Who were the Jomon?



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[1]. 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[2]. Two major routes for these dispersals have been proposed, either from the northern or southern parts of the Himalaya mountains[1,35].

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[15]. 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[15]. 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.

“Principal component analysis (PCA) of ancient and present-day individuals from worldwide populations after the out-of-Africa expansion. Grey labels represent population codes showing coordinates for individuals. Coloured circles indicate ancient individuals.”

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[34] from Hokkaido (Fig.S1), IK002 clusters with the Hokkaido Ainu (Fig.S4), supporting previous findings that they are direct descendants of the Jomon people[14,3441].

200px-Mongoloid_Australoid_Negrito_Asia_Distribution_of_Asian_peoples_Sinodont_Sundadont(I have written previously about the Ainu, who are, of course, still alive:

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.

Ainu Man showing off his beard

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.

The Modern Ainu, pt 2

Welcome back, everyone. Yesterday we were discussing Ainu genetics. Today we’re still discussing Ainu genetics, but this time we’re discussing mtDNA instead of Y DNA.

Modern Ainu (political protest) in 1992

Based on analysis of one sample of 51 modern Ainus, their mtDNA lineages have been reported to consist mainly of haplogroup Yhaplogroup Dhaplogroup M7a … and haplogroup G1[49][52][53] Other mtDNA haplogroups detected in this sample include A (2/51), M7b2 (2/51), N9b (1/51), B4f (1/51), F1b (1/51), and M9a (1/51). Most of the remaining individuals in this sample have been classified definitively only as belonging to macro-haplogroup M.[52] According to Sato et al. (2009), who have studied the mtDNA of the same sample of modern Ainus (n=51), the major haplogroups of the Ainu are N9 (14/51 = 27.5%, including 10/51 Y and 4/51 N9(xY)), D (12/51 = 23.5%, including 8/51 D(xD5) and 4/51 D5), M7 (10/51 = 19.6%), and G (10/51 = 19.6%, including 8/51 G1 and 2/51 G2); the minor haplogroups are A (2/51), B (1/51), F (1/51), and M(xM7, M8, CZ, D, G) (1/51).[54]

Note that Y (confusingly named) is a sub-haplogroup of N9. It’s commonly found in groups around the Sea of Okhotsk, (including the Ainu,) and in Indonesia, similar to the distribution of Sundadont teeth. Haplogroup D is found in Native Americans (highest frequency among the Aleuts,); Siberians, Ainu, east Asians, Japanese, etc. M7 is kind of generically east-Asian, with high frequency in Japan. In other words, Ainu maternal DNA is fairly similar to that of Japan at large + nearby Siberians.

So how closely related are the Ainu to rest of the Japanese?

Given the archaeology of the area and what we now know of the genetics, it looks like the Ainu were descended primarily from two main groups:

  1. Jomon, (the ancient people of Japan,)
  2. Nearby Siberians, (eg, the Nivkhs.)

Over the past hundred years or so, though, the Ainu have purposefully intermarried with the non-Ainu Japanese, who are themselves descended from a mix of:

  1. Jomon
  2. Yayoi, who invaded around 300 BC, conquering the Jomon.

We’d expect therefore for the Ainu and Japanese to share a fair amount of their mtDNA (the Yayoi probably absorbed Jomon women into their groups;) but not much Y DNA. According to Wikipedia:

Studies published in 2004 and 2007 show the combined frequency of M7a and N9b were observed in Jomons and which are believed by some to be Jomon maternal contribution at 28% in Okinawans (7/50 M7a1, 6/50 M7a(xM7a1), 1/50 N9b), 17.6% in Ainus (8/51 M7a(xM7a1), 1/51 N9b), and from 10% (97/1312 M7a(xM7a1), 1/1312 M7a1, 28/1312 N9b) to 17% (15/100 M7a1, 2/100 M7a(xM7a1)) in mainstream Japanese.[55][56]

A recent reevaluation of cranial traits suggests that the Ainu resemble the Okhotsk more than they do the Jōmon.[57] This agrees with the reference to the Ainu being a merger of Okhotsk and Satsumon referenced above.

map of gene-flow in and out of Beringia, from 25,000 years ago to present

Now certainly, if we can use DNA testing to tell that someone is “half Spaniard, a quarter Finnish, and a quarter Czech, with 3% Neanderthal DNA,” then we can use DNA testing to tell what %s of someone’s ancestry are Japanese, Ainu, Jomon, Yayoi, Siberian, etc.–it’s just a matter of getting enough relevant samples. The only major issue I could see getting in the way is if there actually is no such thing as a genetically “pure” Ainu, but rather a bunch of small Ainu groups with varying levels of admixture from all of the other groups. For example, there is no such thing as “Turkic” genetics–all “Turkic” groups speak Turkic languages, take great pride in being Turkic, and presumably have cultural connections, but genetically they are quite diverse. The situation is similar with Jewish groups. 2000 years ago, most Jews were genetically “Jewish,” but today, the vast majority of Jews are at least 50% non-ancient Hebrew by DNA.

