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In human genetics, Haplogroup C3 (M217, P44) is a Y-chromosome DNA haplogroup mainly found in indigenous Mongolians. Haplogroup C3 is the most widespread and frequently occurring branch of the greater Haplogroup C (M130). One particular haplotype within Haplogroup C3 has received a great deal of attention for the possibility that it may represent direct patrilineal descent from Genghis Khan.

Haplogroup C3 is believed to have originated approximately 20,000 years before present in eastern or central Asia. Its closest phylogenetic relatives are found in the general vicinity of South Asia, East Asia, or Oceania. First, Haplogroup C1 has a relictual distribution in Japan, which suggests an origin in the Jōmon people of the prehistoric Japanese Archipelago. Second, Haplogroup C2 appears to have expanded throughout East Indonesia, Melanesia, Micronesia, and Polynesia after the hybridization of Austronesian colonists, ultimately from the Asian mainland, with pre-existing Melanesians. Third, Haplogroup C4 is the predominant male lineage among the indigenous Australians. Finally, Haplogroup C5 is found at an extremely low frequency in South Asia. Haplogroup C* Y-chromosomes, which do not belong to any of the five identified subclades of Haplogroup C, are found at low frequency in Central Asia, South Asia, Southeast Asia, East Asia, and Oceania.

Haplogroup C3 is the modal haplogroup among Mongolians and most indigenous populations of the Russian Far East, such as the Northern Tungusic peoples, Koryaks, and Nivkhs. The subclade C3b-P39 is quite common among males of the indigenous North American peoples whose languages belong to the Na-Dené phylum. The frequency of Haplogroup C3 tends to be negatively correlated with distance from Mongolia and the Russian Far East, but it still comprises more than ten percent of the total Y-chromosome diversity among the Manchus, Koreans, Ainu, and some Turkic peoples of Central Asia although in a genetic study in 2004, haplogroup C3 was more frequent among Koreans than previously thought. Among the Kazakhs, who are a Turkic people of Kazakhstan and neighboring areas in northern Central Asia, Haplogroup C3 once again emerges as the most common haplogroup. Beyond this range of high-to-moderate frequency, which contains mainly the northeast quadrant of Eurasia and the northwest quadrant of North America, Haplogroup C3 continues to be found at low frequencies, and it has even been found as far afield as Northwest Europe, Turkey, Pakistan, Vietnam, the Malay Archipelago, and some aboriginal populations of Colombia and Venezuela. The marginally low frequency of Haplogroup C3 among the Japanese, a mere 2% or 3% (which is lower than the frequency among some regional subgroups of Germans), and its complete absence from the closely related Ryūkyūan population, is another indication of the rather extreme genetic isolation that has shaped the population of the Japanese Archipelago, as Haplogroup C3 is the most frequently occurring haplogroup among the indigenous populations of the neighboring Northeast Asian mainland.

The extremely broad distribution of Haplogroup C3 Y-chromosomes, coupled with the fact that the ancestral paragroup C* is not found among any of the modern Northeast Asian, Siberian, or North American populations among whom Haplogroup C3 predominates, makes the determination of the geographical origin of the defining M217 mutation exceedingly difficult. The presence of Haplogroup C3 at a low frequency but relatively high diversity throughout East Asia and parts of Southeast Asia makes that region one likely source, but it is troubling that the STR profiles of Haplogroup C3 Y-chromosomes suggest that the entire clade has derived from an ancestral Y-chromosome that was more closely related to the Haplogroup C* chromosomes found among modern South Asians than to the Haplogroup C* chromosomes found among the Vietnamese and other Southeast Asians, which for their part appear to be more closely related to the Haplogroup C elements (both C* and C2) found among Melanesian and Austronesian populations. In addition, the C3 haplotypes found among North Eurasian populations appear to belong to a different genealogical branch from the C3 haplotypes found at a low frequency among East and Southeast Asians, which suggests that the marginal presence of C3 among modern East and Southeast Asian populations is not due to recent admixture from Northeast or Central Asia.^[1]

The subclades of Haplogroup C3 with their defining mutation(s), according to the 2006 ISOGG tree:

• C3 (M217, P44) Typical of Mongols, Kazakhs, and indigenous peoples of the Russian Far East, with a moderate distribution throughout Eurasia and the Americas
  • C3*
  • C3a (M93) Observed sporadically among Japanese
  • C3b (P39) Typical of the Na-Dené peoples of North America
  • C3c (M48, M77, M86) Typical of Northern Tungusic peoples, Kazakhs, Oirats, Kalmyks, and Outer Mongolians, with a moderate distribution among Southern Tungusic peoples, Inner Mongolians, Buryats, Tuvinians, Kyrgyz, Uyghurs, Uzbeks, Karakalpaks, and Tajiks
  • C3d (M407) Observed sporadically among Yakuts and Han Chinese

Spread of Haplogroup C3, from The Genographic Project, National Geographic