The steppe- or EHG-related ancestry (if it is in fact from early Corded Ware peoples) in Książnice was thus probably, as in the case of Trypillia, in the form of exogamy with females of neighbouring groups:

The presence of unrelated females and related males in the grave is interesting because it suggests that the community at Koszyce was organized along patrilineal lines of descent, adding to the mounting evidence that this was the dominant form of social organization among Late Neolithic communities in Central Europe. Usually, patrilineal forms of social organization go hand in hand with female exogamy (i.e., the practice of women marrying outside their social group). Indeed, several studies (11, 12) have shown that patrilocal residence patterns and female exogamy prevailed in several parts of Central Europe during the Late Neolithic. (…) the high diversity of mtDNA lineages, combined with the presence of only a single Y chromosome lineage, is certainly consistent with a patrilocal residence system.

funnelbeaker-trypillia-corded-ware
Map of territorial ranges of Funnel Beaker Culture (and its settlement concentrations in Lesser Poland), local Tripolyan groups and Corded Ware Culture settlements (■) at the turn of the 4th/3rd millennia BC.

Since ancient and modern Uralians show predominantly Corded Ware ancestry, and Proto-Uralic must have been in close contact with Proto-Indo-European for a very long time – given the different layers of influence that can be distinguished between them -, it follows as logical consequence that the North Pontic forest-steppes (immediately to the west of the PIE homeland in the Don-Volga-Ural steppes) is the most likely candidate for the expansion of Proto-Uralic, accompanying the spread of Sredni Stog ancestry and a bottleneck under R1a-M417 lineages.

The early TMRCAs in the 4th millennium BC for R1a-M417 and R1a-Z645 support this interpretation, like the R1a-M417 sample found in Sredni Stog. On the other hand, the resurgence of typical GAC-like ancestry in late Corded Ware groups, with GAC lineages showing late TMRCAs in the 3rd millennium BC, proves the disintegration of Corded Ware all over Europe (except in Textile Ceramics- and Abashevo-related groups) as the culture lost its cohesion and different local patrilineal clans used the opportunity to seize power – similar to how eventually I2a-L621 infiltrated eastern (Finno-Ugrian) groups.

Related

Fulani from Cameroon show ancestry similar to Afroasiatic speakers from East Africa

sahel-region-fulani

Open access African evolutionary history inferred from whole genome sequence data of 44 indigenous African populations, by Fan et al. Genome Biology (2019) 20:82.

Interesting excerpts (emphasis mine):

Introduction

To extend our knowledge of patterns of genomic diversity in Africa, we generated high coverage (> 30×) genome sequencing data from 43 geographically diverse Africans originating from 22 ethnic groups, representing a broad array of ethnic, linguistic, cultural, and geographic diversity (Additional file 1: Table S1). These include a number of populations of anthropological interest that have never previously been characterized for high-coverage genome sequence diversity such as Afroasiatic-speaking El Molo fishermen and Nilo-Saharan-speaking Ogiek hunter-gatherers (Kenya); Afroasiatic-speaking Aari, Agaw, and Amhara agro-pastoralists (Ethiopia); Niger-Congo-speaking Fulani pastoralists (Cameroon); Nilo-Saharan-speaking Kaba (Central African Republic, CAR); and Laka and Bulala (Chad) among others. We integrated this data with 49 whole genome sequences generated as part of the Simons Genome Diversity Project (SGDP) [14] (…)

afroasiatic-samples
Locations of samples included in this study. Each dot is an individual and the color indicates the language classification

Results and discussion

We found that the CRHG populations from central Africa, including the Mbuti from the Demographic Republic of Congo (DRC), Biaka from the CAR, and Baka, Bakola, and Bedzan from Cameroon, also form a basal lineage in the phylogeny. The other two hunter-gatherer populations, Hadza and Sandawe, living in Tanzania, group with populations from eastern Africa (Fig. 2). The two Nilo-Saharan-speaking populations, the Mursi from southern Ethiopia and the Dinka from southern Sudan, group into a single cluster, which is consistent with archeological data indicating that the migration of Nilo-Saharan populations to eastern Africa originated from a source population in southern Sudan in the last 3000 years [4, 23, 24, 25].

phylogenetic-relationship-africans
Phylogenetic relationship of 44 African and 32 west Eurasian populations determined by a neighbor joining analysis assuming no admixture. Here, the dots of each node represent bootstrap values and the color of each branch indicates language usage of each population. Human_AA human ancestral alleles

The Fulani people are traditionally nomadic pastoralists living across a broad geographic range spanning Sudan, the Sahel, Central, and Western Africa. The Fulani in our study, sampled from Cameroon, clustered with the Afroasiatic-speaking populations in East Africa in the phylogenetic analysis, indicating a potential language replacement from Afroasiatic to Niger-Congo in this population (Fig. 2). Prior studies suggest a complex history of the Fulani; analyses of Y chromosome variation suggest a shared ancestry with Nilo-Saharan and Afroasiatic populations [24], whereas mtDNA indicates a West African origin [26]. An analysis based on autosomal markers found traces of West Eurasian-related ancestry in this population [4], which suggests a North African or East African origin (as North and East Africans also have such ancestry likely related to expansions of farmers and herders from the Near East) and is consistent with the presence at moderate frequency of the −13,910T variant associated with lactose tolerance in European populations [15, 16].

Phylogenetic reconstruction of the relationship of African individuals under a model allowing for migration using TREEMIX [27] largely recapitulates the NJ phylogeny with the exception of the Fulani who cluster near neighboring Niger-Congo-speaking populations with whom they have admixed (Additional file 2: Figure S1). Interestingly, TREEMIX analysis indicates evidence for gene flow between the Hadza and the ancestors of the Ju|‘hoan and Khomani San, supporting genetic, linguistic, and archeological evidence that Khoesan-speaking populations may have originated in Eastern Africa [28, 29, 30].

afroasiatic-niger-congo-admixture
ADMIXTURE analysis of 92 African and 62 West Eurasian individuals. Each bar is an individual and colors represent the proportion of inferred ancestry from K ancestral populations. The bottom bar shows the language classification of each individual. With the increasing of K, the populations are largely grouped by their current language usage

About the Fulani, this is what the referenced study of Y‐chromosome variation among 15 Sudanese populations by Hassan et al. (2008), had to say:

  • Haplogroups A-M13 and B-M60 are present at high frequencies in Nilo-Saharan groups except Nubians, with low frequencies in Afro-Asiatic groups although notable frequencies of B-M60 were found in Hausa (15.6%) and Copts (15.2%).
  • Haplogroup E (four different haplotypes) accounts for the majority (34.4%) of the chromosome and is widespread in the Sudan. E-M78 represents 74.5% of haplogroup E, the highest frequencies observed in Masalit and Fur populations. E-M33 (5.2%) is largely confined to Fulani and Hausa, whereas E-M2 is restricted to Hausa. E-M215 was found to occur more in Nilo-Saharan rather than Afro-Asiatic speaking groups.
  • In contrast, haplogroups F-M89, I-M170, J-12f2, and JM172 were found to be more frequent in the Afro-Asiatic speaking groups. J-12f2 and J-M172 represents 94% and 6%, respectively, of haplogroup J with high frequencies among Nubians, Copts, and Arabs.
  • Haplogroup K-M9 is restricted to Hausa and Gaalien with low frequencies and is absent in Nilo-Saharan and Niger-Congo.
  • Haplogroup R-M173 appears to be the most frequent haplogroup in Fulani, and haplogroup R-P25 has the highest frequency in Hausa and Copts and is present at lower frequencies in north, east, and western Sudan.
  • Haplogroups A-M51, A-M23, D-M174, H-M52, L-M11, OM175, and P-M74 were completely absent from the populations analyzed.
fulfulde-fulani-language
Image modified from “Fulfulde Language Family Report” Author: Annette Harrison; Cartographer: Irene Tucker; SIL International 2003.

This is what David Reich will talk about in the seminar Insights into language expansions from ancient DNA:

In this talk, I will describe how the new science of genome-wide ancient DNA can provide insights into past spreads of language and culture. I will discuss five examples: (1) the spread of Indo-European languages to Europe and South Asia in association with Steppe pastoralist ancestry, (2) the spread of Austronesian languages to the open Pacific islands in association with Taiwanese aboriginal-associated ancestry, (3) the spread of Austroasiatic languages through southeast Asia in association with the characteristic ancestry type that is also represented in western Indonesia suggesting that these languages were once widespread there, (4) the spread of Afroasiastic languages through in East Africa as part of the Pastoral Neolithic farming expansion, and (5) the spread of Na-Dene languages in North America in association with Proto-Paleoeskimo ancestry. I will highlight the ways that ancient DNA can meaningfully contribute to our understanding of language expansions—increasing the plausibility of some scenarios while decreasing the plausibility of others—while emphasizing that with genetic data by itself we can never definitively determine what languages ancient people spoke.

EDIT (3 MAY 2019): Apparently, there was not much to take from the talk:

neolithic-pastoralist-africa
Pastoralist Neolithic in Africa, through a pale-green Sahelo-Sudanian steppe corridor. See full map.

This seminar (and maybe some new paper on the Neolithic expansion in Africa) could shed light on population movements that may be related to the spread of Afroasiatic dialects. Until now, it seems that Bantu peoples have been more interesting for linguistics and archaeology, and South and East Africans for anthropology.

