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![Simplified phylogenetic tree of the Y chromosome. In each branch, the names of the main Y-SNPs involved and the haplogroups are indicated. The highlighted haplogroups are those listed in the review. For these, the International Society of Genetic Genealogy (ISOGG) nomenclature is also provided (accessed on 16/06/2020) [6]](publication/352949661/figure/fig1/AS:1041712742928396@1625375080803/Simplified-phylogenetic-tree-of-the-Y-chromosome-In-each-branch-the-names-of-the-main.png)
Simplified phylogenetic tree of the Y chromosome. In each branch, the names of the main Y-SNPs involved and the haplogroups are indicated. The highlighted haplogroups are those listed in the review. For these, the International Society of Genetic Genealogy (ISOGG) nomenclature is also provided (accessed on 16/06/2020) [6]
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The Y chromosome has been widely explored for the study of human migrations. Due to its paternal inheritance, the Y chromosome polymorphisms are helpful tools for understanding the geographical distribution of populations all over the world and for inferring their origin, which is really useful in forensics. The remarkable historical context of Eur...
Citations
... Haplogroup I1a is predominant in northern Europe, with the highest frequency in the Scandinavian populations, while haplogroup I1b* is the most common clade in Eastern Europe and the Balkans [36]. Haplogroup I2a, currently predominant in Eastern Europe, has been identified in ancient Y-STR sequences from hunter-gatherers from Switzerland, Hungary, and Scandinavia, as well as in samples from the Neolithic and Bronze Age in Hungary and Germany [37]. The third most common haplogroup found in the population of Roșia Montană is I1, which is also in Harghita County, Transylvania [32]. ...
... BCE the settlement was again defeated by nomads and ceased to exist.[137][138][139][140] Location:49.864876 N, 35.277719 E. Kolomak city, Kharkiv region, Ukraine. The headland on the left bank of a tributary of the Kolomak River, which is a left tributary of the Vorskla River. ...
The North Pontic region, which encompasses present-day Ukraine, was a crossroads of migration as it connected the vast Eurasian Steppe with Central Europe. We generated shotgun-sequenced genomic data for 91 individuals dating from around 7,000 BCE to 1,800 CE to study migration and mobility history in the region, with a particular focus on historically attested migrating groups during the Iron Age and the medieval period, such as Scythian, Chernyakhiv, Saltiv and Nogai associated peoples. We infer a high degree of temporal heterogeneity in ancestry, with fluctuating genetic affinities to present-day Western European, Eastern European, Western Steppe and East Asian groups. We also infer high heterogeneity in ancestry within geographically, culturally and socially defined groups. Despite this, we find that ancestry components which are widespread in Eastern and Central Europe have been present in the Ukraine region since the Bronze Age.
... Poplars are dioecious plants, and another promising sequence for clarifying the systematic relationships of species and hybrids of the genus Populus is the sex-determining region (SDR). Sex chromosomes are actively used in phylogenetic studies (Parker et al., 2020;Navarro-Lopez et al., 2021). The species of sections Aigeiros and Tacamahaca are characterized by an XY sexdetermination system (Gaudet et al., 2008;Pakull et al., 2009;Pakull et al., 2011;Kersten et al., 2014;Geraldes et al., 2015;Pakull et al., 2015;McKown et al., 2017), which allows the examination of poplar relationships in the male lineage. ...
Members of the genus Populus L. play an important role in the formation of forests in the northern hemisphere and are used in urban landscaping and timber production. Populus species of closely related sections show extensive hybridization. Therefore, the systematics of the genus is rather complicated, especially for poplars of hybrid origin. We aimed to assess the efficiency of application of the sex-determining region (SDR) in addition to the nuclear and chloroplast genome loci traditionally used in phylogenetic studies of poplars to investigate relationships in sections Aigeiros Duby and Tacamahaca Spach. Targeted deep sequencing of NTS 5S rDNA, ITS, DSH 2, DSH 5, DSH 8, DSH 12, DSH 29, 6, 15, 16, X18, trnG-psbK-psbI, rps2-rpoC2, rpoC2-rpoC1, as well as SDR and ARR17 gene was performed for 379 poplars. The SDR and ARR17 gene together with traditionally used multicopy and single-copy loci of nuclear and chloroplast DNA allowed us to obtain a clustering that is most consistent with poplar systematics based on morphological data and to shed light on several controversial hypotheses about the origin of the studied taxa (for example, the inexpediency of separating P. koreana, P. maximowiczii, and P. suaveolens into different species). We present a scheme of relationships between species and hybrids of sections Aigeiros and Tacamahaca based on molecular genetic, morphological, and geographical data. The geographical proximity of species and, therefore, the possibility of hybridization between them appear to be more important than the affiliation of species to the same section. We speculate that sections Aigeiros and Tacamahaca are distinguished primarily on an ecological principle (plain and mountain poplars) rather than on a genetic basis. Joint analysis of sequencing data for the SDR and chloroplast genome loci allowed us to determine the ancestors of P. × petrovskoe – P. laurifolia (female tree) × P. × canadensis (male tree), and P. × rasumovskoe – P. nigra (female tree) × P. suaveolens (male tree). Thus, the efficiency of using the SDR for the study of poplars of sections Aigeiros and Tacamahaca and the prospects of its use for the investigation of species of the genus Populus were shown.
