Y-chromosomal Short Tandem Repeat Markers Research Articles

Simultaneous sequencing of 102 Y-STRs on Ion Torrent ™ GeneStudio ™ S5 System

The Precision ID NGS System from Thermo Fisher Scientific is a mainstream next-generation sequencing (NGS) platform used in forensic laboratories to detect almost all commonly used forensic markers, except for Y-chromosomal short tandem repeats (Y-STRs). This study aimed to: 1) develop a Y-STR panel compatible with the automatic workflow of the NGS system using Ion AmpliSeq Technology, 2) evaluate the panel performance following the SWGDAM guidelines, and 3) explore the possibility of using a combination workflow to detect autosomal STRs and Y-STRs (AY-STR NGS workflow). The GrandFiler Y-STR Panel was successfully designed using the ‘separating’ and ‘merging’ strategies, including 102 Y-STRs and Amelogenin with an average amplicon length of 133 bp. It is a mega Y-STR multiplex system in which up to 16 samples can be sequenced simultaneously on an Ion 530 ™ Chip. Developmental validation studies of the performance of the NGS platform, species specificity, reproducibility, concordance, sensitivity, degraded samples, case-type samples, and mixtures were conducted to unequivocally determine whether the GrandFiler Y-STR Panel is suitable for real scenarios. The newly developed Y-STR panel showed compelling run metrics and NGS performance, including 92.47% bases with ≥ Q20, 91.80% effective reads, 2106 × depth of coverage (DoC), and 97.09% inter-locus balance. Additionally, it showed high specificity for human males and 99.40% methodological and bioinformatical concordance, generated complete profiles at ≥ 0.1 ng input DNA, and recovered more genetic information from severely degraded and diverse case samples. Although the outcome when used on mixtures was not as expected, more genetic information was obtained compared to that from capillary electrophoresis (CE) methods. The AY-STR NGS workflow was established by combining the GrandFiler Y-STR Panel with the Precision ID GlobalFiler ™ NGS STR Panel v2 at a 2:1 concentration ratio. The combination workflow on NGS performance, reproducibility, concordance, and sensitivity was as stable as the single Y-STR NGS workflow, providing more options for forensic scientists when dealing with different case scenarios. Overall, the GrandFiler Y-STR Panel was confirmed as the first to effectively detect a large number of Y-STR markers on the Precision ID NGS System, which is compatible with 51 Y-STRs in commercial CE kits and 51 Y-STRs in commercial NGS kits and the STRBase. The panel is as robust, reliable, and sensitive as current CE/NGS kits, and is suitable for solving real cases, especially for severely degraded samples (degradation index > 10).

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.

Mutation analysis for 25 Y-STR markers in Japanese population.

In this study, we analyzed DNA samples from 213 Japanese father son pairs with 25 Y-chromosome short tandem repeat (Y-STR) (DYS576, DYS389I, DYS635, DYS389II, DYS627, DYS460, DYS458, DYS19, YGATAH4, DYS448, DYS391, DYS456, DYS390, DYS438, DYS392, DYS518, DYS570, DYS437, DYS385, DYS449, DYS393, DYS439, DYS481, DYF387S1, and DYS533) markers using the Yfiler™ Plus PCR amplification kit. We calculated Y-STR mutation rates for each locus to evaluate the efficacy of the 25 Y-STR markers for paternity testing and forensic identification using samples from male relatives. Six rapidly mutating Y-STR markers (DYS576, DYS627, DYS518, DYS570, DYS449 and DYF387S1), previously reported to have high mutation rates (>1.0×10-2), are included in the 25 Y-STR markers, but our findings revealed that the mutation rates for all Y-STR markers except for DYS576 and DYS458 were lower than 1.0×10-2. Therefore, the use of these 25 Y-STR markers may be useful for forensic identification in the Japanese population.

