Out of Africa to East Asia: Gleaning the genetic tale of origins and migration from our mitochondria

Early human migration patterns “Out of Africa”

A migratory tale is beginning to emerge from the genes of inhabitants of the Japanese archipelago…

All people living today can trace their maternal ancestry back to one of 26 core mtDNA (mitochondrial DNA) Haplogroups.  Haplogroups are the main “trunks” of the mtDNA phylogenetic tree and represent extremely ancient family groups which arose tens of thousands of years ago.
Over time, the descendents of each Haplogroup formed further subgroups, called “Subclades”.  By discovering which Haplogroup “family” you belong to, you can then trace even further which sub-branch of your Haplogroup you belong to through “Subclade” analysis.

Modern humans left Africa, moving along the tropical coastlines (and the earliest modern human fossil found outside of Africa was) about 100,000 years ago. Hugging the coastline, the early modern human was probably able to expand and occupy or colonize coastal areas by exploiting marine  food resources by that time.

The modern humans were thought to have been possibly forced out of Africa due to the East African mega-droughts (about 135,750 years ago) during the early late-Pleistocene. The period between 80,000-10,000 years ago during the last glacial would have had a huge impact on modern human migration, and the sea level had fallen 50-200 meters below present, which resulted in larger dry lands and possibility for human migration between currently separated lands by ocean, e.g. between Japan and the mainland.

The new arrivals bore lineages (the YAP/M145/M203/SRY4064) that are traceable to an African origin, as the M-174 ancestral allele among YAP+ve lineages is found exclusively in Africa. (M-168 lineages evolved into three distinct sub-clusters: YAP at DYS287 as well as the M-145 and M-203, and two other lineages, defined by the distinct mutations RPS4Y/M216 and M89/M213. These three sub-clusters represent deep structuring of Y-chromosome diversity outside Africa – out of these lineages.) The subcluster found in East Asia  is defined and identified by the M-174 mutation.

Around 60,000 years ago, the first modern humans very likely arrived in Southern East Asia  after having proceeded via the Indian sub-continental coastline.  These earliest of migrating peoples were the bearers of the Haplogroup types C and D. These explorers originally of African origin settled initially in mainland southern East Asia, then migrated northward about 25,000-30,000 years ago, and spread throughout East Asia.

Haplogroup D is believed to represent the Great Coastal Migration along southern Asia, from Arabia to Southeast Asia and thence a northward migration to populate East Asia. It is found today at high frequency among populations in Tibet, the Japanese archipelago, and the Andaman Islands, though curiously not in India. It is found at especially high frequencies among Andaman Islanders and 8-65% in northeast Indian tribes.

However, the fragmented distribution of one East Asian specific Y chromosome lineage – D-M174, which is found at high frequencies only in Tibet, Japan and the Andaman Islands, is inconsistent with this scenario. The Ainu of Japan and the Jarawa and Onge of the Andaman Islands are notable for possessing almost exclusively Haplogroup D chromosomes (although Haplogroup C3 chromosomes also occur among the Ainu at a frequency of approximately 15%). Haplogroup D chromosomes are also found at low to moderate frequencies among populations of Central Asia and northern East Asia as well as the Han and Miao-Yao peoples of China and among several minority populations of Sichuan and Yunnan that speak Tibeto-Burman languages and reside in close proximity to the Tibetans.

Also, the Haplogroup D Y-chromosomes that are found among populations of the Japanese Archipelago are particularly distinctive, bearing a complex of at least five individual mutations along an internal branch of the Haplogroup D phylogeny, thus distinguishing them clearly from the Haplogroup D chromosomes that are found among the Tibetans and Andaman Islanders.

Haplogroup D is believed to have originated in Asia some 60,000 years before present…but where in Asia?

While haplogroup D along with haplogroup E contains the distinctive YAP polymorphism (which indicates their common ancestry), no haplogroup D chromosomes have been found anywhere outside of Asia. Haplogroup D is also remarkable for its rather extreme geographic differentiation, with a distinct subset of Haplogroup D chromosomes being found exclusively in each of the populations that contains a large percentage of individuals whose Y-chromosomes belong to Haplogroup D: Haplogroup D1 among the Tibetans (as well as among the mainland East Asian populations that display very low frequencies of Haplogroup D Y-chromosomes), Haplogroup D2 among the various populations of the Japanese Archipelago, Haplogroup D3 among the inhabitants of Tibet, Tajikistan and other parts of mountainous southern Central Asia, and paragroup D* (probably another monophyletic branch of Haplogroup D) among the Andaman Islanders. Another type (or types) of paragroup D* is found at a very low frequency among the Turkic and Mongolic populations of Central Asia, amounting to no more than 1% in total. This apparently ancient diversification of Haplogroup D suggests that it may perhaps be better characterized as a “super-haplogroup” or “macro-haplogroup.” In one study, the frequency of haplogroup D* found among Thais was 10%.

