Y-chromosomal DNA Research Articles

FamilyTreeDNA Group Project Administrator Stockholm, Sweden

Abstract. Several scholars have in the past hypothesized a northward movement of Hunnic contingents which ultimately reached Scandinavia on the basis of archaeological and philological evidence, an event which should be detectable in both ancient and modern DNA if true. Here I report that when analyzing a combination of ancient and modern DNA samples from across Eurasia one can detect a westward movement from the Altai-Sayan region to Europe which ultimately reached southern Sweden, and also accurately date this migration event to the 4th and 5th centuries CE with the help of carbon-14 dating and estimated TMRCAs of certain Y-DNA lineages. It is possible to identify these individuals and groups as Huns by analyzing their Y-chromosomal and autosomal DNA in combination with burial context. The significance and implications of this become clear when looking at the philological evidence which suggests that the Huns had a formative and lasting impact on the development of the peoples, cultures and beliefs of Scandinavia Keywords: Attila, Huns, Scythians, Y-DNA, Xiongnu

Inferences about the population history of Rangifer tarandus from Y chromosome and mtDNA phylogenies.

Reindeer, called caribou in North America, has a circumpolar distribution and all extant populations belong to the same species (Rangifer tarandus). It has survived the Holocene thanks to its immense adaptability and successful coexistence with humans in different forms of hunting and herding cultures. Here, we examine the paternal and maternal history of Rangifer based on robust Y-chromosomal and mitochondrial DNA (mtDNA) trees representing Eurasian tundra reindeer, Finnish forest reindeer, Svalbard reindeer, Alaska tundra caribou, and woodland caribou. We first assembled Y-chromosomal contigs, representing 1.3 Mb of single-copy Y regions. Based on 545 Y-chromosomal and 458 mtDNA SNPs defined in 55 males, maximum parsimony trees were created. We observed two well separated clades in both phylogenies: the "EuroBeringian clade" formed by animals from Arctic Islands, Eurasia, and a few from North America and the "North American clade" formed only by caribou from North America. The time calibrated Y tree revealed an expansion and dispersal of lineages across continents after the Last Glacial Maximum. We show for the first time unique paternal lineages in Svalbard reindeer and Finnish forest reindeer and reveal a circumscribed Y haplogroup in Fennoscandian tundra reindeer. The Y chromosome in domesticated reindeer is markedly diverse indicating that several male lineages have undergone domestication and less intensive selection on males. This study places R. tarandus onto the list of species with resolved Y and mtDNA phylogenies and builds the basis for studies of the distribution and origin of paternal and maternal lineages in the future.

KozhukhovaE.I., MustafinKh.Kh., SemenovV.A., UchanevaE.N. Reconstructing Ethnocultural Processes in the Sausken Valley (Tuva) during the Later Half of the 1st Millennium BC

The article represents findings of the group research devoted to reconstructing ethnocultural processes of the second half of the 1st millennium BC (Sausken Terrain Feature, Tuva). The research comprehensively studies local population groups who left behind their burial monuments in Eerbek River Valley. The study engages geneticist, ancient technologies experts, anthropologists and archaeologists. Kurgans of the middle and late Uyuk-Sagly Culture (5th–2nd century BC) were excavated in 2011–2016 by Tuva archaeological expedition arranged by the Russian Academy of Sciences Institute for the History of Material Culture. Nearly all burials in the kurgans had been robbed back in the ancient days. The study analyses above-ground structures and internal layouts of the kurgans, the burial ritual and tools (weapons, mirrors, belt accessories, bone items, embellishments). It allows to conclude that the kurgans have varying cultural attributions. The research also implies instrumental process analysis of glass and stone beads, chromatography of fabrics and proteomic analysis of archaeological leather. The paper reveals radiocarbon dating (14C) and correlations with other burial monuments of the Scythian Tuva. Craniological materials analysed allow to determine populations that could have been related to the aliens who arrived at the Eerbek River Valley in the Uyuk times. The Ozen-Ala-Belig groups differ from their peers from other territories in Tuva. It might be explained through the Uyuyk migrants mixing with the Eerbek Valley people who had been living there since the late Bronze Age. The paleogenetic study of 19 items especially focuses on researching the Y-chromosome DNA. For many researched samples the study determines haplogroups Q1b1a3-L330 and R1a1a1b2-Z93 (or its subgroups). The area of spread for these haplogroups is Soviet Central Asia, Central Asia, West and South Siberia. One samples is assigned to I2a1b1-M223 haplogroups with the area of spread in the Balkans and South-Eastern Europe. The obtained findings may indicate that the Western and Eastern nomads kept in touch during the researched period. The archaeological, anthropological and genetic data lead to a conclusion that the Scythian cultures in the given region is complex and multi-faceted.

