Inferring Chinese surnames with Y-STR profiles

Development and validation of YARN: A novel SE-400 MPS kit for East Asian paternal lineage analysis

Y-chromosomal short tandem repeat polymorphisms (Y-STRs) and Y-chromosomal single nucleotide polymorphisms (Y-SNPs) are valuable genetic markers used in paternal lineage identification and population genetics. Currently, there is a lack of an effective panel that integrates Y-STRs and Y-SNPs for studying paternal lineages, particularly in East Asian populations. Hence, we developed a novel Y-chromosomal targeted panel called YARN (Y-chromosome Ancestry and Region Network) based on multiplex PCR and a single-end 400 massive parallel sequencing (MPS) strategy, consisting of 44 patrilineage Y-STRs and 260 evolutionary Y-SNPs. A total of 386 reactions were validated for the effectiveness and applicability of YARN according to SWGDAM validation guidelines, including sensitivity (with a minimum input gDNA of 0.125 ng), mixture identification (ranging from 1:1-1:10), PCR inhibitor testing (using substances such as 50 μM hematin, 100 μM hemoglobin, 100 μM humic acid, and 2.5 mM indigo dye), species specificity (successfully distinguishing humans from other animals), repeatability study (achieved 100% accuracy), and concordance study (with 99.91% accuracy for 1121 Y-STR alleles). Furthermore, we conducted a pilot study using YARN in a cohort of 484 Han Chinese males from Huaiji County, Zhaoqing City, Guangdong, China (GDZQHJ cohort). In this cohort, we identified 52 different Y-haplogroups and 73 different surnames. We found weak to moderate correlations between the Y-haplogroups, Chinese surnames, and geographical locations of the GDZQHJ cohort (with λ values ranging from 0.050 to 0.340). However, when we combined two different categories into a new independent variable, we observed stronger correlations (with λ values ranging from 0.617 to 0.754). Overall, the YARN panel, which combines Y-STR and Y-SNP genetic markers, meets forensic DNA quality assurance guidelines and holds potential for East Asian geographical origin inference and paternal lineage analysis.

Evolutionary profiles and complex admixture landscape in East Asia: New insights from modern and ancient Y chromosome variation perspectives

Human Y-chromosomes are characterized by nonrecombination and uniparental inheritance, carrying traces of human history evolution and admixture. Large-scale population-specific genomic sources based on advanced sequencing technologies have revolutionized our understanding of human Y chromosome diversity and its anthropological and forensic applications. Here, we reviewed and meta-analyzed the Y chromosome genetic diversity of modern and ancient people from China and summarized the patterns of founding lineages of spatiotemporally different populations associated with their origin, expansion, and admixture. We emphasized the strong association between our identified founding lineages and language-related human dispersal events correlated with the Sino-Tibetan, Altaic, and southern Chinese multiple-language families related to the Hmong-Mien, Tai-Kadai, Austronesian, and Austro-Asiatic languages. We subsequently summarize the recent advances in translational applications in forensic and anthropological science, including paternal biogeographical ancestry inference (PBGAI), surname investigation, and paternal history reconstruction. Whole-Y sequencing or high-resolution panels with high coverage of terminal Y chromosome lineages are essential for capturing the genomic diversity of ethnolinguistically diverse East Asians. Generally, we emphasized the importance of including more ethnolinguistically diverse, underrepresented modern and spatiotemporally different ancient East Asians in human genetic research for a comprehensive understanding of the paternal genetic landscape of East Asians with a detailed time series and for the reconstruction of a reference database in the PBGAI, even including new technology innovations of Telomere-to-Telomere (T2T) for new genetic variation discovery.

Inference of population structure and admixture proportion from Y chromosomal data of Chinese population