Unlike haplogroup C, Haplogroup D carriers most likely did not travel from Asia to the New World —  it is found in no modern Native American (North, Central or South) populations (it is however not impossible that Haplogroup D may have traveled to the New World, like Haplogroup C, but that those lineages had died out).

Besides Tibetans and Japanese, D-M174 is also prevalent in several southern ethnic populations in East Asia, including the Tibeto-Burman speaking populations from Yunnan province of southwestern China (14.0–72.3%), one Hmong-Mien population from Guangxi of southern China (30%) and one Daic population from Thailand (10%), which could be explained by fairly recent population admixture. However, a recent study reported a high frequency of D-M174 in Andamanese (56.25%), people who live in the remote islands in the Indian Ocean and considered one of the earliest modern human settlers of African origin in Southeast Asia. Another study suggested that the D-M174 lineage likely reached East Asia about 50,000 years ago. This implies that the YAP lineage in East Asia could be indeed very ancient.
Sub-haplogroup D-M174 is now widely held to have a Tibetan or south China origin.   D1 (M15) is found at high frequencies among Qiang people, 30% with a moderate distribution throughout East Asia; D2 (M55) is found at high frequencies among the Ainu, Japanese, and Ryukyuans. Frequencies: Ainu 87%, Okinawa 56%, Honshu 37% and Kyushu28%.; D3a (P47) Found at high frequencies among Tibetans among the Pumi people at 70%, with a moderate distribution among some other populations of southern Central Asia. The D2 subclade (SNP P37.1 and M55) is very rare outside of Japan and not found in Tibet, the only other region that has substantial amounts of the D haplogroup. Scientists’ calculations show a D2 population founding at 20-37,ooo years ago and an expansion that took place around 12,500 years ago.  Subclade descendants D2a (SNP M116.1), D2a1 (SNP M125) and D2a1b (SNP 022457) are also Japan-specific.  The long diversified branch of Haplogroup D found in Japan fits a model of genetic isolation for a long period of time.

It has also been noted that “Interestingly, the sub-haplogroup D defined by M174 (D-M174) is East Asian specific with abundant appearance in Tibetan and Japanese (30–40%), but rare in most of other East Asian populations and populations from regions bordering East Asia (Central Asia, North Asia and Middle East) (usually less than 5%) . Under D-M174, Japanese belongs to a separate sub-lineage defined by several mutations (e.g. M55, M57 and M64 etc.), which is different from those in Tibetans implicating relatively deep divergence between them. The fragmented distribution of D-M174 in East Asia seems not consistent with the pattern of other East Asian specific lineages, i.e. O3-M122, O1-M119 and O2-M95 under haplogroup O.”(Source of quote)

Given that Haplogroup D is not found in many other regions outside of Tibet and south China,  all of the foregoing suggests that Y-chromosome Haplogroup D2 was the modal Haplogroup in the ancestral population that developed the prehistoric Jomon culture in the Japanese islands and that Tibet and south China are likely to be the origins and birthplace of Haplogroup D (dating ~50-66,000 years before present)”.

Around 60,000, from that ancestral location (possibly Tibet or south China) carriers of the haplogroup D-M174 expanded northward to exploit the food of the “Mammoth Steppelands”. They formed a very ancient lineage of migratory peoples, whose descendents are found today in relic populations of the Andaman Islands, Tibet and Japan. This lineage predates all other northward population movements or throughout East Asia, constituting an ancient Palaeolithic population migration in East Asia. The persistence of this haplogroup in Japan, particularly in Hokkaido, can be explained by its early dispersal into northern Japan, followed by prolonged period of isolation, enabling it to avoid replacement by other expanding populations.

Why Haplogroup D exists in such abundance in Japan and Tibet alone is not well understood. But the spotty and fragmented distribution of D-M174 sub-haplogroup is explained as likely due to the combination of the last glacial phenomenon and the expansion of later Neolithic population or rice-growing cultures which erased or absorbed other populations with early lineages, surrounding the survivors.

