The Ainu, a minority ethnic group from the northernmost island of Japan, was investigated for DNA polymorphisms both from maternal (mitochondrial DNA) and paternal (Y chromosome) lineages extensively. Other Asian populations inhabiting North, East, and Southeast Asia were also examined for detailed phylogeographic analyses at the mtDNA sequence type as well as Y-haplogroup levels. The maternal and paternal gene pools of the Ainu contained 25 mtDNA sequence types and three Y-haplogroups, respectively. Eleven of the 25 mtDNA sequence types were unique to the Ainu and accounted for over 50% of the population, whereas 14 were widely distributed among other Asian populations. Of the 14 shared types, the most frequently shared type was found in common among the Ainu, Nivkhi in northern Sakhalin, and Koryaks in the Kamchatka Peninsula. Moreover, analysis of genetic distances calculated from the mtDNA data revealed that the Ainu seemed to be related to both the Nivkhi and other Japanese populations (such as mainland Japanese and Okinawans) at the population level. On the paternal side, the vast majority (87.5%) of the Ainu exhibited the Asian-specific YAP+ lineages (Y-haplogroups D-M55* and D-M125), which were distributed only in the Japanese Archipelago in this analysis. On the other hand, the Ainu exhibited no other Y-haplogroups (C-M8, O-M175*, and O-M122*) common in mainland Japanese and Okinawans. It is noteworthy that the rest of the Ainu gene pool was occupied by the paternal lineage (Y-haplogroup C-M217*) from North Asia including Sakhalin. Thus, the present findings suggest that the Ainu retain a certain degree of their own genetic uniqueness, while having higher genetic affinities with other regional populations in Japan and the Nivkhi among Asian populations.
The above is from an abstract at Springerlink.com
Atsushi Tajima et al., Genetic origins of the Ainu inferred from combined DNA analyses of maternal and paternal lineages Journal of Human Genetics April 2004, Volume 49, Issue 4, pp 187-193 Date: 02 Mar 2004
Heritage of Japan 
Basic Ainu Y-haplogroups is D, so they originated from South-East Asia, and all similarities with Japanese and Nivkh are result of late mixing.
Also I have to note that in the question of genetic relationship data on Y-haplogroups are much more important than on mtDNA.
Asian origins theory for haplogroup D is on its way out (although D2 mutation may have occurred in SEAsia). See Rare Deep-Rooting Y Chromosome Lineages in Humans http://www.genetics.org/content/165/1/229.full.pdf+html
“Underhill et al. 2000 identified the D-M174 mutation that defines haplogroup D. The M174 allele is found in the ancestral state in all African lineages including haplogroup E. The discovery of M174 mutation meant that haplogroup E could not be a subclade of haplogroup D. These findings effectively neutralized the argument of an Asian origin of the YAP+ based on the character state of the M40 and M96 mutations that define haplogroup E. According to Underhill et al. 2000, the M174 data alone would support an African origin of the YAP insertion”
From there National Geographic Genographic Project comes the:
Current theory of haplogroup D out of Africa migration that would have followed a route from Arabia, Middle East, Afghanistan, Northern India. They posit an earlier trail that took route via India, Sri Lanka, to Southeast Asia. Originating as descendants of the M175 who took a gradual northwards migratory route into South East Asia where D2 originated (and shows itself as P37.1 marker) where it then moved steadily northeast into Japan. D2 occurs at highest frequencies about 50% in some J. populations and highest among Ainu (87.5%).
Genographic Project also posits a later hg D trail, Mongolia-> Tibet
Based on hg YAP+ mutation originating out of Africa assumption, see the genealogical tree at p. 230 of “Rare Deep-Rooting Y Chromosome Lineages in Humans” http://www.genetics.org/content/165/1/229.full.pdf+html the evidence for the “hg D out of Africa-Middle East-Northwest Central Asia” trail thus hinges on two things:
1) the geographical occurrence of DE* and
2) the migratory trail of YAP+ element. YAP occurs in a trail from the Middle East, through Pakistan, Afghanistan, Uzbekistan (Jewish population), Northern India, Yunnan, Yao, Yi, Miao, Tai tribes and then D2 all over Japan.
