Population data for 12 Y-chromosome STR loci in a sample from Honduras

Haplotype, allele frequencies and population data of 12 Y-chromosome STR loci DYS19, DYS385, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438 and DYS439 were determined from a sample of 128 unrelated male individuals from Honduras, Central America. A total of 112 haplotypes were identified by the 12 Y-STR loci of which 98 were unique. The haplotype diversity (98.99%) and the proportion of different haplotypes (87.50%) were estimated. Genetic distances were calculated between Honduras and other populations from Southern and Central America, Europe and Africa. The analysis of a Multi Dimensional Scaling (MDS) plot, based on pairwise R_ST genetic distances, allowed to conclude that Honduras is highly differentiated from the African samples (0.343  R_ST  0.620; P = 0.000) and from a Native American sample from Argentina, Tobas (R_ST = 0.210, P = 0.000). Honduras showed a lower genetic distance to the European cluster (composed by European and South American general population samples from Brazil, Argentina, Colombia and Venezuela) than to the Central American cluster (Mexico and El Salvador).     

Development of an Italian RM Y-STR haplotype database: Results of the 2013 GEFI collaborative exercise

Recently introduced rapidly mutating Y-chromosomal short tandem repeat (RM Y-STR) loci, displaying a multiple-fold higher mutation rate relative to any other Y-STRs, including those conventionally used in forensic casework, have been demonstrated to improve the resolution of male lineage differentiation and to allow male relative separation usually impossible with standard Y-STRs. However, large and geographically-detailed frequency haplotype databases are required to estimate the statistical weight of RM Y-STR haplotype matches if observed in forensic casework. With this in mind, the Italian Working Group (GEFI) of the International Society for Forensic Genetics launched a collaborative exercise aimed at generating an Italian quality controlled forensic RM Y-STR haplotype database. Overall 1509 male individuals from 13 regional populations covering northern, central and southern areas of the Italian peninsula plus Sicily were collected, including both “rural” and “urban” samples classified according to population density in the sampling area. A subset of individuals was additionally genotyped for Y-STR loci included in the Yfiler and PowerPlex Y23 (PPY23) systems (75% and 62%, respectively), allowing the comparison of RM and conventional Y-STRs. Considering the whole set of 13 RM Y-STRs, 1501 unique haplotypes were observed among the 1509 sampled Italian men with a haplotype diversity of 0.999996, largely superior to Yfiler and PPY23 with 0.999914 and 0.999950, respectively. AMOVA indicated that 99.996% of the haplotype variation was within populations, confirming that genetic-geographic structure is almost undetected by RM Y-STRs. Haplotype sharing among regional Italian populations was not observed at all with the complete set of 13 RM Y-STRs. Haplotype sharing within Italian populations was very rare (0.27% non-unique haplotypes), and lower in urban (0.22%) than rural (0.29%) areas. Additionally, 422 father-son pairs were investigated, and 20.1% of them could be discriminated by the whole set of 13 RM Y-STRs, which was very close to the theoretically expected estimate of 19.5% given the mutation rates of the markers used. Results obtained from a high-coverage Italian haplotype dataset confirm on the regional scale the exceptional ability of RM Y-STRs to resolve male lineages previously observed globally, and attest the unsurpassed value of RM Y-STRs for male-relative differentiation purposes.     

Y-chromosomal testing of brown bears (Ursus arctos): Validation of a multiplex PCR-approach for nine STRs suitable for fecal and hair samples

High-resolution Y-chromosomal markers have been applied to humans and other primates to study population genetics, migration, social structures and reproduction. Y-linked markers allow the direct assessment of the genetic structure and gene flow of uniquely male inherited lineages and may also be useful for wildlife conservation and forensics, but have so far been available only for few wild species. Thus, we have developed two multiplex PCR reactions encompassing nine Y-STR markers identified from the brown bear (Ursus arctos) and tested them on hair, fecal and tissue samples. The multiplex PCR approach was optimized and analyzed for species specificity, sensitivity and stutter-peak ratios. The nine Y-STRs also showed specific STR-fragments for male black bears and male polar bears, while none of the nine markers produced any PCR products when using DNA from female bears or males from 12 other mammals. The multiplex PCR approach in two PCR reactions could be amplified with as low as 0.2 ng template input. Precision was high in DNA templates from hairs, fecal scats and tissues, with standard deviations less than 0.14 and median stutter ratios from 0.04 to 0.63. Among the eight di- and one tetra-nucleotide repeat markers, we detected simple repeat structures in seven of the nine markers with 9–25 repeat units. Allelic variation was found for eight of the nine Y-STRs, with 2–9 alleles for each marker and a total of 36 alleles among 453 male brown bears sampled mainly from Northern Europe. We conclude that the multiplex PCR approach with these nine Y-STRs would provide male bear Y-chromosomal specificity and evidence suited for samples from conservation and wildlife forensics.     

