Chromosome Y microsatellites: population genetic and evolutionary aspects

P. de Knijff A1, M. Kayser A2, A. Caglià A3, D. Corach A4, N. Fretwell A5, C. Gehrig A6, G. Graziosi A7, F. Heidorn A8, S. Herrmann A9, B. Herzog A10, M. Hidding A11, K. Honda A12, M. Jobling A5, M. Krawczak A13, K. Leim A14, S. Meuser A15, E. Meyer A16, W. Oesterreich A17, A. Pandya A18, W. Parson A19, G. Penacino A4, A. Perez-Lezaun A20, A. Piccinini A21, M. Prinz A22, C. Schmitt A11, P. M. Schneider A15, R. Szibor A23, J. Teifel-Greding A24, G. Weichhold A25, L. Roewer A2

A1 Forensic Laboratory for DNA Research, MGC-Department of Human Genetics, Leiden University, P.O.Box 9503, 2300 RA Leiden, The Netherlands FAX: +3 (71) 527 4517
A2 Institut für Gerichtliche Medizin, Hannoversche Strasse 6, D-10115 Berlin, Germany
A3 Instituto di Medicina Legale, Universitá Cattolica del S. Cuore, Largo Francesco Vito 1, I-00168 Roma, Italy
A4 Servicio de Huellas Digitales Geneticas, Facultad de Farmacia y Bioquimica UBA, Junin 956, 1113 Buenos Aires, Argentina
A5 Department of Genetics, University of Leicester, University Road, Leicester LEI 7RH, UK
A6 Institut für Rechtsmedizin, Buehlstrasse 20, CH-3012 Bern, Switzerland
A7 Department of Biology, University of Trieste, Via Giorgeri 5, I-34127 Trieste, Italy
A8 Institut für Rechtsmedizin, Hittorfstrasse 18, D-14195 Berlin, Germany
A9 Landeskriminalamt Berlin, Gothaer Strasse 19, D-10823 Berlin, Germany
A10 Institut für Rechtsmedizin, Fürstengraben 2, D-07743 Jena, Germany
A11 Institut für Rechtsmedizin, Melatengürtel 60-62, D-50823 Köln, Germany
A12 Department of Legal Medicine, Osaka University Medical School, 2-2 Yamadaoka, Suita, Osaka 565, Japan
A13 Institute of Medical Genetics, University of Wales, Heath Park, Cardiff CF4 4XN, UK
A14 Institut für Rechtsmedizin, Vosstrasse 2, 69115 Heidelberg, Germany
A15 Institut für Rechtsmedizin, Am Pulverturm 3, D-55131 Mainz, Germany
A16 Institut für Rechtsmedizin, von-Esmarch-Strasse 86, D-48149 Münster, Germany
A17 Landeskriminalamt Brandenburg, Prenzlauer Strasse 66-70, D-16352 Basdorf, Germany
A18 CRC Chromosome Molecular Biology Group, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
A19 Institut für Gerichtliche Medizin, Müllerstrasse 44, A-6020 Innsbruck, Austria
A20 Department Anthropologia, Facultat Biologia, Universitat de Barcelona, Diagonal 645, Barcelona 08028, Spain
A21 Instituto di Medicina Legale, Universitá Milano, Via Mangiagalli 37, I-20133 Milano, Italy
A22 Department of Forensic Biology, OCME, 520 First Avenue, NY 10016 New York, USA
A23 Institut für Rechtsmedizin, Leipziger Strasse 44, D-39112 Magdeburg, Germany
A24 Bayerisches Landeskriminalamt, Maillingerstrasse 15, D-80636 München, Germany
A25 Institut für Rechtsmedizin, Frauenlobstrasse 7a, D-80337 München, Germany


Abstract By means of a multicenter study, a large number of males have been characterized for Y-chromosome specific short tandem repeats (STRs) or microsatellites. A complete summary of the allele frequency distributions for these Y-STRs is presented in the Appendix. This manuscript describes in more detail some of the population genetic and evolutionary aspects for a restricted set of seven chromosome Y STRs in a selected number of population samples. For all the chromosome Y STRs markedly different region-specific allele frequency distributions were observed, also when closely related populations were compared. Haplotype analyses using AMOVA showed that when four different European male groups (Germans, Dutch, Swiss, Italians) were compared, less than 10% of the total genetic variability was due to differences between these populations. Nevertheless, these pairwise comparisons revealed significant differences between most population pairs. Assuming a step-wise mutation model and a mutation frequency of 0.21%, it was estimated that chromosome Y STR-based evolutionary lines of descent can be reliably inferred over a time-span of only 1950 generations (or about 49000 years). This reduces the reliability of the inference of population affinities to a historical, rather than evolutionary time scale. This is best illustrated by the construction of a human evolutionary tree based on chromosome Y STRs in which most of the branches connect in a markedly different way compared with trees based on classical protein polymorphisms and/or mtDNA sequence variation. Thus, the chromosome Y STRs seem to be very useful in comparing closely related populations which cannot probably be separated by e.g. autosomal STRs. However, in order to be used in an evolutionary context they need to be combined with more stable Y-polymorphisms e.g. base-substitutions.