Highlights
- •551 samples of five nearby places differing in size and connection were analyzed.
- •The share of inferred male relatives was inversely related to urbanization degree.
- •Y-chromosomal markers provided genetic evidence for male population sub-structuring.
- •A set of 13 RM Y-STRs featured superior lineage resolution to the 17 Yfiler markers.
- •This gain in male lineage resolution decreased with increasing urbanization degree.
Abstract
In this study we set out to test at a micro-geographic scale for the potential effects
of differences in urbanization degree on Y-chromosomal diversity and the paternal
lineage differentiation of “conventional” and rapidly-mutating (RM) Y-STR markers.
To avoid systematic underrepresentation of common lineages, 551 male samples were
collected under a sampling regime allowing for the inclusion of paternal relatives.
All participants came from a small, topographically highly structured, yet culturally
homogeneous settlement area in the Tyrolean Alps of Austria, a region that is characterized
by a longstanding coexistence of communities differing considerably in size and connection.
The study participants reported provenance in one of the three rural villages Alpbach,
Brandenberg, and Wildschönau – all being separated by topographical barriers from
each other – or in one of the two more urban-like and better connected municipalities
Kitzbühel and St. Johann in Tirol. When compared with the sample pools from the two
larger communities, the three small villages showed distinctly higher rates of self-reported
patrilocality since the paternal grandfather (85–95% vs. ∼42%), and featured evidence
for a considerably higher proportion of close and cryptic paternal relationships among
the study participants. We observed marked differences in the Y-SNP haplogroup frequency
spectra and statistically significant Y-STR-based FST distances among the municipality samples, suggesting population sub-structuring along
municipality borders. While for the two larger settlements a widely used “core” set
of 17 conventional Y-STRs (Yfiler) provided reasonably high lineage resolution (Ĥ: 0.99515 ± 0.00256, 0.99739 ± 0.00224), a markedly reduced haplotype diversity was seen in samples from the rural
villages (Ĥ: 0.96126 ± 0.00701–0.98515 ± 0.00278). This difference largely diminished when instead using a set of 13 RM Y-STRs
(Ĥ: 0.99180 ± 0.00380–0.99922 ± 0.00187, for all groups). Most notably, in the Alpbach sample the number of different
haplotypes rose from 42 (Yfiler) to 99 (RM Y-STRs) and the proportion of matching
haplotypes dropped from nearly 4% (Yfiler) to about 0.4% (RM Y-STRs) of the pairwise
comparisons. Consistent results were obtained with a reduced version of the dataset,
being devoid of inferred close male relatives up to the degree of first cousins. Finally,
consequences potentially arising from a gain in lineage-resolution for population
reference-sample size requirements will be addressed briefly.
Keywords
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References
- Demographic histories, isolation and social factors as determinants of the genetic structure of alpine linguistic groups.PLoS ONE. 2013; 8: e81704
- Migration distance rather than migration rate explains genetic diversity in human patrilocal groups.Mol. Ecol. 2012; 21: 4958-4969
- Heirat als Privileg Obrigkeitliche Heiratsbeschränkungen in Tirol und Vorarlberg 1820 bis 1920.Verlag für Geschichte und Politik, Wien1997
- Toward male individualization with rapidly mutating Y-chromosomal short tandem repeats.Hum. Mutat. 2014; 35: 1021-1032
- The male-specific region on the human Y chromosome is a mosaic of discrete sequence classes.Nature. 2003; 423: 825-837
- Mutability of Y-chromosomal microsatellites: rates, characteristics, molecular bases, and forensic implications.Am. J. Hum. Genet. 2010; 87: 341-353
- A new future of forensic Y-chromosome analysis: rapidly mutating Y-STRs for differentiating male relatives and paternal lineages.Forensic Sci. Int. Genet. 2012; 6: 208-218
- Multiple recurrent mutations at four human Y-chromosomal single nucleotide polymorphism sites in a 37 bp sequence tract on the ARSDP1 pseudogene.Forensic Sci. Int. Genet. 2013; 7: 593-600
- R: A Language and Environment for Statistical Computing.R Foundation for Statistical Computing, Vienna, Austria2016
