YAP-positive element in the Y-chromosomes of the Ainu people

From: Kivisild, T, Tolk, HV, Parik, J, Wang, Y, Papiha, SS, Bandelt, HJ, Villems, R. (2002). The Emerging Limbs and Twigs of the East Asian mtDNA Tree Mol Biol Evol. 19: 1737-1751

“Only four Japanese populations exhibited ht1 (defined only by YAP+) at various frequencies (also see Table 1). 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. Thus, the YAP+ lineage was found in restricted populations among Asian populations, consistent with previous reports (Hammer and Horai 1995; Hammer et al. 1997; Shinka et al. 1999)”

A 2010 study “A genetic analysis of the Sakishima islanders reveals no relationship with Taiwan aborigines but shared ancestry with Ainu and main-island Japanese” American Journal of Physical Anthropology Volume 142, Issue 2, pages 211–223, June 2010 by Hirotaka Matsukusa et al.  about the peoples in the Sakishima Islands reported that a part of the peoples in Miyako Island and Ishigaki Island also show the marks of YAP+ (53% and 26% respectively) http://onlinelibrary.wiley.com/doi/10.1002/ajpa.21212/abstract

“The Sakishima islands are members of the Ryukyu island chain, stretching from the southwestern tip of the Japanese archipelago to Taiwan in the East China Sea. Archaeological data indicate cultural similarities between inhabitants of prehistoric Sakishima and Neolithic Taiwan. Recent studies based on tooth crown traits show remarkably high inter-island diversity among Ryukyu islanders, suggesting that the Sakishima islanders might have genetic backgrounds distinct from main-island Okinawa people. To investigate the genetic diversity of the Ryukyu islanders, we analyzed mtDNA, Y chromosome, and autosomal short tandem repeat loci in a sample of main-island Okinawa people and Sakishima (Miyako and Ishigaki) islanders whose participated in a previous study of tooth crown morphology. Our phylogenetic analysis of maternal (mtDNA) and paternal (Y chromosome) lineages shows that the Sakishima islanders are more closely related to people from the Japanese archipelago than to Taiwan aborigines. Miyako islanders and the Hokkaido Ainu have the first and second highest frequencies (respectively) of the Y-chromosomal Alu-insertion polymorphism, which is a presumable Jomon marker. Genetic diversity statistics show no evidence of demographic reduction or of extreme isolation in each island’s population. Thus, we conclude that 1) Neolithic expansion from Taiwan did not contribute to the gene pool of modern Sakishima islanders, 2) male-lineage of the Ryukyu islanders likely shares a common ancestor with the Hokkaido Ainu who are presumably direct descendants of the Jomon people, and 3) frequent reciprocal gene flow among islands has masked the trace of common ancestry in the Ryukyu island chain”

***

Jomon Genes  By  JOHN TRAVIS

Using DNA, researchers probe the genetic origins of modern Japanese

From that evidence, Hammer and Horai hypothesized that the YAP element was originally carried to Japan by the Jomon and that the Yayoi, who came from the region that now makes up North and South Korea, lacked the marker. More recent research has strengthened this theory.

Working with several colleagues, the two researchers mapped the distribution of YAP-positive chromosomes throughout Japan. While men living in central Japan rarely carry YAP. the Ainu and inhabitants of the southern islands, the two populations apparently least influenced by the Yayoi, frequently do.

Hammer and his colleagues are also studying a second Y chromosome marker that may serve as a sign of the Yayoi migration. This marker is common in Koreans and appears most frequently in the central islands of Japan, says Hammer.

Together, contends Hammer. the two markers tell a story of an initial Yayoi migration into central Japan and a subsequent spread of the people toward the north and south. Since both Y chromosome markers are still found in varying degrees throughout Japan, it appears that the genes of the Jomon and Yayoi peoples did intermingle significantly.

“Our data support the hybridization theory,” says Hammer.

