Yamna/Afanasevo elite males dominated by R1b-L23, Okunevo brings ancient Siberian/Asian population


Open access paper New genetic evidence of affinities and discontinuities between bronze age Siberian populations, by Hollard et al., Am J Phys Anthropol. (2018) 00:1–11.

NOTE. This seems to be a peer-reviewed paper based on a more precise re-examination of the samples from Hollard’s PhD thesis, Peuplement du sud de la Sibérie et de l’Altaï à l’âge du Bronze : apport de la paléogénétique (2014).

Interesting excerpts:

Afanasevo and Yamna

The Afanasievo culture is the earliest known archaeological culture of southern Siberia, occupying the Minusinsk-Altai region during the Eneolithic era 3600/3300 BC to 2500 BC (Svyatko et al., 2009; Vadetskaya et al., 2014). Archeological data showed that the Afanasievo culture had strong affinities with the Yamnaya and pre-Yamnaya Eneolithic cultures in the West (Grushin et al., 2009). This suggests a Yamnaya migration into western Altai and into Afanasievo. Note that, in most current publications, “the Yamnaya culture” combines the so-called “classical Yamnaya culture” of the Early Bronze Age and archeological sites of the preceding Repin culture in the middle reaches of the Don and Volga rivers. In the present article we conventionally use the term Yamnaya in the same sense, in which case the beginning of the “Yamnaya culture” can be dated after the middle of the 4th millennium BC, when the Afanasievo culture appeared in the Altai.

Because of numerous traits attributed to early Indo-Europeans and cultural relations with Kurgan steppe cultures, members of the Afanasievo culture are believed to have been Indo-European speakers (Mallory and Mair, 2000). In a recent whole-genome sequencing study, Allentoft et al. (2015) concluded that Eastern Yamnaya individuals and Afanasievo individuals were genetically indistinguishable. Moreover, this study and one published concurrently by Haak et al. (2015) analyzed 11 Eastern Yamnaya males and showed that all of them belonged to the R1b1a1a (formerly R1b1a) (…)

Early Chalcolithic migrations ca. 3300-2600 BC.

Published works indicate that R1b was a predominant haplogroup from the late Neolithic to the early Bronze Age, notably in the Bell Beaker and Yamnaya cultures (Allentoft et al., 2015; Haak et al., 2015; Lee et al., 2012; Mathieson et al., 2015). Nearly 100% of the Afanasievo men we typed belonged to the R1b1a1a subhaplogroup and, for at least three of them, more precisely to the L23 (xM412) subclade. (…)

(…) our results therefore support the hypothesis of a genetic link between Afanasievo and Yamnaya. This also suggests that R1b was indeed dominant in the early Bronze Age Siberian steppe, at least in individuals that were buried in kurgans (possibly an elite part of the population). The geographical and temporal distribution of subhaplogroup R1b1a1a supports the hypothesis of population expansion from West to East in the Eurasian steppe during this period. It should however be noted that the Yamnaya burials from which the samples for DNA analysis were obtained (Allentoft et al., 2015; Haak et al., 2015; Mathieson et al., 2015) were dated within the limits of the Afanasievo period. Ancestors of both East Yamnaya and Afanasievo populations must therefore be sought in the context of earlier Eneolithic cultures in Eastern Europe. Sufficient Y-chromosomal data from such Eneolithic populations is, unfortunately, not yet available.

Mitochondrial- (A) and Y- (B) haplogroup distribution in studied populations

Okunevo and paternal lineage shift in South Siberia

Results obtained in the current study, from more than a dozen Okunevo individuals belonging to the earliest stage of Okunevo culture, that is the Uibat period (2500–2200 BC) (Lazaretov, 1997), suggest a discontinuity in the genetic pool between Afanasievo and Okunevo cultures. Although Y-chromosomal data obtained for bearers of the Okunevo culture showed that one individual carried haplogroup R1b, most Okunevo Y-haplogroups are representative of an Asian component represented by paternal lineages Q and NO1.

Okunevo carrier of Y-haplogroup Q1b1a-L54, which also supports this hypothesis (L54 being a marker of the lineage from which M3, the main Ameridian lineage, arose). Okunevo people could therefore be a remnant paleo-Siberian population with possible Afanasievo input, as suggested by the presence of the R1b1a1a2a subhaplogroup in one individual.