On the haplogroup D trail
a. Outside of Africa (found in Nigeria and Guinea-Bassau so far), the only confirmed Hg DE* individuals are Sunni Syrian Arabs (around Damascus). Another finding belonged to a Palestinian Arab family of Jerusalem. Other DE* lineages are found in Tibet and the relict populations of the Andaman.
b. There appears to be a clear later migratory trail that of Yunnan->Tibet (50% of men are YAP+)
-> at the same time, from Yunnan, dispersing northeastwards towards Japan, with a later migration
The D haplogroup occurs at a high frequency among Tibetan and Yao populations. Evidence suggests a shared ancestry, originating from ancient tribes of North West China with the derived lineages splitting across Tibet, Mongolia (D1); Southeast Asia (China and Thai-Khmer-YAP+/M15).
On the YAP+ haplogroup trail
There is a clear pattern in the frequencies of the insertion of YAP element: sub-Saharan Africans have the highest frequencies, followed by northern Africans, Europeans, Oceanians, and Asians… with the noted relatively high frequency of the YAP element observed in Japanese. 9 different populations of North India were analysed for YAP insertion and four other single nucleotide polymorphisms (SNPs) to delineate the two lineages. A recent study showed the presence of YAP+ve lineage in only one the North Indian populations — the Shiya Muslims, at a frequency of 11%, the study concluded it reflected an African/Middle Eastern migration into North India.”
Haplogroup D2 is considered to be derived D lineage in Japan, said to be completely restricted to Japan, and is a very diverse lineage within the aboriginal Japanese and in the Japanese population around Okinawa. http://www.chromosomal-labs.com/ancestry/yhaplogroup.pdf
Did hg D enter Japan from the south or from the north? It was formerly thought YDNA hg D entered from the south since hg D is present in all Japanese populations. Hg D bearers were thought to have been from the south (of Asia) and to have mixed with the Mongoloid O hg carriers in Southeast or East Asia.
If so, the puzzling question is this: why then do the Ainu exhibit none of the Southeast Asian Y-haplogroups (O-M175 and O-M122, nor C-M8 all of which are genes common to southerly Southeast Asians) which are common in Okinawans and mainland Japanese? One explanation is D once populated all of the Japanese archipelago before the arrival of the O hg carriers who arrived from the south and across the seas into mainland Japan.
The other explanation for this is the Genographic Project’s scenario of two D lineages one proceeding northeastwards into Japan and the other across China, SEA and eventually into southern Japan, Okinawa.
On the paternal side, while the vast majority of Ainu (87%) exhibit YAP+ D2 (M55 and M125) haplogroups, the rest of the Ainu gene pool is occupied by Y-DNA C-M217 which is characteristic of North Asia.
Maternal haplogroups are important as they help to show where the Y-haplogroup carriers picked up their wives along their migratory trail. Along with the Nivkh genes, the Ainu also have been found with the rare mtDNA X haplogroup (which is not present anywhere Southeast Asia), but which is found in the ancient Basques and Bulgaria-Filand-Italy (Europe); in especially high frequency in the Druze population in Syria, Lebanon, Jordan and Northern Israel, non-Jewish Russians (3.5%); in the Altaic tribes in southern Siberia, and in 3% of Native Americans (Ojibwa tribe of Great Lakes region 25%).
Apart from the Out of Africa-northwest Central Asia original route, analyses of HLA gene, haplotypes, HTLV-I and JC virus markers also place the Ainu squarely with the Northern peoples as hg D/YAP+ carriers moved northeastwards into areas flanking the Pacific Ocean.
Archaeological lithic evidence as well as the distribution of hg D/YAP+ at both ends of Japan suggest separate arrivals. The Japanese Ainu’s lithic culture as well as bear worship culture places their affinity with North Eurasian circumpolar ethnic groups of the Nivkh, Sakhalin-Ainu, Sami, and pre-Christian Finns, not forgetting the Korean legend of ancestry from Dangun’s birth from the union between the bear-woman and the (Manchurian) Tiger.
The bear myths appear to part of the astronomical body of star chart knowledge belonging to the Central Asian-Siberians who crossed the Bering Strait into North America. Their star charts included the Big Dipper as part of a bear that had a long tail, the tail being the handle of the Dipper. The bear myths are thought to have crossed into Native America and survived as their myths about the Big Dipper.
