Notes and bibliography: The unresolved engima of the northern or southern origins of the Jomon people


Seo Y, Y chromosome DNA polymorphisms and their haplotypes in a Japanese population. Leg Med (Tokyo). 1999 Sep;1(3):145-9.
Abstract

Allele frequencies of two Y chromosome-specific short tandem repeats, locus DYS385 and DYS19, in addition to the Y Alu polymorphic (YAP) insert (DYS287) were investigated in blood samples obtained from 270 unrelated Japanese in Miyazaki Prefecture (south Japan). A total of 47 genotypes in DYS385 and 6 in DYS19 were detected, and the frequency of the YAP(+) allele was found to be 35.2% (95270). The allele distributions of each locus revealed significant differences compared with those in other populations. One hundred and twelve different haplotypes were observed in the combined 55 alleles of three loci. The gene diversity values range 0.96 for DYS385 and 0.71 for DYS19, and the combination haplotype diversity value is 0.98.

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Kim W, Y-specific DNA polymorphisms of the YAP element and the locus DYS19 in the Korean population. J Hum Genet. 1998;43(3):195-8.

Abstract

The Y Alu polymorphic (YAP) element (DYS287) and the Y-linked tetranucleotide microsatellite locus DYS19 were examined in samples from a total of 455 unrelated males in the Korean population. The frequency of the YAP allele was found to be 1.3% (6/455) in the Korean population. These results are consistent with previous reports that showed the YAP element to be absent in most Asian populations, with the exception of the high frequency of the YAP allele in the Japanese population. All five common alleles at the DYS19 locus were identified in this study, The C allele was the most frequent (197/455), followed by the D (119/455), B (78/455), E (41/455), and A (20/455) alleles. Seven combination haplotypes (DYS287/DYS19) were found, and the mean combination haplotype diversity in the Korean population appeared to be 0.71. Based on results of these two loci, Japanese and Korean populations may share some common genetic structure that could reflect recent gene flow and some amount of admixture of Y chromosomes between these two populations.

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Abstract

We have examined variations of five polymorphic loci (DYS287, DXYS5Y, SRY465, DYS19, and DXYS156Y) on the Y chromosome in samples from a total of 1260 males in eight ethnic groups of East Asia. We found four unique haplotypes constructed from three biallelic markers in these samples of East Asians. The Japanese population was characterized by a relatively high frequency of either the haplotype I-2b (-/Y2/T) or II-1 (+/Y1/C). These dual patterns of the distribution of Y chromosomes (I-2b/II-1) were also found in Korea, although they were present at relatively low frequencies. The haplotype II-1 was present in Northeast Asian populations (Chinese, Japanese, Koreans, and Mongolians) only, except for one male from the Thai population among the Southeast Asian populations (Indonesians, Philippines, Thais, and Vietnamese). The Japanese were revealed to have the highest frequency of this haplotype (27.5%), followed by Koreans (2.9%), Mongolians (2.6%), and mainland Chinese (2.2%). In contrast, the frequency of the haplotype I-2b was found to be 17.1% in the Japanese, 9.5% in Indonesian, 6.3% in Korean, 3.8% in Vietnamese, and 2.7% in Thai samples. These findings suggested that the chromosomes of haplotype I-2b were likely derived from certain areas of Northeast Asia, the region closest to Southeast Asia. Phylogenetic analysis using the neighbor-joining tree also reflected a general distinction between Southeast and Northeast Asian populations. The phylogeny revealed a closer genetic relationship between Japanese and Koreans than to the other surveyed Asian populations. Based on the result of the dual patterns of the haplotype distribution, it is more likely that the population structure of Koreans may not have evolved from a single ancient population derived from Northeast Asians, but through dual infusions of Y chromosomes entering Korea from two different waves of East Asians.