In the past two decades, Y chromosome data has been generated for human population genetic studies. These Y chromosome datasets were produced with various testing methods and markers, thus difficult to combine them for a comprehensive analysis. In this study, we combine four human Y chromosomal datasets of Han, Tibetan, Hui, and Li ethnic groups. The dataset contains 27 microsatellites and 137 single nucleotide polymorphisms these populations share in common. We assembled a single dataset containing 2439 individuals from 25 nationwide populations in China. A systematic analysis of genetic distance and clustering was performed. To determine the gene flow of the studied population with worldwide populations, we modeled the ancestry informative markers. The reference panel was regarded as a mixture of South Asian (SAS), East Asian (EAS), European (EUR), African (AFR), and American (AMR) populations from 1000 Genomes data of Y chromosome using nonlinear data-fitting. We then calculated the admixture proportion of these four studied populations with 26 worldwide populations. The results showed that the Han and Hui have great genetic affinity, and Hui is the most admixed ethnic group, with 61.53% EAS, 34.65% SAS, 1.91% AFR, 1.56% AMR, and 0.04% EUR ancestry component (the AMR is highly admixed and thus should be ignored). All the other three ethnic groups contained more than 97% EAS ancestry component. The Li is the least admixed population in this study. The combined dataset in this study is the largest of this kind reported to date and proposes reference population data for use in future paternal genetic studies and forensic genealogical identification.

Interpretation of DNA data within the context of UK forensic science - investigation

This article is the second part of a review of the interpretation of DNA data in forensic science. The first part describes the evaluation of autosomal profile for criminal trials where an evidential weight is assigned to the profile of a person of interest (POI) and a crime-scene profile. This part describes the state of the art and future advances in the interpretation of forensic DNA data for providing intelligence information during an investigation. Forensic DNA is crucial in the investigative phase of an undetected crime where a POI needs to be identified. A sample taken from a crime scene is profiled using a range of forensic DNA tests. This review covers investigation using autosomal profiles including searching national and international crime and reference DNA databases. Other investigative methodologies described are kinship analysis; familial searching; Y chromosome (Y-STR) and mitochondrial (mtDNA) profiles; appearance prediction and geographic ancestry; forensic genetic genealogy; and body identification. For completeness, the evaluation of Y-STRs, mtDNA and kinship analysis are briefly described. Taken together, parts I and II, cover the range of interpretation of DNA data in a forensic context.

Development of the decision tree model for distinguishing individuals of Chinese four surnames from Zhanjiang Han population based on Y-STR haplotypes

Co-separation studies between surnames and Y chromosome genetic markers are beneficial to revealing population migrations, surname origins, population formation histories and forensic familial searching. Genetic distributions of 27 Y-STRs in Chinese four surnames (Li, Lin, Chen and Huang) from Zhanjiang Han population were investigated. Meanwhile, we tried to develop a decision tree model for surname predictions based on Y-STR haplotypes. Allelic frequencies of 27 Y-STRs showed that unique alleles were only observed in a certain surname; besides, some alleles displayed higher frequencies in a certain surname than those in other surnames, implying these alleles might be employed as the useful indicators for surname predictions. Haplotype match probability values of 27 Y-STRs in these surnames revealed that the system could be used as a valuable tool for forensic male identification. The developed decision tree model performed well for the training set with the accuracy of 0.9860 and obtained the relatively high accuracy (>0.70) for surname predictions of the testing set. To sum up, we explored the power of the machine learning to the surname predictions based on obtained Y-STR haplotypes, which showed promising application values in forensic familial searching.

Y chromosome analysis for common surnames in the Japanese male population

For many years of Japan's long history, Japanese surnames have been handed down patrilineally. This study investigated relations between major surnames and Y chromosomal polymorphism among the Japanese male population. To analyze genetic phylogeny in namesakes, the Y-single nucleotide polymorphism (SNP) plus Y-short tandem repeat (STR) approach was employed. A haplogroup based on SNPs and haplotypes at 17 STR loci were typed in 567 unrelated volunteers recruited in Kanagawa, Japan. Samples covered 27 common surnames such as Satoh and Suzuki, each name having 10-55 bearers. Significant difference was found for SNP haplogroup compositions and a multidimensional scaling plot using STR haplotypes in several surname groups. By contrast, these common surnames displayed wide diversity with phylogenetic networks, suggesting that no genetic drift event has occurred in their history. In all, 22 descent clusters were found, as judgcriteria ed by ad hoc of groups within five mutational steps in the 15 STR loci with the same haplogroup. The times of the most recent common ancestor ranged from 279 to over 2577 years. According to the approximate millennium span of Japanese surname history, descent criteria are expected to be reasonable for grouping within four step-neighbors. High heterogeneity of common surnames resembles that observed for England and Spain, but not for Ireland. Our results highlight that common Japanese surnames consist of descent clusters and many singletons, reflecting a mixture of long-term bearers and short-term bearers among the population. The genetic study of this population revealed characteristic features of Japanese surnames.

