Two sources of archaic Denisovan ancestry in East Asia, one possibly after the isolation of Native Americans


Open access paper Analysis of Human Sequence Data Reveals Two Pulses of Archaic Denisovan Admixture, by Sharon L. Browning, Brian L. Browning, Zhou, Tucci, & Akey, Cell (2018).


Anatomically modern humans interbred with Neanderthals and with a related archaic population known as Denisovans. Genomes of several Neanderthals and one Denisovan have been sequenced, and these reference genomes have been used to detect introgressed genetic material in present-day human genomes. Segments of introgression also can be detected without use of reference genomes, and doing so can be advantageous for finding introgressed segments that are less closely related to the sequenced archaic genomes. We apply a new reference-free method for detecting archaic introgression to 5,639 whole-genome sequences from Eurasia and Oceania. We find Denisovan ancestry in populations from East and South Asia and Papuans. Denisovan ancestry comprises two components with differing similarity to the sequenced Altai Denisovan individual. This indicates that at least two distinct instances of Denisovan admixture into modern humans occurred, involving Denisovan populations that had different levels of relatedness to the sequenced Altai Denisovan.

Mean detected archaic sequence per individual (Mb)

The discussion on the potential implication of the paper:

Featured image, from the article: Contour Density Plots of Match Proportion of Introgressed Segments to the Altai Neanderthal and Altai Denisovan Genomes.


Iberian prehistoric migrations in Genomics from Neolithic, Chalcolithic, and Bronze Age


New open access paper Four millennia of Iberian biomolecular prehistory illustrate the impact of prehistoric migrations at the far end of Eurasia, by Valdiosera, Günther, Vera-Rodríguez, et al. PNAS (2018) published ahead of print.

Abstract (emphasis mine)

Population genomic studies of ancient human remains have shown how modern-day European population structure has been shaped by a number of prehistoric migrations. The Neolithization of Europe has been associated with large-scale migrations from Anatolia, which was followed by migrations of herders from the Pontic steppe at the onset of the Bronze Age. Southwestern Europe was one of the last parts of the continent reached by these migrations, and modern-day populations from this region show intriguing similarities to the initial Neolithic migrants. Partly due to climatic conditions that are unfavorable for DNA preservation, regional studies on the Mediterranean remain challenging. Here, we present genome-wide sequence data from 13 individuals combined with stable isotope analysis from the north and south of Iberia covering a four-millennial temporal transect (7,500–3,500 BP). Early Iberian farmers and Early Central European farmers exhibit significant genetic differences, suggesting two independent fronts of the Neolithic expansion. The first Neolithic migrants that arrived in Iberia had low levels of genetic diversity, potentially reflecting a small number of individuals; this diversity gradually increased over time from mixing with local hunter-gatherers and potential population expansion. The impact of post-Neolithic migrations on Iberia was much smaller than for the rest of the continent, showing little external influence from the Neolithic to the Bronze Age. Paleodietary reconstruction shows that these populations have a remarkable degree of dietary homogeneity across space and time, suggesting a strong reliance on terrestrial food resources despite changing culture and genetic make-up.

(A) f4 statistics testing affinities of prehistoric European farmers to either early Neolithic Iberians or central Europeans, restricting these reference populations to SNP-captured individuals to avoid technical artifacts driving the affinities. The boxplots in A show the distributions of all individual f4 statistics belonging to the respective groups. The signal is not sensitive to the choice of reference populations and is not driven by hunter-gatherer–related admixture (Datasets S4 and S5). (B) Estimates of ancestry proportions in different prehistoric Europeans as well as modern southwestern Europeans. Individuals from regions of Iberia were grouped together for the analysis in A and B to increase sample sizes per group and reduce noise


We present a comprehensive biomolecular dataset spanning four millennia of prehistory across the whole Iberian Peninsula. Our results highlight the power of archaeogenomic studies focusing on specific regions and covering a temporal transect. The 4,000 y of prehistory in Iberia were shaped by major chronological changes but with little geographic substructure within the Peninsula. The subtle but clear genetic differences between early Neolithic Iberian farmers and early Neolithic central European farmers point toward two independent migrations, potentially originating from two slightly different source populations. These populations followed different routes, one along the Mediterranean coast, giving rise to early Neolithic Iberian farmers, and one via mainland Europe forming early Neolithic central European farmers. This directly links all Neolithic Iberians with the first migrants that arrived with the initial Mediterranean Neolithic wave of expansion. These Iberians mixed with local hunter-gatherers (but maintained farming/pastoral subsistence strategies, i.e., diet), leading to a recovery from the loss of genetic diversity emerging from the initial migration founder bottleneck. Only after the spread of Bell Beaker pottery did steppe-related ancestry arrive in Iberia, where it had smaller contributions to the population compared with the impact that it had in central Europe. This implies that the two prehistoric migrations causing major population turnovers in central Europe had differential effects at the southwestern edge of their distribution: The Neolithic migrations caused substantial changes in the Iberian gene pool (the introduction of agriculture by farmers) (6, 9, 11, 13, 24), whereas the impact of Bronze Age migrations (Yamnaya) was significantly smaller in Iberia than in north-central Europe (24). The post-Neolithic prehistory of Iberia is generally characterized by interactions between residents rather than by migrations from other parts of Europe, resulting in relative genetic continuity, while most other regions were subject to major genetic turnovers after the Neolithic (4, 6, 7, 9, 25, 48). Although Iberian populations represent the furthest wave of Neolithic expansion in the westernmost Mediterranean, the subsequent populations maintain a surprisingly high genetic legacy of the original pioneer farming migrants from the east compared with their central European counterparts. This counterintuitive result emphasizes the importance of in-depth diachronic studies in all parts of the continent.


