Rüdiger Lessig

Mutability of Y-chromosomal microsatellites: rates, characteristics, molecular bases, and forensic implications.

Nonrecombining Y-chromosomal microsatellites (Y-STRs) are widely used to infer population histories, discover genealogical relationships, and identify males for criminal justice purposes. Although a key requirement for their application is reliable mutability knowledge, empirical data are only available for a small number of Y-STRs thus far. To rectify this, we analyzed a large number of 186 Y-STR markers in nearly 2000 DNA-confirmed father-son pairs, covering an overall number of 352,999 meiotic transfers. Following confirmation by DNA sequence analysis, the retrieved mutation data were modeled via a Bayesian approach, resulting in mutation rates from 3.78 × 10(-4) (95% credible interval [CI], 1.38 × 10(-5) - 2.02 × 10(-3)) to 7.44 × 10(-2) (95% CI, 6.51 × 10(-2) - 9.09 × 10(-2)) per marker per generation. With the 924 mutations at 120 Y-STR markers, a nonsignificant excess of repeat losses versus gains (1.16:1), as well as a strong and significant excess of single-repeat versus multirepeat changes (25.23:1), was observed. Although the total repeat number influenced Y-STR locus mutability most strongly, repeat complexity, the length in base pairs of the repeated motif, and the fathers age also contributed to Y-STR mutability. To exemplify how to practically utilize this knowledge, we analyzed the 13 most mutable Y-STRs in an independent sample set and empirically proved their suitability for distinguishing close and distantly related males. This finding is expected to revolutionize Y-chromosomal applications in forensic biology, from previous male lineage differentiation toward future male individual identification.

Signature of recent historical events in the European Y-chromosomal STR haplotype distribution

Previous studies of human Y-chromosomal single-nucleotide polymorphisms (Y-SNPs) established a link between the extant Y-SNP haplogroup distribution and the prehistoric demography of Europe. By contrast, our analysis of seven rapidly evolving Y-chromosomal short tandem repeat loci (Y-STRs) in over 12,700 samples from 91 different locations in Europe reveals a signature of more recent historic events, not previously detected by other genetic markers. Cluster analysis based upon molecular variance yields two clearly identifiable sub-clusters of Western and Eastern European Y-STR haplotypes, and a diverse transition zone in central Europe, where haplotype spectra change more rapidly with longitude than with latitude. This and other observed patterns of Y-STR similarity may plausibly be related to particular historical incidents, including, for example, the expansion of the Franconian and Ottoman Empires. We conclude that Y-STRs may be capable of resolving male genealogies to an unparalleled degree and could therefore provide a useful means to study local population structure and recent demographic history.

ISFG: Recommendations on biostatistics in paternity testing

The Paternity Testing Commission (PTC) of the International Society for Forensic Genetics has taken up the task of establishing the biostatistical recommendations in accordance with the ISO 17025 standards and a previous set of ISFG recommendations specific to the genetic investigations in paternity cases. In the initial set, the PTC recommended that biostatistical evaluations of paternity are based on a likelihood ratio principle - yielding the paternity index, PI. Here, we have made five supplementary biostatistical recommendations. The first recommendation clarifies and defines basic concepts of genetic hypotheses and calculation concerns needed to produce valid PIs. The second and third recommendations address issues associated with population genetics (allele probabilities, Y-chromosome markers, mtDNA, and population substructuring) and special circumstances (deficiency/reconstruction and immigration cases), respectively. The fourth recommendation considers strategies regarding genetic evidence against paternity. The fifth recommendation covers necessary documentation, reporting details and assumptions underlying calculations. The PTC strongly suggests that these recommendations should be adopted by all laboratories involved in paternity testing as the basis for their biostatistical analysis.

Comprehensive mutation analysis of 17 Y-chromosomal short tandem repeat polymorphisms included in the AmpFlSTR® Yfiler® PCR amplification kit

