Y-chromosome Polymorphisms Research Articles

Application of X-STRs for Forensic Identification in Mixed DNA Profile: A Case Report

Autosomal polymorphisms (STRs) or Y-Chromosome polymorphisms (Y-STRs) are usually used for the study and deconvolution of mixed DNA profiles in forensic genetics, accompanying data interpretation with biostatistical evaluations (e.g., RMP, RMNE, LR). Sometimes, however, some mixed DNA profiles are so complex that autosomal and Y markers are not sufficient for correct discrimination and identification. In this work is reported a robbery case in which the analysis of the polymorphic markers of the X Chromosome (X-STRs) was applied to the mixed profiles obtained from the traces. This falls outside the classic use of the X-STRs. Indeed, the aim of the authors is to encourage the usage of X-STRs not only in parental relationships, but also in pure forensic cases for interpreting complex mixed DNA profiles, since their application in case resolution could be more decisive than autosomal STRs and Y-STRs.

Genetic history of the Koryaks and Evens of the Magadan region based on Y chromosome polymorphism data.

In order to clarify the history of gene pool formation of the indigenous populations of the Northern Priokhotye (the northern coast of the Sea of Okhotsk), Y-chromosome polymorphisms were studied in the Koryaks and Evens living in the Magadan region. The results of the study showed that the male gene pool of the Koryaks is represented by haplogroups C-B90-B91, N-B202, and Q-B143, which are also widespread in other peoples of Northeastern Siberia, mainly of Paleo-Asiatic origin. High frequency of haplogroup C-B80, typical of other Tungus-Manchurian peoples, is characteristic of the Evens of the Magadan region. The shared components of the gene pools of the Koryaks and Evens are haplogroups R-M17 and I-P37.2 inherited as a result of admixture with Eastern Europeans (mainly Russians). The high frequency of such Y chromosome haplogroups in the Koryaks (16.7 %) and Evens (37.8 %) is indicative of close interethnic contacts during the last centuries, and most probably especially during the Soviet period. The genetic contribution of the European males' Y chromosome significantly prevails over that of maternally inherited mitochondrial DNA. The study of the Y chromosome haplogroup diversity has shown that only relatively young phylogenetic branches have been preserved in the Koryak gene pool. The age of the oldest component of the Koryak gene pool (haplogroup C-B90-B91) is estimated to be about 3.8 thousand years, the age of the younger haplogroups Q-B143 and N-B202 is about 2.8 and 2.4 thousand years, respectively. Haplogroups C-B90-B91 and N-B202 are Siberian in origin, and haplogroup Q-B143 was apparently inherited by the ancestors of the Koryaks and other Paleo-Asiatic peoples from the Paleo-Eskimos as a result of their migrations to Northeast Asia from the Americas. The analysis of microsatellite loci for haplogroup Q-B143 in the Eskimos of Greenland, Canada and Alaska as well as in the indigenous peoples of Northeastern Siberia showed a decrease in genetic diversity from east to west, pointing to the direction of distribution of the Paleo-Eskimo genetic component in the circumpolar region of America and Asia. At the same time, the Evens appeared in the Northern Priokhotye much later (in the XVII century) as a result of the expansion of the Tungusic tribes, which is confirmed by the results of the analysis of haplogroup C-B80 polymorphisms.

Origin of the Bunun Indigenous People of Taiwan, a Review of Published Material Using Y-Chromosome and Mitochondrial DNA Gene Systems

Anthropological and linguistic studies place the first settlement of Austronesian speaking Taiwanese (AN_Tw) in the mid-Holocene era. However, geneticists have revealed exclusive diversity among the Bunun indigenous people, implying that their ancestral origin needs further study. The mitochondrial DNA (mtDNA) polymorphism of the Bunun shows a homogeneous relationship with other AN_Tw. However, the Y-chromosome polymorphism shows two major haplogroups, O1a2-M50 (60.7%), also seen to a lesser extent among the Northern AN_Tw, and O1b1a1a1a1a1-M88 (37.5%), scarce among all other AN and non-AN groups in Taiwan, but prevailing in Southeast Asia (SEA) and Mainland Southeast Asia (MSEA). While the present-day mtDNA profile of the Bunun typifies the long-term demographic standard for all AN_Tw since the Neolithic era, their Y-chromosome profile suggests an arrival of male settlers in the last two to three millennia from SEA or MSEA, who mixed exclusively with the Bunun indigenous people.