Signal of recent positive selection for African ancestry in the admixed population of Madagascar


Open Access Strong selection during the last millennium for African ancestry in the admixed population of Madagascar, by Pierron, Heiske, Razafindrazaka, et al. Nature Communications (2018) 9: 932.

Abstract (emphasis mine):

While admixed populations offer a unique opportunity to detect selection, the admixture in most of the studied populations occurred too recently to produce conclusive signals. By contrast, Malagasy populations originate from admixture between Asian and African populations that occurred ~27 generations ago, providing power to detect selection. We analyze local ancestry across the genomes of 700 Malagasy and identify a strong signal of recent positive selection, with an estimated selection coefficient >0.2. The selection is for African ancestry and affects 25% of chromosome 1, including the Duffy blood group gene. The null allele at this gene provides resistance to Plasmodium vivax malaria, and previous studies have suggested positive selection for this allele in the Malagasy population. This selection event also influences numerous other genes implicated in immunity, cardiovascular diseases, and asthma and decreases the Asian ancestry genome-wide by 10%, illustrating the role played by selection in recent human history.

This finding is not only interesting in gross evolutionary terms, but this kind of studies may potentially shed light in the distant future to those so-called population ‘resurge’ events after massive migrations over wide regions, which cannot always be explained with anthropological models.


The concept of “Outlier” in Human Ancestry (III): Late Neolithic samples from the Baltic region and origins of the Corded Ware culture


I have written before about how the Late Neolithic sample from Zvejnieki seemed to be an outlier among Corded Ware samples (read also the Admixture analysis section on the IEDDM), due to its position in PCA, even more than its admixture components or statistical comparison might show.

In the recent update to Northern European samples in Mittnik et al. (2018), an evaluation of events similar to the previous preprint (2017) is given:

Computing D-statistics for each individual of the form D(Baltic LN, Yamnaya; X, Mbuti), we find that the two individuals from the early phase of the LN (Plinkaigalis242 and Gyvakarai1, dating to ca. 3200–2600 calBCE) form a clade with Yamnaya (Supplementary Table 7), consistent with the absence of the farmer-associated component in ADMIXTURE (Fig. 2b). Younger individuals share more alleles with Anatolian and European farmers (Supplementary Table 7) as also observed in contemporaneous Central European CWC individuals2.

Sampling locations and dating of 38 ancient Northern European samples introduced in this study. Chronology based on calibrated radiocarbon dates or relative dating

My interpretation of the Zvejnieki sample ca. 2880 BC (and thus also of the only Baltic LN sample forming a close cluster with it) as ‘outlier’ seems thus reinforced as more samples come in. My explanation based on exogamy is one possibility for the region. After all, great mobility and exogamy practices are universally accepted for the Corded Ware territory, and Yamna migrants had settled up along the Prut precisely around this period (ca. 3100-2900 BC), so this kind of relation between Yamna and Baltic samples is to be expected.

NOTE: Information on the Late Neolithic burial of Zvejnieki is scarce, since it is an isolated find in radiocarbon analysis, among Mesolithic burials. You can read more about it from Ilga Zagorska’s studies, such as The use of ochre in Stone Age burials of the East Baltic (2008), The persistent presence of the dead: recent excavations at the hunter-gatherer cemetery at Zvejnieki (Latvia) (Antiquity 2013), or Dietary freshwater reservoir effects and the radiocarbon ages of prehistoric human bones from Zvejnieki, Latvia (J. Archaeol. Sci. 2016).

Samples of Baltic “Late Neolithic / Corded Ware culture”

The only two samples clustering more closely to Yamna cluster also closely to the three previous samples from Khvalynsk in Samara (labelled ‘Steppe Eneolithic’ in the paper), which makes one wonder how strongly connected were cultures from the forest and forest-steppe zones before the expansion of Corded Ware and Yamna settlers.

NOTE: Apart from the scarcity of samples available, which is common in genetic studies, the description of both additional ‘outlier’ samples of the Baltic Late Neolithic – isolated finds based mainly on radiocarbon analysis – leaves a lot to the imagination, because of the lack of cultural context and potential problems with dating methods:

Plinkaigalis 242, >40 year old female (OxA-5936, 4280 ± 75 BP, 3260–2630 calBCE). The burial site is located in the plains of central Lithuania on the eastern bank of the river Šušvė on the outskirts of the Plinkaigalis village, approximately 400 m southeast of an Iron age hill fort and settlement. The burial site was discovered in 1975 when local residents started digging for gravel in the western part of the hill. The same year site was granted a legal protection with archaeological excavations carried out for eight straight years in a row (1977-1984). During the eight years of fieldwork a total of 373 graves (364 inhumation and 9 cremation graves) with all but two of them dating to 3rd to 8th c. AD were uncovered. The two exceptional graves (no. 241, 242) were uncovered in the northern part of the burial site and C14 dated to the Late Neolithic.

Gyvakarai 1, 35-40 year old male (Poz-61584, 4030 ± 30 BP, 2620–2470 calBCE). The burial site is located in the northern part of Lithuania on the steep gravelly bank (elevation up to 79 m a. s. l.) of the rivulet Žvikė, 500 m to the south from where, in the wet grassland valley, it meets the main stem river Pyvesa. The site was discovered in 2000 when local residents started digging for gravel in the central part of the gravelly bank. The same year rescue excavations were conducted in the surrounding area of the highly disturbed grave resulting in discovery of a single grave C14 dated to the Late Neolithic.

