Bioinformatic Amplicon Read Processing Strategies Strongly Affect Eukaryotic Diversity and the Taxonomic Composition of Communities.

Amplicon read sequencing has revolutionized the field of microbial diversity studies. The technique has been developed for bacterial assemblages and has undergone rigorous testing with mock communities. However, due to the great complexity of eukaryotes and the numbers of different rDNA copies, analyzing eukaryotic diversity is more demanding than analyzing bacterial or mock communities, so studies are needed that test the methods of analyses on taxonomically diverse natural communities.

Full likelihood analysis of genetic risk with variable age at onset disease--combining population-based registry data and demographic information.

Background: In genetic studies of rare complex diseases it is common to ascertain familial data from population based registries through all incident cases diagnosed during a pre-defined enrollment period. Such an ascertainment procedure is typically taken into account in the statistical analysis of the familial data by constructing either a retrospective or prospective likelihood expression, which conditions on the ascertainment event. Both of these approaches lead to a substantial loss of valuable data.

Evolution of the capsular regulatory genes in Streptococcus pneumoniae.

The major pneumococcal virulence determinant is its capsule, and pneumococcal epidemiology is based on 91 capsular serotypes, each corresponding to the structure of the capsular polysaccharide determined by the type-specific capsular genome. Here, we provide the beginnings of an approach to intertwine serotype epidemiology, capsular regulatory gene characteristics on the basis of existing sequence information, and the reanalysis of published epidemiological data. We present an approach to explain epidemiological characteristics of serotypes on the basis of genetic differences in their capsular regulatory genes.

Phylogeny of Mysis (Crustacea, Mysida): history of continental invasions inferred from molecular and morphological data.

We studied the phylogenetic history of opossum shrimps of the genus Mysis Latreille, 1802 (Crustacea: Mysida) using parsimony analyses of morphological characters, DNA sequence data from mitochondrial (16S, COI and CytB) and nuclear genes (ITS2, 18S), and eight allozyme loci. With these data we aimed to resolve a long-debated question of the origin of the non-marine (continental) taxa in the genus, i.e.