Updated phylogenetic tree of haplogroup Q-M242 points to Palaeolithic expansions


New paper (behind paywall) Paternal origin of Paleo-Indians in Siberia: insights from Y-chromosome sequences by Wei et al., Eur. J. Hum. Genet. (2018)

Interesting excerpts (for Eurasian migrations):

Differentiation and diffusion in Palaeolithic Siberia

Based on the phylogenetic analyses and the current distributions of relative sub-lineages, we propose that the prehistoric population differentiation in Siberia after the LGM (post-LGM) provided the genetic basis for the emergence of the Paleo-Indian, American aborigine, population. According to the phylogenetic tree of Y-chromosome haplogroup C2-M217 (Fig. 2 and Figure S1), eight sub-lineages emerged in a short period between 15.3 kya and 14.3 kya (Table S5). Within these sub-lineages, haplogroups C2-M48, C2-F1918, and C2- F1756 are predominant paternal lineages in modern Altaic-speaking populations [46, 51, 52]. Samples of haplogroups C2-F8535 and C2-P53.1 were found in two Turkic- and Mongolic-speaking minorities in China (Table S1). Both archeological and genetic data suggest that Altaic-speaking populations are results of population expansion in the past several thousand years in the Altai Mountain, Mongolia Plateau, and Amur River region [51–54].

By contrast, three other sub-lineages, C2-B79, C2-B77, and C2-P39, appear only in Koryaks and Native Americans [16, 35]. The latitude of the Altai Mountain, the Mongolia Plateau, and Amur River region are much lower than that of Beringia, where the ancestors of Native Americans finally separated from their close relatives in Siberia. Therefore, the phylogeographic patterns of sub-lineages of C2-M217 in this study reveal a major splitting event between populations in a lower latitude region of Siberia and ancestors of Koryaks and Native Americans during the post-LGM period.

The sub-lineages of the Y-chromosome Q-M242 haplogroup were found in populations throughout the Eurasia continent. According to available data, the Q1-L804 lineage is exclusively found in Northwest Europe, while Q1-M120 is primarily restricted to East Asia [48]. Additionally, the lineage Q1-L330 is the predominant paternal lineage in Altai, Tuva, and Kets in South Siberia [34–36, 55]. A number of Q1-M242 samples have also been found in ancient remains from South Siberia and adjacent regions [56, 57]. Other sub-lineages of Q-M242 are scattered widely in different geographic regions of Eurasia, including Q1-L275, Q1-M25, and Q1-Y2659 [14, 35, 37, 58]. Additionally, the Y-chromosome of a 6000–5100 BCE sample (I4550) from Zvejnieki, Latvia has been identified as Q1-L56 [59]. These findings suggest that the sub-lineages of Q-M242 started to diffuse throughout Eurasia in a very ancient period.

Founding paternal lineages of American aborigines and their most closely related lineages among Eurasia populations

Emergence of Paleo-Indian populations

The revised phylogenetic tree of Y-chromosome haplogroup Q-M242 in this study provides clues regarding the origin of Native American lineages Q1-M3 and Q1-Z780 (Fig. 3). According to our estimates, haplogroup Q1-L54 expanded rapidly between 17.2 kya and 15.0 kya and finally gave rise to two major founding paternal lineages of Native American populations, known as Q1-Z780 and Q1-M3. Ancient DNA studies indicate that the early population in South Siberia, represented by MA1 genomes, had a genetic influence on both modern western European and Native American populations [7]. Therefore, we conclude that the accumulated diversity of sub-lineages of Q-M242 before 15.3 kya resulted from the in situ differentiation of Q-M242 in Central Eurasia and South Siberia since the Paleolithic Age, and the appearance of the Paleo-Indian population is part of the great human diffusion throughout the Eurasia after the Last Glacial Maximum.

The Southern Caucasus PIE homeland

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. An EHG and a Caucasus ‘clouds’ have been drawn, leaving Pontic-Caspian steppe and derived groups between them.See the original file here.

The origin of Q-M242 in Zvejnieki, like those of Lola (Q1a2-M25) and Steppe Maykop (Q1a2-M25) from Wang et al. (2018) are therefore most likely migrations throughout North Eurasia dated to the Palaeolithic.

As you might remember, the sample of haplogroup Q1a from Khvalynsk was the closest one (in the PCA, see above) to those we now know most likely represent one or more groups of the steppe north of the Caucasus, which were absorbed during the formation and expansion of Khvalynsk.

NOTE. In fact, the position of this early Khvalynsk sample in the PCA is near the Steppe Eneolithic cluster, in turn near ANE (with the Lola sample Q1a2-M25, circle in dark blue/violet above), and Steppe Maykop (which includes the other Q1a2-M25 sample).

It is often assumed that these populations absorbed in the Pontic-Caspian steppe were dominated by haplogroup J, due to the oldest representatives of CHG ancestry (Kotias Klde and Satsurblia).

However, it would not be surprising now to find out that (one or more of) these “CHG/ANE-rich” groups from the steppe (possibly the Kairshak culture in the North Caspian region) were in fact dominated by Q1-M25 subclades.

If this is the case, I don’t know where the proponents of the (south of the) Caucasus homeland will retreat to.