On the Forensic Use of Y-Chromosome Polymorphisms.

Nowadays, the use of Y-chromosome polymorphisms forms an essential part of many forensic DNA investigations. However, this was not always the case. Only since 1992 have we seen that some forensic scientists started to have an interest in this chromosome. In this review, I will sketch a brief history focusing on the forensic use of Y-chromosome polymorphisms. Before describing the various applications of short-tandem repeats (STRs) and single nucleotide polymorphisms (SNPs) on the Y-chromosome, I will discuss a few often ignored aspects influencing proper use and interpretation of Y-chromosome information: (i) genotyping Y-SNPs and Y-STRs, (ii) Y-STR haplotypes shared identical by state (IBS) or identical by descent (IBD), and (iii) Y-haplotype database frequencies.

On the Issue of Genetic Genealogy of the Kazakh Clan Zhagalbayly

The subject of the research is historical sources, oral Kazakh genealogies (shezhire) of the Kazakh-Nogai heroic and lyrical epic, as well as the results of Y-DNA research. The object of research is the Kazakh genus Zhagalbayly. The author examines in detail such aspects of the topic as the entry of the Zhagalbayly clan into the composition of the main peoples who stood out from the imperial super ethnos of the Golden Horde. The data on the places of settlement of Zhagalbayly in various historical periods in the post-Ordyn space are given. Various versions of such works as "Kyz Zhibek", "Kobylandy Batyr" and "Er Sayyn" in Kazakh, Nogai and Kyrgyz languages have been studied as folklore sources. The reasons and time of the emergence of the Kazakh tribal association Zhetiru, which included the genus zhagalbayly, are considered. The main conclusions of the study are to establish the availability of information about the early settlement of the ancestors of modern Kazakh Zhagalbayly clan on a vast territory from the Crimea to Afghanistan. This fact is confirmed by the presence of Zhagalbaila in the list of clans of the Crimean Khanate, Nogai Hordes, the Timurid Empire and the Kazakh Khanate. As a result of the analysis of the data of the oral Kazakh genealogy (shezhire) and the Kazakh-Nogai heroic and lyrical epic, for the purpose of their historical synthesis, the character Karabukan is established. He is represented as a batyr and a soothsayer of the Kiyat tribe troops. It is proposed to consider him as a possible legendary ancestor of the Kazakh Zhagalbayly. The results of studies of Y-chromosome polymorphism of representatives of various divisions of the Kazakh zhagalbayly are presented. When comparing the seven results of the Y-DNA12 samples, the probability that the number of generations before their common ancestor is equal to 24 generations is 91.41%. When comparing the three results for Y-DNA 67, it is equal to 99.61%. This information is consistent with shezhire, in which the distance to the common ancestor is 22-24 generations.

Haplotype Diversity of Mongolian and Tuvan Goat Breeds (Capra hircus) Based on mtDNA and Y-Chromosome Polymorphism

Haplotype Diversity of Mongolian and Tuvan Goat Breeds (Capra hircus) Based on mtDNA and Y-Chromosome Polymorphism

CSYseq: The first Y-chromosome sequencing tool typing a large number of Y-SNPs and Y-STRs to unravel worldwide human population genetics.