- Seeing the wood for the trees: a minimal reference phylogeny for the human Y chromosome.Hum. Mutat. 2014; 35: 187-191
- A nomenclature system for the tree of human Y-chromosomal binary haplogroups.Genome Res. 2002; 12: 339-348
- Pasture names with Romance and Slavic roots facilitate dissection of Y chromosome variation in an exclusively German-speaking alpine region.PLoS ONE. 2012; 7: e41885
- Inter- and intraspecies phylogenetic analyses reveal extensive X-Y gene conversion in the evolution of gametologous sequences of human sex chromosomes.Mol. Biol. Evol. 2014; 31: 2108-2123
- High resolution mapping of Y haplogroup G in Tyrol (Austria).Forensic Sci. Int. Genet. 2013; 7: 529-536
- Development and validation of the AmpFlSTR Yfiler PCR amplification kit: a male specific single amplification 17 Y-STR multiplex system.J. Forensic Sci. 2006; 51: 64-75
- Chromosome Y microsatellites: population genetic and evolutionary aspects.Int. J. Legal Med. 1997; 110: 134-149
- Online reference database of European Y-chromosomal short tandem repeat (STR) haplotypes.Forensic Sci. Int. 2001; 118: 106-113
- DNA commission of the International Society for Forensic Genetics (ISFG): an update of the recommendations on the use of Y-STRs in forensic analysis.Int. J. Legal Med. 2006; 120: 191-200
- Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows.Mol. Ecol. Resour. 2010; 10: 564-567
D. Kahle, H. Wickham, ggmap. a package for spatial visualization with Google Maps and OpenStreetMap, R package version 2.3., (2013), http://goo.gl/CS56q7
- The new Y Chromosome Haplotype Reference Database.Forensic Sci. Int. Genet. 2015; 15: 43-48
- Marine benthic diversity: a comparative study.Am. Nat. 1968; : 243-282
- The nonconcept of species diversity: a critique and alternative parameters.Ecology. 1971; 52: 577-586
- Rarefaction and extrapolation with Hill numbers: a framework for sampling and estimation in species diversity studies.Ecol. Monogr. 2014; 84: 45-67
T.C. Hsieh, K.H., Ma, A. Chao, iNEXT: interpolation and extrapolation for species diversity, 2014, R package version 2.0, http://goo.gl/18u7FS.
- Coverage-based rarefaction and extrapolation: standardizing samples by completeness rather than size.Ecology. 2012; 93: 2533-2547
- Molecular Evolutionary Genetics.Columbia University Press, New York1987
- Microsatellite allele sizes: a simple test to assess their significance on genetic differentiation.Genetics. 2003; 163: 1467-1482
- SPAGeDi: a versatile computer program to analyse spatial genetic structure at the individual or population levels.Mol. Ecol. Notes. 2002; 2: 618-620
- GenAlEx 6.5: genetic analysis in Excel. Population genetic software for teaching and research-an update.Bioinformatics. 2012; 28: 2537-2539
- The control of false discovery rate under dependency.Ann. Stat. 2001; 29: 1165-1188
- The use of confidence or fiducial limits illustrated in the case of the binomial.Biometrika. 1934; 26: 404-413
- A measure of population subdivision based on microsatellite allele frequencies.Genetics. 1995; 139: 457-462
- Microsatellites: simple sequences with complex evolution.Nat. Rev. Genet. 2004; 5: 435-445
- Analysis of 36 Y-STR marker units including a concordance study among 2085 Dutch males.Forensic Sci. Int. Genet. 2015; 14: 174-181
- A global analysis of Y-chromosomal haplotype diversity for 23 STR loci.Forensic Sci. Int. Genet. 2014; 12: 12-23
- Development of an Italian RM Y-STR haplotype database: results of the 2013 GEFI collaborative exercise.Forensic Sci. Int. Genet. 2015; 15: 56-63
- A novel multiplex assay amplifying 13 Y-STRs characterized by rapid and moderate mutation rate.Forensic Sci Int Genet. 2015; 15: 49-55
- Forensic and population genetic analyses of Danes: Greenlanders and Somalis typed with the Yfiler® Plus PCR amplification kit.Forensic Sci Int Genet. 2015; 16: 232-236
- Yfiler® Plus amplification kit validation and calculation of forensic parameters for two Austrian populations.Forensic Sci. Int. Genet. 2016; 21: 90-94
- Forensic genetic value of a 27 Y-STR loci multiplex (Yfiler® Plus kit) in an Italian population sample.Forensic Sci. Int. Genet. 2015; 21: e1-e5
Article info
Publication history
Published online: July 18, 2016
Accepted:
July 17,
2016
Received in revised form:
June 23,
2016
Received:
March 25,
2016
Identification
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