Maximum parsimony tree for the eight haplotypes showed that these haplotypes could be classified into four distinct lineages characterized by three key mutations: an insertion of the Y Alu polymorphic (YAP) element at DYS287, a C-to-G transversion at M9, and a C-to-T transition at RPS4Y(711). Of the four lineages, three major lineages (defined by the allele of YAP(+), M9-G, and RPS4Y-T, respectively) accounted for 98.6% of the Asian populations studied, indicating that these three paternal lineages have contributed to the formation of modern Asian populations. Moreover, phylogenetic analysis revealed three monophyletic Asian clusters, which consisted of north Asian, Japanese, and Han Chinese/southeast Asian populations, respectively. Coalescence analysis in the haplotype tree showed that the estimated ages for three key mutations ranged from 53,000 to 95,000 years, suggesting that the three lineages were separated from one another during early stages of human evolutionary history. The distribution patterns of the Y-haplotypes and mutational ages for the key markers suggest that three major groups with different paternal ancestries separately migrated to prehistoric east and southeast Asia.

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Chandrasekhar A. et al. 2007, YAP insertion signature in South Asia, Annals of Human Biology, 2007, Vol. 34, No. 5 : Pages 582-586   (doi: 10.1080/03014460701556262) HTMLPDF (53 KB)

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.

Chandrasekhar et al. argued for the Asian origin of the YAP+. They state,

The presence of the YAP insertion in Northeast Indian tribes and Andaman Islanders with haplogroup D suggests that some of the M168 chromosomes gave rise to the YAP insertion and M174 mutation in South Asia

They also argue that YAP+ migrated back to Africa with other Eurasian haplogroups. These include Haplogroup R1b1* (18-23kya), which has been observed with especially high frequency among the members of some tribes in northern Cameroon, and Haplogroup T (25-30kya), which has been observed in low frequencies in Africa. Haplogroup E at 50kya is considerably older than these haplogroups and has been observed at frequencies frequencies of 80-92% in Africa.

In a press release concerning a study by Karafet et al. (2008), Michael Hammer, revised the dates for the origin Haplogroup DE from 55,000 years ago to 65,000 years ago. For haplogroup E, Hammer revised the dates from 31,000 years ago to 50,000 years ago. Hammer is also quoted as saying “The age of haplogroup DE is about 65,000 years, just a bit younger than the other major lineage to leave Africa, which is assumed to be about 70,000 years old,” in which he implies that haplogroup DE left Africa along with Haplogroup C. 
Read more: 
http://informahealthcare.com/doi/pdfplus/10.1080/03014460701556262

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Chen F,  et al. Analysis of mitochondrial DNA polymorphisms in Guangdong Han ChineseForensic Sci Int Genet. 2008 Mar;2(2):150-3.

Abstract

Previous investigations on Chinese mitochondrial DNA (mtDNA) variation revealed that the matrilineal gene pool of southern Han Chinese is rather complex, with much higher genetic diversity and more basal/ancient lineages than the northern Hans. The extreme case is Guangdong Han populations, among which pronounced (matrilineal) differentiation has been observed, indicative of complex demography of the region. To get more insights into the maternal makeup of southern Han Chinese, mtDNA variation of a total of 106 individuals sampled from Dongguan, Guangdong Province, China, was analyzed in this study. …. The southern-prevalent haplogroups, such as R9 (20.8%), B (17.9%), M7b (14.2%), show relatively high distribution frequencies in Dongguan Hans; whereas the frequencies of Northern-prevalent haplogroups (with the exception of D) are quite low: C (1.9%), G2 (1.9%) and Z (1.9%), indicating the southern-origin of Dongguan Hans.

The highest frequency (87.5%) was found in JP-Ainu, followed by JP-Okinawa (55.6%) living in the southwestern islands of Japan, JP-Honshu (36.6%), and JP-Kyushu (27.9%). The ht2 haplotype (defined by YAP+/M15+) was found in only two males, one each from Thais and Thai-Khmers; ht3 (defined by YAP+/SRY4064-A) was completely absent in the Asian populations examined, whereas Jewish in the Uzbekistan and African populations had this haplotype with a frequency of 28.3% and 100%, respectively

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Haplogroup DE is found in Africa (Haplogroups E and DE*) and East Asia (Haplogroups D and DE*) but is largely absent in between these two regions. The presence of DE across widely separated regions has confounded investigators trying to reconstruct the migration of humans from Africa to Asia. At some time, there was an extinction of DE lineages in West, South and Central Asia. Autochthonous DE lineages are absent in India, an important region in the dispersal of humans in Asia. However DE lineages have been detected in relict populations of the Andaman Islands. Underhill et al. 2007, suggest the possibility that deleterious mutations in some DE carriers may explain the extinction of DE lineages in India.[9]