Assessing 23 Y-STR loci mutation rates in Chinese Han father–son pairs from southwestern China

In this study, we have analyzed 23 Y-chromosomal short tandem repeats (Y-STRs) (DYS576, DYS389I, DYS389II, DYS448, DYS19, DYS391, DYS481, DYS549, DYS533, DYS438, DYS437, DYS570, DYS635, DYS390, DYS439, DYS392, DYS643, DYS393, DYS458, DYS460, DYS385ab, DYS456 and Y-GATA-H4) in 175 father-son sample pairs using a Microreader™ 24Y Direct ID system. Sixteen repeat mutations of father-son pairs at 10 loci, including three mutations at DYS570, 2 mutations at DYS549, DYS460, DYS458, and DYS576, and 1 mutation at other five loci, were revealed. Furthermore, all of the observed repeat mutations were single repeat changes with 5 (31.25%) repeat insertions and 11 (68.75%) repeat deletions. The deletion rate is more than two fold higher than of insertions (11:5 = 2.2-fold). Locus-specific mutation rates estimated varied between 5.71 × 10-3 (CI from 0.1 × 10-3 to 31.4 × 10-3) and 1.71 × 10-2 (CI from 3.6 × 10-3 to 49.3 × 10-3) for the 23 Y-STRs. An average mutation rate across all 23 Y-STR markers was estimated as 3.97 × 10-3 (CI 2.3 × 10-3 to 6.4 × 10-3). Thus, locus-specific mutation rates in DYS460, DYS458, and DYS438, estimated are much higher than previously published comprehensive data, but an average mutation rate across all 23 Y-STR markers is similar to previous reports (3.97 × 10-3 vs 4.34 × 10-3). These results by characterizing Y-STR mutations will not only provided new information for Y-STR mutations but also might be important for paternal lineage identification, kinship analysis, and family relationship reconstruction in our forensic Y-STR analysis.

Haplotype diversity of 17 Y-STRs in Sheikh population of Punjab.

Y chromosomal short tandem repeat (Y-STR) haplotype diversity of 180 genetically unrelated male individuals from Sheikh population of Punjab Pakistan was studied by amplifying 17 Y-STR markers through the AmpFISTR®Yfiler™ PCR amplification kit. The analysis of data revealed mean discrimination capacity of 0.6438 and matching probability of 0.3561. Sheikh population was also compared with 11 other populations in order to determine its population relationships which indicated that Punjabi Sheikhs have low genetic resemblance with Indian-Balmiki, UAE [Arab], Yousafzai Pathan from Pakistan, and Pathans from Afghanistan. The data of this study could have valuable application in forensic cases, in population genetics studies, and in strengthening the Y-STR database.

Mutation rates of six Y-chromosomal STR loci estimated from 210 pedigrees in Chinese Han population

The Y-chromosomal short tandem repeats (Y-STRs) with low mutation rates as slowly mutating (SM) Y-STRs could be used to refine the construction of phylogenetic trees in evolutionary research. Six Y-STR markers (DYS388, DYS426, DYS461, DYS485, DYS525 and DYS561) were from the previously published paper and considered as SM Y-STRs. Here, we investigated the six Y-STRs from 210 pedigrees in Chinese Han population in Henan province, covering an overall number of 8178 meiotic transfers. The number of mutations of the six Y-STRs ranged from 0 (DYS388 and DYS426) to 12 (DYS561), resulting the observed mutation rates spanned from 0 (95% credible interval [CI], 0∼2.196 × 10−3) to 8.804 × 10−3 (95% CI, 4.557 × 10−3∼1.533 × 10−2). According to the results, only DYS388 and DYS426 could be classified as SM Y-STRs in the Chinese Han population. Although these results will replenish the data of Y-STR mutations as well as be important for paternal genealogy identification, kinship analysis, and phylogenetic tree reconstruction, the mutation rates of the six Y-STRs were significantly different among different populations, which we need to pay attention to in future studies.