The Y-chromosomal short tandem repeat (Y-STR) polymorphisms included in the AmpFlSTR® Yfiler® polymerase chain reaction amplification kit have become widely used for forensic and evolutionary applications where a reliable knowledge on mutation properties is necessary for correct data interpretation. Therefore, we investigated the 17 Yfiler Y-STRs in 1,730–1,764 DNA-confirmed father–son pairs per locus and found 84 sequence-confirmed mutations among the 29,792 meiotic transfers covered. Of the 84 mutations, 83 (98.8%) were single-repeat changes and one (1.2%) was a double-repeat change (ratio, 1:0.01), as well as 43 (51.2%) were repeat gains and 41 (48.8%) repeat losses (ratio, 1:0.95). Medians from Bayesian estimation of locus-specific mutation rates ranged from 0.0003 for DYS448 to 0.0074 for DYS458, with a median rate across all 17 Y-STRs of 0.0025. The mean age (at the time of son’s birth) of fathers with mutations was with 34.40 (±11.63) years higher than that of fathers without ones at 30.32 (±10.22) years, a difference that is highly statistically significant (p < 0.001). A Poisson-based modeling revealed that the Y-STR mutation rate increased with increasing father’s age on a statistically significant level (α = 0.0294, 2.5% quantile = 0.0001). From combining our data with those previously published, considering all together 135,212 meiotic events and 331 mutations, we conclude for the Yfiler Y-STRs that (1) none had a mutation rate of >1%, 12 had mutation rates of >0.1% and four of <0.1%, (2) single-repeat changes were strongly favored over multiple-repeat ones for all loci but 1 and (3) considerable variation existed among loci in the ratio of repeat gains versus losses. Our finding of three Y-STR mutations in one father–son pair (and two pairs with two mutations each) has consequences for determining the threshold of allelic differences to conclude exclusion constellations in future applications of Y-STRs in paternity testing and pedigree analyses.

Significant genetic differentiation between Poland and Germany follows present-day political borders, as revealed by Y-chromosome analysis

To test for human population substructure and to investigate human population history we have analysed Y-chromosome diversity using seven microsatellites (Y-STRs) and ten binary markers (Y-SNPs) in samples from eight regionally distributed populations from Poland (n=913) and 11 from Germany (n=1,215). Based on data from both Y-chromosome marker systems, which we found to be highly correlated (r=0.96), and using spatial analysis of the molecular variance (SAMOVA), we revealed statistically significant support for two groups of populations: (1) all Polish populations and (2) all German populations. By means of analysis of the molecular variance (AMOVA) we observed a large and statistically significant proportion of 14% (for Y-SNPs) and 15% (for Y-STRs) of the respective total genetic variation being explained between both countries. The same population differentiation was detected using Monmonier’s algorithm, with a resulting genetic border between Poland and Germany that closely resembles the course of the political border between both countries. The observed genetic differentiation was mainly, but not exclusively, due to the frequency distribution of two Y-SNP haplogroups and their associated Y-STR haplotypes: R1a1*, most frequent in Poland, and R1*(xR1a1), most frequent in Germany. We suggest here that the pronounced population differentiation between the two geographically neighbouring countries, Poland and Germany, is the consequence of very recent events in human population history, namely the forced human resettlement of many millions of Germans and Poles during and, especially, shortly after World War II. In addition, our findings have consequences for the forensic application of Y-chromosome markers, strongly supporting the implementation of population substructure into forensic Y chromosome databases, and also for genetic association studies.

Homogeneity and distinctiveness of Polish paternal lineages revealed by Y chromosome microsatellite haplotype analysis

Abstract. Different regional populations from Poland were studied in order to assess the genetic heterogeneity within Poland, investigate the genetic relationships with other European populations and provide a population-specific reference database for anthropological and forensic studies. Nine Y-chromosomal microsatellites were analysed in a total of 919 unrelated males from six regions of Poland and in 1,273 male individuals from nine other European populations. AMOVA revealed that all of the molecular variation in the Polish dataset is due to variation within populations, and no variation was detected among populations of different regions of Poland. However, in the non-Polish European dataset 9.3% (P<0.0001) of the total variation was due to differences among populations. Consequently, differences in RST-values between all possible pairs of Polish populations were not statistically significant, whereas significant differences were observed in nearly all comparisons of Polish and non-Polish European populations. Phylogenetic analyses demonstrated tight clustering of Polish populations separated from non-Polish groups. Population clustering based on Y-STR haplotypes generally correlates well with the geography and history of the region. Thus, our data are consistent with the assumption of homogeneity of present-day paternal lineages within Poland and their distinctiveness from other parts of Europe, at least in respect to their Y-STR haplotypes. Electronic supplementary material to this paper can be obtained by using the Springer LINK server located at http://dx.doi.org/10.1007/s00439-002-0728-0.

Child neglect and forensic entomology

Close co-operation between forensic scientists, medico-legal doctors, and police forces made it possible to estimate not only the post-mortem interval but also the time since a child was neglected. On the skin surface under the diaper (anal-genital area), third instar larvae of the false stable fly Muscina stabulans FALLEN, and the lesser house fly Fannia canicularis L. were found. F. canicularis adults are attracted to both feces and urine. From the face, larvae of the bluebottle fly Calliphora vomitoria L. were collected. C. vomitoria maggots are typical early inhabitants of corpses. From the developmental times of the flies, it was estimated that the anal-genital area of the child had not been cleaned for about 14 days (7-21 day range), and that death occurred only 6-8 days prior to discovery of the body. This is the first report where an examination of the maggot fauna on a person illustrated neglect that had occurred prior to death.

