<%@LANGUAGE="JAVASCRIPT" CODEPAGE="65001"%> Haplogroup D (Y-DNA)

Excerpts from Wikipedia.org

Haplogroup D (M174) is a Y-chromosome haplogroup. Both D and E lineages also exhibit the single-nucleotide polymorphism M168 which is present in all Y-chromosome haplogroups except A and B, as well as the YAP unique-event polymorphism, which is unique to Haplogroup DE.

Origins: Haplogroup D is believed to have originated in Asia some 60,000 years before present. While haplogroup D along with haplogroup E contains the distinctive YAP polymorphism (which indicates their common ancestry), no haplogroup D chromosomes have been found anywhere outside of Asia.

Overview: Like haplogroup C, D is believed to represent the Great Coastal Migration along southern Asia, from Arabia to Southeast Asia and thence northward to populate East Asia. It is found today at high frequency among populations in Tibet, the Japanese Archipelago, and the Andaman Islands, though curiously not in India. The Ainu of Japan and the Jarawa and Onge of the Andaman Islands are notable for possessing almost exclusively Haplogroup D chromosomes, although Haplogroup C3 chromosomes also have been found in 15% (3/20) of sampled Ainu males. Haplogroup D chromosomes are also found at low to moderate frequencies among populations of Central Asia and northern East Asia as well as the Han and Miao-Yao peoples of China and among several minority populations of Sichuan and Yunnan that speak Tibeto-Burman languages and reside in close proximity to the Tibetans.

Unlike haplogroup C, Hg D did not travel from Asia to the New World; it is found in no modern Native American (North, Central or South) populations. There is the possibility it traveled to the New World, like Hg C, but those lineages died out.

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

The Haplogroup D Y-chromosomes that are found among populations of the Japanese Archipelago are particularly distinctive, bearing a complex of at least five individual mutations along an internal branch of the Haplogroup D phylogeny, thus distinguishing them clearly from the Haplogroup D chromosomes that are found among the Tibetans and Andaman Islanders and providing evidence that Y-chromosome Haplogroup D2 was the modal haplogroup in the ancestral population that developed the prehistoric Jōmon culture in the Japanese islands.

Subclades: This phylogenetic tree of haplogroup D subclades is based on the ISOGG 2011 tree.

Distribution

D*: This paragroup is found with high frequency among Andaman Islanders and 0%-65% in Northeast Indian tribes. D-M174(xD1-M15, D2-P37, D3a-P47) has been found in approximately 5% of Altayans. Kharkov et al. have found haplogroup D-M174(xD1-M15) in 6.3% (6/96) of a pool of samples of Southern Altaians from three different localities, particularly in Kulada (5/46 = 10.9%) and Kosh-Agach (1/7 = 14%), though they have not tested for any marker of the subclade D2 or D3. Kharkov et al. also have reported finding haplogroup DE-M1(xD-M174) Y-DNA in one Southern Altaian individual from Beshpeltir (1/43 = 2.3%).

D1 (M15): Found frequently among Tibeto-Burman populations of Southwestern China (including approximately 23% of Qiang, approximately 12.5% of Tibetans, and approximately 9% of Yi) and Hmong-Mien speakers in Guangxi-Guizhou boundary regions with a moderate distribution throughout Central Asia, East Asia, and Southeast Asia (Vietnam).

D2 (M55): Found with high frequency among Ainu, Japanese, and Ryukyuans.

D3a (P47): Found with high frequency among Pumi, Naxi, and Tibetans, with a moderate distribution in Central Asia.

 

 

* Y Chromosome Diversity, Human Expansion, Drift, and Cultural Evolution by Jacques Chiaronia, et al.

