Differences in urbanization degree and consequences on the diversity of conventional vs. rapidly mutating Y-STRs in five municipalities from a small region of the Tyrolean Alps in Austria

Niederstätter, Harald; Berger, Burkhard; Kayser, Manfred; Parson, Walther

doi:10.1016/j.fsigen.2016.07.009

Cited by 9 publications

(5 citation statements)

References 37 publications

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“…However, this one does not follow a gradient from north to south but manifests as an enrichment of haplogroup E1b1b-M35 in the eastern part of the country, close to Austria. This pattern fits quite well with data from Tyrol, a region in Western Austria [61], showing an important fraction of 16.9 % haplogroup E in this area, mostly attributed to E-M78, a subclade of E1b1b-M35.…”

Section: Haplogroup Distributionssupporting

confidence: 88%

The Y-chromosomal haplotype and haplogroup distribution of modern Switzerland still reflects the alpine divide as a geographical barrier for human migration

Zieger

Utz

2020

Forensic Science International: Genetics

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A sample of 606 Swiss individuals has been characterized for 27 Y-STR and 34 Y-SNPs, defining major European haplogroups. For the first time, a subsample from the southernmost part of Switzerland, the Italian speaking canton Ticino, has been included. The data reveals significant intra-national differences in the distribution of haplogroups R1b-U106, R1b-U152, I1 and J2a north and south of the alpine divide, with R1b-U152 being the most frequent haplogroup among all Swiss subpopulations, reaching 26 % in average and 53 % in the Ticino sample. In addition, a high percentage of haplogroup E1b1b-M35 in Eastern Switzerland corresponds well with data reported from Western Austria. In general, we detected a low level of differentiation between the subgroups north of the alpine divide. The dataset also revealed a variety of microvariants. Some of them were previously known to be associated with particular haplogroups. However, we discovered one microvariant in DYS533 that seems to be closely associated with haplogroup I2-P215 (xM223). This association had not yet been reported to date. The concordance study with two STR-kits suggests that the DYS533 microvariant is due to an InDel in the flanking regions of the marker. One individual carried a large deletion, frequently detected in people of East Asian ancestry, encompassing the amelogenin locus. To our knowledge, this is the first time that such a deletion has been observed within European haplogroup R1b-U152. This is the first comprehensive Y chromosomal dataset for Switzerland, demonstrating significant population substructure due to an intra-national geographical barrier.

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Section: Haplogroup Distributionssupporting

confidence: 88%

The Y-chromosomal haplotype and haplogroup distribution of modern Switzerland still reflects the alpine divide as a geographical barrier for human migration

Zieger

Utz

2020

Forensic Science International: Genetics

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“…A large empirical Y‐STR mutation rate study conducted with 186 bioinformatically identified Y‐STRs in ∼2000 DNA‐confirmed European father–son pairs, which identified a set of 13 RM Y‐STR markers (DYF387S1, DYF399S1, DYF403S1, DYF404S1, DYS449, DYS518, DYS526, DYS547, DYS570, DYS576, DYS612, DYS626, and DYS627), which are capable of differentiating nearly 70% of father–son pairs, 56% of brothers, and 67% of cousins in 103 pairs from 80 male pedigrees [14]. Subsequently, the possibility of differentiating closely related and unrelated males by the set of 13 RM Y‐STR markers, which allows Y‐STR analysis to approach the level of individual identification, demonstrated by lots of confirmatory literature [15–21]. However, the identified set of 13 RM Y‐STR markers provides limitations for male relative differentiation, particularly regarding close patrilineal relatives and different mutation rates for the same Y‐STR marker in different populations, which limits applications in forensic genetics and genetic genealogy [22].…”

Section: Introductionmentioning

confidence: 99%

The Y‐STR landscape of coastal southeastern Han: Forensic characteristics, haplotype analyses, mutation rates, and population genetics