Updating the Y-chromosomal phylogenetic tree for forensic applications based on whole genome SNPs

The Y-chromosomal phylogenetic tree has a wide variety of important forensic applications and therefore it needs to be state-of-the-art. Nevertheless, since the last ‘official’ published tree many publications reported additional Y-chromosomal lineages and other phylogenetic topologies. Therefore, it is difficult for forensic scientists to interpret those reports and use an up-to-date tree and corresponding nomenclature in their daily work. Whole genome sequencing (WGS) data is useful to verify and optimise the current phylogenetic tree for haploid markers. The AMY-tree software is the first open access program which analyses WGS data for Y-chromosomal phylogenetic applications. Here, all published information is collected in a phylogenetic tree and the correctness of this tree is checked based on the first large analysis of 747 WGS samples with AMY-tree. The obtained result is one phylogenetic tree with all peer-reviewed reported Y-SNPs without the observed recurrent and ambiguous mutations. Nevertheless, the results showed that currently only the genomes of a limited set of Y-chromosomal (sub-)haplogroups is available and that many newly reported Y-SNPs based on WGS projects are false positives, even with high sequencing coverage methods. This study demonstrates the usefulness of AMY-tree in the process of checking the quality of the present Y-chromosomal tree and it accentuates the difficulties to enlarge this tree based on only WGS methods.     

Drawing the history of the Hutterite population on a genetic landscape: inference from Y-chromosome and mtDNA genotypes

Although the North American Hutterites trace their origins to South Tyrol, no attempts have been made to examine the genetic migration history of the Hutterites before emigrating to the United States in the 1870s. To investigate this, we studied 9 microsatellite loci and 11 unique event polymorphism (UEP) markers on the Y-chromosome, the hypervariable region I (HVRI) of the mitochondrial DNA (mtDNA), as well as the complete mtDNA genome of Hutterite and South Tyrolean samples. Only 6 out of 14 Y-chromosome UEP+microsatellite haplotypes and 3 out of 11 mitochondrial haplotypes that were present in the Hutterites were also present in the South Tyrolean population. The phylogenetic relationships inferred from Y-chromosome and mtDNA databases show that the Hutterites have a unique genetic background related to a similar extent to central and eastern European populations. An admixture analysis indicates, however, a relatively high genetic contribution of central European populations to the Hutterite gene pool. These results are consistent with historical records on Hutterite migrations and demographic history. In addition, our data reveal similar numbers of Y and mitochondrial haplotypes in Hutterite male and female founders, respectively. The Hutterite male and female gene pools are similar with respect to genetic diversity and genetic distance measures and comparable with respect to their origins, suggesting a similar evolutionary history.     

Quantitative analysis of microchimerism in systemic sclerosis skin tissue

Abstract It has been reported that more male DNA of presumed fetal origin is present in the blood and skin of women with systemic sclerosis (SSc) as compared with healthy controls after delivery, but these findings are controversial. We sought to determine whether male cell DNA is present in SSc using a quantitative polymerase chain reaction for Y chromosome DNA. The study groups comprised 57 healthy women, 49 patients with SSc and 30 patients with connective tissue diseases other than SSc who had given birth to at least one son and/or had experienced fetal loss. The intensity of the PCR bands on negatives of gel photographs was quantified with a video densitometer linked to a computer analysis system. Positive Y chromosome DNA was found in 20 healthy women, 14 SSc patients and 6 patients with connective tissue diseases other than SSc. The occurrence rate of DNA equivalents of male cells among the three groups showed no significant differences. The number of male cell DNA equivalents per 80 ng tissue DNA in SSc patients (4.59 ± 9.63), however, was significantly higher than in healthy women (1.83 ± 4.96; P < 0.05) and in patients with connective tissue diseases other than SSc (0.27 ± 0.64; P < 0.01). The occurrence rate of fetal loss in male cell DNA-positive SSc (eight) was significantly higher than in male cell DNA-negative SSc patients (four; P < 0.01). No correlation was found between the number of male cell DNA equivalents and birth of sons or clinicolaboratory findings. These results indicate that the elevated amount of male cell DNA in SSc skin tissue may contribute to the pathogenesis of SSc. Received: 19 December 2000 / Revised: 24 March 2001 / Accepted: 2 June 2001     