There were land bridges to the islands of Japan, but like other islands in this region, these land bridges were submerged after around 12,000 years ago (after the Last Glacial Maximum). The land bridge to north connected to Sakhalin Island (itself connected to mainland by land bridge) and in the South it was connected to Korea. Before the end of the Last Glacial Maximum, hunter-gatherers had crossed over from the mainland via the northern route around 30,000 years ago.  These hunter-gatherers were part of the ancient Jomon culture which is thought to have expanded around 20,000 years ago.

Southern East Asia is also thought to be a source for unique ethnic populations that came to inhabit the Andaman and Nicobar Islands in the Bay of Bengal, which is situated between Southern East Asia and South Asia.  Aboriginal hunter-gatherers on these islands have small stature and features resembling pygmies. The physical resemblance to pygmies is believed to be a result of convergent evolution in which two separate populations arrived at similar adaptations, in this case adaptation to environments around the equator.  Andaman populations (aboriginals were all typed with Haplogroup D) are genetically closer to South East Asian populations and are thought to have originated from Palaeolithic era (while Nicobarese have a genetic signature (O2a) more widely throughout Asia and may have arrived during the Neolithic era.  The later origin of Nicobarese would also be consistent with their farming culture). (The Andaman people’s origins thus hint of common ancestry with Haplogroup D descendants of Japan.)
Austro-Asiatic homeland of populations bearers of C and D clades originate possibly around a Daic-speaking source in the mainland around South China and Vietnam (adjacent to the Gulf of Tonkin).    Because most Austro-Asiatic populations have significant levels of Haplogroup C (and other old lineages M1 and K) there is good reason to believe that this language group also has an ancient origin, despite their recent contribution to populations in Oceania.   A case of limited gene flow supports the spread of Austronesian language through the South Pacific more by cultural diffusion than through demic diffusion (i.e. culture and language is likely to be spread more rapidly than genes).
Recent genetic studies have shown that 80 percent of Taiwan’s population also have Austro-Asiatic ancestry.  The Taiwanese aborigines also share genetic heritage and the Austronesian language with SEAS populations and parts of Melanesia.  However, it appears that the spread of this language group did not hop from Taiwan to Melanesia, but rather diffused separately to both regions from a Daic-speaking source in the mainland around South China and Vietnam (adjacent to the Gulf of Tonkin).   The human males moving further east into remote Polynesia, therefore, appear to have combined origins from Austro-Asiatic/Austronesian (SEAS) and non-Austronesian (Melanesia) populations.
At around 20,000 – 30,000 years ago,  the Southern Eastern Asian/Austronesian populations carrying Haplogroup clades C and D  migrated northward, spreading throughout East Asia. A recent archaeological finding supported that modern humans explored the Tibetan plateau about 30,000–40,000 years ago, which is much earlier than the conservative estimates of 20-30,000 years ago.

Meanwhile, a haplogroup subclade D-carrying population enters Japan.  As mentioned earlier, Haplogroup D is thought to be a remnant of more ancient population foundings, to constitute tribes representing relic traces of Haplogroup D connections between Tibet or south China and Japan.  The post-glacial sea level rise eventually led to the separation between Japan and the main continent, which explains the relic distribution of D-M174 in current Japanese populations. The archaeological data suggested that the initial colonization of modern humans in Japan occurred about 30,000 years ago, consistent with the age estimation of D2-M57 (37,678 ± 2,216 years ago).
Around 20-35,000 years ago, a second migration was made by people  — involving carriers of Haplogroup clades O, N and P.
The above population movements taken into consideration are the basis of current theories that the current Tibetan and Japanese populations are probably the admixture of two ancient populations represented by D-M174 and O3-M122 respectively.
Strong evidence in support for this view has also been found for a bottleneck produced during a northward migration of Yakuts from their origin near Lake Baikal in response to an expanding Mongolian Empire.  As they migrated and changed their geographic location, many Yakut populations switched from horse to reindeer herding, though they have maintained their Yakut (Turkic) language amidst many Tungusic speaking Evenk populations.

The peopling of Japan and Korea: Contemporary Japanese have been proposed to spring from two ancestral sources.   Before the end of the Last Glacial Maximum, hunter-gatherers had crossed over from the mainland via the northern route (the land bridge to north connected to Sakhalin Island) around 30,000 years ago.  These hunter-gatherers formed part of the ancient Jomon culture which is thought to have expanded around 20,000 years ago.
The Jomon forerunners of the Japanese are linked to populations with Y-chromosome haplogroup D, which is commonly found in the present-day ethnic Ainu population in the northernmost island of Hokkaido. D subclades in East Asia are most prominent in Tibet and Japan where the D haplogroup has significant levels.  D2 subclades are limited to Japan. The majority of Haplogroup D is found in the south and in Tibet and little diversification of the D lineage can be seen in this territory.

