Are Han Taiwanese genetically distinct from their mainland counterparts, or is it a myth?

Are Han Taiwanese genetically distinct from their mainland counterparts, or is it a myth?
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In short: The Han Taiwanese population, comprising roughly 95 percent of Taiwan, is often defined by a divide between early settlers and those who arrived after 1945. Yet, modern genetic research and historical analysis challenge popular narratives about indigenous ancestry and biological divergence, revealing a complex story of migration and identity.

The Han Chinese, the world's largest ethnic group with over 1.4 billion members, originated in northern China's Yellow River basin. Over millennia, they expanded southward, establishing a cohesive politico-cultural unit. In Taiwan, this group is traditionally categorized into two main segments: the benshengren, whose ancestors arrived in earlier waves, and the waishengren, who migrated with Chiang Kai-Shek following the Chinese Civil War between 1945 and 1949.

A persistent narrative in Taiwanese identity politics suggests that modern Han Taiwanese possess significant indigenous genetic heritage, sometimes cited as high as 85 percent in non-peer-reviewed sources. However, researchers like Shu-juo Chen and Hong-kuan Duan label this the 'myth of indigenous genes.' Scientific studies indicate that genetic markers for aboriginal ancestry constitute only a minute portion of the genome. Evidence suggests that the admixture between East Asian and Austronesian ancestors occurred roughly 4,000 years ago, well before the migration of Han groups to Taiwan.

Historical claims regarding widespread intermarriage between Han men and indigenous women—often summarized by the idiom 'has Tangshan father, no Tangshan mother'—are also contested. Historical sources report only isolated cases of such unions. Because the Han population grew rapidly through mass migration, the demographic scale would have made mass intermarriage impossible. Furthermore, the survival of indigenous tribes until the Japanese colonial period suggests that indigenous women were not integrated into the Han population on a large scale.

Recent precision medicine initiatives, such as the Taiwan Precision Medicine Initiative (TPMI) conducted from 2019 to 2023, have genotyped over half a million participants to better understand the genetic architecture of Han ancestry. These studies confirm that Taiwanese Han cluster most closely with other Sino-Tibetan-speaking groups, such as Cantonese and Singaporean Chinese. Ultimately, attempts to construct a distinct national identity based on unique genetic markers are viewed by many scholars as scientifically unsupported and theoretically meaningless.

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