The forensic landscape and the population genetic analyses of Hainan Li based on massively parallel sequencing DNA profiling

Abstract

Due to the formation of the Qiongzhou Strait by climate change and marine transition, Hainan island isolated from the mainland southern China during the Last Glacial Maximum. Hainan island, located at the southernmost part of China and separated from the Leizhou Peninsula by the Qiongzhou Strait, laid on one of the modern human northward migration routes from Southeast Asia to East Asia. The Hlai-language speaking Li minority, the second largest population after Han Chinese in Hainan island, is the direct descendants of the initial migrants in Hainan island and has unique ethnic properties and derived characteristics, however, the forensic associated studies on Hainan Li population are still insufficient.Hence, 136 Hainan Li individuals were genotyped in this study using the MPS-based ForenSeq™ DNA Signature Prep Kit (DNA Primer Set A) to characterize the forensic genetic polymorphism landscape, and DNA profiles were obtained from 152 different molecular genetic markers (27 autosomal STRs, 24 Y-STRs, 7 X-STRs, and 94 iiSNPs). A total of 419 distinct length variants and 586 repeat sequence sub-variants, with 31 novel alleles (at 17 loci), were identified across the 58 STR loci from the DNA profiles of Hainan Li population. We evaluated the forensic characteristics and efficiencies of DAPA, it demonstrated that the STRs and iiSNPs in DAPA were highly polymorphic in Hainan Li population and could be employed in forensic applications. In addition, we set up three Datasets, which included the genetic data of (Ⅰ). iiSNPs (27 populations, 2640 individuals), (Ⅱ). Y-STRs (42 populations, 8281 individuals), and (Ⅲ). Yhaplogroups (123 populations, 4837 individuals) along with the population ancestries and language families, to perform population genetic analyses separately from different perspectives.In conclusion, the phylogenetic analyses indicated that Hainan Li, with a southern East Asia origin and Tai-Kadai language-speaking language, is an isolated population relatively. But the genetic pool of Hainan Li influenced by the limited gene flows from other Tai-Kadai populations and Hainan populations. Furthermore, the establishment of isolated population models will be beneficial to clarify the exquisite population structures and develop specific genetic markers for subpopulations in forensic genetic fields. Signature Prep Kit; Massively parallel sequencing. mass landings of the Han (since BC 214 in Qin Dynasty) and Lingao people (about BC 500 during the Spring and Autumn period) compressed the living space of Hainan Li, making Li from the north to the south of Hainan island [1,2,9,29,30]. (Nowadays, the main distributions of Hainan Li minority are shown in Fig. 1C.) In all ages, ever since the primordial settlements in Hainan island, Hlai language was the dominant language for the original migrants and their descendants, and the intangible cultural and spiritual heritages within Hainan Li were preserved by oral transmission without ancient writings to hand down. Hlai, which is one important branch of the Tai-Kadai languag...

RETRACTED: Forensic characteristics and phylogenetic analyses of one branch of Tai‐Kadai language‐speaking Hainan Hlai (Ha Hlai) via 23 autosomal STRs included in the Huaxia™ Platinum System

“…To discern the detailed relationship between the Ha Hlai and other language‐speaking populations with different language families, we performed a PCA which included 193 populations (Cadenas, Zhivotovsky, Cavalli‐Sforza, Underhill, & Herrera, 2008; Cai et al, 2011; Chennakrishnaiah et al, 2013; Deng et al, 2013; Fan et al, 2020; Fan, Wang, Chen, Long, et al, 2018; Fan, Zhang, et al, 2018; Gan et al, 2008; Gayden et al, 2007; Khurana et al, 2014; Kwon, Lee, Lee, Yang, & Shin, 2015; Li, Wen, et al, 2008; Regueiro, Cadenas, Gayden, Underhill, & Herrera, 2006; Rowold et al, 2016, 2019; Wells et al, 2001; Wen et al, 2004) from all over the world with eight language families, 11,197 individuals in total (dataset 1). The PC1, PC2, and PC3 of the total variances accounted for 13.97%, 10.83%, and 8.91%, respectively.…”

Comprehensive Insights Into Forensic Features and Genetic Background of Chinese Northwest Hui Group Using Six Distinct Categories of 231 Molecular Markers

“…A disequilibrium in sequencing depth was clearly observed among the different kinds of genetic markers. These sequencing results were within the acceptable criteria defined by the manufacturer and approximately consistent with previous MPS-related studies (Churchill et al, 2017;Guo et al, 2017;Köcher et al, 2018;Hollard et al, 2019;Hussing et al, 2019;Fan et al, 2020). Specifically, partial genetic markers presenting the lowest sequencing depths in this study, such as DYS460, DXS10103, and rs1736442, were also reported to perform poorly in other studies (Almalki et al, 2017;Guo et al, 2017;Jäger et al, 2017;Silvia et al, 2017;Xavier and Parson, 2017;Hollard et al, 2019;Fan et al, 2020).…”

“…These sequencing results were within the acceptable criteria defined by the manufacturer and approximately consistent with previous MPS-related studies (Churchill et al, 2017;Guo et al, 2017;Köcher et al, 2018;Hollard et al, 2019;Hussing et al, 2019;Fan et al, 2020). Specifically, partial genetic markers presenting the lowest sequencing depths in this study, such as DYS460, DXS10103, and rs1736442, were also reported to perform poorly in other studies (Almalki et al, 2017;Guo et al, 2017;Jäger et al, 2017;Silvia et al, 2017;Xavier and Parson, 2017;Hollard et al, 2019;Fan et al, 2020). It was speculated that the constant low detection of these markers might be in relation to amplicon length, low (below recommendations) copy number input DNA, inaccurate library quantification, or overmultiplexing of samples (Guo et al, 2017).…”

“…However, the combined PD value for the 94 IISNPs was higher than those of the 27 A-STRs at both the length and sequence levels. Previous reports also claimed that these 94 IISNPs could be comparable with the 27 A-STRs considering the discrimination power for individual identification (Wendt et al, 2016;Delest et al, 2020;Fan et al, 2020).…”