EDIT (16 FEB 2018): A commentator noted that Gyvakaray1 was also studied for Yersinia pestis, a disease which appears to have expanded first to the west from the steppe, and then to the east, so it is possible that its position in PCA related to Plinkaigalis242 shows a connection to late Yamna settlers or East Bell Beaker migrants.

File modified by me from Mittnik et al. (2018) to include the approximate position of the most common ancestral components, and an identification of potential outliers. Zoomed-in version of the European Late Neolithic and Bronze Age samples. “Principal components analysis of 1012 present-day West Eurasians (grey points, modern Baltic populations in dark grey) with 294 projected published ancient and 38 ancient North European samples introduced in this study (marked with a red outline).

NOTE: I haven’t had the time and patience to work with my virtual computer on the PCA of these new samples – my CPU is reaching everyday its limit and my fans work half the time – , so I don’t know exactly which of them is Plinkaigalis242 and which Gyvakarai1, I just made a wild guess (based on ADMIXTURE) that the earlier Plinkaigalis242 forms a common ‘outlier’ group with Zvejnieki; if they are reversed or otherwise wrong in the image, please correct me. It will be much appreciated.

We can see from the additional samples in Mittnik et al. (2018) that the common cluster formed by most Baltic LN samples in PCA (most of them with clear cultural context among Late Neolithic or Corded Ware material, unlike the two ‘outliers’ and Gyvakarai1) is among Ukraine Eneolithic samples, European Corded Ware samples, and also Mesolithic-Neolithic samples from the Baltic. This is a logical find in light of the mainstream opinion that the expansion of the third horizon of the Corded Ware culture seems to have begun in the Dnieper-Dniester region (a corridor of steppe, steppe-forest, and forest zones) ca. 3300 BC.

PCA and ADMIXTURE analysis reflecting three time periods in Northern European prehistory. a Principal components analysis of 1012 present-day West Eurasians (grey points, modern Baltic populations in dark grey) with 294 projected published ancient and 38 ancient North European samples introduced in this study (marked with a red outline). Population labels of modern West Eurasians are given in Supplementary Fig. 7 and a zoomed-in version of the European Late Neolithic and Bronze Age samples is provided in Supplementary Fig. 8. b Ancestral components in ancient individuals estimated by ADMIXTURE (k = 11)

Corded Ware culture origins

If we take the most recent reliable radiocarbon analyses of material culture, and interpretations based on them of Corded Ware as a ‘complex’ similar to Bell Beaker (accepted more and more by disparate academics such as Anthony or Klejn), it seems that the controversial ‘massive’ Corded Ware migration must have begun somehow later than previously thought, which leaves these early Baltic samples still less clearly part of the initial Corded Ware culture, and more as outliers waiting for a more precise cultural context among Late Neolithic changes in the region.

Their situation in PCA among Khvalynsk (Samara), Baltic Mesolithic, East Hunger-Gatherer samples, Yamna and Eneolithic Ukraine leaves us without enough information to understand their actual origin.

EDIT (3 FEB 2018): In the first edition of my IEDDM paper I based the potential expansion of the Corded Ware culture mainly on Piezonka’s detailed analyses of the evolution of Mesolithic and Neolithic cultures in the forest-steppe and Forest Zone, and on later phylogeographic finds, since there were no samples from these regions in this interesting period. I revised it in the second edition to accomodate the model to the Indo-Uralic proto-language supported by the Leiden school, and identified it with a a close Neolithic-Chalcolithic steppe community based on common language guesstimates and – after the latest revision of Mathieson et al. (2017) – on the appearance of steppe admixture in the steppe.

However, if traditional Uralicists are right in supposing a loose Neolithic community in the Forest Zone, and Kristiansen is right in supposing long-lasting contacts in the Dniester-Dnieper region, we might actually be seeing with these ‘outliers’ the first proof that Neolithic samples from the forest-steppe and Forest Zone of the 4th millenium – unrelated to the Corded Ware culture – clustered closely to Khvalynsk, Sredni Stog, or Yamna samples, which is compatible with Piezonka’s accounts of intercultural contacts.

Martin Furholt‘s assessment of the origin of the A-horizon of the Corded Ware culture would put the early dates of Late Neolithic in the Baltic coinciding with or just before the initial expansion of Corded Ware migrants. For example, here are some excerpts (emphasis mine) from Re-evaluating Corded Ware Variability in Late Neolithic Europe (2014), in Proceedings of the Prehistoric Society (you can read it free at

Radiocarbon analysis

Acceptance of the results of radiometric dating meant that the concept of the so called ‘A-Horizon’ also had to be reformulated. If we are dealing with such a phase at all, it is not a classic typological period that is defined by a uniform material culture inventory, but rather a set of types which show a wide distribution, but which are always integrated into a locally specific and thus regionally variable context.

The situation resembles that of the Bell Beakers, where a few supra-regional types are associated with local forms of ‘Begleitkeramik’ (i.e. pottery that accompanies Bell Beakers: Strahm 1995; Besse 1996).

The distribution data indicate that this set of forms (namely the A-Beaker, ‘A-Amphora’, and A-Battle Axe, as well as Herringbone-decorated Beakers) was to be found over much of Europe around 2700 BC, and that the currency of these forms was not short: they seem to have been used continuously during the Final Neolithic, perhaps even until 2000 BC (Fig. 3; Furholt 2004). Analysis of the radiometric and dendrochronological determinations also indicates that the A-Horizon is not the earliest Corded Ware phase. Instead, it appears to follow an apparent earlier phase in Poland during which Corded Ware pottery was in use from as early as 2900 BC (Furholt 2003; 2008a; Wödarczak 2006; Ullrich 2008).