The only person in the world to be confirmed in Hg DE* by commercial testing is Ruslan bin Makin Al Bitar[10], maternal half-brother to Yomal Sidoroff-Biarmskii[11], who ordered the testing. The Al Bitar family are Sunni Syrian Arabs of Damascus, Syria. In yhrd.org , a similar haplotype was found only in Syrian Arabs of provincial Syria from the work “Donbak2006″[12] (9 out of 9 markers, 1 out of 113 individuals). This implies that Syria has some small share of Hg DE* (never reported anywhwre outside West Africa & Tibet by academic studies). However, all the other studies of Syria have yet failed to find this Hg. The only haplotype outside Africa that is anywhere close to the above can be found in the smgf.org database belonging to the Othman family, a Palestinian Arab family of Jerusalem.

Discovery

The YAP insertion was discovered by scientists led by Michael Hammer of the University of Arizona.[13] Between 1997 and 1998 Hammer published three articles relating to the origins of haplogroup DE.[14][15][16] These articles state that YAP insertion occurred in Asia. As recently as 2007, some studies such as Chandrasekar et al. 2007, cite the publications by Hammer when arguing for an Asian origin of the YAP insertion.[5]

The scenarios outlined by Hammer include an out of Africa migration over 100,000 years ago, the YAP+ insertion on an Asian Y-chromosome 55,000 years ago and a back migration of YAP+ from Asia to Africa 31,000 years ago by its subclade haplogroup E.[16] This analysis was based on the fact that older African lineages, such as haplogroups A and B, were YAP negative whereas the younger lineage, haplogroup E was YAP positive. Haplogroup D, which is YAP positive, was clearly an Asian lineage, being found only in East Asia with high frequencies in Japan and Tibet. Because the mutations that define haplogroup E were observed to be in the ancestral state in haplogroup D, and haplogroup D at 55kya, was considerably older than haplogroup E at 31kya, Hammer concluded that haplogroup E was a subclade of haplogroup D.[16]

Contemporary studies

In 2000 a number of scientists had started to reassess the hypothesis of an Asian origin of the YAP insertion. 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.[17]

Further arguments were made supporting and African origin of the YAP in Underhill et al. 2001. The arguments for an African origin include.[3]

Africa has the highest frequency of YAP(>80%). Whereas the YAP+ in Asia has a fairly restricted geographic distribution, mainly at low to moderate frequencies (average 9.6%) in East Asia.[8]
It was claimed that there was no archaeological evidence of a back-migration to Africa, and at the time of writing that there was no unequivocal Y DNA, mitochondrial DNA orautosomal DNA evidence of a back migration to Africa.[3]
Although Haplogroup C seems to have originated in Asia at a similar time to Haplogroup DE’s origin, Haplogroup C shows no sign of back migration to Africa.
The African origin of the YAP+ is also supported by studies concerning haplogroup E.

In Altheide and Hammer 1997, the authors argue that haplogroup E arose in Asia on an ancestral YAP+ allele before migrating back to Africa.[15]

However some studies, such as Semino et al., indicate that the highest frequency and diversity of haplogroup E is in Africa, and Africa is the most likely place of origin of the haplogroup.[8][18]

The models supporting an African origin or an Asian origin of the YAP+ insertion both required the extinction of the ancestral YAP chromosome to explain the current distribution of the YAP+ polymorphism. Paragroup DE* possesses neither the mutations that define haplogroup D or haplogroup E. If paragroup DE* was found in one location but not the other, it would boost one theory of the other.[19] Haplogroup DE* has recently been found in Nigeria,[6] Guinea-Bissau[7] and also in Tibet.[8] The phylogenetic relationship of three DE* sequences has yet to be determined, but it is known that the Guinea Bissau sequences differ from the Nigerian sequences by at least one mutation.[7] Weale et al. state that the discovery of DE* among Nigerians pushes back the date for the most recent common ancestor (MRCA) of African YAP chromosomes. This, in his view, has the effect of reducing the time window through which a possible back migration from Asia to Africa could occur.[6]

