Dissecting the genetic admixture and forensic signatures of ethnolinguistically diverse Chinese populations via a 114-plex NGS InDel panel

Abstract

Comprehensive characterizations of genetic diversity and demographic models of ethnolinguistically diverse Chinese populations are essential for elucidating their forensic characteristics and evolutionary past. We developed a 114-plex NGS InDel panel to genotype 114 genome-wide markers and investigated the genetic structures of Zhuang, Hui, Miao, Li, Tibetan, Yi, and Mongolian populations, encompassing five language families. This panel demonstrated robust performance, with exceptional potential for forensic individual identification and paternity testing, evidenced by the combined power of discrimination for 77 autosomal InDels (ranged from 1-3.6400 × 10^-30 to 1-3.5713 × 10^-32) and the combined power of exclusion (ranged from 1-2.1863 × 10^-6 to 1-2.1261 × 10^-7). The cumulative mean exclusion chance for 32 X-chromosomal InDels varied between 0.99996 and 0.99999 for trios and 0.99760 to 0.99898 for duos. We also analyzed genetic similarities and differences between these populations and 27 global populations, revealing distinct clusters among African, South Asian, East Asian, and European groups, with a close genetic affinity to East Asians. Notably, we identified geography-related genetic substructures: Inner Mongolia Mongolians and Gansu Huis formed a northern branch, Tibetans and Yis from Sichuan constituted a highland branch, and Guangxi Zhuangs exhibited close ties with Hainan Lis and Guangxi Miaos in the southern branch. Additionally, many InDels proved to be ancestry-informative markers for biogeographic ancestry inference. Collectively, these findings underscore the utility of the 114-plex NGS InDel panel as a complementary tool for forensic investigations and as a source of insights into the genetic architecture of ethnolinguistically distinct Chinese populations.

Keywords: Forensic characterization; Genetic diversity; InDel; Next-generation sequencing; Population structure.

Fig. 1

Geographical distribution of the 34 populations and box plots illustrating the depth of coverage (DOC), allele coverage ratio (ACR), and noise level (NL) values derived from 114 InDel loci across the studied groups. A Map showing the geographic locations of the seven studied populations, Guangdong Han, and 26 global reference populations. B Box plot of DOC values for 77 A-InDels in both males and females. C DOC values of 32 X-InDels for females. D DOC values of 32 X-InDels and 5 Y-InDels for males. E ACR values of 77 A-InDels and 32 X-InDels. F NL values of 114 InDels

Fig. 2

Violin plots depicting forensic parameter distributions for the 77 A-InDels across the seven studied populations

Fig. 3

Allele frequency divergence of insertion alleles for the 108 InDels was analyzed across 34 populations. Insertion frequencies and In values were compared among populations from three continents (Africa, Europe, and East Asia), four continents (Africa, Europe, East Asia, and South Asia), and five continents (Africa, Europe, East Asia, South Asia, and America)

Fig. 4

Genetic relationships among the seven studied populations and 27 reference populations analyzed using 76 A-InDels. A A heatmap depicting pairwise Fst and DA distance values highlights population differentiation. B-C Principal component analysis (PCA) based on insertion allele frequencies. D PCA conducted on genotype data provides additional insight into genetic variation across populations

Fig. 5

Genetic relationships and population structures were explored using 76 A-InDels across seven studied populations and 27 reference populations. A Multidimensional scaling plots based on the Fst distance matrix. B A phylogenetic tree illustrates the evolutionary relationships among populations. C Ancestry component proportion in 34 populations with K ranging from 2 to 6