The place of Slovakian paternal diversity in the clinal European landscape

Background: Several demographic events have been postulated to explain the contemporaneous structure of European genetic diversity. First, an initial settlement of the continent by anatomically modern humans; second, the re-settlement of northern latitudes after the Last Glacial Maximum; third, the demic diffusion of Neolithic farmers from the Near East; and, fourth, several historical events such as the Slavic migration.

Aim: The aim of this study was to provide a more integrated picture of male-specific genetic relationships of Slovakia within the broader pan-European genetic landscape.

Subjects and methods: This study analysed a new Y-chromosome data-set (156 individuals) for both SNP and STR polymorphisms in population samples from five different Slovakian localities.

Results: It was found that the male diversity of Slovakia is embedded in the clinal pattern of the major R1a and R1b clades extending over the continent and a similar pattern of population structure is found with Y-specific SNP or STR variation.

Conclusion: The highly significant correlation between the results based on fast evolving STRs on one hand and slow evolving SNPs on the other hand suggests a recent timeframe for the settlement of the area.     

Y-chromosomal analysis identifies the skeletal remains of Swiss national hero Jörg Jenatsch (1596–1639)

Jörg Jenatsch was a Swiss defender of independence and a fighter for liberty in the 17th century. With the help of three living male members of the Jenatsch family, we successfully identified a skeleton exhumed from Chur cathedral as the remains of Jörg Jenatsch. Our conclusion was based upon complete Y-STR and Y-SNP profiles that could be generated by replicate analyses of a bone sample available to us. The skeleton and the three living family members carried the same Y-SNP haplogroup, but were discordant at three of 23 Y-STR loci. This notwithstanding, conservative biostatistical evaluation of the data suggests that the Chur skeleton is at least 20 times more likely than not to be Jörg Jenatsch.     

Y-chromosomal analysis identifies the skeletal remains of Swiss national hero Jörg Jenatsch (1596–1639)

Jörg Jenatsch was a Swiss defender of independence and a fighter for liberty in the 17th century. With the help of three living male members of the Jenatsch family, we successfully identified a skeleton exhumed from Chur cathedral as the remains of Jörg Jenatsch. Our conclusion was based upon complete Y-STR and Y-SNP profiles that could be generated by replicate analyses of a bone sample available to us. The skeleton and the three living family members carried the same Y-SNP haplogroup, but were discordant at three of 23 Y-STR loci. This notwithstanding, conservative biostatistical evaluation of the data suggests that the Chur skeleton is at least 20 times more likely than not to be Jörg Jenatsch.     

Reprint of: High resolution mapping of Y haplogroup G in Tyrol (Austria)

The distribution of Y-chromosomal haplogroup G2a (G-P15) in present-day paternal lineages in Tyrol (Austria) was analyzed by applying a high-density regional sampling scheme that also covered remote mountain areas. There is evidence from ancient genetic data for a high frequency of Y-chromosomal haplogroup G in prehistoric populations of Central Europe, whilst nowadays levels well below 10% are routinely observed. A population sample comprising ∼3700 specimens was analyzed for Y-chromosomal variation by genotyping Y-SNPs and Y-STRs. The set of binary markers included nine SNPs specific for sub-lineages of haplogroup G. The frequency of haplogroup G in 2379 unrelated men born in Tyrol amounted to 11.3%. Nearly all of these Y chromosomes belonged to haplogroup G2a. The main sub-haplogroup within G2a was defined by the SNP L497 (G2a3b1c) and reached a population frequency of 8.6%. Although this average level is higher than reported for other countries the geographical distribution of haplogroup G-L497 showed a differentiated pattern with a clustered distribution within some alpine valleys, where maxima above 40% were found. Both, the estimation of coalescent times and a principle coordinates analysis based on R_ST values derived from Y-STR haplotypes from different sub-regions of Tyrol revealed evidence for an old settlement history associated with Y chromosomes belonging to haplogroup G in the Tyrolean Alps.     

六色荧光标记同步检测27个STR基因座的法医学应用评估

目的探讨同步检测27个STR基因座多态性及法医学应用价值。方法用Power PlexFusion 6C荧光标记系统对274份广东汉族无关个体的DNA进行PCR扩增,在3130XL遗传分析仪上进行电泳分析。用Gene MapperID-X软件分析基因型,用Power Stats v1.2软件分析群体遗传学参数。并观察该系统对微量及混合检材的检验效果。结果 23个常染色体STR基因座遗传多态性高,在广东汉族人群的累积个人识别率为1-2.3×10-28,累积非父排除率为0.999 999 999。DYS391、DYS570和DYS576的GD值分别为0.481、0.791和0.751,共检出58种单倍型,单倍型多态性为0.337。微量检材STR基因座检出率为93.33%,混合检材Y-STR基因座检出率为96.67%。结论 Power PlexFusion 6C系统遗传多态性高,可以用于亲缘鉴定、个体识别以及数据库建设。     

Developmental validation of the Yfiler® Plus PCR Amplification Kit: An enhanced Y-STR multiplex for casework and database applications

