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.

Microsatellites' mutation modeling through the analysis of the Y-chromosomal transmission: Results of a GHEP-ISFG collaborative study

The Spanish and Portuguese Speaking Working Group of the International Society for Forensic Genetics (GHEP-ISFG) organized a collaborative study on mutations of Y-chromosomal short tandem repeats (Y-STRs). New data from 2225 father-son duos and data from 44 previously published reports, corresponding to 25,729 duos, were collected and analyzed. Marker-specific mutation rates were estimated for 33 Y-STRs. Although highly dependent on the analyzed marker, mutations compatible with the gain or loss of a single repeat were 23.2 times more likely than those involving a greater number of repeats. Longer alleles (relatively to the modal one) showed to be nearly twice more mutable than the shorter ones. Within the subset of longer alleles, the loss of repeats showed to be nearly twice more likely than the gain. Conversely, shorter alleles showed a symmetrical trend, with repeat gains being twofold more frequent than reductions. A positive correlation between the paternal age and the mutation rate was observed, strengthening previous findings. The results of a machine learning approach, via logistic regression analyses, allowed the establishment of algebraic formulas for estimating the probability of mutation depending on paternal age and allele length for DYS389I, DYS393 and DYS627. Algebraic formulas could also be established considering only the allele length as predictor for DYS19, DYS389I, DYS389II-I, DYS390, DYS391, DYS393, DYS437, DYS439, DYS449, DYS456, DYS458, DYS460, DYS481, DYS518, DYS533, DYS576, DYS626 and DYS627 loci. For the remaining Y-STRs, a lack of statistical significance was observed, probably as a consequence of the small effective size of the subsets available, a common difficulty in the modeling of rare events as is the case of mutations. The amount of data used in the different analyses varied widely, depending on how the data were reported in the publications analyzed. This shows a regrettable waste of produced data, due to inadequate communication of the results, supporting an urgent need of publication guidelines for mutation studies.

Male Pedigree Toolbox: A Versatile Software for Y-STR Data Analyses

Y-chromosomal short tandem repeats (Y-STRs) are widely used in forensic, genealogical, and population genetics. With the recent increase in the number of rapidly mutating (RM) Y-STRs, an unprecedented level of male differentiation can be achieved, widening and improving the applications of Y-STRs in various fields, including forensics. The growing complexity of Y-STR data increases the need for automated data analyses, but dedicated software tools are scarce. To address this, we present the Male Pedigree Toolbox (MPT), a software tool for the automated analysis of Y-STR data in the context of patrilineal genealogical relationships. The MPT can estimate mutation rates and male relative differentiation rates from input Y-STR pedigree data. It can aid in determining ancestral haplotypes within a pedigree and visualize the genetic variation within pedigrees in all branches of family trees. Additionally, it can provide probabilistic classifications using machine learning, helping to establish or prove the structure of the pedigree and the level of relatedness between males, even for closely related individuals with highly similar haplotypes. The tool is flexible and easy to use and can be adjusted to any set of Y-STR markers by modifying the intuitive input file formats. We introduce the MPT software tool v1.0 and make it publicly available with the goal of encouraging and supporting forensic, genealogical, and other geneticists in utilizing the full potential of Y-STRs for both research purposes and practical applications, including criminal casework.

Genetic Polymorphism Analysis of 24 Y-STRs in a Han Chinese Population in Luzhou, Southwest China

Han is the largest of China's 56 ethnic groups and the most populous ethnic group in the world. The Luzhou region is located in southwest China, at the junction of three provinces. The unique historical factors contribute to the genetic polymorphism information. Short tandem repeats (STRs) are highly polymorphic, but the polymorphism of the Y chromosomal STRs (Y-STRs) loci in the Luzhou region is still unclear. It is of great significance to provide Y-STRs genetic data for the Han population from the Luzhou areas of southwest China. A total of 910 unrelated male individuals of the Han population from the Luzhou area were recruited, and 24 Y-STRs were analyzed. The population structure and phylogenetic relationships were compared with those of another 11 related Han populations. A total of 893 different haplotypes were achieved from 910 samples, of which 877 (98.21%) haplotypes were unique. Haplotype diversity and discrimination were 0.999956 and 0.981319, respectively. The lowest genetic diversity of DYS437 is 0.4321, and the highest genetic diversity of DYS385a/b is 0.9642. Pair-to-pair genetic distance and relative probability values indicate that Luzhou Han people are close to Sichuan Han people, Guangdong Han people, and Hunan Han people, which is consistent with geographical distribution, historical influence, and economic development. The 24 Y-STR markers of the southwest Luzhou Han population were highly polymorphic, which provided us with genetic polymorphism information and enriched the population genetic database. Therefore, it is of great value to our forensic applications and population genetics research.

Genetic portrait of the Amazonian communities of Peru and Bolivia: The legacy of the Takanan-speaking people

During the colonial period in South America, many autochthonous populations were affected by relocation by European missionary reductions and other factors that impacted and reconfigured their genetic makeup. Presently, the descendants of some "reduced" and other isolated groups are distributed in the Amazonian areas of Peru, Bolivia, and Brazil, and among them, speakers of Takanan and Panoan languages. Based on linguistics, these peoples should be closely related, but so far no DNA comparison studies have been conducted to corroborate a genetic relationship. To clarify these questions, we used a set of 15 short tandem repeats of the non-recombining part of the Y-chromosome (Y-STRs) and mitochondrial DNA (mtDNA) control region sequence data. Paternal line comparisons showed the Takanan-speaking peoples from Peru and Bolivia descended from recent common ancestors; one group was related to Arawakan, Jivaroan, and Cocama and the other to Panoan speakers, consistent with linguistics. Also, a genetic affinity for maternal lines was observed between some Takanan speakers and individuals who spoke different Amazonian languages. Our results supported a shared ancestry of Takanan, Panoan, Cocama, and Jivaroan-speaking communities who appeared to be related to each other and came likely from an early Arawak expansion in the western Amazonia of South America.

Analysis of Y-STR diversity and DNA methylation variation among Black and Indian males from KwaZulu-Natal, South Africa

Y-chromosome short tandem repeats (Y-STRs) are essential in understanding genetic structure and diversity of human populations and, most importantly, in identification of male perpetrators in criminal investigations. DNA methylation differences have been reported in human populations and methylation pattern at the CpG sites found within or flanking the Y-STR sites could also aid in human identification. Studies based on DNA methylation (DNAm) at Y-STRs are currently limited. The current study aimed to analyze the Y-STR diversity in South African Black and Indian individuals living in KwaZulu-Natal, Durban, South Africa, with the Yfiler™ Plus Kit and to analyze DNAm patterns in Y-STR markers CpG sites. DNA from 247 stored saliva samples were isolated and quantified. Across the 27 Y-STR loci in the Yfiler™ Plus Kit, 253 alleles were observed in 113 South African Black and Indian males, 112 unique haplotypes were observed, and one haplotype appeared twice (two Black individuals). No statistically significant differences were observed in the genetic diversity between the two population groups (Fst = 0.028, p-value ≥ 0.05). The kit showed a high discrimination capacity (DC) of 0.9912 and an overall haplotype diversity (HD) = 0.9995 among the sampled population groups. DYS438 and DYS448 markers displayed 2 and 3 CpG sites, respectively. Based on the two-tailed Fisher's Exact test, there were no statistically significant differences in the DNAm levels at DYS438 CpGs of Black and Indian males (p > 0.05). The Yfiler™ Plus Kit can be considered highly discriminatory among South African Black and Indian males. Studies on the South African population using Yfiler™ Plus Kit are scarce. Hence, accumulating Y-STR data on the diverse South African population will enhance the representation of South Africa in STR databases. Knowing which Y-STR markers are significantly informative for South Africa is essential for developing Y-STR kits better suited for the different ethnic groups. And to the best of our knowledge, DNA methylation analysis in Y-STR for different ethnic groups has never been done before. Complementing Y-STR data with methylation knowledge could provide population-specific information for forensic identification.