Estimating Y-Str Mutation Rates and Tmrca Through Deep-Rooting Italian Pedigrees

In the population genomics era, the study of Y-chromosome variability is still of the greatest interest for several fields ranging from molecular anthropology to forensics and genetic genealogy. In particular, mutation rates of Y-chromosomal Short Tandem Repeats markers (Y-STRs) are key parameters for different interdisciplinary applications. Among them, testing the patrilineal relatedness between individuals and calculating their Time of Most Recent Common Ancestors (TMRCAs) are of the utmost importance. To provide new valuable estimates and to address these issues, we typed 47 Y-STRs (comprising Yfiler, PowerPlex23 and YfilerPlus loci, the recently defined Rapidly Mutating [RM] panel and 11 additional markers often used in genetic genealogical applications) in 135 individuals belonging to 66 deep-rooting paternal genealogies from Northern Italy. Our results confirmed that the genealogy approach is an effective way to obtain reliable Y-STR mutation rate estimates even with a limited number of samples. Moreover, they showed that the impact of multi-step mutations and backmutations is negligible within the temporal scale usually adopted by forensic and genetic genealogy analyses. We then detected a significant association between the number of mutations within genealogies and observed TMRCAs. Therefore, we compared observed and expected TMRCAs by implementing a Bayesian procedure originally designed by Walsh (2001) and showed that the method yields a good performance (up to 96.72%), especially when using the Infinite Alleles Model (IAM).

A comprehensive mutation study in wide deep-rooted R1b Serbian pedigree: mutation rates and male relative differentiation capacity of 36 Y-STR markers

Haplotyping of Y-chromosomal short tandem repeats (Y-STRs) reflects the paternal lineage, although, the father-son pair profiles may differ due to the germline mutations. In order to discriminate between closely related males in criminal cases, as well as for the correct application of Y-STRs in the paternity/kinship analysis and determination of the most recent common ancestor in the familial searching or genealogy research, the assessment of mutation rates of routinely used Y-STRs is of a great importance. We genotyped 120 males belonging to one wide deep-rooted pedigree separated by 1–20 meiosis. The haplotypes of analyzed males distributed over 12 different families (according to their surnames), with 113 originating from one ancestor, and the remaining 7 from the second, closely related to the previous one, belong to the R1b haplogroup. The analysis was performed using Powerplex® Y23 kit, Yfiler™ plus kit and 13 rapidly mutating (RM13) Y-STRs. In 20,855 allele transmissions, 175 mutations (61% repeat losses and 39% gains) and one gene conversion event were found at 25 out of 36 markers. The medians of locus-specific mutation rates estimated using the Bayesian approach ranged from 1.42 × 10−3 (95% credible interval (CI): 0.05 × 10−3 - 7.56 × 10−3) for loci with no observed mutations to 130.91 × 10−3 (95% CI: 102.91 × 10−3 - 162.78 × 10−3) for DYF399S1, with a median rate across all 36 markers of 10.06 × 10−3 (95% CI: 8.65 × 10−3 - 11.61 × 10−3). In 6349 male relative pairs, the 36 Y-STR set distinguished 98.4% relative pairs by at least one mutation, compared to 95.9%, 65.5% and 57.4% for RM13, Yfiler™ plus, and Powerplex® Y23 set, respectively. The extra-pair paternity rate was estimated at 11.9 × 10−3 (95% CI: 4.4 × 10−3 – 25.8 × 10−3) fitting within the range reported for some European populations. A significant positive correlation was observed between fathers’ ages at the time of the Y chromosome transmission and mutability rates (R2 = 0.9495, p = 0.0256), with more significant results when analyzing RM markers (R2 = 0.9827, p = 0.0087).

