Symbiotic fungi living in plants as endophytes, and in lichens as endolichenic fungi, cause no apparent symptoms to their hosts. They are ubiquitous, ecologically important, hyperdiverse, and represent a rich source of secondary compounds for new pharmaceutical and biocontrol products. Due in part to the lack of visible reproductive structures and other distinctive phenotypic traits for many sp...

In this paper, we use the EcoRI centromeric satellite DNA family conserved in Sparidae as a taxonomic and a phylogenetic marker. The analyses of 56 monomeric units (187 bp in size) obtained by means of cloning and PCR from 10 sparid species indicate that this repetitive DNA evolves by concerted evolution. Different phylogenetic inference methods, such as neighbor-joining and UPGMA, group the 56...

Phylogenetic relationships within the suborder Trypanosomatina were inferred from the kinetoplast DNA minicircle conserved region sequences. Trees built using distance-matrix (Neighbor-Joining) and maximum parsimony methods showed that the minicircle conserved regions (CRs) provide a sensitive and specific molecular marker suitable for phylogenetic analyses of subspecies and strains of trypanos...

Phylogenetic networks are rooted, directed, acyclic graphs that model reticulate evolutionary histories. Recently, statistical methods were devised for inferring such networks from either gene tree estimates or the sequence alignments of multiple unlinked loci. Bi-allelic markers, most notably single nucleotide polymorphisms (SNPs) and amplified fragment length polymorphisms (AFLPs), provide a ...

This study was designed to clarify the differences in the internal transcribed spacer (ITS) 1 and 5.8S nucleotide sequences of Moniezia expansa, M. benedeni and M. monardi isolated from ruminants in Japan and to determine their phylogenetic relationships. A 98% similarity in the 5.8S sequences was observed among the 3 Moniezia species, whereas many nucleotide indels and substitutions were obser...

Using RecA as the phylogenetic marker, the relationships of the green sulfur bacterium Chlorobium tepidum and the green non-sulfur bacterium Chloroflexus aurantiacus to other eubacteria were investigated. The recA genes of the two organisms were cloned, and the resulting protein sequences aligned with 86 other eubacterial RecA sequences. Cb. tepidum was placed as the nearest relative to the Cyt...

A Borrelia burgdorferi secA homologue was cloned and the complete DNA sequence was determined. The deduced protein sequence consists of 899 amino acids and shows a high degree of homology to SecA homologues from other Bacteria and photosynthetic plastids. The presence of the secA gene in Spirochetes suggests that this gene is present in most if not all major lineages within Bacteria. The ease o...

Phylogenetic research is often stymied by selection of a marker that leads to poor phylogenetic resolution despite considerable cost and effort. Profiles of phylogenetic informativeness provide a quantitative measure for prioritizing gene sampling to resolve branching order in a particular epoch. To evaluate the utility of these profiles, we analyzed phylogenomic data sets from metazoans, fungi...

Right whales (genus: Eubalaena) are among the most endangered mammals, yet their taxonomy and phylogeny have been questioned. A phylogenetic hypothesis based on mitochondrial DNA (mtDNA) variation recently prompted a taxonomic revision, increasing the number of right whale species to three. We critically evaluated this hypothesis using sequence data from 13 nuclear DNA (nuDNA) loci as well as t...

Acari harbor numerous minute species of agricultural economic importance, mainly Tetranychidae and Phytoseiidae. Great efforts have been established by means recovering morphological, molecular, phylogenetic traits for identification. Traditional identification still relies on external diagnostic characters, which are limited usually exhibit large phenotypic plasticity within the species, rende...