Distribution of Y-chromosome haplogroups in Serbian population groups originating from historically and geographically significant distinct parts of the Balkan Peninsula

Our study enrolled 1200 Serbian males originating from three geographical regions in the Balkan Peninsula inhabited by Serbs: present-day Serbia, regions of Old Herzegovina and Kosovo and Metohija. These samples were genotyped using the combination of 23 Y-chromosomal short tandem repeats (Y-STRs) loci and 17 Ychromosomal single nucleotide polymorphisms (Y-SNPs) loci for the haplotype and haplogroup analysis in order to characterize in detail Y chromosome flow in the recent history. Serbia's borders have changed through history, forcing Serbs constantly to migrate to different regions of Balkan Peninsula. The most significant migration waves in the recent history towards present-day Serbia occurred from the regions of Old- Herzegovina and Kosovo and Metohija that lie in the south-west/south. High haplotype diversity and discrimination capacity were observed in all three datasets, with the highest number of unique haplotypes (381) and discrimination capacity (0.97) detected in the samples originating from the present-day Serbia. Haplogroup composition didn't differ significantly among datasets, with three dominant haplogroups (I-M170, E-P170 and R-M198), and haplogroup I-M170 being the most frequent in all three datasets. Haplogroup E-P170 was the second most dominant in the dataset originating from geographical region of Kosovo and Metohija, whereas haplogroup R-M198 was the second most prevalent in the dataset from historical region of Old Herzegovina. Based on the phylogenetic three for haplogroup I constructed within this study, haplogroup I2a1-P37.2 was the most dominant within all three datasets, especially in the dataset from historical region of Old Herzegovina, where 182 out of 400 samples were derived for SNP P37.2. Genetic distances between three groups of samples, evaluated by the Fst and Rst statistical values, and further visualized through multidimensional scaling plot, showed great genetic similarity between datasets from Old Herzegovina and present-day Serbia. Genetic difference in the haplogroup distribution and frequency between datasets from historical region of Old Herzegovina and from geographical region of Kosovo and Metohija was confirmed with highest Fst and Rst vaules. In this study we have distinguished genetic structure, diversity and haplogroup frequencies within 1200 Serbian males from three datasets, relationships among them as well as with other Balkan and European populations, which is useful for studying recent demographic history.

Genetic characteristics and forensic features of Xibe ethnic group revealed via extended set of Y-STRs

BACKGROUND

Xibe is the fifth largest minority population of Liaoning province. Predominately they live in Liaoning province (69.52%), followed by Xinjiang (18.06%), Heilongjiang (3.99%), Jilin (1.63%) and Inner Mongolia provinces (1.57%).

AIM

To provide an updated and precise population database on an extended set of Y STRs not available before and explore the forensic characteristics of 26 Y chromosomal STRs.

SUBJECTS & METHODS

In this study, we genotyped 406 unrelated Xibe male individuals from Liaoning province using Goldeneye® 26Y System kit and calculated the forensic parameters of these 26 Y STRs loci.

RESULTS

All haplotypes generated for 406 Xibe samples using Goldeneye^® 26Y kit were unique with a discrimination capacity (DC) of 1. On restricting the haplotypes to the Y-filer® set of 17 Y-STRs, we observed 392 haplotypes. Among them 93.53% (380) were unique with a DC of 0.9655 and haplotype diversity (HD) of 0.9998, showing high discrimination power of the extended set of markers in this population. Allelic frequencies ranged from 0.0024 to 0.7684 across 26 Y STRs loci. DYS385 showed the highest gene diversity (0.9691) among all markers.

CONCLUSION

According to pairwise R_ST genetic distances among Xibe populations from China, the Liaoning Xibe population showed the closest genetic distance (0.0035) followed by Xinjiang Xibe population (0.0218). Multidimensional scaling (MDS) analysis among Xibe and 29 other Chinese populations showed that local populations such as Manchu from Liaoning and Han from Beijing had a close affinity while Tibetans from Aba, China, were most distant from Xibe populations. Moreover, 12 individuals showed a null allele at DYS448 in Xibe population samples. We submitted Y-STRs data in the Y-Chromosome Haplotype Reference Database (YHRD) for future forensic and other usage.

Forensic features and phylogenetic analyses of the population of Nayagarh (Odisha), India using 23 Y-STRs

AIM

The present study was designed to explore the STR diversity and genomic history of the inhabitants of Nayagarh district of Odisha, India. We also tested the proficiency of the most recent, new generation PowerPlex^R Y23 multiplex system for forensic characterisation and to decipher the phylogenetic affinities.

SUBJECTS AND METHODS

The genetic diversity and polymorphism among 236 healthy unrelated male volunteers from Nayagarh district of Odisha, India was investigated. This investigation was carried out via 23 Y-chromosomal STRs using capillary electrophoresis.

RESULT

A total 223 unique haplotypes were reported. Discrimination capacity (DC), gene diversity (GD) and power of discrimination (PD) were observed as 0.945, 0.999999999998333, and 0.99999999999794, respectively. Polymorphic information content (PIC) and matching probability (PM) were reported as 0.999999999925535 and 2.06 × 10^-12, respectively. Simultaneously, the haplogroup analysis characterised with C2, E1b1a, E1b1b, G2a, H1, I2a, J2a, J2b, L, O, O1, O2, Q, R1a, R2, and T haplogroups, disclosing the possible geographical relatedness of the studied population to different areas of the world.

CONCLUSION

Phylogenetic analysis with previously reported Indian and Asian populations showed the genetic closeness of the studied population to different Indian populations and the Bangladeshi population of Dhaka, whereas the Bhotra population of Odisha and Han population of China showed much less genetic affinity.

The Ancestry of Eastern Paraguay: A Typical South American Profile with a Unique Pattern of Admixture

Immigrants from diverse origins have arrived in Paraguay and produced important demographic changes in a territory initially inhabited by indigenous Guarani. Few studies have been performed to estimate the proportion of Native ancestry that is still preserved in Paraguay and the role of females and males in admixture processes. Therefore, 548 individuals from eastern Paraguay were genotyped for three marker sets: mtDNA, Y-SNPs and autosomal AIM-InDels. A genetic homogeneity was found between departments for each set of markers, supported by the demographic data collected, which showed that only 43% of the individuals have the same birthplace as their parents. The results show a sex-biased intermarriage, with higher maternal than paternal Native American ancestry. Within the native mtDNA lineages in Paraguay (87.2% of the total), most haplogroups have a broad distribution across the subcontinent, and only few are concentrated around the Paraná River basin. The frequency distribution of the European paternal lineages in Paraguay (92.2% of the total) showed a major contribution from the Iberian region. In addition to the remaining legacy of the colonial period, the joint analysis of the different types of markers included in this study revealed the impact of post-war migrations on the current genetic background of Paraguay.

RMplex: An efficient method for analyzing 30 Y-STRs with high mutation rates

Y-chromosomal short tandem repeats (Y-STRs) with high mutation rates are recognized as valuable genetic markers for differentiating paternally related men, who typically cannot be separated with standard Y-STRs, and were shown to provide paternal lineage differentiation on a higher resolution level than standard Y-STRs. Both features make Y-STRs with high mutation rates relevant in criminal casework, particularly in sexual assault cases involving highly unbalanced male-female DNA mixtures that often fail autosomal forensic STR profiling for the male donor. Previously, the number of known Y-STRs with mutation rates higher than 10^-2 per locus per generation termed rapidly mutating Y-STRs (RM Y-STRs) was limited to 13, which has recently been overcome by the discovery and characterization of 12 additional RM Y-STRs. Here, we present the development and validation of RMplex, an efficient genotyping system for analyzing 30 Y-STRs with high mutation rates, including all currently known RM Y-STRs, using multiplex PCR with capillary electrophoresis (CE) or massively parallel sequencing (MPS), overall targeting a total of 44 male-specific loci. If previously unavailable, repeat number assignations were provided based on newly generated MPS data. Validation tests based on the CE method demonstrated that the results were both repeatable and reproducible, full profiles were achieved with minimal input DNA of 250 pg for RMplex 1 and 100 pg for RMplex 2, and in the presence of inhibitors, or with a surplus of female DNA, the assays performed reasonably well. Application of RMplex to differentiate between paternally related men was exemplified in 32 males belonging to five different paternal pedigrees. Given further successful forensic validation testing, we envision the future application of RMplex in criminal cases where it is suspected, or cannot be excluded, that the crime scene trace originated from a male relatives of the suspect who is highlighted with standard Y-STR matching. Other applications of RMplex are in criminal cases without known suspects to differentiate between male relatives highlighted in familial searching based on standard Y-STR matching.