Y Chromosome Haplogroup D Geographic Frequency Distribution Map

 

 

Andamanese People

The Andamanese people are the various aboriginal inhabitants of the Andaman Islands, which is the northern district of the Andaman and Nicobar Islands union territory of India, located in the southeastern part of the Bay of Bengal. They include the Great Andamanese, Jarawa, Onge, Sentinelese, and the extinct Jangil. Anthropologically, they are usually classified as Negritos (sometimes also called Proto-Australoids), represented also by the Semang of Malaysia and the Aeta of the Philippines. Their ancestors are thought to have arrived in the islands 60,000 years ago from coastal India (or crossed over a land bridge from Burma during a glacial period) as part of the first human peopling of India and Southeast Asia, in the initial Great Coastal Migration on what is now the Continental shelf of the northern Indian Ocean that was the first expansion of humanity Out of Africa that began 60,000 years ago. With very little contact with external societies or each other for nearly all this period the tribes have mutually unintelligible languages. This comparatively long-lasting isolation and separation from external influences is unequaled, except perhaps by the aboriginal inhabitants of Tasmania.

Genetic Legacy: The Andamans are theorized to be a part of the great coastal migration of humans from Africa along the coastal regions of the Indian mainland and towards Southeast Asia, Japan and Oceania.

The Andamanese belong to the broad Y-chromosome lineage designated as M130 (haplogroup C) by Spencer Wells, who leads the Genographic Project. This is the lineage that seems to have emigrated from East Africa at least 50,000 years ago along the south coast of Asia eastwards to Australia. Within this lineage, the Andamanese (Onges and Jarawas) belong almost exclusively to the subtype designated Haplotype D, which is also common in Tibet and Japan, but rare on the Indian mainland. However, this is a subclade of the D haplogroup which has not been seen outside of the Andamans, marking the insularity of these tribes. The only other group that is known to predominantly belong to haplogroup D are the Ainu aboriginal people of Japan. Male Great Andamanese, on the other hand, have a mixed presence of Y-chromosome haplogroups O, L, K and P, which places them between mainland Indian and Asian populations.

The results concerning nuclear DNA stress the uniqueness of the Andamanese people. First, they show a very small genetic variation, which is indicative of populations that have experienced a population bottleneck and then developed in isolation for a long period. Second, an allele has been discovered among the Jarawas which is found nowhere else in the world. Third, they present no specific affinity to any other population in the world. This has led some geneticists to conclude that the Andamanese "seem to have remained in isolation for a much longer period than any known ancient population of the world." A likely causal explanation for their uniqueness is that the Andamanese are the surviving descendants of early human migrants from Africa who remained genetically isolated in their habitat in the Andaman Islands since their arrival. This is in contrast to the neighboring Nicobarese, who are believed to mostly descend from more recent immigrants from mainland Asia.

Some anthropologists postulate that Southern India and Southeast Asia was once populated largely by Negritos similar to those of the Andamans, and that some tribal populations in the south of India, such as the Irulas are remnants of that period. A 2009 genetic study of Indian populations that traced most South Asian ethnicities to genomic contributions from two original founding populations also found that, of all modern-day Indians, only the Andamanese possess Ancestral South Indian lineage without admixture of any Ancestral North Indian genetic heritage.

 

 

Andaman and Nicobar Islands

 

 

* YAP Insertion Signature in South Asia by Chandrasekar A, et al.

Abstract: 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.

 

 

Ainu People

The Ainu are indigenous people or groups in Japan and Russia. Historically they spoke the Ainu language and related varieties and lived in Hokkaidō, the Kuril Islands, and much of Sakhalin. Most of those who identify themselves as Ainu still live in this same region, though the exact number of living Ainu is unknown. This is due to ethnic issues in Japan resulting in those with Ainu backgrounds hiding their identities and confusion over mixed heritages. In Japan, because of intermarriage over many years with Japanese, the concept of a pure Ainu ethnic group is no longer feasible. Official estimates of the population are of around 25,000, while the unofficial number is upward of 200,000 people.

Origins: The origins of the Ainu have often been considered Jōmon-jin, natives to Japan from the Jōmon period. "The Ainu lived in this place a hundred thousand years before the Children of the Sun came" is told in one of their Yukar Upopo (Ainu legends).