Finally, the Ainu creation deity sending down a water wagtail have affinity with the earth diver stories of Central Asia and Native American cultures.
Thus the Ainu even though they share haplogroup D/YAP+ with the other regional Japanese populations, they are distinctively not the descendants of Mongoloid peoples, unlike other Southeast Asians.
All the YAP+ readings and references may be found at this page.
D haplogroup obviously has southern origin:
Moreover I am to tell you, that similar myths can be easily created independently among different ethnic groups (all hunters have bear myth and bear rite), so myths can’t be proof of contacts or genetic relationship of certain ethnic groups.
Where myths are found in highly different regions, such highly general myths of sun and moon, earth fertility … may (or may not) have occurred independently, but where they occur in a geographical belt and a number of the components of the myths may be established to be the same, as well as identifiable cultural practices, symbolic traditions(Bear Festival), a case may be made of either demic diffusion or cultural diffusion (taboos, sacrifices)…which is the case of the Siberian and North Eurasian circumpolar ethnic groups … and a strong case can be made particularly when you can trace the genetic trails. Concrete bodies of star chart astronomical knowledge belonging to the Central Asian-Siberians who crossed the Bering Strait into North America including the Big Dipper as part of a bear that had a long tail, the tail being the handle of the Dipper … certainly had to have been taught / transmitted between adjacent populations and cannot be dismissed so easily. See “Tracing the Bear Myth in Northeast Asia” by Juha Janhunen http://src-h.slav.hokudai.ac.jp/publictn/acta/20/asi20-001-janhunen.pdf /also The Great circumpolar bear cult (ISSN: 0196-3147) / Bledsoe, Brandon. “The Significance of the Bear Ritual Among the Sami and Other Northern Cultures” http://www.utexas.edu/courses/sami/diehtu/siida/religion/bear.htm see map here /.Kindaichi, Kyōsuke; Yoshida, Minori (Winter, 1949). “The Concepts behind the Ainu Bear Festival (Kumamatsuri)”. Southwestern Journal of Anthropology (University of New Mexico) 5 (4): 345–350. JSTOR 3628594
One or two observable similarities, you may put down to coincidence, but a host of similarities, you have to consider their value as evidence of a pattern.
You are a diffusionist. Bear feast and bear myth is spread in all ethnicities which deal with bear. Local bear feasts and myths have much more differences than similarities so it’s obvious that such practices were elaborated independently among different ethnicities that deal with bear. Moreover, if we speak of common origin of certain myths we have to provide some evidences of anthropological and linguistic relationship.
Again, read the theses written on bear cults – referenced at the bottom of the article, before you react so cavalierly. The symbolic similarities are striking in the important aspects, that they remain the same despite ethnic groups that have evolved separately over vast amounts of time is remarkable. Moreover, we are not talking merely about mere similarity of cultural practices, you can overlay the distinctive traits to ethnic populations that share the same genetic components too. Even the Saami and Finnish populations that are so far removed from northern Asia, with their characteristic bear festivals and shamanic practices that make them stand out from other European populations, the Asian genetic components and connection in those populations have been traced by genetic research to the B and Z haplogroups of East Eurasia. People stubbornly carry their myths, their culture, their technology and their worship and burial practices with them wherever they go…that is fact, changes are seldom drastic, only erased over time by strong admixtures or replacement. Nomadic tribal tendencies to intermarry and exchanges of genes, the admixtures also serve to hasten exchanges and adaptions of material or other culture. Do not slap a label on me … the facts and evidence have been raised on these pages on many fronts, find the time to study and consider them objectively.
The hypothesis that “D-M174 has a southern origin and its northward expansion occurred about 60,000 years ago, predating the northward migration of other major East Asian lineages. The Neolithic expansion of Han culture and the last glacial maximum are likely the key factors leading to the current relic distribution of D-M174 in East Asia” was the position established in Spencer Well’s (et al.) paper (http://www.geocities.jp/ikoh12/kennkyuuno_to/012_4Y_chromosome_no_kennkyuu.html)
However, it is but one interpretation and the position of D having a southern origin is being challenged. See YAP insertion signatures in India (http://www.ansi.gov.in/download/YAP_INSERTION_SIGNATURES_IN_SOUTH_ASIA.pdf ):
“Haplotype D* is also found in central Asia (Karafet et al. 2001). The phylogenetic order of YAP lineages D* and E* is still uncertain. Presence of paragroup DE* among five Nigerians led Weale et al. (2003) to dissect the interior branching order of the YAP lineages and opine that it is impossible to impute the origin of the YAP clade with certainty. Regardless of the branching order of DE*, D*, and E*, the view that male Andaman Islanders descended from Asian colonizers needs further scrutiny.”
Background and distribution of Hg D: Haplogroup D is an old lineage that evolved in Asia where it is hypothesized to have been widely distributed. This Haplogroup was present in the first people to colonize Japan. This Haplogroup was later displaced from much of Asia by other colonizing groups, but is still present at intermediate frequencies in the aboriginal Japanese and on the Tibetan plateau. It is also found at low frequencies in Mongolian populations and the Altais people of central Asia. Haplogroup D1 lineage is a descendent of the D lineage and is currently present in Southeast Asia and Tibet. Like its progenitor it is also found in low frequencies in Mongolian populations, but unlike D it is completely absent from Japan. Haplogroup D2 most likely derived from the D lineage in Japan. It is completely restricted to Japan, and is a very diverse lineage within the aboriginal Japanese and in the Japanese population around Okinawa (Source: http://www.roperld.com/ybiallelichaplogroups.htm)
The Y Alu Polymorphism or YAP for short, is characterized by a mutational event known as Alu insertion, a 300 nucleotide fragment of DNA that on rare occasion gets inserted into different parts of the human genome during cell replication. A man living around 50,000 years ago (somewhere in southern Asia) acquired this fragment on his Y-chromosome and passed it on to his descendants. Over time the YAP lineage split into two distinct groups: One, Haplogroup D is found in Asia and is defined by the M174 mutation. See Genographic Project’s map of migratory path of M174 http://blogimg.goo.ne.jp/user_image/38/1b/a5943a2c971360a38da9fd0a1595b168.jpg The other, Haplogroup E is found primarily in Africa and the Mediterranean and is defined by marker M96.
Since DE are determined to have split from YAP, the distribution of both YAP genes (see source readings elsewhere on our blog for this) and DE* hgs found predominantly all in the north, particularly in the Northeast Indian corridor trail to Mongolia is calling into question this interpretation of Hg D originating in the south. Hg D is found in Andaman islanders but otherwise nowhere else in the southern mainland India.
The DNA chart you referred to lacks resolution, it only shows that that D hgs are found in TB, CAS populations. Look at this next chart, one sees that the D (yellow) in the south appears derived from DE (green) in the north http://www.angelfire.com/droid/ross/china/index.album/fig-2-distribution-of-y-haplogroups-in-east-asia-circle-area-is-proportional-to-sample-size-and-the-nine-haplogroups-are-represented-by-different-colors?i=2&s=1 Where a mutation diversified or expanded (high frequency, bottlenecks) is easier to locate than where it branched off from or originated (a very small clan /population) the signals of which having possibly either been diluted or erased by later arrivals.
In another 2003 paper (by Hammer et al.) on NE Asian nature of Korean genes,a northern origin for these chromosomes was suggested:
“Haplogroup DE-YAP (the YAP+ allele) was present at high frequency only in the Japanese and was rare in other parts of east Asia (Table 2, Fig. 2). This result is consistent with previous findings of YAP+ chromosomes only in populations from Japan and Tibet in east Asia (Hammer and Horai 1995; Hammer et al. 1997; Kim et al. 2000; Tajima at al. 2002). However, haplogroup DE-YAP is also found at low frequencies in all the other northeast Asian populations sampled here (2.4% overall, excluding the Japanese; 9.6%, including the Japanese), but only in two of the southern populations (0.8% overall), suggesting that the Korean YAP+ chromosomes are unlikely to have been derived from a southeast Asian source.
