The modern people of Japan are descended from two main groups–the Yayoi, rice farmers who arrived in the archipelago around 800 BC, and the Jomon, hunter-gatherers who arrived thousands of years before.
The oldest known skeletons in Japan are about 30,000 years old. The first 20,000 years of Japanese history are the Paleolithic; the Jomon period, marked by distinct pottery, begins around 14,000 BC.
Despite being hunter-gatherers, the Jomon reached a relatively high level of cultural sophistication (Wikipedia has a nice collection of Jomon art and buildings,) probably because Japan is a naturally lush and pleasant place to live. (The popular perception of hunter-gatherers as poor and constantly on the brink of death is due to the best land having been conquered by farmers over the past few thousand years and enormous population growth over the past hundred. Neither of these factors affected the Jomon at their peak.)
Who were the Jomon? Were they descended directly from the paleolithic peoples of Japan, or were they (relative) newcomers? And what happened to them when the Yayoi arrived? Did they inter-marry? Are the Ainu their modern descendants?
An interesting new paper posted on BioRxiv, Jomon genome sheds light on East Asian population history, examines the DNA of a 2,500 year old individual:
After the major Out-of-Africa dispersal of Homo sapiens around 60 kya, modern humans rapidly expanded across the vast landscapes of Eurasia. Both fossil and ancient genomic evidence suggest that groups ancestrally related to present-day East Asians were present in eastern China by as early as 40 kya. Two major routes for these dispersals have been proposed, either from the northern or southern parts of the Himalaya mountains[1,3–5].
So far the genetic studies have suggested a southern migration route, but archaeological evidence suggests a northern route or at least significant northern trade routes.
Note: the paper claims that the Jomon invented the world’s first pottery, but this appears to be incorrect; according to Wikipedia, the oldest known pottery is from China. However, the Jomon are very close.
To identify the origin of the Jomon people, we sequenced a 1.85-fold genomic coverage of a 2,500-years old Jomon individual (IK002) excavated from the central part of the Japanese archipelago. Comparing the Jomon whole-genome sequence with ancient Southeast Asians, we previously reported genetic affinity between IK002 and the 8,000-years old Hòabìnhian hunter-gatherer. This direct evidence on the link between the Jomon and Southeast Asians, thus, confirms the southern route origin of East Asians.
Ideally, it would be nice to have a bunch of much older samples, but is difficult to get older DNA from Japanese skeletons because Japan is generally warm and humid, which interferes with preservation. It’s really amazing that we can get what little old DNA we can.
I’m going to call IK002 “Ikari” from here on.
Ikari’s mother hails from mitochondrial haplogroup N9b1, which previous studies have established as common in ancient Jomon people. It’s quite rare in modern Japan, however–which is somewhat unusual, since invading armies usually like to turn the local women into war brides rather than wipe them out entirely. The mitochondrial DNA of Latin American people, for example, hails primarily from native women, while their Y chromosomes hail primarily from Spanish conquistadors.
Then we get to the exciting part.
The authors use numerous methods to compare Ikari’s DNA to that of other people, ancient and modern. The graph at right shows Ikari (the red diamod) closest to the Kusunda, a modern day people living in Nepal! According to Wikipedia, there are only 164 Kusunda left, with only one surviving speaker of their native language, itself an isolate. (Though the Wikipedia page on the Kusunda language claims that 7 or 8 more speakers were recently discovered.)
The other shapes close to Ikari on this graph are are Sherpas and another iron-age individual from Tibet.
The Ainu are not shown on this graph, but Ikari is closely related to them, as well.
Second, when using a smaller number of SNPs (41,264 SNPs) including the present-day Ainu from Hokkaido (Fig.S1), IK002 clusters with the Hokkaido Ainu (Fig.S4), supporting previous findings that they are direct descendants of the Jomon people[14,34–41].
Taken together, all of the evidence is still kind of scanty, but points to the possibility of a Melanesian-derived group that spread across south Asia, made it into Tibet and the Andaman Islands, walked into Indonesia, and then split up, with one branch heading up the coast to Taiwan, Okinawa, Japan, and perhaps across the Bering Strait and down to Brazil, while another group headed out to Australia.
Later, the ancestors of today’s east Asians moved into the area, largely displacing or wiping out the original population, except in the hardest places to reach, like Tibet, the Andaman Islands, Papua New Guinea, the Amazon Rainforest, and Hokkaido–the fringe.)
That was quite speculative, but an actual genetic link between Tibetans (broadly speaking, peoples of the Tibetan plateau) and the modern Ainu is pretty exciting.
Of course, the Jomon did not die out entirely when the Yayoi arrived–about 10% of the modern Japanese genome resembles Ikari’s, along with 6% of the nearby Siberian Ulchi people’s.
By contrast, the Yayoi are more closely related to the modern Han Chinese.
Further analysis reveals more fascinating details about the ancient peopling of Asia and the Americas: Ikari’s ancestors likely split off from the other Asians before the Native Americans headed to Alaska, giving us a rough time estimate for the Jomon’s arrival–older than the 26,000 year old split between East Asians vs Siberians & Native Americans, but younger than a particular 40,000 year old group that split off in China, found in Tianyuan.
This indicates that the Jomon are most likely descended from the Japanese Paleolithic people, who arrived around 30,000 years ago and simply developed pottery a few thousand years later, rather than more recent migrants.
People have long speculated about whether the Ainu are related to Caucasians (whites, Europeans, Westerners, whatever you want to call them,) due to their abundantly bushy beards. There is some West-Eurasian admixture in the ancestors of East Siberians and Native Americans that pre-dates the peopling of the New World, but this admixture is not found in Ikari; the Ainu likely did not get their beards from wandering European hunter-gatherers.
As the tooth studies suggested, however, the Jomon and Ainu are related to the Taiwanese Aborigines, like the Ami and Atayal. (However, the final portion of the paper is a little confusing, so I may have misinterpreted something. Hopefully the authors can clarify a bit in their final form.) It is otherwise a fine paper, and I encourage you to read it.