Koreans v. Japanese v. Chinese Genetic Ancestry

A new paper purports to be able to distinguish almost perfectly between Koreans, the Japanese, and Chinese individuals based upon autosomal genetics. This is something that consumer genetic services such as 23andMe struggle with right now.

For example, 23andMe claims that my son has more Japanese ancestry than Korean ancestry, when, in fact, he probably has no recent Japanese ancestry and has entirely North Korean ancestry on his mother's side (something upon which we have very solid genealogical support from living memory back to his great-great grandparents because his last great-grandparent died just a few years ago at the age of 98).

In the case of 23andMe, this is probably because ancestry in Japanese people from Yayoi people (including mounted warriors) who invaded Japan from Korea ca. 1000 BCE is being classified as Japanese in origin, rather than Korean, despite the fact that these genetic component originated in Korea, because there are more Japanese individuals in their samples than there are Koreans. 

The paper also controversially suggests that these three populations have a common origin at about 1200 BCE (in the Shang Dynasty of China). 

Indeed, we are pretty much certain that this is not true in the case of the Japanese who have substantial Jomon ancestry that has a much greater time depth. 

The common origin hypothesis is also contrary to the hypothesis that the non-Jomon genetic component of the Koreans and Japanese has a significant "Altaic" component (also hypothesized linguistically) derived from Manchuria and Mongolia and the vicinity, in addition to substantial Chinese admixture in both Korean and Japanese populations, which is well documented historically at least in the case of the Japanese.

So, this 1200 BCE common origin date may be due to some methodological artifact (i.e. flaw) that might, perhaps, simply be measuring a common origin for the Chinese admixture component in all three populations that is significant in all of them, since this is around the time that the Chinese component of these nations would have diverged historically.

Both the linguistic and genetic origins of the Yayoi prior to their migration from Korea to Japan are disputed. Wikipedia (from the link above) notes that:

Origin 

There are several hypotheses about the origin of the Yayoi people. 

The most popular one is that they were the people who brought wet rice cultivation to Japan from the Korean peninsula and Jiangnan near the Yangtze River Delta in China.[1] This is supported by archeological researches and bones found in today southeastern China.[2] 

Another is that they are from Primorskaya Oblast or northern part of the Korean peninsula. It is because the human bones of the Doihigahama ruins resemble the ancient human bones of the northern part of the Korean peninsula, and pottery is similar to the "Engraved band sentence pottery", widely used during the Yayoi period, was discovered in the Sini-Gai culture in the southwestern coastal province of Primorskaya Oblast.[3] 

The theory that Yayoi people have multiple origins is suggested and influential.[4][5] 

It is estimated that Yayoi people mainly belonged to [Ed. Y-DNA] Haplogroup O-M176 and Haplogroup O-M122 which are typical for East- and Southeast-Asians.[6] 

Language 

The Yayoi may have spoken an Austroasiatic language or Tai-Kadai language, based on the reconstructed Japonic terms *(z/h)ina-Ci 'rice (plant)', *koma-Ci '(hulled) rice', and *pwo 'ear of grain' which Vovin assumes to be agricultural terms of Yayoi origin. Vovin suggests that Japonic was in contact with Austronesian, before the migration from Southern China to Japan, pointing to an ultimate origin of Japonic in southern China.[7][8] Although Vovin (2014)[8]does not consider Japonic to be genetically related to Tai-Kadai, he suggests that Japonic was later in contact with Tai-Kadai, pointing to an ultimate origin of Japonic in southern China with possible genetic relation to Austroasiatic. 

There is typological evidence that Proto-Japonic may have been a monosyllabic, SVO syntax and isolating language; which are features that the Austroasiatic languages also famously exhibit.[8] 

A 2015 analysis using the Automated Similarity Judgment Program resulted in the Japonic languages being grouped with the Austroasiatic languages. The same analysis also showed a connection to Ainu languages, but this is possibly because of heavy influence from Japonic to Ainu.[9]

Many linguistic scholars, however, think that Japonic and Korean are distant members of the Altaic language family which also includes the Turkish, Mongolian and Manchurian (a.k.a. Tungistic) languages.

Japanese has borrowed heavily in the historic era from the Chinese language, without changing its underlying grammar and structure, and has virtually no linguistic connection to the Ainu language which was related to the language of the Jomon people who were invaded by the Yayoi. 

This lack of linguistic borrowing from the Jomon is the case even though Jomon genetic input into the modern Japanese gene pool was very substantial for a hunter-gatherer population, perhaps because hunter-gatherers who fish, like those in Japan, the Pacific Northwest and the Baltic-Finnish region, seem to have more staying power than terrestrial hunter-gatherers, vis-a-vis farmers and herders.