Genomic history and forensic characteristics of Sherpa highlanders on the Tibetan Plateau inferred from high-resolution InDel panel and genome-wide SNPs

RETRACTED: Investigating the effectiveness of forensic genetics and population genetic diversity using a multi-InDel system in Chinese Hezhou and Southern Shaanxi Han populations

INTRODUCTION

Multiple insertion-deletion (multi-InDel) has greater potential in forensic genetics than InDel, and its efficacy in kinship testing, individual identification, DNA mixture detection and ancestry inference remains to be explored.

METHODS

Consequently, we designed an efficient and robust system consisting of 41 multi-InDels to evaluate its efficacy in forensic applications in Chinese Hezhou Han (HZH) and Southern Shaanxi Han (SNH) populations and explore the genetic relationships between the SNH, HZH, and 26 reference populations.

RESULTS AND CONCLUSION

The obtained results showed that 38 out of the 41 multi-InDels had fairly high genetic variations. The the cumulative probability of discrimination and exclusion values of the multi-InDels (except MI38) in HZH and SNH populations both exceeded 1-e-25 and 1-e-6, correspondingly. The genetic compositions of HZH and SNH individuals were similar to that of East Asians and the Naive Bayes model could well distinguish East Asians, Africans and Americans. These results indicated that the multi-InDel systerm can serve as an effective tool to provide important evidence for the development of multi-InDels in forensic practice and better analyse the genetic background of the Han Chinese populations.

Comprehensive elucidation on the genetic profile of the Hezhou Han population via an efficient InDel panel

The Han nationality is widely distributed in different regions, and it is one of the most populous nationalities in China. Compared with the ethnic minorities in Guangxi Zhuang Autonomous Region, there is relatively less research on Han individuals dwelled in Guangxi as a part of Chinese Han population. In this study, the genetic polymorphisms of 57 autosomal insertion/deletion (InDel) loci were explored in Hezhou Han (HZH) population. Forensic-related parameters revealed that these 57 InDel loci had high forensic validity and could be used in forensic practice application. In addition, the genetic relationships between the HZH population and 30 worldwide reference populations were explored using a variety of analytical methods, such as phylogenetic tree, principal component analysis, and genetic structure analysis. These results demonstrated that there were closer genetic relationships between the HZH and nine populations from East Asia (EAS). The prediction accuracy rates of five inter-continental cross-validation analyses for individuals from EAS was >0.9, and the prediction accuracy rates of three inter-continental cross-validation analyses for individuals from EAS, Europe, and Africa were all >0.95. In addition, 24 of the 57 InDel loci could be served as ancestral information inference loci, which could effectively distinguish individuals of EAS, Europe, and Africa. In conclusion, these InDel loci could be used not only as a good tool for individual identification and paternity testing in HZH population, but also as an auxiliary tool for ancestry information inference research.

Genetic Mechanism Analysis Related to Cold Tolerance of Red Swamp Crayfish, Procambarus clarkii

In China, the red swamp crayfish (Procambarus clarkii), a notorious invasive species, has become an important economic freshwater species. In order to compare the genetic diversity and population structure of crayfish from northern and southern China, we collected 60 crayfish individuals from 4 crayfish populations in northern China and 2 populations in southern China for sequencing using the 2b-RAD technique. Additionally, the whole genome sequence information obtained by 2b-RAD of 90 individuals from 2 populations in northern China and 7 populations in southern China were downloaded from NCBI. After quality control, a total of 25,371 SNPs were detected from approximately 54.22 billion raw reads. Based on these SNPs, high genetic diversity was observed in the 15 crayfish populations in China. The pairwise FST values indicated that there was a large genetic differentiation of crayfish populations in northern and southern China. Despite common genetic backgrounds, due to geographical barriers, genetic divergence has been observed in northern and southern China crayfishes. The principal component analysis in combination with Admixture and Neighbor-Joining tree analysis showed that the crayfish fell into two clusters corresponding to geographical regions. The integrated analysis of whole genome and transcriptome data showed that two genes (CETN4 and CPEB2) might play important roles during crayfish resistance to a cold environment. This study reveals the genetic differentiation of crayfish populations in northern and southern China and provides clues to the genetic mechanism related to cold adaptation.

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

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.