Male-specific age prediction based on Y-chromosome DNA methylation with blood using pyrosequencing

Age prediction is an important aspect of forensic science that offers valuable insight into identification. In recent years, extensive studies have been conducted on age prediction based on DNA methylation, and numerous studies have demonstrated that DNA methylation is a reliable biomarker for age prediction. However, almost all studies on age prediction based on DNA methylation have focused on age-related CpG sites in autosomes, which are concentrated on single-source DNA samples. Mixed samples, especially male-female mixed samples, are common in forensic casework. The application of Y-STRs and Y-SNPs can provide clues for the genetic typing of male individuals in male-female mixtures, but they cannot provide the age information of male individuals. Studies on Y-chromosome DNA methylation can address this issue. In this study, we identified five age-related CpG sites on the Y chromosome (Y-CpGs) and developed a male-specific age prediction model using pyrosequencing combined with a support vector machine algorithm. The mean absolute deviation of the model was 5.50 years in the training set and 6.74 years in the testing set. When we used a male blood sample to predict age, the deviation between the predicted and chronological age was 1.18 years. Then, we mixed the genomic DNA of the male and a female at ratios of 1:1, 1:5, 1:10, and 1:50, the range of deviation between the predicted and chronological age of the male in the mixture was 1.16–1.74 years. In addition, there was no significant difference between the methylation values of bloodstains and blood in the same sample, which indicates that our model is also suitable for bloodstain samples. Overall, our results show that age prediction using DNA methylation of the Y chromosome has potential applications in forensic science and can be of great help in predicting the age of males in male-female mixtures. Furthermore, this work lays the foundation for future research on age-related applications of Y-CpGs.

Application of bioluminescence assay to assess PCR carryover contamination in forensic DNA laboratories

In forensic DNA testing, PCR-based multilocus short tandem repeat (STR) profiling kits, which have high sensitivity and discriminatory power, are generally used to analyze autosomal and Y-chromosomal DNA profiles. Forensic DNA laboratories require strict quality control for DNA testing, as contamination during analyses leads to incorrect interpretation of DNA profiles. Here, we aimed to apply bioluminescence assay to detect and monitor residual PCR products on laboratory work area and equipment surfaces by targeting dATP in the PCR product and allelic ladder marker. Two commercially available bioluminescence assay kits (CheckLite HS Plus and UltraSnap™) were examined for their sensitivity after confirming their reactivity to dATP. In the assay using CheckLite HS Plus, the lower detectable sample volumes were calculated as 10 pl of PCR product of GlobalFiler and PowerPlex Fusion and 1 pl of PCR product of Yfiler Plus and the allelic ladder marker of GlobalFiler, whereas those in the assay using UltraSnap™ were calculated as 1 nl of PCR product and allelic ladder marker. The sample volumes of these kits were lower than those detected through electrophoresis. Thus, the sensitivity of these kits was sufficient to control PCR carryover contamination in the post-PCR areas. Furthermore, residual PCR products in the post-PCR areas were continuously monitored using a bioluminescence assay. The results showed that the bioluminescence values increased after handling PCR samples for electrophoresis and decreased after decontamination. Therefore, we concluded that the bioluminescence assay is useful for assessing PCR carryover contamination in post-PCR processes in forensic DNA laboratories.