Relating Clans Ao and Aisin Gioro from northeast China by whole Y-chromosome sequencing

The Y-chromosome haplogroup C2b1a3a2-F8951 is the paternal lineage of the Aisin Gioro clan, the most important brother branch of the famous Mongolic-speaking population characteristic haplogroup C2*-Star Cluster (C2b1a3a1-F3796). However, investigations on its internal phylogeny are still limited. In this study, we used whole Y-chromosome sequencing to update its phylogenetic tree. In the revised tree, C2b1a3a2-F8951 and C2*-Star Cluster differentiated 3852 years ago (95% CI = 3295-4497). Approximately 3558 years ago (95% CI = 3013-4144), C2b1a3a2-F8951 was divided into two main subclades, C2b1a3a2a-F14753 and C2b1a3a2b-F5483. Currently, samples of C2b1a3a2-F8951 were mainly from the House of Aisin Gioro clan, the Ao family from Daur and some individuals mainly from northeast China. Although other haplogroups are also found in the Ao family, including C2b1a2-M48, C2b1a3a1-F3796, C2a1b-F845, and N1c-M178, the haplogroup C2b1a3a2-F8951 is still the most distinct genetic component. For haplogroup C2b1a3a2-F8951, the time of the most recent common ancestor of the House of Aisin Gioro clan and the Ao family were both very late, just a few hundred years ago. Some family-specific Y-SNPs of the House of Aisin Gioro and the Ao family were also discovered. This revision evidently improved the resolving power of Y-chromosome phylogeny in northeast Asia, deepening our understanding of the origin of these two families, even the Mongolic-speaking population.

An index of Chinese surname distribution and its implications for population dynamics

Objective

We propose an index to characterize the key feature of Chinese surname distributions and investigate its implications for population structure and dynamics.

Materials and methods

The surname dataset was obtained from the National Citizen Identity Information Center, which contains 1.28 billion Chinese citizens enrolled in 2007, excluding those of Hong Kong, Macao, and Taiwan. An index, the coverage ratio of stretched exponential distribution (CRSED), is proposed based on the crossover point of stretched exponential truncated power‐law distribution, where the stretched exponential term and the power‐law term contribute equally. We use multidimensional scaling technique to demonstrate the dependence of the similarity of one prefecture to the others on the CRSED.

Results

The CRSEDs of 362 prefectures exhibit an uneven distribution. The consistency of this index is evident by strong positive correlations of CRSEDs at the three administrative levels. This new index has a strong negative correlation with the proportion of the rare surnames. The prefectures with similar CRSEDs tend to adjoin each other on the administrative map, resulting in several distinct regions, each of which shares similar terrain features or historical migrations. The prefectures with lower CRSEDs are more dissimilar to the other prefectures, while the ones with higher CRSEDs are more similar to the others.

Discussion

The population dynamics of the prefectures with higher CRSEDs are more likely dominated by migratory movements, the dominant evolutionary forces of the prefectures with lower CRSEDs can be attributed to drift and mutation.

Regional surname affinity: A spatial network approach

Objective

We investigate surname affinities among areas of modern‐day China, by constructing a spatial network, and making community detection. It reports a geographical genealogy of the Chinese population that is result of population origins, historical migrations, and societal evolutions.

Materials and methods

We acquire data from the census records supplied by China's National Citizen Identity Information System, including the surname and regional information of 1.28 billion registered Chinese citizens. We propose a multilayer minimum spanning tree (MMST) to construct a spatial network based on the matrix of isonymic distances, which is often used to characterize the dissimilarity of surname structure among areas. We use the fast unfolding algorithm to detect network communities.

Results

We obtain a 10‐layer MMST network of 362 prefecture nodes and 3,610 edges derived from the matrix of the Euclidean distances among these areas. These prefectures are divided into eight groups in the spatial network via community detection. We measure the partition by comparing the inter‐distances and intra‐distances of the communities and obtain meaningful regional ethnicity classification.

Discussion

The visualization of the resulting communities on the map indicates that the prefectures in the same community are usually geographically adjacent. The formation of this partition is influenced by geographical factors, historic migrations, trade and economic factors, as well as isolation of culture and language. The MMST algorithm proves to be effective in geo‐genealogy and ethnicity classification for it retains essential information about surname affinity and highlights the geographical consanguinity of the population.