Spread of Indo-European and Uralic speakers in ADMIXTURE

indo-european-uralic-admixture

The following are updated files for unsupervised ADMIXTURE of most available ancient Eurasian samples with K=7. For reference, see PCA of ancient and modern Eurasian samples.

NOTE. For a precise interpretation of ancestry evolution, be sure to first check the posts on the expansion of “Steppe ancestry”, on the spread of Yamnaya ancestry with Indo-Europeans, and on the evolution of Corded Ware ancestry typical of modern Uralic populations.

ADMIXTURE timeline

This is a YouTube video similar to the one on Indo-Europeans and Y-DNA evolution:

admixture-video-youtube

Some comments

  • 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.
plot-admixture-7
Unsupervised ADMIXTURE (K=7). See full image.

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.

  1. Anatomically Modern Humans (PDF)
  2. Upper Palaeolithic (PDF)
  3. Epipalaeolithic (PDF)
  4. Early Mesolithic (PDF)
  5. Late Mesolithic (PDF)
  6. Neolithic and hunter-gatherer pottery (PDF)
  7. Early Eneolithic (PDF)
  8. Late Eneolithic (PDF)
  9. Early Chalcolithic (PDF)
  10. Late Chalcolithic (PDF)
  11. Early Bronze Age (PDF)
  12. Middle Bronze Age (PDF)
  13. Late Bronze Age (PDF)
  14. Early Iron Age (PDF)
  15. Late Iron Age (PDF)
  16. Antiquity (PDF)
  17. Middle Ages (PDF)

Natural interpolation maps of ADMIXTURE

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.

WHG ancestry

whg-ancestry

AHG ancestry

anatolia-hg-ancestry

ANE ancestry

ane-ancestry

“Siberian” ancestry

This ancestry peaks among Baikal HG, Ust’Belaya, Nganasans, or Ulchi, hence the different labels used.

siberian-ancestry

Iran HG ancestry

iran-hg-ancestry

ADMIXTURE maps by period

Click on each image for a higher resolution version.

Mesolithic

1-mesolithic-admixture

Neolithic

2-neolithic-admixture

Early Eneolithic

3-eneolithic-early-admixture

Late Eneolithic

4-eneolithic-late-admixture

Early Chalcolithic

5-chalcolithic-early-admixture

Late Chalcolithic

6-chalcolithic-late-admixture

Early Bronze Age

7-bronze-age-early-admixture

Middle Bronze Age

8-bronze-age-middle-admixture

Late Bronze Age

9-bronze-age-late-admixture

Early Iron Age

10-iron-age-early-admixture

Late Iron Age

11-iron-age-late-admixture

Antiquity

12-antiquity-admixture

Middle Ages

13-middle-ages-admixture

Modern populations

14-modern-admixture

Samples

These are the samples used for interpolations in each period (except for modern populations, which are those included in the Reich Lab curated dataset):

See also

Ancient genomes from North Africa evidence Neolithic migrations to the Maghreb

BioRxiv preprint now published (behind paywall) Ancient genomes from North Africa evidence prehistoric migrations to the Maghreb from both the Levant and Europe, by Fregel et al., PNAS (2018).

NOTE. I think one of the important changes in this version compared to the preprint is the addition of the recent Iberomaurusian samples.

Abstract (emphasis mine):

The extent to which prehistoric migrations of farmers influenced the genetic pool of western North Africans remains unclear. Archaeological evidence suggests that the Neolithization process may have happened through the adoption of innovations by local Epipaleolithic communities or by demic diffusion from the Eastern Mediterranean shores or Iberia. Here, we present an analysis of individuals’ genome sequences from Early and Late Neolithic sites in Morocco and from Early Neolithic individuals from southern Iberia. We show that Early Neolithic Moroccans (∼5,000 BCE) are similar to Later Stone Age individuals from the same region and possess an endemic element retained in present-day Maghrebi populations, confirming a long-term genetic continuity in the region. This scenario is consistent with Early Neolithic traditions in North Africa deriving from Epipaleolithic communities that adopted certain agricultural techniques from neighboring populations. Among Eurasian ancient populations, Early Neolithic Moroccans are distantly related to Levantine Natufian hunter-gatherers (∼9,000 BCE) and Pre-Pottery Neolithic farmers (∼6,500 BCE). Late Neolithic (∼3,000 BCE) Moroccans, in contrast, share an Iberian component, supporting theories of trans-Gibraltar gene flow and indicating that Neolithization of North Africa involved both the movement of ideas and people. Lastly, the southern Iberian Early Neolithic samples share the same genetic composition as the Cardial Mediterranean Neolithic culture that reached Iberia ∼5,500 BCE. The cultural and genetic similarities between Iberian and North African Neolithic traditions further reinforce the model of an Iberian migration into the Maghreb.

north-africa-genomes-pca
Ancestry inference in ancient samples from North Africa and the Iberian Peninsula. PCA analysis using the Human Origins panel (European, Middle Eastern, and North African populations) and LASER projection of aDNA samples.

