In Xiaoming Zhang et al., "A Late Pleistocene human genome from Southwest China" (2022), the authors discuss their analysis of 14,000 year old ancient DNA from a woman at the Red Deer Cave named Mengzi Ren (MZR). (I tip my hat to Bernard's blog and to Razib who together alerted me to this paper.) I previously blogged this find, before ancient DNA analysis was available, on December 18, 2015.
Her "mosaic" of seemingly partially archaic bone features suggested that she might be an archaic hominin-modern human hybrid in Southwest China.
As was the case with seemingly archaic featured remains in South America that were later genotyped to be ordinary indigenous Americans genetically, the reality was less flashy and was largely paradigm affirming.
The results disfavor the late persistence of archaic hominins in mainland Asia, and demand a non-genetic explanation for her seemingly archaic features, as she is genetically a typical Southeast and southern East Asian anatomically modern human.
Perhaps the most novel conclusion of the paper is that it substantiates a strong genetic affinity between the Red Deer Cave people of Southwest China ca. 14,000 years ago, and the main founding population of the Americas which broke away from Asia at roughly the same time or a few thousand years earlier.
Her mtDNA was a now extinct basal branch of mtDNA M9, a non-African modern human mtDNA clade, that is fairly closely related to the mtDNA M9 clades that are common in China's interior and central Asia (and to a lesser extent in the rest of China). Her mtDNA deviates by just one mutation from the mtDNA M9 root.
In island Southeast Asia and Vietnam, in contrast, mtDNA E which is also a basal branch of mtDNA M is more common.
She is definitively an anatomically modern human based upon her autosomal DNA, which is close on a PCA chart of overall genetic similarity to Hoabinhian hunter-gatherers who occupied Southeast Asia and adjacent regions in China from sometime in the Upper Paleolithic, a.k.a. Late Pleistocene, era until about 2000 BCE.
There has been considerable genetic continuity from her to modern populations that were until recently hunter-gathers in the region over the last 14,000 years.
She shows an even greater autosomal genetic affinity to contemporaneous Northeast Asians on the brink of the Bering land bridge and to the oldest Native American ancient genomes, than she does with mainland Southeast Asian Hoabinhians.
Her autosomal DNA reflected most strongly an ancestral DNA component now associated with Southeast Asia with a significant minority of ancestry that was distinctively Northeast Asian, in addition to trace ancestry components that were distinctive African, specifically Native American, European or Papuan (and she has no distinctive South Asian ancestry component).
This indicates that 14,000 years ago, there was already differentiation and population structure between Northeast Asia and mainland Southeast Asia that had formed, and then produced admixed populations again, of which she was a member.
Archaic Hominin Ancestry
Her percentages of Neanderthal (1.27%) and Denisovan (1.29%) autosomal DNA admixture is similar to that other modern humans of that era and does not show enhanced or recent archaic admixture. Her Neanderthal and Denisovan ancestry percentages are broadly similar to modern Asian people from this region today.
This is what the paradigm would expect since there are no really definitive examples of archaic hominins in mainland Southeast Asia or China more recent than about 100,000 years ago.
Evidence of a Neanderthal presence has never been found east of South Asia in places south of the Altai.
The History Of Two Asian Genetic Variants
She lacks a derived genetic variant associated with light skin in modern East Asians that an analysis of many ancient and modern DNA samples in the papers concludes arose only in the early Holocene era (i.e. in the last 10,000 years) with the oldest isolated example from 7,500 years ago and some examples in the las 5,000 years and predominance in the last hundred years.
The paper also analyzes the emergence of the derived EDAR variant which is the source of some of the distinctively "Asian" phenotype. This arises many thousands of years earlier than the light skin genetic variant, but apparently the ancient DNA sample from this woman was missing the part of her genome that would have contains the EDAR variant, so we don't know if she had it or not. The oldest example of the derived EDAR variant is from the Amur region in Northeast Asia from about 19,000 years ago (although mutation rate estimates suggest it originated 30,000 years ago), and it is fairly widespread in East Asia, Northeast Asia, and the Americas from 11,600 years ago onward, becoming predominant in Southeast Asia, East Asia, Northeast Asia and the Americas by 4,900 years ago.
Both of these derived genetic variants that are distinguishing features of modern Southeast and East Asians post-dated the Last Glacial Maximum which led to essentially total population replacement in Northern Asia (and preceded any significant modern human population that left lasting traces in the Americas).
The Paper's Analysis
The discussion section of the paper generally sums up these themes and adds some additional cross-disciplinary speculation, most of which is plausible, although the bold underlined conjecture really has no solid support.