Molecular characterization of 23 Y chromosomal STR markers in the Gurjar population of National Capital Region (NCR), India

In the present study, DNA samples of 202 unrelated male individuals of Gurjar population were evaluated for the molecular diversity at 23 Y chromosomal Y-STR markers. Out of selected individuals, results showed 143 unique haplotypes. Highest degree of gene diversity (GD), polymorphic information content (PIC), and power of discrimination (PD) was observed as 0.7941, 0.7590, and 0.7902, respectively, for the locus DYS385a/b. Haplotype diversity (HD), gene diversity (GD), polymorphic information content (PIC), and power of discrimination (PD) was found to be 0.7079, 0.999999999989, 0.9999999996, and 0.999999999986, respectively, for the studied 23 Y-STR markers. Allele 11 of locus DYS392 was found to be the most frequent allele with the frequency of 0.762. In inter-population relationship, studied population showed genetic relatedness with the population of Jammu and Kashmir, India, and Ladakh, India. The haplotype data of the present study will not only enrich the existing Indian Y-STR data but will also be useful for forensic DNA application.

Genetic reconstruction and phylogenetic analysis by 193 Y-SNPs and 27 Y-STRs in a Chinese Yi ethnic group

Yi is the seventh-largest ethnic group in China and features mountainous regional characteristics. The Liangshan Yi Autonomous Prefecture is the largest Yi agglomeration with isolated geographical conditions, profoundly impeding genetic communication. Here, we investigated 427 unrelated males of Liangshan from 193 Y-chromosome single nucleotide polymorphisms (Y-SNPs) and 27 Y-chromosome short tandem repeats (Y-STRs) to reveal the genetic structure and paternal phylogeny of the group. The haplogroup diversity reached 0.9169 with 46 different subhaplogroups by 193 Y-SNPs, and the haplotype diversity reached 0.9999 by 27 Y-STR loci. Multidimensional scaling (MDS), N-J tree, and Network were constructed to decipher and visualize the genetic relations between Yi and worldwide groups. Our results revealed: (1) the Network by Y-STRs and Y-SNPs showed the haplogroup D1a1a-M15 in the Liangshan Yi population was a ramification of Tibetan groups' expansion from west to east on the plateau; (2) the haplogroup distribution and the mismatch mutation analysis indicated the haplogroup O2a2b1a1a1a4a2-Z25929 of Liangshan Yi derived from manifold Southeast Asian immigrants; (3) a high-resolution Y-SNPs panel is vital to depict accurate paternal derivations and build an integrated and refining genetic structure of ethnic groups.

Tibetan Y-STR trait in the eleven regions of the Qinghai-Tibet Plateau

Y-Chromosomal short-tandem repeats (Y-STRs) could provide highly valuable information for forensic investigation and demographic studies. However, there is still no systematic Y-STR information on Tibetan as obtained from different regions of the broad Qinghai-Tibet Plateau. In this study, an analysis was conducted on 585 male individuals, classed into 3 different dialect branches as Ü-Tsang, Amdo, and Khams and originating from 11 scattered regions of the Qinghai-Tibet Plateau. The gene diversity values of the 41 Y-STRs in Tibetan ranged from 0.3636 to 0.9322. Additionally, a total of 563 distinct haplotypes were obtained with an overall haplotype diversity of 0.9999 and a discrimination capacity of 0.9624. As suggested by the inter-population diversity analysis, there were two main separated clades of Tibetan subgroups. The visualization of pairwise genetic distances between 11 Tibetan subgroups and 59 reference populations using cladogram revealed the distribution of various populations, which was basically consistent with the patterns of geographic origin and linguistic affinity.

Genetic structure and forensic characterization of 36 Y-chromosomal STR loci in Tibeto-Burman-speaking Yi population

BACKGROUND

Male-specifically inherited Y-STRs have been widely used in population genetics and forensic investigations.

METHODS

We genotyped and analyzed Y chromosome haplotypes of 408 unrelated Tibeto-Burman-speaking Yi male individuals from Guizhou using Goldeneye® Y-PLUS kit. Population comparisons between the Guizhou Yi and 67 reference groups were performed via the AMOVA, MDS, and phylogenetic relationship reconstruction.

RESULTS

A total of 389 alleles and 396 haplotypes could be detected, and the allelic frequencies ranged from 0.0025 to 0.9875. The haplotype diversity, random match probability, and discrimination capacity values were 0.9999, 0.0026, and 0.9900, respectively. The gene diversity (GD) of 36 Y-STR loci in the studied group ranged from 0.0248 (DYS645) to 0.9601 (DYS385a/b). Our newly genotyped Yi samples show a close affinity with other Tibeto-Burman speaking groups in China and Southeast Asia.

CONCLUSIONS

The population stratification was almost consistent with the geographic distribution and language-family, both among Chinese and worldwide ethnic groups. Our data may provide useful information for paternal lineage in the forensic application and population genetics, as well as evidence for archaeological and historical research.

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.

A Y-chromosomal survey of Ecuador's multi-ethnic population reveals new insights into the tri-partite population structure and supports an early Holocene age of the rare Native American founder lineage C3-MPB373

Ecuador is a multiethnic and pluricultural country with a complex history defined by migration and admixture processes. The present study aims to increase our knowledge on the Ecuadorian Native Amerindian groups and the unique South American Y-chromosome haplogroup C3-MPB373 through the analysis of up to 23 Y-chromosome STRs (Y-STRs) and several Y-SNPs in a sample of 527 Ecuadorians from 7 distinct populations and geographic areas, including Kichwa and non-Kichwa Native Amerindians, Mestizos and Afro-Ecuadorians. Our results reveal the presence of C3-MPB373 both in the Amazonian lowland Kichwa with frequencies up to 28 % and, for the first time, in notable proportions in Kichwa populations from the Ecuadorian highlands. The substantially higher frequencies of C3-MPB373 in the Amazonian lowlands found in Kichwa and Waorani individuals suggest a founder effect in that area. Notably, estimates for the time to the most recent common ancestor (TMRCA) in the range of 7.2-9.0 kya point to an ancient origin of the haplogroup and suggest an early Holocene expansion of C3-MPB373 into South America. Finally, the pairwise genetic distances (R_ST) separate the Kichwa Salasaka from all the other Native Amerindian and Ecuadorian groups, indicating a so far hidden diversity among the Kichwa-speaking populations and suggesting a more southern origin of this population. In sum, our study provides a more in-depth knowledge of the male genetic structure of the multiethnic Ecuadorian population, as well as a valuable reference dataset for forensic use.

Haplotype analysis of 36 Y-STR loci in a Chinese Han population from Anhui Province, Eastern China

We analyzed haplotypes for 36 Y chromosomal STRs (Y-STRs), including 27 Yfiler Plus loci and 9 additional STRs (DYS549, DYS643, DYS508, DYS447, DYS596, DYS444, DYS557, and DYS527a/b) in 2018 unrelated Chinese Han individuals from Anhui Province using DNATyper^TM 36Y Kit. Phylogenetic analysis was performed to determine the genetic relationship of the Anhui Han population with other neighboring and/or linguistically close populations.