Chronological model following from radiocarbon dating. Mark the contrast to the traditional model of the A-horizon as the earliest phase and a successive increase in regional variability later on

Corded Ware and Yamna/Bell Beaker

While widening networks and a change in the mechanism of exchange appears to have contributed to the emergence of the Corded Ware archaeological phenomenon, and also the contemporaneous Yamnaya graves (Harrison & Heyd 2007) and the following Bell Beaker and Early Bronze Age phenomena, it remains to be seen exactly what factors contributed to the development of these systems. It may be that there were changes in subsistence practices, perhaps involving a rising importance of animal herding that subsequently required higher mobility (for a discussion see Dörfler & Müller 2008), but considering the obvious diversity in subsistence patterns present in different Corded Ware groups, such an explanation would seem appropriate for the transformation in some regions, but surely not for the eastern hunterfisher-gatherer groups of the Baltic (Bläuer & Kantanen 2013). Also, trade with amber and copper might have played its role, but there are so far no indications for a significant rise in quantity or reach of these two materials in connection with Corded Ware graves or settlements (Furholt 2003, 125–7).

The impacts of animal traction and the wagon are also to be taken into account, as they are present since 3400 BC (Mischka 2011) but does at least not play any visible role in Corded Ware burial rituals, very much in contrast to the previous periods (Johannsen & Laursen 2010). There is no evidence for horse riding, but the domesticated horse seems to be present in central Europe since before 3000 BC (Becker 1999) and have also been found in Corded Ware settlements (Becker 2008), but again the evidence of domesticated horses is much more abundant in the period before 3000 BC.

So, concerning amber and copper exchange, or the impact of the wheel and animal traction, there is the recurrent motive of stronger evidence for the period before 3000 BC than during or in connection to Corded Ware finds after 2700 BC.

Summary table for the chronological positions (extent of name plus vertical lines) of the most important traditional archaeological ‘cultures’, ‘Groups’ or pottery styles discussed in this paper. Note that the definitions of those units are far from consistent or comparable, because they derive from different national and regional research traditions. Bold letters indicate a unit connected to the Corded Ware phenonomenon


The evidence strongly points towards a long period of coalescence from 3000 to 2700 BC, when several innovations in burial customs, pottery, and tool types sprung forth from different places and subsequently spread via different networks of exchange and interaction. These surely showed a significant rise in scale, reach, and impact on local practices, but the same is true for the contemporary Globular Amphora and Yamnaya ‘Cultures’. This exchange resulted, roughly spoken, in a phenomenon like the A-Horizon.


Thus, it seems reasonable to explain the wide regional reach of those Corded Ware elements as the result of a general increase in mobility and thus an increase in the spatial extension of regional networks, triggered by the long-term effects of technological innovations and connected economic and social transformations in Europe since 3400 BC. It is the increase in mobility and regional networks that is new to the European Neolithic Societies after this time, and it is not only the Corded Ware elements, that are spread through these channels but also Yamnaya, Globular Amphorae, Bell Beaker ‘Cultures’, and copper and bronze artefacts in later periods. Those are archaeological classification units, heuristic tools for the ordering of finds, while brushing over variability and overlapping traits, and so they should not be confused with real social groups.

Network analysis based on the quantitative occurrence of Corded Ware pottery forms, pottery ornamentation styles, tools, weapons and ornaments as stated in Table 1, based on the catalogues given in Table 2, line thickness representing similarity

As a summary, we can say that there is still much work to be done on the origins and expansion of the Corded Ware culture, and that speculative interpretations of recent genetic papers (especially since 2015), based solely on scarce genetic finds, are not doing much in favour of sound anthropological models by connecting directly Yamna to Corded Ware (and the latter to Bell Beaker), as the multiple new anthropological ‘steppe’ models (and their unending revisions due to the gradual corrections from ‘Yamnaya’ to ‘steppe’ admixture in genetic papers) are showing.

Featured image, from Furholt’s article: Map of the Corded Ware regions discussed for central Europe. The dark shading indicates those regions where Corded Ware burial rituals are present regularly.


Admixture of Srubna and Huns in Hungarian conquerors


New preprint at BioRxiv, Mitogenomic data indicate admixture components of Asian Hun and Srubnaya origin in the Hungarian Conquerors, by Neparáczki et al. (2018), at BioRxiv.

Abstract (emphasis mine):

It has been widely accepted that the Finno-Ugric Hungarian language, originated from proto Uralic people, was brought into the Carpathian Basin by the Hungarian Conquerors. From the middle of the 19th century this view prevailed against the deep-rooted Hungarian Hun tradition, maintained in folk memory as well as in Hungarian and foreign written medieval sources, which claimed that Hungarians were kinsfolk of the Huns. In order to shed light on the genetic origin of the Conquerors we sequenced 102 mitogenomes from early Conqueror cemeteries and compared them to sequences of all available databases. We applied novel population genetic algorithms, named Shared Haplogroup Distance and MITOMIX, to reveal past admixture of maternal lineages. Phylogenetic and population genetic analysis indicated that more than one third of the Conqueror maternal lineages were derived from Central-Inner Asia and their most probable ultimate sources were the Asian Huns. The rest of the lineages most likely originated from the Bronze Age Potapovka-Poltavka-Srubnaya cultures of the Pontic-Caspian steppe, which area was part of the later European Hun empire. Our data give support to the Hungarian Hun tradition and provides indirect evidence for the genetic connection between Asian and European Huns. Available data imply that the Conquerors did not have a major contribution to the gene pool of the Carpathian Basin, raising doubts about the Conqueror origin of Hungarian language.

