I have tried running supervised ADMIXTURE models by selecting distant populations based on PCAs and qpAdm results. The most accurate approximations to what the software should offer appear with a small K number, between K=5 and K=7, whether supervised or unsupervised, and adding more ancestral populations gives some weird results the more distant (in time) populations are from these selected samples.
Labels for ancestral components are used following those commonly referred to in the literature, although supervised ADMIXTURE using corresponding available samples (viz. Anatolia Neolithic for AHG, Iran Hotu and/or CHG for IHG, AG2, AG3 and Mal’ta for ANE, etc.) offer slightly different, less smooth outputs for some periods, especially among more recent populations.
Outputs depend on many different factors, and these files are intended as an overview of the evolution of these simplistic components. The number of available samples per period, the potential ancestry changes within each conventionally selected period, or whether or not each available sample is representative of the territory they were recovered from, among many other factors, influence the outputs and the maps.
NOTE. In summary, ADMIXTURE results like these below might be used to develop new ideas, to be then formally tested; they cannot be used to support anything. Don’t be like the Copenhagen group, randomly selecting “Steppe ancestry” with K=4, identifying this component as “Indo-Europeans”, and correlating its evolution with changes in vegetation composition in yet another obvious correlation = causation argument among many confounding factors left unaccounted for…
Static ADMIXTURE + culture maps
Colours correspond to the components as labelled in the video and in the files below.
The following maps offer natural neighbour interpolations of ancestral components in ancient DNA samples grouped by periods (conventionally selected following the same pattern as in the Prehistory Atlas).
Extrapolation (inferred ancestry beyond the frame created by available samples per map) is obtained by adding distant external locations (such as Greenland, Arctic, Alaska…) with a value of 0.
Videos offer a dynamic timeline.
Click on the images to see a version with higher resolution.
This ancestry peaks among Baikal HG, Ust’Belaya, Nganasans, or Ulchi, hence the different labels used.
Iran HG ancestry
ADMIXTURE maps by period
Click on each image for a higher resolution version.
Early Bronze Age
Middle Bronze Age
Late Bronze Age
Early Iron Age
Late Iron Age
These are the samples used for interpolations in each period (except for modern populations, which are those included in the Reich Lab curated dataset):
Grotta d’Oriente is a small coastal cave located on the island of Favignana, the largest (~20 km2) of a group of small islands forming the Egadi Archipelago, ~5 km from the NW coast of Sicily.
The Oriente C funeral pit opens in the lower portion of layer 7, specifically sublayer 7D. Two radiocarbon dates on charcoal from the sublayers 7D (12149±65 uncal. BP) and 7E, 12132±80 uncal. BP are consistent with the associated Late Epigravettian lithic assemblages (Lo Vetro and Martini, 2012; Martini et al., 2012b) and refer the burial to a period between about 14200-13800 cal. BP, when Favignana was connected to the main island (Agnesi et al., 1993; Antonioli et al., 2002; Mannino et al. 2014).
The anatomical features of Oriente C are close to those of Late Upper Palaeolithic populations of the Mediterranean and show strong affinity with other Palaeolithic individuals of Sicily. As suggested by Henke (1989) and Fabbri (1995) the hunter-gatherer populations were morphologically rather uniform.
We confirmed the originally reported mitochondrial haplogroup assignment of U2’3’4’7’8’9. This haplogroup is present in both pre- and post-LGM populations, but is rare by the Mesolithic, when U5 dominates (Posth et al.2016).
Lipson et al. (2018) (their supplementary Figure S5.1) and Villalba-Mouco et al. (2019) (their Figure 2A) showed that European Late Palaeolithic and Mesolithic hunter-gatherers fall along two main axes of genetic variation. Multidimensional scaling (MDS) of f3-statistics shows that these axes form a “V” shape (Fig. 3). (…)
Focusing further on Oriente C, we find that it shares most drift with individuals from Northern Italy, Switzerland and Luxembourg, and less with individuals from Iberia, Scandinavia, and East and Southeast Europe (Fig. 4A-B). Shared drift decreases significantly with distance (Fig. 4C) and with time (Fig. 4D) although in a linear model of drift with distance and time as a covariate, only distance (p=1.3×10-6) and not time (p=0.11) is significant. Consistent with the overall E-W cline in hunter-gatherer ancestry, genetic distance to Oriente C increases more rapidly with longitude than latitude, although this may also be affected by geographic features. For example, Oriente C shares significantly more drift with the 8,000 year-old 1,400 km distant individual from Loschbour in Luxembourg (Lazaridis et al.,2014), than with the 9,000 year old individual from Vela Spila in Croatia (Mathieson et al.,2018) only 700 km away as shown by the D-statistic (Patterson et al.,2012) D (Mbuti, Oriente C, Vela Spila, Villabruna); Z=3.42. Oriente C’s heterozygosity was slightly lower than Villabruna (14% lower at 1240k transversion sites), but this difference is not significant (bootstrap P=0.12).
