STRAF 2: New features and improvements of the STR population data analysis software.

Population data in forensic genetics must be checked for a variety of statistical parameters before it can be employed for casework. Several tools exist to perform such tasks; however, it can become challenging to obtain the right results due to the number of software to use and the broad range of input formats. Furthermore, a substantial amount of experience is required to use some of these programs.

Genomes of Microtus Rodents Highlight the Importance of Olfactory and Immune Systems in Their Fast Radiation.

The characterization of genes and biological functions underlying functional diversification and the formation of species is a major goal of evolutionary biology. In this study, we investigated the fast radiation of Microtus voles, one of the most speciose group of mammals, which shows strong genetic divergence despite few readily observable morphological differences. We produced an annotated reference genome for the common vole, Microtus arvalis, and resequenced the genomes of 10 different species and evolutionary lineages spanning the Microtus speciation continuum.

A holistic approach for the selection of forensic DNA swabs.

In the present study, we compared the performance of five different ISO 18385 certified forensic swabs for DNA sampling in practice over a time period of five months. Comparisons were made for DNA profiling success rates, measured as the percentage of CODIS (Combined DNA Index System) suitable profiles as well as for practical suitability during sampling at the scene, measured through a survey among collaborators. More than forty members of our crime scene investigation (CSI) unit took part in the test series and provided structured feedback concerning different aspects of swab handling.

Human background DNA on stones in an urban environment.

Stones are frequently used as tools in criminal acts. In our department, around 5 % of all analysed crime scene related trace samples are contact or touch DNA traces swabbed from stones. These samples are primarily related to cases of damage to property and burglary.

Population genetic analysis of 12 X-chromosomal STRs in a Swiss sample.

X-chromosomal STRs are a powerful tool to assess a broad variety of complex kinship scenarios. We introduce herewith the first Swiss X-STR dataset based on 1198 individuals (592 female, 606 male), characterized with the Qiagen Investigator® Argus X-12 QS multiplex kit. Anomalous allele patterns, allele and haplotype frequencies, and forensic and population genetic parameters are presented.

Expanding the Swiss autosomal marker set to 32 STRs.

By genotyping 1198 individuals with the Qiagen Investigator® HDplex Kit, we expand the Swiss autosomal STR dataset to 32 loci, providing additional resources for complex kinship cases. We present the first high-quality allele frequency dataset for loci D2S1360, D5S2500, D7S1517, and D10S2325 that will be accessible through the ENFSI reference database STRidER. For loci D3S1744, D4S2366, D6S474, D8S1132, and D21S2055, we provide a first European STRidER dataset.

Recent Evolutionary History of Tigers Highlights Contrasting Roles of Genetic Drift and Selection.

Species conservation can be improved by knowledge of evolutionary and genetic history. Tigers are among the most charismatic of endangered species and garner significant conservation attention. However, their evolutionary history and genomic variation remain poorly known, especially for Indian tigers.

Polygenic Patterns of Adaptive Introgression in Modern Humans Are Mainly Shaped by Response to Pathogens.

Anatomically modern humans carry many introgressed variants from other hominins in their genomes. Some of them affect their phenotype and can thus be negatively or positively selected. Several individual genes have been proposed to be the subject of adaptive introgression, but the possibility of polygenic adaptive introgression has not been extensively investigated yet.

Relaxed Selection During a Recent Human Expansion.

Humans have colonized the planet through a series of range expansions, which deeply impacted genetic diversity in newly settled areas and potentially increased the frequency of deleterious mutations on expanding wave fronts. To test this prediction, we studied the genomic diversity of French Canadians who colonized Quebec in the 17th century. We used historical information and records from ∼4000 ascending genealogies to select individuals whose ancestors lived mostly on the colonizing wave front and individuals whose ancestors remained in the core of the settlement.

Detecting gene subnetworks under selection in biological pathways.

Advances in high throughput sequencing technologies have created a gap between data production and functional data analysis. Indeed, phenotypes result from interactions between numerous genes, but traditional methods treat loci independently, missing important knowledge brought by network-level emerging properties. Therefore, detecting selection acting on multiple genes affecting the evolution of complex traits remains challenging.

STRAF-A convenient online tool for STR data evaluation in forensic genetics.

Population data in forensic genetics has to be checked for a variety of statistical parameters before it can be employed for case work. A lot of very powerful statistical tools are available for this task, most of them developed by labs having their research focus on population genetics or evolution. However, most of these programs require a substantial amount of experience.

The summary-likelihood method and its implementation in the Infusion package.

In recent years, simulation methods such as approximate Bayesian computation have extensively been used to infer parameters of population genetic models where the likelihood is intractable. We describe an alternative approach, summary likelihood, that provides a likelihood-based analysis of the information retained in the summary statistics whose distribution is simulated. We provide an automated implementation as a standard R package, Infusion, and we test the method, in particular for a scenario of inference of population-size change from genetic data.