“Comparison of major Hg distributions from modern and ancient populations. Asian main Hg-s are designated with brackets. Major Hg distribution of Conqueror samples from this study are very similar to that of other 91 Conquerors taken from previous studies [11,12]. Scythians and ancient Xiongnus show similar Hg composition to the bracketed Asian fraction of the Conqueror samples, but Hg B is present just in Xiongnus. Modern Hungarians have very small Asian components pointing at small contribution from the Conquerors. Of the 289 modern Hungarian mitogenomes 272 are published in [29]. Scythian Hg-s are from [48,49,55,59,71–74]. Xiongnu Hg-s are from [66–69].”

Just recently another article contributed to a similar idea. I already talked about the Bronze Age R1a-z93 sample with high steppe ancestry found in the Balkans, and its likely origin in an expansion of the Srubna or a related culture. No truce, therefore, for those looking for autochthonous continuity anywhere in Europe.

We are seeing how multiple migrations shaped the history of the Carpathian basin (and its complex genetic structure) – and of Europe in general -, often from the Pontic-Caspian steppe. That is clear from many different prehistorical and historical times, such as the expansions of Suvorovo-Novodanilovka, Yamna, Srubna, Thraco-Cimmerians, Sarmatians, Scythians, Huns,…

About the linguistic interpretations based on genetics contained in the paper (Hungarian language as a legacy of Huns), well, you know my stance regarding the Yamnaya ancestral concept (and the wrong linguistic interpretations derived from it, which many sadly keep to this day), and genetics in general to solve language questions

This is yet another example of how (what some people would call) “scientific data” is useless without sound anthropological models.

Featured image, from the article: “Hypothetic origin and migration route of different components of the Hungarian Conquerors. Bluish line frames the Eurasian steppe zone, within which all presumptive ancestors of the Conquerors were found. Yellow area designates the Xiongnu Empire at its zenith from which area the East Eurasian lineages originated. Phylogeographical distribution of modern East Eurasian sequence matches (Fig. 1) well correspond to this territory, especially considering that Yakuts, Evenks and Evens lived more south in the past [108], and European Tatars also originated from this area. Regions where Asian and European Scythian remains were found are labeled green, pink is the presumptive range of the Srubnaya culture. Migrants of Xiongnu origin most likely incorporated descendants of these groups. The map was created using QGIS 2.18.4[109]”.

Article available under a CC-BY-NC-ND 4.0 International license.

Discovered via Razib Khan.

See also:

Differences in ADMIXTURE between Khvalynsk/Yamna and Sredni Stog/Corded Ware


Looking for differences among steppe cultures in Genomics is like looking for a needle in a haystack.

It means, after all, looking for differences among closely related cultures, such as between South-Western and North-Western Anatolian Neolithic cultures, or among Old European cultures (such as Vinča or Cucuteni–Trypillia), or between Iberian cultures after the arrival of steppe-related populations.

These differences between closely related regions, in all these cases and especially among steppe cultures, even when they are supported by Archaeology and anthropological models of migration (and compatible with linguistic models), are expected to be minimal.

Fortunately, we have phylogeography, which helps us point in the right direction when assessing potential migrations using genomic data.

User Tomenable recently pointed out a curious finding on Anthrogenica, from data available in Mathieson et al (2017): in ADMIXTURE results with K=12, a different ancestral component (in light green in the paper, see below) is traceable from the North Caspian steppe since the Neolithic. This is also partially distinguishable on K=10 and K=11, although not so clearly differentiating among later cultures.

NOTE: Read more on the controversy regarding the ideal number of ancestral populations, the absurd use of ADMIXTURE to solve language questions, and the meaning of cross-validation (CV) values

Unsupervised ADMIXTURE plot from k=10 to 12, on a dataset consisting of 1099 present-day individuals and 476 ancient individuals. We show newly reported ancient individuals and some previously published individuals for comparison.

Explanations for this finding might include, as the user points out, a greater contribution of CHG ancestry in the eastern steppe cultures (Khvalynsk/Yamna) compared to the North Pontic steppe (Sredni Stog/Corded Ware), which is probably one of the main genomic differences among both cultures, as I pointed out in the Indo-European demic diffusion model (see accounts on the origins of Khvalynsk and Sredni Stog populations and on contacts between Yamna and the Caucasus, and see below also my sketch of Eurasian genomic history).

Interesting is also the appearance of similar ancestral components later in Vučedol – which probably received admixture from Yamna settlers (see admixture components in West Yamna samples and in the Yamna settler from Bulgaria) – , and later still in the Balkans.

On the other hand, previous ancestral components in outliers from the Balkans seem to be more similar to Sredni Stog samples, giving still more strength to the hypothesis that this common (“steppe”) component expanded westward within the Pontic-Caspian steppe with the spread of Suvorovo-Novodanilovka chiefs.

Problems with this interpretation include:

1) The scarce samples available, the different cultures included, and the CV values of the K populations selected in ADMIXTURE.

2) The lack of data for comparison with Bell Beaker peoples (from Olalde et al. 2017).

3) The sample classified as Latvia_LN/CWC has this component. I have already said before that, given the differences with all other Corded Ware samples, this quite early sample might be an outlier, with Khvalynsk/Yamna population connected directly to the ancestors of this individual, possibly through exogamy (as it is clear from my sketch below). Whether or not this is an outlier among CWC populations in the Baltic, only future samples can tell.

4) Three later individuals from Corded Ware in Germany have the component, in a minimal amount. I would bet – judging by their position in the graphic – that this might be explained through the Esperstedt family. These individuals might have in turn got the contribution directly from the oldest member, who shows what seems (in PCA) like a recent admixture from contemporary steppe cultures (such as the Catacomb culture).