Improving the efficiency of Y-chromosome detection and the quality of STR typing in forensic casework with an in-house made qPCR and HRM system based on SYTO™ 9 chemistry

DNA quantification prior to STR amplification is a crucial step in forensic casework. Obtaining good-quality genetic STR profiles depends mainly on the amount and integrity of the DNA input in the PCR. In addition, the detection of male trace DNA provides key information for forensic investigation. AimTo evaluate the correlation between the quantification results obtained with the previously developed Amel-Y system, and its ability to detect Y-chromosome DNA by HRM, with the resulting STR profiles, and to ultimately show that Amel-Y can be routinely used in forensic casework to improve STR and Y-STR results. Material & methodsBiological samples derived from forensic casework (85 reference and 391 evidence samples) were quantified by the Amel-Y system (a duplex qPCR/HRM based on SYTO™ 9 chemistry) using Rotor-Gene 6000. STRs were amplified and analyzed with GeneAmp™ PCR System 9700 or Veriti™ Thermal Cyclers and ABI 3500 Genetic Analyzer, respectively. ResultsAfter DNA normalization, a total of 386 STR profiles were obtained (305 full and 81 partial). Sex typing by HRM was 100% successful in reference samples. Male DNA was detected by HRM in 210 evidence samples. 80/201 were mixed with an excess of female DNA. In addition, Amel-Y was able to detect Y-chromosome DNA in mixed samples that did not amplify the Y-variant of Amelogenin marker with commercial STR kits. The reproducibility and precision of the Amel-Y system were demonstrated (CVCt% ≤ 9.55) within the dynamic range analyzed (0.016–50 ng/µL; 41 independent runs). Amel-Y also proved to be compatible with other real-time PCR platforms. ConclusionWe demonstrated that Amel-Y is a robust quantification system that can be routinely used in forensic casework to obtain reliable autosomal STR profiles and can be suitable as a predictor for Y-STR typing success when male DNA is detected. HRM can be used as a rapid screening tool for male DNA detection in mixed samples. Alternative designs like Amel-Y offer independence from commercial quantification kits in forensic labs.

Impact of Cell-Debris and Room-Temperature Storage on Urine Circulating Tumor DNA from Hepatocellular Carcinoma

This study evaluated the impact of cell debris and 7-day room temperature storage on the quality and yield of transrenal DNA. Archived urine specimens collected from five hepatocellular carcinoma (HCC) patients and two pregnant women carrying male fetuses were used to assess the impact of cell debris on urine cell-free DNA (ucfDNA) isolation as measured by quantitative PCR for Y-chromosome DNA, or HCC-associated mutation and methylation markers, and by capillary electrophoresis. Prospectively collected urine from 21 HCC patients was aliquoted after collection for paired immediate freezing versus 7-day room temperature storage followed by freezing for further analysis. Cell debris contained more Y-chromosome DNA than supernatant in three of the six urine specimens tested from pregnant women, suggesting that cell debris can be associated with 20.6% to 84.9% of transrenal ucfDNA. Ninety-five percent (20 of 21) of frozen and room temperature urine pairs had overlapping DNA size distribution. ucfDNA quantity determined by quantitative PCR for TP53, CTNNB1, TERT, and HCC-associated urine circulating tumor DNA markers were statistically similar between room temperature and frozen samples. This suggests no significant difference in DNA degradation between the groups. The association of transrenal ucfDNA with cell debris and HCC circulating DNA stability at room temperature is significant to further the understanding of transrenal circulating tumor DNA pre-analytical handling for HCC screening.

