Asian Ancestry based on Studies of Y-DNA Variation: Part 3. Recent demographics and ancestry of the male East Asians – Empires and Dynasties
Learning Center» Paternal Ancestry (Y-DNA)» Y-DNA Haplogroups (SNPs)» Asian Ancestry based on Studies of Y-DNA Variation: Part 3. Recent demographics and ancestry of the male East Asians – Empires and Dynasties
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This article is Part 3 of a 3 part series.
Part 1.  Early origins – the emergence of modern humans in East Asia 
Part 2.  Additional migrations and reach.  Travels south to Oceania, north to the Americas and in between. 
Part 3.  Recent demographics and ancestry of the male East Asians – Empires and Dynasties  <<== You are here

There have been many relatively recent migration events that have created the present Y-chromosome landscape across East Asia.  Some of these episodes have strong correlations to the spread of agricultural practices while others can be linked to historical conquests and empire-building and both may have been the impetus in the spread of languages.  The most notable of the recent colonizations is the creation of the Mongol Empire by Genghis Khan.

Genghis Khan’s Legacy

Genghis Khan, born as Temujin, was a Mongolian ruler living in the 12th century (1162-1227 AD).  His rise to power initially came through the consolidation of warring nomadic tribes in NEAS and his tactics of incorporating defeated tribes into his expanding army and awarding military posts based on performance and loyalty, i.e. meritocracy, helped to sustain the growth of his empire.  By continued assimilation, the Mongol Empire eventually spread from the Caspian Sea to the Sea of Japan and is typically regarded as the largest single empire in human history (see Figure 18).  After his death, his brothers, sons and grandsons continued to expand and control territory in Asia.  His grandson, Kublai Khan, eventually conquered and united all of China in the Yuan Dynasty (1271-1368).

Figure 18.  Extent of the Mongol Empire around Genghis Khan’s death (1227).  Approximate routes of Marco Polo’s travels into East Asia (~1260) are marked in blue and national borders are marked in red.

The genetic legacy of Genghis Khan has received considerable attention.  The genetic signature of Genghis Khan was uncovered in a study of >32 Y STR markers in more than 2,000 men from Asia.  The results showed an unusual sharing of haplotypes by individuals spread over many populations and many regions.  The regions where these haplotypes were found overlapped closely with the Mongol Empire.  These related haplotypes formed a tightly-knit or ‘star cluster’ in the C*(xC3c) lineage (i.e SNP RPS4Y or M130 positive and M48 negative).  This ‘star cluster’ in the C*(xC3c) network contained haplotype 10-16-25-10-11-13-14-12-11-11-11-12-8-10-10 corresponding to loci DYS389I-DYS389b-DYS390-DYS391-DYS392-DYS393-DYS388-DYS425-DYS426-DYS434-DYS435-DYS436-DYS437-DYS438-DYS439.  This STR profile is thought to be carried by male-line descendants of Genghis Khan.  Testing of Hazaras who live in Pakistan and claim direct descent from Genghis Khan revealed a high frequency of the modal haplotype and 1-step relatives.  The origin date for the ancestor to this population is estimated to be 600-1,300 years ago and, therefore, matches well with the known dates for Genghis Khan’s exploits.  Similarly, the Kalmyks who are located to the west of the Volga River and Caspian Sea have a high percentage of haplotypes in the ‘star cluster’ (and a common ancestor dating ~900 years ago) and show the tremendous genetic reach of Mongolian Empire to the west. 

If we extrapolate the frequency (~8%) of the modal haplotype found in this sampling of Asian males, we would expect that ~16 million men currently share this Y-chromosome signature haplotype and may trace their ancestry to Genghis Khan.  While this indirect or circumstantial evidence does not tell us the actual haplogroup or haplotype of Genghis Khan or his family members, the evidence is consistent with the hypothesis that he was a grand patriarch of an extremely large population living in Asia today.   In fact this is largest male lineage so far ascribed to a common founder.  This proposal also has interest since it would be a clear example of positive selection of a genetic heritage based on social status rather than biological merits. 

Interestingly, the Mongolian Empire probably also paved the way for population and genetic mixing in Asia by unifying control and trade along the Silk Road.   For example, Marco Polo conducted his expeditions (c. 1255-95 AD) along Silk Road routes shortly after the death of Genghis Khan and helped to spur extensive trade with Europe.  For example, West China near the Silk Road (see Figure 2) has some affinity with Europe marked by the occurrence of Haplogroups L and P, although the region still retains high level of Haplogroups O and C. 

