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:

Another hint at the role of Corded Ware peoples in spreading Uralic languages into north-eastern Europe, found in mtDNA analysis of the Finnish population

corded-ware-migration-yamna

Open article at Scientific Reports (Nature): Identification and analysis of mtDNA genomes attributed to Finns reveal long-stagnant demographic trends obscured in the total diversity, by Översti et al. (2017).

Of special interest is its depiction of Finland’s past as including the expansion of Corded Ware population of mtDNA U5b1b2 (and probably Y-DNA R1a-M417 subclades), most likely Uralic speakers of the Forest Zone, to the north of the Yamna culture (where Late Proto-Indo-European was spoken).

A later expansion of other subclades – particularly Y-DNA N1c -, was probably associated with the later western expansion of the Eurasian Seima-Turbino phenomenon, and its current prevalence in Finnish Y-DNA haplogroups might have been the consequence of the population decline ca. 1500 BC, and later Iron Age population bottleneck (with the population peak ca. 500 AD) described in the article.

That would more naturally explain the ‘cultural diffusion’ of Finnic languages into invading eastern N1c lineages, a diffusion which would have been in fact a long-term, quite gradual replacement of previously prevalent Y-DNA R1a subclades in the region, as supported by the prevalent “steppe” component in genome-wide ancestry of Finns.

Therefore, there were probably no sudden, strong population (and thus cultural) changes associated with the arrival of N1c lineages, like the ones seen with R1a (Corded Ware / Uralic) and R1b (Yamna / Proto-Indo-European) expansions in Europe.

How the Saami fit into this scheme is not yet obvious, though.

Abstract:

In Europe, modern mitochondrial diversity is relatively homogeneous and suggests an ubiquitous rapid population growth since the Neolithic revolution. Similar patterns also have been observed in mitochondrial control region data in Finland, which contrasts with the distinctive autosomal and Y-chromosomal diversity among Finns. A different picture emerges from the 843 whole mitochondrial genomes from modern Finns analyzed here. Up to one third of the subhaplogroups can be considered as Finn-characteristic, i.e. rather common in Finland but virtually absent or rare elsewhere in Europe. Bayesian phylogenetic analyses suggest that most of these attributed Finnish lineages date back to around 3,000–5,000 years, coinciding with the arrival of Corded Ware culture and agriculture into Finland. Bayesian estimation of past effective population sizes reveals two differing demographic histories: 1) the ‘local’ Finnish mtDNA haplotypes yielding small and dwindling size estimates for most of the past; and 2) the ‘immigrant’ haplotypes showing growth typical of most European populations. The results based on the local diversity are more in line with that known about Finns from other studies, e.g., Y-chromosome analyses and archaeology findings. The mitochondrial gene pool thus may contain signals of local population history that cannot be readily deduced from the total diversity.

From its results:

In general, there appears to be two loose and largely overlapping clusters among the Finn-characteristic haplogroups: the first between 1,000–2,000 ybp and the second around 3,300–5,500 ybp. The age of the older cluster coincides temporally with the arrival of the Corded-Ware culture and, notably, the spread of agriculture in Finland. The arrival and spread of agriculture, temporally corresponding with the age estimates for most of the haplogroups characteristic of Finns, might be a sign of population size increase enabled by the new mode of subsistence, resulting in reduced drift and accumulation of genetic diversity in the population.

(…)

Another insight in the past population sizes in Finland is based on radiocarbon-dated archaeological findings in different time periods. These analyses suggest two prehistoric population peaks in Finland, the Stone Age peak (c. 5,500 ybp) and the Metal Age peak (~1,500 ybp). Both of these peaks were followed by a population decline, which appears to have reached its ebb around 3,500 ybp. These developments are not distinguishable in the BSPs. However, these ages correspond well to the two haplogroup age clusters described above. The presumably less severe Iron Age population bottleneck seen in the archaeological data, 1,500–1,300 ybp, temporally coincides with the population size reduction visible for the Finn-characteristic subhaplogroups.

Related:

Discovered via Eurogenes.