Pediococci are found in foods and on plants and as beer-spoilage agents. The goal of the present study was to use the DNA sequences of the first three variable regions of the 165 rRNA gene, the 16S-23S rRNA internally transcribed spacer region sequence and approximately a third of the 60 kDa heat-shock protein gene to elucidate phylogenetic groupings within the genus Pediococcus. Phylogenetic t...

The use of some multiple-sequence alignments in phylogenetic analysis, particularly those that are not very well conserved, requires the elimination of poorly aligned positions and divergent regions, since they may not be homologous or may have been saturated by multiple substitutions. A computerized method that eliminates such positions and at the same time tries to minimize the loss of inform...

After decades of debate, a mostly satisfactory resolution of relationships among the 11 recognized holometabolan orders of insects has been reached based on nuclear genes, resolving one of the most substantial branches of the tree-of-life, but the relationships are still not well established with mitochondrial genome data. The main reasons have been the absence of sufficient data in several ord...

Poison frogs (Dendrobatidae) have been the subject of scientific interest for a long time due to their bright colouration, astonishing phenotypic variability and complex breeding behaviour (Daly and Myers, 1967; Savage, 1968; Myers et al., 1983). In the past, species were diagnosed and their relationships evaluated mainly using morphological characteristics. However, the high phenotypic variati...

Combined analysis of multiple phylogenetic data sets can reveal emergent character support that is not evident in separate analyses of individual data sets. Previous parsimony analyses have shown that this hidden support often accounts for a large percentage of the overall phylogenetic signal in cladistic studies. Here, reanalysis of a large comparative genomic data set for yeast (genus Sacchar...

The increasing availability of complete genome sequences and the development of new, faster methods for phylogenetic reconstruction allow the exploration of the set of evolutionary trees for each gene in the genome of any species. This has led to the development of new phylogenomic methods. Here, we have compared different phylogenetic and phylogenomic methods in the analysis of the monophyleti...