Haplogroup J, which is strongly associated with the Middle East and CAS, was found in Mongolian Khalkh, Zakhchin, Khoton tribes.  Haplogroup J is generally very low to absent among East Asian populations and its moderate presence in CAS is likely a recent contribution from Silk Road trade with Europe or a result of Muslim expansion along this same route.  The Khoton show further affinity with CAS, through the shared presence of R1a1.  The Khoton tribe is very small group found in the northwest of Mongolia and may be of Turkish origin – moving into Mongolia during the 17th century, although the TMRCA dating puts the origin of the R1a1 subclade in Mongolia at ~3kya.  The Khoton population displayed very low diversity of haplogroups and haplotypes and their low complexity can be best explained by a bottleneck event.  Haplogroup D was also found among the Mongolian ethnic tribes and is likely a remnant of more ancient population foundings.  These tribes may represent traces of Haplogroup D connections between Tibet and Japan.  Strong evidence has been found for a bottleneck produced during a northward migration of Yakuts from their origin near Lake Baikal in response to an expanding Mongolian Empire.  In response to this switch in geographic location, many Yakut populations have switched from horse to reindeer herding, though they have maintained their Yakut (Turkic) language amidst many Tungusic speaking Evenk populations.    
A word of caution should be spoken here regarding the occurrence of common haplotypes, such as that for the star cluster attributed to Genghis Khan. When a large number of STR loci are tested, the haplotype obtained can be predictive for ancient Y-chromosome ancestry of haplogroups, which are based on more slowly evolving SNP markers.  This is the case for the Genghis Khan star cluster haplotype and the C*(xC3c) haplogroup.  However, because haplotypes are rapidly-evolving signatures, they are not stable and not necessarily confined to a haplogroup.  The same haplotype or a very similar one might occur in another haplogroup lineage.   Such a mistake occurred in the recent pronouncement made that a university professor in the U.S. was a likely descendant of Genghis Khan after 7/9 STR sites matched the profile in the Genghis Khan star cluster.  However, additional results gained through SNP testing indicated that his Y-chromosome was not from the C*(xC3c) haplogroup and he did not in fact share this unique Asian ancestry.  In sum, it is always better to base conclusions about ancestry on as many STR and SNP markers as possible.   

The rise of the Manchu and the last dynasty of China

Another significant paternal legacy fostered during the Qing Dynasty (1644-1912) in East Asia was found through an analysis of Y-chromosome haplotypes very similar to that for the reported heritage of Genghis Khan.   As with the study of ‘star cluster’ haplotypes linked to Genghis Khan, the investigators noticed the unusual abundance of a haplotype shared among many distantly located populations.  This haplotype cluster in this case (the modal haplotype and two-step neighbors) falls within the C3c subclade (SNP M48), indicating a haplogroup lineage separate from the ‘star cluster’ of Genghis Khan, which is characterized by not being found in the C3c subclade (as in CxC3c notation).  This new cluster was designated the ‘Manchu cluster’, since the northeastern area of China and Mongolia have the highest concentration of this genetic lineage (see Figures 10 and 11 for C3c frequency), although it is not limited to this location and can be found in the Xibe of northwest China.  The ‘Manchu’ modal haplotype is 13-10-16-24-9-11-13-12-11-11-11-12-8-10-11 for the STR loci DYS388-DYS389I-DYS389b-DYS390-DYS391-DYS392-DYS393-DYS425-DYS426-DYS434-DYS435-DYS436-DYS437-DYS438-DYS439.

The date for the origin of the common ancestor to this lineage was estimated near 500 years ago and puts the theoretical patriarch in the historical context of the establishment of the Qing Dynasty.  Giocangga’s (c. ?-1582) grandson Nurhaci (1559-1612) is credited with founding the Qing Dynasty, which was characterized by a noble class made up of male descendants of Giocangga.  Nurhaci’s son, Hung Taiji, was to continue to rule the Qing Dynasty until his death in 1643.  This elite class system, known as the Eight Banners, was perpetuated over centuries of rule.  An estimate for the current number of descendants stemming from the grand patriarch Giocangga is on the order of 1 million.  Thus, another system of social prestige is linked to a remarkable expansion of particular male ancestry in East Asia. (see Figure 19 for the origin and spread of this dynasty). 