Genetic diversity and income inequality: The case for Y-chromosome DNA diversity

This paper examines how patrilineal genetic diversity affects income inequality. We create a new measure of genetic diversity by implementing the notion of Y chromosome diversity. Using a cross section of more than 120 countries and controlling for other geographic and economic variations, we find that countries with higher genetic diversity also have higher income inequality. We show that this measure captures variations in income inequality that is unexplained by previous popular diversity indices and overcomes some of the empirical issues of those measures. Additionally, we find that countries with higher degree of genetic diversity have lower levels of social cooperation and government efficiency, which then leads to a decrease in redistribution and an increase in income inequality.

Archaeological questions and genetic answers: Male paternal kinship in a copper age multiple burial from the eastern Italian Alps

In 2010, a detailed anthropological study regarding two adult individuals and one foetus-newborn buried in a Copper Age (ca. 3000–2700 cal. BC) multiple grave site found in Ora/Auer in the eastern Italian Alps (Alto Adige/ Südtirol) was published. This exceptional archaeological finding provides a rare insight into an inhumation prehistoric ritual discovered within a natural alpine rock shelter.Due to the presence of an infant in the grave, the authors were doubtful of the anthropological male sex assignment given to both adult individuals found there. Additionally, correlation of non-metric traits suggested a possible kinship between them. To determine the biological sex and to investigate genetic relatedness, we performed a paleogenetic investigation (shotgun and enrichment data of ∼2 million SNPs) of the two adults.We successfully analyzed the ancient DNA of these individuals, confirming that biologically, both were males (XY). Moreover, through kinship analyses and data from unilinear-transmitted markers (Y-Chromosome and mitochondrial DNA), we detected a first-degree paternal kinship (most likely father-son).This study underlines the importance of interdisciplinary dialogue between archaeology, anthropology and palaeogenomics, demonstrating how the latter can significantly support the interpretation of funerary contexts.

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.

The Idaho Student Homicides and the Future of Forensic Genetic Genealogy

The Idaho Student Homicides and the Future of Forensic Genetic Genealogy

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.

Genetic Examination of Remains from the Two Largest Mass Burials of 1238 in Yaroslavl Detynets

The article presents the results of genetic studies of the remains of people who died and were buried in 1238 on the territory of the citadel in the city of Yaroslavl. The analysis of ancient DNA allows us to directly study the composition of the population of this ancient Russian city along the Volga at the time of the Mongol conquest. By the genetic profile of both Y-chromosomal and mitochondrial DNA, we can say that about 40% of the samples studied do not belong to the dominant haplogroups. The lowest homogeneity in the Y-chromosome is typical for the burial in pit No. 110, which was located near the fortifications. It also contained the remains of two men belonging to the haplogroup R1a (Z93), marking the possible "eastern" origin of their ancestors. In the authors’ opinion, not only ordinary residents of the city and its environs, but also professional defenders, as well as attackers, could get into the burials near the walls of the citadel. Absence of grave goods and in the conditions of a sanitary burial, makes not possible to determine who the men of "eastern" origin were. However, their presence undoubtedly affects the genetic diversity of the city's population.

Sheep Post-Domestication Expansion in the Context of Mitochondrial and Y Chromosome Haplogroups and Haplotypes.

Mitochondrial DNA and nonrecombinant parts of Y-chromosome DNA are a great tool for looking at a species’ past. They are inherited for generations almost unaffected because they do not participate in recombination; thus, the time of occurrence of each mutation can be estimated based on the average mutation rate. Thanks to this, male and female haplogroups guide confirming events in the distant past (potential centers of domestication, settlement of areas, trade connections) as well as in modern breeding (crossbreeding, confirmation of paternity). This research focuses mainly on the development of domestic sheep and its post-domestication expansion, which has occurred through human trade from one continent to another. So far, five mitochondrial and five Y-chromosome haplogroups and dozens of their haplotypes have been detected in domestic sheep through studies worldwide. Mitochondrial DNA variability is more or less correlated with distance from the domestication center, but variability on the recombinant region of the Y chromosome is not. According to available data, central China shows the highest variability of male haplogroups and haplotypes.