Archaeology in Africa appears to be in its infancy, as is population genomics. From the latest publication by Carina Schlebusch, Population migration and adaptation during the African Holocene: A genetic perspective, a chapter from Modern Human Origins and Dispersal (2019):

The process behind the introduction and development of farming in Africa is still unclear. It is not known how many independent invention events there were in the continent and to which extent the various first instances of farming in northern Africa are linked. Based on the archeological record, it was proposed that at least three regions in Africa may have developed agriculture independently: the Sahara/Sahel (around 7 ka), the Ethiopian highlands (7-4 ka), and western Africa (5-3 ka). In addition to these developments, the Nile River Valley is thought to have adopted agriculture (around 7.2 ka), from the Neolithic Revolution in the Middle East (Chapter 12 – Jobling et al. 2014; Chapter 35, 37 – Mitchell and Lane 2013). From these diverse centers of origin, farmers or farming practices spread to the rest of Africa, with domesticate animals reaching the southern tip of Africa ~2 ka and crop farming ~1,8 ka (Mitchell 2002; Huffman 2007)

african-popularion-movements
Schematic representation of possible migration routes related to the expansion of herders and crop farmers during Holocene times. Arrow color indicate source populations; Brown-Eurasian, Green-western African, Blue-eastern African.

Similar to the case in Europe and the 1990s-2000s wrong haplogroup history based on the modern distribution of R1b, R1a, N, or I2, it is possible that neither of the most often mentioned haplogroups linked to the Afroasiatic expansion, E and J, were responsible for its early spread within Africa, despite their widespread distribution in certain modern Afroasiatic-speaking areas. The fact that such assessments include implausible glottochronological dates spanning up to 20,000 years for the parent language, combined with regional language continuities despite archaeological changes, makes them even more suspicious.

Similar to the case with Indo-Europeans and the “steppe ancestry” concept of the 2010s, it may be that the often-looked-for West Eurasian ancestry among Africans is the effect of recent migrations, unrelated to the Afroasiatic expansion. The results of this paper could be offering another sign of how this ancestry may have expanded only quite recently westwards from East Africa through the Sahel, after the Semitic expansion to the south:

1. From approximately 1000 BC, accompanying Nilo-Saharan peoples.

2. From approximately AD 1500, with the different population movements related to the nomadic Fulani:

sahel-nomadic-sedentary
Image from Sahel in West African History – Oxford Research Encyclopedia of African History.
  • Arguably, since the Fulani caste system wasn’t as elaborate in northern Nigeria, eastern Niger, and Cameroon, these specific groups would be a good example of the admixture with eastern populations, based on the (proportionally) huge amount of slaves they dealt with.
  • Similarly, it could be argued that the castes-based social stratification in most other territories (including Sudan) would have helped them keep a genetic make-up similar to their region of origin in terms of ancient lineages, hence similar to Chadic populations from west to east.

Reich’s assertion of the association of the language expansion with the spread of Pastoral Neolithic is still too vague, but – based on previous publications of ancient DNA in Africa and the Levant – I don’t have high hopes for a revolutionary paper in the near future. Without many samples and proper temporal transects, we are stuck with speculations based on modern distributions and scarce historical data.

fula-people-distribution
A distribution map of Fula people. Dark green: a major ethnic group; Medium: significant; Light: minor. Modified from image by Sarah Welch at Wikipedia.

About the potential genetic make-up of Cameroon before the arrival of the Neolithic, from the recent SAA 84th Annual Meeting (Abstracts in PDF):

Lipson, Mark (Harvard Medical School), Mary Prendergast (Harvard University), Isabelle Ribot (Université de Montréal), Carles Lalueza-Fox (Institute of Evolutionary Biology CSIC-UPF) and David Reich (Harvard Medical School)

[253] Ancient Human DNA from Shum Laka (Cameroon) in the Context of African Population History We generated genome-wide DNA data from four people buried at the site of Shum Laka in Cameroon between 8000–3000 years ago. One individual carried the deeply divergent Y chromosome haplogroup A00 found at low frequencies among some present-day Niger-Congo speakers, but the genome-wide ancestry profiles for all four individuals are very different from the majority of West Africans today and instead are more similar to West-Central African hunter-gatherers. Thus, despite the geographic proximity of Shum Laka to the hypothesized birthplace of Bantu languages and the temporal range of our samples bookending the initial Bantu expansion, these individuals are not representative of a Bantu source population. We present a phylogenetic model including Shum Laka that features three major radiations within Africa: one phase early in the history of modern humans, one close to the time of the migration giving rise to non-Africans, and one in the past several thousand years. Present-day West Africans and some East Africans, in addition to Central and Southern African hunter-gatherers, retain ancestry from the first phase, which is therefore still represented throughout the majority of human diversity in Africa today.

Related

Ancient Sardinia hints at Mesolithic spread of R1b-V88, and Western EEF-related expansion of Vasconic

nuragic-sardinia-neolithic

New preprint Population history from the Neolithic to present on the Mediterranean island of Sardinia: An ancient DNA perspective, by Marcus et al. bioRxiv (2019)

Interesting excerpts (emphasis mine, edited for clarity):

On the high frequency of R1b-V88

Our genome-wide data allowed us to assign Y haplogroups for 25 ancient Sardinian individuals. More than half of them consist of R1b-V88 (n=10) or I2-M223 (n=7).

Francalacci et al. (2013) identi fied three major Sardinia-specifi c founder clades based on present-day variation within the haplogroups I2-M26, G2-L91 and R1b-V88, and here we found each of those broader haplogroups in at least one ancient Sardinian individual. Two major present-day Sardinian haplogroups, R1b-M269 and E-M215, are absent.

Compared to other Neolithic and present-day European populations, the number of identi fied R1b-V88 carriers is relatively high.

(…)ancient Sardinian mtDNA haplotypes belong almost exclusively to macro-haplogroups HV (n = 16), JT (n = 17) and U (n = 9), a composition broadly similar to other European Neolithic populations.

r1b-v88-europe
Geographic and temporal distribution of R1b-V88 Y-haplotypes in ancient European samples. We plot the geographic position of all ancient samples inferred to carry R1b-V88 equivalent markers. Dates are given as years BCE (means of calibrated 2s radio-carbon dates). Multiple V88 individuals with similar geographic positions are vertically stacked. We additionally color-code the status of the R1b-V88 subclade R1b-V2197, which is found in most present-day African R1b-V88 carriers.

On the origin of a Vasconic-like Paleosardo with the Western EEF

(…) the Neolithic (and also later) ancient Sardinian individuals sit between early Neolithic Iberian and later Copper Age Iberian populations, roughly on an axis that differentiates WHG and EEF populations and embedded in a cluster that additionally includes Neolithic British individuals. This result is also evident in terms of absolute genetic differentiation, with low pairwise FST ~ 0.005 +- 0.002 between Neolithic Sardinian individuals and Neolithic western mainland European populations. Pairwise outgroup-f3 analysis shows a very similar pattern, with the highest values of f3 (i.e. most shared drift) being with Neolithic and Copper Age Iberia, gradually dropping off for temporally and geographically distant populations.

In explicit admixture models (using qpAdm, see Methods) the southern French Neolithic individuals (France-N) are the most consistent with being a single source for Neolithic Sardinia (p ~ 0:074 to reject the model of one population being the direct source of the other); followed by other populations associated with the western Mediterranean Neolithic Cardial Ware expansion.

sardinians-ancient-eef
Principal Components Analysis based on the Human Origins dataset. A: Projection of ancient individuals’ genotypes onto principal component axes de fined by modern Western Eurasians (gray labels).

Pervasive Western Hunter-Gatherer ancestry in Iberian/French/Sardinian population

Similar to western European Neolithic and central European Late Neolithic populations, ancient Sardinian individuals are shifted towards WHG individuals in the top two PCs relative to early Neolithic Anatolians Admixture analysis using qpAdm infers that ancient Sardinian individuals harbour HG ancestry (~ 17%) that is higher than early Neolithic mainland populations (including Iberia, ~ 8%), but lower than Copper Age Iberians (~ 25%) and about the same as Southern French Middle-Neolithic individuals (~ 21%).

sardinia-modern-ancient-nuragic-pca
Principal Components Analysis based on the Human Origins dataset. B: Zoom into the region most relevant for Sardinian individuals.

Continuity from Sardinia Neolithic through the Nuragic

We found several lines of evidence supporting genetic continuity from the Sardinian Neolithic into the Bronze Age and Nuragic times. Importantly, we observed low genetic differentiation between ancient Sardinian individuals from various time periods.

A qpAdm analysis, which is based on simultaneously testing f-statistics with a number of outgroups and adjusts for correlations, cannot reject a model of Neolithic Sardinian individuals being a direct predecessor of Nuragic Sardinian individuals (…) Our qpAdm analysis further shows that the WHG ancestry proportion, in a model of admixture with Neolithic Anatolia, remains stable at ~17% throughout three ancient time-periods.

sardinians-modern-ancient-pca-admixture
Present-day genetic structure in Sardinia reanalyzed with aDNA. A: Scatter plot of the rst two principal components trained on 1577 present-day individuals with grand-parental ancestry from Sardinia. Each individual is labeled with a location if at least 3 of the 4 grandparents were born in the same geographical location (\small” three letter abbreviations); otherwise with \x” or if grand-parental ancestry is missing with \?”. We calculated median PC values for each Sardinian province (large abbreviations). We also projected each ancient Sardinian individual on to the top two PCs (gray points). B/C: We plot f-statistics that test for admixture of modern Sardinian individuals (grouped into provinces) when using Nuragic Sardinian individuals as one source population. Uncertainty ranges depict one standard error (calculated from block bootstrap). Karitiana are used in the f-statistic calculation as a proxy for ANE/Steppe ancestry (Patterson et al., 2012).