The Han culture and other recent perspectives on Asian Ancestry

Another historical scenario for Y-chromosome ancestry in Asia underwent scrutiny recently.  A study was conducted to determine if the Liqian in China carried ancestry from Roman mercenaries that purportedly arrived in this region after many years of travel once they had disbanded.  Haplogroup testing in Liqians indicated that 78% of the haplogroups were of East Asian origin, and most closely aligned with the Han Chinese and Mongols (71% O3, 7% C).  None of the haplogroups found were Roman or European-specific, although a low level of R1a1 (SNP M17) was found, which is prominent in East Europe and CAS, though it has a rather low frequency in Italy.  Haplogroups I, J and H, which are abundant in Europe, were not found.  Therefore the Liqian lacked any clear Y-chromosome ancestry from these remote populations and were deemed more likely to be related to the Han, who were contemporaries of the Romans.   

We have made a few mentions of the Han Chinese population, but have not discussed their ancestry directly. The Han are currently the single largest ethnic group in China today (92% of the population or about 1.2 billion people).  This also makes the Han the largest ethnic group in the world.  Their origin is suggested to arise from Huaxia tribes in north China near the Yellow River basin and their population has expanded considerably over last 2,000 years.  The Han are major carriers of the O3 subclade (O3 constitutes an average of 54% of Han Y-chromosomes).  From their point of origin in the north, they generally spread into other populations in the south; in many cases out-pacing the expansion of indigenous populations and supplanting them. (see Figure 19)  For example, the Zhuang, which are the second largest Chinese ethnic group after the Han, are found in the South next to the border with Vietnam.  The aboriginal Zhuang are thought to be related to the Baiyue, and carry the O* and O2a Y-chromosomes, but a significant fraction of O3 (~20%) is also found in the current population and it is likely that this is a contribution from Han migrations.  Likewise, the O2 subclades are only found in southern Han and not northern Han.  Parallel findings have been obtained with the O1 lineage that is generally limited to SEAS.   Thus, there has been mixing between southern Han and ethnic southern populations – in effect creating a third population (and admixture) that has dual ancestry.  Comparison to maternal ancestry (studies of mtDNA haplogroups) has also shown that Han males contributed to a larger extent than females in the migration south and admixture with native populations.  

Figure 19.  Proposed recent migrations of male H. s. sapiens populations through East Asia.  The map displays probable routes of migrations for modern humans across China, generally in the north to south direction.  Color-coding is used to delineate Y-chromosome haplogroup subclade lineages.  Note that this is a general model and many detailed migration routes have been omitted for clarity. 

A very similar story of admixture between north and south has been revealed by studies of Tibeto-Burman populations.  Tibetans and the Tibeto-Burman language originate with the Di-Qiang around the Upper Yellow River in northwest China.  The migration of the populations and language moved southward along the Tibeto-Burman (Zang-Mien) corridor ~2600ya.  They came to occupy territory covered by Hmong-Mien, Daic and Austro-Asiatic languages.  The Tibeto-Burman populations were rather rich in the O3 haplogroup and these populations like the Han, helped to spread their genetic heritage south and helped to create some similarity between NEAS and SEAS.  The Hmong-Mien have also contributed to some gene flow further into the south.  This population prominently carries the O3 subclade, O3a3b (SNP M7).  

Thus, the early expansions of SEAS populations into the north were countered by later NEAS (Han and Tibeto-Burmans) populations migrations into the south.  Indeed, a recent study aimed at examining the north-south division (or any spatial genetic differentiation) in detail has shown that such a boundary is difficult to detect when examining paternal ancestry in China.  Therefore, the different trajectories of modern humans across East Asia throughout time have made this region of the world a complex genetic mixture with no simple patterns. 

In our discussion of male Asian Ancestry, express train models have been contrasted with slow boats and vast empires have emerged next to small, nomadic hunter-gatherer tribes.  While this study of Y-chromosome variation has informed many current hypotheses for the dispersal of males across Asia, the inclusion of additional genetic tools (mtDNA and autosomal inheritance patterns) and findings from other disciplines such as linguistics, paleogeography and ethnobotany will continue to reveal secrets of Asian Ancestry.  Indeed, the discovery human ancestry in East Asia seems to unfold in layers as a Chinese Box or a Russian Matryoshka doll - themselves modeled after dolls representing the Japanese Seven Gods of Fortune.  We are still discovering many of the steps taken in the journeys of our ancestors.    


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Asian Ancestry based on Studies of Y-DNA Variation: Part 3. Recent demographics and ancestry of the male East Asians – Empires and Dynasties. Genebase Tutorials. Retrieved November 22, 2014, from
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