Male-specific Y-chromosome (chrY) polymorphisms are interesting components of the DNA for population genetics. While single nucleotide polymorphisms (Y-SNPs) indicate distant evolutionary ancestry, short tandem repeats (Y-STRs) are able to identify close familial kinships. Detailed chrY analysis provides thus both biogeographical background information as paternal lineage identification. The rapid advancement of high-throughput massive parallel sequencing (MPS) technology in the past decade has revolutionized genetic research. Using MPS, single-base information of both Y-SNPs as Y-STRs can be analyzed in a single assay typing multiple samples at once. In this study, we present the first extensive chrY-specific targeted resequencing panel, the ‘CSYseq’, which simultaneously identifies slow mutating Y-SNPs as evolution markers and rapid mutating Y-STRs as patrilineage markers. The panel was validated by paired-end sequencing of 130 males, distributed over 65 deep-rooted pedigrees covering 1,279 generations. The CSYseq successfully targets 15,611 Y-SNPs including 9,014 phylogenetic informative Y-SNPs to identify 1,443 human evolutionary Y-subhaplogroup lineages worldwide. In addition, the CSYseq properly targets 202 Y-STRs, including 81 slow, 68 moderate, 27 fast and 26 rapid mutating Y-STRs to individualize close paternal relatives. The targeted chrY markers cover a high average number of reads (Y-SNP = 717, Y-STR = 150), easy interpretation, powerful discrimination capacity and chrY specificity. The CSYseq is interesting for research on different time scales: to identify evolutionary ancestry, to find distant family and to discriminate closely related males. Therefore, this panel serves as a unique tool valuable for a wide range of genetic-genealogical applications in interdisciplinary research within evolutionary, population, molecular, medical and forensic genetics.

Middle eastern genetic legacy in the paternal and maternal gene pools of Chuetas

Chuetas are a group of descendants of Majorcan Crypto-Jews (Balearic Islands, Spain) who were socially stigmatized and segregated by their Majorcan neighbours until recently; generating a community that, although after the seventeenth century no longer contained Judaic religious elements, maintained strong group cohesion, Jewishness consciousness, and endogamy. Collective memory fixed 15 surnames as a most important defining element of Chueta families. Previous studies demonstrated Chuetas were a differentiated population, with a considerable proportion of their original genetic make-up. Genetic data of Y-chromosome polymorphism and mtDNA control region showed, in Chuetas’ paternal lineages, high prevalence of haplogroups J2-M172 (33%) and J1-M267 (18%). In maternal lineages, the Chuetas hallmark is the presence of a new sub-branching of the rare haplogroup R0a2m as their modal haplogroup (21%). Genetic diversity in both Y-chromosome and mtDNA indicates the Chueta community has managed to avoid the expected heterogeneity decrease in their gene pool after centuries of isolation and inbreeding. Moreover, the composition of their uniparentally transmitted lineages demonstrates a remarkable signature of Middle Eastern ancestry—despite some degree of host admixture—confirming Chuetas have retained over the centuries a considerable degree of ancestral genetic signature along with the cultural memory of their Jewish origin.

Analysis of Clan Structure of Tuvans by Y-Chromosome Markers

According to the data on the Y-chromosome polymorphism, an assessment of the influence of two factors (tribal (clan) and administrative (kozhuuns) subdivision) on the structure of the gene pool of Tuvans is provided. The ten most common Tuvan clans (Ak, Baraan, Irgit, Kol, Kyrgyz, Mongush, Oorzhak, Oyun, Khertek, Choodu) are included in this analysis. They cover two-thirds of the total sample (N = 545) of Tuvans from six kozhuuns (Barun-Khemchiksky, Tandinsky, Tere-Kholsky, Todzhinsky, Chaa-Kholsky, Erzinsky). Genetic portraits of clans created on the basis of 52 SNP markers of the Y chromosome reveal the founder effect for all clans, except the two largest—Kyrgyz and Mongush. Making up one-third of the sample, these two clans are conglomerates. Analysis of molecular variance (AMOVA) indicates an equal degree of genetic separation of clans (5.2%) and kozhuuns (6.8%). But the Mantel test detects a high correlation (r = 0.50) between the genetic and clan structure against the low correlation (r = 0.25) between the genetic and geographical distances. The reason for the difference between the AMOVA and Mantel test lies in the fact that the four most numerous kozhuuns are “monoclan,” in which one clan prevails, and only two kozhuuns (Todzhinsky and Tere-Kholsky) include representatives of three different clans. The selection of the western and eastern clusters on the graph of multidimensional scaling fits in well with the anthropological data (Sayansky and Katangsky anthropological types), but does not confirm any of the ethnographic versions of the Tuvan ethnogenesis (“Samoyedic,” “Mongolian,” “Turkic”). The sum of results indicates that the tribal structure most fully reflects the architectonics of the Tuvan gene pool, and for this reason, it must be taken into account in population genetic research.