Steppe influx in Modern Sardinians

While contemporary Sardinian individuals show the highest affinity towards EEF-associated populations among all of the modern populations, they also display membership with other clusters (Fig. 5). In contrast to ancient Sardinian individuals, present-day Sardinian individuals carry a modest “Steppe-like” ancestry component (but generally less than continental present-day European populations), and an appreciable broadly “eastern Mediterranean” ancestry component (also inferred at a high fraction in other present-day Mediterranean populations, such as Sicily and Greece).

Related

Spread of Y. pestis, earlier than previously thought, may have caused Neolithic decline

spread-yersinia-pestis

Open access Emergence and Spread of Basal Lineages of Yersinia pestis during the Neolithic Decline, by Rascovan et al. Cell (2018)

Abstract (emphasis mine):

Between 5,000 and 6,000 years ago, many Neolithic societies declined throughout western Eurasia due to a combination of factors that are still largely debated. Here, we report the discovery and genome reconstruction of Yersinia pestis, the etiological agent of plague, in Neolithic farmers in Sweden, pre-dating and basal to all modern and ancient known strains of this pathogen. We investigated the history of this strain by combining phylogenetic and molecular clock analyses of the bacterial genome, detailed archaeological information, and genomic analyses from infected individuals and hundreds of ancient human samples across Eurasia. These analyses revealed that multiple and independent lineages of Y. pestis branched and expanded across Eurasia during the Neolithic decline, spreading most likely through early trade networks rather than massive human migrations. Our results are consistent with the existence of a prehistoric plague pandemic that likely contributed to the decay of Neolithic populations in Europe.

spread-yersinia-trypillia
(A) Schematic representation of the trajectories and time periods (thousand years before present, kyr) of major known human migrations in Eurasia during the Neolithic and Bronze Age. The observed geographic distribution and divergence times of Y. pestis strains from the Gok2 and Bronze Age clades cannot be explained by the timings and routes of these human movements.
(B) Geographic distribution of the use of animal traction and wheeled transport across Neolithic and Bronze Age populations in Eurasia, which broadly expanded during the period of 5,500 and 5,000 BP. The expansion of these technological innovations overlaps the predicted period for the expansion of the basal Y. pestis strains.
(C) Timeline indicating the proposed key historical events that contributed to the emergence and spread of plague during the Neolithic.

We have evolved in the interpretation of the plague from 1) a Corded Ware-driven disease, to 2) a steppe disease that was spread by Yamna and Corded Ware, and now 3) a (potentially) Trypillia-driven disease that spread to the west earlier than Yamna and Corded Ware, but probably also later east and west with both.

At least it still seems that the plague and its demographic consequences were a good reason for the expansion of Indo-Europeans and Uralians into Europe, as we thought…

Featured image, from the paper: “The predicted model of early dispersion of Y. pestis during Neolithic and Bronze Age was built by integrating phylogenetic information of Y. pestis strains from this period (Figure 1E), their divergence times (Figure 3), the geographic locations, carbon dating and genotypes of the individuals, and the archaeological record. The model suggests that early Y. pestis strains likely emerged and spread from mega-settlements in Eastern Europe (built by the Trypillia Culture) into Europe and the Eurasian steppe, most likely through human interaction networks. This was facilitated by wheeled and animal-powered transports, which are schematized in the map with red lines with arrows pointing in both senses. Our model builds upon a previous model (Andrades Valtuena et al., 2017) that proposed the spread of plague to be associated with large-scale human migrations (blue line).

Related

“Steppe ancestry” step by step: Khvalynsk, Sredni Stog, Repin, Yamna, Corded Ware

dzudzuana_pca-large

Wang et al. (2018) is obviously a game changer in many aspects. I have already written about the upcoming Yamna Hungary samples, about the new Steppe_Eneolithic and Caucasus Eneolithic keystones, and about the upcoming Greece Neolithic samples with steppe ancestry.

An interesting aspect of the paper, hidden among so many relevant details, is a clearer picture of how the so-called Yamnaya or steppe ancestry evolved from Samara hunter-gatherers to Yamna nomadic pastoralists, and how this ancestry appeared among Proto-Corded Ware populations.

anatolia-neolithic-steppe-eneolithic
Image modified from Wang et al. (2018). Marked are in orange: equivalent Steppe_Maykop ADMIXTURE; in red, approximate limit of Anatolia_Neolithic ancestry found in Yamna populations; in blue, Corded Ware-related groups. “Modelling results for the Steppe and Caucasus cluster. Admixture proportions based on (temporally and geographically) distal and proximal models, showing additional Anatolian farmer-related ancestry in Steppe groups as well as additional gene flow from the south in some of the Steppe groups as well as the Caucasus groups.”

Please note: arrows of “ancestry movement” in the following PCAs do not necessarily represent physical population movements, or even ethnolinguistic change. To avoid misinterpretations, I have depicted arrows with Y-DNA haplogroup migrations to represent the most likely true ethnolinguistic movements. Admixture graphics shown are from Wang et al. (2018), and also (the K12) from Mathieson et al. (2018).

1. Samara to Early Khvalynsk

The so-called steppe ancestry was born during the Khvalynsk expansion through the steppes, probably through exogamy of expanding elite clans (eventually all R1b-M269 lineages) originally of Samara_HG ancestry. The nearest group to the ANE-like ghost population with which Samara hunter-gatherers admixed is represented by the Steppe_Eneolithic / Steppe_Maykop cluster (from the Northern Caucasus Piedmont).

Steppe_Eneolithic samples, of R1b1 lineages, are probably expanded Khvalynsk peoples, showing thus a proximate ancestry of an Early Eneolithic ghost population of the Northern Caucasus. Steppe_Maykop samples represent a later replacement of this Steppe_Eneolithic population – and/or a similar population with further contribution of ANE-like ancestry – in the area some 1,000 years later.

PCA-caucasus-steppe-samara

This is what Steppe_Maykop looks like, different from Steppe_Eneolithic:

steppe-maykop-admixture

NOTE. This admixture shows how different Steppe_Maykop is from Steppe_Eneolithic, but in the different supervised ADMIXTURE graphics below Maykop_Eneolithic is roughly equivalent to Eneolithic_Steppe (see orange arrow in ADMIXTURE graphic above). This is useful for a simplified analysis, but actual differences between Khvalynsk, Sredni Stog, Afanasevo, Yamna and Corded Ware are probably underestimated in the analyses below, and will become clearer in the future when more ancestral hunter-gatherer populations are added to the analysis.

2. Early Khvalynsk expansion

We have direct data of Khvalynsk-Novodanilovka-like populations thanks to Khvalynsk and Steppe_Eneolithic samples (although I’ve used the latter above to represent the ghost Caucasus population with which Samara_HG admixed).

We also have indirect data. First, there is the PCA with outliers:

PCA-khvalynsk-steppe

Second, we have data from north Pontic Ukraine_Eneolithic samples (see next section).

Third, there is the continuity of late Repin / Afanasevo with Steppe_Eneolithic (see below).

3. Proto-Corded Ware expansion

It is unclear if R1a-M459 subclades were continuously in the steppe and resurged after the Khvalynsk expansion, or (the most likely option) they came from the forested region of the Upper Dnieper area, possibly from previous expansions there with hunter-gatherer pottery.

Supporting the latter is the millennia-long continuity of R1b-V88 and I2a2 subclades in the north Pontic Mesolithic, Neolithic, and Early Eneolithic Sredni Stog culture, until ca. 4500 BC (and even later, during the second half).

Only at the end of the Early Eneolithic with the disappearance of Novodanilovka (and beginning of the steppe ‘hiatus’ of Rassamakin) is R1a to be found in Ukraine again (after disappearing from the record some 2,000 years earlier), related to complex population movements in the north Pontic area.

NOTE. In the PCA, a tentative position of Novodanilovka closer to Anatolia_Neolithic / Dzudzuana ancestry is selected, based on the apparent cline formed by Ukraine_Eneolithic samples, and on the position and ancestry of Sredni Stog, Yamna, and Corded Ware later. A good alternative would be to place Novodanilovka still closer to the Balkan outliers (i.e. Suvorovo), and a source closer to EHG as the ancestry driven by the migration of R1a-M417.

PCA-sredni-stog-steppe

The first sample with steppe ancestry appears only after 4250 BC in the forest-steppe, centuries after the samples with steppe ancestry from the Northern Caucasus and the Balkans, which points to exogamy of expanding R1a-M417 lineages with the remnants of the Novodanilovka population.

steppe-ancestry-admixture-sredni-stog

4. Repin / Early Yamna expansion

We don’t have direct data on early Repin settlers. But we do have a very close representative: Afanasevo, a population we know comes directly from the Repin/late Khvalynsk expansion ca. 3500/3300 BC (just before the emergence of Early Yamna), and which shows fully Steppe_Eneolithic-like ancestry.

afanasevo-admixture

Compared to this eastern Repin expansion that gave Afanasevo, the late Repin expansion to the west ca. 3300 BC that gave rise to the Yamna culture was one of colonization, evidenced by the admixture with north Pontic (Sredni Stog-like) populations, no doubt through exogamy:

PCA-repin-yamna

This admixture is also found (in lesser proportion) in east Yamna groups, which supports the high mobility and exogamy practices among western and eastern Yamna clans, not only with locals:

yamnaya-admixture

5. Corded Ware

Corded Ware represents a quite homogeneous expansion of a late Sredni Stog population, compatible with the traditional location of Proto-Corded Ware peoples in the steppe-forest/forest zone of the Dnieper-Dniester region.