Discussion and Conclusion
The robust record of radiocarbon dates proves that they reached Sicily not before 15-14 ka cal. BP, several millennia after the LGM peak. In our opinion, in fact, the hypothesis about an early colonization of Sicily by Aurignacians (Laplace, 1964; Chilardi et al., 1996) must be rejected, on the basis of a recent reinterpretation of the techno-typological features of the lithic industries from Riparo di Fontana Nuova (Martini et al., 2007; Lo Vetro and Martini, 2012; on this topic see also Di Maida et al., 2019).
These analyses have implications for understanding the origin and diffusion of the hunter-gatherers that inhabited Europe during the Late Upper Palaeolithic and Mesolithic. Our findings indicate that Oriente C shows a strong genetic relationship with Western European Late Upper Palaeolithic and Mesolithic hunter-gatherers, suggesting that the “Western hunter-gatherers” was a homogeneous population widely distributed in the Central Mediterranean, presumably as a consequence of continuous gene flow among different groups, or a range expansion following the LGM.
The South Italian corridor
Once again, a hypothesis based on phylogeography – apart from scarce archaeological and palaeolinguistic data (“Semitic”-like topo-hydronymy and substrates in Europe) – seems to be confirmed step by step. Since the finding of the Villabruna individual of hg. R1b-L754 (likely R1b-V88, like south-eastern European lineages expanded with WHG ancestry), it was quite likely to find out that southern Europe was the origin of the expansion of R1b-V88 into Africa.
The most likely explanation for the presence of “archaic” R1b-V88 subclades among modern Sardinians was, therefore, that they represented a remnant from a Late Upper Palaeolithic/Early Mesolithic population that had not been replaced in subsequent migrations, and thus that the migration of these lineages into Northern Africa and the Green Sahara happened during a period when Italy was connected by a shallower Mediterranean (and more land connections) to Northern Africa.
Nevertheless, the arguments for a quite recent expansion of R1b-V88 through the Mediterranean and into Africa keep being repeated, probably based on ancestry from the few ancient (and many modern) populations that have been investigated to date, a simplistic approach prone to important errors that overarch whole migration models.
For example, in the recent paper by Marcus et al. (2019) the presence of these lineages among ancient Sardinians (from the late 4th millennium BC on) is interpreted as an expansion of R1b-V88 with the Cardial Neolithic based on their ancestry, disregarding the millennia-long gap between these samples and the presence of this haplogroup in Palaeolithic/Mesolithic Northern Iberia and Northern Italy, and the comparatively much earlier splits in the phylogenetic tree and dispersal among African populations.
Afroasiatic and Nostratic
I was asked recently if I really believed that we could reconstruct Proto-Nostratic and connect it with any ancestral population. My answer is simple: until the Chalcolithic – when the whole picture of Indo-Europeans, Uralians, Egyptians or Semites becomes quite clear – we have just very few (linguistic, archaeological, genetic) dots which we would like to connect, and we do so the best we can. The earlier the population and proto-language, the more difficult this task becomes.
2) After that, I though it was more likely to be connected to AME ancestry and the Middle East, because of the apparent expansion of WHG from south-eastern Europe, and the potential association of Afroasiatic and (Elamo-?)Dravidian to Middle Eastern populations.
3) However, after finding more and more R1b samples expanding through northern Eurasia, spreading through the (then wider) steppe regions; and R1a essentially surviving among other groups in eastern Europe for thousands of years without being associated to significant migrations (like, say, hg. C after the Palaeolithic), it didn’t seem like this division was accurate, hence my most recent version.
But, in essence, it’s all about connecting the dots, and we have very few of them…
In linguistics, I trust traditional linguists who tend to trust other more experimental linguists (like Hyllested or Kortlandt) who consider that – in their experience – an Indo-Uralic and a Eurasiatic phylum can be reconstructed. Similarly, linguists like Kortlandt are apparently (partially) supportive of attempts like that of Allan Bomhard with Nostratic – although almost everyone is critic of the Muscovite school‘s attachment to the Brugmannian reconstruction, stuck in pre-laryngeal Proto-Indo-Anatolian and similar archaisms.