The research on YAP has also addressed another controversial question: Where did the Jomon come from? Some researchers have long held the idea that the Jomon originated in southeast Asia and spread to Japan about 12,000 years ago. Analyses of dental remains, shared aspects of language, and even some genetic studies have offered support for this scenario.

Several years ago, Nei offered an alternative. Working from his own analysis of more than a dozen genetic markers on a variety of chromosomes and from archaeological data showing habitation of Japan dating back 30,000 years, Nei argued that the Jomon actually came from northeastern Asia and settled in Japan far earlier than supporters of the Southeast Asia theory had proposed.

While the YAP data do not appear to support the transformation theory favored by Nei, they may bolster Nei’s vision of the Jomon’s origin, says Hammer. He and his colleagues surveyed more than 1,000 men from 20 populations in Southeast Asia. “We didn’t find a single example of a YAP-positive chromosome”, says Hammer.

In contrast, a survey of 700 men from 13 northern Asian populations did reveal areas with YAP-positive chromosomes.

About 3 percent of men from southwestern Siberia and Mongolia have the marker. The most spectacular finding was that more than 50 percent of men from Tibet harbor the YAP element.

While Tibet is part of central Asia, Nei suggests that the YAP data support his theory that the Jomon originated in the northeast. Other researchers have concluded that the Tibetans arrived in their current homeland only several thousand years ago, after a migration from northeast Asia, Nei points out.

The new Y chromosome research by Hammer and Horai is unlikely to settle the century-old debate about the origin of the Jomon and their genetic contribution to modern Japanese, caution researchers following the issue.

“You may get a different story when you look at the Y chromosome than when you look at mitochondrial DNA or when you look at other nuclear genes,” warns Brace, who adds that any genetic data must also be reconciled with traditional archaeological evidence. “They all have to mesh to tell a complete story.”

Courtesy of National Science Museum at Ueno/Shinjuku

[Former] mainstream hypothesis of migrations into the Japanese islands from Siberia and Korea. Red=Jomon/Ainu (native islanders), Yellow=Yayoi (korean/chinese)

Predicted distribution of Ainu/Jomon Japanese. The red stands for the Ainu ethnicity in modern japanese in molecular levels, and the yellow indicates the yayoi japanese.

Most recently, the latest writings indicate that the consensus is now that YAP’s origin is in West Africa (Nigeria), with a founding derivative clade in the ancestors of the Shiya Muslims who made their way to South Asia (India), Central Asia and eventually to Japan. The sources below refer:

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 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.”

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.

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

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)

ABSTRACT The blood samples of 66 Ahmadiyya Muslim males from Qadian, district Gurdaspur of Punjab have been analysed to study the Y-chromosome Alu insertion polymorphism (YAP). Y-chromosomes carrying the YAP element
were found in many populations in India and Pakistan. However, the absence of YAP insertion element in the present Ahmadiyya population has suggested that this isolated population is not likely to have been affected by many
migrations in Indian history.

“…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. It is an effort to identify their geographic affinity with their Pakistani counterparts.

… 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).

The absence of YAP insertion element in present Ahmadiyya Muslim isolate validates that there is no paternal lineages connection with Pakistani Muslims, which are reported in the literature with some instances of positive insertion
(Qamar et al. 1999; Hammer et al. 1997). 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). It also appears that Ahmadiyya Muslims have not been affected by many migrations to Indian subcontinent. 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. Saha et al. (2005) also screened five regional populations groups of India from Punjab, Uttar Pradesh, Bihar,
West Bengal and South India for the YAP polymorphism but could not find this
polymorphism in any of the population group.
The present study like many earlier studies failed to find any polymorphism of YAP insertion in the Ahmaddiya Muslims…”

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.

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:10.1186/1741-7007-6-45PMC 2605740PMID 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 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.