Ainu culture as it is known today dates from around the year 1200 and recent research suggests that it originated in a merger of the Okhotsk and Satsumon cultures, one of the ancient Japanese cultures. Their economy was based on farming as well as hunting, fishing and gathering.

Full-blooded Ainu are lighter skinned than their Japanese neighbors and have more body hair. Many early investigators proposed a Caucasian ancestry, although recent DNA tests have not shown any genetic similarity with modern caucasian Europeans.

Genetic testing of the Ainu people has shown them to belong mainly to Y-haplogroup D2. Y-DNA haplogroup D2 is found frequently throughout the Japanese Archipelago including Okinawa. The only places outside of Japan in which Y-haplogroup D is common are Tibet and the Andaman Islands in the Indian Ocean.

In a study by Tajima et al. (2004), two out of a sample of sixteen (or 12.5%) Ainu men have been found to belong to Haplogroup C3, which is the most common Y-chromosome haplogroup among the indigenous populations of the Russian Far East and Mongolia. Hammer et al. (2006) have tested a sample of four Ainu men and have found that one of them belongs to haplogroup C3. Some researchers have speculated that this minority of Haplogroup C3 carriers among the Ainu may reflect a certain degree of unidirectional genetic influence from the Nivkhs, a traditionally nomadic people of northern Sakhalin Island and the adjacent mainland, with whom the Ainu have long-standing cultural interactions.

A recent reevaluation of cranial traits suggests that the Ainu resemble the Okhotsk more than they do the Jōmon. This agrees with the reference to the Ainu culture being a merger of Okhotsk and Satsumon cultures referenced above.

Some have speculated that the Ainu may be descendants of a prehistoric group of humans that also produced indigenous Australian peoples. In Steve Olson's book Mapping Human History, page 133, he describes the discovery of fossils dating back 10,000 years, representing the remains of the Jōmon, a group whose facial features more closely resemble those of the indigenous peoples of New Guinea and Australia.

After a new wave of immigration, probably from the Korean Peninsula some 2,300 years ago, of the Yayoi people, the Jōmon were pushed into northern Japan. Genetic data suggest that modern Japanese are descended from both the Yayoi and the Jōmon.

 

 

Evolution of Skin Color

Rogers et al. (2004) performed an examination of the variation in MC1R nucleotide sequences for people of different ancestry and compared the sequences for chimpanzees and humans from various regions of the Earth. Rogers concluded that roughly five million years ago, at the time of the evolutionary separation of chimpanzees and humans, the common ancestors of all humans had light skin that was covered by dark hair. Over time the hair disappeared to allow better heat dissipation through sweating and the skin tone grew darker to protect from folate depletion to the increased exposure to sunlight. By 1.2 million years ago, shortly after the final speciation of homo sapiens from homo ergaster, the ancestors of all people living today had exactly the same receptor protein as modern Africans. Evolutionary pressure meant that any gene variations that resulted in lighter skin were unable to survive under the intense African sun, and human skin remained dark for the next 1.1 million years.

Approximately 70,000–100,000 years ago modern humans began to migrate away from the tropics to the north where they were exposed to less intense sunlight, possibly in part due to the need for greater use of clothing to protect against the colder climate. Under these conditions there was less photodestruction of folate and so the evolutionary pressure stopping lighter-skinned gene variants from surviving was reduced. In addition, lighter skin is able to generate more vitamin D (cholecalciferol) than darker skin so would have represented a health benefit in reduced sunlight if there were limited sources of vitamin D. Hence the leading hypothesis for the evolution of human skin color proposes that:-

  1. From ~1.2 million years ago to less than 100,000 years ago, the ancestors of all people alive were as dark as modern Africans.
  2. As populations began to migrate, the evolutionary constraint keeping skin dark decreased proportionally to the distance North a population migrated, resulting in a range of skin tones within northern populations.
  3. At some point northern populations experienced positive selection for lighter skin due to the increased production of vitamin D from sunlight and the genes for darker skin disappeared from these populations.