Genetic history of esophageal cancer group in southwestern China revealed by Y-chromosome STRs and genomic evolutionary connection analysis

Genetic and environmental factors play crucial roles in the development of esophageal cancer (EC) and contribute uniquely or cooperatively to human cancer susceptibility. Sichuan is located in the interior of southwestern China, and the northern part of Sichuan is one of the regions with a high occurrence of EC. However, the factors influencing the high incidence rate of EC in the Sichuan Han Chinese population and its corresponding genetic background and origins are still poorly understood. Here, we utilized genome-wide single nucleotide polymorphisms (SNPs) and Y-chromosome short tandem repeats (Y-STRs) to characterize the genetic structure, connection, and origin of cancer groups and general populations. We generated Y-STR-based haplotype data from 214 Sichuan individuals, including the Han Chinese EC population and a control group of Han Chinese individuals. Our results, obtained from Y-STR-based population statistical methods (analysis of molecular variance (AMOVA), principal component analysis (PCA), and phylogenetic analysis), demonstrated that there was a genetic substructure difference between the EC population in the high-incidence area of northern Sichuan Province and the control population. Additionally, there was a strong genetic relationship between the EC population in the northern Sichuan high-incidence area and those at high risk in both the Fujian and Chaoshan areas. In addition, we obtained high-density SNP data from saliva samples of 60 healthy Han Chinese individuals from three high-prevalence areas of EC in China: Sichuan Nanchong, Fujian Quanzhou, and Henan Xinxiang. As inferred from the allele frequency of SNPs and sharing patterns of haplotype segments, the evolutionary history and admixture events suggested that the Han population from Nanchong in northern Sichuan Province shared a close genetic relationship with the Han populations from Xinxiang in Henan Province and Quanzhou in Fujian Province, both of which are regions with a high prevalence of EC. Our study illuminated the genetic profile and connection of the Northern Sichuan Han population and enriched the genomic resources and features of the Han Chinese populations in China, especially for the Y-STR genetic data of the Han Chinese EC population. Populations living in different regions with high incidences of EC may share similar genetic backgrounds, which offers new insights for further exploring the genetic mechanisms underlying EC.

Distinguished biological adaptation architecture aggravated population differentiation of Tibeto-Burman-speaking people

Tibeto-Burman (TB) people have endeavored to adapt to the hypoxic, cold, and high-UV high-altitude environments in the Tibetan Plateau and complex disease exposures in lowland rainforests since the late Paleolithic period. However, the full landscape of genetic history and biological adaptation of geographically diverse TB-speaking people, as well as their interaction mechanism, remain unknown. Here, we generate a whole-genome meta-database of 500 individuals from 39 TB-speaking populations and present a comprehensive landscape of genetic diversity, admixture history, and differentiated adaptative features of geographically different TB-speaking people. We identify genetic differentiation related to geography and language among TB-speaking people, consistent with their differentiated admixture process with incoming or indigenous ancestral source populations. A robust genetic connection between the Tibetan-Yi corridor and the ancient Yellow River people supports their Northern China origin hypothesis. We finally report substructure-related differentiated biological adaptative signatures between highland Tibetans and Loloish speakers. Adaptative signatures associated with the physical pigmentation (EDAR and SLC24A5) and metabolism (ALDH9A1) are identified in Loloish people, which differed from the high-altitude adaptative genetic architecture in Tibetan. TB-related genomic resources provide new insights into the genetic basis of biological adaptation and better reference for the anthropologically informed sampling design in biomedical and genomic cohort research.

Genetic polymorphism analysis and forensic application evaluation of 57 insertion/deletion polymorphisms from Yi ethnic group in Yunnan

BACKGROUND

As a new kind of diallelic genetic marker, insertion/deletion (InDel) polymorphisms have recently been used in forensic science. However, there are relatively few studies on the forensic evaluation of InDel genetic polymorphisms from different populations.

AIM

The aim of the present work is to assess the genetic polymorphism and forensic applicability of 57 InDels from the Yi ethnic group and explore the genetic background of this group.

SUBJECTS AND METHODS

A total sample of 122 unrelated individuals of Yi group from the Yunnan province were genotyped by the AGCU indel 60 Kit. Multiplex population genetic analyses on the same 57 InDels were carried out among the Yunnan Yi group and 29 reference populations.

RESULTS

The average allele frequency of these loci in the Yi ethnic group was 0.485. Heterozygosity, polymorphism information content, and the power of discrimination were 0.477, 0.362, and 0.612, respectively. The combined power of discrimination and the combined power of exclusion reached to 0.99999999999999999669 and 0.999962965, respectively. The results showed that 57 InDels polymorphisms have high genetic polymorphisms in the Yi ethnic group.

CONCLUSIONS

The 57 InDels could be used for forensic individual identification, paternity testing, and intercontinental population discrimination, with the potential for use in biogeographic ancestry inference.