Our previous studies showed that the dominant and East Asian specific Y haplogroup O-M175 (44.3% on average) reflected possibly the earliest modern human expansion in East Asia [8,9,13]. Unlike the prevalence of O-M175 in most of the East Asian populations, populations with relatively high frequencies of D-M174 are mostly located at the peripheral regions of mainland East Asia with fragmented distribution [7,9-11,13-18], implying two possible explanations of human prehistory. Firstly, like O-M175, D-M174 may also be just one of the lineages going northward during the suggested Paleolithic migration of modern humans in East Asia [8,9]. Subsequently, due to population substructure (the last glacial is likely a key factor) and recent expansion of Han culture [18], the distribution of D-M174 was fragmented into the current geographic pattern. The other possible scenario would suggest an independent earlier migration different from the one we proposed previously [8,9]. To address this question, we conducted a systematic sampling and genetic analysis of more than 5,000 male individuals from 73 East Asian and Southeast Asian populations. Based on the Y chromosome SNP and STR data and the estimated ages of the major D-M174 lineages, we proposed that there was an independent Paleolithic northward migration of modern humans in East Asia, predating the previously suggested northward population movement.

the antiquity of D-M174 likely reflects the true prehistory of human populations in East Asia. The age estimation model developed by Zhivotovsky (2001) is not sensitive to effective population size and recent population expansion though the effect of population substructure cannot be totally ruled out. The antiquity of D-M174 was also supported by a previous study in which the origin of D-M174 was estimated more than 50,000 years ago [5].

The divergence time of haplogroup D is about 60,000 years ago, considering the wide though fragmented geographic distribution of D-M174, the proposed Paleolithic migration would be the first northward population movement of modern humans after their initial settlement in southern East Asia. As the last glacial occurred during 80,000–10,000 years ago, the northward migration of D-M174 is consistent with the proposed notion that modern humans might exploit the food of “Mammoth Steppe” [39]. Besides the later population expansion, the cold weather during the last glacial may also contribute to the current fragmented distribution of D-M174. Interestingly, a recent archaeological finding supported that modern humans explored the Tibetan plateau about 30,000–40,000 years ago, which is much earlier than previously suggested [40], but consistent with our hypothesis. The after-glacial sea level rise eventually led to the separation between Japan and the main continent, which explains the relic distribution of D-M174 in current Japanese populations. The archaeological data suggested that the initial colonization of modern humans in Japan occurred about 30,000 years ago [41,42], consistent with our age estimation of D2-M57 (37,678 ± 2,216 years ago). Taken together, the current Tibetan and Japanese populations are probably the admixture of two ancient populations represented by D-M174 and O3-M122 respectively…

Conclusion: In summary, we demonstrated an ancient Paleolithic population migration in East Asia, predating the previously suggested northward population movement. The current fragmented distribution of D-M174 is likely due to the combination of later Neolithic population expansion and the last glacial.”

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 1715891PMID 9311756.

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.

DNA-101 based on Deep Ancestry the Genographic Project by Spencer Wells

The Y Alu Polymorphism or YAP for short, is characterized by a mutational event known as Aluinsertion, 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.  The other, Haplogroup E is found primarily in Africa and the Mediterranean and is defined by marker M96.

The geographic polymorphisms of Y chromosome at YAP locus among 25 ethnic groups in Yunnan, ChinaSci China C Life Sci. 2003 Apr;46(2):135-40. by Shi H et al.

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.Sci China C Life Sci. 2003 Apr;46(2):135-140.
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%). The other 15 populations are YAP-including Lahu (2 populations), Hani, Achang, Drung, Lisu, Sui, Bouyei, Va, Bulang, Deang, Man and Hui and Mongol of Yunnan and Bai of Hunan. The YAP+ frequencies varied among the different ethnic groups studied, and even different among the same ethnic group living in different geographic locations. 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

(See also Y-DNA of Qiangs and Hanis from Xue et al., “Male demography in East Asia: a north-south contrast in human population expansion times,” Genetics (2006) – full text here)

