Wednesday, January 11, 2017

Mark Lipson, David Reich , A working model of the deep relationships of diverse modern human genetic lineages outside of Africa, Molecular Biology and Evolution, is not a good model for the Out of Africa Exit

Mark Lipson, David Reich (2017), A working model of the deep relationship Humans genetic lineages outside of Africa  fails to live up to the hype associated with the new study. Articles about this study claim that it “the new model shows there was a major eastern-western population split once modern humans left Africa”. Read more: Here

In reality, the article does no such thing it fails to explain how Ust’-Ishim  can represent the western  ancestral Eurasian population, when this individual has no living descendants, and there appears to be two ancestral populations for the eastern Eurasians, since Tianyuan man is characterized by mtDNA B, while the Australasians mainly carry the mtDNA M clade.

As I pointed out elsewhere you can analyze genetic research papers via my  “ A PROTOCOL TO EVALUATE POPULATION GENETICS PAPERS”Here

The Protocol provide a framework for analyzing and int erpreting population genetics articles. Bayesian Statistics combines prior beliefs and sample DNA information to make inferences about the sample based on the researchers prior beliefs.

The authors claims that “Here, we report a model that provides a good statistical fit to allele-frequency correlation patterns among East Asians, Australasians, Native Americans, and ancient western and northern Eurasians, together with archaic human groups. The model features a primary eastern/western bifurcation dating to at least 45,000 years ago, with Australasians nested inside the eastern clade, and a parsimonious set of admixture events. “  These clades are represented by the Tianyuan individual (the eastern type) the  Malta individual (the western type) .The evidence in the paper does not support this conclusion.

The sample used in the study were the archaic humanoids: Altai Neanderthals, and the Denisova; the western Eurasian clade was represented by Mal’ta 1 and , Ust’-Ishim  individuals;  indigenous populations from , New Guinea, Australia,  Onge ( from the Andaman Islands), and the Ami (aboriginal Taiwanese) represented the eastern clade.

The basic error in this method is that the authors are comparing ancient and modern DNA, with the full knowledge that the ancient DNA, rarely corresponds to contemporary populations. In addition the authors use the date of the Ust’-Ishim individual as the terminal date for the separation of the eastern and western clades.

Granted, the authors acknowledge that the Ust’-Ishim individual shows no  admixture in Australasians . But this is not surprising , there are no living descendants of Ust’-Ishim. As a result, s/ he  can not represent the point when the eastern and western clades separated .

Interestingly, the Tianyuan DNA, belongs to the mtDNA R macrohaplogroup, namely haplogroup B, in addition a deletion of a 9-bp motif (5′-CCCCCTCTA-3′, revised Cambridge reference sequence positions 8,281–8,289). This haplogroup is not carried by the  indigenous populations from , New Guinea, Australia,  Onge ( from the Andaman Islands), and the Ami (aboriginal Taiwanese) that represented the eastern clade in this study.

The authors of this article failed to discuss the Tianyuan DNA which also dates to 40kya, while the eastern sample used in the study are all modern. The failure to adequately discuss the Tianyuan DNA, makes the conclusion of the paper suspect, since the authors are claiming that the Australasians, represent the eastern clade, eventhough the Tianyuan individual is 45ky old. Moreover, the presence of the 9-bp motif clearly indicates an African influence among the Tianyuan.

Qiaomei Fu et al. DNA analysis of an early modern human from Tianyuan Cave, China. PNAS, published online before print January 22, 2013.