Haplotype data and forensic evaluation of 23 Y-STR and 12 X-STR loci in eight ethnic groups from Eritrea

Eritrea is a multi-ethnic country of over 3 million of people consisting of different ethnic groups, having each its own language and cultural tradition. Due to the lack of population genetic data for markers of forensic interest, in this study, we analyzed the genetic polymorphisms of 23 Y-chromosome STR loci and of 12 X-chromosome STR loci in a sample of 255 unrelated individuals from 8 Eritrean ethnic groups, with the aim to generate a reference haplotype database for anthropological and forensic applications. X- and Y-chromosomes markers may indeed offer information especially in personal identification and kinship testing, when relying on the availability of large local population data to derive sufficiently accurate frequency estimates. The population genetic analyses in the Eritrean sample for both the two set of Y- and X-STR markers showed high power of discrimination both at country-based and population levels. Comparison population results highlight the importance of considering the ethnic composition within the analyzed country and the necessity of increasing available data especially when referring to heterogeneous populations such as the African ones.

Massively parallel sequencing of sex-chromosomal STRs in Saudi Arabia reveals patrilineage-associated sequence variants

Massively parallel sequencing (MPS) of forensic STRs has the potential to reveal additional allele diversity compared to conventional capillary electrophoresis (CE) typing strategies, but population studies are currently relatively few in number. The Verogen ForenSeq™ DNA Signature Prep Kit includes both Y-STRs and X-STRs among its targeted loci, and here we report the sequences of these loci, analysed using Verogen's ForenSeq™ Universal Analysis Software (UAS) v1.3 and STRait Razor v3.0, in a representative sample of 89 Saudi Arabian males. We identified 56 length variants (equivalent to CE alleles) and 75 repeat sequence sub-variants across the six X-STRs analysed; equivalent figures for the set of 24 Y-STRs were 147 and 192 respectively. We also observed two flanking sequence variants for the X-, and six for the Y-STRs. Recovery of sequence data and concordance with CE data (where available) across the tested loci was good, though rare flanking variation affected interpretation and allele calling at DYF387S1 and DXS7132. Examination of flanking sequences of the Y-STRs revealed five SNPs (L255, M4790, BY7692, Z16708 and S17543) previously shown to define specific haplogroups by Y-chromosome sequencing. These define Y-haplogroups in 62 % of our sample, a proportion that increases to 91 % when haplogroup-associated repeat-sequence motifs are also considered. A population-level comparison of the Saudi Arabian X-STRs with a global sample showed our dataset to be part of a large cluster of populations of West Eurasian and Middle Eastern origin.

Ethnic fragmentation and degree of urbanization strongly affect the discrimination power of Y-STR haplotypes in central Sahel

Y chromosome short tandem repeats (Y-STRs) are commonly used to identify male lineages for investigative and judicial purposes and could represent the only source of male-specific genetic information from unbalanced female-male mixtures. The Yfiler Plus multiplex, which includes twenty conventional and seven rapidly-mutating Y-STRs, represents the most discriminating patrilineal system commercially available to date. Over the past five years, this multiplex has been used to analyze several Eurasian populations, with a reported discrimination capacity (DC) approaching or corresponding to the highest possible value. However, despite the inclusion of rapidly mutating Y-STRs, extensive haplotype sharing was still reported for some African populations due to a number of different factors affecting the effective population size. In the present study, we analyzed 27 Y-STRs included in the Yfiler Plus multiplex and 82 Y-SNPs in central Sahel (northern Cameroon and western Chad), an African region characterized by a strong ethnic fragmentation and linguistic diversity. We evaluated the effects of population sub-structuring on genetic diversity by stratifying a sample composed of 431 males according to their ethnicity (44 different ethnic groups) and urbanization degree (four villages and four towns). Overall, we observed a low discrimination capacity (DC = 0.90), with 71 subjects (16.5 %) sharing 27 Y-STR haplotypes. Haplotype sharing was essentially limited to subjects with the same binary haplogroup, coming from the same location and belonging to the same ethnic group. Haplotype sharing was much higher in rural areas (average DC = 0.83) than urban settlements (average DC = 0.96) with a significant correlation between DC and census size (r = 0.89; p = 0.003). Notably, we found that genetic differentiation between villages from the same country (Φ_ST = 0.14) largely exceeded that found among countries (Φ_ST = 0.02). These findings have important implications for the choice of the appropriate reference population database to evaluate the statistical relevance of forensic Y-haplotype matches.

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

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.

Joint Genetic Analyses of Mitochondrial and Y-Chromosome Molecular Markers for a Population from Northwest China

The genetic markers on mitochondria DNA (mtDNA) and Y-chromosome can be applied as a powerful tool in population genetics. We present a study to reveal the genetic background of Kyrgyz group, a Chinese ethnic group living in northwest China, and genetic polymorphisms of 60 loci on maternal inherited mtDNA and 24 loci on paternal inherited Y-chromosome short tandem repeats (Y-STRs) were investigated. The relationship between the two systems was tested, and the result indicated that they were statistically independent from each other. The genetic distances between Kyrgyz group and 11 reference populations for mtDNA, and 13 reference populations for Y-STRs were also calculated, respectively. The present results demonstrated that the Kyrgyz group was genetically closer to East Asian populations than European populations based on the mtDNA loci but the other way around for the Y-STRs. The genetic analyses could largely strengthen the understanding for the genetic background of the Kyrgyz group.

The construction and application of a new 17-plex Y-STR system using universal fluorescent PCR

Y-chromosomal short tandem repeat (Y-STR) polymorphisms are useful in forensic identification, population genetics, and human structures. However, the current Y-STR systems are limited in discriminating distant relatives in a family with a low discrimination power. Increasing the capacity of detecting Y chromosomal polymorphisms will drastically narrow down the matching number of genealogy populations or pedigrees. In this study, we developed a system containing 17 Y-STRs that are complementary to the current commercially available Y-STR kits. This system was constructed by multiplex PCR with expected sizes of 126-400 bp labeled by different fluorescence molecules (DYS715, DYS709, DYS716, DYS713, and DYS607 labeled by FAM; DYS718, DYS723, DYS708, and DYS714 labeled by JOE; DYS712, DYS717, DYS721, and DYS605 labeled by TAMRA; and DYS719, DYS726, DYS598, and DYS722 labeled by ROX). The system was extensively tested for sensitivity, male specificity, species specificity, mixture, population genetics, and mutation rates following the Scientific Working Group on DNA Analysis Methods (SWGDAM) guidelines. The genetic data were obtained from eight populations with a total of 1260 individuals. Our results showed that all the 17 Y-STRs are human- and male-specific and include only one copy of the Y-chromosome. The 17 Y-STR system detects 143 alleles and has a high discrimination power (0.996031746). Mutation rates were different among the 17 Y-STRs, ranging from 0.30 to 3.03%. In conclusion, our study provides a robust, sensitive, and cost-effective genotyping method for human identification, which will be beneficial for narrowing the search scope when applied to genealogy searching with the Y-STR DNA databank.

Comprehensive genetic structure analysis of Han population from Dalian City revealed by 20 Y-STRs

BACKGROUND

Dalian is a city formed in the 1880s in Liaoning province, Northeastern China with a population of 6.69 million now. Han is the largest ethnic group not only across Mainland China (92%) and Taiwan (97%) but also considered to be the largest ethnic group of the world contributing to above 18% of world's population.

METHODS

In the current study, we genotyped Goldeneye® 20Y System loci in 879 unrelated male individuals from the Han ethnic group in Dalian city and calculated the forensic parameters of the 20 Y-STR loci.

RESULTS

In total, we observed 855 haplotypes, among which 835 (94.99%) were unique. The discrimination capacity (DC) of overall Goldeneye® 20Y System is 97.27% and it slightly reduces to 96.93% when only Y-filer® set of 17 Y-STRs were used, which mitigates using the extended set of markers in this population. We found DYS388 showed the lowest gene diversity (0.5151), whereas DYS389II showed the highest gene diversity (0.7621) in single copy Y-STR, and DYS385 showed the highest gene diversity (0.9683) among all.