Y-chromosomal loci have proven useful in solving investigations where low levels of male DNA are present in a high female DNA background. An intrinsic limitation of Y-STRs compared with autosomal STRs is a reduced power of discrimination due to a lack of recombination throughout most of the Y-chromosome. Thus, in an effort to increase the power of discrimination we have developed a new 6-dye, 27-plex Y-STR system that includes the 17 loci from the Yfiler^® and Yfiler^® Direct kits (DYS19, DYS385a/b, DYS389I/II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS635 (Y GATA C4), and Y GATA H4) plus three highly polymorphic Y-STR loci (DYS460, DYS481, and DYS533), and seven rapidly mutating Y-STR loci (DYF387S1a/b, DYS449, DYS518, DYS570, DYS576, DYS627) which allow for improved discrimination of related individuals. The Yfiler^® Plus PCR Amplification Kit is a dual application assay designed to amplify DNA from extracted casework and database samples from storage cards and swab lysates via direct amplification. Compared to the Yfiler PCR Amplification Kit, the new multiplex shows increased discrimination of male lineages and also improved performance in inhibited samples, improved balance in male DNA samples mixed with female DNA at ratios >1:1000, and faster time to results. The Yfiler Plus Kit shows very high concordance to the Yfiler Kit but discordance with the PowerPlex^® Y23 Kit at the DYS481 locus was observed in 2 out of 30 samples tested. This developmental validation work follows the SWGDAM guidelines and demonstrates that the assay is robust and suitable for use on forensic casework and database samples.     

Analysis of 24 Y chromosomal STR haplotypes in a Chinese Han population sample from Henan Province,Central China

We analyzed haplotypes for 24 Y chromosomal STRs (Y-STRs), including 17 Yfiler loci (DYS19, DYS385a/b, DYS389I/II, DYS390, DYS391, DYS392, DYS393, DYS437, DY438, DYS439, DYS448, DYS456, DYS458, DYS635 and Y-GATA-H4) and 7 additional STRs (DYS388, DYS444, DYS447, DYS449, DYS522 and DYS527a/b) in 1100 unrelated Chinese Han individuals from Henan Province using AGCU Y24 STR kit systems. The calculated average gene diversity (GD) values ranged from 0.4105 to 0.9647 for the DYS388 and DYS385a/b loci, respectively. The discriminatory capacity (DC) was 72.91% with 802 observed haplotypes using 17 Yfiler loci, by the addition of 7 Y-STRs to the Yfiler system, the DC was increased to 79.09% while showing 870 observed haplotypes. Among the additional 7 Y-STRs, DYS449, DYS527a/b, DYS444 and DYS522 were major contributors to enhancing discrimination. In the analysis of molecular variance, the Henan Han population clustered with Han origin populations and showed significant differences from other Non-Han populations. In the present study, we report 24 Y-STR population data in Henan Han population, and we emphasize the need for adding additional markers to the commonly used 17 Yfiler loci to achieve more improved discriminatory capacity in a population with low genetic diversity.     

云南白族人群13个快速突变(RM)Y-STR基因座多态性研究

目的 调查分析13个RM Y-STR基因座等位基因频率及多态性分布.方法 采用PCR复合扩增和ABI 31 00遗传分析仪,检测白族110例无关个体13个RM Y-STR位点遗传多态性分布.结果 在DYS570、DYS576、DYS518、DYS526、DYS626、DYS627、DYS449、DYS547、DYS612、DYF387S1、DYF399S1、DYF403S1和DYF404S1等13个RM Y-STR基因座中,基因多态性(GD)分布在0.7262 (DYS526 A) ～ 0.8711(DYF403S1 A)之间.由13个RM Y-STR基因座组成的单倍型系统中单倍型有110种,单倍型多样性为1.结论 上述13个RM Y-STR基因座组成的单倍型系统在白族群体中具有很高的遗传多态性,在法医学的个人识别鉴定中有重要应用价值.     

新Y-STR基因座DYS721在山西汉族人群中的遗传多态性

目的：为了使法医学及人类遗传学研究方面能应用更多Y染色体基因座，本实验从Y染色体基因组候选基因座中筛选出新Y—STR基因DYS721，调查其在山西汉族人群中的等位基因频率分布情况。方法：根据GDB基因库提供的引物序列进行引物合成，用其对该基因座进行PCR扩增；非变性PAGE电泳分离，银染显带后保存。结果：研究发现山西地区111例汉族男性DYS721共观察到17、18、19、20、21五个等位基因，其基因多样性为0．6256，在法医学应用方面，其个人识别能力（DP）和非父排除率（PE）均为0．6256。20例女性对照无扩增产物且50组家系调查无突变，同一男性不同组织检测结果分型一致。结论：该基因座有很好的基因多态性和稳定性，是法医学和人类遗传学研究的理想遗传标记。     

RMplex reveals population differences in RM Y-STR mutation rates and provides improved father-son differentiation in Japanese

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.