Polymorphisms and microvariant sequences in the Japanese population for 25 Y-STR markers and their relationships to Y-chromosome haplogroups

Y-chromosomal short tandem repeat (Y-STR) markers have been used for forensic purposes such as kinship analysis of male-linage and detection of a male DNA component in a mixture of male and female DNA. Recently, rapidly mutating Y-STR (RM Y-STR) markers were reported that are expected to help distinguish close male relatives. This study provides data of Y-chromosomal haplotypes for 25 Y-STR markers, including six RM Y-STR markers (DYS576, DYS627, DYS518, DYS570, DYS449 and DYF387S1) typed with the Yfiler™ Plus kit in 1299 males of the Japanese population. Discrimination capacity increased from 87.2% for 16 Y-STR markers with the Yfiler™ kit to 99.6% for 25 Y-STR markers with the Yfiler™ Plus kit. We characterized sequences of observed microvariant alleles of eight Y-STR markers and a low-amplified allele of DYS390 by Sanger sequencing. DYF387S1, a multi-locus Y-STR marker that is located at two positions on the human Y-chromosome, was observed in tri-allelic patterns in 51 of 1299 samples (3.9%) and we found an extremely high frequency of the tri-allelic pattern of DYF387S1 in haplogroup C-M131. We also analyzed Y-STR gene diversity in each haplogroup and its relevance to mutation rates.

Mutation analysis of 13 RM Y-STR loci in Han population from Beijing of China.

Two five-color fluorescence multiplex amplification systems of 13 Y chromosome short tandem repeat (Y-STR) loci (DYF387S1, DYF399S1, DYF403S1a/b, DYF404S1, DYS449, DYS518, DYS526a/b, DYS547, DYS570, DYS576, DYS612, DYS626, and DYS627) have been designed. A study was conducted measuring the mutation rates of the 13 Y-STRs in 501 father-son pairs of Han origin in Beijing, China. Among 7515 allele transmissions in 501 father-son pairs, 75 single-step and 2 two-step mutations were observed. Two father-son pairs had mutations at two different loci in 13 Y-STRs. The estimated mutation rates ranged from 2.00 × 10-3 (95% CI 1.00 × 10-4 to 1.11 × 10-2) for the DYF387S1, DYF403S1b, DYS526a, and DYS449 loci to 4.59 × 10-2 (95% CI 2.93 × 10-2 to 6.81 × 10-2) for the DYF399S1 locus. The average mutation rate is 1.02 × 10-2 (95% CI 8.10 × 10-3 to 1.28 × 10-2). Among these Y-STR markers, only DYF399S1, DYS627, DYF403S1a, DYS547, DYS612, and DYS626 had mutation rates higher than 1.00 × 10-2.

A comprehensive portrait of Y-STR diversity of Indian populations and comparison with 129 worldwide populations

India, known for its rich cultural, linguistic and ethnic diversity, has attracted the attention of population geneticists to understand its genetic diversity employing autosomal, Y-chromosomal and mitochondrial DNA markers. Y-chromosomal short tandem repeats (Y-STRs) are useful in understanding population substructures and reveal the patrilineal affinities among populations. Previous studies on Indian populations based on Y-STR markers were either limited to restricted number of markers or focused on few selected populations. In this study we genotyped 407 unrelated male individuals from 12 states in India employing the suite of Y-STRs present in PowerPlex Y23 (Promega, Madison, WI, USA). These populations clustered genetically close to each other irrespective of their geographic co-ordinates and were characterized primarily by R1a, H and L haplogroups. Interestingly, comparison with 129 worldwide populations showed genetic affinity of the Indian populations with few populations from Europe and Levantine. This study presents the first pan-Indian landscape of 23 Y-STRs and serves as a useful resource for construction of an Indian Y-STR database.

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 multiplex PCR system for 13 RM Y-STRs with separate amplification of two different repeat motif structures in DYF403S1a