In a press release concerning a study by Karafet et al. (2008), Michael Hammer, revised the dates for the origin Haplogroup DE from 55,000 years ago to 65,000 years ago. For haplogroup E, Hammer revised the dates from 31,000 years ago to 50,000 years ago. Hammer is also quoted as saying “The age of haplogroup DE is about 65,000 years, just a bit younger than the other major lineage to leave Africa, which is assumed to be about 70,000 years old,” in which he implies that haplogroup DE left Africa along with Haplogroup CF.[20]

Peter Underhill states that there will always be uncertainty regarding the precise origins of DNA sequence variants such as YAP because of a lack of knowledge concerning prehistoric demographics and population movements. However Underhill contends that with all the available information, the African origin of the YAP+ polymorphism is more parsimonious and more plausible than the Asian origin hypothesis.[9] Other authors who have published or co-published works in support of an African origin the YAP+ include Luigi Luca Cavalli-Sforza,[17] Toomas Kivisild,[9] Spencer Wells,[19] Linda Stone and Paul F. Lurquin.[21]

Source: Haplogroup DE, Wikipedia

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.” 

see also ‘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) – abstract above.
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.

Hammer MF (September 1994). “A recent insertion of an alu element on the Y chromosome is a useful marker for human population studies”Mol. Biol. Evol. 11 (5): 749–61. PMID 7968488.

Abstract: A member of the Alu family of repeated DNA elements has been identified on the long arm of the human Y chromosome, Yq11. This element, referred to as the Y Alu polymorphic (YAP) element, is present at a specific site on the Y chromosome in some humans and is absent in others. Phylogenetic comparisons with other Alu sequences reveal that the YAP element is a member of the polymorphic subfamily-3 (PSF-3), a previously undefined subfamily of Alu elements. The evolutionary relationships of PSF-3 to other Alu subfamilies support the hypothesis that recently inserted elements result from multiple source genes. The frequency of the YAP element is described in 340 individuals from 14 populations, and the data are combined with those from other populations. There is both significant heterogeneity among populations and a clear pattern in the frequencies of the insertion: sub-Saharan Africans have the highest frequencies, followed by northern Africans, Europeans, Oceanians, and Asians. An interesting exception is the relatively high frequency of the YAP element in Japanese. The greatest genetic distance is observed between the African and non-African populations. The YAP is especially useful for studying human population history from the perspective of male lineages.

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National Geo’s Atlas of the Human Journey Genographic suggests two scenarios for Hg D:

Hg D migrated out of Africa at 50K years ago, following southern Arabian peninsula, India, Sri Lanka and into Southeast Asia (pockets in SEAsia, Andaman, but not mainland India)

First migratory lineage went north into Japan

Second, a later lineage from Mongolia into Tibet.

From there Nat. Geo Genographic comes …

The current theory of haplogroup D out of Africa would have followed a route from Arabia, Middle East, Afghanistan, Northern India

An earlier trail 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%).

Later trail, Mongolia (Hammer) -> Tibet according to NatGeo Genographic Project???

Based on hg YAP+ mutation

According to some (see Underhill references below), Asian origins theory for haplogroup D is on its way out (see Rare Deep-Rooting Y Chromosome Lineages in Humans):

“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”.

Underhill (2001). “The case for an African rather than an Asian origin of the human Y-chromosome YAP insertion”. Genetic, Linguistic and Archaeological Perspectives on Human Diversity in Southeast Asia. New Jersey: World Scientific. ISBN 9810247842.

Underhill et al (2000). The phylogeography of Y chromosome binary haplotypes and the origins of modern human populations

See 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.

The above paper concluded:

“…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. The Tibetan and Japanese populations are the admixture of two ancient populations represented by two major East Asian specific Y chromosome lineages, the O and D haplogroups.”

“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 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 [1]. 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 [8,9]”

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The Haplogroup D/YAP Riddle: From the south or north?

