Additionally, know that some Mongols also have R1a1a. It’s hard to differentiate different periods of admixture. But to me the presence of R2 and J2 point to a Central/South Asian origin of a lot of the Hui R1a as well.
To review, Muslims in China are multi-ethnic. The two largest groups, the Hui and Uyghurs, comprise nearly 90% of Chinese Muslims. There are marginally more Hui than Uyghurs.
Who are the Hui? The Chinese government defines Hui as an ethnic group, but really they are differentiated by their adherence to Islam. Hui speak a dialect of Chinese specific to their locality. They do not have a “Hui language.” Physically they resemble the Han. Because of their long period of isolation in China after the collapse of the Yuan dynasty, the Hui have gone through several indigenizing phases.In the 18th century in eastern China the Hui intellectual classes synthesized Chinese cultural frameworks with Islam in a fascinating manner. The whole project is recounted in The Dao of Muhammad.
These periods of Sinicization are often followed a reformist globalist revival triggered by missionaries or those who went on pilgrimage to Mecca. Islam with Chinese characterizes recedes for a generation or two, only to come back.
In the 19th century to a great extent the project of social accommodation with the Han by the Hui collapsed in the face of social disorder, anti-Muslim policies by the Manchus, and reformist movements inspired by broader currents in the Islamic world. Though the Hui are a very small minority, unlike the Han a military career was not low status for them, so they “punched above” their weight.
In the 20th and 21st centuries the Hui have been relatively quiescent. Why? There are numerous reasons, but it is important to emphasize that there are many strong contrasts with how the Hui are treated and perceived, and how they perceive China, in relation to what is meted out to the Uyghurs. The Hui are no less Muslim than Uyghurs, but they are not the political and social problem in China that Uyghurs are.
Though the Chinese state defines Hui as one of the minority “nationalities,” that is really a semantic obfuscation. The Hui are most easily conceptualized as Han Muslims, even though some of their customs separate them very strongly from the Han (e.g., no consumption of pork), and traditionally Han identity has been seen as exclusive from an Islamic identity. That is, a Han who converts to Islam becomes a Hui by definition.
Though in a Chinese context one could never call the Hui “Han Muslims,” from a non-Chinese perspective it is very informative of the relationship and difference of the Hui from the Han, as opposed to the Uyghur from the Han.
Obviously the Uyghur are not Han, they are Turkic. Uyghur nationalists have pan-Turkic associations, and many Uyghurs live in Turkey. As a Turkic people Uyghurs, unlike Hui, do not speak Chinese as their first language. The attempt to educate Uyghur children in Mandarin Chinese to enable them to assimilate and succeed economically has faced resistance because Uyghurs see in this the first steps to assimilation and eventually alienation.
Though Hui are very distinctive in China proper, and live in their own segregated areas in much of the north (in southern China this is less common, and Hui assimilation into Han identity has also been widespread), they are still part of the Chinese landscape. Muslims have lived in China proper since the Tang dynasty, 1,300 years ago. Large numbers of Muslims arrived with the Mongols 800 years ago, and many stayed on. As a minority in a non-Muslim society these people had to navigate how to be both Chinese and Muslim, when much of Chinese identity deviated from world normative Islam in deep ways.
The Uyghurs did not go through any of this because they were not part of China until the 20th century. Though Chinese garrisons and hegemony did exist in Xinjiang during portions of the Han and Tang dynasty, up until the Manchu conquest of these territories in the mid-18th century the Uyghurs had not been part of the same political unit with Han Chinese for over 1,000 years, with the exception of the short Mongol interlude. In fact, the ethnogenesis of modern Uyghurs, as a blending of Turkic migrants from the north and native Indo-Eurpean speaking groups in the Tarim basin, was concurrent with the collapse of Chinese influence in what became the eastern edge of the Turkic world.
Notice I was very specific in saying that they became part of the same political unit with Han Chinese in the middle of the 18th century. This because outside of China proper the Manchu emperors did not necessarily rule as Chinese potentates. Rather, they took on different forms for their different subject peoples, and the conquest of the heart of Eurasia was not a conquest by the state of China, but of the Manchu ruling caste. Any attempts to Sinicize Xinjiang came later, and were halting at best. While Chinese speaking Muslims in Beijing were theorizing how Muhammad actually completed the Confucian vision better than most Chinese, the Uyghurs simply swapped the rule of nearby Tibetan Buddhist Oirat Mongols for a distant Manchu ruler, who was also sympathetic to Tibetan Buddhist religion and claimed a kinship with the Mongols through descent from Genghis Khan’s younger brother.
The problem that the modern Chinese state has is that it rejects the feudal multicultural compromises of the imperial past. Though Communist regimes pay lip service to national self-determination, the reality in Communist regimes has always been that the party has enforced a normative ethnic identity as one that is aspirational for minorities. The Chinese state suppression of the religion of the Uyghurs, the promotion of Mandarin, the encouragement of migration to Xinjiang by Han, and even inducements in some cases for Uyghurs to intermarry with Han, are all part of a general pattern of activity which will result in the assimilation of the Uyghur nation.
It is apparently a fact that while Islamic belief and practice by Uyghurs is sharply frowned upon by Han authorities in Xinjiang, in most of China proper Hui religiosity is relatively tolerated. Hui are even seen as appropriate ambassadors to Muslim nations for purposes of diplomacy and business, because they show how China can accommodate Islam. Unlike the Uyghurs the Hui do not have a geographical region where they are dominant (Muslims are 35% of the population of the small province set aside for Hui). Their national home is China. Additionally, obviously they would not resist Mandarin Chinese instruction, because they are already Chinese speakers. Unlike the Uyghur, who have substantial West Eurasian ancestry, the Hui are also physically no different from Han.
In Central Asia the Hui have a different name. They are called Dungans. And traditionally they have been overrepresented among soldiers and merchants from China. Within China the Hui are exotic and somewhat out of place due to their religion. But in Central Asia the Hui are exotic and somewhat out of place due to their Chineseness. Hui were important in keeping Xinjiang in the Manchu fold after the conquest. Many Uyghurs know this history of cooperation between Han and Hui. In the 2009 Urumqi riots the Uyghurs reportedly chanted “Kill the Han, kill the Hui”.
None of this is to deny that Islam presents challenges as a minority religion within a non-Muslim nation. The Hui rebellions of the 19th century, and periodic flare ups between Hui and Han in the Chinese heartland, attest to this. But differences between Uyghurs and Hui illustrate that excessive focus on Islam misses that Uyghur violence in response to Chinese coercion likely has multiple causes. Islam over the last generation has been the most powerful binding ideology for national resistance among Uyghurs. But it would be far less relevant if the Uyghurs were not a nation in the first place, which they are.
Another way to say it is that Tibet and Xinjiang have many of the same underlying parameters as to why they are hotbeds of ethnic tension and separatism. Religion is part of the story.