From Ingold


But of course, genetics doesn’t tell you much about the lives of modern Ainu.

Many people theorize recent connections between all of the peoples along the north Pacific rim, from Japan to Oregon, and northward across Canada, based on similar abstract, geometric art styles; lifestyles; and documented contacts. The eternally-controversial Kennewick man (a 9,000 year old skeleton discovered in Washington State,) was initially described by some anthropologists as resembling an Ainu man. Mister Kennewick has since been proven to be related to modern Native Americans–Native Americans may simply have looked different 9,000 years ago.

I look forward to more research on connections between circum-polar and circum-Pacific peoples.

For further reading and interesting photos, I recommend The Ainu and their Culture by Dubreuil.

By Request: The Modern Ainu pt 1

Old photograph of an Ainu man

Most of the information easily available on the internet speaks of the Ainu in the past tense: The Ainu were hunter-gatherers; the Ainu worshiped; the Ainu were conquered. The photographic situation is similar: an image search for “Ainu” brings up a few dozen century-old photos and not much else.

But the modern Ainu, of course, do not live in the past–they live in today, primarily in the very modern city of Sapporo. The modern Ainu are not hunter-gatherers (although the entire nation of Japan remains highly dependent on fishing for its nutrition;) they are doctors and shop-keepers, office workers and artists. They go to school, keep up with modern fashions, play video games, and ride the shinkansen just like everyone else in Japan.

Wikipedia (and everyone else) estimates that about 25,000 Ainu live today in Japan, with the caveat that since the Ainu don’t always bother to mention their ancestry, there could be a couple hundred thousand who just haven’t been counted.

Due to years of inter-marrying, the vast majority of today’s Ainu are at least part Japanese. One reference I recall estimated that about 300 pure-blooded Ainu remained in 1950; another estimated that 200 remain today.

There are also some Ainu living in Russia; according to Wikipedia, about 100 Russians tried to identify as Ainu in the 2010 census, and nearly a thousand people with some degree of Ainu ancestry live in the area.

Alas for my purposes as a writer, these few remaining folks appear to be living their lives out in anthropological anonymity, rather than posting selfies tagged #RealAinu all over the internet.

The one thing everyone likes to argue about in threads about the Ainu is whether or not they look like white people.

It’s kind of dumb to fight about, since obviously Ainu look like Ainu.

Okay, okay. Don’t start a flame war. According to Wikipedia:

Cavalli-Sforza places the Ainu in his “Northeast and East Asian” genetic cluster.[42] …

Turner found remains of Jōmon people of Japan to belong to Sundadont pattern similar with the Southern Mongoloid living populations of Taiwanese aborigines, Filipinos, Indonesians, Thais, Borneans, Laotians, and Malaysians. …

Genetic testing has shown them to belong mainly to Y-haplogroup D-M55.[49] Y-DNA haplogroup D2 is found frequently throughout the Japanese Archipelago including Okinawa. The only places outside Japan in which Y-haplogroup D is common are Tibet in China and the Andaman Islands in the Indian Ocean.[50]

Your Y-haplogroup traces your paternal ancestry, because men (and only men) inherit their Y-chromosomes from their fathers. Your M or Mt-DNA, (short for mitochondrial DNA,) hails exclusively from your mother (and both men and women have Mt-DNA, because we all have mitochondria.)

Often when one group of people conquers another group of people, their descendants end up with Y-DNA from the conquerors and MtDNA from the conquered, but there are other ways people come together, like folks intermarrying with their neighbors.

(Presumably this study was done with relatively pure-blooded Ainu.)

The distribution of Haplogroup D-M174 is quite suggestive: Ainu, Tibetans, and Andaman Islanders. These are three (historically) highly isolated groups–one of the world’s few remaining basically uncontacted peoples, the Sentinelese, (they’ll put a spear in you if you land on their island) live in the Andaman Islands. The Tibetans, as I’ve mentioned, have inherited DNA from the Denisovans–cousins of the Neanderthals who interbred with their ancestors–that lets them breathe more easily at high altitudes than anyone else on Earth, making it rather hard for non-Tibetans move there, much less conquer and occupy it [Note: I wouldn’t be surprised if the Nepalese or other folks who also live up in the Himalayas also have the adaptation; this isn’t meant to be a discussion of modern political borders.] And the Ainu basically live on the far edge of Asian at the southern edge of Siberia–northern Japan is the snowiest populated place in the world.