The only person in the world to be confirmed in Hg DE* by commercial testing is Ruslan bin Makin Al Bitar[10], maternal half-brother to Yomal Sidoroff-Biarmskii[11], who ordered the testing. The Al Bitar family are Sunni Syrian Arabs of Damascus, Syria. In yhrd.org , a similar haplotype was found only in Syrian Arabs of provincial Syria from the work “Donbak2006″[12] (9 out of 9 markers, 1 out of 113 individuals). This implies that Syria has some small share of Hg DE*The only haplotype outside Africa that is anywhere close to the above can be found in the smgf.org database belonging to the Othman family, a Palestinian Arab family of Jerusalem. However DE lineages have been detected in relict populations of the Andaman Islands. Underhill et al. 2007, suggest the possibility that deleterious mutations in some DE carriers may explain the extinction of DE lineages in India.[9]

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.[17] Haplogroup DE* has recently been found in Nigeria,[6] Guinea-Bissau[7] and also in Tibet.[8]

Underhill contends that with all the available information, the African origin of the YAP+ polymorphism is more parsimonious and more plausible than the Asian origin hypothesis.[9] Other authors who have published or co-published works in support of an African origin the YAP+ include Luigi Luca Cavalli-Sforza,[17] Toomas Kivisild,[9] Spencer Wells,[19] Linda Stone and Paul F. Lurquin.[21]

Haplogroup D first appeared approximately 50,000 years ago and likely accompanied the people of haplogroup C on their great coastal migration through the Southern Arabian Peninsula, India, Southeast Asia and ultimately Australia. In modern times, this haplogroup appears along the ancient migration route in the Andaman Islands and Southeast Asia, although not in India. This haplogroup occurs at a high frequency among Tibetan and Yao populations. Evidence suggests a shared ancestry, originating from ancient tribes of North West China. Haplogroup D1 evolved from the D lineage and is found in Southeast Asia and Tibet. It is also found at low frequencies in Mongolian populations, but completely absent from Japan. Haplogroup D2 is 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.chromosomal-labs.com/ancestry/yhaplogroup.pdf

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 relatively high frequency of the YAP element observed in Japanese.  nine 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 one North Indian populations, the Shiya Muslims, at a frequency of 11%, concluding 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

So, did hg D enter Japan from the south or from the north? It was formerly thought D entered from the south.  Hg D bearers were thought to have been from the south have mixed with the Mongoloid O hg carriers in Southeast or East Asia.

If so, 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 explanation for this is the Genographic Project’s scenario of two D lineages one proceeding northeastwards into Japan and the other across China and eventually into southern Japan, Okinawa.

For an explanation of the hg D lineage in Northeast Asia, see

Altheide TK, Hammer MF (August 1997). “Evidence for a Possible Asian Origin of YAP+ Y Chromosomes“. Am. J. Hum. Genet. 61 (2): 462–6. doi:10.1016/S0002-9297(07)64077-4.PMC 1715891. PMID 9311756.

The nonrecombining portion of the human Y chromonary dysplasia/hypoplasia, and hypospadias suggest the some has become an important tool for evolutionary studies … Its exclusive paternal inheritance and lack of recombination with the X chromosome preserve a unique record of mutational events from previous generations. Mutational changes
that have occurred a single time in human evolution can be used to construct bifurcating haplotype trees that reflect the history of human Y-chromosome lineages. These haplotype trees, in turn, can be used to generate and test hypotheses about the origin and migration of human populations.

One of the most useful and widely studied Y-linked based on the distribution of a GrA transition in the polymorphisms is known as the ‘‘Y Alu polymorphic’’ (YAP) element (Hammer 1994). This polymorphism has resulted from the single and stable insertion of a member of the repetitive Alu family at a specific site (locus polymorphism at nucleotide site 4064 (referred to here DYS287) on the long arm of the human Y chromosome during the past 29,000–334,000 years (Hammer 1995). The frequency of Y chromosomes carrying the YAP element(YAP+) varies greatly among human populations from different geographic locations (Hammer 1994); Spurdle et al. 1992a and 1994b; Hammer and Horai 1995; Hammer et al. 1997; Karafet et al. 1997) For example, global surveys have shown that sub-Saharan African populations have the highest overall frequency of YAP+ chromosomes, followed by populations from northern Africa, Asia, Europe, the New World, and Oceania. Hammer (1995) sequenced a 2.6-kb region encompassing the YAP insertion in 16 humans, found three polymorphic nucleotide sites (PN1, PN2, and PN3) plus a variable-length poly(A) tail associated with the YAP element, and constructed a haplotype tree composed of five YAP haplotypes. Haplotypes 1 and 2 were YAP- (lacking the YAP element, which is the ancestral state), whereas haplotypes 3-5 were YAP+ (see fig. 1). YAP haplotype 3 represented the most ancestral YAP+ lineage and was initially identified in a single African and two Japanese males. A global survey of these five haplotypes in 1,500 individuals revealed both the presence of all five YAP haplotype s in sub-Saharan African populations and subsets of these in non-African populations (Hammer et al. 1997). For instance, YAP haplotypes 1 and 4 were present in European populations, and haplotypes 1 and 3 were present in Asian populations.