NOTE: See my graphics with interesting members of the Espersted family marked: ADMIXTURE and PCA (outlier).

Tentative sketch modelling the genetic history of Europe and West Eurasia from ancient populations up to the Neolithic, according to results in recent genetic papers and archaeological models of known migrations.

Again, needle in a haystack… And confirmation bias by me, indeed.

But interesting nonetheless.

EDIT (4 JAN 2017): A reader points out that the interpretation of Unsupervised ADMIXTURE should work backwards (i.e. different contributions into different modern populations), and not based solely on ancestral populations, which seems probably right. So again, confirmation bias (and potentially wrong direction fallacy) by me…


Genomic history of Northern Eurasians includes East-West and North-South gradients


Open Access article on modern populations (including ancient samples), Between Lake Baikal and the Baltic Sea: genomic history of the gateway to Europe, by Triska et al., BMC Genetics 18(Suppl 1):110, 2017.


The history of human populations occupying the plains and mountain ridges separating Europe from Asia has been eventful, as these natural obstacles were crossed westward by multiple waves of Turkic and Uralic-speaking migrants as well as eastward by Europeans. Unfortunately, the material records of history of this region are not dense enough to reconstruct details of population history. These considerations stimulate growing interest to obtain a genetic picture of the demographic history of migrations and admixture in Northern Eurasia.

We genotyped and analyzed 1076 individuals from 30 populations with geographical coverage spanning from Baltic Sea to Baikal Lake. Our dense sampling allowed us to describe in detail the population structure, provide insight into genomic history of numerous European and Asian populations, and significantly increase quantity of genetic data available for modern populations in region of North Eurasia. Our study doubles the amount of genome-wide profiles available for this region.

We detected unusually high amount of shared identical-by-descent (IBD) genomic segments between several Siberian populations, such as Khanty and Ket, providing evidence of genetic relatedness across vast geographic distances and between speakers of different language families. Additionally, we observed excessive IBD sharing between Khanty and Bashkir, a group of Turkic speakers from Southern Urals region. While adding some weight to the “Finno-Ugric” origin of Bashkir, our studies highlighted that the Bashkir genepool lacks the main “core”, being a multi-layered amalgamation of Turkic, Ugric, Finnish and Indo-European contributions, which points at intricacy of genetic interface between Turkic and Uralic populations. Comparison of the genetic structure of Siberian ethnicities and the geography of the region they inhabit point at existence of the “Great Siberian Vortex” directing genetic exchanges in populations across the Siberian part of Asia.

f3 values to estimate (a) Eastern European Hunter-Gatherer, b Neolithic Farmer, c Caucasus hunter-gatherer, and d) Mal’ta (Ancient North Eurasian) ancestry in modern humans

Slavic speakers of Eastern Europe are, in general, very similar in their genetic composition. Ukrainians, Belarusians and Russians have almost identical proportions of Caucasus and Northern European components and have virtually no Asian influence. We capitalized on wide geographic span of our sampling to address intriguing question about the place of origin of Russian Starovers, an enigmatic Eastern Orthodox Old Believers religious group relocated to Siberia in seventeenth century. A comparative reAdmix analysis, complemented by IBD sharing, placed their roots in the region of the Northern European Plain, occupied by North Russians and Finno-Ugric Komi and Karelian people. Russians from Novosibirsk and Russian Starover exhibit ancestral proportions close to that of European Eastern Slavs, however, they also include between five to 10 % of Central Siberian ancestry, not present at this level in their European counterparts.

Admixture proportions in studied populations, K = 6. Populations from the Extended dataset. Abbreviated population codes: NSK – Russians from Novosibirsk; STV -Starover Russians; ARK: Bashkirs from Arkhangelskiy district; BRZ – Bashkirs from Burzyansky district

Our project has patched the hole in the genetic map of Eurasia: we demonstrated complexity of genetic structure of Northern Eurasians, existence of East-West and North-South genetic gradients, and assessed different inputs of ancient populations into modern populations.

Featured image, from the article: “Departures from the expected IBD. Shown populations exceed the expected IBD sharing by more than two standard deviations.”


Review article on the origin of modern humans: the multiple-dispersal model and Late Pleistocene Asia


Review article On the origin of modern humans: Asian perspectives, by Christopher J. Bae, Katerina Douka, and Michael D. Petraglia, Science (2017)


The earliest fossils of Homo sapiens are located in Africa and dated to the late Middle Pleistocene. At some point later, modern humans dispersed into Asia and reached the far-away locales of Europe, Australia, and eventually the Americas. Given that Neandertals, Denisovans, mid-Pleistocene Homo, and H. floresiensis were present in Asia before the appearance of modern humans, the timing and nature of the spread of modern humans across Eurasia continue to be subjects of intense debate. For instance, did modern humans replace the indigenous populations when moving into new regions? Alternatively, did population contact and interbreeding occur regularly? In terms of behavior, did technological innovations and symbolism facilitate dispersals of modern humans? For example, it is often assumed that only modern humans were capable of using watercraft and navigating to distant locations such as Australia and the Japanese archipelago—destinations that would not have been visible to the naked eye from the departure points, even during glacial stages when sea levels would have been much lower. Moreover, what role did major climatic fluctuations and environmental events (e.g., the Toba volcanic super-eruption) play in the dispersal of modern humans across Asia? Did extirpations of groups occur regularly, and did extinctions of populations take place? Questions such as these are paramount in understanding hominin evolution and Late Pleistocene Asian paleoanthropology.