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

“Insertion/deletion polymorphism of YAP (DYS287), M96 and M120 polymorphisms in Bidayuh ethnic populations of Sarawak, Malaysia were analyzed in this study. Genomic DNA was extracted from 180 buccal samples and amplified by Hot-Start PCR method. The amplified PCR products were separated by using 2% agarose gel electrophoresis. 26 out of 180 samples (14.44%) have shown insertion (YAP+) polymorphism, while the rest of the samples (85.56%) have shown deletion (YAP-) polymorphism. M96 derived and ancestral allele reveal 102 (56.67%) and 78 (43.33%), respectively and 96 (53.33%), while for

M120 derived allele and 84 (46.67%) for M120 ancestral allele. This study has provided the information about the distribution of YAP, M96 and M120 polymorphisms in Bidayuh ethnic population of Sarawak.
This study has to be continued with more samples to determine the YAP polymorphism and also the biallelic markers in Bidayuh population.

The indigenous people make up about 50% of Sarawak population. Among the known groups and sub-groups are Iban, Bidayuh, Kenyah, Kelabit and Penan. Iban is the largest indigenous group in Sarawak, making up almost 38% of the state while Bidayuh make up about 10% of the state. The Bidayuh people are generally known as Land Dayak. They can be found mainly in Lundu and Bau area. The 11 related sub-groups of Bidayuh are Bekati, Binyadu, Jongkang, Ribun, Salako…

The YAP+ was successfully amplified as a 450 bp amplicon (Figure 1). The frequency of YAP+ and YAPpolymorphism in 180 Bidayuh ethnics are  summarized in Table 3. Out of the 180 subjects, 14.44% of subjects show YAP+ while 85.56% of subjects are having YAP polymorphism.

This percentage indicates that there is lack of YAP insertion polymorphism in Bidayuh ethnic of Sarawak population. An extensive study of YAP insertion/deletion polymorphism in European, African, Asian and Oceanian populations was carried out by Hammer (1994). He found that the frequency of YAP insertion polymorphism (YAP+) was significantly high in the African populations, followed by the Europeans, Oceanians and lastly, Asians with exception to the Japanese population. Another study done by Hammer
and Horai (1995) observed that in Japanese population, 43% of Japanese subjects have YAP+ polymorphism, the highest frequency ever discovered in Asian population among Ahmadiyya Muslim males from Qadian, district
Gurdaspur of Punjab (Badaruddoza et al., 2008) YAP+ insertion was not found. In all Middle Eastern Muslim populations the frequency of YAP insertion is found to be in the range of 11 to 25% but none of the north Indian and South Indian populations had this insertion (Deka et al., 1996; Al-Zahery et al., 2003). The result obtained from the study on Bidayuh subjects is consistent with the study done by Hammer (1994) and Badaruddoza et al. (2008) which concluded that most Asian populations lack the YAP+ with the exception of the Japanese population.

This may be due to the fact that 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). Silva et al. (2007) has studied the Y-chromosome genetic variation in 127 male subjects from Rio de Janeiro of Brazilian populations. This study has utilized 28 Y chromosome-specific biallelic markers including M96. They found that the frequency of M96 in Rio de Janeiro population was at 0.018 (N = 112) after removing all chromosomes of Sub-saharan Africa or Amerindian origin. Like M96, M120 biallelic polymorphism is a novel Yspecific biallelic marker characterized by single base substitution from T to C (T > C). From the result, 53.33% of Bidayuh subjects show the ancestral allele, while 46.67% have derived allele. M120 biallelic polymorphism originated in Asia and represent recent founder paternal Native American radiation into the Americas. Sharma et al. (2007) has studied the Y-specific biallelic markers in Indian population including the M120. 630 samples belonging to different regions of India were screened for M120 polymorphism, only one individual was found to have M120 polymorphism, representing Q1 lineage.”

Lara, Sanggau, Sara, Tringgus, Semandang and Ahe.

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