Thursday, September 22, 2016

Some comments on "Genomic analyses inform on migration events during the peopling of Eurasia"

Pagani et al
Published online

"High-coverage whole-genome sequence studies have so far focused on a limited number[1] of geographically restricted populations [2–5], or been targeted at specific diseases, such as cancer[6]. Nevertheless,  the availability of high-resolution genomic data has led to the development of new methodologies for inferring population history[7–9] and refuelled the debate on the mutation rate in humans [10].  Here we present the Estonian Biocentre Human Genome Diversity Panel (EGDP), a dataset of 483 high-coverage human genomes from 148 populations worldwide, including 379 new genomes from 125 populations, which we group into diversity and selection sets.  We analyse this dataset to refine estimates of continent-wide patterns of heterozygosity, long- and short-distance gene flow, archaic admixture, and changes in effective population size through time as well as for signals of positive or balancing selection. We find a genetic signature in present-day Papuans that suggests that at least 2% of their genome originates from an early and largely extinct expansion of anatomically modern humans (AMHs) out of Africa. Together with evidence from the western Asian fossil record [11], and admixture between AMHs and Neanderthals predating the main Eurasian expansion [12], our results contribute to the mounting evidence for the presence of AMHs out of Africa earlier than 75,000 years ago."

My comments: 

Sounds good to me.  I would add that it is pretty backward to think that there is no "Eurasian" ancestry in Africans.  And if there is "Eurasian" ancestry in Africans, due to obvious high mobility of hominins backward and forwards across and between continents for hundreds of thousands of years, (and most large mammals for that matter) then most of these calculations regarding the degree of archaic and modern admixture in the hominin past are grossly under-estimated (since the degree of admixture in non-Africans has been inferred against Africans, and assumes that Africans [incorrectly] have no Neanderthal or Denisovan admixture.)  Furthermore, the time estimates of population splits would be different if we started to include the idea of high mobility and "soft" splits between hominin populations and continents.

Unfortunately, we rarely see sophisticated models accounting for bidirectional gene flow, high mobility, and other possible confounding phenomena.   The models reflect the same "just so" human origin genetic story, with ever so minor a variation, and are carefully crafted so as not to too directly tread on the toes of a small number of prominent and entrenched paleoanthropologists and human origin geneticists.

At least this paper managed to state the obvious that AMH was present in Eurasia earlier than 75,000 years ago (given those "80,000 year old" Daoxian AMH teeth).


Yes, I'm smiling, but only because I don't work professionally in any field related to the cloying, over specialized, highly politicized and narrow field of human origin genetics.

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