Outcomes for offspring of men having ICSI for male factor infertility

Since the introduction of intracytoplasmic sperm injection (ICSI) using single sperm isolated from testicular tissue in men with obstructive and non-obstructive azoospermia, or using ejaculated sperm in those with poor semen quality, there have been concerns that this might have adverse effects on the offspring compared to conventional in vitro fertilisation (IVF) and natural conceptions. ICSI is done for reasons other than male factor infertility, and on the whole has not been shown to have any more negative effects than those seen with IVF. There have however, been very few studies of ICSI with a focus on, or large enough numbers to examine, the specific outcomes associated with male factor infertility. From the limited information available in relation to the source of the sperm and aetiology of infertility in the presence of ICSI, there appears to be no increased risk of congenital malformations. There is, however, a small increase in both de novo and inherited chromosome abnormalities. In terms of growth and neurodevelopment, there are very few studies, and so far, no adverse outcomes have been found in young children whose fathers have a sperm defect. The origin of the sperm used in ICSI does not have a major influence on the early life outcomes for the offspring, but transgenerational and epigenetic effects remain unknown. When the male factor infertility is known or thought to be due to a Y-chromosome deletion, this information should be given to the young male offspring at a time that will ensure his own reproductive health and plans are optimized.     

Y-Chromosome haplotypes reveal relationships between populations of the Arabian Peninsula,North Africa and South Asia

Background: The United Arab Emirates (UAE) is positioned at the crossroads of human migration out of Africa and through to Asia and Europe.

Aim: To compare the degree of genetic diversity of the Arabian UAE population with populations in other countries from the Middle East, South Asia and North Africa.

Subjects and methods: Twenty-seven Y-STR were analysed in 217 individuals. Y-STR haplotypes from this study were compared to population data stored in YHRD, using MDS and AMOVA.

Results: Two hundred and twelve haplotypes were observed in the 217 individuals studied. Although the reduction in Y-STR loci from 27 to 17 resulted in a decrease in discriminatory power, comparisons of populations were possible. The UAE population clustered closer with other populations of the Middle East. The South Asian and North African populations were separated by Middle Eastern populations in between both clusters.

Conclusion: This is the first study to report the diversity of a population of the Arabian Peninsula using 27 Y-STR. MDS plots show that Middle Eastern populations are positioned in the centre, with African, Asian and European populations around the Arab population cluster. The findings of this study are consistent with this region being at the epicentre of human migration between continents.     

中国广东汉族与新疆维吾尔族24个Y-STR基因座的多态性分析

目的应用GFS 24Y试剂盒,对中国广东汉族和新疆维吾尔族共584个无关男性样本进行24个Y-STR基因座分型,统计其基因座、单倍型的遗传多态性,并分析其群体差异。方法采用磁珠法提取样本DNA后用GFS24Y试剂盒扩增,3130XL遗传分析仪进行基因分型,根据分型结果进行统计分析。结果获得了中国广东汉族与新疆维吾尔族共584个样本24个Y-STR基因座的分型结果及各等位基因频率分布资料。在广东汉族群体中,各基因座的基因多样性(GD值)为0.560 6~0.963 9,由24个基因座组成的单倍型共有299个,单倍型多样性(HD值)为0.999 93;在新疆维吾尔族中,GD值为0.443 9~0.957 9,共观察到282个单倍型,HD值为0.999 85。两个民族未观察到共有单倍型。通过两个群体间的比较,共有22个Y-STR基因座等位基因频率分布在两个民族之间存在差异(P0.05),各基因座在两个民族的遗传分化系数(Fst值)为0.000 767 9(DYS481)~0.247 946(DYS520)。结论 24个Y-STR基因座在中国广东汉族与新疆维吾尔族人群中均有较高的多态性,并显示出明显的民族特征,在法医亲权鉴定和个体识别、群体遗传学等领域均有重要的应用价值。