Differentiated genomic footprints suggest isolation and long-distance migration of Hmong-Mien populations

BACKGROUND

The underrepresentation of Hmong-Mien (HM) people in Asian genomic studies has hindered our comprehensive understanding of the full landscape of their evolutionary history and complex trait architecture. South China is a multi-ethnic region and indigenously settled by ethnolinguistically diverse HM, Austroasiatic (AA), Tai-Kadai (TK), Austronesian (AN), and Sino-Tibetan (ST) people, which is regarded as East Asia's initial cradle of biodiversity. However, previous fragmented genetic studies have only presented a fraction of the landscape of genetic diversity in this region, especially the lack of haplotype-based genomic resources. The deep characterization of demographic history and natural-selection-relevant genetic architecture of HM people was necessary.

RESULTS

We reported one HM-specific genomic resource and comprehensively explored the fine-scale genetic structure and adaptative features inferred from the genome-wide SNP data of 440 HM individuals from 33 ethnolinguistic populations, including previously unreported She. We identified solid genetic differentiation between HM people and Han Chinese at 7.64‒15.86 years ago (kya) and split events between southern Chinese inland (Miao/Yao) and coastal (She) HM people in the middle Bronze Age period and the latter obtained more gene flow from Ancient Northern East Asians. Multiple admixture models further confirmed that extensive gene flow from surrounding ST, TK, and AN people entangled in forming the gene pool of Chinese coastal HM people. Genetic findings of isolated shared unique ancestral components based on the sharing alleles and haplotypes deconstructed that HM people from the Yungui Plateau carried the breadth of previously unknown genomic diversity. We identified a direct and recent genetic connection between Chinese inland and Southeast Asian HM people as they shared the most extended identity-by-descent fragments, supporting the long-distance migration hypothesis. Uniparental phylogenetic topology and network-based phylogenetic relationship reconstruction found ancient uniparental founding lineages in southwestern HM people. Finally, the population-specific biological adaptation study identified the shared and differentiated natural selection signatures among inland and coastal HM people associated with physical features and immune functions. The allele frequency spectrum of cancer susceptibility alleles and pharmacogenomic genes showed significant differences between HM and northern Chinese people.

CONCLUSIONS

Our extensive genetic evidence combined with the historical documents supported the view that ancient HM people originated from the Yungui regions associated with ancient "Three-Miao tribes" descended from the ancient Daxi-Qujialing-Shijiahe people. Then, some have recently migrated rapidly to Southeast Asia, and some have migrated eastward and mixed respectively with Southeast Asian indigenes, Liangzhu-related coastal ancient populations, and incoming southward ST people. Generally, complex population migration, admixture, and adaptation history contributed to the complicated patterns of population structure of geographically diverse HM people.

Exploring Genomics and Microbial Ecology: Analysis of Bidens pilosa L. Genetic Structure and Soil Microbiome Diversity by RAD-Seq and Metabarcoding

Bidens pilosa L., native to South America and commonly used for medicinal purposes, has been understudied at molecular and genomic levels and in its relationship with soil microorganisms. In this study, restriction site-associated DNA markers (RADseq) techniques were implemented to analyze genetic diversity and population structure, and metabarcoding to examine microbial composition in soils from Palmira, Sibundoy, and Bogotá, Colombia. A total of 2,984,123 loci and 3485 single nucleotide polymorphisms (SNPs) were identified, revealing a genetic variation of 12% between populations and 88% within individuals, and distributing the population into three main genetic groups, FST = 0.115 (p < 0.001) and FIT = 0.013 (p > 0.05). In the soil analysis, significant correlations were found between effective cation exchange capacity (ECEC) and apparent density, soil texture, and levels of Mg and Fe, as well as negative correlations between ECEC and Mg, and Mg, Fe, and Ca. Proteobacteria and Ascomycota emerged as the predominant bacterial and fungal phyla, respectively. Analyses of alpha, beta, and multifactorial diversity highlight the influence of ecological and environmental factors on these microbial communities, revealing specific patterns of clustering and association between bacteria and fungi in the studied locations.

Comprehensive evaluations of individual discrimination, kinship analysis, genetic relationship exploration and biogeographic origin prediction in Chinese Dongxiang group by a 60-plex DIP panel

BACKGROUND

Dongxiang group, as an important minority, resides in Gansu province which is located at the northwest China, forensic detection system with more loci needed to be studied to improve the application efficiency of forensic case investigation in this group.