In forensic science and human genetics, Y-chromosomal short tandem repeats (Y-STRs) have been used as very useful markers. Recently, more Y-STR markers have been analyzed to enhance the resolution power in haplotype analysis, and 13 rapidly mutating (RM) Y-STRs have been suggested as revolutionary tools that can widen Y-chromosomal application from paternal lineage differentiation to male individualization. We have constructed two multiplex PCR sets for the amplification of 13 RM Y-STRs, which yield small-sized amplicons (<400bp) and a more balanced PCR efficiency with minimum PCR cycling. In particular, with the developed multiplex PCR system, we could separate three copies of DYF403S1a into two copies of DYF403S1a and one of DYF403S1b1. This is because DYF403S1b1 possesses distinguishable sequences from DYF403S1a at both the front and rear flanking regions of the repeat motif; therefore, the locus could be separately amplified using sequence-specific primers. In addition, the other copy, defined as DYF403S1b by Ballantyne et al., was renamed DYF403S1b2 because of its similar flanking region sequence to DYF403S1b1. By redefining DYF403S1 with the developed multiplex system, all genotypes of four copies could be successfully typed and more diverse haplotypes were obtained. We analyzed haplotype distributions in 705 Korean males based on four different Y-STR subsets: Yfiler, PowerPlex Y23, Yfiler Plus, and RM Y-STRs. All haplotypes obtained from RM Y-STRs were the most diverse and showed strong discriminatory power in Korean population.

Characterization of genetic sequence variation of 58 STR loci in four major population groups

Massively parallel sequencing (MPS) can identify sequence variation within short tandem repeat (STR) alleles as well as their nominal allele lengths that traditionally have been obtained by capillary electrophoresis. Using the MiSeq FGx Forensic Genomics System (Illumina), STRait Razor, and in-house excel workbooks, genetic variation was characterized within STR repeat and flanking regions of 27 autosomal, 7 X-chromosome and 24 Y-chromosome STR markers in 777 unrelated individuals from four population groups. Seven hundred and forty six autosomal, 227 X-chromosome, and 324 Y-chromosome STR alleles were identified by sequence compared with 357 autosomal, 107 X-chromosome, and 189 Y-chromosome STR alleles that were identified by length. Within the observed sequence variation, 227 autosomal, 156 X-chromosome, and 112 Y-chromosome novel alleles were identified and described. One hundred and seventy six autosomal, 123 X-chromosome, and 93 Y-chromosome sequence variants resided within STR repeat regions, and 86 autosomal, 39 X-chromosome, and 20 Y-chromosome variants were located in STR flanking regions. Three markers, D18S51, DXS10135, and DYS385a-b had 1, 4, and 1 alleles, respectively, which contained both a novel repeat region variant and a flanking sequence variant in the same nucleotide sequence. There were 50 markers that demonstrated a relative increase in diversity with the variant sequence alleles compared with those of traditional nominal length alleles. These population data illustrate the genetic variation that exists in the commonly used STR markers in the selected population samples and provide allele frequencies for statistical calculations related to STR profiling with MPS data.

Improving empirical evidence on differentiating closely related men with RM Y-STRs: A comprehensive pedigree study from Pakistan

Y-chromosomal short tandem repeat (Y-STR) markers are commonly used in forensic genetics. Male-specific haplotypes provided by commercial Y-STR kits allow discriminating between many – but not all – unrelated men, while they mostly fail to separate related ones. Aiming to improve male relative and paternal lineage differentiation, a set of 13 rapidly-mutating (RM) Y-STRs was previously identified and introduced to forensic Y-chromosome analysis. Recently, their value was highlighted by separating 99% of over 12,200 unrelated men from 111 global populations, as well as 29% of over 2500 male relative pairs, the vast majority were father-sons. Here, we provide improved empirical evidence on differentiating closely related men with RM Y-STRs, most notably beyond father-sons, where previous data were limited. After careful quality control including genetic relationship testing, we used 572 Pakistani men belonging to 99 2–4 generation pedigrees covering 1568 pairs of men related by 1–6 meioses. Of those, 45% were differentiated by one or more of the 13 RM Y-STR markers. In contrast, only 14.7% of a subset of 1484 pairs from 94 pedigrees were separated by the commercial AmpFlSTR Y-filer kit. Combining previously published and new data, an overall differentiation rate of 35.3% was revealed for the RM Y-STR set based on 4096 pairs of men related by 1–20 meioses, compared to 9.6% with Y-filer based on 3645 pairs. Using father-son pair data from the present and previous studies, we provide updated RM Y-STR mutation rates. Locus-specific mutation rates ranged from 2.0×10−3 (7.0×10−4–4.3×10−3) to 6.9×10−2 (6.1×10−2–7.9×10−2) based on 2741–3143 meioses, with an average rate across all 13 RM Y-STR markers of 1.8×10−2 (1.7×10−2–1.9×10−2) based on 800 mutations from 44,922 meioses. The high haplotype diversity (h=0.9996) we observed among the unrelated men (N=105) underlines the value of this RM Y-STR set to differentiate paternal lineages even from endogamous populations such as from Pakistan.