Mitogenomes from the middle of the Merovingian period in the Lorraine region


Investigating the kinship between individuals deposited in exceptional Merovingian multiple burials through aDNA analysis: The case of Hérange burial 41 (Northeast France), by Deguilloux et al. Journal of Archaeological Science: Reports (2018) 20:784-790.

Interesting excerpts (emphasis mine):

The Merovingian period in Northeast France (developing from 440/450 to 700/710 CE; Legoux et al., 2004) represents [a case of multiple burial], where a large majority of the types of deposits encountered consists of individual burials. In this context, whereas hundreds of individual burials are known, the syntheses recently conducted have enabled the inventory of only six multiple burials (Lefebvre and Lafosse, 2016). These observations naturally raised questions about the exceptional circumstances that led the members of the community to set up such unusual burials. The archaeological site of Hérange, excavated in 2014 (Lorraine, Grand Est region; Fig. S1), holds a key position in the debate surrounding the interpretation of multiple burials during the Merovingian period since it contains one of these rare multiple burials: burial 41, which was dated through archaeological material to the period 530–640 CE.

(…) The biological analysis of the human remains recovered in the second burial (“burial 41”) enabled the demonstration of the combined presence of a woman of approximately 40 years old (A) and three immature individuals, including a 4–5-year-old child (B), a 14–16-year-old teenager (C) and a 2,5–3-month-old infant (D) (Lefebvre and Lafosse, 2016) (Fig. 1). Since rare multiple burials described for the Merovingian period in Northeast France mainly contained two or rarely three deceased, the discovery of a burial grouping four individuals reinforced its exceptional nature. (…) Intriguingly, great care was observed in the treatment of the dead, as illustrated through a special arrangement of the deceased in the grave (Fig. 1). Indeed, the woman A occupied a central position in the grave, with her left arm covering part of the body of child D, her right arm covering the torso of child B and her right hand covering the legs of children B and C. Several arguments, such as the close contact or the imbrication of the bones of individuals A, B and C, have attested to the simultaneity of their deposits in the burial (Lefebvre and Lafosse, 2016).

Geographic distribution of the extant European individuals sharing mitochondrial haplotypes with the Hérange human remains.

Interestingly, studies have demonstrated an important chronological homogeneity for the rare multiple burials discovered for the Merovingian period in the Lorraine region (Lefebvre and Lafosse, 2016). The collected data support the existence of an epiphenomenon arisen around the middle of the Merovingian period and that may have linked the multiple burials to (i) a funerary “fashion trend” for a special group of the community, (ii) an increase in cases of violence or (iii) an epidemic crisis linked to infectious disease. In other Lorraine sites, none of the available indices permitted the specification of the cause of death for the individuals recovered in these specific burials. The deceased could well have died of natural causes, violent acts or infectious diseases that had left no visible evidence on the skeletal.

Nuclear data (Y chromosome SNPs and nuclear STRs) typed on the four Hérange human remains (STRs alleles shown in grey were not fully replicated).

The aDNA analyses conducted on the four individuals discovered in the exceptional multiple burial 41 from Hérange (Lorraine) have demonstrated strong biological links between three individuals. Notably, we could propose that the woman A was the mother of the two immatures B and D deposited just besides her whereas she was not genetically closely related to the teenager C deposited along her legs. Consequently, we propose that the special arrangement of the deceased in the grave clearly reflected the degree of biological links between the deposited individuals. In Hérange, the bereaved were well aware of kinship among the deceased, wanted to express this close linkage through their relative location within the burial, and intentionally arranged body positions consequently. In conclusion, the collected archaeological, archaeo-anthropological and genetic data suggest that the special setup of the multiple burial 41 in the Hérange necropolis and the great care in the treatment of the dead, could be explained by the contemporaneous death of the four related individuals. Data gathered for other archaeological sites from the region or in Germany suggested an epidemic crisis (plague epidemic?) during the middle of the Merovingian period that may explain the contemporaneous death of related individuals living in close contact and easily sharing pathogens.


Reported mtDNA haplogroups include U* for samples A, B, and D, and H for sample C.


Expansion of domesticated goat echoes expansion of early farmers


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

Interesting excerpts (emphasis mine):

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

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

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

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


Recent Africa origin with hybridization, and back to Africa 70,000 years ago


Open access Carriers of mitochondrial DNA macrohaplogroup L3 basal lineages migrated back to Africa from Asia around 70,000 years ago, by Cabrera et al. BMC Evol Biol (2018) 18(98).

Abstract (emphasis mine):


The main unequivocal conclusion after three decades of phylogeographic mtDNA studies is the African origin of all extant modern humans. In addition, a southern coastal route has been argued for to explain the Eurasian colonization of these African pioneers. Based on the age of macrohaplogroup L3, from which all maternal Eurasian and the majority of African lineages originated, the out-of-Africa event has been dated around 60-70 kya. On the opposite side, we have proposed a northern route through Central Asia across the Levant for that expansion and, consistent with the fossil record, we have dated it around 125 kya. To help bridge differences between the molecular and fossil record ages, in this article we assess the possibility that mtDNA macrohaplogroup L3 matured in Eurasia and returned to Africa as basal L3 lineages around 70 kya.