The genetic mutations leading to light skin, though different among East Asians and Europeans, suggest the two groups experienced a similar selective pressure due to settlement in northern latitudes.

There is a long-standing hypothesis that the selection for lighter skin due to higher vitamin D absorption occurred soon after the Out of Africa migration sometime before 40,000 years ago. A number of researchers disagree with this and suggest that the northern latitudes permitted enough synthesis of vitamin D combined with food sources from hunting to keep populations healthy, and only when agriculture was adopted was there a need for lighter skin to maximize the synthesis of vitamin D. The theory suggests that the reduction of game meat, fish, and some plants from the diet resulted in skin turning white many thousands of years after settlement in Europe and Asia. This theory is supported by a study into the SLC24A5 gene which found that the allelle associated with light skin in Europe may have originated as recently as 6,000–10,000 years ago which is in line with the earliest evidence of farming.

 

 

* Y Chromosome Evidence of Earliest Modern Human Settlement in East Asia and Multiple Origins of Tibetan and Japanese Populations by Hong Shi, et al.

Abstract

Background: The phylogeography of the Y chromosome in Asia previously suggested that modern humans of African origin initially settled in mainland southern East Asia, and about 25,000– 30,000 years ago, migrated northward, spreading throughout East Asia. However, the fragmented distribution of one East Asian specific Y chromosome lineage (D-M174), which is found at high frequencies only in Tibet, Japan and the Andaman Islands, is inconsistent with this scenario.

Results: In this study, we collected more than 5,000 male samples from 73 East Asian populations and reconstructed the phylogeography of the D-M174 lineage. Our results suggest that D-M174 represents an extremely ancient lineage of modern humans in East Asia, and a deep divergence was observed between northern and southern populations.

Conclusion: We proposed 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 Sub-Haplogroup/Haplotype Distribution of D-M174 in Eastern Asia

 

 

* Dual Origins of the Japanese: Common ground for hunter-gatherer and farmer Y chromosomes by Michael F. Hammer, et al.

Abstract: Historic Japanese culture evolved from at least two distinct migrations that originated on the Asian
continent. Hunter-gatherers arrived before land bridges were submerged after the last glacial maximum (>12,000 years ago) and gave rise to the Jomon culture, and the Yayoi migration brought wet rice agriculture
from Korea beginning 2,300 years ago. A set of 81 Y chromosome single nucleotide polymorphisms (SNPs) was used to trace the origins of Paleolithic and Neolithic components of the Japanese paternal gene pool, and to determine the relative contribution of Jomon and Yayoi Y chromosome lineages to modern Japanese. Our global sample consisted of >2,500 males from 39 Asian populations, including six populations sampled from across the Japanese archipelago. Japanese populations were characterized by the presence of two major (D and O) and two minor (C and N) clades of Y chromosomes, each with several sub-lineages. Haplogroup D chromosomes were present at 34.7% and were distributed in a U-shaped pattern with the highest frequency in the northern Ainu and southern Ryukyuans. In contrast, haplogroup O lineages (51.8%) were distributed in an inverted U-shaped pattern with a maximum frequency on Kyushu. Coalescent analyses of Y chromosome short tandem repeat diversity indicated that haplogroups D and C began their expansions in Japan 20,000 and 12,000 years ago, respectively, while haplogroup O-47z began its expansion only 4,000 years ago. We infer that these patterns result from separate and distinct genetic contributions from both the Jomon and the Yayoi cultures to modern Japanese, with varying levels of admixture between these two populations across the archipelago. The results also support the hypothesis of a Central Asian origin of Jomonese ancestors, and a Southeast Asian origin of the ancestors of the Yayoi, contra previous models based on morphological and genetic evidence.