... 21 European Y chromosomes are primarily comprised of the haplogroups E, G, I, J, N and R, with the R haplogroup comprising the majority of the Y chromosomes. 22,23,24,25 While many previous studies are limited by short tandem repeats (STR's) and/or low resolution single nucleotide polymorphisms (SNPs) panels, 22,24,25,26,27,28 they provide information on the composition and frequency of major haplogroups in Europeans. ...
... 21 European Y chromosomes are primarily comprised of the haplogroups E, G, I, J, N and R, with the R haplogroup comprising the majority of the Y chromosomes. 22,23,24,25 While many previous studies are limited by short tandem repeats (STR's) and/or low resolution single nucleotide polymorphisms (SNPs) panels, 22,24,25,26,27,28 they provide information on the composition and frequency of major haplogroups in Europeans. ...
... Unlike I1, the I2a haplogroup and its subclades are much less frequent in Scandinavia but are reported to comprise 10% of Irish and 6% of Basque Y haplogroups. 24,25,26,28 While the presence of I2a, which is clustered in the Northwest region of the province (Figure 3, Table 3), is consistent with English-settled communities in NL, it also could be indicative of the presence of Iberian/Basque Y-DNA that originated from Portuguese and Spanish fishermen. 8,9 Similarly, the J haplogroup, comprising ~10% of the current Portuguese population 48 may also have originated in NL with the presence of Portuguese ancestors. ...
The population of Newfoundland and Labrador (NL) is largely derived from settlers who migrated primarily from England and Ireland in the 1700-1800s. Previously described as an isolated founder population, based on historical and demographic studies, data on the genetic ancestry of this population remains fragmentary. Here we describe the largest investigation of patrilineal ancestry in NL. To determine the paternal genetic structure of the population, 1,110 Y chromosomes from an NL based cohort were analyzed using 5,761 Y-specific markers. We identified 160 distinct paternal haplotypes, the majority of which (71.4%) belong to the R1b haplogroup. When NL is compared with global reference populations, the haplotype composition and frequencies of the NL paternal lineages primarily resemble the English and Irish ancestral source populations. There is also evidence for genetic contributions from Basque, French, Portuguese, and Spanish fishermen and early settlers that frequented NL. The population structure shows geographical and religious clustering that can be associated with the settlement of ancestral source populations from England and Ireland. For example, the R1b-M222 haplotype, seen in people of Irish descent, is found clustered in the Irish-settled Southeast region of NL. The clustering and expansion of Y haplotypes in conjunction with the geographical and religious clusters illustrate that limited subsequent in-migration, geographic isolation and societal factors have contributed to the genetic substructure of the NL population and its designation as a founder population.
... When comparing the most common Y-SNP haplogroups in the Japanese sample set (Figure 3), it became evident that the longer Y-STR alleles at DYS712 were especially common in males belonging to a subgroup of haplogroup O1b2 (O-P49). This was the most frequently observed haplogroup in the current Japanese sample and is completely absent from Europeans [21]. It is widely established that longer STR alleles are more prone to mutations [15,16]. ...
Rapidly mutating Y chromosomal short tandem repeat markers (RM Y-STRs) –characterized by at least one mutation per 100 generations– are suitable for differentiating both related and unrelated males. The recently introduced multiplex method RMplex allows for the efficient analysis of 30 Y-STRs with increased mutation rates, including all 26 currently known RM Y-STRs. While currently available RM Y-STR mutation rates were established mostly from European individuals, here we applied RMplex to DNA samples of 178 genetically confirmed father-son pairs from East Asia. For several Y-STRs, we found significantly higher mutation rates in Japanese compared to previous estimates. The consequent father-son differentiation rate based on RMplex was significantly higher (52%) in Japanese than previously reported for Europeans (42%), and much higher than with Yfiler Plus in both sample sets (14% and 13%, respectively). Further analysis suggests that the higher mutation and relative differentiation rates in Japanese can in part be explained by on average longer Y-STR alleles relative to Europeans. Moreover, we show that the most striking difference, which was found in DYS712, could be linked to a Y-SNP haplogroup (O1b2-P49) that is common in Japanese and rare in other populations. We encourage the forensic Y-STR community to generate more RMplex data from more population samples of sufficiently large sample size in combination with Y-SNP data to further investigate population effects on mutation and relative differentiation rates. Until more RMplex data from more populations become available, caution shall be placed when applying RM Y-STR mutation rate estimates established in one population, such as Europeans, to forensic casework involving male suspects of paternal origin from other populations, such as non-Europeans.
