How Han are Taiwanese Han? Genetic inference of Plains Indigenous ancestry among Taiwanese Han and its implications for Taiwan identity

Taiwanese Han have been searching for new cultural or historical grounds upon which to resist Beijing's "Keep Taiwan Chinese" policies. Despite the fact that ancestors of most Taiwanese Han were immigrants from China during the last four hundred years, many Taiwanese Han have sought to establish a unique sense of identity expressed in the well-known folk saying: "There were mainland grandfathers but no mainland grandmothers." They believe Taiwanese Han are genetically different from Chinese Han because the female ancestors of most Taiwanese Han were not Han, but Plains Indigenes, a group of Taiwan Austronesian speakers.;The proportion of Plains Indigenous ancestry among Taiwanese Han was not known before this study because Plains Indigenes are not officially recognized today. The ethnic labeling in the Japanese household registry is the most conclusive reliable resource to identify Plains Indigenes. In this thesis, Plains Indigenes identified from the Japanese household registry and censuses are sampled and genotyped. A genetic distinction between Plains Indigenes and Taiwanese Han is confirmed by their Y chromosome and mtDNA variations. The great number of Han immigrants after the 18th century is the main reason to consider that the early genetic contribution from Plains Indigenes to Taiwanese Han has been largely diluted and no longer exists in any meaningful way.;However, Taiwan blood nationalists and some geneticists have misinterpreted the genetic evidence and misled people in Taiwan into believing the opposite. The "myth of Indigenous genes"---the belief that the majority of people in Taiwan have Indigenous ancestors---is widely accepted. Taiwan blood nationalists have called for Taiwan's independence based on this myth.;The descendants of Plains Indigenes are extremely opposed to using their ancestors in such calls for Taiwan independence. In efforts to revive their traditional culture, maintaining group solidarity among their villagers is more important than differentiating the ancestral origins of village members. "Keep the Village Siraya" is important in the propaganda used in their appeals for official recognition.;While Taiwan blood nationalists use Plains Indigenous ancestors as a template to create a Taiwan nation based on blood, the value of Plains Indigenous ancestors is destroyed by their descendants. Plains Indigenes and Taiwan blood nationalists have different cultural and socioeconomic contexts and the significance of having unique ancestral origins based on blood is treated totally differently. However, no one can deny that the Plains Indigenes have the highest authority to define the values attributed to their ancestors' blood. In this struggle, the denial of the importance of ancestors' blood also destroys the importance of genetic evidence. The claim of Plains Indigenous ancestry among Taiwanese Han becomes socially meaningless.