Experiences in tsunami victim identification.

Sir, On 26 December 2004, giant tsunami waves devastated the coast lines of 12 south-east Asian countries, with the number of persons confirmed dead or still missing exceeding 300,000 as of 30 June 2005. Directly after the tsunami had struck Thailand’s holiday resorts on the southwestern coast, tens of thousands of locals and Western holidaymakers were missing, and hourly, more and more were confirmed dead by local authorities via the national and international media. As members of the German Federal Police’s disaster victim identification (DVI), these authors arrived on the island of Phuket, Thailand, on 28 and 30 December 2004, and worked in the region of Phuket and Khao Lak until returning to Germany on 14 January 2005. During the first 2 days after the tsunami had struck, hurried disposal of corpses by cremation or mass burials was performed in the region of Phuket and Khao Lak at some places under the surveillance of local authorities, resulting in bodies being either wrongly or not identified. Thai (local) tsunami victims had been visually “identified” by relatives and friends and were hastily cremated at Wat Yan Yao, at least until 29 December 2004; in addition, mass burials of corpses of believed Thai citizens (as determined by their black hair color, in contrast to those with blonde hair who were believed to be foreigners) were conducted during the first 2 weeks of January 2005 near the city of Phang Nga, not far from the region of Khao Lak (Fig. 1). Under the leadership of the Thai police, the German DVI team worked at three different provisional mortuaries during the early phase of the tsunami operation, handling approximately 400 bodies during the first 3 weeks after the tsunami. Over the first days, identification procedures had to be performed in the open, at a site not far from Phuket airport, since no provisional mortuaries were installed in the region at that time. Most of the deceased that underwent identification procedures at this work site were tsunami victims who had died in Phuket hospital shortly after the disaster had occurred. Since the Thai medical system was not prepared to give those who survived the tsunami immediate and appropriate medical care directly after the disaster—as the medical supply system of any country confronted with a disaster of such vast dimensions would be overstretched—at least hundreds of tsunami victims who initially survived died during the first days after the disaster from respiratory tract infections as a sequel of near-drowning, blunt force trauma or sepsis originating from wound infections. M. Tsokos (*) Institute of Legal Medicine, Department of Forensic Pathology, University of Hamburg, Butenfeld 34, 22529 Hamburg, Germany e-mail: mtsokos@web.de Tel.: +49-40-428032748 Fax: +49-40-428033934

Y chromosome polymorphisms and haplotypes in West Saxony (Germany)

In order to apply a set of useful and high polymorphic Y-STRs in paternity testing, we performed a population genetic study from Saxony. The allele distributions of the systems DYS19, DYS385, DYS389I/II and DYS390 were investigated in a sample of 250 unrelated males from the area of Leipzig. PCR products were detected using native polyacrylamide gel electrophoresis as well as capillary electrophoresis and GenScan Software on the ABI Prism 310 DNA sequencer. Haplotype frequency data of 164 different types were obtained which show that these four systems are very useful for special cases of paternity and forensic stain analysis. In addition several confirmed father-son pairs were examined using the paternity cases of the institute. One mutation was found in the system DYS390 and sequencing data are presented.

Fatal trauma to the neck: immunohistochemical study of local injuries

As fatal trauma to the neck is often associated with short survival times, proof of vitality may often be difficult using standard histochemical techniques. Soft tissue neck injuries resulting from strangulation by ligature or manual strangulation were examined immunohistochemically using antibodies to myoglobin, fibronectin, C5b-9 and MRP14, and compared to controls consisting of accidental soft tissue neck injuries as well as undamaged neck soft tissue. Although survival times in the study and control groups were unknown and certainly some individual variation may be expected in the time course of normal wound development, both the study and control groups demonstrated similar time courses in the immunohistochemical detection of antigen. Myoglobin was always found in those samples in which only one antigen was shown to be involved in an injury-specific pattern; myoglobin and fibronectin were found in samples with dual antigen involvement. Samples involving three antigens always included C5b-9 in addition to myoglobin and fibronectin. The single positive MRP14 sample in the study and control groups was simultaneously positive for the other markers used. Myoglobin, fibronectin, C5b-9 and MRP14 are therefore suitable for immunohistochemical detection of vital reactions and estimation of temporal relationships in the early posttraumatic period after neck trauma.