Wednesday, September 22, 2021

A Grab Bag Paper On East Asian Historical Genetics

In the course of looking into the three component story of the formation of the Japanese people that I posted yesterday, I came across a gem of a preprint from March 25, 2020 covering all manner of only vaguely related subjects. I may have previously blogged some of its findings, but it really is all over the place and could have legitimately spawned five distinct articles.
The deep population history of East Asia remains poorly understood due to a lack of ancient DNA data and sparse sampling of present-day people. We report genome-wide data from 191 individuals from Mongolia, northern China, Taiwan, the Amur River Basin and Japan dating to 6000 BCE – 1000 CE, many from contexts never previously analyzed with ancient DNA. We also report 383 present-day individuals from 46 groups mostly from the Tibetan Plateau and southern China. 
We document how 6000-3600 BCE people of Mongolia and the Amur River Basin were from populations that expanded over Northeast Asia, likely dispersing the ancestors of Mongolic and Tungusic languages. 
In a time transect of 89 Mongolians, we reveal how Yamnaya steppe pastoralist spread from the west by 3300-2900 BCE in association with the Afanasievo culture, although we also document a boy buried in an Afanasievo barrow with ancestry entirely from local Mongolian hunter-gatherers, representing a unique case of someone of entirely non-Yamnaya ancestry interred in this way. The second spread of Yamnaya-derived ancestry came via groups that harbored about a third of their ancestry from European farmers, which nearly completely displaced unmixed Yamnaya-related lineages in Mongolia in the second millennium BCE, but did not replace Afanasievo lineages in western China where Afanasievo ancestry persisted, plausibly acting as the source of the early-splitting Tocharian branch of Indo-European languages. 
Analyzing 20 Yellow River Basin farmers dating to ∼3000 BCE, we document a population that was a plausible vector for the spread of Sino-Tibetan languages both to the Tibetan Plateau and to the central plain where they mixed with southern agriculturalists to form the ancestors of Han Chinese. 
We show that the individuals in a time transect of 52 ancient Taiwan individuals spanning at least 1400 BCE to 600 CE were consistent with being nearly direct descendants of Yangtze Valley first farmers who likely spread Austronesian, Tai-Kadai and Austroasiatic languages across Southeast and South Asia and mixing with the people they encountered, contributing to a four-fold reduction of genetic differentiation during the emergence of complex societies. 
We finally report data from Jomon hunter-gatherers from Japan who harbored one of the earliest splitting branches of East Eurasian variation, and show an affinity among Jomon, Amur River Basin, ancient Taiwan, and Austronesian-speakers, as expected for ancestry if they all had contributions from a Late Pleistocene coastal route migration to East Asia.


Ryan said...

Interesting results, especially since the Amur River populations seem to be key to the peopling of northern North America.

DDeden said...
Article on genomes of Polynesians identify route over 400 years migrations from Samoa to Easter Island, with AmerInd traces

DDeden said...

22ka footprints in New Mexico

That "genetic evidence" claim is probably not including the newer data of the Surui of the Amazon and some groups in Columbia that have Andaman-like genetic traces indicating a plausibly much earlier migration (using bark canoes?). Those footprints may have been made by people who resembled Andaman people more than today's Asians or Amer. Indians. That could explain the lack of dog tracks amongst the children's footprints?

andrew said...


Thanks for the tips.

I noticed the Polynesian article and was weighing if it really added anything meaningful to my prior posts on the subject.

I also noticed the New Mexico footprints story and have been pausing a bit to look at what others have to say about it, and the analyze that data and muse about it. At first blush, the dating and identification of the footprints as modern human seems reliable, but I'd like to hear more informed commentary.

For the reasons I stated in a previous post on the subject of Paleoasian ancestry in South America, I do not think that the "Paleoasian" ancestry in the Surui and elsewhere in South America has that much time depth, primarily because there is no plausible way that it could have such high intrapopulation variation in genetic proportion as the most recent study revealed. The law of averages says that this ancestry had to be relatively recent and there is a well established vector and time frame for that from Polynesians ca. 1200 CE (which the new Polynesian paper tends to confirm) that could provide about the right level of variability.

The more plausible hypothesis is that modern human populations in the Americas from before the main founding population wave, either left no discernible genetic trace and reached or almost reached extinction during the LGM or upon first contact with the newcomers, or that their introgression into the Founding population of the Americas was proportionately small enough and substantively similar enough genetically the the Founding population that arrived a few thousand years later, that it can't be discerned as distinct from the Founding population. The amount of genetic divergence that occurs over time is a function of both the number of generations and the effective population size of the populations in question. And, on both sides of the Bering Strait the amount of divergence would have been limited by small population size and would have begun from a common ancestral population in NE Asia. The loss of Y-DNA and mtDNA haplogroups in the pre-Founding population would also be expected if there was a stable or declining population in the Americas and if the effective population size was small.

Onur Dincer said...


or that their introgression into the Founding population of the Americas was proportionately small enough and substantively similar enough genetically the the Founding population that arrived a few thousand years later, that it can't be discerned as distinct from the Founding population.

They need not be genetically so similar to the founding population of modern-day Amerindians, being composed of a single component of the modern-day Amerindian genetics would be enough. They may, for instance, have been entirely composed of ANE (Ancient North Eurasian) ancestry, which is indeed one of the components of modern-day Amerindian genetics; their dating is compatible with them being entirely composed of ANE ancestry as Siberia was full of pure or close to pure ANE populations back then. But of course the bulk of the ANE ancestry of modern-day Amerindians must still be from an East Eurasian-ANE mixture event within Siberia or Beringia later in time and not from them, otherwise we would expect to see strong signals of them in the dating of the East Eurasian-ANE mixture of modern-day Amerindians.

andrew said...


I really didn't intend to say otherwise.

The idea is that the Paleo-Asian component, and the places where most claims of evidence of pre-LGM or LGM era migration are made, are among the least genetically diverse. Meso-America and South America have far less genetic diversity than any other part of the Americas (prior to the Southern migration of Na-Dene migration to what is now the American Southwest ca. 1000 CE, and of course in the pre-Columbian era ca. 1492 CE). That isn't a good fit for ANE.

Onur Dincer said...


Irrespective of however the ancestry of the hypothesized earliest modern human inhabitants of the Americas was, they probably have contributed nothing or very little to the genetics of modern-day Amerindians we know due to the later estimated date of the East Eurasian-ANE mixture of modern-day Amerindians. So the earliest modern human inhabitants of the Americas could hypothetically have any kind of modern human ancestry. I hypothesize a largely or fully ANE type of ancestry for them due to the ANE type genetics of large parts of Siberia during the time of their colonization of the Americas.

andrew said...

@Onur A reasonable hypothesis.