CONCLUSION

Multidimensional scaling (MDS) analysis based upon pairwise Rst genetic distance showed difference among Han population from the east to the west and from the north to the south. We also predicted haplogroups using Y-STR haplotypes, which showed the dominance of Haplogroup O (65.2%) followed by Haplogroup C (14.5%) in Dalian Han population. Moreover, we found 10 individuals showed a null allele at the DYS448 in our samples. We also performed linear discriminatory analysis (LDA) between Han and other prominent Chinese minority ethnic groups. We presented Y-STRs data in the Y-Chromosome Haplotype Reference Database (YHRD) for the future forensic and other usage.

Population genetics of 27 Y-STRs for the Yi population from Liangshan Yi Autonomous Prefecture, China

Liangshan Yi Autonomous Prefecture locates at the south of Sichuan, China, and this area has the largest population of Yi ethnic nationally. In order to study the population data of Y-STRs of this area and contribute to the worldwide Y-STR database, we genotyped 628 unrelated individuals using commercially available Goldeneye® DNA ID 27Y system. Gene diversity (GD) values and haplotype diversity (HD) were calculated. Population comparison results showed that Liangshan Yi population was significantly differently from other populations.

Paternal lineages and forensic parameters based on 23 Y-STRs (Powerplex® Y23) in Mestizo males from Mexico City

We analyzed 307 Mexican-Mestizo (admixed) males from Mexico City with the Powerplex® Y23 system. The complete list of Y-STR haplotypes was uploaded into the YHRD database (accession number YA004275). The discriminatory capacity (98.70 %) and gene diversity (D = 99.99 %) were calculated, improving the haplotype diversity regarding previous studies in Mexico based on 17 Y-STRs and 12 Y-STRs. Haplogroup distribution assignment was inferred by means of two different online-available algorithms. The Native American Q* haplogroup was the most frequent (66.2 %), followed by the European R1b lineage (19.5 %). In addition, eight Eurasian (3.9%) and two African (6.6%) haplogroups were observed in this population sample from Mexico City. Interestingly, AMOVA test showed a low but significant differentiation among Mexican-Mestizos (Fst = 1.52%; p = 0.0000), suggesting that four population clusters allow to explain their genetic structure according to geographic criteria: north, west, center, and south.

Genetic characteristics of 23 Y-chromosomal STRs in the Kinh population in Northern Vietnam

We collected and analysed the genetic characteristics of 23 Y-STR data of 200 unrelated Kinh individuals living in the North of Vietnam. Haplotype frequencies and forensic parameters were calculated, showing high discrimination value. Population comparison analysis was performed to determine the genetic relationship with neighbouring ethnicities, in particular with Thai and Han populations.

Genetic ancestry of families of putative Inka descent

This study focuses on the descendants of the royal Inka family. The Inkas ruled Tawantinsuyu, the largest pre-Columbian empire in South America, which extended from southern Colombia to central Chile. The origin of the royal Inkas is currently unknown. While the mummies of the Inka rulers could have been informative, most were destroyed by Spaniards and the few remaining disappeared without a trace. Moreover, no genetic studies have been conducted on present-day descendants of the Inka rulers. In the present study, we analysed uniparental DNA markers in 18 individuals predominantly from the districts of San Sebastian and San Jerónimo in Cusco (Peru), who belong to 12 families of putative patrilineal descent of Inka rulers, according to documented registries. We used single-nucleotide polymorphisms and short tandem repeat (STR) markers of the Y chromosome (Y-STRs), as well as mitochondrial DNA D-loop sequences, to investigate the paternal and maternal descent of the 18 alleged Inka descendants. Two Q-M3* Y-STR clusters descending from different male founders were identified. The first cluster, named AWKI-1, was associated with five families (eight individuals). By contrast, the second cluster, named AWKI-2, was represented by a single individual; AWKI-2 was part of the Q-Z19483 sub-lineage that was likely associated with a recent male expansion in the Andes, which probably occurred during the Late Intermediate Period (1000-1450 AD), overlapping the Inka period. Concerning the maternal descent, different mtDNA lineages associated with each family were identified, suggesting a high maternal gene flow among Andean populations, probably due to changes in the last 1000 years.

Rapidly mutating Y-STRs study in Chinese Yi population

Y-chromosomal short tandem repeats (Y-STRs) have been widely used in forensic analysis and population genetics. With low to moderate mutation rates, conventional Y-STR panels, including commercially available Y-STR kits, enable the identification of male pedigrees but typically fail to differentiate related male individuals. The introduction of rapidly mutating Y-chromosomal short tandem repeats (RM Y-STRs) with higher mutation rates (μ > 10^-2) has been demonstrated to increase the discrimination capacity of unrelated men and the differentiation rate of related men compared with standard Y-STRs. To date, several studies have been performed worldwide. Here, 260 father-son pairs from Chinese Yi population were investigated, and 18.8% of them were differentiated with the 13 RM Y-STR markers, which was close to the theoretical estimate of 19.5% based on the mutation rates of these markers. Among the 57 mutations observed, repeat gains were more common than repeat losses (1.48:1), and one-step mutations were more common than two-step mutations (27.5:1). Locus-specific mutation rates ranged from < 3.85 × 10^-3 (95% CI 0.00-1.41 × 10^-2) to 3.85 × 10^-2 (95% CI 1.86 × 10^-2-6.96 × 10^-2), with an average mutation rate of 1.46 × 10^-2 (95% CI 1.11 × 10^-2-1.89 × 10^-2). Furthermore, we combined the father-son pair data from the present study with the data from the previous studies, generating an overall mutation rate of 1.70 × 10^-2. The high differentiation rate obtained in the present study indicates the suitability of RM Y-STRs to distinguish paternal lineages in Chinese Yi population.

A phylogenetic framework facilitates Y-STR variant discovery and classification via massively parallel sequencing

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23 Y-chromosomal STRs (PPY23) reanalysed by massively parallel sequencing.

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Phylogeny-based approach captures wide range of sequence variants in 100 samples.

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STR variants described in phase with their flanking sequences.

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Phylogenetic framework clarifies allele nomenclature and mutation processes.

Short tandem repeats on the male-specific region of the Y chromosome (Y-STRs) are permanently linked as haplotypes, and therefore Y-STR sequence diversity can be considered within the robust framework of a phylogeny of haplogroups defined by single nucleotide polymorphisms (SNPs). Here we use massively parallel sequencing (MPS) to analyse the 23 Y-STRs in Promega’s prototype PowerSeq™ Auto/Mito/Y System kit (containing the markers of the PowerPlex® Y23 [PPY23] System) in a set of 100 diverse Y chromosomes whose phylogenetic relationships are known from previous megabase-scale resequencing. Including allele duplications and alleles resulting from likely somatic mutation, we characterised 2311 alleles, demonstrating 99.83% concordance with capillary electrophoresis (CE) data on the same sample set. The set contains 267 distinct sequence-based alleles (an increase of 58% compared to the 169 detectable by CE), including 60 novel Y-STR variants phased with their flanking sequences which have not been reported previously to our knowledge. Variation includes 46 distinct alleles containing non-reference variants of SNPs/indels in both repeat and flanking regions, and 145 distinct alleles containing repeat pattern variants (RPV). For DYS385a,b, DYS481 and DYS390 we observed repeat count variation in short flanking segments previously considered invariable, and suggest new MPS-based structural designations based on these. We considered the observed variation in the context of the Y phylogeny: several specific haplogroup associations were observed for SNPs and indels, reflecting the low mutation rates of such variant types; however, RPVs showed less phylogenetic coherence and more recurrence, reflecting their relatively high mutation rates. In conclusion, our study reveals considerable additional diversity at the Y-STRs of the PPY23 set via MPS analysis, demonstrates high concordance with CE data, facilitates nomenclature standardisation, and places Y-STR sequence variants in their phylogenetic context.