 

 

Ryukyu Islands

 

 

* Extended Y-Chromosome Investigation Suggests Post-Glacial Migrations of Modern Humans into East Asia Via the Northern Route by Hua Zhong, et al.

Abstract: Genetic diversity data, from Y chromosome and mitochondrial DNA as well as recent genome-wide autosomal SNPs, suggested that mainland Southeast Asia was the major geographic source of East Asian populations. However, these studies also detected Central-South Asia- and/or West Eurasia-related genetic components in East Asia, implying either recent population admixture or ancient migrations via the proposed northern route. To trace the time period and geographic source of these Central-South Asia- and West Eurasia-related genetic components, we sampled 3,826 males (116 populations from China and one population from South Korea) and performed high-resolution genotyping according to the well-resolved Y-chromosome phylogeny. Our data, in combination with the published East Asian Y-haplogroup data, show that there are four dominant haplogroups (accounting for 92.87% of the East Asian Y chromosomes), O-M175, D-M174, C-M130 (not including C5-M356) and N-M231, in both southern and northern East Asian populations, which is consistent with the proposed southern route of modern human origin in East Asia. However, there are other haplogroups (6.79% in total) (E-SRY4064, C5-M356, G-M201, H-M69, I-M170, J-P209, L-M20, Q-M242, R-M207 and T-M70) detected primarily in northern East Asian populations, and were identified as Central-South Asian and/or West Eurasian origin based on the phylogeographic analysis. In particular, evidence of geographic distribution and Y-STR diversity indicate that haplogroup Q-M242 (the ancestral haplogroup of the native American-specific haplogroup Q1a3a-M3) and R-M207 probably migrated into East Asia via the northern route. The age estimation of Y-STR variation within haplogroups suggests the existence of post-Glacial (∼18 thousand years ago, kya) migrations via the northern route as well as recent (∼3 kya) population admixture. We propose that although the Paleolithic migrations via the southern route played a major role in modern human settlement in East Asia, there are ancient contributions, though limited, from western Eurasia which partly explain the genetic divergence between current southern and northern East Asian populations.

 

 

Coastal Migration

Coastal Migration is a term sometimes used in modern anthropology and genetics for the concept that, from a single origin in Africa 100-200 thousand years before present (kybp), humanity first spread eastwards to areas outside Africa along routes that were predominantly located around coastlines. Other terms, such as Southern Coastal Route, Rapid Coastal Settlement, Coastal Migration Theory and Coastal Migration Model, are also used.

Coastal migration theory in Asia and Oceania: The coastal route is primarily used to describe the initial that peopling of the Arabian peninsula, India, Southeast Asia, New Guinea, Australia, coastal China and Japan, and is linked with the presence and dispersal of mtDNA haplogroup M and haplogroup N, as well as the specific distribution patterns of Y-DNA haplogroup C and haplogroup D, in these regions. The theory proposes that humans, likely similar to the Negritos or Proto-Australoids of modern times, arrived in the Arabian peninsula from Africa, then on the southern coastal regions of the Indian mainland, followed by spread to the Andaman Islands and modern-day Indonesia, and thence branching southwards to Australia and northwards towards Japan. National Geographic's Genographic Project uses the term 'Coastal Clan' to describe the initial human groups of Y-DNA haplogroup C who expanded eastwards out from Africa along the coastal route around 50 kybp.

Roger Blench discusses the theory in relation to language families.

 

 

Negrito

The Negrito are a class of several ethnic groups that inhabit isolated parts of Southeast Asia.

Their current populations include 12 Andamanese tribes of the Andaman Islands, six Semang tribes of Malaysia, the Mani of Thailand, and the Aeta, Agta, Ati, and 30 other tribes of the Philippines. Reports from British traders also speak of negrito tribes on Borneo (Sarawak). (Journal of the Malayan Branch Royal Asiatic Society, Vol. XXIX, part 1, 1956)

Negritos share some common physical features with African pygmy populations, including short stature, natural afro-hair texture, and dark skin; however, their origin and the route of their migration to Asia is still a matter of great speculation. They are the most genetically distant human population from Africans at most loci studied thus far (except for MC1R, which codes for dark skin).