Objective To compare the differences in the haplogroup classification and population discrimination abilities of five Y-SNP panels based on next-generation sequencing and to provide references for the forensic application of these panels. Methods The haplogroup classification and genetic structure analysis of 1,600 samples from the high-depth sequencing project of 1,000 Human Genomes were analyzed. The Y-SNP loci, Y-InDel loci, and haplogroup information provided by the five published panels were used to perform statistical analysis. and Results There were obvious differences in the proportion of haplogroups and haplogroup resolution among different panels. The 639 Y-SNP panel has the highest average resolution for the haplogroups C, D and O, and the CSYseq panel has the highest average resolution for the haplogroups N and Q. The three panels developed for Chinese populations showed higher population specificity, among which the 639 Y-SNP panel showed a highest resolution level in the three Chinese populations and was closest to the fineness level of the ISOGG 2019 phylogenetic tree. Except the 859 Y-SNP panel, other four panels exhibited good discrimination abilities for Asian populations. Conclusion The three Y-SNP panels developed by Chinese research groups showed outstanding
Y chromosomal short tandem repeats (Y-STRs) are used in forensic investigations as a useful complementary tool to autosomal markers. The ongoing development of new kits with an increasing number of markers makes it necessary to update populations typed in the Y-STR Haplotype Reference Database to reach at least 23 Y-STRs. A novel Y-STR multiplex panel was developed to offer a cost-efficient alternative to update Y-STR haplotypes from 12 to 23 loci. This panel includes the eleven markers, DYS448, DYS456, DYS458, DYS635, Y-GATA H4, DYS576, DYS481, DYS549, DYS533, DYS570 and DYS643, as well as DYS385a/b for traceability purpose. Developmental validation of this panel was conducted following the recommendations of the Scientific Working Group on DNA Analysis Methods (SWGDAM), showing high sensitivity, tolerance to common inhibitors as well as high species specificity. It was efficient for degraded DNA samples and for detection of male mixtures. When applying it for extending the current data of the Ibiza population, both the discrimination capacity and the haplotype diversity increased from 0.5952 to 0.9048 and from 0.9808 to 0.9977, respectively. Together, the study demonstrates the suitability of this panel in forensic casework.
The Y chromosome can yield a unique perspective into the study of human demographic history. However, due to the repetitive nature of part of its sequence, only a small set of regions are suitable for variant calling and discovery from short-read sequencing data. These regions combined represent 8.9 Mbp or 0.14% of a diploid human genome. Consequently, investing in whole-genome sequencing to resolve Y-chromosome questions is poorly efficient. Here we use, as an alternative, target enrichment technology to greatly increase sequencing effectiveness, validating and applying the technique to 181 males, for 162 of whom we obtained a positive result. Additionally, 75 samples sequenced for the whole genome were also included, for a total sample size of 237. These samples were chosen for their Y chromosome haplogroup: R1b-DF27. In the context of European populations, and particularly in Iberia, this haplogroup stands out for its high frequency and its demographic history. Current evidence indicates that the diffusion of this haplogroup is related to the population movements that mark the cultural Bronze Age transition, making it remarkably interesting for population geneticists. The results of this study show the effects of the rapid radiation of the haplogroup in Spain, as even with the higher discriminating power of whole sequences, most haplotypes still fall within the R1b-DF27* paragroup rather than in the main derived branches. However, we were able to refine the ISOGG 2019–2020 phylogeny, and its two main subbranches, namely L176.2 and Z272, which present geographical differentiation between the Atlantic and Mediterranean coasts of Iberia.
Structural rearrangements like copy number variations (CNVs) in the male-specific Y chromosome (MSY) have been associated with male fertility phenotypes in human and mouse but have been sparsely studied in other mammalian species. Here we designed digital droplet PCR (ddPCR) assays for seven horse MSY multi-copy genes and SRY and evaluated their absolute copy numbers (CN) in 209 normal male horses of 22 breeds, 73 XY horses with disorders of sex development (DSD) and/or infertility, five Przewalski's horses and two kulans. This established baseline CN for these genes in horses. The TSPY gene showed the highest CN and was the most CN variable between individuals and breeds. SRY was a single-copy gene in most horses but had two to three copies in some indigenous breeds. Since SRY is flanked by two copies of RBMY, their CNVs were interrelated and may lead to SRY-negative XY DSD. The Przewalski's horse and kulan had one copy of SRY and RBMY. TSPY and ETSTY2 showed significant CNVs between cryptorchid and normal males (p < 0.05). No significant CNVs were observed in subfertile/infertile males. Notably, CN of TSPY and ETSTY5 differed between successive male generations and between cloned horses, indicating germline and somatic mechanisms for CNVs. We observed no correlation between MSY gene CNVs and MSY haplotypes. We conclude that the ampliconic MSY reference assembly has deficiencies and further studies with an improved MSY assembly are needed to determine selective constraints over horse MSY gene CN and their relation to stallion reproduction and male biology.