Late Chalcolithic migrations ca. 2600-2250 BC.

Replacement of Asian Indo-European elite lineages by R1a

Published genetic data from the late Bronze Age Andronovo culture from the Minusinsk Basin (Keyser et al., 2009), the Sintashta culture from Russia (Allentoft et al., 2015) and the Srubnaya culture from the region of Samara (Mathieson et al., 2015), show that males did not belong to Y-haplogroup R1b but mostly to R1a clades: there appears to have been a change in the dominant Y-chromosomal haplogroup between the early and the late Bronze Age in these regions. Moreover, as described in Allentoft et al. (2015), the Andronovo and Sintashta peoples were closely related to each other but clearly distinct from both Yamnaya and Afanasievo. Although these results do not imply that Y-haplogroup R1b was entirely absent in these later populations, they could correspond to a replacement of the elite between these two main periods and therefore a difference in the haplogroups of the men that were preferentially buried.

Early Bronze Age migrations ca. 2250-1750 BC.

Afanasevo and the Tarim Basin

The discovery, in the Tarim Basin, of well-preserved mummies from the Bronze Age allows for the construction of two hypotheses regarding the peopling of the Xinjiang province at this period. The “steppe hypothesis,” argues for a link with nomadic steppe herders (Hemphill and Mallory, 2004), possibly represented in this case by Afanasievo populations and their descendants (Mallory and Mair, 2000). However, newly published cultural data from the burial grounds of Gumugou (Wang, 2014) and Xiaohe (Xinjiang, 2003, 2007) shows material culture and burial rites incompatible with the Afanasievo culture. The earliest 14C date for Tarim Basin burials would place them at the turn of the 2nd millenium BC (Wang, 2013), 500 years after the Afanasievo period.

Instead, early Gumugou and Xiaohe burial grounds were contemporary with the start of the Andronovo period. Likewise, the Bronze Age population of the Xinjiang at Gumugou/Qäwrighul is not phenotypically closest to Afanasievo but to the Andronovo (Fedorovo) group of northeastern Kazakhstan and western Altai (Kozintsev, 2009). Our investigations demonstrate that Y-chromosomal lineage composition is also compatible with the notion that the ancient Tarim population was genetically distinct from the Afanasievo population. The only Y-haplogroup found by Li et al. (2010) in the Bronze Age Tarim Basin population was Y-haplogroup R1a, which suggests a proximity of this population with Andronovo groups rather than Afanasievo groups.

I don’t think these finds are much of a surprise based on what we already know, or need much explanation…

I would add that, once again, we have more proof that the movement of Okunevo and related ancient Siberian migrants from Central or North Asia will not be able to explain the presence of Uralic languages spread over North-East Europe and Scandinavia already during the Bronze Age.

Also interesting is to read in more peer-reviewed papers the idea of Late Indo-European speakers clearly linked to the expansion of patrilineally-related elite males marked by haplogroup R1b-L23, most likely since Eneolithic Khvalynsk/Repin cultures.


North Asian mitogenomes hint at the arrival of pastoralists from West to East ca. 2800-1000 BC


Open access Investigating Holocene human population history in North Asia using ancient mitogenomes, by Kılınç et al., Scientific Reports (2018) 8: 8969.

Abstract (emphasis mine):

Archaeogenomic studies have largely elucidated human population history in West Eurasia during the Stone Age. However, despite being a broad geographical region of significant cultural and linguistic diversity, little is known about the population history in North Asia. We present complete mitochondrial genome sequences together with stable isotope data for 41 serially sampled ancient individuals from North Asia, dated between c.13,790 BP and c.1,380 BP extending from the Palaeolithic to the Iron Age. Analyses of mitochondrial DNA sequences and haplogroup data of these individuals revealed the highest genetic affinity to present-day North Asian populations of the same geographical region suggesting a possible long-term maternal genetic continuity in the region. We observed a decrease in genetic diversity over time and a reduction of maternal effective population size (Ne) approximately seven thousand years before present. Coalescent simulations were consistent with genetic continuity between present day individuals and individuals dating to 7,000 BP, 4,800 BP or 3,000 BP. Meanwhile, genetic differences observed between 7,000 BP and 3,000 BP as well as between 4,800 BP and 3,000 BP were inconsistent with genetic drift alone, suggesting gene flow into the region from distant gene pools or structure within the population. These results indicate that despite some level of continuity between ancient groups and present-day populations, the region exhibits a complex demographic history during the Holocene.