They have also been shown to have separated early from Asians, suggesting that they are either surviving descendants of settlers from an early migration out of Africa, commonly referred to as the Proto-Australoids, or that they are descendants of one of the founder populations of modern humans.

Historical Distribution: Negritos may have also possibly lived in Taiwan, where they were called the "Little Black People". Apart from being short-statured, they were also said to be broad-nosed and dark-skinned with curly hair. The little black population shrank to the point up to 100 years ago only one small group lived near the Saisiyat tribe. A festival celebrated by the Saisiyat gives evidence to their formal habitation of Taiwan. The Saisiyat tribe celebrate the black people in a festival called Ritual of the Little Black People (矮靈祭).

After the negritos on Taiwan, thousands of years before any Han came to Taiwan in 1600, the Aboriginal Austronesians moved into Taiwan. Estimates of their arrival date from 6,000-1,000 years ago from the Malay Archipelago, although it is controversial. Chinese historians called them "black dwarfs" in the Three Kingdoms period (AD 220 to AD 280) and they were still to be found in China during the Qing dynasty (1644 to 1911). There are other stories about them in other aboriginals and some archeological sites are attributed to them.

According to James J.Y. Liu, a professor of comparative literature, the Chinese term Kun-lun (崑崙) means Negrito. There are many stories about them. Shandao, Geji (戈基), Juho, Wa and Koro-pok-guru peoples, are also said to be pygmies. Haplogroup D (Y-DNA) are found frequently among some peoples living in the same area. In China, stone coffins were used by these peoples.

 

 

Prehistory of Taiwan

Reconstruction of the Zhuojhen man

The prehistory of Taiwan includes the late Paleolithic era. During that time, roughly 50,000 BC to 10,000 BC, people were already living in Taiwan.

Evidence shows that the earliest archaeological culture found in Taiwan was the Changbin culture (長濱文化), this prehistoric site was found in Eastern Taiwan. Human skeletons were also found in Zuozhen, Tainan County (now part of Tainan City, therefore called the Zuojhen people (左鎮人). Yuanshan (圓山遺址) and other prehistoric sites were found in Taipei Basin. However, there isn't enough evidence to be sure which group of people left the artifacts.

Taiwan is the urheimat of the Austronesian languages. Archaeological evidence (e.g., Bellwood 1997) suggests that speakers of pre-Proto-Austronesian spread from the South Chinese mainland to Taiwan at some time around 8,000 years ago. Evidence from historical linguistics suggests that it is from this island that seafaring peoples migrated, perhaps in distinct waves separated by millennia, to the entire region encompassed by the Austronesian languages (Diamond 2000). It is believed that this migration began around 6,000 years ago (Blust 1999). However, evidence from historical linguistics cannot bridge the gap between those two periods.

 

 

* 臺灣原住民族的Y 染色體多樣性與華南史前文化的關連性 by 陳叔倬

D*: Taiwanese aborigines 0%, D1: Taiwanese aborigines 0%

 

 

* Recent Anthropological Genetic Study of Taiwan Indigenous Populations by Shu-Juo Chen, et al.

Map Showing the Locations of the Studied Populations

 

Y-Chromosome Haplotype Frequency Distribution in Asian and Oceanic Populations

H2 YAP DE*(xD1):Taiwanese aborigines 0%, Taiwan Han Chinese 0%
H3 M15 D1: Taiwanese aborigines 0%, Taiwan Han Chinese 4.3%

 

Markers in Su's Nomenclature System from A Nomenclature System for the Tree of Human Y-Chromosomal Binary Haplogroups by The Y Chromosome Consortium

 

 

* Y-DNA Haplogroups by Populations of East and Southeast Asia by wikipedia.org

D: Taiwan (Han) 0.3%, Taiwanese aborigines 0%

* Haplotype Frequencies of Nine Y-Chromosome STR Loci in the Taiwanese Han Population by Tsai LC, et al.
* A Predominantly Indigenous Paternal Heritage for the Austronesian-Speaking Peoples of Insular Southeast Asia and Oceania by Cristian Capelli, et al.