I mostly use Nostratic as a way to give a simplistic ethnolinguistic label to the genetically related prehistoric peoples whose languages we will probably never know. I think it’s becoming clear that the strongest connection right now with the expansion of potential Eurasiatic dialects is offered by ANE-related populations (hence Y-chromosome bottlenecks under hg. R, Q, probably also N), however complicated the reconstruction of that hypothetic community (and its dialectalization) may be.
What should be clear to anyone is that the attempt of many modern Afroasiatic speakers to connect their language to their own (or their own community’s main) haplogroups, frequently E and/or J, is flawed for many reasons; it was simplistic in the 2000s, but it is absurd after the advent of ancient DNA investigation and more recent investigation on SNP mutation rates. R1b-V88 should have been on the table of discussions about the expansion of Afroasiatic communities through the Green Sahara long ago, whether one supports a Nostratic phylum or not.
The fact that the role of R1b bottlenecks and expansions in the spread of Afroasiatic is usually not even discussed despite their likely connection with the most recent population expansions through the Green Sahara fitting a reasonable time frame for Proto-Afroasiatic reconstruction, a reasonable geographical homeland, and a compatible dialectal division – unlike many other proposed (E or J) subclades – reveals (once again) a lot about the reasons behind amateur interest in genetics.
NOTE. That evident interest notwithstanding, it is undeniable that we have a much better understanding of the expansions of R1b subclades than other haplogroups, probably due in great part to the easier recovery of ancient DNA from Eurasia (and Europe in particular), for many different – sociopolitical, geographical, technological – reasons. It is quite possible that a more thorough temporal transect of ancient DNA from the Middle East and Africa might radically change our understanding of population movements, especially those related to the Afroasiatic expansion. I am referring in this post to interpretations based on the data we currently have, despite that potential R1b-based bias.
Scythian population genetics and settlement patterns
Genetic continuity in the western Eurasian Steppe broken not due to Scythian dominance, but rather at the transition to the Chernyakhov culture (Ostrogoths), by Järve et al.
The long-held archaeological view sees the Early Iron Age nomadic Scythians expanding west from their Altai region homeland across the Eurasian Steppe until they reached the Ponto-Caspian region north of the Black and Caspian Seas by around 2,900 BP1. However, the migration theory has not found support from ancient DNA evidence, and it is still unclear how much of the Scythian dominance in the Eurasian Steppe was due to movements of people and how much reflected cultural diffusion and elite dominance. We present new whole-genome results of 31 ancient Western and Eastern Scythians as well as samples pre- and postdating them that allow us to set the Scythians in a temporal context by comparing the Western Scythians to samples before and after within the Ponto-Caspian region. We detect no significant contribution of the Scythians to the Early Iron Age Ponto-Caspian gene pool, inferring instead a genetic continuity in the western Eurasian Steppe that persisted from at least 4,800–4,400 cal BP to 2,700–2,100 cal BP (based on our radiocarbon dated samples), i.e. from the Yamnaya through the Scythian period.
However, the transition from the Scythian to the Chernyakhov culture between 2,100 and 1,700 cal BP does mark a shift in the Ponto-Caspian genetic landscape, with various analyses showing that Chernyakhov culture samples share more drift and derived alleles with Bronze/Iron Age and modern Europeans, while the Scythians position outside modern European variation. Our results agree well with the Ostrogothic origins of the Chernyakhov culture and support the hypothesis that the Scythian dominance was cultural rather than achieved through population replacement.
Detail of the slide with admixture of Scythian groups in Ukraine:
Interesting to read in combination with yesterday’s re-evaluation of Scythian mobility and settlement patterns in the west (showing adaptation to the different regional cultures), The Steppe was Sown – multi-isotopic research changes our understandings of Scythian diet and mobility, by Ventresca Miller et al.
Nomadic pastoralists conventionally known as the Scythians occupied the Pontic steppe during the Iron Age, c. 700-200 BC, a period of unprecedented pan-regional interaction. Popular science accounts of the Scythians promote narratives of roving bands of nomadic warriors traversing the steppe from the Altai Mountains to the Black Sea coastline. The quantity and scale of mobility in the region is usually emphasized based on the wide distribution of material culture and the characterization of Iron Age subsistence economies in the Pontic steppe and forest-steppe as mobile pastoralism. Yet, there remains a lack of systematic, direct analysis of the mobility of individuals and their animals. Here, we present a multi-isotopic analysis of humans from Iron Age Scythian sites in Ukraine. Mobility and dietary intake were documented through strontium, carbon and oxygen isotope analyses of tooth enamel. Our results provide direct evidence for mobility among populations in the steppe and forest-steppe zones, demonstrating a range of localized mobility strategies. However, we found that very few individuals came from outside of the broader vicinity of each site, often staying within a 90 km radius. Dietary intake varied at the intrasite level and was based in agro-pastoralism.