Male Individualization Based on Y-Chromosomal Short Tandem Repeats: A Comparative Information Theoretical Analysis of 16 Y-STR Loci in Central Anatolia and Iraqi Populations

The aim of this study is to investigate the discrimination capacity of 16 Y-Chromosomal Short Tandem Repeat markers (Y-STRs) based on their joint entropy for the purpose of male individualization o...

Shannon's equivocation for forensic Y-STR marker selection

Short tandem repeat (STR) markers are widely and continuously used in forensic applications. However, past research has demonstrated substantial allelic association between STR markers on both autosomes and the X chromosome, leading to partially redundant information that these markers can provide. Here, we quantify the allelic association between Y-chromosomal STR markers that are part of established forensic panels, separately for three different continental groups. We further propose a sequential marker selection procedure that is based on Shannon’s equivocation and that accounts for allelic association between STR markers, leading to a maximal gain in independent information. In application to three real-world data sets, we demonstrate the procedure’s superior performance when compared to single-locus diversity selection strategies, resulting in the optimal marker set for a given data set in the majority of marker subsets. Noting the inferior performance of the established Y-STR marker panels in a retrospective investigation, we suggest that future forensic marker selection should be guided, besides by other technical selection criteria, by an equivocation-based approach to obtain maximally discriminatory marker sets at minimal cost.

Human paternal lineages, languages, and environment in the Caucasus.

Publications that describe the composition of the human Y-DNA haplogroup in diffferent ethnic or linguistic groups and geographic regions provide no explicit explanation of the distribution of human paternal lineages in relation to specific ecological conditions. Our research attempts to address this topic for the Caucasus, a geographic region that encompasses a relatively small area but harbors high linguistic, ethnic, and Y-DNA haplogroup diversity. We genotyped 224 men that identified themselves as ethnic Georgian for 23 Y-chromosome short tandem-repeat markers and assigned them to their geographic places of origin. The genotyped data were supplemented with published data on haplogroup composition and location of other ethnic groups of the Caucasus. We used multivariate statistical methods to see if linguistics, climate, and landscape accounted for geographical diffferences in frequencies of the Y-DNA haplogroups G2, R1a, R1b, J1, and J2. The analysis showed significant associations of (1) G2 with wellforested mountains, (2) J2 with warm areas or poorly forested mountains, and (3) J1 with poorly forested mountains. R1b showed no association with environment. Haplogroups J1 and R1a were significantly associated with Daghestanian and Kipchak speakers, respectively, but the other haplogroups showed no such simple associations with languages. Climate and landscape in the context of competition over productive areas among diffferent paternal lineages, arriving in the Caucasus in diffferent times, have played an important role in shaping the present-day spatial distribution of patrilineages in the Caucasus. This spatial pattern had formed before linguistic subdivisions were finally shaped, probably in the Neolithic to Bronze Age. Later historical turmoil had little influence on the patrilineage composition and spatial distribution. Based on our results, the scenario of postglacial expansions of humans and their languages to the Caucasus from the Middle East, western Eurasia, and the East European Plain is plausible.

