Monday, July 12, 2021

Inferring Ancient Arabian Genetics From Modern Populations

Researchers in a preprint earlier this year use modern Arabian and Iranian whole genomes to infer the makeup of ancient Arabian population genetics. 

Their results suggest that the hypothetical ghost population of "basal Eurasians" (who did not experience Neanderthal admixture) may have a real world counterpart in ancient East Arabians and in the ancient Iberomaurusian hunter-gatherers of what is now Morocco, Algeria, Tunisia and Libya, in the period between the Last Glacial Maximum and the Holocene. As Wikipedia describes this an ancient archaeological culture:
The name of the Iberomaurusian means "of Iberia and Mauretania", the latter being a Latin name for Northwest Africa. Pallary (1909) coined this term to describe assemblages from the site of La Mouillah in the belief that the industry extended over the strait of Gibraltar into the Iberian peninsula. This theory is now generally discounted (Garrod 1938), but the name has stuck.

In Algeria, Tunisia, and Libya, but not in Morocco, the industry is succeeded by the Capsian industry, whose origins are unclear. The Capsian is believed either to have spread into North Africa from the Near East, or to have evolved from the Iberomaurusian. In Morocco and Western Algeria, the Iberomaurusian is succeeded by the Cardial culture after a long hiatus.

We know a fair amount about these people genetically from ancient DNA and my own remote Y-DNA E-V13 ancestor is probably from this archaeological culture.

In 2013, Iberomaurusian skeletons from the prehistoric sites of Taforalt and Afalou were analyzed for ancient DNA. All of the specimens belonged to maternal clades associated with either North Africa or the northern and southern Mediterranean littoral, indicating gene flow between these areas since the Epipaleolithic. The ancient Taforalt individuals carried the mtDNA Haplogroup N subclades like U6 and M which points to population continuity in the region dating from the Iberomaurusian period.

Loosdrecht et al. (2018) analysed genome-wide data from seven ancient individuals from the Iberomaurusian Grotte des Pigeons site near Taforalt in north-eastern Morocco. The fossils were directly dated to between 15,100 and 13,900 calibrated years before present. 
The scientists found that all males belonged to haplogroup E1b1b, common among Afroasiatic males. The male specimens with sufficient nuclear DNA preservation belonged to the paternal haplogroup E1b1b1a1 (M78), with one skeleton bearing the E1b1b1a1b1 parent lineage to E-V13, one male specimen belonged to E1b1b (M215*). These Y-DNA clades 24,000 years BP had a common ancestor with the Berbers and the E1b1b1b (M123) subhaplogroup that has been observed in skeletal remains belonging to the Epipaleolithic Natufian and Pre-Pottery Neolithic cultures of the Levant
Maternally, the Taforalt remains bore the U6a and M1b mtDNA haplogroups, which are common among modern Afroasiatic-speaking populations in Africa. 
A two-way admixture scenario using Natufian and modern sub-Saharan samples (including West Africans and the Tanzanian Hadza) as reference populations inferred that the seven Taforalt individuals are best modeled genetically as of 63.5% Natufian-related and 36.5% sub-Saharan ancestry (with the latter having both West African-like and Hadza-like affinities), with no apparent gene flow from the Epigravettian culture of Paleolithic southern Europe. The scientists indicated that further ancient DNA testing at other Iberomaurusian archaeological sites would be necessary to determine whether the Taforalt samples were representative of the broader Iberomaurusian gene pool.
The paper and its abstract are as follows (emphasis mine):
Arabian Peninsula is strategic for investigations centred on the structuring of the modern human population in the three main groups, in the awake of the out-of-Africa migration. Despite the poor climatic conditions for recovery of ancient DNA human evidence in Arabia, the availability of genomic data from neighbouring ancient specimens and of informative statistical tools allow better modelling the ancestry of these populations. 
We applied this approach to a dataset of 741,000 variants screened in 291 Arabians and 78 Iranians, and obtained insightful evidence. 
The west-east axis was a strong forcer of population structure in the Peninsula, and, more importantly, there were clear continuums throughout time linking west Arabia with Levant, and east Arabia with Iran and Caucasus. East Arabians also displayed the highest levels of the basal Eurasian lineage of all tested modern-day populations, a signal that was maintained even after correcting for possible bias due to recent sub-Saharan African input in their genomes. Not surprisingly, east Arabians were also the ones with higher similarity with Iberomaurusians, who were so far the best proxy for the basal Eurasians amongst the known ancient specimens. The basal Eurasian lineage is the signature of ancient non-Africans that diverged from the common European-East Asian pool before 50 thousand years ago, and before the later interbred with Neanderthals. Our results are strong evidence to include the exposed basin of the Arabo-Persian Gulf as possible home of basal Eurasians, to be investigated further on namely by searching ancient Arabian human specimens.

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