While terrestrial protein did form a portion of the diet for some individuals, there were also high levels of a 13C-enriched food source among many individuals, which has been interpreted as millet consumption. Individuals exhibiting 87Sr/86Sr ratios that fell outside the local range were more likely to have lower rates of millet consumption than those that fell within the local range. This suggests that individuals moving to the site later in life had different economic pursuits and consumed less millet. There is also strong evidence that children and infants moved at the pan-regional scale. Contrary to the popular narrative, the majority of Scythians engaged in localized mobility as part of agricultural lifeways while pan-regional movements included family groups.
Only small component of these pops highly mobile (in range of early childhood to adolescence), w/ interesting dietary composition correlates. Ongoing turn in Eurasian steppe archaeology towards seeing many of the iconically Scythian expressions of personal & warrior prestige…
North-Africans show ancestry from the ancient Near East and sub-Saharan Africa
Pleistocene North Africans show dual genetic ancestry from the ancient Near East and sub-Saharan Africa, by van de Loosdrecht et al.
North Africa, connecting sub-Saharan Africa and Eurasia, is important for understanding human history. However, the genetic history of modern humans in this region is largely unknown before the introduction of agriculture. After the Last Glacial Maximum modern humans, associated with the Iberomaurusian culture, inhabited a wide area spanning from Morocco to Libya. The Iberomaurusian is part of the early Later Stone Age and characterized by a distinct microlithic bladelet technology, complex hunter-gathering and tooth evulsion.
Here we present genomic data from seven individuals, directly dated to ~15,000-year-ago, from Grotte des Pigeons, Taforalt in Morocco. Uni-parental marker analyses show mitochondrial haplogroup U6a for six individuals and M1b for one individual, and Y-chromosome haplogroup E-M78 (E1b1b1a1) for males. We find a strong genetic affinity of the Taforalt individuals with ancient Near Easterners, best represented by ~12,000 year old Levantine Natufians, that made the transition from complex hunter-gathering to more sedentary food production. This suggests that genetic connections between Africa and the Near East predate the introduction of agriculture in North Africa by several millennia. Notably, we do not find evidence for gene flow from Paleolithic Europeans into the ~15,000 year old North Africans as previously suggested based on archaeological similarities. Finally, the Taforalt individuals derive one third of their ancestry from sub-Saharan Africans, best approximated by a mixture of genetic components preserved in present-day West Africans (Yoruba, Mende) and Africans from Tanzania (Hadza). In contrast, modern North Africans have a much smaller sub-Saharan African component with no apparent link to Hadza. Our results provide the earliest direct evidence for genetic interactions between modern humans across Africa and Eurasia.
Exploring the genomic impact of colonization in north-eastern Siberia by Seguin-Orlando et al.
Yakutia is the coldest region in the northern hemisphere, with winter record temperatures below minus 70°C. The ability of Yakut people to adapt both culturally and biologically to extremely cold temperatures has been key to their subsistence. They are believed to descend from an ancestral population, which left its original homeland in the Lake Baykal area following the Mongol expansion between the 13th and 15th centuries AD. They originally developed a semi-nomadic lifestyle, based on horse and cattle breeding, providing transportation, primary clothing material, meat, and milk. The early colonization by Russians in the first half of the 17th century AD, and their further expansion, have massively impacted indigenous populations. It led not only to massive epidemiological outbreaks, but also to an important dietary shift increasingly relying on carbohydrate-rich resources, and a profound lifestyle transition with the gradual conversion from Shamanism to Christianity and the establishment of new marriage customs. Leveraging an exceptional archaeological collection of more than a hundred of bodies excavated by MAFSO (Mission Archéologique Française en Sibérie Orientale) over the last 15 years and naturally kept frozen by the extreme cold temperatures of Yakutia, we have started to characterize the (epi)genome of indigenous individuals who lived from the 16th to the 20th century AD. Current data include the genome sequence of approximately 50 individuals that lived prior to and after Russian contact, at a coverage from 2 to 40 fold. Combined with data from archaeology and physical anthropology, as well as microbial DNA preserved in the specimens, our unique dataset is aimed at assessing the biological consequences of the social and biological changes undergone by the Yakut people following their neolithisation by Russian colons.