The Early Mediaeval Slav-German border (Limes Sorabicus) in the light of research into Y-chromosome polymorphism in contemporary and historical German populations

n the 8th century, the first political boundary between Germany (the land of the Franks) and the Slav people – known as Limes Sorabicus – followed the line of the Rivers Elbe and its tributary the Saale. In later centuries this was breached under the influence of an eastwards political expansion of Germany also characterised by developing German colonisation in that same direction (of the so-called Ostsiedlung). The consequence was for German regional communities to take shape to the east of the old Limes Sorabicus. Alongside the emigrants from the west, further participants in the process where autochthonous Slavs and Balts. This mixed origin of the new communities arising is revealed in historical accounts, but also via the results of scientific analyses of various profiles. The genetic research carried out to date supports the above contention, as well as a conclusion that the zone around the old Limes Sorabicus, despite its running through the centre of what is today an ethnically-German area, continues to represent a separation of populations whose ancestors are mainly of distinct origins.

Анализ генофонда юго-восточных башкир в контексте их родовой структуры (по данным о полиморфизме Y-хромосомы)

Анализ генофонда юго-восточных башкир в контексте их родовой структуры (по данным о полиморфизме Y-хромосомы)

Генофонд трех восточных родов тувинцев по данным полиморфизма Y-хромосомы

Генофонд трех восточных родов тувинцев по данным полиморфизма Y-хромосомы

Structure and Forming of Mitochondrial Gene Pool of Russian Population of Eastern Europe

Phylogeographic analysis of the variability of whole mitochondrial genomes in the Russian populations of Eastern Europe (n = 557) showed that, in the Russian mitochondrial gene pool, there were subgroups of mtDNA characteristic only of Russians and other Eastern Slavs (11.7%), as well as of Slavs as a whole (12.2%), Slavs and Germans (6.6%), and Slavs and Baltic Finns (5.7%). The results of molecular dating suggest that the mitochondrial subgroups characteristic of Russians and Slavs in general began to arise 2700–3500 years ago. The results of the study of the dynamics of the effective population size based on the Bayesian analysis of data on the variability of mtDNA haplotypes specific to Russians and Slavs showed that a rapid increase in population sizes occurred immediately after its decline 4000–5000 years ago. The data obtained are discussed in comparison with the results of the analysis of Y-chromosome polymorphism in European populations.

Molecular Genetic Analysis of Population Structure of the Great Zhuz Kazakh Tribal Union Based on Y-Chromosome Polymorphism

Historically, the Kazakhs formed through an amalgam of nomadic tribes that previously belonged to the Golden Horde. The Kazakh tribes were geographically divided into three tribal associations—the Great, the Middle, and the Lesser zhuzes. One of the unsolved problems in the Kazakhs’ ethnic history remains the issue of the genetic relationships between tribes composing the zhuzes. The aim of the current work was to study intertribal genetic relations in the Great zhuz. To achieve this goal, we investigated the biallelic polymorphisms of Y chromosome in the 12 tribes of the Great zhuz. Twenty-seven haplogroups of Y chromosome were identified. The comparative analysis of the haplogroup distribution revealed complexity of the Great zhuz gene pool. The results obtained suggest that the Great zhuz was formed by combining not only genetically related, but also quite remote, groups of tribes.