METHODS

A 60-plex system including 57 autosomal deletion/insertion polymorphisms (A-DIPs), 2 Y chromosome DIPs (Y-DIPs) and the sex determination locus (Amelogenin) was explored to evaluate the forensic application efficiencies of individual discrimination, kinship analysis and biogeographic origin prediction in Gansu Dongxiang group based on the 60-plex genotype results of 233 unrelated Dongxiang individuals. The 60-plex genotype results of 4582 unrelated individuals from 33 reference populations in five different continents were also collected to analyze the genetic background of Dongxiang group and its genetic relationships with other continental populations.

RESULTS

The system showed high individual discrimination power, as the cumulative power of discrimination (CPD), cumulative power of exclusion (CPE) for trio and cumulative match probability (CMP) values were 0.99999999999999999999997297, 0.999980 and 2.7029E^- 24, respectively. The system could distinguish 98.12%, 93.78%, 82.18%, 62.35% and 39.32% of full sibling pairs from unrelated individual pairs, when the likelihood ratio (LR) limits were set as 1, 10, 100, 1000 and 10,000 based on the simulated family samples, respectively. Additionally, Dongxiang group had the close genetic distances with populations in East Asia, especially showed the intimate genetic relationships with Chinese Han populations, which were concluded from the genetic affinities and genetic background analyses of Dongxiang group and 33 reference populations. In terms of the effectiveness of biogeographic origin inference, different artificial intelligent algorithms possessed different efficacies. Among them, the random forest (RF) and extreme gradient boosting (XGBoost) algorithm models could accurately predict the biogeographic origins of 99.7% and 90.59% of three and five continental individuals, respectively.

CONCLUSION

This 60-plex system had good performance for individual discrimination, kinship analysis and biogeographic origin prediction in Dongxiang group, which could be used as a powerful tool for case investigation.

Genetic admixture history and forensic characteristics of Tibeto-Burman-speaking Qiang people explored via the newly developed Y-STR panel and genome-wide SNP data

Fine-scale patterns of population genetic structure and diversity of ethnolinguistically diverse populations are important for biogeographical ancestry inference, kinship testing, and development and validation of new kits focused on forensic personal identification. Analyses focused on forensic markers and genome-wide single nucleotide polymorphism (SNP) data can provide new insights into the origin, admixture processes, and forensic characteristics of targeted populations. Qiang people had a large sample size among Tibeto-Burmanspeaking populations, which widely resided in the middle latitude of the Tibetan Plateau. However, their genetic structure and forensic features have remained uncharacterized because of the paucity of comprehensive genetic analyses. Here, we first developed and validated the forensic performance of the AGCU-Y30 Y-short tandem repeats (STR) panel, which contains slowly and moderately mutating Y-STRs, and then we conducted comprehensive population genetic analyses based on Y-STRs and genome-wide SNPs to explore the admixture history of Qiang people and their neighbors. The validated results of this panel showed that the new Y-STR kit was sensitive and robust enough for forensic applications. Haplotype diversity (HD) ranging from 0.9932 to 0.9996 and allelic frequencies ranging from 0.001946 to 0.8326 in 514 Qiang people demonstrated that all included markers were highly polymorphic in Tibeto-Burman people. Population genetic analyses based on Y-STRs [RST, FST, multidimensional scaling (MDS) analysis, neighboring-joining (NJ) tree, principal component analysis (PCA), and median-joining network (MJN)] revealed that the Qiang people harbored a paternally close relationship with lowland Tibetan-Yi corridor populations. Furthermore, we conducted a comprehensive population admixture analysis among modern and ancient Eurasian populations based on genome-wide shared SNPs. We found that the Qiang people were a genetically admixed population and showed closest relationship with Tibetan and Neolithic Yellow River farmers. Admixture modeling showed that Qiang people shared the primary ancestry related to Tibetan, supporting the hypothesis of common origin between Tibetan and Qiang people from North China.

Genetic substructure of Guizhou Tai-Kadai-speaking people inferred from genome-wide single nucleotide polymorphisms data

