Research paper
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

https://doi.org/10.1016/j.fsigen.2016.07.009Get rights and content

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.

Introduction

Alpine landscapes constitute a highly structured matrix for human migration, occupation, and settlement. Mountains can act as physical barriers to dispersal and permanently habitable regions are largely confined to valleys, which also act as the main corridors for human movement. This topographical segmentation results in a heterogeneous area of settlement, which is characterized by the coexistence of communities differing in size and degree of isolation (e.g. [1]). In addition to this, also social practices, as for instance patrilocality (e.g. [2]) or constrained access to marriage and reproduction for parts of the population (e.g. [3]), can act as barriers of limited permeability to gene flow, lower the effective population size, and support non-random mating. The interplay of these forces shapes local genetic variation and population sub-structuring sometimes might be observed even at fine-scale geographic resolution. It appears reasonable to surmise that in isolated communities a considerable proportion of the population’s Y chromosomes will be embedded in a network of both close and cryptic paternal relatives. Such a scenario is of great relevance in forensic genetics, as the Y-chromosomal short tandem repeat (Y-STR) sets routinely used in this field usually fail in resolving Y chromosomes from close male relatives (e.g. [4]). Furthermore, the existence of strong population sub-structure is relevant for choosing the appropriate population to estimate haplotype (HT) frequencies in forensic investigations with matching Y-STR evidence.

In this study, we tested at the micro-geographic scale for evidence pointing toward sub-structuring of a Y-chromosomal sample pool due to differences in urbanization degree. For this purpose, molecular genetic markers on the male-specific portion of the human Y chromosome [5] were analyzed. Yet, factors like community size, patrilocality rate, and the proportion of inferred close male relatives were considered as well. The group of biomolecular markers comprised 26 phylogenetically informative single nucleotide polymorphisms (Y-SNPs) and 17 “conventional” Y-STRs. These markers were analyzed in 551 men from five municipalities located in the “Tiroler Unterland”, a culturally homogeneous region in the eastern part of North-Tyrol (Austria, Fig. 1), which was chosen for its highly structured alpine landscape. Coexistence of small and in historical as well as topographical terms isolated villages and in contrast rather urban communities is a typical feature of this area of limited extent. The five addressed municipalities were pre-selected as they cover both settlement types. Against this backdrop we tested the rapidly-mutating Y-STRs’ (RM Y-STRs) [4], [6], [7] power to enhance resolution of Y-chromosomal lineages in the municipality samples analyzed.

Section snippets

Biological samples, ethics statement, and personal metadata

The DNA extracts used herein were obtained within the framework of a larger study [8] aiming at the genetic diversity of human Y chromosomes from Tyrol, Austria. This project was approved by the ethics commission of the Medical University of Innsbruck (study classification number UN2598, session number 241/4.5). All voluntary blood donors provided written informed consent as well as personal metadata (full name, date of birth, and provenance). Additionally, they were asked to report their

Geographical background of male lineages

The participants reported 72 and 65 different places of birth for their fathers and paternal grandfathers, respectively. Most of the donors’ ancestors in the male lineage were assigned to Tyrolean municipalities (fathers: 93.4%, grandfathers: 92.0%) and within this Tyrolean group, 98.2% of the fathers and 98.8% of the grandfathers could be attributed to the Tiroler Unterland by means of their place of birth information. Regarding birth-places located outside of modern-day Austria, only those

Characterization of the sampling area and the sampling sites

In Tyrol, geographical isolation in a strict sense no longer exists, as the modern transportation network is well-developed. This supports movement of individuals among communities, which is a fundamental requirement for gene flow. However, it is reasonable to assume that changes due to current demographic processes will not immediately result in a new equilibrium of the genetic structure and diversity of human communities. Thus, signs for markedly differing degrees of genetic isolation and

Conflicts of interest

The authors declare that there are no conflicts of interest.

Acknowledgements

Above all we are indebted to all voluntary blood donors participating in this study. Harald Schennach, Christoph Gassner and their colleagues of the “Central Institute for Blood Transfusion and Immunological Department” (Landeskrankenhaus Innsbruck) are acknowledged for providing us the opportunity to collect samples during the blood drive campaigns. We are also obliged to Stefan Troger for programming and maintaining the in-house database, to Hannelore Volderauer for sample management and

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