Y-chromosome variation in Basrah population.

Y-chromosome DNA profiles are promising tools in population genetics and forensic science. Analysis of Y-chromosome variety was performed on a total of 191 unrelated males throughout different regions in Basrah. The Y-chromosome variety was explored utilizing 17 markers system. For the uniparental system, the large majority of the haplogroups observed in the Basrah population are (R1b, E1b1b, G2a, and J1) considered to have begun in the Middle East and to have later spread all over Western Eurasia. 30% of the Y-chromosomes, in all likelihood, represent landings from inaccessible distant geographic regions. The level of haplotype diversity and its implication for statistics are evaluated. The distinctive extent of long go genetic input observed for the Y chromosome shows that gene flow events to this area might have involved mainly males.

The possibility of molecular genetic identity testing of an unidentified body from the second world war

Background: In the current forensic scenario, molecular genetic analyzes are used to identify the remains of victims of natural and man-made disasters, emergencies, and war conflicts. Aim: This study aimed to summarize forensic molecular genetic examinations conducted at the RCFME for identifying the victims of the Second World War in the Russian Federation. This was conducted to assess the prospects of using DNA identification analysis for unidentified remains of bodies buried in 19391945. Material and methods: We studied 30 expert reports from 2007 to 2021 of 171 skeletal bodies from exhumed graves. The total number of objects studied was 421 (bone fragments and teeth, from 1 to 5 objects from 1 body). Results: Using the remains, genotypes of 167 people were established. The success rate of evidence-based molecular genetic identification was 98% (171 cases). Of these, positive identification was noted for 10 body remains and negative identification for 157 remains. Four skeletal bodies (2%) were deemed unsuitable for research. In most cases, indirect identification schemes were used a comparative study with putative relatives by biostatistical analysis of allelic variants of polymorphic loci of autosomal DNA as well as by direct comparative analysis of the polymorphism at the Y-chromosome DNA and mitochondrial DNA. Conclusions: Molecular genetic studies are highly effective for identifying the remains of victims of natural and man-made disasters, military conflicts, and other emergencies. The success of molecular genetic studies regarding the identification of victims of the Second World War conducted at the RCFME clearly demonstrate these possibilities. Simultaneously, it should be emphasized that this type of expertise falls to the category of rather complex molecular genetic studies, which requires the use of expanded panels of analytical test systems as well as the use of special methodological techniques and hardware and software.

Label-free E-DNA biosensor based on PANi-RGO-G*NPs for detection of cell-free fetal DNA in maternal blood and fetal gender determination in early pregnancy

In this study, a DYS14 aptamer/polyaniline–reduced graphene oxide–gold nanoparticles/gold (Apt/PANi–RGO–G*NPs/Au) electrode was fabricated to detect the Y-chromosome DYS14 DNA sequence in cffDNA in the blood plasma of pregnant women and used on real and laboratory samples with high success rate. The electrochemical properties of the prepared E-DNA biosensor were characterized by CV, SWV, XRD, and EIS. The E-DNA biosensor morphological characteristics were investigated by TEM, SEM, and EDX. Phosphorothioate was used to link the aptamer to PANi–RGO–G*NPs modified gold electrode. This is due to control of the adsorption polarity and increase adsorption stability. Under optimized conditions, the linear range of the analytical technique with respect to the logarithm of the target sequence concentration was 1.0 × 10−16–1.0 × 10−8 M, the detection limit was 4.26 × 10−17 M, and the limit of quantitation was 1.422 × 10−16 M. The E-DNA biosensor displayed high selectivity and sensitivity, high efficiency, and acceptable repeatability. For fetal sex detection, 12 pregnant women from the 5th to the 15th week of gestation participated in the study. Results indicated the fabricated Apt/PANi–RGO–G*NPs/Au E-DNA biosensor to be appropriate for fetal sex determination in pregnant women between the 7th and 9th week of gestation. Notably, this method can be used as a model for the study of pathogens like bacteria and viruses.