The genome-wide characteristics and admixture history of the Tai-Kadai-speaking populations are essential for understanding the population genetic diversity in southern China. We genotyped about 700,000 single nucleotide polymorphisms (SNPs) of 239 individuals from six Tai-Kadai-speaking populations residing in the mountainous Guizhou Province of southwestern China. We merged the genome-wide data with available populations and ancients in East and Southeast Asia to infer Tai-Kadai-speaking populations’ admixture history and genetic structure. We observed a genetic substructure within the studied six populations in the PCA, ADMIXTURE, ChromoPainter, GLOBETROTTER, f-statistics, and qpWave analysis. The Dong, Zhuang, and Bouyei people had a strong genetic affinity with other Tai-Kadai-speaking and Austronesian groups in the surrounding area. However, Gelao showed an affinity to Sino-Tibetan groups, and Mulao people were genetically close to Hmong-Mien populations. qpAdm further illuminated that Gelao and Dong_Tongren composited more Han-related ancestry than Dong, Zhuang, Bouyei, and Mulao people. Meanwhile, we observed high frequencies of Y-chromosome haplogroup O in studied Tai-Kadai-speaking groups except for Gelao people with a high haplogroup N frequency. From the maternal side, haplogroup M7 was frequent in studied populations except for Tongren Dong, who had a high frequency of haplogroup B5. Our newly reported data are helpful for further exploring population dynamics in southern China.

Genomic insight into the population history and biological adaptations of high-altitude Tibetan highlanders in Nagqu

Tibetan, one of the largest indigenous populations living in the high-altitude region of the Tibetan Plateau (TP), has developed a suite of physiological adaptation strategies to cope with the extreme highland environment in TP. Here, we reported genome-wide SNP data from 48 Kham-speaking Nagqu Tibetans and analyzed it with published data from 1,067 individuals in 167 modern and ancient populations to characterize the detailed Tibetan subgroup history and population substructure. Overall, the patterns of allele sharing and haplotype sharing suggested (1) the relatively genetic homogeny between the studied Nagqu Tibetans and ancient Nepalese as well as present-day core Tibetans from Lhasa, Nagqu, and Shigatse; and (2) the close relationship between our studied Kham-speaking Nagqu Tibetans and Kham-speaking Chamdo Tibetans. The fitted qpAdm models showed that the studied Nagqu Tibetans could be fitted as having the main ancestry from late Neolithic upper Yellow River millet farmers and deeply diverged lineages from Southern East Asians (represented by Upper Paleolithic Guangxi_Longlin and Laos_Hoabinhian), and a non-neglectable western Steppe herder-related ancestry (∼3%). We further scanned the candidate genomic regions of natural selection for our newly generated Nagqu Tibetans and the published core Tibetans via FST, iHS, and XP-EHH tests. The genes overlapping with these regions were associated with essential human biological functions such as immune response, enzyme activity, signal transduction, skin development, and energy metabolism. Together, our results shed light on the admixture and evolutionary history of Nagqu Tibetan populations.

Genetic Admixture History and Forensic Characteristics of Guizhou Sui People Inferred From Autosomal Insertion/Deletion and Genome-Wide Single-Nucleotide Polymorphisms

Insertion-deletion (Indel) serves as one of the important markers in forensic personal identification and parentage testing, especially for cases with degraded samples. However, the genetic diversity and forensic features in ethnolinguistically diverse southwestern Chinese populations remain to be explored. Sui, one Tai-Kadai-speaking population residing in Guizhou, has a complex genetic history based on linguistic, historic, and anthropological evidence. In this study, we genotyped 30 Indels from 511 Guizhou Sui individuals and obtained approximately 700,000 genome-wide single-nucleotide polymorphisms (SNPs) in 15 representative Sui individuals to comprehensively characterize the genetic diversity, forensic characteristics, and genomic landscape of Guizhou Sui people. The estimated forensic statistically allele frequency spectrum and parameters demonstrated that this Indels panel was polymorphic and informative in Tai-Kadai populations in southern China. Results of principal component analysis (PCA), STRUCTURE, and phylogenetic trees showed that Guizhou Sui had a close genetic relationship with geographically close Tai-Kadai and Hmong-Mien people. Furthermore, genomic analysis based on the Fst and f4-statistics further suggested the genetic affinity within southern Chinese Tai-Kadai-speaking populations and a close relationship with geographically adjoining Guizhou populations. Admixture models based on the ADMIXTURE, f4, three-way qpAdm, and ALDER results demonstrated the interaction between the common ancestor for Tai-Kadai/Austronesian, Hmong-Mien, and Austroasiatic speaking populations played a significant role in the formation of modern Tai-Kadai people. We observed a sex-biased influence in Sui people by finding that the dominant Y chromosomal type was a Hmong-Mien specific lineage O2a2a1a2a1a2-N5 but the mtDNA lineages were commonly found in Tai-Kadai populations. The additional southward expansion of millet farmers in the Yellow River Basin has impacted the gene pool of southern populations including Tai-Kadai. The whole-genome sequencing in the future will shed more light on the finer genetic profile of Guizhou populations.