The C3 subclade (SNP M217) is however found among the Ainu and Sakhalin Island and Kamchatka Peninsula populations.  C3* haplotype diversity was also found to be high in Japan, in support of an old age for this paternal genealogy in Japan.  The C3c subclade is prevalent in Siberian (Koryak) populations but is not represented in the Japanese island archipelago populations to the southeast.

There is also the C1 subclade that is unique to Japan. Early Japanese founders from the C1 (SNP M8, age ~20kya) lineage have also been proposed, but this lineage is missing from the Ainu in Hokkaido so it may not have entered Japan from the north (but via the land bridge in the South by which it was connected to Korea)

Explaining the C subclade and who are the Ainu people    Genetic mapping studies (by Cavalli-Sforza) have shown a pattern of genetic expansion from the area of the Sea of Japan towards the rest of eastern Asia. This appears as the third most important genetic movement in Eastern Asia (after the “Great expansion” from the African continent, and a second expansion from the area of Northern Siberia), which suggests geographical expansion during the early Jomon period.

The origins of the Ainu have often been considered Jomon-jin, natives to Japan from the Jomon period. “The Ainu lived in this place a hundred thousand years before the Children of the Sun came” is told in one of their Yukar Upopo (Ainu legends). Ainu culture as it is known today however dates from only around 1,200 CE.  Genetically, this puzzle needs to be explained. While genetic testing of the Ainu people has shown them to belong mainly to Y-haplogroup D2  and Y-DNA haplogroup D2 is found frequently throughout the Japanese Archipelago including among ancient Ryukyuans, and modern Okinawas (and outside of Japan, in Tibet and the Andaman Islands in the Indian Ocean) —  in another study, two out of a sample of sixteen (or 12.5%) Ainu men were found to belong to Haplogroup C3.
Haplogroup C3 is the most common Y-chromosome haplogroup among the indigenous populations of the Russian Far East and Mongolia. It is also thought that the Jomon population expansion may have reached America along a path following the Pacific coast. Incidentally, two waves of migration carrying haplogroups C and Q are believed to have crossed the Bering Strait in the colonization of the Americas with North East Asia as the point of departure to America although the populations have remained independent of one another.
Some researchers think this minority of Haplogroup C3 carriers among the Ainu may reflect a certain degree of genetic influence from the Nivkhs, a traditionally nomadic people of northern Sakhalin Island and the adjacent mainland, with whom the Ainu have long-standing cultural interactions (the Nivkhs’  mtDNA lineages# mainly consist of:
– haplogroup Y (11/51 = 21.6%),
– haplogroup M7a(xM7a1) (8/51 = 15.7%),
– haplogroup D (especially D4), and
– haplogroup G).

Recent research suggests that the Ainu culture originated in a merger of the Okhotsk and Satsumon hunter-fishing-gathering cultures, one of the ancient Japanese cultures. A recent study examining comparative cranial traits suggests that the Ainu resemble the Okhotsk more than they do the Jomon. Thus another theory follows from the evidence which posits that the Ainu culture is a merger of Okhotsk and Satsumon cultures.
Northeast populations bearing haplogroup subclades N and P stayed mainly in the North, while bearers of Haplogroup O followed a route south.
Relatively latecomers to East Asia, the Haplogroup O expansion was however robust and rapid.

The Haplogroup O expansion A second immigration wave arrived in Japan 2,000-4,000 years ago, and was composed of Yayoi people who brought rice cultivation (as well as weaving and metal working) from Korea and North Eastern Asia. At this date, the land bridges to Japanese islands were submerged and sea-faring migrations must have been responsible for the spread of the Yayoi.  Japanese are also carriers of O — subclade O3 is major branch represented in East Asia — which is connected to agricultural revolution in Neolithic Era.  The Yayoi origins are estimated to have contributed approximately 52% of the current population, while the Jomon contribution is estimated at 40%.

Beside the O3 subclade, Yayoi have also been identified with the O2b1 subclade (SNP 47z).  The analysis of haplotypes in the O2b1 subclade reveals a star-like network, which fits well with a model of a major or single founding lineage contributing to a Japanese population.  The precursor to the O2b1 subclade, O2b (SNP SRY465), is also abundant in Japan. STR haplotyping in the O2b subclade shows a higher diversity in the Korean population versus the Japanese population, supporting an older age and probable origin in the Korean Peninsula.

