View Full Version : Genetic admixture in the culturally unique Peranakan Chinese population in ISEA

07-04-2021, 03:08 PM
Genetic admixture in the culturally unique Peranakan Chinese population in Southeast Asia

Degang Wu, Peter Yiqing Li, Bangfen Pan, Zenia Tiang, Jinzhuang Dou, Ivanna Williantarra, Amadeus Yeremia Pribowo, Rizky Nurdiansyah, The SG Peranakan Project, Roger S Y Foo, Chaolong Wang



The Peranakan Chinese are culturally unique descendants of immigrants from China who settled in the Malay Archipelago ∼300-500 years ago. Today, among large communities in Southeast Asia, the Peranakans have preserved Chinese traditions with strong influence from the local indigenous Malays. Yet, whether or to what extent genetic admixture co-occurred with the cultural mixture has been a topic of ongoing debate. We performed whole-genome sequencing (WGS) on 177 Singapore (SG) Peranakans and analyzed the data jointly with WGS data of Asian and European populations. We estimated that Peranakan Chinese inherited ∼5.62% (95% confidence interval [CI]: 4.75-6.46%) Malay ancestry, much higher than that in SG Chinese (1.08%, 0.69-1.53%), southern Chinese (0.86%, 0.57-1.31%), and northern Chinese (0.25%, 0.18-0.33%). A sex-biased admixture history, in which the Malay ancestry was contributed primarily by females, was supported by X chromosomal variants, and mitochondrial (MT) and Y haplogroups. Finally, we identified an ancient admixture event shared by Peranakan Chinese and SG Chinese ∼1,612 (95% CI: 1,345-1,923) years ago, coinciding with the settlement history of Han Chinese in southern China, apart from the recent admixture event with Malays unique to Peranakan Chinese ∼190 (159-213) years ago. These findings greatly advance our understanding of the dispersal history of Chinese and their interaction with indigenous populations in Southeast Asia.

This confirms my phenotype-based suspicion that Malaysian and Singaporean Chinese have non-negligible native Indonesian-like ancestry. I would imagine the percentage is even higher for Indoneaian Chinese.



07-04-2021, 05:58 PM

Population structure

We constructed a reference ancestry space by applying principal component analysis (PCA) on genotypes across 944,059 autosomal SNPs for 996 Chinese, 399 Malays, 629 Indians, selected from the SG10K Pilot Project (Wu, et al. 2019), and 190 Europeans from 1KGP (The 1000 Genomes Project Consortium 2015) (Materials and Methods). These four reference populations, who are well separated by the top three PCs (Figure 1A), represent local and immigrant populations in Singapore. We then projected Peranakans into the reference ancestry space (Wang, et al. 2014; Wang, et al. 2015). Peranakans largely overlapped with Chinese, except for a few outliers falling between the four reference populations (Figure 1A), consistent with their self-reported ancestry of Peranakan Indians, Eurasians or Caucasians. In addition, some outliers might be introduced by very recent admixture events (i.e., within two generations), which may mask the admixture signals further back in time. Therefore, we excluded 15 Peranakan samples who were more than 3 standard deviations (SD) from the mean coordinates of Peranakans in any of the top 3 PCs, and focused on the remaining 115 samples, whom we labeled as Peranakan Chinese (Materials and Methods). PCA results based on 113,037 SNPs on the X chromosome resembled the autosomal PCA results for the reference populations (Procrustes similarity t0=0.91 for the top 3 PCs) (Wang, et al. 2010), but had a noisier distribution for the Peranakans, indicating different admixture fractions on the X chromosome compared to the autosomes (Figure S2).

After removing the outliers, we projected Peranakan Chinese, SG Chinese, and Han Chinese sampled from northern and southern China (CHB and CHS from 1KGP, respectively) onto the reference ancestry map spanned by the top two PCs of Chinese, Malays, and Indians (Figure 1B ). Despite the substantial overlap between Peranakan Chinese and the reference Chinese, an enlarged view of the projected coordinates revealed a different distribution of Peranakan Chinese in comparison to SG Chinese, southern Chinese, and northern Chinese (Figure 1C). Specifically, we observed a trend of Peranakan Chinese tilted towards the reference Malays, indicating a low level of Malay admixture in Peranakan Chinese. Compared to the projected coordinates of southern Chinese, the mean shift towards Malays was insignificant for SG Chinese (p=0.31, t-test) but highly significant for Peranakan Chinese (p=7.510-12 147 , Figure 1D).

It makes sense that "Northern Han" is CHB (cosmopolitan sample of university students) and "Southern Han" is CHS (Hunan + Fujian).

Subgraph D shows that the SG Chinese sample has a bimodal distribution- with one peak that's slightly more "northern" (or less Malay-shifted) than the CHS peak, plus another smaller peak that lines up with the smallest "most SEA-shifted" peak in CHB and the "most SEA-shifted" portion of CHS. Subgraph C shows that the Northern (northern-shifted) Chinese in CHB are also shifted towards Europeans relative to CHS and SG Chinese.