Relevant excerpts:

FST and outgroup-f3 distances indicate a high similarity between IAM and Taforalt. As observed for IAM, most Taforalt sample ancestry derives from Epipaleolithic populations from the Levant. However, van de Loosdrecht et al. (17) also reported that one third of Taforalt ancestry was of sub-Saharan African origin. To confirm whether IAM individuals show a sub-Saharan African component, we calculated f4(chimpanzee, African population; Natufian, IAM) in such a way that a positive result for f4 would indicate that IAM is composed both of Levantine and African ancestries. Consistent with the results observed for Taforalt, f4 values are significantly positive for West African populations, with the highest value observed for Gambian and Mandenka (Fig. 3 and SI Appendix, Supplementary Note 10). Together, these results indicate the presence of the same ancestral components in ∼15,000-y old and ∼7,000-y-old populations from Morocco, strongly suggesting a temporal continuity between Later Stone Age and Early Neolithic populations in the Maghreb. However, it is important to take into account that the number of ancient genomes available for comparison is still low and future sampling can provide further refinement in the evolutionary history of North Africa.

Genetic analyses have revealed that the population history of modern North Africans is quite complex (11). Based on our aDNA analysis, we identify an Early Neolithic Moroccan component that is (i) restricted to North Africa in present-day populations (11); (ii) the sole ancestry in IAM samples; and (iii) similar to the one observed in Later Stone Age samples from Morocco (17). We conclude that this component, distantly related to that of Epipaleolithic communities from the Levant, represents the autochthonous Maghrebi ancestry associated with Berber populations. Our data suggests that human populations were isolated in the Maghreb since Upper Paleolithic times. Our hypothesis is in agreement with archaeological research pointing to the first stage of the Neolithic expansion in Morocco as the result of a local population that adopted some technological innovations, such as pottery production or farming, from neighboring areas.

By 3,000 BCE, a continuity in the Neolithic spread brought Mediterranean-like ancestry to the Maghreb, most likely from Iberia. Other archaeological remains, such as African elephant ivory and ostrich eggs found in Iberian sites, confirm the existence of contacts and exchange networks through both sides of the Gibraltar strait at this time. Our analyses strongly support that at least some of the European ancestry observed today in North Africa is related to prehistoric migrations, and local Berber populations were already admixed with Europeans before the Roman conquest. Furthermore, additional European/ Iberian ancestry could have reached the Maghreb after KEB people; this scenario is supported by the presence of Iberian-like Bell-Beaker pottery in more recent stratigraphic layers of IAM and KEB caves. Future paleogenomic efforts in North Africa will further disentangle the complex history of migrations that forged the ancestry of the admixed populations we observe today.

north-africa-iberia-admixture
Ancestry inference in ancient samples from North Africa and the Iberian Peninsula. (B) ADMIXTURE analysis using the Human Origins dataset (European, Middle Eastern, and North African populations) for modern and ancient samples (K = 8). (D) Detail of ADMIXTURE analysis using the Human Origins dataset (European, Middle Eastern, North African, and sub-Saharan African populations) for modern and ancient samples, including Taforalt.

Also, from the main author’s Twitter account:

I just realized that the paragraph with information on data availability is missing! Sequence data in the European Nucleotide Archive (PRJEB22699). Consensus mtDNA sequences are available at the National Center of Biotechnology Information (Accession Numbers MF991431-MF991448).

I find it hard to believe that this genetic continuity from Upper Palaeolithic to Late Neolithic could be representative of an autochthonous development of Afroasiatic. An important population movement – likely more than one – must be found in ancient DNA influencing North-Central and North-East Africa, probably during the time of the Green Sahara corridor.

See here:

Pleistocene North African genomes link Near Eastern and sub-Saharan African human populations

taforalt-samples

Pleistocene North African genomes link Near Eastern and sub-Saharan African human populations, by van de Loosdrecht et al. Science (2018).

Abstract

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.

Excerpts:

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)).

taforalt-admixture
A summary of the genetic profile of the Taforalt individuals. (A) The top two PCs calculated from present-day African, Near Eastern and South European individuals from 72 populations. The Taforalt individuals are projected thereon (red-colored circles). Selected present-day populations are marked by colored symbols. Labels for other populations (marked by small grey circles) are provided in fig. S8. (B) ADMIXTURE results of chosen African and Middle Eastern populations (K = 10). Ancient individuals are labeled in red color. Major ancestry components in Taforalt are maximized in early Holocene Levantines (green), West Africans (purple) and East African Hadza (brown). The ancestry component prevalent in pre-Neolithic Europeans (beige) is absent in Taforalt.

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.
  • That the North African connection with Natufians is quite old – for which we already had modern Y-DNA investigation – , and therefore unlikely to be related to the Afroasiatic expansion.

I am glad I had some more time this week to read at least some interesting parts of the published papers, because the information to process is becoming insanely huge…

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