Cultural hitchhiking and competition between patrilineal kin groups explain the post-Neolithic Y-chromosome bottleneck Tian Chen Zeng, Alan J. Aw & Marcus W. Feldman Nature Communicationsvolume 9, Article number: 2077(2018) doi:10.1038/s41467-018-04375-6 Download Citation AnthropologyEvolutionary geneticsEvolutionary theory Received: 20 November 2017 Accepted: 24 April 2018 Published: 25 May 2018 Abstract In human populations, changes in genetic variation are driven not only by genetic processes, but can also arise from cultural or social changes. An abrupt population bottleneck specific to human males has been inferred across several Old World (Africa, Europe, Asia) populations 5000–7000 BP. Here, bringing together anthropological theory, recent population genomic studies and mathematical models, we propose a sociocultural hypothesis, involving the formation of patrilineal kin groups and intergroup competition among these groups. Our analysis shows that this sociocultural hypothesis can explain the inference of a population bottleneck. We also show that our hypothesis is consistent with current findings from the archaeogenetics of Old World Eurasia, and is important for conceptions of cultural and social evolution in prehistory.
All Japanese emperors and shoguns and most daimyo shared the same Y-DNA lineage
The Emperors of Japan belonged to haplogroup D1b1a2 based on the tests of various descendants. Another presumed descendant of the imperial family tested at samples of many Japanese genoms and also belonged to that haplogroup, and more precisely to the D-Z1504 subclade. Many database claimed that 6 million Japanese men (10% of the male population of Japan) carry the same Y-DNA lineage as the Imperial family and that they share a common ancestor about 1000 years ago.
Many medieval emperors had illegitimate offspring (Emperor Saga alone fathered 49 children), who were bestowed the surnames Minamoto (Genji), Taira (Heike) or Tachibana, who in turn became powerful aristocratic clans of their own. The Minamoto and Taira became the ancestors of dozens of samurai clans (see below), while the Tachibana became one of the four most powerful kuge (court nobility) families in Japan's Nara and early Heian periods. A few samurai clans descend from Japanese emperors through imperial princes. This is the case of the Asakura clan.
I have made my own research and found that the Minamoto are the patrilineal ancestors of daimyo clans such as the Akamatsu, Akechi, Amago, Ashikaga (Muromachi-era shoguns), Hatakeyama, Hosokawa, Ikeda, Imagawa, Kitabatake, Kuroda, Matsudaira, Miyoshi, Mogami, Mori, Nanbu, Nitta, Ogasawara, Ota, Rokkaku, Sakai, Sasaki, Satake, Satomi, Shiba, Shimazu, Takeda, Toki, Tokugawa (Edo-era shoguns), and Tsuchiya. A few kuge (court aristocracy) families also descend from the Minamoto, such as the Koga.
If this is correct, it could mean that all Japanese emperors and a great number of daimyo (feudal lords) and samurai families would have belonged to haplogroup D1b1a2, if non-paternity events did not occur.
The Taira clan descends from four 9th-century emperors (Kanmu, Ninmyo, Montoku and Koko) and were the ancestors of several daimyo families such as the Ashina, Chiba, Hojo (Kamakura-era shoguns), Miura, Soma, and Oda (whose most famous member was Oda Nobunaga, who started the reunification of Japan during the Sengoku period).
Only a few daimyo clans did not descend from the Y-DNA line of the Imperial family. Most, however, descend from the Fujiwara family, who intermarried with the Imperial family almost every generation during the Heian period(794-1185) and therefore can be considered the same family (the maternal branch). The Fujiwara clan customarily served as regents and ministers (sadaijin and udaijin), which allowed them to dominate Japanese politics throughout the Heian period. Their descendant remained court nobles until 1945. Only a few notable samurai families descend from the Fujiwara Y-DNA line. These include the Adachi, Ashikaga (Fujiwara), Azai, Date, Gamo, Honda, Ii, Ito, Niwa, Tsugaru, Uesugi and Utsunomiya. Among them the Date and Uesugi in eastern and northern Honshu distinguished themselves during the Sengoku period. The HTsugaruonda and Ii were retainers of the Matsudaira/Tokugawa clan and became powerful after Tokugawa Ieyasu established the last shogunate.
At least many descendants from the Fujiwara clan tested their Y-DNA at samples of many Japanese genoms and all belonged to haplogroup O1b2a1 (formerly known as O2b1a), and more specifically to O-47Z(aka CTS10674 or CTS11986). This haplogroup is found in 24% of the Japanese population. Y-full list a few deeper branches but more research is needed to determine the deep clade associated specifically with the Fujiwara.
I could only find a handful of notable daimyo clans that didn't descend either from the Imperial lineage or from the Fujiwara lineage. The most prominent was the Mori clan (not to be confused with the Mori clan above), who were descended from the Oe, a court aristocratic lineage from the Heian period related by marriage to the Imperial family.
Another one was the Abe clan, one of the oldest in Japan, said to be one of the original clans of the Yamato people. The Hata clan is equally old and was founded by Chinese immigrants with the surname Qin (秦 ; Hata being the Japanese reading of that Chinese character) during the Kofun period (250-538). They became the ancestors of a number of samurai clans, such as the Akizuki, Chosokabe, Kawakatsu and Tamura. Descendant testing at many database showed that that lineaged belonged to haplogroup O2a2b1a1 (formerly known as O3a2c1a), the most common lineage among Han Chinese, and specifically to the O-CTS10738 subclade found in both China and Japan.
During the Sengoku period, there was also the Saito clan (founded by a merchant who seized power in Mino province and became Oda Nobunaga's father-in-law) and the Toyotomi clan, founded by Toyotomi Hideyoshi, Oda Nobunaga's general who gradually rose in power a peasant family. They were recent parvenus whose lineage didn't last more than a few generations.
It all looks like a big family feud between different branches of the Imperial family vying for supremacy and never leaving any space for outsiders (except very briefly as with Toyotomi Hideyoshi). What is amazing is that all the famous samurai in history were members of the imperial paternal lineage, and that basically the same family controlled every aspect of society in Japan, from religious (emperor) to cultural and socio-economic (ministers and court nobles) to military (daimyo) for over 1000 years, since Japan exists as a unified country. Many of these aristocratic and samurai families still play an important role today, as politicians or presidents/chairmans of companies or organisations. For example, Morihiro Hosokawa, the head of the Hosokawa clan, served as Prime Minister of Japan in 1993-94.
It's approximately 1000 years, which corresponds to the Heian period, when emperors were particularly prolific sexually. The Taira clan dates back to the 9th century. The Minamoto clan started with Emperor Saga (also in the 9th century) who had 49 children. 18 emperors gave the Minamoto surname to their illegitimate offspring between the 9th and 17th centuries, but the most successfully lineage by far was the one descending from Emperor Seiwa (Seiwa Genji branch of the Minamoto) who included most of the daimyo clans listed above under Minamoto. Many of them descend from the Ashikaga shoguns (e.g. the Hosokawa, Imagawa, Hatakeyama, Shiba, Mogami, Takeda, Ogasawara, Nitta, Matsudaira, Tokugawa, Kira, Hachisuke, Ueno, Sakurai, etc.). Only the Nitta branch of the Ashikaga spawned the Tokugawa, Matsudaira, Yamana, Wakiya, Horiguchi, Odachi, Iwamatsu and Sakai. There are so many surnames because every time a cadet branch moves to a new fief, they adopt the name of the village/town where they settle.