Extensive geographical and social structure in the paternal lineages of Saudi Arabia revealed by analysis of 27 Y-STRs

Saudi Arabia's indigenous population is organized into patrilineal descent groups, but to date, little has been done to characterize its population structure, in particular with respect to the male-specific region of the Y chromosome. We have used the 27-STR Yfiler^® Plus kit to generate haplotypes in 597 unrelated Saudi males, classified into five geographical regions (North, South, Central, East and West). Overall, Yfiler^® Plus provides a good discrimination capacity of 95.3%, but this is greatly reduced (74.7%) when considering the reduced Yfiler^® set of 17 Y-STRs, justifying the use of the expanded set of markers in this population. Comparison of the five geographical divisions reveals striking differences, with low diversity and similar haplotype spectra in the Central and Northern regions, and high diversity and similar haplotype spectra in the East and West. These patterns likely reflect the geographical isolation of the desert heartland of the peninsula, and the proximity to the sea of the Eastern and Western areas, and consequent historical immigration. We predicted haplogroups from Y-STR haplotypes, testing the performance of prediction by using a large independent set of Saudi Arabian Y-STR + Y-SNP data. Prediction indicated predominance (71%) of haplogroup J1, which was significantly more common in Central, Northern and Southern groups than in East and West, and formed a star-like expansion cluster in a median-joining network with an estimated age of ∼2800 years. Most of our 597 participants were sampled within Saudi Arabia itself, but ∼16% were sampled in the UK. Despite matching these two groups by home sub-region, we observed significant differences in haplotype and predicted haplogroup constitutions overall, and for most sub-regions individually. This suggests social structure influencing the probability of leaving Saudi Arabia, correlated with different Y-chromosome compositions. The UK-recruited sample is an inappropriate proxy for Saudi Arabia generally, and caution is needed when considering expatriate groups as representative of country of origin. Our study shows the importance of geographical and social structuring that may affect the utility of forensic databases and the interpretation of Y-STR profiles.

Genetic variations of 15 autosomal and 17 Y-STR markers in Sindhi population of Pakistan

This study comprises genetic characterization of 15 autosomal and 17 Y-chromosomal STR loci in 103 unrelated male inhabitants of the Sindhi population to establish its lineage and parameters of forensic interest. The examined autosomal STRs revealed high combined power of discrimination, combined power of exclusion, and the combined matching probability as 0.99999999999999999042580, 0.9999977141, and 9.5742 × 10^-18, respectively. A total of 89 unique haplotypes were obtained, of which 84 were observed once with a haplotype diversity value of 0.999677. The resulted Y-STR haplotypes exhibited a high degree of geographical demarcation by comparing with other populations at the local and global levels.

Genetic polymorphisms of 17 Y-chromosomal STRs in the Chengdu Han population of China

Chengdu is located at the center of Sichuan Province in southwestern China, and its primary demographic group is the Han population. The aim of this study was to contribute data detailing 17 Y-short tandem repeat (Y-STR) loci from 3291 Chengdu Han male samples analyzed with the AmpFLSTR^® Yfiler^® PCR Amplification Kit. We observed 2228 different haplotypes, and haplotype diversity (HD) was 0.9992. Gene diversity (GD) values for the 17 Y-STR loci of the Chengdu Han population ranged from 0.4156 to 0.9529. Haplotype match probability (HMC) was 0.0011. Compared with 13 reference populations of six provinces surrounding Chengdu, we observed that the Chengdu Han population was significantly different from each of these populations.

On the Bantu expansion

Here we report the results of fine resolution Y chromosomal analyses (Y-SNP and Y-STR) of 267 Bantu-speaking males from three populations located in the southeast region of Africa. In an effort to determine the relative Y chromosomal affinities of these three genotyped populations, the findings are interpreted in the context of 74 geographically and ethnically targeted African reference populations representing four major ethno-linguistic groups (Afro-Asiatic, Niger Kordofanin, Khoisan and Pygmoid). In this investigation, we detected a general similarity in the Y chromosome lineages among the geographically dispersed Bantu-speaking populations suggesting a shared heritage and the shallow time depth of the Bantu Expansion. Also, micro-variations in the Bantu Y chromosomal composition across the continent highlight location-specific gene flow patterns with non-Bantu-speaking populations (Khoisan, Pygmy, Afro-Asiatic). Our Y chromosomal results also indicate that the three Bantu-speaking Southeast populations genotyped exhibit unique gene flow patterns involving Eurasian populations but fail to reveal a prevailing genetic affinity to East or Central African Bantu-speaking groups. In addition, the Y-SNP data underscores a longitudinal partitioning in sub-Sahara Africa of two R1b1 subgroups, R1b1-P25* (west) and R1b1a2-M269 (east). No evidence was observed linking the B2a haplogroup detected in the genotyped Southeast African Bantu-speaking populations to gene flow from contemporary Khoisan groups.

More comprehensive forensic genetic marker analyses for accurate human remains identification using massively parallel DNA sequencing

BACKGROUND

Although the primary objective of forensic DNA analyses of unidentified human remains is positive identification, cases involving historical or archaeological skeletal remains often lack reference samples for comparison. Massively parallel sequencing (MPS) offers an opportunity to provide biometric data in such cases, and these cases provide valuable data on the feasibility of applying MPS for characterization of modern forensic casework samples. In this study, MPS was used to characterize 140-year-old human skeletal remains discovered at a historical site in Deadwood, South Dakota, United States. The remains were in an unmarked grave and there were no records or other metadata available regarding the identity of the individual. Due to the high throughput of MPS, a variety of biometric markers could be typed using a single sample.

RESULTS

Using MPS and suitable forensic genetic markers, more relevant information could be obtained from a limited quantity and quality sample. Results were obtained for 25/26 Y-STRs, 34/34 Y SNPs, 166/166 ancestry-informative SNPs, 24/24 phenotype-informative SNPs, 102/102 human identity SNPs, 27/29 autosomal STRs (plus amelogenin), and 4/8 X-STRs (as well as ten regions of mtDNA). The Y-chromosome (Y-STR, Y-SNP) and mtDNA profiles of the unidentified skeletal remains are consistent with the R1b and H1 haplogroups, respectively. Both of these haplogroups are the most common haplogroups in Western Europe. Ancestry-informative SNP analysis also supported European ancestry. The genetic results are consistent with anthropological findings that the remains belong to a male of European ancestry (Caucasian). Phenotype-informative SNP data provided strong support that the individual had light red hair and brown eyes.

CONCLUSIONS

This study is among the first to genetically characterize historical human remains with forensic genetic marker kits specifically designed for MPS. The outcome demonstrates that substantially more genetic information can be obtained from the same initial quantities of DNA as that of current CE-based analyses.

Y-STR markers from Ladakh in the Himalayas

A total of 223 samples from the general population of Ladakh in Northwestern India were amplified at 17 Y-STR loci using the AmpFlSTR® Yfiler™ system. The DNA profiles generated were employed to generate allelic frequencies, gene diversity, haplotype diversity and discrimination capacity values as well as number of different haplotypes, fraction of unique haplotypes and Rst pair wise genetic distances. Multidimensional Scaling (MDS) and Correspondence Analysis (CA) were performed with the Rst values and allelic frequencies, respectively. The 17-loci discrimination capacity of Ladakh was found to be 0.8093. Eleven out of the 16 loci have diversity values greater than 0.6, and 13 loci possess values greater than 0.5. Ladakh exhibits no significant genetic difference to seven of the 15 reference forensic databases after Bonferroni correction, three of which are located in South Central Asian and four are from the Himalayan region. Rst genetic distance values before and after Bonferroni corrections illustrate the capacity of the Yfiler system to discriminate among Himalayan populations. The intermediate position of the Ladakh population in the MDS and CA plots likely reflects genetic flow and admixture with neighboring populations. In addition, the longitudinal partition of populations in the MDS and CA plots likely reflect human dispersals such as the silk road migrations.

