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.

Insights From Y-STRs: Forensic Characteristics, Genetic Affinities, and Linguistic Classifications of Guangdong Hakka and She Groups

“…The predominantly detected haplogroups were O2-M122 (45.75%), O2a2a1a2-M7 (25.47%), O1a-M119 (10.38%), O1b1a1a-M95 (8.02%), O-M175 (7.08%), and O2a2b1a1-M117 (3.30%), which were determined according to ISOGG, 2019 2 . In addition, a PCA graph was performed among 77 populations ( Wen et al, 2004 ; Gan et al, 2008 ; Li et al, 2008 ; Cai et al, 2011 ; Deng et al, 2013 ; Fan et al, 2018c ; Rowold et al, 2019 ; Luo et al, 2020 ; Fan et al, 2021 ), which were composed of 4,195 individuals in total, including Tai-Kadai, Hmong-Mien, Tibeto-Burman, and Chinese (Southern and Northern Han) populations from Southeast and East Asia, which included three She groups (Fujian, Guangdong Chaoshan, and Guangdong She). From the diagram in Figure 7 , the first and second principal components could explain 33.07% of the total variances.…”

Systematic Evaluation of a Novel 6-dye Direct and Multiplex PCR-CE-Based InDel Typing System for Forensic Purposes

“…The Hainan Li, inhabiting in the south of Hainan island, is a relatively isolated minority group in China, which is beneficial to clarify the exquisite population structure and develop specific genetic markers for subpopulations in the forensic genetic field ( Liu et al, 2020b ; Fan et al, 2021a ). Hence, a total of 279 healthy Hainan Li individuals were collected for forensic evaluations of 57 A-InDel loci in EAIS.…”

“…Therefore, the UAIS could supply additional information for the paternity tests. The Hainan Li, inhabiting in the south of Hainan island, is a relatively isolated minority group in China, which is beneficial to clarify the exquisite population structure and develop specific genetic markers for subpopulations in the forensic genetic field (Liu et al, 2020b;Fan et al, 2021a (mean He: 0.4666 ± 0.0560). Moreover, the CPE and CPD of the 57 A-InDels in the Hainan Li group was 0.999965 and 1-1.32 × 10 -23 , which demonstrated that the EAIS have good performances for individual identification and paternity test in the Hainan Li group (Table 2).…”

“…Therefore, based on the underlying genome-wide data of the EAS populations from the 1,000 Genome Project (1KG) Phase 3 ( Genomes Project et al, 2010 ; Genomes Project et al, 2015 ) and the engineering fundamental logic for the maximum utilization of multiplex PCR-CE system, a novel 6-dye direct and multiplex PCR-CE-based typing system with relatively short amplicons (<230 bp), consisting of 57 autosomal InDels (A-InDels), 2 Y-chromosomal InDels (Y-InDels), and Amelogenin, was studied to expand application scenarios for forensic purposes in EAS populations, especially for different Chinese populations. Moreover, forensic efficiencies and population genetic analyses of the direct and multiplex PCR-CE-based InDel typing system were further evaluated in 26 globally dispersed populations and the Hainan Li (HNL) group, which is a relatively isolated Chinese group revealed by the previous studies ( Fan et al, 2018b ; Fan et al 2019b ; Fan et al 2021a ; Wang et al, 2021 ).…”

Microhaplotype and Y-SNP/STR (MY): A novel MPS-based system for genotype pattern recognition in two-person DNA mixtures

“…With the development of massive parallel sequencing (MPS) technology [13][14][15][16][17][18][19][20][21][22][23][24], emerging microhaplotypes (i.e., microhaps or MHs, generally <200 bp and consisting of two or more closely linked single nucleotide polymorphisms (SNPs) with three or more allelic combinations [7,25,26]) exhibit promising characteristics for further enhancing the deconvolution of DNA mixtures. MHs present some advantages over standard STRs: (1) a multiallelic nature and the absence of STR structures, which prevents Taq polymerase slippage and stutter peak generation; (2) balanced PCR amplification due to the similar lengths of MH amplicons (preferential PCR amplification for shorter alleles commonly occurs with STRs); and (3) lower mutation rates than STRs.…”