Challenges in the identification of dead migrants in the Mediterranean: The case study of the Lampedusa shipwreck of October 3rd 2013

Every year thousands of migrants die during the endeavour to reach the Italian coasts, making the Mediterranean the theatre of one of the greatest tragedies of mankind. Over 60% of these victims is buried unidentified: one of the reasons behind this is related to the specific difficulties and lack of strategies concerning AM and PM data collection. The present article describes how Italy is trying to face the problem of migrant identification, thanks to the collaboration between government, the Italian national police and universities. In particular, this is the first pilot study carried out to identify the victims of the second greatest tragedy of its kind off the Italian coast, near Lampedusa, on October 3rd 2013, which caused 366 victims. The present article shows the strategies conceived to collect postmortem and especially antemortem data and to compare them to identify matches, using medicolegal, anthropological, odontological and genetic approaches. Thirty-one victims out of 53 missing sought by relatives were identified (58.5%). The type and the quality of antemortem data available, generally photos and videos, pinpoints the importance of the face and the body for identification when the bodies are well preserved and how DNA analyses may at times present difficulties. In fact, critical points emerged concerning especially the lack of genetic information of the populations to which the victims belonged, the number of genetic markers needed to reach a statistical support for the identification and the need to adopt lineage markers such as mitochondrial DNA and Y-chromosome polymorphisms to identify parental relationships. This pilot study however has proven that families continue to seek their relatives and that it is possible, as well as mandatory, to identify migrant victims in spite of the difficulties in the collection of antemortem and postmortem data. In addition, considering the peculiar scenario, novel strategies for positive identification have to be defined in each field (anthropological, odontological and genetic) as well as in combination.

Y-chromosome polymorphisms of the domestic Bactrian camel in China

Single-nucleotide polymorphisms (SNPs), microsatellites and copy number variation (CNV) were studied on the Y chromosome to understand the paternal origin and phylogenetic relationships for resource protection, rational development and utilization of the domestic Bactrian camel in China. Our sample set consisted of 94 Chinese domestic Bactrian camels from four regions (Inner Mongolia, Gansu, Qinghai and Xinjiang), we screened 29 Y-chromosome-specific loci for SNPs, analysed 40 bovine-derived microsatellite loci and measured CNVs of HSFY and SRY through Sanger sequencing, automated fluorescence-based microsatellite analysis and quantitative real-time PCR, respectively. A multicopy gene, SRY, was first found, and sequence variation was only detected in SRY in a screen of 29 loci in 13 DNA pools of individual camels. In addition, a TG repeat in the USP9Y gene was identified as the first polymorphic microsatellite in the camel Y chromosome, whereas microsatellite based on bovine sequences were not detected. The frequency of each allele varied among different populations. For the Nanjiang, Hexi and Alashan populations, a 243-bp allele was found. For the Sunite population, 241-bp, 243-bp and 247-bp alleles were detected, and the frequencies of these alleles were 22.2%, 44.5% and 33.3%, respectively; 241-bp and 243-bp alleles were found in other populations. Finally, CNVs in two Y-chromosomal genes were detected; CNV for HSFY and SRY ranged from 1 to 3 and from 1 to 9, respectively.

Molecular genetic analysis of population structure of kazakh tribal union great zhuz based on y-chromosome polymorphism

Molecular genetic analysis of population structure of kazakh tribal union great zhuz based on y-chromosome polymorphism

Whole sequence analysis indicates a recent southern origin of Mongolian Y-chromosome C2c1a1a1-M407.