In addition to the other O subclades, the O2a subclade is found in Japan and was also probably introduced at a more recent date with the expansion of rice cultivation. O2a is however associated with Southern East Asia and with speakers of Austro-Asiatic languages (non Austro-Asiatic groups also have good levels of O2a ~ 15%).  (O2a is also very abundant in India, and another proposed as the ancestral home of this Y-chromosome type) but the frequency of O2a (97%) peaks in the unique population of the Mang.   A study of the Mang population who live near the border between China and Vietnam in SEAS found only 3 haplogroups:  O2a (SNP M95), O3a3b (SNP M7) and O3a3c (SNP M134).  The genetic signature is unique and suggests that this is an indigenous population.  The Mang have a short stature, live by foraging and have a language related to Mon Khmer.

Because the Yayoi spread from south to north – their highest influence is in Kyushu, which lies closest to the Korean Peninsula. However, the Haplogroup O genetic signature of the Yayoi is not found in Hokkaido, the northernmost island.  The geographically separate southern Ryukyu Islands (the largest island is Okinawa) were also spared the domination by Yayoi.  Essentially, the distribution of Haplogroup O (highest central location) is the reciprocal of Haplogroup D (highest in north and south).  Thus, the island archipelago structure helped to create barriers and genetic structure throughout Japan.
[#Note: Mitochondrial DNA haplogroup Y is otherwise found mainly among Nivkhs, and with lower frequency among Tungusic peoples, Koreans, Mongols (including Kalmyks and Buryats), Chinese, Japanese, Tajiks and other Central Asians, South Siberian Turkic peoples (e.g. Tuvans, Todjins, Soyots), Koryaks, Alyutors, Itelmens, Taiwanese aborigines, Filipinos, Indonesians, and Malaysians.
Haplogroup M7a, on the other hand, has been found elsewhere mainly among Japanese and Ryukyuans, and with lower frequency among Koreans, Chinese, Filipinos, Taiwanese aborigines, Buryats, Central Asians, and Waars of the Jaintia Hills in Meghalaya, India.]

Source references:
Shi H, Zhong H, Peng Y, et al. (2008). Y chromosome evidence of earliest modern human settlement in East Asia and multiple origins of Tibetan and Japanese populations. BMC Biol. 6: 45. doi:10.1186/1741-7007-6-45. PMC 2605740. PMID 18959782. http://www.biomedcentral.com/1741-7007/6/45
Jomon Genes, by John Travis c 1997 Society for Science & the Public. Source: http://www.jstor.org/pss/3980542
Tajima et al. (2004)’s study was confirmed by another study by Hammer et al. (2006) tested another sample of four Ainu men and found that one of them belonged to haplogroup C3.
YAP, signature of an African-Middle Eastern migration into northern India. Current Science 88: 12. Suraksha Agrawal, et al. (25 June 2005).
The History and Geography of Human Genes: (Abridged paperback edition) [ABRIDGED] (Paperback)
~ Luigi Luca Cavalli-Sforza (Author), Paolo Menozzi (Author), Alberto Piazza (Author)
ISBN:9780415399234 (Hard cover book)  456 p. Sanchez-Mazas, Alicia (EDT) / Blench, Roger (EDT) / Ross, Malcolm D. (ED 2008/10 Routledge

4 responses to “Out of Africa to East Asia: Gleaning the genetic tale of origins and migration from our mitochondria

  1. Here’s a question, though not specifically aimed at Japanese history:

    My understanding is that about 74,000 years ago, humanity nearly went extinct from the Toba supereruption, which plunged the planet into a 6-to-10-year volcanic winter, and caused the world’s population to plummet to an estimated 2,000 thus forming a genetic bottleneck, from whom all modern humans are presumed to be descended.

    Presupposing this is more-or-less what happened, why is this not regarded as a mass extinction event for all species? (There being 5 prior mass extinction events). Was it just humanity that suffered near-extinction? Surely all species would have been severely affected?

    • I’m sure I agree with you that there was a near-extinction event, more likely a great many along the evolutionary path, and I think I once saw a BBC documentary mention that humans, more accurately, hominids (hominins) have undergone many extinction events, leaving many branches extinct. However, hominids are still overrunning the earth and decimating other species thanks to luck and the adaptability and innovation of homo sapiens sapiens, so perhaps extinction might not be the best word. Also the debate is still not totally resolved over whether other branches might not be around or admixed with homo sapiens, like homo erectus, or the Neandertal, homo flores, or Asian species. Every year new “news” resurface despite prominent geneticists declaring with confidence that the genetic studies show that all populations today are traceable only to the Out-of-Africa homo sapiens sapiens. .

  2. Thank you for your kind response.

  3. EnlIghtening!

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