The coalescence ages of all Eurasian (M,N) and African (L3 ) lineages, both around 71 kya, are not significantly different. The oldest M and N Eurasian clades are found in southeastern Asia instead near of Africa as expected by the southern route hypothesis. The split of the Y-chromosome composite DE haplogroup is very similar to the age of mtDNA L3. An Eurasian origin and back migration to Africa has been proposed for the African Y-chromosome haplogroup E. Inside Africa, frequency distributions of maternal L3 and paternal E lineages are positively correlated. This correlation is not fully explained by geographic or ethnic affinities. This correlation rather seems to be the result of a joint and global replacement of the old autochthonous male and female African lineages by the new Eurasian incomers.


These results are congruent with a model proposing an out-of-Africa migration into Asia, following a northern route, of early anatomically modern humans carrying pre-L3 mtDNA lineages around 125 kya, subsequent diversification of pre-L3 into the basal lineages of L3, a return to Africa of Eurasian fully modern humans around 70 kya carrying the basal L3 lineages and the subsequent diversification of Eurasian-remaining L3 lineages into the M and N lineages in the outside-of-Africa context, and a second Eurasian global expansion by 60 kya, most probably, out of southeast Asia. Climatic conditions and the presence of Neanderthals and other hominins might have played significant roles in these human movements. Moreover, recent studies based on ancient DNA and whole-genome sequencing are also compatible with this hypothesis.


You can also read the recent interesting open access review How did Homo sapiens evolve? by Julia Galway-Witham, Chris Stringer, Science (2018) 360:6395 1296-1298.


Reconstruction of Y-DNA phylogeny helps also reconstruct Tibeto-Burman expansion


New paper (behind paywall) Reconstruction of Y-chromosome phylogeny reveals two neolithic expansions of Tibeto-Burman populations by Wang et al. Mol Genet Genomics (2018).

Interesting excerpts:

Archeological studies suggest that a subgroup of ancient populations of the Miaodigou culture (~ 6300–5500 BP) moved westward to the upper stream region of the Yellow River and created the Majiayao culture (~ 5400–4900 BP) (Liu et al. 2010), which was proposed to be the remains of direct ancestors of Tibeto-Burman populations (Sagart 2008). On the other hand, Han populations, the other major descendant group of the Yang-Shao culture (~ 7000–5500 BP), are composed of many other sub-lineages of Oα-F5 and extremely low frequencies of D-M174 (Additional files 1: Figure S1; Additional files 2: Table S1). Therefore, we propose that Oα-F5 may be one of the dominant paternal lineages in ancient populations of Yang-Shao culture and its successors.

In this study, we demonstrated that both sub-lineages of D-M174 and Oα-F5 are founding paternal lineages of modern Tibeto-Burman populations. The genetic patterns suggested that the ancestor group of modern Tibeto-Burman populations may be an admixture of two distinct ancient populations. One of them may be hunter–gatherer populations who survived on the plateau since the Paleolithic Age, represented by varied sub-lineages of sub-lineages of D-M174. The other one was comprised of farmers who migrated from the middle Yellow River basin, represented by sub-lineages of Oα-F5. In general, the genetic evidence in this study supports the conclusion that the appearance of the ancestor group of Tibeto-Burman populations was triggered by the Neolithic expansion from the upper-middle Yellow River basin and admixture with local populations on the Tibetan Plateau (Su et al. 2000).

Simplified phylogenetic tree showing sample locations. The size of the circle for each sampling location corresponds to the number of samples

Two neolithic expansion origins of Tibeto‑Burman populations

We also observed significant differences in the paternal gene pool of different subgroups of Tibeto-Burman populations. Haplogroup D-M174 contributed ~ 54% percent in a sampling of 2354 Tibetan males throughout the Tibetan Plateau (Qi et al. 2013). Previous studies have also found high frequencies of D-M174 in other populations on the Tibetan Plateau (Shi et al. 2008), including Sherpa (Lu et al. 2016) and Qiang (Wang et al. 2014). In contrast, haplogroup D-M174 is rare or absent from Tibeto-Burman populations from Northeast India and Burma (Shi et al. 2008). In populations of the Ngwi-Burmese language subgroup, the average frequencies of haplogroup D-M174 are ~ 5% (Dong et al. 2004; Peng et al. 2014). Furthermore, we found that lineage Oα1c1b-CTS5308 is mainly found in Tibeto-Burman populations from the Tibetan Plateau. In contrast, lineage Oα1c1a-Z25929 was found in Tibeto-Burman populations from Northeast India, Burma, and the Yunan and Hunan provinces of China (Additional files 1: Figure S1; Additional files 2: Table S1). In general, enrichment of lineage Oα1c1b- CTS5308 and high frequencies of D-M174 can be found in most Tibeto-Burman populations on the Tibetan Plateau and adjacent regions, whereas Tibeto-Burman populations from other regions tend to have lineage Oα1c1a-Z25929 and a little to no percentage of D-M174.