An increasing number of multidisciplinary field and laboratory projects focused on archaeological sites and fossil localities from different areas of Asia are producing important findings, allowing researchers to address key evolutionary questions that have long perplexed the field. For instance, technological advances have increased our ability to successfully collect ancient DNA from hominin fossils, providing proof that interbreeding occurred on a somewhat regular basis. New finds of H. sapiens fossils, with increasingly secure dating associations, are emerging in different areas of Asia, some seemingly from the first half of the Late Pleistocene. Cultural variability discerned from archaeological studies indicates that modern human behaviors did not simply spread across Asia in a time-transgressive pattern. This regional variation, which is particularly distinct in Southeast Asia, could be related at least in part to environmental and ecological variation (e.g., Palearctic versus Oriental biogeographic zones).

Recent findings from archaeology, hominin paleontology, geochronology, and genetics indicate that the strict “out of Africa” model, which posits that there was only a single dispersal into Eurasia at ~60,000 years ago, is in need of revision. In particular, a multiple-dispersal model, perhaps beginning at the advent of the Late Pleistocene, needs to be examined more closely. An increasingly robust record from Late Pleistocene Asian paleoanthropology is helping to build and establish new views about the origin and dispersal of modern humans.

Map of sites with ages and postulated early and later pathways associated with modern humans dispersing across Asia during the Late Pleistocene.

Read more about the article in Materials provided by the Max Planck Institute for the Science of Human History.


The concept of “Outlier” in Human Ancestry (II): Early Khvalynsk, Sredni Stog, West Yamna, Iron Age Bulgaria, Potapovka, Andronovo…


I already wrote about the concept of outlier in Human Ancestry, so I am not going to repeat myself. This is just an update of “outliers” in recent studies, and their potential origins (here I will repeat some of the examples):

Early Khvalynsk: the three samples from the Samara region have quite different positions in PCA, from nearest to EHG (of Y-DNA haplogroup R1a) to nearest to ANE ancestry (of Y-DNA haplogroup Q). This could represent the initial consequences of the second wave of ANE ancestry – as found later in Yamna samples from a neighbouring region -, possibly brought then by Eurasian migrants related to haplogroup Q.
With only 3 samples, this is obviously just a tentative explanation of the finds. The samples can only be reasonably said to show an unstable time for the region in terms of admixture (i.e. probably migration), judging by the data on PCA.

Ukraine Eneolithic samples offer a curious example of how the concept of outlier can change radically: from the third version (May 30th) of the preprint paper of Mathieson et al. (2017), when the Ukraine Eneolithic sample with steppe ancestry (and clustering with central European samples) was the ‘outlier’, to the fourth version (September 19th), when two samples with steppe ancestry clustering close to Corded Ware samples were now the ‘normal’ ones (i.e. those representing Ukraine Eneolithic population), and the outlier was the one clustering closely with Ukraine Mesolithic samples…

PCA and Admixture for south-eastern Europe. Image modified from Mathieson et al. (2017) – Third revision (May 30th), used in the 2nd edition of the Indo-European demic diffusion model.

This is one of the funny consequences of the wrong interpretation of the ‘yamnaya component’, that made geneticists believe at first that, out of two samples (!), the ‘outlier’ was the one with ‘yamnaya’ ancestry, because this component would have been brought by an eastern immigrant from early Khvalynsk…

This example offers yet another reason why precise anthropological context is necessary to offer the right interpretation of results. Within the Indo-European demic diffusion model – based mainly on Archaeology and Linguistics – , the sample with steppe ancestry was the most logical find in the region for a potential origin of the Corded Ware culture, and it was interpreted as such, well before the publication of the fourth version of Mathieson et al. (2017).

PCA of South-East European and other European samples. Image modified from Mathieson et al. (2017) – Fourth revision (September 19th), used in the 3rd edition of the Indo-European demic diffusion model.

West Yamna (to insist on the same question, the ‘yamnaya’ component): we have only four western Yamna samples, two of them showing Anatolian Neolithic ancestry (one of them, from Ukraine, with a strong ‘southern’ drift). On the other hand, Corded Ware migrants do not show this. So we could infer that their migrations were not coetaneous: whereas peoples of Corded Ware culture expanded ca. 3300 BC to the north – in the natural corridor to the Baltic that has been proposed for this culture in Archaeology for decades (and that is well represented by Ukraine Eneolithic samples) -, peoples of Yamna culture expanded to the west, replacing the Ukraine Eneolithic population (i.e. probably those of ‘Proto-Corded Ware culture’), and eventually mixing with Balkan populations of Anatolian Neolithic ancestry.

Potapovka, Andronovo, and Srubna: while Potapovka clusters closely to the steppe, and Andronovo (like Sintashta) clusters closely to Corded Ware (i.e. Ukraine Neolithic / Central-East European), both have certain ‘outliers’ in PCA: the former has one individual clustering closely to Corded Ware, and the latter to the steppe. Both ‘outliers’ fit well with the interpretation of the recent mixture of Corded Ware peoples with steppe populations, and they offer a different image for the evolution of populations of Potapovka and Sintashta-Petrovka, potentially influencing their language. The position of Srubna samples, nearer to Sintashta and Andronovo (but occupying the same territory as the previous Potapovka) offers the image of a late westward conquest from Corded Ware-related populations.