PCA-latvia-ln-steppe

We don’t have a comparison with Ukraine_Eneolithic or Corded Ware samples in Wang et al. (2018), but we do have proximate sources for Abashevo, when compared to the Poltavka population (with which it admixed in the Volga-Ural steppes): Sintashta, Potapovka, Srubna (with further Abashevo contribution), and Andronovo:

sintashta-poltavka-andronovo-admixture

The two CWC outliers from the Baltic show what I thought was an admixture with Yamna. However, given the previous mixture of Eneolithic_Steppe in north Pontic steppe-forest populations, this elevated “steppe ancestry” found in Baltic_LN (similar to west Yamna) seems rather an admixture of Baltic sub-Neolithic peoples with a north Pontic Eneolithic_Steppe-like population. Late Repin settlers also admixed with a similar population during its colonization of the north Pontic area, hence the Baltic_LN – west Yamna similarities.

NOTE. A direct admixture with west Yamna populations through exogamy by the ancestors of this Baltic population cannot be ruled out yet (without direct access to more samples), though, because of the contacts of Corded Ware with west Yamna settlers in the forest-steppe regions.

steppe-ancestry-admixture-latvia

A similar case is found in the Yamna outlier from Mednikarovo south of the Danube. It would be absurd to think that Yamna from the Balkans comes from Corded Ware (or vice versa), just because the former is closer in the PCA to the latter than other Yamna samples. The same error is also found e.g. in the Corded Ware → Bell Beaker theory, because of their proximity in the PCA and their shared “steppe ancestry”. All those theories have been proven already wrong.

NOTE. A similar fallacy is found in potential Sintashta→Mycenaean connections, where we should distinguish statistically that result from an East/West Yamna + Balkans_BA admixture. In fact, genetic links of Mycenaeans with west Yamna settlers prove this (there are some related analyses in Anthrogenica, but the site is down at this moment). To try to relate these two populations (separated more than 1,000 years before Sintashta) is like comparing ancient populations to modern ones, without the intermediate samples to trace the real anthropological trail of what is found…Pure numbers and wishful thinking.

Conclusion

Yamna and Corded Ware show a similar “steppe ancestry” due to convergence. I have said so many times (see e.g. here). This was clear long ago, just by looking at the Y-chromosome bottlenecks that differentiate them – and Tomenable noticed this difference in ADMIXTURE from the supplementary materials in Mathieson et al. (2017), well before Wang et al. (2018).

This different stock stems from (1) completely different ancestral populations + (2) different, long-lasting Y-chromosome bottlenecks. Their similarities come from the two neighbouring cultures admixing with similar populations.

If all this does not mean anything, and each lab was going to support some pre-selected archaeological theories from the 1960s or the 1980s, coupled with outdated linguistic models no matter what – Anthony’s model + Ringe’s glottochronological tree of the early 2000s in the Reich Lab; and worse, Kristiansen’s CWC-IE + Germano-Slavonic models of the 1940s in the Copenhagen group – , I have to repeat my question again:

What’s (so much published) ancient DNA useful for, exactly?

See also

Related

Waves of Palaeolithic ANE ancestry driven by P subclades; new CWC-like Finnish Iron Age

New preprint The population history of northeastern Siberia since the Pleistocene, by Sikora et al. bioRxiv (2018).

Interesting excerpts (emphasis mine; most internal references removed):

ANE ancestry

The earliest, most secure archaeological evidence of human occupation of the region comes from the artefact-rich, high-latitude (~70° N) Yana RHS site dated to ~31.6 kya (…)

The Yana RHS human remains represent the earliest direct evidence of human presence in northeastern Siberia, a population we refer to as “Ancient North Siberians” (ANS). Both Yana RHS individuals were unrelated males, and belong to mitochondrial haplogroup U, predominant among ancient West Eurasian hunter-gatherers, and to Y chromosome haplogroup P1, ancestral to haplogroups Q and R, which are widespread among present-day Eurasians and Native Americans.

Symmetry tests using f4 statistics reject tree-like clade relationships with both Early West Eurasians (EWE; Sunghir) and Early East Asians (EEA; Tianyuan); however, Yana is genetically closer to EWE, despite its geographic location in northeastern Siberia

Using admixture graphs (qpGraph) and outgroup-based estimation of mixture proportions (qpAdm), we find that Yana can be modelled as EWE with ~25% contribution from EEA

Among all ancient individuals, Yana shares the most genetic drift with Mal’ta, and f4 statistics show that Mal’ta shares more alleles with Yana than with EWE (e.g. f4(Mbuti,Mal’ta;Sunghir,Yana) = 0.0019, Z = 3.99). Mal’ta and Yana also exhibit a similar pattern of genetic affinities to both EWE and EEA, consistent with previous studies.The ANE lineage can thus be considered a descendant of the ANS lineage, demonstrating that by 31.6 kya early representatives of this lineage were widespread across northern Eurasia, including far northeastern Siberia.

siberian-samples-haplogroup

Ancient Palaeosiberian

(…) the 9.8 kya Kolyma1 individual, representing a group we term “Ancient Paleosiberians” (AP). Our results indicate that AP are derived from a first major genetic shift observed in the region. Principal component analysis (PCA), outgroup f3-statistics and mtDNA and Y chromosome haplogroups (G1b and Q1a1a, respectively) demonstrate a close affinity between AP and present-day Koryaks, Itelmen and Chukchis, as well as with Native Americans.

For both AP and Native Americans, ANS ancestry appears more closely related to Mal’ta than Yana, therefore rejecting a direct contribution of Yana to later AP or Native American groups.

Lake Baikal Neolithic – Bronze Age

(…) the newly reported genomes from Ust’Belaya and recently published neighbouring Neolithic and Bronze Age sites show a succession of three distinct genetic ancestries over a ~6 ky time span. The earliest individuals show predominantly East Asian ancestry, closely related to the ancient individuals from DGC. In the early Bronze Age (BA), we observe a resurgence of AP ancestry (up to ~50% ancestry fraction), as well as influence of West Eurasian Steppe ANE ancestry represented by the early BA individuals from Afanasievo in the Altai region (~10%) This is consistent with previous reports of gene flow from an unknown ANE-related source into Lake Baikal hunter-gatherers.

Our results suggest a southward expansion of AP as a possible source, which is also consistent with the replacement of Y chromosome lineages observed at Lake Baikal, from predominantly haplogroup N in the Neolithic to haplogroup Q in the BA. Finally, the most recent individual from Ust’Belaya, dated to ~600 years ago, falls along the Neosiberian cline, similar to the ~760 year-old ‘Young Yana’ individual from northeastern Siberia, demonstrating the widespread distribution of Neosiberian ancestry in the most recent epoch.

finnish_ia_palaeosiberian
Genetic structure of ancient northeast Siberians. PCA of ancient individuals projected onto a set of modern Eurasian and American individuals. Abbreviations in group labels: UP – Upper Palaeolithic; LP – Late Palaeolithic; M – Mesolithic; EN – Early Neolithic; MN – Middle Neolithic; LN – Late Neolithic; EBA – Early Bronze Age; LBA – Late Bronze Age; IA – Iron Age; PE – Paleoeskimo; MED – Medieval

Finland Saami

At the western edge of northern Eurasia, genetic and strontium isotope data from ancient individuals at the Levänluhta site documents the presence of Saami ancestry in Southern Finland in the Late Holocene 1.5 kya. This ancestry component is currently limited to the northern fringes of the region, mirroring the pattern observed for AP ancestry in northeastern Siberia. However, while the ancient Saami individuals harbour East Asian ancestry, we find that this is better modelled by DGC rather than AP, suggesting that AP influence was likely restricted to the eastern side of the Urals. Comparison of ancient Finns and Saami with their present-day counterparts reveals additional gene flow over the past 1.6 kya, with evidence for West Eurasian admixture into modern Saami. The ancient Finn from Levänluhta shows lower Siberian ancestry than modern Finns .

EDIT (27 OCT 2018): By comparing the three, I see these are samples published already (at least two) in Lamnidis et al. (2018), but here with added (1) specific radiocarbon dates, (2) comparison with Neosiberian populations and (3) strontium isotope analyses.

Finnish_IA (ca. 350 AD) is probably a Saami-speaking individual, just like the Saami_IA with newly reported radiocarbon dates from Levänluhta ca. 400-600 AD (since Fennic peoples were then likely around the Gulf of Finland).

The conflicting strontium isotope data on marine dietary resources on certain samples from the supplementary material hint at possible external origin of the diet of some of the previously reported (and possibly one newly reported) Saami Iron Age individuals, from some 25-30 km. to the northwest through the river up to hundreds of km. to the southwest of Levänluhta (i.e. the whole coast of the Bothnian Sea). It is unclear why they would prefer an origin of the dietary source in southern Baltic regions instead of some km. to the west, though, unless that’s what they want to propose based on the sample’s admixture…

The coast of the Bothnian Sea (=the northern part of the Baltic Sea, between Sweden and Finland) lay only 25-30 km to the northwest, and accessible to the Iron Age people of the Levänluhta region via the Kyrönjoki river. (…) For individual JA2065/DA236, the low 87Sr/86Sr value (0.71078) would imply an exceptionally heavy reliance on Baltic Sea resources. The δ13C and δ15N values of the individual are near comparable (especially considering within-Baltic latitudinal gradients in δ13C; Torniainen et al. 2017) to the δ13C and δ15N values of a Middle Neolithic population on the Baltic island of Gotland (Eriksson, 2004) interpreted to have subsisted primarily on seals.

