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Wednesday, May 1, 2019

Archaic Ghost population admixed with Modern Humans in Africa


A paper published on April 26, 2019, Whole-genome sequence analysis of a Pan African set of samples reveals archaic gene flow from an extinct basal population of modern humans into sub-Saharan populations by Belen Lorente-Galdos et al. (Genome Biology201920:77 https://doi.org/10.1186/s13059-019-1684-5) looks into a "Ghost" archaic population (XAf) in Africa which admixed archaic genes into humans (AMH or anatomically modern humans) there.


The authors write:


"We identify the fingerprint of an archaic introgression event in the sub-Saharan populations included in the models (~ 4.0% in Khoisan, ~ 4.3% in Mbuti Pygmies, and ~ 5.8% in Mandenka) from an early divergent and currently extinct ghost modern human lineage."

These are quite high values. The authors continue:


"Our results suggest interbreeding of AMHs with an archaic ghost population that diverged from the AMH lineage at a temporal scale similar to the one between the Neanderthals and Denisovans.
This observation would indicate the presence of a deep archaic population substructure also in the African continent and contrasts with previous studies that suggested that a basal lineage had a major impact only on particular western African populations.
Furthermore, our analyses showed that the estimated proportion of Neanderthal ancestry in Eurasian populations is highly sensitive to the presence of XAf population, increasing by a threefold the amount of archaic introgression.
This result suggests that the amount of Neanderthal ancestry out of Africa that so far has been estimated could be an underestimation by not having considered events of archaic introgression in Africa in the tested models.
"

I find the last part very interesting, the paper is suggesting that we -non-Africans- may have even more Neanderthal genes than current studies suggest, because they have not considered this XAf admixture into the humans leaving Africa.


The paper downplays a possible "Into Africa" event where Neanderthal genes were passed on to Africans by Neanderthals and assume the source of those genes are more recent: Europeans or Asians. The authors write:


"Traces of Neanderthal introgression have been observed not only in North African populations, who are in fact historically and genetically different from sub-Saharan peoples, but also in other African populations, for instance in Yoruba genomes, although they were most likely introduced through recent Eurasian admixture."

They defined some timelines (we quote them below):


"The AMH lineage and the one from the archaic Eurasian populations diverged 603 kya" the CI is 495.85 to 796.86 kya


"The ghost XAf archaic population and the AMH lineage split 528 kya" (CI 230.16 to 700.06 kya)


"The Denisovan and Neanderthal lineages split 426 kya" (CI 332.77 to 538.37 kya)


Admixture of XAf was significant, considering that Neanderthal genes account for less than 2% of Eurasian genetic makeup. These are the African values of admixture:


  • 3.8% (95% CI 1.7 to 4.8%) in Khoisan
  • 3.9% (95% CI 1.3 to 4.9%) in Mbuti
  • 5.8% (95% CI 0.7 to 0.97%) in West Africa

The paper found that there was high levels of inbreeding as they "observed that ... both Khoisan and Pygmies show higher levels of ROH that are closer to the ones found in North African or Eurasian populations". ROH or Runs of Homozygosity are are regions of the chromosomes where there are many consecutive homozygoous loci and are an indication of inbreeding.


So the supposedly ancient Khoshian are very similar in their ROH to the "more recent" Eurasians, which are supposed to have undergone bottlenecks and later inbreeding.


The issue of African diversity is not addressed clearly. Although they identify some introgression regions:


"Specific candidate introgressed regions have also been identified, for instance, a 20 kbp block found exclusively in sub-Saharan populations that covers the entire MUC7 gene, a protein abundantly expressed in saliva and associated with the composition of oral microbiome [40], or 265 loci spanning ~ 20 Mbp spread across the genome that were detected in two Western African Pygmy populations"

Read more about the MUC7 gene introgresion here.


The impact of 4% archaic genes in the overall diversity of modern Africans must be significant, and that means that their diversity is not due to Africa being the cradle of mankind but to an admixture of archaic DNA.



Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2019 by Austin Whittall © 

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