Bo Simonsen

Population structure of African buffalo inferred from mtDNA sequences and microsatellite loci : High variation but low differentiation

The African buffalo (Syncerus caffer) is widespread throughout sub‐Saharan Africa and is found in most major vegetation types, wherever permanent sources of water are available, making it physically able to disperse through a wide range of habitats. Despite this, the buffalo has been assumed to be strongly philopatric and to form large aggregations that remain within separate home ranges with little interchange between units, but the level of differentiation within the species is unknown. Genetic differences between populations were assessed using mitochondrial DNA (control region) sequence data and analysis of variation at six microsatellite loci among 11 localities in eastern and southern Africa. High levels of genetic variability were found, suggesting that reported severe population bottlenecks due to outbreak of rinderpest during the last century did not strongly reduce the genetic variability within the species. The high level of genetic variation within the species was found to be evenly distributed among populations and only at the continental level were we able to consistently detect significant differentiation, contrasting with the assumed philopatric behaviour of the buffalo. Results of mtDNA and microsatellite data were found to be congruent, disagreeing with the alleged male‐biased dispersal. We propose that the observed pattern of the distribution of genetic variation between buffalo populations at the regional level can be caused by fragmentation of a previous panmictic population due to human activity, and at the continental level, reflects an effect of geographical distance between populations.

Hybridization between subspecies of waterbuck ( Kobus ellipsiprymnus ) in zones of overlap with limited introgression

Two subspecies of waterbuck (Kobus ellipsiprymnus), common (Kobus ellipsiprymnus ellipsiprymnus) and defassa (Kobus ellipsiprymnus defassa), are recognized based on differences in rump pattern, coat colour and geographical distribution. These forms are parapatrically distributed with an area of range overlap in East Africa, where phenotypically intermediate populations occur. Variation in 478 bp of the mitochondrial DNA control region and 14 polymorphic microsatellite loci were used to describe the genetic structure and phylogeographical pattern of the species, and to assess if the intermediate populations are the results of hybridization. In total, 186 individuals from 11 localities were analysed. A high degree of genetic differentiation was found between subspecies, although this was most evident from the microsatellite data. Hybridization was suggested in the phenotypically and geographically intermediate Nairobi NP population in Kenya. A neighbour‐joining (NJ) tree based on microsatellite population genetic distances grouped Nairobi between the common and defassa populations, and a Bayesian analysis clearly showed introgression. Individuals sampled in Samburu NP, Kenya, had a common waterbuck phenotype, but introgression was suggested by both markers. Although a high degree of maternal defassa input was indicated from the sequence data, the Samburu population grouped with the common waterbuck in the microsatellite population genetic distance tree, with high support. Analyses of linkage disequilibrium and maximum‐likelihood estimates of genetic drift suggested that admixture between subspecies is a recent event. The fact that introgression is limited between subspecies could be caused by chromosomal differences, hindering gene flow between common and defassa waterbuck.

A report of the 2002–2008 paternity testing workshops of the English speaking working group of the International Society for Forensic Genetics

The English Speaking Working Group (ESWG) of the International Society for Forensic Genetics (ISFG) offers an annual Paternity Testing Workshop open to all members of the group. Blood samples, a questionnaire and a paper challenge are sent to the participants. Here, we present the results of the 2002-2008 Paternity Testing Workshops with the objective to evaluate the uniformity of DNA-profiling and conclusions of the participating laboratories as well as to clarify tendencies in typing strategies and biostatistical evaluations of the laboratories. The numbers of participating laboratories increased from 46 in 2002 to 68 in 2008. The results showed an increasing degree of concordance concerning methods and DNA systems used and a high degree of uniformity in typing results with discrepancies in 0.1 and 0.3 % of all submitted PCR-based results. The paper challenges showed uniformity in the calculation of the weight of evidence for simple cases with straight-forward genetic constellations. However, a high degree of variation existed in complex scenarios with rare genetic constellations such as genetic inconsistencies/possible silent alleles, rare alleles and haplotypes.

Understanding geographic origins and history of admixture among chimpanzees in European zoos, with implications for future breeding programmes

Despite ample focus on this endangered species, conservation planning for chimpanzees residing outside Africa has proven a challenge because of the lack of ancestry information. Here, we analysed the largest number of chimpanzee samples to date, examining microsatellites in >100 chimpanzees from the range of the species in Africa, and 20% of the European zoo population. We applied the knowledge about subspecies differentiation throughout equatorial Africa to assign origin to chimpanzees in the largest conservation management programme globally. A total of 63% of the genotyped chimpanzees from the European zoos could be assigned to one of the recognized subspecies. The majority being of West African origin (40%) will help consolidate the current breeding programme for this subspecies and the identification of individuals belonging to the two other subspecies so far found in European zoos can form the basis for breeding programmes for these. Individuals of various degree of mixed ancestry made up 37% of the genotyped European zoo population and thus highlight the need for appropriate management programmes guided by genetic analysis to preserve maximum genetic diversity and reduce hybridization among subspecies.

Y-chromosome STR haplotypes in males from Greenland.

A total of 272 males from Greenland were typed for 11 Y-chromosome STRs DYS19, DYS385a/b, DYS389-I, DYS389-II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438 and DYS439 with the PowerPlex Y System (Promega). A total of 146 different haplotypes were observed and the haplotype diversity was 0.9887. The number of haplotypes seen once was 108 and the most common haplotype was observed in 12 males. A significant F(ST) value was observed (F(ST)=0.012, P<0.00001) when comparing the population of 15 locations in Greenland assigned to 7 groups. The significance could mainly be attributed to the subpopulation of males from Tasiilaq (East of Greenland). The R(ST) value was not statistically significant (R(ST)=0.016, P=0.15).

Adaptable component frameworks: using vector from the C++ standard library as an example

The CPH STL is a special edition of the STL, the containers and algorithms part of the C++ standard library. The specification of the generic components of the STL is given in the C++ standard. Any implementation of the STL, e.g. the one that ships with your standard-compliant C++ compiler, should provide at least one realization for each container that has the specified characteristics with respect to performance and safety. In the CPH STL project, our goal is to provide several alternative realizations for each STL container. For example, for associative containers we can provide almost any kind of balanced search tree. Also, we do provide safe and compact versions of each container. To ease the maintenance of this large collection of implementations, we have developed component frameworks for the STL containers. In this paper, we describe the design and implementation of a component framework for vector, which is undoubtedly the most used container of the C++ standard library. In particular, we specify the details of a vector implementation that is safe with respect to referential integrity and strong exception safety. Additionally, we report the experiences and lessons learnt from the development of component frameworks which we hope to be of benefit to persons engaged in the design and implementation of generic software libraries.

Results of the 2003 paternity testing workshop of the English Speaking Working Group of the International Society of Forensic Genetics

Abstract We present the results of the 2003 paternity testing workshop of the English Speaking Working Group (ESWG) of the International Society of Forensic Genetics (ISFG). The scenario was an alleged father, one child and the mother. All 51 participating laboratories drew the correct conclusion. The laboratories used a total of 30 autosomal and 17 Y-chromosomal PCR-based STR systems and 7 RFLP-based VNTR systems. The percentage of typing errors was 0.12% for the autosomal systems and 2% for the Y-chromosomal systems. The results from a paper challenge showed that occurrences of rare events such as mutations and possible silent alleles were treated differently among the participating laboratories. Participating laboratories reported mutational events observed in STR systems. Considerable differences between mutation rates in STR loci were reported. There were marked differences between paternal and maternal mutation rates as well as between single-step and multiple-step mutation rates.