Human Paternal Lineages, Languages, and Environment in the Caucasus

Human Paternal Lineages, Languages, and Environment in the Caucasus David Tarkhnishvili, Alexander Gavashelishvili, Marine Murtskhvaladze, Mariam Gabelaia, and Gigi Tevzadze abstract Publications that describe the composition of the human Y-DNA haplogroup in different ethnic or linguistic groups and geographic regions provide no explicit explanation of the distribution of human paternal lineages in relation to specific ecological conditions. Our research attempts to address this topic for the Caucasus, a geographic region that encompasses a relatively small area but harbors high linguistic, ethnic, and Y-DNA haplogroup diversity. We genotyped 224 men that identified themselves as ethnic Georgian for 23 Y-chromosome short tandem-repeat markers and assigned them to their geographic places of origin. The genotyped data were supplemented with published data on haplogroup composition and location of other ethnic groups of the Caucasus. We used multivariate statistical methods to see if linguistics, climate, and landscape accounted for geographical differences in frequencies of the Y-DNA haplogroups G2, R1a, R1b, J1, and J2. The analysis showed significant associations of (1) G2 with well-forested mountains, (2) J2 with warm areas or poorly forested mountains, and (3) J1 with poorly forested mountains. R1b showed no association with environment. Haplogroups J1 and R1a were significantly associated with Daghestanian and Kipchak speakers, respectively, but the other haplogroups showed no such simple associations with languages. Climate and landscape in the context of competition over productive areas among different paternal lineages, arriving in the Caucasus in different times, have played an important role in shaping the present-day spatial distribution of patrilineages in the Caucasus. This spatial pattern had formed before linguistic subdivisions were finally shaped, probably in the Neolithic to Bronze Age. Later historical turmoil had little influence on the patrilineage composition and spatial distribution. Based on our results, the scenario of postglacial expansions of humans and their languages to the Caucasus from the Middle East, western Eurasia, and the East European Plain is plausible. key words Y-DNA Haplogroup, Paternal Lineage, Caucasus, Glacial Refugia, Human Ecology, Landscape Genetics, Ethnogenesis, Language Y-DNA haplogroup diversity is most commonly used to analyze ancestry of individual ethnic groups or linguistic families (Kayser et al. 1997; Brisighelli 2012), because Y-DNA haplogroups generally show more distinct ethnogeographic patterns than does matrilineally inherited mitochondrial DNA (Comas et al. 2000; Nasidze et al. 2003, 2004a), most likely because of higher dispersal rates of women (Seielstad et al. 1998; Oota et al. 2001; Nasidze et al. 2004b), the effects of selective pressures on the mitochondrial genome (Mishmar et al. 2003), and/or sex ratio [End Page 113] in favor of women causing more genetic drift in males (Dupanloup et al. 2003). Moreover, there is a popular nomenclature of the haplogroups linked to a well-established phylogenetic pattern (Underhill et al. 2001; Y Chromosome Consortium 2002; Karafet et al. 2008; Chiaroni et al. 2009). The Caucasus is among the most linguistically and culturally diverse regions of Eurasia (Comrie 2008; Nasidze et al. 2004a; Marchani et al. 2008; Balanovsky et al. 2011; Yunusbayev et al. 2012). Currently, the region hosts dozens of languages that are grouped into three language families (Comrie 2008): Caucasian, Indo-European, and Turkic. The Caucasian language family traditionally includes Adyghean, Vainakh, Daghestanian, and Kartvelian languages (Catford 1977), although the common origin of these languages is disputed (Starostin 1989). A recent study by Pagel et al. (2013) shows that the Kartvelian and Dravidic language families are the most basal in relation to the other Eurasian language families. Diakonoff and Starostin (1988) suggest that Vainakh and Daghestanian (i.e., Northeast Caucasian languages) are related to extinct Hurro-Urartian. Armenian and Ossetian languages belong to the Indo-European language family, and Oghuz and Kipchak subgroups of the Turkic language group are spoken in the Caucasus as well (Catford 1977; Comrie 2008). Linguistic differences, along with the differences in political history, influence (but do not determine) the ethnic identities of the people inhabiting the region. Some ethnic boundaries (e.g., that of Armenians or Ossetians) coincide with the linguistic boundaries, but those of the other ethnic groups do so only partly. Some groups speaking several mutually unintelligible but related languages consider themselves to be part of a single ethnos (e.g., Georgians...