These new data on the samples give us some more information than what we already had, because the early date of Finnish_IA implies that there was few East Asian admixture (if any at all) in west Finland during the Roman Iron Age, which pushes still farther forward in time the expected appearance of Siberian ancestry among Saamic (first) and Fennic populations (later). It is unclear whether this East Asian ancestry found in Finnish_IA is actually related to DGC, or it is rather related to the ENA-like ancestry found already in Baltic hunter-gatherers (i.e. in some EHG samples from Karelia), for which Baikal_EN is a good proxy in Lazaridis et al. (2018).

Since Bronze Age and Iron Age samples from Estonia show more Baltic_HG drift compared to Corded Ware samples, it is likely that this supposedly DGC-related ancestry (here considered part of the ‘Siberian ancestry’) is actually an EHG-related ENA component of north-east European hunter-gatherers, with whom Finno-Saamic peoples admixed during the expansion of the Corded Ware culture into Finland.

The paper finds thus increased (probably the actual) Siberian ancestry in modern Finns compared to this Iron Age Saami individual. Coupled with the later Saami Iron Age samples, from between one to three centuries later – showing the start of Siberian ancestry influx – , we can begin to establish when the expansion of Siberian ancestry happened in central Finland, and thus quite likely when the Saami began to expand to the north and east and admix with Palaeo-Laplandic peoples.

siberian-population-expansions
Admixture modelling using qpAdm. Maps showing locations and ancestry proportions of ancient (left) and modern (right) groups.

One sample of haplogroup N1a1a1a1a4a1-M1982, Yana_MED, is found in the Arctic region (north-eastern Yakutia) ca. 1100 AD. Since it is derived from N1a1a1a1a-L392, it might be a surprise for some to find it in a clearly non-Uralic speaking environment at the same time other subclades of this haplogroup were admixing in the west with well-established Finno-Saamic, Volga-Finnic, Ugric, and Samoyedic populations…

On the growing doubts that these data – contradicting the CWC=IE theory – are creating among geneticists (from the supplementary materials):

NOTE. This paper comes from the Copenhagen group, also signed by Kristiansen, one of today’s strongest supporters of this connection

The Proto-Saami language evolved in southern Finland and Karelia in the Early Iron Age, an area now host to Finnish and the closely related Karelian, but with Saami toponyms showing that the latter two languages are intrusive here (Saarikivi 2004). Saami-speaking populations are thought to have retreated to Lapland during the Middle Iron Age (300–800 AD), where it diverged into the modern Saami dialects. Genetically, the northward retreat of the Saami language correlates with the documented decrease of Saami ancestry in Southern Finland between the Iron Age and the modern period (cf. Lamnidis et al. 2018).

On the way to Lapland, the Saami replaced at least two linguistically obscure groups. This can be inferred from 1) an influx of non-Uralic loanwords into Proto-Saami in the Finnish Lakeland area, and 2) an influx of non-Uralic, non-Germanic words into Saami dialects in Lapland (Aikio 2012). Both of these borrowing events imply contact with non-Saami-speaking groups, e.g. non-Uralic-speaking hunter-gatherers that may have left a genetic and linguistic footprint on modern Saami populations.

The linguistic prehistory of Finland thus does not allow for a straightforward interpretation of the genetic data. The detection of East Asian ancestry in the genetically Saami individual is indicative of a population movement from the east (cf. Lamnidis et al. 2018, Rootsi et al. 2007), one that given the affinities with the ~7.6 ky old individuals from the Devil’s Gate Cave may have been a western extension of the Neosiberian turnover. However, it remains unclear whether this gene flow should be associated with the arrival of Uralic speakers, thus providing further support for a Uralic homeland in Eastern Eurasia, or with an earlier immigration of pre-Uralic, so-called “Paleo-Lakelandic” groups.

I think the genetic interpretation is already straightforward, though. We had a sneak peek at how this late admixture with non-Uralians (mainly Palaeo-Lakelandic and Palaeo-Laplandic peoples from Lovozero and related asbestos ware cultures) is going to unfold among expanding Saami-speaking populations thanks to Lamnidis et al. (2018):

saamic-lovozero-pca
PCA plot of 113 Modern Eurasian populations, with individuals from this study projected on the principal components. Uralic speakers are highlighted in light purple. Image modified from Lamnidis et al. (2018)

Also, still no trace of R1a in far East Asia (reported as M17 ca. 5300 BC near Lake Baikal by Moussa et al. 2016), so I still have doubts about my previous assessment that R1a split into M17 (and thus also M417) in Siberia, with those expanding hunter-gatherer pottery.

Related

Dzudzuana, Sidelkino, and the Caucasus contribution to the Pontic-Caspian steppe

hunter-gatherer-pottery

It has been known for a long time that the Caucasus must have hosted many (at least partially) isolated populations, probably helped by geographical boundaries, setting it apart from open Eurasian areas.

David Reich writes in his book the following about India:

The genetic data told a clear story. Around a third of Indian groups experienced population bottlenecks as strong or stronger than the ones that occurred among Finns or Ashkenazi Jews. We later confirmed this finding in an even larger dataset that we collected working with Thangaraj: genetic data from more than 250 jati groups spread throughout India (…)

Rather than an invention of colonialism as Dirks suggested, long-term endogamy as embodied in India today in the institution of caste has been overwhelmingly important for millennia. (…)

The Han Chinese are truly a large population. They have been mixing freely for thousands of years. In contrast, there are few if any Indian groups that are demographically very large, and the degree of genetic differentiation among Indian jati groups living side by side in the same village is typically two to three times higher than the genetic differentiation between northern and southern Europeans. The truth is that India is composed of a large number of small populations.

There is little doubt now, based on findings spanning thousands of years, that the Mesolithic and Neolithic Caucasus hosted various very small populations, even if the ancestral components may be reduced to the few known to date (such as ANE, EHG, AME*, ENA, CHG, and other “deep” ancestral components).

NOTE. I will call the ancestral component of Dzudzuana/Anatolian hunter-gatherers Ancient Middle Easterner (AME), to give a clear idea of its likely extension during the Late Upper Palaeolithic, and to avoid using the more simplistic Dzudzuana, unless it is useful to mention these specific local samples.

dzudzuana-pca
Image modified from Lazaridis et al. (2018), including Caucasus, Don-Volga-Ural, and North Pontic Mesolithic-Neolithic populations. “Ancient West Eurasian population structure. (a) Geographical distribution of key ancient West Eurasian populations. (b) Temporal distribution of key ancient West Eurasian populations (approximate date in ky BP). (c) PCA of key ancient West Eurasians, including additional populations (shown with grey shells), in the space of outgroup f4-statistics (Methods).”

Genetic labs have a strong fixation with ancestry. I guess the use of complex statistical methods gives professionals and laymen alike the feeling of dealing with “Science”, as opposed to academic fields where you have to interpret data. I think language reveals a lot about the way people think, and the fact that ancestral components are called ‘lineages’ – while not wrong per se – is a clear symptom of the lack of interest in the true lineages: Y-DNA haplogroups.

Y-DNA bottlenecks

It has become quite clear that male-biased migrations are often the ones which can be confidently followed for actual population movements and ethnolinguistic identification, at least until the Iron Age. The frequently used Palaeolithic clusters offer a clear example of why ancestry does not represent what some people believe: They merely give a basic idea of sizeable population replacements by distant peoples.

Both concepts are important: sizeable and distant peoples. For example, during the Upper Palaeolithic in Europe there was a sizeable population replacement of the Aurignacian Goyet cluster by the Gravettian Vestonice cluster (probably from populations of far eastern Russia) coupled with the arrival of haplogroup I, although during the thousands of years that this material culture lasted, the previously expanded C1a2 lineages did not disappear, and there were probably different resurgence and admixture events.

Haplogroup I certainly expanded with the Gravettian culture to Iberia, where the Goyet ancestry did not change much – probably because of male-driven migrations -, to the extent that during the Magdalenian expansions haplogroup I expanded with an ancestry closer to Goyet, in what is called a ‘resurge’ of the Goyet cluster – even though there is a clear replacement of male lines.

The Villabruna (WHG) cluster is another good example. It probably spread with haplogroup R1b-L754, which – based on the extra ‘East Asian’ affinity of some samples and on modern samples from the Middle East – came probably from the east through a southern route, and not too long before the expansion of WHG likely from around the Black Sea, although this is still unclear. The finding of haplogroup I in samples of mostly WHG ancestry could confuse people that do not care about timing, sub-structured populations, and gene flow.

palaeolithic-expansions-reich
Image from David Reich’s Who We Are and How We Got Here. Having migrated out of Africa and the Near East, modern human pioneer populations spread throughout Eurasia (1). By at least thirty-nine thousand years ago, one group founded a lineage of European hunter-gatherers that persisted largely uninterrupted for more than twenty thousand years (2). Eventually, groups derived from an eastern branch of this founding population of European huntergatherers spread west (3), displaced previous groups, and were eventually themselves pushed out of northern Europe by the spread of glacial ice, shown at its maximum extent (top right). As the glaciers receded, western Europe was repeopled from the southwest (4) by a population that had managed to persist for tens of thousands of years and was related to an approximately thirty-five-thousand-year old individual from far western Europe. A later human migration, following the first strong warming period, had an even larger impact, with a spread from the southeast (5) that not only transformed the population of western Europe but also homogenized the populations of Europe and the Near East. At a single site—Goyet Caves in Belgium—ancient DNA from individuals spread over twenty thousand years reflects these transformations, with representatives from the Aurignacian, Gravettian, and Magdalenian periods.