 

* Partial Duplication at AZFc on the Y Chromosome Is a Risk Factor for Impaired Spermatogenesis in Han Chinese in Taiwan by Yi-Wen Lin, et al.

The Y Chromosome Haplogroups of Han Taiwanese

(M145, M174 D: Han Taiwanese 0.3%)

 

 

* Genetic Evidence Supports Demic Diffusion of Han Culture by Bo Wen, et al.

NRY Haplogroup Distribution in Han Populations

D/E YAP: Fujian 2.7%
D1 M15: Fujian 0%
Population n C* D/E D1 F* K* O3* O3d O3e O1* O1b O2a* O2a1 Q1 P*
    M130 YAP M15 M89 M9 M122 M7 M134 M119 M110 M95 M88 M120 M45
Northern Han
                              
Gansu
60
7
5
  
6
10
11
  
11
5
   1  
3
1
Hebei
14
      
2
1
3
  
7
1
          
Henan
50
2
    
2
11
16
  
10
4
      
4
1
Liaoning
48
1
1
  
11
8
13
  
9
2
  
1
  
2
  
Neimeng
60
12
3
  
4
8
13
  
16
1
  
1
  
2
  
Shandong 1
85
14
1
2
3
12
36
  
12
    
1
  
4
  
Shandong 2
100
4
    
11
13
32
  
30
6
  
1
  
3
  
Shannxi 1
63
2
3
  
4
11
16
  
22
1
  
1
  
1
2
Shannxi 2
27
      
3
9
5
  
8
1
      
1
  
Xinjiang
51
2
1
  
3
9
15
  
15
2
      
2
2
Southern Han
                              
Anhui
22
3
      
4
6
  
4
4
      
1
  
148
4
1
  
3
21
80
6
24
3
1
4
  
1
  
Guangdong
64
3
  
1
  
8
15
  
19
5
  
7
5
1
  
Guangxi
26
2
      
4
4
  
5
4
  
2
5
    
Hubei
18
1
      
2
5
1
6
3
          
Hunan
15
        
2
5
  
4
2
  
2
      
Jiangsu
100
6
2
  
3
19
25
2
19
18
  
4
  
2
  
Jiangxi
21
1
1
  
2
4
4
  
5
3
  
1
      
Shanghai
55
4
2
    
9
14
1
9
14
      
2
  
Sichuan
63
3
  
1
  
10
16
2
18
5
  
6
2
    
Yunnan 1
27
3
    
1
1
5
  
15
1
  
1
      
Yunnan 2
66
4
  
2
2
15
25
4
10
    
2
  
2
  
Zhejiang
106
10
      
6
26
  
28
29
  
5
  
2
  

 

 

YAP Insertion

Most parsimonious phylogeny of YAP based on Underhill and Kivisild 2007 by Wapondaponda

The YAP insertion was discovered by scientists led by Michael Hammer of the University of Arizona. Between 1997 and 1998 Hammer published three articles relating to the origins of haplogroup DE. 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.

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. 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 considerable older than haplogroup E at 31kya, Hammer concluded that haplogroup E was a subclade of haplogroup D.

By 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.

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

  1. 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.
  2. 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 or autosomal 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 recent 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. However recent 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.

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. Haplogroup DE* has recently been found in Nigeria, Guinea-Bissau and also in Tibet. 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. 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.

Chandrasekhar et al. 2007, have 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 CF.

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. Other authors who have published or co-published works in support of an African origin the YAP+ include Luigi Luca Cavalli-Sforza, Toomas Kivisild, Spencer Wells, Linda Stone and Paul F. Lurquin.

