Nanoflagellate protists are algae and protozoa (2– 20 mm in size) that play important ecological roles in freshwater and marine microbial communities as primary producers and as consumers of prokaryotic and eukaryotic prey. There is little biogeographical information for most of these minute protists despite their significant role in aquatic food webs. In addition, the evolutionary relationship...

Systematists must frequently deal with substantial uncertainty in their phylogenetic estimates. Nonparametric bootstrapping (59) and Markov chain Monte Carlo (MCMC) simulations used for Bayesian phylogenetic inference (65; 64; 60) are two of the most popular computational approaches for assessing support for different parts of a phylogenetic tree. Both of these techniques produce large collecti...

Neotropical cichlid fishes comprise approximately 60 genera and at least 600 species, but despite this diversity, their phylogeny is only partially understood, which limits taxonomic, ecological and evolutionary research. We report the largest molecular phylogeny of Neotropical cichlids produced to date, combining data from three mitochondrial and two nuclear markers for 57 named genera and 154...

We describe a rapid and easily automated phylogenetic grouping technique based on analysis of bacterial genome single-nucleotide polymorphisms (SNPs). We selected 13 SNPs derived from a complete sequence analysis of 11 essential genes previously used for multilocus sequence typing (MLST) of 30 Escherichia coli strains representing the genetic diversity of the species. The 13 SNPs were localized...

BACKGROUND Phylogenetic relationships among Asian and African colobine genera have been disputed and are not yet well established. In the present study, we revisit the contentious relationships within the Asian and African Colobinae by analyzing 44 nuclear non-coding genes (>23 kb) and mitochondrial (mt) genome sequences from 14 colobine and 4 non-colobine primates. PRINCIPAL FINDINGS The com...

MOTIVATION We explored the feasibility of using unaligned rRNA gene sequences as DNA barcodes, based on correlation analysis of composition vectors (CVs) derived from nucleotide strings. We tested this method with seven rRNA (including 12, 16, 18, 26 and 28S) datasets from a wide variety of organisms (from archaea to tetrapods) at taxonomic levels ranging from class to species. RESULT Our res...

Although much progress has been made recently in teleostean phylogeny, relationships among the main lineages of the higher teleosts (Acanthomorpha), containing more than 60% of all fish species, remain poorly defined. This study represents the most extensive taxonomic sampling effort to date to collect new molecular characters for phylogenetic analysis of acanthomorph fishes. We compiled and an...

Identification of orthologous genes, which are defined as homologous genes derived from speciation in the history of evolution [1], is a crucial step for comparative analysis of multiple genomes. Basically, evidence to identify orthologs includes: i) highest level of similarity, ii) conservation of gene arrangement on the chromosome, iii) consistency between gene phylogeny and species phylogeny...