OGRe: a relational database for comparative analysis of mitochondrial genomes

Organellar Genome Retrieval (OGRe) is a relational database of complete mitochondrial genome sequences for over 250 Metazoan species. OGRe provides a resource for the comparative analysis of mitochondrial genomes at several levels. At the sequence level, OGRe allows the retrieval of any selected set of mitochondrial genes from any selected set of species. Species are classified using a taxonomic system that allows easy selection of related groups of species. Sequence alignments are also available for some species. At the level of individual nucleotides, the system contains information on base frequencies and codon usage frequencies that can be compared between organisms. At the level of whole genomes, OGRe provides several ways of visualizing information on gene order. Diagrams illustrating the genome arrangement can be generated for any selected set of species automatically from the information in the database. Searches can be done based on gene arrangement to find sets of species that have the same order as one another. Diagrams for pairwise comparison of species can be produced that show the positions of break-points in the gene order and use colour to highlight the sections of the genome that have moved. OGRe is available from http://www.bioinf.man.ac.uk/ogre

Phylogenetic relationships among cirrate octopods (Mollusca: Cephalopoda) resolved using mitochondrial 16S ribosomal DNA sequences

Phylogenetic relationships among the cirrate octopods (Mollusca: Cephalopoda) were investigated using partial sequences of the 16S rRNA mitochondrial gene. The derived phylogeny supports the traditional separation of cirrate families based on web form. Genera with a single web (Opisthoteuthis, Grimpoteuthis, Luteuthis, and Cirroctopus) are clearly distinct from those with an intermediate or secondary web (Cirroteuthis, Cirrothauma, and Stauroteuthis). The cirrates with a single web are separated into three groups. The first group is represented by Opisthoteuthis species, the second by Grimpoteuthis and Luteuthis, and the third by members of the genus Cirroctopus. There is no support for the isolation of Luteuthis in a separate family (Luteuthidae). There is, however, evidence of two groupings within the genus Opisthoteuthis. The data suggest the following revisions in the systematic classification of the cirrates: (1) Cirrothauma, Cirroteuthis, and Stauroteuthis be united in the Cirroteuthidae; (2) Grimpoteuthis and Luteuthis be placed in the Grimpoteuthidae; (3) Opisthoteuthis in the Opisthoteuthidae, and; (4) Cirroctopus be considered sufficiently distinct from both Opisthoteuthidae and Grimpoteuthidae to warrant placement in a new family

Molecular phylogeny of the helicoid land snails (Pulmonata: Stylommatophora: Helicoidea), with special emphasis on the Camaenidae

The superfamily Helicoidea is a large and diverse group of land snails belonging to the Pulmonate suborder Stylommatophora. It has an almost worldwide distribution, absent from only sub-Saharan Africa, southern South America, New Zealand and some Pacific islands (Scott, 1996, 1997). The composition of the superfamily has remained somewhat controversial. Morphological studies have suggested the inclusion of between three and nine families, with only the Helicidae and Bradybaenidae common to all classifications (Thiele, 1931; Zilch, 1959–1960; Taylor & Sohl, 1962; Shileyko, 1979; Solem, 1979; Boss, 1982; Nordsieck, 1985, 1986; Tillier, 1989; Vaught, 1989; Scott, 1997; Bouchet & Rocroi, 2005). Our recent molecular study of the Stylommatophora has demonstrated the monophyly of a ‘Helicoidea’ comprising the Helicidae, Bradybaenidae, Helminthoglyptidae, Hygromiidae, Camaenidae, Polygyridae and Sagdidae (Wade, Mordan & Naggs, 2006). In this study, we apply molecular phylogenetic techniques to investigate specifically the evolutionary relationships within this ‘helicoid’ group

RNA-based phylogenetic methods: application to mammalian mitochondrial RNA sequences

The PHASE software package allows phylogenetic tree construction with a number of evolutionary models designed specifically for use with RNA sequences that have conserved secondary structure. Evolution in the paired regions of RNAs occurs via compensatory substitutions, hence changes on either side of a pair are correlated. Accounting for this correlation is important for phylogenetic inference because it affects the likelihood calculation. In the present study we use the complete set of tRNA and rRNA sequences from 69 complete mammalian mitochondrial genomes. The likelihood calculation uses two evolutionary models simultaneously for different parts of the sequence: a paired-site model for the paired sites and a single-site model for the unpaired sites. We use Bayesian phylogenetic methods and a Markov chain Monte Carlo algorithm is used to obtain the most probable trees and posterior probabilities of clades. The results are well resolved for almost all the important branches on the mammalian tree. They support the arrangement of mammalian orders within the four supra-ordinal clades that have been identified by studies of much larger data sets mainly comprising nuclear genes. Groups such as the hedgehogs and the murid rodents, which have been problematic in previous studies with mitochondrial proteins, appear in their expected position with the other members of their order. Our choice of genes and evolutionary model appears to be more reliable and less subject to biases caused by variation in base composition than previous studies with mitochondrial genomes.