“Sinodont” and “sundadont” actually refer to two different tooth shapes.

East Asian genetic tree, showing Ainu, Japanese, Koreans, etc

Tibetans and Andaman Islanders are definitely Asians–they clade with other Asians in the Greater Asian Clade–but they don’t look much alike. You wouldn’t mistake them for Caucasians, though.

Haplogroup D-M174 is believed to have evolved about 50-60-thousand years ago, presumably in Asia. This was shortly after the Out-of-Africa event, which occurred about 70,000 (or possibly 100,000 years ago [there might have been more than one OOA.]) D-M174 is so old that its “parent” haplogroup is DE, which is found in Africa and Asia.

By contrast, the mutation to the EDAR-gene which gives Han Chinese (the Asian ethnic group Americans are most familiar with) and Japanese their characteristic hair, skin, tooth shape, build, etc., (EDAR is pretty incredible in that way) only occurred 30,000 years ago–that is, the Ainu split off from other Asians 20-30 thousand years before what we think of as “the Asian look” had even evolved.

For that matter, Caucasian themselves only appear to have split off from Asians around 40,000 years ago–10,000 years before EDAR mutated, but 10-20,000 years after D-M174 arose.

Or to put it another way:

About 70,000 years ago, an intrepid band of explorers left Africa. Presumably, these people looked African, but I don’t know exactly which Africans these ancient people looked like–perhaps they didn’t really look like any modern group; perhaps they looked a lot like most Sub-Saharan Africans; perhaps they looked like the Bushmen, noted for their tawny skin tones and more “Asian” look than other Sub-Saharans. I don’t know yet.

About 60,000 years ago, the band split, and one group spread far across Asia. Their modern descendants are the Ainu, Tibetans, and Andaman Islanders.

The other group presumably hung out in central Eurasia, until about 40,000 years ago, when it definitively split. One group went west and became the Caucasians; the other became the Han.

Around 30,000 years, the distinctive EDAR mutation that gives east-Asians their “typical” appearance evolved.

Around 10,000 years ago, more or less, Europeans began getting lighter, and “whiteness” as we know it evolved.

Oki Kano, Ainu Musician

So… could the Ainu retain some traits or have never obtained some traits–like epicanthic folds at the corners of their eyes–which make them look more like their ancestral group, to which the ancestors of both Asians and Caucasians belonged? Sure. Could they have just evolved traits to deal with the extremely cold, near-Siberian environment they lived in that happened to resemble traits that evolved in European populations dealing with a similarly cold environment? Sure.

But are they Caucasians? Not even remotely.

And in my opinion, they don’t look Caucasian, at least not when their faces aren’t covered with big, bushy beards. (The modern Ainu tend to shave.) Take, for example, Oki Kano, an Ainu musician. Nothing about his appearance says, “Mysterious tribe of lost Caucasians.”

Back to Wikipedia:

In a study by Tajima et al. (2004), two out of a sample of sixteen (or 12.5%) Ainu men have been found to belong to Haplogroup C-M217, which is the most common Y-chromosome haplogroup among the indigenous populations of Siberia and Mongolia.[49] … Some researchers have speculated that this minority of Haplogroup C-M217 carriers among the Ainu may reflect a certain degree of unidirectional genetic influence from the Nivkhs, a traditionally nomadic people of northern Sakhalin and the adjacent mainland, with whom the Ainu have long-standing cultural interactions.[49]

The Nivkhs live basically next door and have a lot of cultural similarities–for example, both groups traditionally had shamanic rituals involving bears, which they raised and then sacrificed:

Nivkh Shamans also presided over the Bear Festival, a traditional holiday celebrated between January and February depending on the clan. Bears were captured and raised in a corral for several years by local women, treating the bear like a child.[34] The bear was considered a sacred earthly manifestation of Nivkh ancestors and the gods in bear form (see Bear worship). During the Festival, the bear would be dressed in a specially made ceremonial costume. It would be offered a banquet to take back to the realm of gods to show benevolence upon the clans.[29] After the banquet, the bear would be sacrificed and eaten in an elaborate religious ceremony. Often dogs were sacrificed as well. The bear’s spirit returned to the gods of the mountain ‘happy’ and would then reward the Nivkh with bountiful forests.[35]

A very similar ceremony, Iomante, is practiced by the Ainu people of Japan.

While haplogroup D-M174 shows affinity with more southerly Asian groups, like the Tibetans or Andaman Islanders, haplogroup C-M217 is found throughout northern Asia (principally Siberia) and northern North America.

To be continued…