About Ancestors

ABSTRACT Though regularly studied as different academic domains, Asian and Oceanian studies are deeply intertwined not only through longstanding political, economic, immigrant – and colonial – ties, but by questions about common ancestry. From popular commercial DNA testing to historical studies in linguistics, folklore, archaeology, biological anthropology, and sophisticated genome sequencing, deep histories of Oceanian Islander peoples have long been tied to ‘origin’ traditions and reconstructions of lineages from the Asian mainland, notably through the Austronesian diaspora. From 19th-century linguistic theories and Lapita sites, to 20th-century ABO blood groupings and contemporary mitochondrial and Y-chromosome DNA assays, scholars have proposed at times conflicting interpretations of Oceania’s possible Asian human heritage. These analyses have themselves been consistently challenged by Indigenous genealogical traditions such as Māori whakapapa and Islander assertions of origins based on ancestral and localized narratives decolonized of Western scientific practices.

A New Method for Improving Extraction Efficiency and Purity of Urine and Plasma Cell-Free DNA.

This study assessed three commercially available cell-free DNA (cfDNA) extraction kits and the impact of a PEG-based DNA cleanup procedure (DNApure) on cfDNA quality and yield. Six normal donor urine and plasma samples and specimens from four pregnant (PG) women carrying male fetuses underwent extractions with the JBS cfDNA extraction kit (kit J), MagMAX Cell-Free DNA Extraction kit (kit M), and QIAamp Circulating Nucleic Acid Kit (kit Q). Recovery of a PCR product spike-in, endogenous TP53, and Y-chromosome DNA was used to assess kit performance. Nucleosomal-sized DNA profiles varied among the kits, with prominent multi-nucleosomal-sized peaks present in urine and plasma DNA isolated by kits J and M only. Kit J recovered significantly more spike-in DNA than did kits M or Q (p < 0.001) from urine, and similar amounts from plasma (p = 0.12). Applying DNApure to kit M- and Q-isolated DNA significantly improved the amplification efficiency of spike-in DNA from urine (p < 0.001) and plasma (p ≤ 0.013). Furthermore, kit J isolated significantly more Y-chromosome DNA from PG urine compared to kit Q (p = 0.05). We demonstrate that DNApure can provide an efficient means of improving the yield and purity of cfDNA and minimize the effects of pre-analytical biospecimen variability on liquid biopsy assay performance.

Male-specific age estimation based on Y-chromosomal DNA methylation.

Although DNA methylation variation of autosomal CpGs provides robust age predictive biomarkers, no male-specific age predictor exists based on Y-CpGs yet. Since sex chromosomes play an important role in aging, a Y-chromosome-based age predictor would allow studying male-specific aging effects and would also be useful in forensics. Here, we used blood-based DNA methylation microarray data of 1,057 males from six cohorts aged 15-87 and identified 75 Y-CpGs with an interquartile range of ≥0.1. Of these, 22 and six were significantly hyper- and hypomethylated with age (p(cor)<0.05, Bonferroni), respectively. Amongst several machine learning algorithms, a model based on support vector machines with radial kernel performed best in male-specific age prediction. We achieved a mean absolute deviation (MAD) between true and predicted age of 7.54 years (cor=0.81, validation) when using all 75 Y-CpGs, and a MAD of 8.46 years (cor=0.73, validation) based on the most predictive 19 Y-CpGs. The accuracies of both age predictors did not worsen with increased age, in contrast to autosomal CpG-based age predictors that are known to predict age with reduced accuracy in the elderly. Overall, we introduce the first-of-its-kind male-specific epigenetic age predictor for future applications in aging research and forensics.