NOTE. If you don’t understand why ‘clusters’ that span thousands of years don’t really matter for the many Palaeolithic population expansions that certainly happened among hunter-gatherers in Europe, just take a look at what happened with Bell Beakers expanding from Yamna into western Europe within 500 years.

If we don’t thread carefully when talking about population migrations, these terms are bound to confuse people. Just as the fixation on “steppe ancestry” – which marks the arrival in Chalcolithic Europe of peoples from the Pontic-Caspian region – has confused a lot of researchers to this day.

When I began to write about the Indo-European demic diffusion model, my concern was to find a single spot where a North-West Indo-European proto-language could have expanded from ca. 2000 BC (our most common guesstimate). Based on the 2015 papers, and in spite of their conclusions, I thought it had become clear that Corded Ware was not it, and it was rather Bell Beakers. I assumed that Uralic was spoken to the north (as was the traditional belief), and thus Corded Ware expanded from the forest zone, hence steppe ancestry would also be found there with other R1a lineages.

With the publication of Mathieson et al. (2017) and Olalde et al. (2017), I changed my mind, seeing how “steppe ancestry” did in fact appear quite late, hence it was likely to be the result of very specific population movements, probably directly from the Caucasus. Later, Mathieson published in a revision the sample from Alexandria of hg R1a-M417 (probably R1a-Z645, possibly Z93+), which further supported the idea that the migration of Corded Ware peoples started near the North Pontic forest-steppe (as I included in a the next revision).

The question remains the same I repeated recently, though: where do the extra Caucasus components (i.e. beyond EHG) of Eneolithic Ukraine/Corded Ware and Khvalynsk/Yamna come from?

Steppe ancestry: “EHG” + “CHG”?

About EHG ancestry

From Lazaridis et al. (2018):

Considering 2-way mixtures, we can model Karelia_HG as deriving 34 ± 2.8% of its ancestry from a Villabruna-related source, with the remainder mainly from ANE represented by the AfontovaGora3 (AG3) sample from Lake Baikal ~17kya.

AG3 was likely of haplogroup Q1a (as reported by YFull, see Genetiker), and probably the ANE ancestry found in Eastern Europe accompanied a Palaeolithic migration of Q1a2-M25 (formed ca. 22600 BC, TMRCA ca. 14300 BC).

NOTE. You can read more about the expansion of Q lineages during the Palaeolithic.

Combined with what we know about the Eneolithic Steppe and Caucasus populations – it is likely that ANE ancestry remained the most important component of some of the small ghost populations of the Caucasus until their emergence with the Lola culture.

pca-caucasus-dzudzuana
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. To understand the drawn potential Caucasus Mesolithic cluster, see above the PCA from Lazaridis et al. (2018).

The first sample we have now attributed to the EHG cluster is Sidelkino, from the Samara region (ca. 9300 BC), mtDNA U5a2. In Damgaard et al. (Science 2018), Yamnaya could be modelled as a CHG population related to Kotias Klde (54%) and the remaining from ANE population related to Sidelkino (>46%), with the following split events:

  1. A split event, where the CHG component of Yamnaya splits from KK1. The model inferred this time at 27 kya (though we note the larger models in Sections S2.12.4 and S2.12.5 inferred a more recent split time).
  2. A split event, where the ANE component of Yamnaya splits from Sidelkino. This was inferred at about about 11 kya.
  3. A split event, where the ANE component of Yamnaya splits from Botai. We inferred this to occur 17 kya. Note that this is above the Sidelkino split time, so our model infers Yamnaya to be more closely related to the EHG Sidelkino, as expected.
  4. An ancestral split event between the CHG and ANE ancestral populations. This was inferred to occur around 40 kya.

Other samples classified as of the EHG cluster:

  • Popovo2 (ca. 6250 BC) of hg J1, mtDNA U4d – Po2 and Po4 from the same site (ca. 6550 BC) show continuity of mtDNA.
  • Karelia_HG, from Juzhnii Oleni Ostrov (ca. 6300 BC): I0211/UzOO40 (ca. 6300 BC) of hg J1(xJ1a), mtDNA U4a; and I0061/UzOO74 of hg R1a1(xR1a1a), mtDNA C1
  • UzOO77 and UzOO76 from Juzhnii Oleni Ostrov (ca. 5250 BC) of mtDNA R1b.
  • Samara_HG from Lebyanzhinka (ca. 5600 BC) of hg R1b1a, mtDNA U5a1d.

From the analysis of Lazaridis et al. (2018), we have some details about their admixture:

dzudzuana-admixture-sidelkino
Image modified from Lazaridis et al. (2018). 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 split of Ust’Ishim, Tianyuan, and West Eurasians and can include both ‘Basal Eurasian’ and other (e.g., Sub-Saharan African) ancestry. (Left) ‘Conservative’ estimates. Each population 367 cannot be modeled with fewer admixture events than shown. (Right) ‘Speculative’ estimates. The highest number of sources (≤5) with admixture estimates within [0,1] are shown for each population. Some of the admixture proportions are not significantly different from 0 (Supplementary Information section 4).

About Anatolia_Neolithic ancestry

About the enigmatic Anatolia_Neolithic-related ancestry found in Pontic-Caspian steppe samples, this is what Wang et al. (2018) had to say:

We focused on model of mixture of proximal sources such as CHG and Anatolian Chalcolithic for all six groups of the Caucasus cluster (Eneolithic Caucasus, Maykop and Late Makyop, Maykop-Novosvobodnaya, Kura-Araxes, and Dolmen LBA), with admixture proportions on a genetic cline of 40-72% Anatolian Chalcolithic related and 28-60% CHG related (Supplementary Table 7). When we explored Romania_EN and Greece_Neolithic individuals as alternative southeast European sources (30-46% and 36-49%), the CHG proportions increased to 54-70% and 51-64%, respectively. We hypothesize that alternative models, replacing the Anatolian Chalcolithic individual with yet unsampled populations from eastern Anatolia, South Caucasus or northern Mesopotamia, would probably also provide a fit to the data from some of the tested Caucasus groups.

Also:

The first appearance of ‘Near Eastern farmer related ancestry’ in the steppe zone is evident in Steppe Maykop outliers. However, PCA results also suggest that Yamnaya and later groups of the West Eurasian steppe carry some farmer related ancestry as they are slightly shifted towards ‘European Neolithic groups’ in PC2 (Fig. 2D) compared to Eneolithic steppe. This is not the case for the preceding Eneolithic steppe individuals. The tilting cline is also confirmed by admixture f3-statistics, which provide statistically negative values for AG3 as one source and any Anatolian Neolithic related group as a second source

yamnaya-caucasus-dzudzuana
Modified image from Wang et al. (2018). In blue, Yamna-related populations. In red, Corded Ware-related populations, and two elevated Anatolia_Neolithic values in Yamna. Notice how only GAC-related admixture increases the Anatolian_N-related ancestry in the Yamna outlier from Ozero, and the late Yamna sample from Hungary, related to the homogeneous Yamna population. “Supplementary Table 14. P values of rank=3 and admixture proportions in modelling Steppe ancestry populations as a four-way admixture of distal sources EHG, CHG, Anatolian_Neolithic and WHG using 14 outgroups.Left populations: Steppe cluster, EHG, CHG, WHG, Anatolian_Neolithic. Right populations: Mbuti.DG, Ust_Ishim.DG, Kostenki14, MA1, Han.DG, Papuan.DG, Onge.DG, Villabruna, Vestonice16, ElMiron, Ethiopia_4500BP.SG, Karitiana.DG, Natufian, Iran_Ganj_Dareh_Neolithic.”

Detailed exploration via D-statistics in the form of D(EHG, steppe group; X, Mbuti) and D(Samara_Eneolithic, steppe group; X, Mbuti) show significantly negative D values for most of the steppe groups when X is a member of the Caucasus cluster or one of the Levant/Anatolia farmer-related groups (Supplementary Figs. 5 and 6). In addition, we used f- and D-statistics to explore the shared ancestry with Anatolian Neolithic as well as the reciprocal relationship between Anatolian- and Iranian farmer-related ancestry for all groups of our two main clusters and relevant adjacent regions (Supplementary Fig. 4). Here, we observe an increase in farmer-related ancestry (both Anatolian and Iranian) in our Steppe cluster, ranging from Eneolithic steppe to later groups. In Middle/Late Bronze Age groups especially to the north and east we observe a further increase of Anatolian farmer related ancestry consistent with previous studies of the Poltavka, Andronovo, Srubnaya and Sintashta groups and reflecting a different process not especially related to events in the Caucasus.