“Exploring the genomic impact of colonization in North-Eastern #Siberia” – Andaine Seguin-Orlando #ISBA8#aDNA with shotgun data from 110 #Yakut individuals over 4 regions and multiple archaeological phases of #Yakutia including 71 >1x coverage and 2 sequenced to high depth. pic.twitter.com/BGpecQPcGE
North Africa is a key region for understanding human history, but the genetic history of its people is largely unknown. We present genomic data from seven 15,000-year-old modern humans from Morocco, attributed to the Iberomaurusian culture. We find a genetic affinity with early Holocene Near Easterners, best represented by Levantine Natufians, suggesting a pre-agricultural connection between Africa and the Near East. We do not find evidence for gene flow from Paleolithic Europeans into Late Pleistocene North Africans. The Taforalt individuals derive one third of their ancestry from sub-Saharan Africans, best approximated by a mixture of genetic components preserved in present-day West and East Africans. Thus, we provide direct evidence for genetic interactions between modern humans across Africa and Eurasia in the Pleistocene.
We analyzed the genetic affinities of the Taforalt individ-uals by performing principal component analysis (PCA) and model-based clustering of worldwide data (Fig. 2). When pro-jected onto the top PCs of African and West Eurasian popu-lations, the Taforalt individuals form a distinct cluster in an intermediate position between present-day North Africans (e.g., Amazighes (Berbers), Mozabite and Saharawi) and East Africans (e.g., Afar, Oromo and Somali) (Fig. 2A). Consist-ently, we find that all males with sufficient nuclear DNA preservation carry Y haplogroup E1b1b1a1 (M-78; table S16). This haplogroup occurs most frequently in present-day North and East African populations (18). The closely related E1b1b1b (M-123) haplogroup has been reported for Epipaleolithic Natufians and Pre-Pottery Neolithic Levantines (“Levant_N”) (16). Unsupervised genetic clustering also suggests a connection of Taforalt to the Near East. The three major components that comprise the Taforalt genomes are maximized in early Holocene Levantines, East African hunter-gatherer Hadza from north-central Tanzania, and West Africans (K = 10; Fig. 2B). In contrast, present-day North Africans have smaller sub-Saharan African components with minimal Hadza-related contribution (Fig. 2B).
Taforalt harboring an ancestry that contains additional affinity with South, East and Central African outgroups. None of the present-day or ancient Holocene African groups serve as a good proxy for this unknown ancestry, because adding them as the third source is still insufficient to match the model to the Taforalt gene pool.
Mitochondrial consensus sequences of the Taforalt indi-viduals belong to the U6a (n = 6) and M1b (n = 1) haplogroups (15), which are mostly confined to present-day populations in North and East Africa (7). U6 and M1 have been proposed as markers for autochthonous Maghreb ancestry, which might have been originally introduced into this region by a back-to-Africa migration from West Asia (6, 7). The occurrence of both haplogroups in the Taforalt individuals proves their pre-Holocene presence in the Maghreb.
(…) the diversification of haplogroup U6a and M1 found for Taforalt is dated to ~24,000 yBP (fig. S23), which is close in time to the earliest known appearance of the Iberomaurusian in Northwest Africa (25,845-25,270 cal. yBP at Tamar Hat (26)).
The relationships of the Iberomaurusian culture with the preceding MSA, including the local backed bladelet technologies in Northeast Africa, and the Epigravettian in southern Europe have been questioned (13). The genetic profile of Taforalt suggests substantial Natufian-related and sub-Saharan African-related ancestries (63.5% and 36.5%, respec-tively), but not additional ancestry from Epigravettian or other Upper Paleolithic European populations. Therefore, we provide genomic evidence for a Late Pleistocene connection between North Africa and the Near East, predating the Neolithic transition by at least four millennia, while rejecting a potential Epigravettian gene flow from southern Europe into northern Africa within the resolution of our data.
It seems that the Taforalt gene pool (ca. 13000-12000 BC) cannot be explained by a connection with Upper Palaeolithic Europeans, but a more archaic admixture, so the authors cannot prove a migration through the Strait of Gibraltar or Sicily.
Nevertheless, these results apparently suggest:
That there is no contact before ca. 12000 BC through the Strait of Gibraltar; therefore the Sicilian route I support for the migration of R1b-V88 lineages is still the most likely one.