The Y-chromosome haplogroup C2c1a1a1-M407 is a predominant paternal lineage in Mongolic-speaking populations, especially in Buryats and Kalmyks. However, the origin and internal phylogeny of C2c1a1a1-M407 have not been investigated in detail. In this study, we analyzed twenty-three Y-chromosome sequences of haplogroup C2c1a1a1-M407 and its most closely related clades. We generated a high-resolution phylogenetic tree of haplogroup C2c1a1a1-M407 and its upstream clade C2c1a1-CTS2657, including 32 subclades and 144 non-private Y-chromosome polymorphisms. We discover that all available C2c1a1a1-M407 samples from Mongolic-speaking populations belong to its newly defined downstream clade C2c1a1a1b-F8465, whereas all samples of C2c1a1-CTS2657(xF8465) come from northern Han Chinese, Korean, and Japanese. Furthermore, we observe that C2c1a1a1b-F8465 and its subclade C2c1a1a1b1-F8536 expanded at approximately 0.86 and 0.44 thousand years ago, respectively. Therefore, we conclude that C2c1a1a1-M407 in Mongolic-speaking populations has originated from northeastern Asia. C2c1a1a1b1-F8536, the newly defined subclade of C2c1a1a1-M407, probably represents the genetic relationships between ancient Oyrats, modern Kalmyks, Mongolians, and Buryats.

Preliminary results of the genetic identifications of the Lampedusa 2013 shipwreck victims

In the last years, the migration flow across the Mediterranean Sea increased rapidly. More than 20,000 persons, included young men, women and children, died trying to reach the European coasts, 60% of which remained with no identity. In this scenario, forensic genetics can give a support to the positive identification of the victims. To this aim, the DNA extracted from the victims is analysed and compared to reference samples supplied by relatives, in order to find out familiar relationships. In collaboration with LABANOF, University of Milan, our laboratory is trying to set up a genetic and statistic approach suitable for victim identification of the migrants died during the shipwreck occurred near the Lampedusa island, in October 3rd, 2013. The genetic profiles of the 363 victims, collected by the Forensic Genetics Lab of the Scientific Police Service (Palermo, Italy), were initially compared among them and subsequently between victims and subsequently with the reference samples, using the software Familias3, setting up the DVI interface. The statistical approach identified four familiar groups among the victims, generally composed by a parent with two or more children, and five parent-child relationships. In addition, 20 matches were detected between the subjects seeking a relative and 17 victims, with a positive statistical support. Some critical points emerged during the analyses among which the most important were the number of relatives and genetic markers needed to reach a statistical support to identification, the lack of genetic information about the populations to which the victims belonged and the option to use lineage markers such as Y-chromosome and mtDNA polymorphisms. In conclusion, these results support the reliability of the approach and highlight the importance to collaborate with other forensic experts in order to achieve positive identifications of the bodies.

Y-chromosome polymorphisms in the United Arab Emirates population

Y chromosome short tandem repeats (Y-STR) has been widely used in forensic DNA profiling and lineages analysis. The aim of this study is to establish a database of an extensive Y-STR profiles of the United Arab Emirates (UAE) population and to investigate the distribution of 17 Y-STR loci. Samples of 345 Emirati males using 17 Y-STR loci included in the AmpFLSTR® Y-filer® PCR Amplification kit (Life Technologies) (DYS456, DYS3891, DYS390, DYS389II, DYS458, DYS19, DYS385a/b, DYS393, DYS391, DYS439, DYS635, DYS392, GATA-H4, DYS437, DYS438 and DYS448). Statistical analysis of allele frequency, haplotype diversity and discrimination capacity were performed for the samples using Arlequin software version 3.5A total of 301 unique haplotypes were identified, 271 haplotypes were found to be unique and 22 haplotypes were shared between two individuals. In addition, there were four different haplotypes shared between more than two individuals. The haplotype diversity (HD) was found to be equal to 0.99885. The highest gene diversity was estimated to be 0.94142 for DYS385a/b whereas the lowest was estimated to be 0.4369 for DYS392. The discrimination capacity (DC) was calculated to be 90.03%