Diachronic map of migrations ca. 2250-1750 BC

Iron Age Bulgaria: a sample of haplogroup R1a-z93, with more ‘yamnaya’ ancestry than any other previous sample from the Balkans. For some, it might mean continuity from an older time. However – as with the Corded Ware outlier from Esperstedt before it – it is more likely a recent migrant from the steppe. The most likely origin of this individual is therefore people from the steppe, i.e. either the Srubna culture or a related group. Its relatively close cluster in PCA to certain recent Slavic populations can be interpreted in light of the multiple back and forth migrations in the region: of steppe populations to the west (Srubna, Cimmerians, Scythians, Sarmatians,…), and of Slavic-speaking populations:

Diachronic map of Bronze Age migrations ca. 1750-1250 BC.

Well-defined outliers are, therefore, essential to understand a recent history of admixture. On the other hand, the very concept of “outlier” can be a dangerous tool – when the lack of enough samples makes their classification as as such unjustified -, leading to the wrong interpretations.


Globular Amphora not linked to Pontic steppe migrants – more data against Kristiansen’s Kurgan model of Indo-European expansion


New open access article, Genome diversity in the Neolithic Globular Amphorae culture and the spread of Indo-European languages, by Tassi et al. (2017).


It is unclear whether Indo-European languages in Europe spread from the Pontic steppes in the late Neolithic, or from Anatolia in the Early Neolithic. Under the former hypothesis, people of the Globular Amphorae culture (GAC) would be descended from Eastern ancestors, likely representing the Yamnaya culture. However, nuclear (six individuals typed for 597 573 SNPs) and mitochondrial (11 complete sequences) DNA from the GAC appear closer to those of earlier Neolithic groups than to the DNA of all other populations related to the Pontic steppe migration. Explicit comparisons of alternative demographic models via approximate Bayesian computation confirmed this pattern. These results are not in contrast to Late Neolithic gene flow from the Pontic steppes into Central Europe. However, they add nuance to this model, showing that the eastern affinities of the GAC in the archaeological record reflect cultural influences from other groups from the East, rather than the movement of people.

(a) Principal component analysis on genomic diversity in ancient and modern individuals. (b) K = 3,4 ADMIXTURE analysis based only on ancient variation. (a) Principal component analysis of 777 modern West Eurasian samples with 199 ancient samples. Only transversions considered in the PCA (to avoid confounding effects of post-mortem damage). We represented modern individuals as grey dots, and used coloured and labelled symbols to represent the ancient individuals. (b) Admixture plots at K = 3 and K = 4 of the analysis conducted only considering the ancient individuals. The full plot is shown in electronic supplementary material, figure S7. The ancient populations are sorted by a temporal scale from Pleistocene to Iron Age. The GAC samples of this study are displayed in the box on the right.

Excerpt, from the discussion:

In its classical formulation, the Kurgan hypothesis, i.e. a late Neolithic spread of proto-Indo-European languages from the Pontic steppes, regards the GAC people as largely descended from Late Neolithic ancestors from the East, most likely representing the Yamna culture; these populations then continued their Westward movement, giving rise to the later Corded Ware and Bell Beaker cultures. Gimbutas [23] suggested that the spread of Indo-European languages involved conflict, with eastern populations spreading their languages and customs to previously established European groups, which implies some degree of demographic change in the areas affected by the process. The genomic variation observed in GAC individuals from Kierzkowo, Poland, does not seem to agree with this view. Indeed, at the nuclear level, the GAC people show minor genetic affinities with the other populations related with the Kurgan Hypothesis, including the Yamna. On the contrary, they are similar to Early-Middle Neolithic populations, even geographically distant ones, from Iberia or Sweden. As already found for other Late Neolithic populations [18], in the GAC people’s genome there is a component related to those of much earlier hunting-gathering communities, probably a sign of admixture with them. At the nuclear level, there is a recognizable genealogical continuity from Yamna to Corded Ware. However, the view that the GAC people represented an intermediate phase in this large-scale migration finds no support in bi-dimensional representations of genome diversity (PCA and MDS), ADMIXTURE graphs, or in the set of estimated f3-statistics.

Scheme summarizing the five alternative models compared via ABC random forest. We generated by coalescent simulation mtDNA sequences under five models, differing as to the number of migration events considered. The coloured lines represent the ancient samples included in the analysis, namely Unetice (yellow line), Bell Beaker (purple line), Corded Ware (green line) and Globular Amphorae (red line) from Central Europe, Yamnaya (light blue line) and Srubnaya (brown line) from Eastern Europe. The arrows refer to the three waves of migration tested. Model NOMIG was the simplest one, in which the six populations did not have any genetic exchanges; models MIG1, MIG2 and MIG1, 2 differed from NOMIG in that they included the migration events number 1, 2 (from Eastern to Central Europe, respectively before and after the onset of the GAC), or both. Model MIG2, 3 represents a modification of MIG2 model also including a back migration from Central to Eastern Europe after the development of the Corded Ware culture.

Together with Globular Amphora culture samples from Mathieson et al. (2017), this suggests that Kristiansen’s Indo-European Corded Ware Theory is wrong, even in its latest revised models of 2017.

The background shading indicates the tree migratory waves proposed by Marija Gimbutas, and personally
checked by her in 1995. The symbols refer to the ancient populations considered in the ABC analysis

On the other hand, the article’s genetic finds have some interesting connections in terms of mtDNA phylogeography, but without a proper archaeological model it is difficult to explain them.

Haplogroup frequencies were obtained for Early Neolithic (EN), Middle Neolithic (MN), Chalcolithic (CA), and Late Neolithic (LN). The color assigned to each haplogroup is represented on the lower right part of each plot. Haplogroup frequencies were plotted geographically using QGIS v2.14.

Text and images from the article under Creative Commons Attribution 4.0 license.

Discovered first via Bernard Sécher’s blog.

See also: