DNA analyses and inferred genetic origins of the Ainu

SATO, Takehiro, et al.,Mitochondrial DNA haplogrouping of the Okhotsk people based on analysis of ancient DNA: an intermediate of gene flow from the continental Sakhalin people to the Ainu Anthropological Science; ISSN:0918-7960; VOL.117; NO.3; PAGE.171-180; (2009) Full text version

Abstract:

In order to further understand the genetic status of the Okhotsk people, who were distributed in southern coastal regions of the Okhotsk Sea during the 5th–13th centuries, nucleotide variations in the hypervariable region (HVR) and the coding regions of mitochondrial DNA (mtDNA) were analyzed. Targeting the coding regions provides reliable genetic information even from ancient DNAs that may have suffered post-mortem damage. MtDNA haplogroups of 38 individuals were classified according to mtDNA lineages known in northeastern Asian people. Comparisons of mtDNA haplogroup frequencies between the Okhotsk people and other Asian populations revealed that the genetic structures of the Okhotsk people are very similar to those of populations currently living around lower regions of the Amur River and the Ainu of Hokkaido. The results support our previous study on molecular phylogeny of mtDNA HVR 1 sequences, and strongly suggest that the Okhotsk people originated around the lower regions of the Amur River and became an intermediate of gene flow from the continental Sakhalin people to the Ainu.

Excerpts:

“The haplogroup frequencies in the Okhotsk specimens were as follows: A, 8.1%; B5, 2.7%; C3, 5.4%; G1, 24.3%; M7, 5.4%; N9, 10.8%; Y, 43.2% (Table 2). Thus, in the mitochondrial gene pool of the Okhotsk people, haplogroup Y was major. This genetic feature is similar to those of populations currently living around the lower regions of the Amur River, such as the Ulchi, Nivkhi, and Negidal (Table 2). Table 3 shows values of pairwise Fst, estimated by haplogroup frequencies, among northern Asian populations. The exact test demonstrated that differentiations in any pair of the populations were statistically significant (P < 0.05). The genetic relationships between the Okhotsk people and the other northeastern Asian populations were shown using the multidimensional scaling method (Figure 3). Based on this, the Okhotsk people were closely related to the Ulchi, Ainu, and Negidal. Although the Nivkhi also neighbored the Okhotsk people (Figure 3), the Fst values between the Nivkhi and Okhotsk people were 0.1556: this high value is probably due to a high frequency of haplogroup Y (66.1%) in the Nivkhi. The findings show that the Okhotsk people are genetically closer to populations currently living around the lower regions of the Amur River as well as to the Ainu people of Hokkaido….
On the other hand, some of the Okhotsk people shared haplogroup A, which is not seen in populations currently living around the lower regions of the Amur River and in the Jomon people of Hokkaido (Table 1, Table 2). Haplogroup A is shared by many northeastern Asian populations except for the Nivkhi, Ulchi, and Negidal. The HVR 1 sequence of haplogroup A observed among the Okhotsk people is shared by the Koryak living around the Kamchatka peninsula. This sequence of HVR 1 corresponds with Type 3 reported by Sato et al. (2007). In addition, the Koryak are closely related to the Okhotsk people (Figure 3). These suggest that gene flows between the ancient Koryak and Okhotsk people also occurred (Figure 4).

Haplogroups N9 and G1 were also major among the Okhotsk people (Table 1, Table 2). The two haplogroups are also major among northeastern Asian populations. Haplogroup N9 is shared by both of the Hokkaido Jomon people (65.9%) and the Udegey (30.4%) at high frequencies (Table 2). Meanwhile, haplogroup G1 is observed among native populations of the Kamchatka peninsula (68.1% in the Itelmen and 41.9% in the Koryak) at high frequencies (Table 2), and is also shared by the populations around the lower regions of the Amur River (10.3% in the Ulchi; 5.4% in the Nivkhi; and 27.2% in the Negidal) and the Hokkaido Jomon people (13.6%). These facts suggest that haplogroup frequencies of the Okhotsk people were increased as a result of interactions with neighboring northeastern Asian populations.

In conclusion, mtDNA haplogrouping in the present study demonstrated that the Okhotsk people were closely related to populations living around lower regions of the Amur River and the Ainu. This finding indicates that the Okhotsk people could have originated around the lower regions of the Amur River and must have merged with the ancestors (the Epi-Jomon and/or Satsumon people) of the Ainu. This supports the results of the HVR 1 analysis (Sato et al., 2007) and the morphological analyses (Ishida, 1988, 1996; Kozintsev, 1990, 1992; Komesu et al., 2008). Moreover, the present study indicates that the Okhotsk people were also affected by the gene flow from the Kamchatka peninsula. To further clarify the gene flow relating to the Okhotsk people, genetic information on the paternal and biparental gene lineages would be very useful.”

See also: Ana T. Dugga, Investigating the Prehistory of Tungusic Peoples of Siberia and the Amur-Ussuri Region with Complete mtDNA Genome Sequences and Y-chromosomal Markers PLoS One. 2013; 8(12): e83570. Dec 12, 2013. doi: 10.1371/journal.pone.0083570
PMCID: PMC3861515

Genetic origins of the Ainu inferred from combined DNA analyses of maternal and paternal lineages

Source: Journal of Human Genetics, Volume 49, Number 4, April 2004 , pp. 187-193(7)

Abstract:

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.

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KANZAWA-KIRIYAMA Hideaki et al. , Ancient mitochondrial DNA sequences of Jomon teeth samples from Sanganji, Tohoku district, Japan

Abstract We investigated mitochondrial DNA haplogroups of four Jomon individuals from the Sanganji shell mound in Fukushima, Tohoku district, Japan. Partial nucleotide sequences of the coding and control region of mitochondrial DNA were determined. The success rate of sequencing increased when we analyzed short DNA sequences. We identified haplogroups from all four samples that were analyzed; haplogroup frequencies were 50% (n = 2) for N9b and 50% (n = 2) for M7a2. Haplogroup N9b has been previously observed in high frequencies in the other Tohoku Jomon, Hokkaido Jomon, Okhotsk, and Ainu peoples, whereas its frequency was reported to be low in the Kanto Jomon and the modern mainland Japanese. Sub-haplogroup M7a2 has previously been reported in the Hokkaido Jomon, Okhotsk, and modern Udegey (southern Siberia) peoples, but not in the Kanto Jomon, Ainu, or Ryukyuan peoples. Principal component analysis and phylogenetic network analysis revealed that, based on haplogroup frequencies, the Tohoku Jomon was genetically closer to the Hokkaido Jomon and Udegey people, than to the Kanto Jomon or mainland modern Japanese. The available evidence suggests genetic differences between the Tohoku and Kanto regions in the Jomon period, and greater genetic similarity between the Tohoku Jomon and the other investigated ancient (Hokkaido Jomon, Okhotsk) and modern (Siberian, Udegey in particular) populations. At the same time, the Tohoku and Hokkaido Jomon seem to differ in sub-haplotype representations, suggesting complexity in Jomon population structure and history.

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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.

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 [of North India] 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 African/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.

Mekel-Bobrov N, Gilbert SL, Evans PD, et al (September 2005). “Ongoing adaptive evolution of ASPM, a brain size determinant in Homo sapiens”. Science 309 (5741): 1720–2. doi:10.1126/science.1116815.PMID 16151010.

In this 2005 study of ASPM gene variants, Mekel-Bobrov et al. found that the Kalash people of Pakistan [a Dardic indigenous people residing in the Chitral District of Khyber-Pakhtunkhwa province of Pakistan, considered a unique tribe among the Indo-Aryan peoples] have among the highest rate of the newly-evolved ASPM haplogroup D, at 60% occurrence of the approximately 6,000-year-old allele. The Kalash also have been shown to exhibit the exceedingly rare 19 allele value at autosomal marker D9S1120 at a frequency higher than the majority of other world populations which do have it…[ Another study with Qasim Ayub, and S. Qasim Mehdi, and led by Quintana-Murci claims that “the western Eurasian presence in the Kalash population reaches a frequency of 100%, the most prevalent [mtDNA] haplogroup being U4, (pre-HV)1, U2e, and J2,” and that they show “no detectable East or South Asian lineages… a western Eurasian origin for this population is likely, in view of their maternal lineages, which can ultimately be traced back to the Middle East”. [ However, dual origins or an Indian admixture is also possible given the genetic study by Sengupta et al. (2006), found the Kalash to comprise high frequencies of Haplogroup L3 (25%), R1a (20%), H1* (20%), Haplogroup G2a (20%), R* (5%), J2a and J2b2 at (5%) each[33]. Haplogroup L originates from prehistoric South Asia…See Sengupta, S et al. (February 2006).“Polarity and Temporality of High-Resolution Y-Chromosome Distributions in India Identify Both Indigenous and Exogenous Expansions and Reveal Minor Genetic Influence of Central Asian Pastoralists”. Am J Hum Genet. 78 (2): 202–21.doi:10.1086/499411. PMC 1380230. PMID 16400607.]

Chandrasekar A et al., YAP insertion signature in South Asia. Ann Hum Biol. 2007 Sep-Oct;34(5):582-6

A total of 2169 samples from 21 tribal populations from different regions of India were scanned for the Y-chromosome Alu polymorphism. This study reports, for the first time, high frequencies (8-65%) of Y Alu polymorphic (YAP) insertion in northeast Indian tribes. All seven Jarawa samples from the Andaman and Nicobar islands had the YAP insertion, in conformity with an earlier study of Andaman Islanders. One isolated case with haplotype E* was found in Dungri Bhill, a western Indian population, while YAP insertion in northeast India and Andaman tribes was found in association with haplotype D* (M168, M174). YAP insertion frequencies reported in the mainland Indian populations are negligible, according to previous studies. Genetic drift may be the causative factor for the variable frequency of the YAP insertion in the mainland populations, while the founder effect may have resulted in the highest incidence of haplotype D among the Andaman Islanders. The results of YAP insertion and the evidence of previous mtDNA studies indicate an early out of Africa migration to the Andaman and Nicobar Islands. The findings of YAP insertion in northeast Indian tribes are very significant for understanding the evolutionary history of the region.

Wang HW et al, Mitochondrial DNA evidence supports northeast Indian origin of the aboriginal Andamanese in the Late Paleolithic. J Genet Genomics. 2011 Mar 20;38(3):117-22. Epub 2011 Mar 29

To solve this question and better understand the origin of the aboriginal Andamanese, we screened for haplogroups M31 (from which Andaman-specific lineage M31a1 branched off) and M32 among 846 mitochondrial DNAs (mtDNAs) sampled across Myanmar. As a result, two Myanmar individuals belonging to haplogroup M31 were identified, and completely sequencing the entire mtDNA genomes of both samples testified that the two M31 individuals observed in Myanmar were probably attributed to the recent gene flow from northeast India populations. Since no root lineages of haplogroup M31 or M32 were observed in Myanmar, it is unlikely that Myanmar may serve as the source place of the aboriginal Andamanese. To get further insight into the origin of this unique population, the detailed phylogenetic and phylogeographic analyses were performed by including additional 7 new entire mtDNA genomes and 113 M31 mtDNAs pinpointed from South Asian populations, and the results suggested that Andaman-specific M31a1 could in fact trace its origin to northeast India. Time estimation results further indicated that the 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.

Study of YAP Element among an Endogamous Human Isolate in Punjab, AJS Badaruddoza et al. Kamla-Raj 2008. Int J Hum Genet, 8(3): 269-271 (2008)

“…polymorphic sites are useful for tracing the origin of paternal lineages in human population (Qamar et al. 1999) and can be often traced among populations within limited geographic areas (Hammer et al. 1998; Jobling and Tyler-Smith 1995, 2000, 2003) and specific ethnic groups (Qamar et al. 1999; Underhill et al. 2001). However, from some large scale surveys of human Y-chromosome polymorphism (Hammer 1994; Hammer et al. 1997; Jobling and Tyler-Smith 1995, 2000, 2003), it has been found a simple and stable polymorphism from the recent insertion of an Alu-family member on the long arm of the Y chromosome. This element, referred to as the Y Alu polymorphic element is present at a specific site on the Ychromosome in some humans and absent in others. One such Alu insertion is the Y Alu polymorphic element (YAP). This polymorphism is particularly useful because of its low rate of parallel and back mutation, which makes it suitable for identifying stable parental lineages that can be traced back in time over thousands of years.

Here, we report for the first time the YAP element in an isolated endogamous Ahmadiyya Muslim population of Punjab. …In none of the samples of the present study any YAP+ insertion was found as is shown in figure I. The study was carried out to evaluate the YAP in Muslim isolate population of Punjab since it is believed that all migrations to this part of continent took place from Middle East and Central Asia and in neighbouring Pakistan many groups exhibit this insertion (Qamar et al. 1999; Hammer et al. 1997). In all Middle Eastern Muslim populations the YAP insertion is found to be in the frequency of 11-25% but none of the North Indian and South Indian population had this insertion (Deka et al. 1996; Al-Zahery et al. 2003)…. In the study of YAP in nine populations of UP, North India, Agrawal et al. (2005) also did not find YAP insertion in any of the population groups, except for the Shia Muslims. Interestingly they did not find it in Sunni Muslims as observed in the present study, despite the fact that both groups have a common origin historically (Agrawal et al. 2005). … However, it is hypothesized that invasions of Aryans, Arabs and Mongols have significantly contributed to the ethnic variety of Indian population. The other population where the YAP insertion is found in very high frequency of 40% is the Siddis, a population of known East African ancestry found in Southern Andhra Pradesh (Ramana et al. 2001). Whereas, Thangaraj et al. (2003) observed 100% frequency of Asian specific lineage (D) of YAP, both in Onges and Jarawas population groups of

Andaman Islands, though representing the descendents of early colonisers of South East Asia later replaced in most of the continent by
Palaeolithic and Neolithic agriculturists…

See also Thangarai K. et al, Reconstructing the origin of Andaman Islanders as well as the comment which revealed ”mitochondrial DNA from two northeast Indian Rajbanshi individuals that shares three specific mutations with the M31a lineage observed in the Great Andamanese, which suggests that the predecessor of haplogroup M31 originated on the Indian subcontinent.”

Wang HW et al, Mitochondrial DNA evidence supports northeast Indian origin of the aboriginal Andamanese in the Late Paleolithic. J Genet Genomics. 2011 Mar 20;38(3):117-22. Epub 2011 Mar 29

Rare deep rooting Y-chromosome lineages in humans: Lessons for Phylogeography, Genetics. 2003 Sep;165(1):229-34., by Michael E. Weale et al.

The discovery of DE macrohaplogroups in Nigerians report a new very rare deep-rooting YAP clade (Figure 1). — because group E represents the great major- group, so far found only in five Nigerians, being the least derived of Y chromosomes found in sub-Saharan Africa, leads to the opposite conclusion—of significant evidence in human migration patterns for range expansion from West Africa to Asia.

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. Full text here.

“The Y chromosome Alu polymorphism (YAP, also called M1) defines the deep-rooted haplogroup D/E of the global Y-chromosome phylogeny [1]. This D/E haplogroup is further branched into three sub-haplogroups DE*, D and E (Figure 1). The distribution of the D/E haplogroup is highly regional, and the three subgroups are geographically restricted to certain areas, therefore informative in tracing human prehistory (Table 1). The sub-haplogroup DE*, presumably the most ancient lineage of the D/E haplogroup was only found in Africans from Nigeria [2], supporting the “Out of Africa” hypothesis about modern human origin. The sub-haplogroup E (E-M40), defined by M40/SRY4064 and M96, was also suggested [that it] originated in Africa [3-6], and later dispersed to Middle East and Europe about 20,000 years ago [3,4]. 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%) [5-7]. 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.

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 [9-11]. 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 [12]. Another study by Underhill et al. suggested that the D-M174 lineage likely reached East Asia about 50,000 years ago [5]. This implies that the YAP lineage in East Asia could be indeed very ancient.

Over time the YAP lineage split into two distinct groups: One, Haplogroup D is found in Asia and is defined by the M174 mutation.  The other, Haplogroup E is found primarily in Africa and the Mediterranean and is defined by marker M96.

[Possibly related to the Tibetan haplogroup D-bearing populations is that of the Bhutias, who inhabit large parts of the Himalayan areas of India including Sikkim, and who are thought to originate from Tibet.]

The geographic polymorphisms of Y chromosome at YAP locus among 25 ethnic groups in Yunnan, China. Sci China C Life Sci. 2003 Apr;46(2):135-40. by Shi H et al. [alternatively titled YAP IN 25 ETHNIC GROUPS FROM YUNNAN CHINA)Sci China C Life Sci. 2003 Apr;46(2):135-140.

YAP defines haplogroup DE of the human Y-chromosome phylogeny, which joins together the haplogroup E, found in Negroids and Caucasoids, with haplogroup D, found mainly among Mongoloids, including the archaic Ainu, but also non-Mongoloid populations such as the Andaman Islanders. The YAP frequencies listed here are, in all probability mostly of haplogroup D.

The geographic polymorphisms of Y chromosome at YAP locus among 25 ethnic groups in Yunnan, China. Shi H, Dong Y, Li W, Yang J, Li K, Zan R, Xiao C.The genetic polymorphisms of Y chromosome at YAP locus in 25 ethnic groups (33 populations) of China were analyzed in a total of 1294 samples. The average YAP+ frequency of the 33 populations was 9.2%, coinciding with published data of Chinese populations. Primi [or Pumi] has the highest YAP+ frequency (72.3%), which is also the highest YAP+ among all the eastern Asian populations studied. The YAP+ occurred in 17 populations studied including Tibetan (36.0%), Naxi (37.5% and 25.5%), Zhuang (21.3%), Jingpo (12.5%), Miao (11.8%), Dai (11.4%, 10.0%, 3.3% and 2.0%), Yi (8.0%), Bai of Yunnan (6.7% and 6.0%), Mongol of Inner Mongolia (4.3%), Tujia of Hunan (2.6%), Yao (2.2%) and Nu (1.8%). … Using the genetic information, combined with the knowledge of ethnology, history and archaeology, the origin and prehistoric migrations of the ethnic groups in China, especially in Yunnan Province were discussed. Source: Link

R. Vasudevan et al. Analysis of three polymorphisms in Bidayuh ethnic of Sarawak population: A report from Malaysia African Journal of Biotechnology Vol. 10(22), pp. 4544-4549, 30 May, 2011 DOI: 10.5897/AJB10.2241 Available from http://www.academicjournals.org/AJB

Alu element was originally inserted on the chromosome of the Subsaharan African populations, which explains the lack of YAP+ in the Asian population. The small percentage of YAP+ found in Bidayuh ethnics suggest that the probability of population admixture have taken place many years ago …

M96 biallelic polymorphism is a single base substitution polymorphism, where the base G has been substituted to C (G > C). 56.67% of Bidayuh subjects possess the ancestral state, while the remaining 43.33% of subjects have the derived state of the allele (Table 3). M96 originated in Africa and later dispersed to Middle East and Europe about 20,000 years ago (Hong et al., 2008)

For more details on the YAP+ lineage genetic component (and possible migratory path) of the Ainu, see this page.

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Is an Ainu-Native American connection detected through DNA analyses?

A hitherto unknown migratory lineage, carriers of the X haplogroup has been detected. This X haplogroup is not found in Asia but is present in the Ainu population.

In 1997, a fifth mtDNA haplogroup X was identified and found present in 3% in Native Americans with apparent widespread dispersal (from Canada and Washington State, to Arizona, to the Plains, to the Great Lakes area), with a particular linkage to the Iroquois.  Among other native American tribes, X haplogroup has also been detected in small numbers in the Yakima, Sioux and Navajo  tribes, and to greater numbers among the Ojibway, Onecta, and Nuu-Chah-Nulth tribes. The X haplogroup thought to have entered America around 34,000 B.C., but emerged in larger numbers between 12,000 – 10,000 B.C.  –  the haplogroup has not been detected in South nor Central American tribes including the Maya. It has however, also turned up in ancient remains in Illinois near Ohio and a few places near the Great Lakes. Source: DNA evidence for Atlantis Beyond the Bering Strait – DNA Evidence Rocks the Boat  

In addition, X haplogroup has been found mainly in Europe in the remains of the ancient Basques and elsewhere in Europe (Bulgaria, Finland, Italy).

The study mtDNA haplogroup X: an ancient link between Europe/Western Asia? (American Journal of Human Genetics, 1998 ISSN: 0002-9297),  concluded that Native American founders may have had Caucasian ancestry.

On the other hand, a study on the HLA gene (alleles and haplotypes) frequencies on North, Meso, South American AmeriIndians showed that AmerIndians have little relatedness with Asians, according to genealogy studies except for the one haplotype (A*24-B*40-DRB1*1401-DQB1*0503)  that Japanese share with North-Americans in low frequencies. Source: The Peopling of the Americas: A Complex Issue AmeriIndian, Na-Dene, Aleut and Eskimo first inhabitants  (International Journal of Modern Anthropology, Int. J. Mod. Anthrop. 3  (2010) Available online at   www.ata.org.tn)

It has also turned up in the Middle East (Israel). In July 2001, a research letter was published in the American Journal of Human Genetics reporting that the X haplogroup had been detected in a tribe called Altaics or Altasians (by Russian geneticists) located in extreme southern Siberia. These people have always inhabited the Gobi Desert area.

An important finding of the 2004 research paper “Mitochondrial DNA variation in the aboriginal populations of the Altai-Baikal region: impl”  was the presence of type X in the Altaians, which had not yet been detected in Asia. Computer analysis showed this DNA sequence is not a late European admixture. Rather, the Altai variant X is ancient and can be close to the ancestral form of the variants of contemporary Europeans and Amerinds. The presented results prove that of all nations in Asia, the Turkic-speaking nations living between Altai and Baikal along the Sayan mountains are genetically closest to the Amerinds. [and thereby possibly a contributory Altaic genetic component of the ancestry of the Ainu populations too?] 

Analysis of HLA genes and haplotypes in Ainu (from Hokkaido, northern Japan) supports the premise that they descend from Upper Paleolithic populations of East Asia
Authors: Bannai, M.1; Ohashi, J.2; Harihara, S.3; Takahashi, Y.1; Juji, T.4; Omoto, K.5; Tokunaga, K.2

Source: Tissue Antigens, Volume 55, Number 2, 1 February 2000 ,

The Ainu people are assumed to be the descendants of pre-agricultural native populations of northern Japan, while the majority of population of present-day Japan (Hondo-Japanese) is considered to have descended mainly from post-neolithic migrants. Sequence-level polymorphisms of the HLA-class I (HLA-A and HLA-B) genes were investigated in DNA samples of 50 Ainu living in Hidaka district, Hokkaido. HLA-A*2402, A*0201, A*0206, A*2601, A*3101, B*1501, B*5101, B*3901, and B*3501 were observed at frequencies of more than 10% and most of these have previously been found in populations of not only Asians but also North and South American Indians. A*68012, which has not so far been detected in Hondo-Japanese, was found in the Ainu (3%). On the other hand, several alleles common in Hondo-Japanese, including HLA-A*3303, A*1101, B*4403, B*5201, B*5401, B*4601, and B*0702 were infrequent in Ainu (0-1%). Correspondence and neighbor-joining analyses of various populations based on HLA-A, -B and -DRB1 gene frequencies enabled distinction between Asian, Native South American, European, and African populations. The Ainu, as well as Tlingit (Na-Dene), were placed midway between other East Asians, including Hondo Japanese, and Native South Americans (Amerindians) in the correspondence analysis. Furthermore, several HLA-A-B and HLA-B-DR-DQ haplotypes common in the Ainu, are shared with some Native American populations. These observations strongly suggest a unique place for the Ainu as descendants of some Upper Paleolithic populations of East Asia, from whom some Native Americans may have descended.

Genetic link between Asians and native Americans: evidence from HLA genes and haplotypes

Katsushi Tokunaga, , a, Jun Ohashia, Makoto Bannaib and Takeo Jujic

Received 16 May 2001; accepted 15 June 2001 Available online 30 August 2001.

Abstract
We have been studying polymorphisms of HLA class I and II genes in East Asians including Buryat in Siberia, Mongolian, Han Chinese, Man Chinese, Korean Chinese, South Korean, and Taiwan indigenous populations in collaboration with many Asian scientists. Regional populations in Japan, Hondo-Japanese, Ryukyuan, and Ainu, were also studied. HLA-A, -B, and -DRB1 gene frequencies were subjected to the correspondence analysis and calculation of DA distances. The correspondence analysis demonstrated several major clusters of human populations in the world. “Mongoloid” populations were highly diversified, in which several clusters such as Northeast Asians, Southeast Asians, Oceanians, and Native Americans were observed. Interestingly, an indigenous population in North Japan, Ainu, was placed relatively close to Native Americans in the correspondence analysis. Distribution of particular HLA-A, -B, -DRB1 alleles and haplotypes was also analyzed in relation to migration and dispersal routes of ancestral populations. A number of alleles and haplotypes showed characteristic patterns of regional distribution. For example, B39-HR5-DQ7 (B*3901-DRB1*1406-DQB1*0301) was shared by Ainu and Native Americans. A24-Cw8-B48 was commonly observed in Taiwan indigenous populations, Maori in New Zealand, Orochon in Northeast China, Inuit, and Tlingit. These findings further support the genetic link between East Asians and Native Americans. We have proposed that various ancestral populations in East Asia, marked by different HLA haplotypes, had migrated and dispersed through multiple routes. Moreover, relatively small genetic distances and the sharing of several HLA haplotypes between Ainu and Native Americans suggest that these populations are descendants of some Upper Paleolithic populations of East Asia.

If the Ainu  (or a group related distantly to them) contributed to the native American DNA pool, it was probably at a very low level. No Y chromosome or mt DNA have shown up in native Americans yet.

Strains of JC virus in Amerin-speakers of North America (Salish) and South America (Guarani), Na-Dene-speakers of New Mexico (Navajo), and modern Japanese suggest links through an ancestral Asian population.  Am J Phys Anthropol. 2002 Jun;118(2):154-68.

The final clarification may now have come from a study showing that all type 2A JC Virus strains from North and South Americans are closely related to strains in present-day Japan.  The strains of JC virus  present in Navajo in New Mexico (speakers of an Athapaskan language in the Na-Dene language phylum) were found to be of a prototype type 2A strain of a northeast Asian genotype found in Japan. The partial VP1 gene sequences of the JC virus from the Salish people in Montana (speakers of a language in the Salishan group in the Amerind family) and from the Guarani Indians of Argentina (speakers of the Tupi-Guarani language and Equatorial branch of the Amerind family) were however shown to be closely related to several strains variants of strains found in Japan.

Other references:

Bannai M. et al., Analysis of HLA genes and haplotypes in Ainu (from Hokkaido, northern Japan) supports the premise that they descent from Upper Paleolithic populations of East Asia  Tissue Antigens, Volume 55, Number 2, 1 February 2000, pp. 128-139(12)

For more readings on the origins of the Ainu:

• Ainu populations share genetic affinities with Nivkhi and other peoples from North Asia including Sakhalin.
• YAP-positive element in the Y-chromosomes of the Ainu people
• Ainu’s affinity to northeast Asian Ul’chis (Orochis) – prehistoric Paleo-Siberian neighbours and cousins of the Ainu and Jomon people
• DNA news: Migrants from Northeast Siberia move into the Okhotsk and into Hokkaido