The inconsistent pattern we observed in the paternal gene pool of modern Tibeto-Burman populations suggested that there may be two distinct ancestor groups (Fig. 3). The proposed migration routes shown in Fig. 3 are somewhat different from those proposed by Su et al. (2000). According to our age estimation, most of the D1a2a-P47 samples belong to sub-lineage PH116, a young lineage that emerged ~ 2500 years ago (95% CI 1915–3188 years). On the other hand, continuous differentiation can be observed on a phylogenetic tree of lineages D1a1a1a1-PH4979 and D1a1a1a2-Z31591 since 6000 years ago. Therefore, we proposed that a group of ancient populations may have moved to the upper basin of the Yellow River and admixed intensively with local populations with high frequencies of haplogroup D-M174, including its sub-lineage D1a2a-P47 (Fig. 3). This ancestor group eventually gave birth to modern Tibeto-Burman populations on the Tibetan Plateau and adjacent regions. The other ancestor group moved toward the southwest and finally reached South East Asia (Burma and other locations) and the northeastern part of India (Fig. 3). This ancestor group may have had no or a minor admixture of D-M174 in their paternal gene pool.

Two proposed ancestor groups and migration routes for Tibeto-Burman populations

Long‑term admixture before expansion to a high‑altitude region

It is interesting to investigate the time gap between the appearance of Neolithic cultures in the northeastern part of the Tibetan Plateau and the final phase of human expansion across the Tibetan Plateau. The Majiayao culture (~ 5400–4900 BP) is the earliest Neolithic culture in the northeastern part of the Tibetan Plateau (Liu et al. 2010). However, previous archeological study has suggested that the final phase of diffusion into the high-altitude area of the Tibetan Plateau occurred at approximately 3.6 kya (Chen et al. 2015). Our genetic evidence in this study is consistent with this scenario based on archeological evidence. Based on Y-chromosome analysis in this study, many unique lineages of Tibeto-Burman populations emerged between 6000 years ago and 2500 years ago (Additional files 3: Table S2). The most recent common age of D1a2-PH116, a sub-lineage that spread throughout the Tibetan Plateau, is only 2500 years ago.

We propose that there may be two important factors for the observed age gap. First, living in a high-altitude environment may require some crucial physical characteristics that were lacking from Neolithic immigrants from the middle Yellow River Basin. Intense genetic admixture with local people who had survived on the Tibetan Plateau since the Paleolithic Age may have actually guaranteed the expansion of humans across the Tibetan Plateau. Therefore, a long period of admixture, lasting from 5.4 to 3.6 kya, may be necessary for the appearance of a population with beneficial genetic variants that was genetically adapted to the high-altitude environment. Second, technological innovations, such as the domestication of wheat and highland barley (Chen et al. 2015), establishment of yak pastoralism (Rhode et al. 2007), and introduction of other culture elements in the Bronze Age (Ma et al. 2016), are also important factors that facilitated permanent settlements with large population sizes in the high-altitude area of the Tibetan Plateau.


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.


Canid Y-chromosome phylogeny reveals distinct haplogroups among Neolithic European dogs


Open access Analysis of the canid Y-chromosome phylogeny using short-read sequencing data reveals the presence of distinct haplogroups among Neolithic European dogs, by Oetjens et al., BMC Genomics (2018) 19:350.

Interesting excerpts (modified for clarity, emphasis mine):


Canid mitochondrial phylogenies show that dogs and wolves are not reciprocally monophyletic. The mitochondrial tree contains four deeply rooted clades encompassing dogs and many grey wolf groups. These four clades form the basis of dog mitochondrial haplogroup assignment, known as haplogroups A-D. The time of the most recent common ancestor (TMRCA) of haplogroups A-D significantly predates estimates for domestication based on archeological and genetic evidence. Instead, these clades may represent variation present among the founding population of the dog lineage or the results of wolf introgressions into dog populations. The relative frequencies of mitochondria haplogroups are not stable over time, with changes reflecting processes such as drift, migration, and population growth. Although the mitochondria A and B haplogroups are most common in contemporary European dogs, surveys of ancient samples indicate that the majority of ancient European dogs carried the C or D mitochondrial haplotype. This apparent turnover in mitochondrial haplogroups may reflect the migration of a distinct dog population into Europe over the past 15,000 years.

Maximum likelihood phylogeny of 118 candid Y-chromosomes A Y-chromosome haplogroup tree produced by RAxML (8.1.13) using the GTR+ I model is depicted. Clades in the tree have been collapsed by haplogroup assignment. The number of samples within each collapsed node is indicated in parentheses next to the haplogroup assignment. For each node, percent bootstrap support out of 1000 iterations is indicated above the branch. The locations of three ancient samples, based on the presence of diagnostic mutations, are indicated in red


Using the variation discovered from sequence data, we applied a Bayesian MCMC approach to estimate TMRCAs for each haplotype group. Our estimated Y-chromosome mutation rate (3.07 × 10− 10 substitutions per site per year, relaxed clock model) falls within the range of a previous estimate by Ding et al. who used a similar calibration and estimate 1.35 × 10− 10– 4.31 × 10− 10 substitutions per site per year. The TMRCAs we estimated are substantially older than mitochondria phylogenies calibrated with tip dates of ancient samples, which report clade-specific TMRCAs < 25,000 years ago. We note that our Y-chromosome TMRCA estimates are extremely sensitive to our assumptions about the age of the root of the tree and should be interpreted with caution due to the uncertainty in this single calibration point. However, the relative ages of the branches and the chronological order of haplogroup divergences are more robust than the absolute estimated dates.

In general, the relationships between Y-chromosome haplogroups and autosomal ancestry we report are very similar to the relationships described in Shannon et al. As noted earlier, our dataset includes a subset of wolves with Y-chromosomes assigned to a dog Y-haplogroup. However, ADMIXTURE analysis does not indicate substantial recent dog ancestry in these samples, suggesting that their placement on the Y-chromosome phylogeny reflects variation in Y-chromosome haplotypes that was present in the ancestral population and therefore predates the domestication process or is the result of ancient introgression events whose signature of autosomal ancestry has been diluted.

The relationship between autosomal ancestry and Y-chromosome haplogroups Major groupings of canine ancestry are shown based on a principal components analysis of autosomal markers from 499 village dogs from Shannon et al. a. The geographic origin of each sample is indicated by color. The 104 male dogs used in this study are projected onto the resulting principal components and colored based on haplogroup (b). Village dogs from (a) are shown as transparent dots in (b)


Using sequencing data, we find that the estimated TMRCA of dog Y haplogroups predates dog domestication. We further reveal the placement of several wolf Y-chromosomes within deep branches of dog haplogroup clades. Using an expanded set of mutations diagnostic for each haplogroup, we find that distinct Y haplogroups were present in Europe during the Neolithic and that CTC, a ~ 4700 year old ancient dog from Germany has a Y-chromosome that shares diagnostic alleles with wolves found in India.

Other studies

On the same subject, you can read another recent study, bioRxiv preprint New Evidence of the Earliest Domestic Dogs in the Americas, by Perri et al. (2018); and also a recent, open access paper (see above featured image) Ancient European dog genomes reveal continuity since the Early Neolithic, by Botigué et al., Science Communications (2017).

While Proto-Indo-European- and Proto-Uralic-speakers had a close relationship with dogs (revealed in their reconstructed language and attributed archaeological cultures), I think it will be very difficult to ascertain any population movement based on them, unless there is a clear, well-established archaeological relationship between a specific culture and dog-breeding.

Nevertheless, I would say that this kind of studies are more likely to give some information related to these and other cultures than, for example, the study of honeybees in honey-hunting vs. beekeeping cultures (see e.g. The Complex Demographic History and Evolutionary Origin of the Western Honey Bee, Apis Mellifera, by Cridland, Tsutsui, and Ramírez GBE 2017), which was also related to the development of both PIE and PU cultures.

See also:

Domesticated horse population structure, selection, and mtDNA geographic patterns


Open access Detecting the Population Structure and Scanning for Signatures of Selection in Horses (Equus caballus) From Whole-Genome Sequencing Data, by Zhang et al, Evolutionary Bioinformatics (2018) 14:1–9.

Abstract (emphasis mine):

Animal domestication gives rise to gradual changes at the genomic level through selection in populations. Selective sweeps have been traced in the genomes of many animal species, including humans, cattle, and dogs. However, little is known regarding positional candidate genes and genomic regions that exhibit signatures of selection in domestic horses. In addition, an understanding of the genetic processes underlying horse domestication, especially the origin of Chinese native populations, is still lacking. In our study, we generated whole genome sequences from 4 Chinese native horses and combined them with 48 publicly available full genome sequences, from which 15 341 213 high-quality unique single-nucleotide polymorphism variants were identified. Kazakh and Lichuan horses are 2 typical Asian native breeds that were formed in Kazakh or Northwest China and South China, respectively. We detected 1390 loss-of-function (LoF) variants in protein-coding genes, and gene ontology (GO) enrichment analysis revealed that some LoF-affected genes were overrepresented in GO terms related to the immune response. Bayesian clustering, distance analysis, and principal component analysis demonstrated that the population structure of these breeds largely reflected weak geographic patterns. Kazakh and Lichuan horses were assigned to the same lineage with other Asian native breeds, in agreement with previous studies on the genetic origin of Chinese domestic horses. We applied the composite likelihood ratio method to scan for genomic regions showing signals of recent selection in the horse genome. A total of 1052 genomic windows of 10 kB, corresponding to 933 distinct core regions, significantly exceeded neutral simulations. The GO enrichment analysis revealed that the genes under selective sweeps were overrepresented with GO terms, including “negative regulation of canonical Wnt signaling pathway,” “muscle contraction,” and “axon guidance.” Frequent exercise training in domestic horses may have resulted in changes in the expression of genes related to metabolism, muscle structure, and the nervous system.

Bayesian clustering output for 5 K values from K = 2 to K = 8 in 45 domestic horses. Each individual is represented by a vertical line, which is partitioned into colored segments that represent the proportion of the inferred K clusters.

Interesting excerpts:

Admixture proportions were assessed without user-defined population information to infer the presence of distinct populations among the samples (Figure 2). At K = 3 or K = 4, Franches-Montagnes and Arabian forms one unique cluster; at K = 5, Jeju pony forms one unique cluster. For other breeds, comparatively strong population structure exists among breeds, and they can be assigned to 2 (or 3) alternate clusters from K = 3 to K = 5 including group A (Duelmener, Fjord, Icelandic, Kazakh, Lichuan, and Mongolian) and group B (Hanoverian, Morgan, Quarter, Sorraia, and Standardbred). For group A, geographically this was unexpected, where Nordic breeds (Norwegian Fjord, Icelandic, and Duelmener) clustered with Asian breeds including the Mongolian. Previous results of mitochondrial DNA have revealed links between the Mongolian horse and breeds in Iceland, Scandinavia, Central Europe, and the British Isles. The Mongol horses are believed to have been originally imported from Russia subsequently became the basis for the Norwegian Fjord horse.31 At K = 6, Sorraia forms one unique cluster. The Sorraia horse has no long history as a domestic breed but is considered to be of a nearly ancestral type in the southern part of the Iberian Peninsula.32 However, our result did not support Sorraia as an independent ancestral type based on result from K = 2 to K = 5, and the unique cluster in K = 6 may be explained by the small population size and recently inbreeding programs. Genetic admixture of Morgan reveals that these breeds are currently or traditionally continually crossed with other breeds from K = 2 to K = 8. The Morgan horse has been a largely closed breed for 200 years or more but there has been some unreported crossbreeding in recent times.33

Principal component analysis results of all 48 horses. The x-axis denotes the value of PC1, whereas the y-axis denotes the value of PC2. Each dot in the figure represents one individual.

Bayesian clustering and PCA demonstrated the relationships among the horse breeds with weak geographic patterns. The tight grouping within most native breeds and looser grouping of individuals in admixed breeds have been reported previously in modern horses using data from a 54K SNP chip.33,34 Cluster analysis reveals that Arabian or Franches-Montagnes forms one unique cluster with relatively low K value, which is consistent with former study using 50K SNP chip 33,34 Interestingly, Standardbred forms a unique cluster with relatively high K value in this study, different from previous study.33 To date, no footprints are available to describe how the earliest domestic horses spread into China in ancient times. Our study found that Kazakh and Lichuan were assigned to the same lineage as other native Asian breeds, in agreement with previous studies on the origin of Chinese domestic horses.4,5,35,36 The strong genetic relationship between Asian native breeds and European native breeds have made it more difficult to understand the population history of the horse across Eurasia. Low levels of population differentiation observed between breeds might be explained by historical admixture. Unlike the domestic pig in China,8  we suggest that in China, Northern/Southern distinct groups could not be used to genetically distinct native Chinese horse breeds. We consider that during domestication process of horse, gene flow continued among Chinese-domesticated horses.

Open access Some maternal lineages of domestic horses may have origins in East Asia revealed with further evidence of mitochondrial genomes and HVR-1 sequences, by Ma et al., PeerJ (2018).


There are large populations of indigenous horse (Equus caballus) in China and some other parts of East Asia. However, their matrilineal genetic diversity and origin remained poorly understood. Using a combination of mitochondrial DNA (mtDNA) and hypervariable region (HVR-1) sequences, we aim to investigate the origin of matrilineal inheritance in these domestic horses.

To investigate patterns of matrilineal inheritance in domestic horses, we conducted a phylogenetic study using 31 de novo mtDNA genomes together with 317 others from the GenBank. In terms of the updated phylogeny, a total of 5,180 horse mitochondrial HVR-1 sequences were analyzed.

Eighteen haplogroups (Aw-Rw) were uncovered from the analysis of the whole mitochondrial genomes. Most of which have a divergence time before the earliest domestication of wild horses (about 5,800 years ago) and during the Upper Paleolithic (35–10 KYA). The distribution of some haplogroups shows geographic patterns. The Lw haplogroup contained a significantly higher proportion of European horses than the horses from other regions, while haplogroups Jw, Rw, and some maternal lineages of Cw, have a higher frequency in the horses from East Asia. The 5,180 sequences of horse mitochondrial HVR-1 form nine major haplogroups (A-I). We revealed a corresponding relationship between the haplotypes of HVR-1 and those of whole mitochondrial DNA sequences. The data of the HVR-1 sequences also suggests that Jw, Rw, and some haplotypes of Cw may have originated in East Asia while Lw probably formed in Europe.

Our study supports the hypothesis of the multiple origins of the maternal lineage of domestic horses and some maternal lineages of domestic horses may have originated from East Asia.

Median joining network constructed based on the 247- bp HVR-1 sequences. Circles are proportional to the number of horses represented and a scale indicator (for node sizes) was provided. The length of lines represents the number of variants that separate nodes (some manual adjustment was made for visually good). In the circles, the colors of solid pie slices indicate studied horse populations: Orange, European horses; Blue, horses of West Asia; Light Green, horses from East Asia; Grey, ancient horses; Purper, Przewalskii horses.

Geographic distributions of horse mtDNA haplogroups

The analysis of geographic distribution of the mitochondrial genome haplogroups showed that horse populations in Europe or East Asia included all haplogroups defined from the mtDNA genome sequences. The lineage Fw comprised entirely of Przewalskii horses. The two haplogroups Iw and Lw displayed frequency peaks in Europe (14.08% and 37.32%, respectively) and a decline to the east (9.33% and 8.00% in the West Asia, and 6.45% and 12.90% in East Asia, respectively), especially for Lw, which contained the largest number of European horses (Table 2). However, an opposite distribution pattern was observed for haplogroups Aw, Hw, Jw, and Rw, which were harbored by more horses from East Asia than those from other regions. The proportions of horses from East Asia for the four haplogroups were 38%, 88%, 62%, and 54%, respectively.

Schematic phylogeny of mtDNAs genome from modern horses. This tree includes 348 sequences
and was rooted at a donkey (E. asinus) mitochondrial genome (not displayed). The topology was inferred by a beast approach, whereas a time divergence scale (based on rate substitutions) is shown on the bottom (age estimates were indicated with thousand years (KY)). The percentages on each branch represent Bayesian posterior credibility and the alphabets on the right represent the names of haplogroups. Additional details concerning ages were given in Tables S3 and S6.


A multidisciplinary approach to Neolithic life reconstruction


Open access A Multidisciplinary Approach to Neolithic Life Reconstruction, by Goude et al. J Archaeol Method Th (2018).

Abstract (emphasis mine):

The expansion of Neolithic stable isotope studies in France now allows distinct regional population-scale food patterns to be linked to both local environment influences and specific economic choices. Carbon and nitrogen isotope values of more than 500 humans and of animal samples also permit hypotheses on sex-biased human provenance. To advance population scale research, we here present the first study that draws together carbon (C), nitrogen (N), sulphur (S) and strontium (Sr), dental calculus, aDNA, and palaeoparasitology analysis to infer intra-population patterns of diet and provenance in a Middle Neolithic population from Le Vigneau 2 (human = 40; fauna = 12; 4720–4350 cal. BC) from north-western France. The data of the different studies, such as palaeoparasitology to detect diet and hygiene, CNS isotopes and dental calculus analysis to examine dietary staples, Sr and S isotopes to discriminate non-locals, and aDNA to detect maternal (mtDNA) versus paternal lineages (Y chromosome), were compared to anthropological information of sex and age. Collagen isotope data suggest a similar diet for all individuals except for one child. The provenance isotopic studies suggest no clear differences between sexes, suggesting both males and females used the territory in a similar pattern and had access to foods from the same environments.

Radiogenic strontium isotope ratios from human teeth

Relevant excerpt:

With regard to aDNA analysis and the information this reveals on genetic provenance, Table 1 presents the mitochondrial haplogroups (SNPs typing) retrieved from the human remains. SNPs typing made it possible to assign one individual (LVH3, male < 60 years old) to maternal lineage K (or derivatives), and another individual (LVH12) to lineage H (or derivatives), whereas the low number of SNPs recovered for the last sample (LVH26) did not make it possible to assign any haplogroup. No Y chromosome SNP, as well as no reproducible result for HVR-I sequences, could be obtained for any Le Vigneau 2 individual. Unfortunately, major DNA degradation prevents precise identification of the maternal and paternal lineages, and these two mitochondrial haplogroups do not allow any assessment about female mobility. However, we can note that maternal lineages characterized in the Le Vigneau 2 site are quite common in Neolithic farmer groups and fit within the French Middle Neolithic variability (from 14 to 25.5% for haplogroup K and from 7.9 to 40.9% for haplogroup H; Beau et al. 2017), including farmers from the Paris Basin (35% of H and 18.33% of K for the Gurgy site; Rivollat et al. 2015).

Haplogroup J spread in the Mediterranean due to Phoenician and Greek colonizations


Open access A finely resolved phylogeny of Y chromosome Hg J illuminates the processes of Phoenician and Greek colonizations in the Mediterranean, by Finocchio et al. Scientific Reports (2018) Nº 7465.

Abstract (emphasis mine):

In order to improve the phylogeography of the male-specific genetic traces of Greek and Phoenician colonizations on the Northern coasts of the Mediterranean, we performed a geographically structured sampling of seven subclades of haplogroup J in Turkey, Greece and Italy. We resequenced 4.4 Mb of Y-chromosome in 58 subjects, obtaining 1079 high quality variants. We did not find a preferential coalescence of Turkish samples to ancestral nodes, contradicting the simplistic idea of a dispersal and radiation of Hg J as a whole from the Middle East. Upon calibration with an ancient Hg J chromosome, we confirmed that signs of Holocenic Hg J radiations are subtle and date mainly to the Bronze Age. We pinpointed seven variants which could potentially unveil star clusters of sequences, indicative of local expansions. By directly genotyping these variants in Hg J carriers and complementing with published resequenced chromosomes (893 subjects), we provide strong temporal and distributional evidence for markers of the Greek settlement of Magna Graecia (J2a-L397) and Phoenician migrations (rs760148062). Our work generated a minimal but robust list of evolutionarily stable markers to elucidate the demographic dynamics and spatial domains of male-mediated movements across and around the Mediterranean, in the last 6,000 years.