(…) Surprisingly, we found that a minimum of four streams of ancestry is needed to explain all eleven steppe ancestry groups tested, including previously published ones (Fig. 2; Supplementary Table 12). Importantly, our results show a subtle contribution of both Anatolian farmer-related ancestry and WHG-related ancestry (Fig.4; Supplementary Tables 13 and 14), which was likely contributed through Middle and Late Neolithic farming groups from adjacent regions in the West. The discovery of a quite old AME ancestry has rendered this probably unnecessary, because this admixture from an Anatolian-like ghost population could be driven even by small populations from the Caucasus.

yamna-caucasus-cwc-anatolia-neolithic
Image modified from Wang et al. (2018). Marked are: in red, approximate limit of Anatolia_Neolithic ancestry found in Yamna populations; in blue, Corded Ware-related groups. “Modelling results for the Steppe and Caucasus 1128 cluster. Admixture proportions based on (temporally and geographically) distal and proximal models, showing additional Anatolian farmer-related ancestry in Steppe groups as well as additional gene flow from the south in some of the Steppe groups as well as the Caucasus groups (see also Supplementary Tables 10, 14 and 20).”

NOTE. For a detailed account of the possibilities regarding this differential admixture in the North Pontic area in contrast to the Don-Volga-Ural region, you can read the posts Sredni Stog, Proto-Corded Ware, and their “steppe admixture”, and Corded Ware culture origins: The Final Frontier.

While it is not yet fully clear, the increased Anatolian_Neolithic-like ancestry in Ukraine_Eneolithic samples (see below) makes it unlikely that all such ancestry in Corded Ware groups comes from a GAC-related contribution. It is likely that at least part of it represents contributions from populations of the Caucasus, based on the mostly westward population movements in the steppe from ca. 4600 BC on, including the Suvorovo-Novodanilovka expansion, and especially the Kuban-Maykop expansion during the final Eneolithic into the North Pontic area.

NOTE. Since CHG-like groups from the Caucasus may have combinations of AME and ANE ancestry similar to Yamna (which may thus appear as ‘steppe ancestry’ in the North Pontic area), it is impossible to interpret with precision the following ADMIXTURE graphic:

ukraine-whg-ehg-steppe
Modified image from Mathieson et al. (2018). Supervised ADMIXTURE analysis, modelling each ancient individual (one per row) as a mixture of population clusters constrained to contain northwestern-Anatolian Neolithic (grey), Yamnaya from Samara (yellow), EHG (pink) and WHG (green) populations. Dates in parentheses indicate approximate range of individuals in each population.

North-Eastern Technocomplex

The East Asian contribution to samples from the WHG samples (like Loschbour or La Braña), as specified in Fu et al. (2016), does not seem to be related to Baikal_EN, and appears possibly (in the ADMIXTURE analysis) integrated into he Villabruna component. I guess this implies that the shared alleles with East Asians are quite early, and potentially due to the expansion of R1b-L754 from the East.

It would be interesting to know the specific material culture Sidelkino belonged to – i.e. if it was related to the expansion of the North-Eastern Technocomplex – , and its Y-DNA. The Post-Swiderian expansion into eastern Europe, probably associated with the expansion of R1b-P297 lineages (including R1b-M73, found later in Botai and in Baltic HG) is supposed to have begun during the 11th millennium BC, but migrations to the Urals and beyond are probably concentrated in the 9th millennium, so this sample is possibly slightly early for R1b.

NOTE. User Rozenfeld at Anthrogenica posted this, which I think is interesting (in case anyone wants to try a Y-SNP call):

there is something strange with Sidelkino EHG: first, its archaeological context is not described in the supplementary. Second, its sex is not listed in the supplementary tables. Third, after looking for info about this sample, I found that: “Сиделькино-3. Для снятия вопроса о половой принадлежности индивида была проведена генетическая экспертиза, выявившая принадлежность останков мужчине.”(translation: Sidelkino-3. To resolve the question about sex of the remains, the genetic analysis was conducted, which showed that remains belonged to male), source: http://static.iea.ras.ru/books/7487_Traditsii.pdf

So either they haven’t mentioned his Y-DNA in the paper for some reason, or there are more than one Sidelkino sample and the male one has not yet been published. The coverage of the Sidelkino sample from the paper is 2.9, more than enough to tell Y-DNA haplogroup.

zaliznyak-post-swiderian
The map of spreading of Post-Swiderian and Post-Krasnosillian sites in Mesolithic of Eastern Europe in the 8th millennia BC. From Zaliznyak (see here).

My speculative guess right now about specific population movements in far eastern Europe, based on the few data we have:

  • The expansion of the North-Eastern Technocomplex first around the 9th millennium BC, most likely expanded R1b-P279 ca. 11300 BC, judging by its TMRCA, with both R1b-M73 (TMRCA 5300) and R1b-M269 (TMRCA 4400 BC) info (with extra El Mirón ancestry) back, and thus Eurasiatic.
  • The expansion of haplogroup J1 to the north may have happened before or after the R1b-P279 expansion. Judging by the increase in AG3-related ancestry near Karelia compared to Baltic_HG, it is possible that it expanded just after R1b-P279 (hence possibly J1-Y6304? TMRCA 9700 BC). Its long-lasting presence in the Caucasus is supported by the Satsurblia (ca. 11300 BC) and the Dolmen BA (ca. 1300 BC) samples.
  • The expansion of R1a-M17 ca. 6600 BC is still likely to have happened from the east, based on the R1a-M17 samples found in Baikalic cultures slightly later (ca. 5300 BC). The presence of elevated Baikal_EN ancestry in Karelia HG and in Samara HG, and the finding of R1a-M417 samples in the Forest Zone after the Mesolithic suggests a connection with the expansion of Hunter-Gatherer pottery, from the Elshanka culture in the Samara region northward into the Forset Zone and westward into the North Pontic area.
  • The expansion of R1b-M73 ca. 5300 BC is likely to be associated with the emergence of a group east of the Urals (related to the later Botai culture, and potentially Pre-Yukaghir). Its presence in a Narva sample from Donkalnis (ca. 5200 BC) suggest either an early split and spread of both R1b-P297 lineages (M73 and M269) through Eastern Europe, or maybe a back-migration with hunter-gatherer pottery.
  • R1b-M269 spread successfully ca. 4400 BC (and R1b-L23 ca. 4100 BC, both based on TMRCA), and this successful expansion is probably to be associated with the Khvalynsk-Novodanilovka expansion. We already know that Samara_HG ca. 5600 was R1b1a, so it is likely that R1b-M269 appeared (or ‘resurged’) in the Volga-Ural region shortly after the expansion of R1a-M17, whose expansion through the region may be inferred by the additional AG3 and Baikal_EN ancestry. Interesting from Samara_HG compared to the previous Sidelkino sample is the introduction of more El Mirón-related ancestry, typical of WHG populations (and thus proper of Baltic groups).

NOTE. The TMRCA dates are obviously gross approximations, because a) the actual rate of mutation is unknown and b) TMRCA estimates are based on the convergence of lineages that survived. The potential finding of R1a-Z645 (possibly Z93+) in Ukraine Eneolithic (ca. 4000 BC), and the potential finding of R1b-L23 in Khvalynsk ca. 4250 BC complicates things further, in terms of dates and origins of any subclade.

The question thus remains as it was long ago: did R1b-M269 lineages expand (‘return’) from the east, near the Urals, or directly from the north? Were they already near Samara at the same time as the expansion of hunter-gatherer pottery, and were not much affected by it? Or did they ‘resurge’ from populations admixed with Caucasus-related ancestry after the expansion of R1a-M17 with this pottery (since there are different stepped expansions from the Samara region)? We could even ask, did R1a-M17 really expand from the east, i.e. are the dates on Baikalic subclades from Moussa et al. (2016) reliable? Or did R1a-M17 expand from some pockets in the Pontic-Caspian steppe, taking over the expansion of HG pottery at some point?

hunger-gatherer-pottery
Early Neolithic cultures in eastern and central Europe: 1–Yelshanian; 2–North Caspian; 3–Rakushechnyj Yar; 4–Surskian; 5–Dnieper-Donetsian; 6– Bug-Dniesterian; 7–Upper Volga; 8–Narvian; 9–Linear Pottery. White arrows: expansion of early farming; black arrows: spread of pottery-making traditions. From Dolukhanov et al. (2009).

Maglemose-related migrations

The most interesting aspect from the new paper (regarding Indo-Uralic migrations) is that Ancestral Middle Easterner ancestry will probably be a better proxy for the Anatolia_Neolithic component found in Ukraine Mesolithic to Eneolithic, and possibly also for some of the “more CHG-like” component found among Pontic-Caspian steppe populations, all likely derived from different admixture events with groups from the Caucasus.

NOTE. Even the supposed gene flow of Neolithic Iranian ancestry into the Caucasus can be put into question, since that means possibly a Dzudzuana-like population with greater “deep ancestry” proportion than the one found in CHG, which may still be found within the Caucasus.

If it was not clear already that following ‘steppe ancestry’ wherever it appears is a rather lame way of following Indo-European migrations, every single sample from the Caucasus and their admixture with Pontic-Caspian steppe populations will probably show that “steppe ancestry” is in fact formed by a variety of steppe-related ancestral components, impossible to follow coherently with a single population. Exactly what is happening already with the Siberian ancestry.

If the paper on the Dzudzuana samples has shown something, is that the expansion of an ANE-like population shook the entire Caucasus area up to the Zagros Mountains, creating this ANE – AME cline that are CHG and Iran_N, with further contributions of “deep ancestries” (probably from the south) complicating the picture further.

If this happens with few known samples, and we know of an ANE-like ghost population in the Caucasus (appearing later in the Lola culture), we can already guess that the often repeated “CHG component” found in Ukraine_Eneolithic and Khvalynsk will not be the same (except the part mediated by the Novodanilovka expansion).