Tree: This phylogenetic tree of para-haplogroup DE is based on the YCC 2008 tree and subsequent published research.

 

 

* The Eurasian Heartland: A continental perspective on Y-chromosome diversity by R. Spencer Wells, et al.

Geographic Distribution of Y-Chromosome Haplotypes in Selected Eurasian Populations

(YAP lineage)

 

 

Haplogroup D1

Haplogroup D1 (M15) is a Y-chromosome DNA haplogroup. Haplogroup D1 is a descendant branch of the greater Haplogroup D.

Its phylogenetically closest relatives are found among the peoples of Japan, Central Asia, and the Andaman Islands in the Bay of Bengal. It is more distantly related to the Haplogroup E, whose sub-clades are common throughout Africa, West Asia, and Europe.

Distribution: Haplogroup D1 is widely distributed throughout populations that dwell to the northwest, north, northeast, east, and southeast of the Himalaya. It is not found among the populations of India to the south and southwest. The distribution of Haplogroup D1 in Southeast Asia is also very limited, as it is found there only at low frequency and only among populations that speak Tibeto-Burman or Miao-Yao languages, which have ancestral ties to the north.

The distribution of Haplogroup D1 is much more regular in the north, as it is found among nearly all the populations of Central Asia and Northeast Asia south of the Russian border, although generally at a low frequency of 2% or less. A dramatic spike in the frequency of Haplogroup D1 occurs as one approaches the Qinghai-Tibetan Plateau of western China: among some local populations in Qinghai, it has been found to reach as high as 100%. Its frequency gradually fades as one travels south through the territory of the Tibetan peoples, as Haplogroup O3, which is the most common haplogroup among the Han Chinese and also generally found among Southeast Asian populations, becomes dominant. Haplogroup D1 continues to occur at an overall very low frequency among the Han people to the east; however, there are some indications that the frequency of D1 among the Hans may vary significantly between localities. A secondary, minor spike in the frequency of Haplogroup D1 occurs again in Korea, where it may reach as high as 5% to 8%; this somewhat heightened frequency does not stretch into Manchuria to the north or Japan to the east, which may corroborate historical accounts of immigration from the country of Qin in the far west of ancient China to the country of Jinhan, which is believed to have been located somewhere in the southern half of the Korean Peninsula. Ancient Chinese historians are known for their habit of drawing what often seem to be forced connections between contemporary peoples and putative ancestors of misty antiquity, and the comments about immigration from Qin to Jinhan might have been motivated by the similarity that the ancient central Chinese perceived between the languages of Qin and Jinhan. Nevertheless, on this occasion the genetic evidence seems to provide the story with some independent corroboration.

As for the ultimate origin of Haplogroup D1, one can only speculate that it might share a recent common ancestor with the Haplogroup D* (M174) Y-chromosomes that are found at a vanishingly low frequency among modern populations of Central Asia.

In regards to the ethnic affiliation of the original carriers of Haplogroup D1, it is notable that Haplogroup D1 Y-chromosomes have not been found to occur at all among many populations of Tibeto-Burman speakers, but Y-chromosomes belonging to the Haplogroup O3a5-M134 clade are commonly found among all Tibeto-Burman-speaking populations outside of Qinghai in addition to being the modal haplogroup among speakers of Sino-Tibetan languages in general, which suggests that the Haplogroup D1 Y-chromosomes found at high frequency among the populations of the Qinghai-Tibetan Plateau may reflect:

(1) A severe founder effect and/or genetic drift

(2) Descent from a Tibeticized Paleolithic substrate distantly related to modern populations of Central and/or Northeast Asia

(3) A massive incursion of foreign Y-chromosomes belonging to a now linguistically extinct tribe of ultimately Central Asian or Northeast Asian derivation, subsequent to the establishment of Sino-Tibetan-speaking Neolithic populations in the general area.