Orthologs are widely used for phylogenetic analysis of species; however, identifying genuine orthologs among distantly related species is challenging, because genes obtained through horizontal gene transfer (HGT) and out-paralogs derived from gene duplication before speciation are often present among the predicted orthologs. We developed a program, "Ortholog-Finder," to obtain ortholog data set...

The coastal octopus at Saint Paul and Amsterdam Islands is Octopus vulgaris Cuvier 1797. Meristic and morphological characters, along with phylogenetic analysis of COI and COIII DNA sequences, were used to identify 11 animals collected in 2000 or 2001. The range of the species is therefore expanded to include the oceanic islands of the central southern Indian Ocean. The trees also depicted the ...

Magnetotactic bacteria is a kind of polyphyletic group of prokaryotes with the characteristics of magnetotaxis that make them orient and swim along geomagnetic field lines. A magnetotactic bacteria optimization algorithm(MBOA) inspired by the characteristics of magnetotactic bacteria is researched in the paper. Experiment results show that the MBOA is effective in function optimization problems...

The markedly different mode of mesoderm formation in anuran and urodelan amphibians (which is related to the early double-layered nature of the anuran blastula wall in contrast to its single-layered nature in the urodeles), but particularly the fundamentally different place and mode of origin of the primordial germ cells in the two groups of amphibians, strongly pleads in favour of a very ancie...

Allopolyploid species contain more than two sets of related chromosomes (homoeologs) that must be sorted during meiosis to ensure fertility. As polyploid species usually have multiple origins, one intriguing, yet largely underexplored, question is whether different mechanisms suppressing crossovers between homoeologs may coexist within the same polyphyletic species. We addressed this question u...

DNA barcoding of aquatic macroinvertebrates holds much promise as a tool for taxonomic research and for providing the reliable identifications needed for water quality assessment programs. A prerequisite for identification using barcodes is a reliable reference library. We gathered 4165 sequences from the barcode region of the mitochondrial cytochrome c oxidase subunit I gene representing 264 n...

A phylogeny for the Rhodophyta has been inferred by parsimony analysis of plastid rbcL sequences representing 81 species, 68 genera, 38 families, and 17 orders of red algae; rbcL encodes the large subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase. Levels of sequence divergence among species, genera, and families are high in red algae, typically much greater than those reported for flow...

Pentatomomorpha is the second suborder in size only to Cimicomorpha in Heteroptera. However, the phylogenetic relationships among members of the suborder are not well established. Sequences from partial nuclear ribosomal 18S gene and mitochondrial COX1 gene were analyzed separately and in combination to generate a preliminary molecular phylogeny of Pentatomomorpha based on 40 species representi...

Cowpox virus (CPXV) was considered as uniform species within the genus Orthopoxvirus (OPV). Previous phylogenetic analysis indicated that CPXV is polyphyletic and isolates may cluster into different clades with two of these clades showing genetic similarities to either variola (VARV) or vaccinia viruses (VACV). Further analyses were initiated to assess both the genetic diversity and the evoluti...