Fan

Zeng

et al. 2021

Electrophoresis

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The Y‐STR landscape of Coastal Southeastern Han (CSEH) living in Chinese southeast areas (including Guangdong, Fujian, and Zhejiang provinces) is still unclear. We investigated 62 Y‐STR markers in a reasonably large number of 1021 unrelated males and 1027 DNA‐confirmed father‐son pairs to broaden the genetic backgrounds of CSEH. In total, 85 null alleles, 121 off‐ladder alleles, and 95 copy number variants were observed, and 1012 distinct haplotypes were determined with the overall HD and DC values of 0.999974 and 0.9912. We observed 369 mutations in 76 099 meiotic transfers, and the average estimated Y‐STR mutation rate was 4.85 × 10–3 (95% CI, 4.4 × 10–3–5.4 × 10–3). The Spearman correlation analyses indicated that GD values (R2 = 0.6548) and average allele sizes (R2 = 0.5989) have positive correlations with Y‐STR mutation rates. Our RM Y‐STR set including 8 candidate RM Y‐STRs, of which DYS534, DYS630, and DYS713 are new candidates in CSEH, distinguished 18.52% of father–son pairs. This study also clarified the population structures of CSEH which isolated in population‐mixed South China relatively. The strategy, SM Y‐STRs for familial searching and RM Y‐STRs for individual identification regionally, could be applicable based on enough knowledge of the Y‐STR mutability of different populations.

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“…This situation changed in 2010 with the publication of a large empirical Y‐STR mutation rate study analyzing 186 Y‐STRs in nearly 2,000 DNA‐confirmed father–son pairs, which highlighted 13 Y‐STR markers with mutation rates > 10 −2 mutations per marker per meiosis termed rapidly mutating (RM) Y‐STRs (Ballantyne et al, 2010). Followed by the first empirical demonstrations of their suitability for male relative differentiation (Ballantyne et al, 2012, 2014), many subsequent studies provided increasing evidence on the value of RM Y‐STRs for differentiating related, including closely related, and also unrelated men (Adnan, Ralf, Rakha, Kousouri, & Kayser, 2016; Alghafri, Goodwin, & Hadi, 2013; Boattini et al, 2016, 2019; Lang et al, 2017; Niederstätter, Berger, Kayser, & Parson, 2016; Robino et al, 2015; Salvador et al, 2019; Turrina, Caratti, Ferrian, & De Leo, 2016; Westen et al, 2015; Zgonjanin, Alghafri, Antov et al, 2017). In genetic genealogy too, RM Y‐STRs are advantageous as they provide improved differentiation of unrelated individuals (Ballantyne et al, 2014) and they allow distinguishing closely related from more distantly related males by taking the number of observed mutations into account (Larmuseau et al, 2019).…”

Section: Introductionmentioning

confidence: 99%

Identification and characterization of novel rapidly mutating Y‐chromosomal short tandem repeat markers

et al. 2020

Self Cite

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Short tandem repeat polymorphisms on the male‐specific part of the human Y‐chromosome (Y‐STRs) are valuable tools in many areas of human genetics. Although their paternal inheritance and moderate mutation rate (~10−3 mutations per marker per meiosis) allow detecting paternal relationships, they typically fail to separate male relatives. Previously, we identified 13 Y‐STR markers with untypically high mutation rates (>10−2), termed rapidly mutating (RM) Y‐STRs, and showed that they improved male relative differentiation over standard Y‐STRs. By applying a newly developed in silico search approach to the Y‐chromosome reference sequence, we identified 27 novel RM Y‐STR candidates. Genotyping them in 1,616 DNA‐confirmed father–son pairs for mutation rate estimation empirically highlighted 12 novel RM Y‐STRs. Their capacity to differentiate males related by 1, 2, and 3 meioses was 27%, 47%, and 61%, respectively, while for all 25 currently known RM Y‐STRs, it was 44%, 69%, and 83%. Of the 647 Y‐STR mutations observed in total, almost all were single repeat changes, repeat gains, and losses were well balanced; allele length and fathers' age were positively correlated with mutation rate. We expect these new RM Y‐STRs, together with the previously known ones, to significantly improving male relative differentiation in future human genetic applications.

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Differences in urbanization degree and consequences on the diversity of conventional vs. rapidly mutating Y-STRs in five municipalities from a small region of the Tyrolean Alps in Austria

Cited by 9 publications

References 37 publications

The Y-chromosomal haplotype and haplogroup distribution of modern Switzerland still reflects the alpine divide as a geographical barrier for human migration

The Y-chromosomal haplotype and haplogroup distribution of modern Switzerland still reflects the alpine divide as a geographical barrier for human migration

The Y‐STR landscape of coastal southeastern Han: Forensic characteristics, haplotype analyses, mutation rates, and population genetics

Identification and characterization of novel rapidly mutating Y‐chromosomal short tandem repeat markers

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