This ANE-like expansion happened probably in the Late Upper Palaeolithic, and reached Northern Europe probably after the expansion of the Villabruna cluster (ca. 12000 BC), judging by the advance of AG3-like and ENA-like ancestry in later WHG samples.

The population movements during the Mesolithic and Early Neolithic in the North Pontic area are quite complicated: the extra AME ancestry is probably connected to the admixture with populations from the Caucasus, while the close similarity of Ukraine populations with Scandinavian ones (with an increase in Villabruna ancestry from Mesolithic to Neolithic samples), probably reveal population movements related to the expansion of Maglemose-related groups.

maglemose-mesolithic
Etno-cultural situation in Central and Eastern Europe in the Late Mesolithic — Early Neolithic (VI—V Mill. BC) (after Конча 2004: 201, карта 1; made after ideas by L. L. Zaliznyak). Legend: 1 — Maglemose circle in the VII Mill. BC (after Gr. Clark); 2—7 — Mesolithic cultures of the Post-Maglemose tradition, VI Mill. BC (after S. Kozłowsky, L. L. Zaliznyak): 2 — de Leyen-Wartena; 3 — Oldesloe — Godenaa; 4 — Chojnice — Peńki; 5 — Janisłavice; 6 — finds of Janisłavice artefacts outside of the main area; 7 — Donets culture; 8 — directions of the settling of Janisłavice people (after S. Kozłowsky and L. L. Zaliznyak); 9 — the south border of Mesolithic and Early Neolithic cultures of post-Swidrian and post-Arensburgian traditions; 10 — northern border of settlement of the Balkan-Danubian farmers; 11 — Bug- Dniester culture; 12 — Neolithic cultures emerged on the ethno-cultural basis of post-Maglemose: Э — Ertebölle-Ellerbeck, Н — Neman, Д — Dnieper-Donets, М — Mariupol (western variants). From Klein (2017).

These Maglemose-related groups were probably migrants from the north-west, originally from the Northern European Plains, who occupied the previous Swiderian territory, and then expanded into the North Pontic area. The overwhelming presence of I2a (likely all I2a2a1b1b) lineages in Ukraine Neolithic supports this migration.

The likely picture of Mesolithic-Neolithic migrations in the North Pontic area right now is then:

  1. Expansion of R1a-M459 from the east ca. 12000 BC – probably coupled with AG3 and also some Baikal_EN ancestry. First sample is I1819 from Vasilievka (ca. 8700 BC), another is from Dereivka ca. 6900 BC.
  2. Expansion of R1b-V88 from the Balkans in the west ca. 9700 BC, based on its TMRCA and also the Balkan hunter-gatherer population overwhemingly of this haplogroup from the 10th millennium until the Neolithic. First sample is I1734 from Vasilievka (ca. 7252 BC), which suggests that it replaced the male population there, based on their similar EHG-like adxmixture (and lack of sizeable WHG increase), and shared mtDNA U5b2, U5a2.
  3. Expansion of I2a-Y5606 probably ca. 6800 based on its TMRCA with Janislawice culture. Supporting this is the increase in WHG contribution to Neolithic samples, including the spread of U4 subclades compared to the previous period.
  4. Expansion of R1a-M17 starting probably ca. 6600 BC in the east (see above).

NOTE. The first sample of haplogroup I appears in the Mesolithic: I1763 (ca. 8100 BC) of haplogroup I2a1, probably related to an older Upper Palaeolithic expansion.

janislawice
Distribution of archeological cultures in the North Pontic Region during the Mesolithic (7th – 6th millennium BCE). Dotted, dashed and solid lines with corresponding arrows indicate alternative models of the spread of the Grebenyky culture groups. (After Bryuako IV., Samojlova TL., Eds, Drevnie kul’tury Severo-­‐Zapadnogo Prichernomor’ya, Odessa: SMIL, 2013.) Nikitin – Ivanova 2017.

Conclusion

It is becoming more and more clear with each new paper that – unless the number of very ancient samples increases – the use of Y-chromosome haplogroups remains one of the most important tools for academics; this is especially so in the steppes, in light of the diversity found in populations from the Caucasus. A clear example comes from the Yamna – Corded Ware similarities:

After the publication of the 2015 papers, it was likely that Yamna expanded with haplogroup R1b-L23, but it has only become crystal clear that Yamna expanded through the steppes into Bell Beakers, now that we have data about the strict genetic homogeneity of the whole Yamna population from west to east (including Afanasevo), in contrast with contemporary Corded Ware peoples which expanded from a different forest-steppe population.

The presence of haplogroups Q and R1a-M459 (xM17) in Khvalynsk along with a R1b1a sample, which some interpreted as being akin to modern ‘mixed’ populations in the past, is likely to point instead to a period of Khvalynsk-Novodanilovka expansion with R1b-M269, where different small populations from the steppe were being integrated into the common Khvalynsk stock, but where differences are seen in material culture surrounding their burials, as supported by the finding of R1b1 in the Kuban area already in the first half of the 5th millennium. The case would be similar to the early ‘mixed’ Icelandic population.

Only after the emergence of the Samara culture (in the second half of the 6th millennium BC), with a sample of haplogroup R1b1a, starts then the obvious connection with Early Proto-Indo-Europeans; and only after the appearance of late Sredni Stog and haplogroup R1a-M417 (ca. 4000 BC) is its connection with Uralic also clear. In previous population movements, I think more haplogroups were involved in migrations of small groups, and only some communities among them were eventually successful, expanding to be dominant, creating ever growing cultures during their expansions.

Indeed, if you think in terms of Uralic and Indo-European just as converging languages, and forget their potential genetic connection, then the genetic + linguistic picture becomes simplified, and the upper frontier of the 6th millennium BC with a division North Pontic (Mariupol) vs. Volga-Ural (Samara) is enough. However, tracing their movements backwards – with cultural expansions from west to east (with the expansion of farming), and earlier east to west (with hunter-gatherer pottery), and still earlier west to east (with the north-eastern technocomplex), offers an interesting way to prove their potential connection to macrofamilies, at least in terms of population movements.

corded-ware-uralic-qpgraph
Modified image from Tambets et al. (2018) 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. The NeolL (Neolithic Levant) ancestry selected in this qpGraph is likely to correspond (at least in part) to a specific Dzudzuana-like component present in the CHG-like population that admixed in the North Pontic area.

I am quite convinced right now that it would be possible to connect the expansion of R1b-L754 subclades with a speculative Nostratic (given the R1b-V88 connection with Afroasiatic, and the obvious connection of R1b-L297 with Eurasiatic). Paradoxically, the connection of an Indo-Uralic community in the steppes (after the separation of Yukaghir) with any lineage expansion (R1a-M17, R1b-M269, or even Q, I or J1) seems somehow blurrier than one year ago, possibly just because there are too many open possibilities.

David Reich says about the admixture with Neanderthals, which he helped discover:

At the conclusion of the Neanderthal genome project, I am still amazed by the surprises we encountered. Having found the first evidence of interbreeding between Neanderthals and modern humans, I continue to have nightmares that the finding is some kind of mistake. But the data are sternly consistent: the evidence for Neanderthal interbreeding turns out to be everywhere. As we continue to do genetic work, we keep encountering more and more patterns that reflect the extraordinary impact this interbreeding has had on the genomes of people living today.

I think this is a shared feeling among many of us who have made proposals about anything, to fear that we have made a gross, evident mistake, and constantly look for flaws. However, it seems to me that geneticists are more preoccupied with being wrong in their developed statistical methods, in the theoretical models they are creating, and not so much about errors in the true ancient ethnolinguistic picture human population genetics is (at least in theory) concerned about. Their publications are, after all, constantly associating genetic finds with cultures and (whenever possible) languages, so this aspect of their research should not be taken lightly.

Seeing how David Anthony or Razib Khan (among many others) have changed their previously preferred migration models as new data was published, and they continue to be respected in their own fields, I guess we can be confident that professionals with integrity are going to accept whatever new picture appears. While I don’t think that genetic finds can change what we can reconstruct with comparative grammar, I am also ready to revise guesstimates and routes of expansion of certain dialects if R1a-Z645 is shown to have accompanied Late Proto-Indo-Europeans during their expansion with Yamna, and later integrated somehow with Corded Ware.

However, taking into account the obsession of some with an ancestral, uninterrupted R1a—Indo-European association, and the lack of actual political repercussion of Neanderthal admixture, I think the most common nightmare that all genetic researchers should be worried about is to keep inflating this “Yamnaya ancestry”-based hornet’s nest, which has been constantly stirred up for the past two years, by rejecting it – or, rather, specifying it into its true complex nature.

This succession of corrections and redefinitions, coupled with the distinct Y-DNA bottleneck of each steppe population, will eventually lead to a completely different ethnolinguistic picture of the Pontic-Caspian region during the Eneolithic, which is likely to eventually piss off not only reasonable academics stubbornly attached to the CWC-IE idea, but also a part of those interested in daydreaming about their patrilineal ancestors.

Sometimes it’s better to just rip off the band-aid once and for all…

Featured image from The oldest pottery in hunter-gatherer communitiesand models of Neolithisation of Eastern Europe (2015), by Andrey Mazurkevich and Ekaterina Dolbunova.

Related

Interesting is today’s post in Ancient DNA Era: Is Male-driven Genetic Replacement always meaning Language-shift?

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