The prevalence of the YAP+ allele in central Asian populations suggests a genetic contribution to the east Asian populations from the northwest, probably from central Asia (Altheide and Hammer 1997; Jin and Su 2000; Karafet et al. 2001).” Y-chromosomal DNA haplogroups and their implications for the dual origins of the Koreans. (Abstract http://www.ncbi.nlm.nih.gov/pubmed/14505036 / Read in full http://online4kim.net/xe/bbs_pub/13343)
Gm markers research (MATSUMOTO, The origin of the Japanese race based on genetic markers of immunoglobulin G http://www.jstage.jst.go.jp/article/pjab/85/2/69/_pdf) and archaeological-anthropological data (Han 1995; Choi and Rhee 2001) show both early Japanese and Korean populations to have had a common origin in the northern regions of the Altai Mountains and Lake Baikal of southeastern Siberia. See the 2009 paper Jin H-J, Tyler-Smith C, Kim W (2009) The Peopling of Korea Revealed by Analyses of Mitochondrial DNA and Y-Chromosomal Markers. PLoS ONE 4(1): e4210. doi:10.1371/journal.pone.0004210http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0004210
A Japanese clustering with northern populations was also shown in a 2008 paper Yoshihiko Katsuyama, Hidetoshi Inoko, Tadashi Imanishi, Nobuhisa Mizuki, Takashi Gojobori, and Masao Ota. “Genetic Relationships among Japanese, Northern Han, Hui, Uygur, Kazakh, Greek, Saudi Arabian, and Italian Populations Based on Allelic Frequencies at Four VNTR (D1S80, D4S43, COL2A1, D17S5) and One STR (ACTBP2) Loci.” Human Heredity 48 (1998): pages 126-137.:
“The genetic polymorphism at four variable number of tandem repeats (D1S80, D4S43, COL2A1, D17S5) and one short tandem repeat (ACTBP2) loci was assessed by polymerase chain reaction analysis of genomic DNA obtained from blood samples of eight human populations (Japanese, Northern Han, Hui, Uygur, Kazakh, Saudi Arabian, Greek, Italian). […] A dendrogram constructed by the neighbor-joining method based on the allele frequencies of the five loci suggested that the five Asian populations (Japanese, Northern Han, Hui, Uygur, and Kazakh) formed one cluster
On YAP see:
‘YAP insertion signature in South, Asia‘,Annals of Human Biology,34:5,582 — 586, (2007) Chandrasekar, A.,et al.2007, Vol. 34, No. 5 , Pages 582-586 (doi:10.1080/03014460701556262)
YAP, signature of an African-Middle Eastern migration into India CURRENT SCIENCE, VOL. 88, NO. 12, 25 JUNE 2005 by Suraksha Agrawal et al. /
“The present study has been envisaged to ascertain the presence of the YAP insertion in various North Indian groups of Brahmins, Bhargavas, Chaturvedis, Kayastha, Rastogis, Vaish, Mathurs, Sunni and Shiya Muslims.
YAP+ve lineage has been further analysed for M-145 and M-203 markers, which are equivalent to YAP insertion and M-174 and SRY-4064 markers, to delineate the two different lineages specific to African/Middle East Asian and East Asian/Japanese populations respectively. …
Y-chromosome is present in two lineages worldwide, corresponding to M145/M203/SRY4064 (haplogroup E) and M145/M203/M174 (haplogroup D) polymorphisms respectively.
First lineage belonging to haplogroup D is specific to Japan and other Southeast Asian populations, while haplogroup E is confined to Sub-Saharan African, Middle Eastern and Southern European populations.
There is both significant heterogeneity among populations and…
The YAP is especially useful for studying human population history from the perspective of male lineages. The greatest genetic distance is observed between the African and non-African populations. In the present study, 1021 Y-chromosomes belonging to nine different populations of North India were analysed for YAP insertion and four other single nucleotide polymorphisms (SNPs) to delineate the two lineages. Out of nine populations only one, i.e. Shiya Muslims revealed presence of YAP element at a frequency of 11%.
Further analysis based on four additional SNPs revealed that all the YAP+ve samples could be categorized under Africa-Nigeria to Middle East-specific haplogroup E lineage. Interestingly, Sunni Muslims who historically have the same origin, i.e. from the Middle East showed a complete lack of YAP+ve lineage similar to other castes. We hypothesize that unlike Sunnis, Shiya Muslims due to their lesser number and less admixture with other caste groups of India, still carry the ancestral YAP+ve lineage, which in all probabilities is one of the founder haplogroups. All Middle Eastern populations show the presence of this lineage in almost similar frequency. Our study shows the presence of YAP+ve lineage in North Indian populations, reflecting an African/Middle Eastern migration into North India.”