Similar patterns of variation at non–Y chromosome loci have been interpreted to support a recent African origin of contemporary human genetic lineages (Cann et al. 1987; Armour et al. 1996; Tishkoff et al. 1996); however, Hammer et al. (1997) have raised the possibility that YAP haplotype 3 originated in Asia and migrated to Africa. This hypothesis is supported by the finding of high frequencies of haplotype 3 in some Asian populations (i.e., Ç50% in Tibet) and by the observation of higher levels of diversity (based on the number and frequency of alleles at the DYS19 microsatellite locus) associated with Asian versus African haplotype 3 chromosomes. Because YAP haplotypes 4 and 5 evolved from haplotype 3 and account for the majority of Y chromosomes in Africa (table 1), this hypothesis implies a substantial Asian contribution to the African paternal gene pool (Hammer et al. 1997)

We now report additional evidence in support of the based on the distribution of a G–>A transition in the SRY region.

… A clear-cut geographic trend was apparent in the distribution of YAP+/SRY4064 chromosomes in the populations studied by Hammer et al. (1997). Remarkably, the ancestral YAP lineage represented by haplotype 3G was present only in Asian populations, and the derived 3A haplotype was present only in African populations and in a single European individual (table 1). No population was found to be polymorphic for both the 3G haplotype and the 3A haplotype.

We present three alternative hypotheses to explain this pattern (table 2). …

A global analysis of 240 Y chromosomes sampled from Africa, Europe, Asia, and South America indicated that only a single ah type (ahV) was shared between YAP+ and YAP- chromosomes. Thus, the YAP insertion was postulated to have occurred on an ahV Y chromosome, and all other ah types associated with YAP+ chromosomes were assumed to be derivatives of ahV (Santos et al. 1996). In the same global survey, several YAP+/ahV chromosomes were identified in males from Africa, Mongolia, and the New World, whereas only two YAP-/ahV chromosomes were found (Santos et al. 1996). One of the YAP- /ahV chromosomes was also from the Mongolian population, the only population found to possess both YAP+/ahV and YAP-/ahV chromosomes (the other YAP-/ahV chromosome was found in a cell line of uncertain geographic region.

Interestingly, we have found several YAP DNA and human chromosomes in Mongolia (Karafet et al. 1997), and all of these are associated with the ancestral SRY the Y chromosome is a useful marker for human population allele (data not shown).

We infer that Mongolian populations have both the ancestral YAP-/SRY4064-G/ahV haplotye and the ancestral YAP+/SRY4064-G/ahV haplotype, and we tentatively take this take this as additional evidence in support of the hypothesis of an Asian origin of YAP+/chromosomes. We have begun to type the ah system in our global sample of chromosomes and now have confirmed the presence of the YAP+/SRY4064-G/ahV haplotype in another Asian population—Tibetans (M. Hammer and N. Bianchi, un-published data). Continued global studies of the ah and SRY4064 polymorphisms, in conjunction with study of both YAP+ and YAP- chromosomes, should provide a sound framework for testing hypotheses about the geographic origin of the original YAP element –insertion event.

[note: ah refers to the alpha sign which could not be produced on this keyboard]

To read Hammer’s letter to the Editor in its entirety, go to this page.

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On the paternal side, while the vast majority of Ainu 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,The Druze: A Population Genetic Refugium of the Near East. PLoS ONE. 2008 May 7;3(5):e2105. Source 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, 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.

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