J2-L397. The star indicates the centroid of derived alleles. The solid square indicates the centroid of ancestral alleles, with its 95% C.I. (ellipse). In the insets: distributions of the pairwise sampling distances (in Km) for the carriers of the ancestral (black) and derived (white) allele, with solid and dashed lines indicating the respective averages. At right: median joining network of 7-STR haplotypes and SNPs in the same groups, with sectors coloured according to sampling location. Haplotype structure is detailed for some nodes, in the order YCA2a-YCA2b-DYS19-DYS390-DYS391-DYS392-DYS393 (in italics).

Interesting excerpts:

Two features of our tree are at odds with the simplistic idea of a dispersal of Hg J as a whole from the Middle East towards Greece and Italy and an accompanying radiation26. First, there is little evidence of sudden diversification between 15 and 5 kya, a period of likely population increase and pressure for range expansion, due to the Agricultural revolution in the Fertile Crescent. Second, within each subclade, lineages currently sampled in Turkey do not show up as preferentially ancestral. Both findings are replicated and reinforced by examining the previous landmark studies. Our Turkish samples do not coalesce preferentially to ancestral nodes when mapped onto these studies’ trees.

Additional relevant information on the entire Hg J comes from the discontinuous distribution of J2b-M12. The northern fringe of our sample is enriched in the J2b-M241 subclade, which reappears in the gulf of Bengal38,45, with low frequencies in the intervening Iraq46 and Iran47. No J2b-M12 carriers were found among 35 modern Lebanese, as contrasted to one of two ancient specimens from the same region35.

In summary, a first conclusion of our sequencing effort and merge with available data is that the phylogeography of Hg J is complex and hardly explained by the presence of a single population harbouring the major lineages at the onset of agriculture and spreading westward. A unifying explanation for all the above inconsistencies could be a centre of initial radiation outside the area here sampled more densely, i.e. the Caucasus and regions North of it, from which different Hg J subclades may have later reached mainland Italy, Greece and Turkey, possibly following different routes and times. Evidence in this direction comes from the distribution of J2a-M41045,48 and the early-49 or mid-Holocene50 southward spread of J1.

Supplemental Figure 7. Maps of sampling locations for the carriers of the derived allele (white triangle point down) at the indicated SNP vs carriers of the ancestral allele (black triangle point-up), conditioned on identical genotype at the same most terminal marker. Coastlines were drawn with the R packages18 “map” and “mapproj” v. 3.1.3 (https://cran.r-project.org/web/packages/mapproj/index.html), and additional features added with default functions. The star triangle indicates the centroid of derived alleles. The solid square indicates the centroid of ancestral alleles, with its 95% C.I. (ellipse). In the insets: distributions of the pairwise sampling distances (in Km) for the carriers of the ancestral (black) and derived (white) allele, with solid and dashed lines indicating the respective averages. At right: median joining network of 7-STR haplotypes and SNPs in the same groups, with sectors coloured according to sampling location. Haplotype structure is detailed for some nodes, in the order YCA2a-YCA2b-DYS19-DYS390-DYS391-DYS392-DYS393 (in italics).

The lineage defined by rs779180992, belonging to J2b-M205, and dated at 4–4.5 kya, has a radically different distribution, with derived alleles in Continental Italy, Greece and Northern Turkey, and two instances in a Palestinian and a Jew. The interpretation of the spread of this lineage is not straightforward. Tentative hypotheses are linked to Southward movements that occurred in the Balkan Peninsula from the Bronze Age29,53, through the Roman occupation and later54.

The slightly older (5.6–6.3 kya) branch 98 lineage displays a similar trend of a Eastward positioning of derived alleles, with the notable difference of being present in Sardinia, Crete, Cyprus and Northern Egypt. This feature and the low frequency of the parental J2a-M92 lineage in the Balkans27 calls for an explanation different from the above.

Finally, we explored the distribution of J2a-L397 and three derived lineages within it. J2a-L397 is tightly associated with a typical DYS445 6-repeat allele. This has been hypothesized as a marker of the Greek colonizations in the Mediterranean55, based on its presence in Greek Anatolia and Provence (France), a region with attested Iron Age Greek contribution. All of our chromosomes in this clade were characterized also by DYS391(9), confirming their Anatolian Greek signature. We resolved the J2a-L397 clade to an unprecedented precision, with three internal markers which allow a finer discrimination than STRs. The ages of the three lineages (2.0–3.0 kya) are compatible with the beginning of the Greek colonial period, in the 8th century BCE. The three subclades have different distributions (Fig. 2B), with two (branches 57, 59) found both East and West to Greece, and one only in Italy (branch 58). As to Mediterranean Islands, J2a-L397 was found in Cyprus56 and Crete43. Its presence as one of the three branches 57–59 will represent an important test. In Italy all three variants were found mainly along the Western coast (18/25), which hosted the preferred Greek trade cities. The finding of all three differentiated lineages in Locri excludes a local founder effect of a single genealogy. Interestingly, an important Greek colony was established in this location, with continuity of human settlement until modern times. The sample composed of the same subjects displayed genetic affinities with Eastern Greece and the Aegean also at autosomal markers57. In summary, the distributions of branches 57–59 mirror the variety of the cities of origin and geographic ranges during the phases of the colonization process58.

So, there you have it, another proof that haplogroup J and CHG-related ancestry in the Mediterranean was mainly driven by different (and late) expansions of historic peoples.