Another possible hypothesis that is looking to be knocked off the “established” pedestal is the idea that haplgroup O originated in the south. See Vikrant Kumar’s “Y-chromosome evidence suggests a common paternal heritage of Austro-Asiatic populations”http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1851701/
“…Our results suggest a strong paternal genetic link, not only among the subgroups of Indian Austro-Asiatic populations but also with those of Southeast Asia. However, maternal link based on mtDNA is not evident. The results also indicate that the haplogroup O-M95 had originated in the Indian Austro-Asiatic populations ~65,000 yrs BP (95% C.I. 25,442 – 132,230) and their ancestors carried it further to Southeast Asia via the Northeast Indian corridor. Subsequently, in the process of expansion, the Mon-Khmer populations from Southeast Asia seem to have migrated and colonized Andaman and Nicobar Islands at a much later point of time. Conclusion: Our findings are consistent with the linguistic evidence, which suggests that the linguistic ancestors of the Austro-Asiatic populations have originated in India and then migrated to Southeast Asia. ” [More discussions of O’s origins here: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2065843/ and here ]
Bottomline: What is not in question is that whether the branching off YAP-DE* took place in Altai-Mongolia or Onge/Jarawa remains or NW Asia remains a complex question for debate – see Rare Deep-Rooting Y Chromosome Lineages in Humans: Lessons for Phylogeography and also “Paternal Population of East Asia…“: “the peopling of East Asia was more complex than earlier models had proposed-that is, a multilayered, multidirectional, and multidisciplinary framework is necessary. For instance, in addition to the previously recognized genetic and dental dispersal signals from SEAS to NEAS populations, CAS has made a significant contribution to the contemporary gene pool of NEAS, and the Sino-Tibetan expansion has left traces of a genetic trail from northern to southern China
mtDNA is more useful than you think. It may be the nail in the coffin on the origins of the Andaman Islanders. See Hua-Wei Wang’s 2011 “Mitochondrial DNA evidence supports northeast Indian origin of the aboriginal Andamanese in the Late Paleolithic“: “Andaman archipelago was likely settled by modern humans from northeast India via the land-bridge which connected the Andaman archipelago and Myanmar around the Last Glacial Maximum (LGM), a scenario in well agreement with the evidence from linguistic and palaeoclimate studies.” Also found by Fornarino S, “Mitochondrial and Y-chromosome diversity of the Tharus (Nepal): a reservoir of genetic variation”http://www.ncbi.nlm.nih.gov/pubmed/19573232 was “a Japanese deep lineage [22] indicating an ancient link between India and Japan. A more recent connection with Japan is, in turn, revealed by the F1d haplogroup showing a tight linkage between an Eastern Tharu sequence and two Japanese mtDNAs….The complete sequencing of mtDNAs from unresolved haplogroups also provided informative markers that greatly improved the mtDNA phylogeny and allowed the identification of ancient relationships between Tharus and Malaysia, the Andaman Islands and Japan as well as between India and North and East Africa. Overall, this study gives a paradigmatic example of the importance of genetic isolates in revealing variants not easily detectable in the general population..” Also Derenko M’s “Origin and post-glacial dispersal of mitochondrial DNA haplogroups C and D in northern Asia” showed that northern mtDNA genes decline in frequency from CAS-Mongolia to Japan and Korea, which suggests that maternal gene pool in E Asia may comprise more southern ones (although the paternal gene pool is predominantly from the north) – supported by Tanaka’s “Mitochondrial Genome Variation in Eastern Asia and the Peopling of Japan Genome”
More references:http://genome.cshlp.org/content/14/10a/1832.full.html#ref-list-1
What the above recent research suggest is that haplogroups O and YAP/DE could have arrived via the Northeast Indian corridor (The Northeast Indian Passageway: A Barrier or Corridor for Human Migrations? http://mbe.oxfordjournals.org/content/21/8/1525.full) into Mongolia, Tibet as well as to E. Asia including Japan.