The Genetic History of Peruvian Quechua-Lamistas and Chankas: Uniparental DNA Patterns among Autochthonous Amazonian and Andean Populations

This study focuses on the genetic history of the Quechua‐Lamistas, inhabitants of the Lamas Province in the San Martin Department, Peru, who speak their own distinct variety of the Quechua family of languages. It has been suggested that different pre‐Columbian ethnic groups from the Peruvian Amazonia, like the Motilones or “shaven heads”, assimilated the Quechua language and then formed the current native population of Lamas. However, many Quechua‐Lamistas claim to be direct descendants of the Chankas, a famous pre‐Columbian indigenous group that escaped from Inca rule in the Andes. To investigate the Quechua‐Lamistas and Chankas’ ancestries, we compared uniparental genetic profiles (17 STRs of Q‐M3 Y‐chromosome and mtDNA complete control region haplotypes) among autochthonous Amazonian and Andean populations from Peru, Bolivia and Ecuador. The phylogeographic and population genetic analyses indicate a fairly heterogeneous ancestry for the Quechua‐Lamistas, while they are closely related to their neighbours who speak Amazonian languages, presenting no direct relationships with populations from the region where the ancient Chankas lived. On the other hand, the genetic profiles of self‐identified Chanka descendants living in Andahuaylas (located in the Apurimac Department, Peru, in the Central Andes) were closely related to those living in Huancavelica and the assumed Chanka Confederation area before the Inca expansion.

Analysis of Rapidly Mutating Y Chromosome Short Tandem Repeats (RM Y-STRs)

Rapidly mutating (RM) Y-STRs were recently identified and can help to differentiate between paternally related males in paternity and forensic casework. Normal Y-STRs are often used in casework due to their paternal inheritance, which can help to resolve kinship cases, and identify male components in male/female mixtures; however, more discriminating profiles are obtained if rapidly mutating Y-STRs are used. Previously two or three multiplex PCRs have been used to amplify 13 RM Y-STRs; here, an assay amplifying these 13 markers in a single multiplex PCR is described. Commercially available male control DNA samples have been genotyped during the validation of this assay, thus providing a tool for calibrating genotyping results. It is expected that the assay will provide a niche tool for genotyping casework samples.

Genetic diversity and haplotype structure of 21 Y-STRs, including nine noncore loci, in South Tunisian Population: Forensic relevance

Y chromosome STRs (Y-STRs) are being used frequently in forensic laboratories. Previous studies of Y-STR polymorphisms in different groups of the Tunisian population identified low levels of diversity and discrimination capacity (DC) using various commercial marker sets. This definitely limits the use of such systems for Y-STRs genotyping in Tunisia. In our investigation on South Tunisia, 200 unrelated males were typed for the 12 conventional Y-STRs included in the PowerPlex® Y System. Additional set of nine noncore Y-STRs including DYS446, DYS456, DYS458, DYS388, DYS444, DYS445, DYS449, DYS710, and DYS464 markers were genotyped and evaluated for their potential in improving DC. Allele frequency, gene diversity, haplotype diversity (HD), and DC calculation revealed that DYS464 was the most diverse marker followed by DYS710 and DYS449 markers. The standard panel of 12 Y-STRs (DC = 80.5%) and the nine markers were combined to obtain DC of 99%. Among the 198 different haplotypes observed, 196 haplotypes were unique (HD = 99.999). Out of the nine noncore set, six Y-STRs (DYS458, DYS456, DYS449, DYS710, DYS444, and DYS464) had the greatest impact on enhancing DC. Our data provided putative Y-STRs combination to be used for genetic and forensic applications.

Genetic population study of Y-chromosome markers in Benin and Ivory Coast ethnic groups

Ninety-six single nucleotide polymorphisms (SNPs) and seventeen short tandem repeat (STRs) were investigated on the Y-chromosome of 288 unrelated healthy individuals from populations in Benin (Bariba, Yoruba, and Fon) and the Ivory Coast (Ahizi and Yacouba). We performed a multidimensional scaling analysis based on FST and RST genetic distances using a large extensive database of sub-Saharan African populations. There is more genetic homogeneity in Ivory Coast populations compared with populations from Benin. Notably, the Beninese Yoruba are significantly differentiated from neighbouring groups, but also from the Yoruba from Nigeria (FST>0.05; P<0.01). The Y-chromosome dataset presented here provides new valuable data to understand the complex genetic diversity and human male demographic events in West Africa.

A novel multiplex assay for simultaneously analysing 13 rapidly mutating Y-STRs

A multiplex polymerase chain reaction (PCR) assay (RM-Yplex) was developed which is capable of simultaneously amplifying 13 recently introduced rapidly mutating Y-STR markers (RM Y-STRs). This multiplex assay is expected to aid human identity testing in forensic and other applications to improve differentiating unrelated males and allow separating related males. The 13 RM Y-STR markers included in the multiplex are: DYF387S1, DYF399S1, DYF403S1ab, DYF404S1, DYS449, DYS518, DYS526ab, DYS547, DYS570, DYS576, DYS612, DYS626 and DYS627. This study reflects the proof of concept to analyse all currently known RM Y-STRs simultaneously and describes the optimization of the multiplex assay. The RM-Yplex assay generated complete RM Y-STR profiles down to 62.5pg of male template DNA, and from male-female DNA mixtures at all ratios tested. We herewith introduce and make available for widespread use in forensic and anthropological studies, an effective and sensitive single multiplex assay for simultaneous genotyping of 13 RM Y-STRs.

Polymorphisms at 17 Y-STR loci in Botswana populations

Seventeen Y-chromosomal short tandem repeats (YSTRs)-DYS19, DYS389I, DYS389II, DYS385a/b, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS635, and Y-GATA-H4-were analyzed in 252 unrelated male individuals from Botswana. A total of 238 unique haplotypes were identified. The discrimination capacity (DC) was 0.9444 whereas the haplotype diversity (HD) was 0.9990. A database search of the 238 unique haplotypes in the Y chromosome haplogroup database (YHRD) yielded three African American, six Sub-Saharan African, and two admixed South American matches. Five additional African-American matches were detected in the Applied Biosystems Y-STR database. RST, multi-dimensional scaling (MDS) and AMOVA were used to investigate population differentiation in Sub-Saharan Africa and in Botswana. The populations in Sub-Saharan Africa were found to be heterogeneous, with Botswana showing significant differences from its neighbors. No geographic regional or ethnic differentiation was observed within Botswana. Regional and ethnic variation can be useful in forensic working hypotheses.

The Y-chromosome tree bursts into leaf: 13,000 high-confidence SNPs covering the majority of known clades

Many studies of human populations have used the male-specific region of the Y chromosome (MSY) as a marker, but MSY sequence variants have traditionally been subject to ascertainment bias. Also, dating of haplogroups has relied on Y-specific short tandem repeats (STRs), involving problems of mutation rate choice, and possible long-term mutation saturation. Next-generation sequencing can ascertain single nucleotide polymorphisms (SNPs) in an unbiased way, leading to phylogenies in which branch-lengths are proportional to time, and allowing the times-to-most-recent-common-ancestor (TMRCAs) of nodes to be estimated directly. Here we describe the sequencing of 3.7 Mb of MSY in each of 448 human males at a mean coverage of 51×, yielding 13,261 high-confidence SNPs, 65.9% of which are previously unreported. The resulting phylogeny covers the majority of the known clades, provides date estimates of nodes, and constitutes a robust evolutionary framework for analyzing the history of other classes of mutation. Different clades within the tree show subtle but significant differences in branch lengths to the root. We also apply a set of 23 Y-STRs to the same samples, allowing SNP- and STR-based diversity and TMRCA estimates to be systematically compared. Ongoing purifying selection is suggested by our analysis of the phylogenetic distribution of nonsynonymous variants in 15 MSY single-copy genes.