Relationship between ancient North Asians and other populations based on haplogroup frequencies. Ancient North Asians as a single group (SIB, n = 41) and as divided into three different regional groups including Cis-Baikal (CISB, n = 23), Trans-Baikal (TRAB, n = 7) and Yakutia (YAK, n = 9) or as divided into three temporal groups including Early (7,000 BP, n = 11), Middle (4800 BP, n = 16) and Late (3000 BP, n = 11). Two individuals from Krasnoyarsk and Blagoveshensk are not included in regional groups due to their distinct geographical locations. (a) Barplot showing haplogroup frequencies on a dataset of 1,780 individuals. PCA plot based on haplogroup frequencies calculated using (b) 291 individuals with full mitochondrial sequences. Ancient North Asians are included as a single population. (c) 1,780 individuals. Ancient North Asians are included as three different regional groups in the analysis. See also Supplementary Tables S1, S4–S12 and Fig. S3a and b in Supplementary Information.

Interesting excerpts:

Although highly dependent on sample size and thus prone to generalization, haplotype sharing analysis between three spatial groups and other modern and ancient populations (Supplementary Table S15) revealed that the TRAB group shared most lineages with ancient Kazakh Altai (KA) and modern Nganasan (NGN)39,40,41,42. The CISB group shared most lineages with Tubalar39,42, KA43 and Early Bronze Age groups of Russia (BO)12, which might reflect the Siberian roots of BO, consistent with MDS based on Fst (Fig. 3b). The YAK group shared most lineages with the CISB, BO and Tubalar groups. These results showed that despite being from different sides of the Lake Baikal, the CISB and YAK groups shared most lineages with the Tubalar and also both of them were to a certain degree affiliated to the BO of the Cis-Baikal region, thus, reflecting a shared common ancestry. Furthermore, the CISB and YAK groups share lineages supporting the hypothesis of a lasting continuity in this large geographical territory. However, the TRAB group may have different legacy with affinities to ancient Kazakh Altai and modern Nganasan groups (that, actually, may have relocated from the Trans-Baikal region in times post-dating our sample).

Relationship between ancient North Asians and other ancient and present-day populations based on Slatkin’s linearized pairwise FST. MDS plot based on Slatkin’s linearized pairwise FST calculated using (a) full mitochondrial DNA sequences. (b) HVRI sequences. See also Fig. S3c and d in Supplementary Information, Supplementary Tables S13–S15.

Two findings, however, were intriguing. One was the discovery of only weak support for a single regional population in comparisons between Early vs. Late as well as Middle vs. Late groups in the region. This may be explained by population structure, as the Late group comprised geographically very distant individuals, such as individuals from Krasnoyarsk Krai and Amur Oblast, not represented in the other diachronic groups (Table S9). Another explanation for rejecting the null hypothesis of continuity between the Middle and Late (4,800–3,000 BP) groups might be due to an interruption and the arrival of pastoralists at the beginning of the Iron Age between 3,670 to 2,760  BP as suggested by the archaeological record32. Thus, the introduction of the new lifeways, technologies and material culture expressions might also here be associated to an increased mobility into the area.

The second point was the estimated reduction in maternal effective population size and haplotype diversity around 7,000 BP. Intriguingly, climate modelling and radiocarbon dating studies53 suggest that climatic change and a collapse of the riverine ecosystems might have affected the human populations in Cis Baikal between 7,000–6,000 BP in line with our results. This finding was further supported by archaeological studies pointing to a possible hiatus38,54,55.

Although our results provide a first glimpse into population structure and diversity in North Asia during the Holocene which link to trend in the archaeological record, complete genome sequences will provide a higher resolution of more complex demographic events in the region.

Yet another hint at the west-east (and not east-west) population movement in Eurasia after the Corded Ware and Yamna expansions, without any significant change in the other direction until the Iron Age (as we know from Fennoscandian samples), which leaves still less space to propose incoming Uralic-speaking groups from Asia…