The rest of Japan's patrilineal ancestry (outside the Ainu indigeneous minority population) is largely traceable to historic era migration from Korea and China which brought the Japanese language to the island chain and gave birth to what became the modern Japanese culture as these rice growing, horse riding, metal sword wielding new comers (the Yaoyi) admixed with the sedentary fishing populations that preceded them (a remarkably high percentage of ancestral survival for a pre-Neolithic population whose language leaves almost no trace in the modern Japanese language).
Partial samples of ancient Jomon autosomal DNA seem to largely confirm this analysis.
The abstract of a symposium paper soon to be presented on the subject states:
Hideaki Kanzawa-Kiriyama, Nuclear Genome Analysis of Ancient Japanese Archipelago HumansI have some doubts about the sequencing. There is a good case to be made that the Jomon arrive after the first wave of modern humans in East Asia, rather than before, and settle in places like Tibet, the Andaman Islands, and Japan because it is all that is left that hasn't been claimed at that time, and because they have superior maritime capabilities compared to their contemporaries.
The Jomon period, characterized by chord-marked potteries, lasted from ~16,000 to less than 3,000 years before present (YBP), and abundant human skeletal remains have been excavated from shell mounds and other sites throughout the Japanese Archipelago. However, their genetic origin and the relationships with modern populations are largely unknown. Here we determined 10% and 80% of the genomic DNA sequences from two Jomon individuals, excavated at Yugura cave site, Nagano, and Shitsukariabe cave site, Aomori, respectively, and compared their genome sequences with worldwide populations. We found a unique genetic position of the Jomon people who had diverged before the diversification of most of present-day East Eurasian populations including East Eurasian Islanders. This indicates that Jomon people were a basal population in East Eurasia and genetically isolated from other East Eurasians for long time. However, their genetic affinities to modern East Eurasians are uneven. The heterogeneity might be a hint to clarify human migration and gene flow in East Eurasia after the divergence of Jomon ancestors.
Background on the issue of Jomon DNA can be ground here. An ancient Jomon DNA study from 2009 is here. A 2013 study is here. Realistically, about 43% of Japanese Y-DNA and a third of Japanese mtDNA is attributable to Jomon ancestors, with more in Northern Japan and less in Western Japan, consistent with the history of Yaoyi migration in Japan starting ca. 1000 BCE, or perhaps a century or two later, with full control of the Japanese islands secured only many centuries after that point.
A new paper also documents archaeologically, the arrival of Fertile Crescent crops like barley and wheat strengthen agriculture in Tibet ca. 1600 BCE that previously relied on crops such as broomcorn and foxtail millet, and this cemented the much older human presence there. Sheep may also have arrived in Tibet around this time.