Genetic substructure and forensic characteristics of Chinese Hui populations using 157 Y-SNPs and 27 Y-STRs

Xie, Mingkun; Song, Feng; Li, Jienan; Lang, Min; Luo, Haibo; Wang, Zheng; Jin, Wook; Li, Changzheng; Tian, Chenchen; Wang, Weizhi; Ma, Hong; Song, Zhen; Fan, Yujie; Hou, Yiping

doi:10.1016/j.fsigen.2019.03.022

Cited by 58 publications

(70 citation statements)

References 43 publications

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“…Four samples displayed .2 microvariants present in the DYF387S1 virtual ladder (39.2 and 41.2), and all were predicted to belong to haplogroup B2 which is often associated with such microvariants at this locus (Iacovacci et al 2017 ). Similarly, a DYS481 25.1 microvariant allele in five men was wholly concordant with the NevGen prediction of the R1b-PH155 subclade, which is a globally rare basal R1b lineage previously recorded in several Bahrainis who have very similar haplotypes to those typed here, and have submitted their Y-STR and Y-SNP profiles to the YFull Tree database (Roewer 2017 ; Xie et al 2019 ). The same allele (25.1) has also been recorded in a Han Chinese individual who was derived for the Y-SNP M343 but ancestral for SNP L389, which also implies a basal R1b lineage (Guo 2017 ).…”

Section: Resultssupporting

confidence: 83%

Geographical structuring and low diversity of paternal lineages in Bahrain shown by analysis of 27 Y-STRs

et al. 2020

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We have determined the distribution of Y-chromosomal haplotypes and predicted haplogroups in the ethnically diverse Kingdom of Bahrain, a small archipelago in the Arabian Gulf. Paternal population structure within Bahrain was investigated using the 27 Y-STRs (short tandem repeats) in the Yfiler Plus kit to generate haplotypes from 562 unrelated Bahraini males, sub-divided into four geographical regions—Northern, Capital, Southern and Muharraq. Yfiler Plus provided a significant improvement over the 17-locus Yfiler kit in discrimination capacity (from 77% to 87.5% overall), but discrimination capacity differed widely between regions from 98.4% in Muharraq to 75.2% in the Northern region, an unusually low value possibly resulting from recent rapid population expansion. Clusters of closely related male lineages were seen, with only 79.4% of donors displaying unique haplotypes and 59% of instances of shared haplotypes occurring within, rather than between, regions. Haplogroup prediction indicated diverse origins of the population with a predominance of haplogroups J2 and J1, both typical of the Arabian Peninsula, but also haplogroups such as B2 and E1b1a likely originating in Africa, and H, L and R2 likely indicative of migration from South Asia. Haplogroup frequencies differed significantly between regions, with J2 significantly more common in the Northern region compared with the Southern, possibly due to differential settlement by Baharna and Arabs. Our study shows that paternal lineage population structure can exist even over small geographical scales, and that highly discriminating genetic tools are required where rapid expansions have occurred within tightly bounded populations.

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Section: Resultssupporting

confidence: 83%

Geographical structuring and low diversity of paternal lineages in Bahrain shown by analysis of 27 Y-STRs

et al. 2020

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“…Furthermore, to make additionally population differentiations between Hainan Li and populations which had relatively close distances in geographical scale , and populations in Hainan island [89,91], we collected publicly published Y-STR data in literatures and our house-in Hainan Y-STR dataset for Dataset Ⅱ (in Table 1) to evaluate the differences between Hainan populations including Hainan Li and the populations from south China [89,91,[147][148][149][150][151][152][153][154][155][156][157][158], Southeast Asia [159][160][161][162] and Australia [163] with different language families. The details of Dataset Ⅱ, a total of 8281 individuals with 17 Yfiler data (DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS385a/b, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS635 and Y_GATA_H4), were presented in Supplementary Table S16 and the elaborate geographic positions of the 42 populations which belonged to five language families were orientated in Fig.…”

Section: Population Differentiation Based On Y-strsmentioning

confidence: 99%

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

Fan

Wang

et al. 2020

Preprint

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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...

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“…The obtained results provided evidence for the East Asian origin of the studied Hui group, which might be related to the greater gene flow between the Hui group and East Asian populations. However, genetic distribution analyses of the genetic markers on the Y chromosomes in the Hui groups from different regions revealed their genetic substructures [13]. Therefore, further analyses of the genetic components in the Hui groups from other regions should be conducted based on the developed AISNP panel.…”

Section: Phylogenetic Relationships and Population Structure Analysesmentioning

confidence: 99%

“…And they found that these Hui groups presented genetic differentiations and could be classified into Hui group in northwest China, Hui groups in Sichuan and Shandong provinces and the Hui group in Yunnan province. Therefore, the authors suggested that different genetic databases should be employed for forensic investigations into these Hui groups [13]. In previous studies, our research team conducted a series of population genetic analyses of Hui group based on autosomal InDels [14], autosomal STR [10,15], Y-STR [16] and X-STR [17] loci and found that the Hui group had close genetic relationships with the Chinese Han populations.…”

Section: Introductionmentioning

confidence: 99%

Ancestry Prediction Comparisons of Different AISNPs for Five Continental Populations and Population Structure Dissection of the Xinjiang Hui Group via a Self-Developed Panel

Jin

Guo

Chen

et al. 2020

Genes

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Ancestry informative markers are genetic markers that show distinct genetic divergences among different populations. These markers can be utilized to discern population substructures and estimate the ancestral origins of unknown individuals. Previously, we developed a multiplex system of 30 ancestry informative single nucleotide polymorphism (AISNP) loci to facilitate ancestral inferences in different continental populations. In the current study, we first compared the ancestry resolutions of the 30 AISNPs and the other previously reported AISNP panels for African, European, East Asian, South Asian and American populations. Next, the genetic components of the Xinjiang Hui group were further explored in comparison to these continental populations based on the 30 AISNPs. Genetic divergence analyses of the 30 AISNPs in these five continental populations revealed that most of the AISNPs showed high genetic differentiations between these populations. Ancestry analysis comparisons of the 30 AISNPs and other published AISNPs revealed that these 30 AISNPs had comparable efficiency to other AISNP panels. Genetic relationship analyses among the studied Hui group and other continental populations demonstrated that the Hui group had close genetic affinities with East Asian populations and might share the genetic ancestries with East Asian populations. Overall, the 30 AISNPs can be used to predict the bio-geographical origins of different continental populations. Moreover, the obtained genetic data of 30 AISNPs in the Hui group can further enrich the extant reference data, which can be used as reference data for ancestry analyses of the Hui group.

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Genetic substructure and forensic characteristics of Chinese Hui populations using 157 Y-SNPs and 27 Y-STRs

Cited by 58 publications

References 43 publications

Geographical structuring and low diversity of paternal lineages in Bahrain shown by analysis of 27 Y-STRs

Geographical structuring and low diversity of paternal lineages in Bahrain shown by analysis of 27 Y-STRs

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

Ancestry Prediction Comparisons of Different AISNPs for Five Continental Populations and Population Structure Dissection of the Xinjiang Hui Group via a Self-Developed Panel

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