Testing Central and Inner Asian admixture among contemporary Hungarians

Historically, the Carpathian Basin was the final destination for many nomadic peoples who migrated westward from Inner and Central Asia towards Europe. Proto-Hungarians (Steppe Magyars) were among those who came from the East, the Eurasian Steppe in the early middle ages. In order to detect the paternal genetic contribution from nomadic Steppe tribes, we tested 966 samples from Central Asian (Uzbekistan, Kazakhstan), Inner Asian (Mongolians and Buryats in Mongolia) and Hungarian-speaking European (Hungarian, Sekler and Csango) populations. We constructed median-joining networks of certain haplogroups in Hungarian-speaking European, and Altaic-speaking Central and Inner Asian populations. We estimated that the possible paternal genetic contribution from the above described populations among contemporary Hungarian speaking populations ranged between 5% and 7.4%. It is lowest among Hungarians from Hungary (5.1%), while higher among Hungarian-speaking groups in Romania, notably Sekler (7.4%) and Csango (6.3%). However, these results represent only an upper limit. Actual Central/Inner Asian admixture might be somewhat lower as some of the related lineages may have come from a common third source. The main haplogroups responsible for the Central/Inner Asian admixture among Hungarians are J2*-M172 (xM47, M67, M12), J2-L24, R1a-Z93; Q-M242 and E-M78. Earlier studies showed very limited Uralic genetic influence among Hungarians, and based on the present study, Altaic/Turkic genetic contribution is also not significant, although significantly higher than the Uralic one. The conclusion of this study is that present-day Hungarian speakers are genetically very similar to neighbouring populations, isolated Hungarian speaking groups having relatively higher presence of Central and Inner Asian genetic elements. At the same time, the reliable historical and genetic conclusions require an extension of the study to a significantly larger database with deep haplogroup resolution, including ancient DNA data.

At the southeast fringe of the Bantu expansion: genetic diversity and phylogenetic relationships to other sub-Saharan tribes

Here, we present 12 loci paternal haplotypes (Y-STR profiles) against the backdrop of the Y-SNP marker system of Bantu males from the Maputo Province of Southeast Africa, a region believed to represent the southeastern fringe of the Bantu expansion. Our Maputo Bantu group was analyzed within the context of 27 geographically relevant reference populations in order to ascertain its genetic relationship to other Bantu and non Bantu (Pygmy, Khoisan and Nilotic) sub-equatorial tribes from West and East Africa. This study entails statistical pair wise comparisons and multidimensional scaling based on YSTR Rst distances, network analyses of Bantu (B2a-M150) and Pygmy (B2b-M112) lineages as well as an assessment of Y-SNP distribution patterns. Several notable findings include the following: 1) the Maputo Province Bantu exhibits a relatively close paternal affinity with both east and west Bantu tribes due to high proportion of Bantu Y chromosomal markers, 2) only traces of Khoisan (1.3%) and Pygmy (1.3%) markers persist in the Maputo Province Bantu gene pool, 3) the occurrence of R1a1a-M17/M198, a member of the Eurasian R1a-M420 branch in the population of the Maputo Province, may represent back migration events and/or recent admixture events, 4) the shared presence of E1b1b1-M35 in all Tanzanian tribes examined, including Bantu and non-Bantu groups, in conjunction with its nearly complete absence in the West African populations indicate that, in addition to a shared linguistic, cultural and genetic heritage, geography (e.g., east vs. west) may have impacted the paternal landscape of sub-Saharan Africa, 5) the admixture and assimilation processes of Bantu elements were both highly complex and region-specific.

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Maputo Bantus exhibit close affinities with other West and East African Bantus.

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Traces of Khoisan and Pygmy markers persist in the Maputo Province Bantus.

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R1a1a-M17/M198 in the Maputo Province may represent back or recent migration.

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Linguistic, cultural and genetic heritages are reflected in Maputo's gene pool.

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Admixture and assimilation processes of Bantu elements were region-specific.

Male lineage strata of Brazilian population disclosed by the simultaneous analysis of STRs and SNPs

Brazil has a large territory divided in five geographical regions harboring highly diverse populations that resulted from different degrees and modes of admixture between Native Americans, Europeans and Africans. In this study, a sample of 605 unrelated males was genotyped for 17 Y-STRs and 46 Y-SNPs aiming a deep characterization of the male gene pool of Rio de Janeiro and its comparison with other Brazilian populations. High values of Y-STR haplotype diversity (0.9999±0.0001) and Y-SNP haplogroup diversity (0.7589±0.0171) were observed. Population comparisons at both haplotype and haplogroup levels showed significant differences between Brazilian South Eastern and Northern populations that can be explained by differences in the proportion of African and Native American Y chromosomes. Statistical significant differences between admixed urban samples from the five regions of Brazil were not previously detected at haplotype level based on smaller size samples from South East, which emphasizes the importance of sample size to detected population stratification for an accurate interpretation of profile matches in kinship and forensic casework. Although not having an intra-population discrimination power as high as the Y-STRs, the Y-SNPs are more powerful to disclose differences in admixed populations. In this study, the combined analysis of these two types of markers proved to be a good strategy to predict population sub-structure, which should be taken into account when delineating forensic database strategies for Y chromosome haplotypes.

Toward male individualization with rapidly mutating y-chromosomal short tandem repeats

Relevant for various areas of human genetics, Y-chromosomal short tandem repeats (Y-STRs) are commonly used for testing close paternal relationships among individuals and populations, and for male lineage identification. However, even the widely used 17-loci Yfiler set cannot resolve individuals and populations completely. Here, 52 centers generated quality-controlled data of 13 rapidly mutating (RM) Y-STRs in 14,644 related and unrelated males from 111 worldwide populations. Strikingly, >99% of the 12,272 unrelated males were completely individualized. Haplotype diversity was extremely high (global: 0.9999985, regional: 0.99836–0.9999988). Haplotype sharing between populations was almost absent except for six (0.05%) of the 12,156 haplotypes. Haplotype sharing within populations was generally rare (0.8% nonunique haplotypes), significantly lower in urban (0.9%) than rural (2.1%) and highest in endogamous groups (14.3%). Analysis of molecular variance revealed 99.98% of variation within populations, 0.018% among populations within groups, and 0.002% among groups. Of the 2,372 newly and 156 previously typed male relative pairs, 29% were differentiated including 27% of the 2,378 father–son pairs. Relative to Yfiler, haplotype diversity was increased in 86% of the populations tested and overall male relative differentiation was raised by 23.5%. Our study demonstrates the value of RM Y-STRs in identifying and separating unrelated and related males and provides a reference database.

Northern Slavs from Serbia do not show a founder effect at autosomal and Y-chromosomal STRs and retain their paternal genetic heritage

Studies on Y-chromosomal markers revealed significant genetic differentiation between Southern and Northern (Western and Eastern) Slavic populations. The northern Serbian region of Vojvodina is inhabited by Southern Slavic Serbian majority and, inter alia, Western Slavic (Slovak) and Eastern Slavic (Ruthenian) minorities. In the study, 15 autosomal STR markers were analysed in unrelated Slovaks, Ruthenians and Serbs from northern Serbia and western Slovakia. Additionally, Slovak males from Serbia were genotyped for 17 Y-chromosomal STR loci. The results were compared to data available for other Slavic populations. Genetic distances for autosomal markers revealed homogeneity between Serbs from northern Serbia and Slovaks from western Slovakia and distinctiveness of Serbian Slovaks and Ruthenians. Y-STR variation showed a clear genetic departure of the Slovaks and Ruthenians inhabiting Vojvodina from their Serbian neighbours and genetic similarity to the Northern Slavic populations of Slovakia and Ukraine. Admixture estimates revealed negligible Serbian paternal ancestry in both Northern Slavic minorities of Vojvodina, providing evidence for their genetic isolation from the Serbian majority population. No reduction of genetic diversity at autosomal and Y-chromosomal markers was found, excluding genetic drift as a reason for differences observed at autosomal STRs. Analysis of molecular variance detected significant population stratification of autosomal and Y-chromosomal microsatellites in the three Slavic populations of northern Serbia, indicating necessity for separate databases used for estimations of frequencies of autosomal and Y-chromosomal STR profiles in forensic casework. Our results demonstrate that regarding Y-STR haplotypes, Serbian Slovaks and Ruthenians fit in the Eastern European metapopulation defined in the Y chromosome haplotype reference database.