ProtTest is available under the GNU license from http://darwin.uvigo.es

We present TranslatorX, a web server designed to align protein-coding nucleotide sequences based on their corresponding amino acid translations. Many comparisons between biological sequences (nucleic acids and proteins) involve the construction of multiple alignments. Alignments represent a statement regarding the homology between individual nucleotides or amino acids within homologous genes. As protein-coding DNA sequences evolve as triplets of nucleotides (codons) and it is known that sequence similarity degrades more rapidly at the DNA than at the amino acid level, alignments are generally more accurate when based on amino acids than on their corresponding nucleotides. TranslatorX novelties include: (i) use of all documented genetic codes and the possibility of assigning different genetic codes for each sequence; (ii) a battery of different multiple alignment programs; (iii) translation of ambiguous codons when possible; (iv) an innovative criterion to clean nucleotide alignments with GBlocks based on protein information; and (v) a rich output, including Jalview-powered graphical visualization of the alignments, codon-based alignments coloured according to the corresponding amino acids, measures of compositional bias and first, second and third codon position specific alignments. The TranslatorX server is freely available at http://translatorx.co.uk.

The phylogenetic relationships of 106 European cyprinid taxa were determined based on the complete nucleotide sequence (1140 bp) of the mitochondrial cytochrome b gene. The molecular phylogeny was used (1) to revise the current systematics of European cyprinids, (2) to establish the phylogenetic utility of traditional morphological characters that are widely used in Cyprinidae systematics, and (3) to discuss alternative hypotheses on the biogeography of the family in Europe. The age of the major lineages within European cyprinids was tentatively estimated with a molecular clock and showed full agreement with the fossil record of the group. Moreover, the results provided unambiguous evidence for a close phylogenetic affinity of some Caucasian and Greek endemic cyprinid taxa (e.g., B. capito and B. brachycephalus and Leuciscus keadicus, Barbus graecus, and B. albanicus, respectively) to Iberian and North African, but not Central European, cyprinids. The existence of such unexpected phylogenetic relationships refutes the classical hypothesis on the biogeography of European cyprinids, which assumes a dispersal of the cyprinid fauna from central Europe to southern Europe and northern Africa during the Miocene (and, hence, predicts a close phylogenetic relationship of all Caucasian, Greek, Iberian, and North African cyprinids to central European taxa). Instead, the existence of a Mediterranean realm independent of the central European route seems plausible based on the molecular evidence. It is likely that the new biogeographical scenario proposed here might apply to other primary freshwater European animals with low dispersal abilities, including fish, amphibians, and invertebrates.

A large number of studies in evolutionary biology utilize phylogenetic information obtained from mitochondrial DNA. Researchers place trust in this molecule and expect it generally to be a reliable marker for addressing questions ranging from population genetics to phylogenies among distantly related lineages. Yet, regardless of the phylogenetic method and weighting treatment, individual mitochondrial genes might potentially produce misleading evolutionary inferences and hence might not constitute an adequate representation neither of the entire mitochondrial genome nor of the evolutionary history of the organisms from which they are derived. We investigated the performance of all mitochondrial protein-coding genes to recover two expected phylogenies of tetrapods and mammals. According to these tests, mitochondrial protein-coding genes can be roughly classified into three groups of good (ND4, ND5, ND2, cytb, and COI), medium (COB, COIII, NDl, and ND6), and poor (ATPase 6, ND3, ATPase 8, and ND4L) phylogenetic performers in recovering these expected trees among phylogenetically distant relatives. How general our findings are is unclear. Simple length differences and rate differences between these genes cannot account for their different phylogenetic performance. The phylogenetic performance of these mitochondrial genes might depend on various factors that play a role in determining the probability of discovering the correct phylogeny such as the density of lineage creation events in time, the phylogenetic "depth" of the question, lineage-specific rate heterogeneity, and the completeness of taxa representation.

BackgroundGastropod mitochondrial genomes exhibit an unusually great variety of gene orders compared to other metazoan mitochondrial genome such as e.g those of vertebrates. Hence, gastropod mitochondrial genomes constitute a good model system to study patterns, rates, and mechanisms of mitochondrial genome rearrangement. However, this kind of evolutionary comparative analysis requires a robust phylogenetic framework of the group under study, which has been elusive so far for gastropods in spite of the efforts carried out during the last two decades. Here, we report the complete nucleotide sequence of five mitochondrial genomes of gastropods (Pyramidella dolabrata, Ascobulla fragilis, Siphonaria pectinata, Onchidella celtica, and Myosotella myosotis), and we analyze them together with another ten complete mitochondrial genomes of gastropods currently available in molecular databases in order to reconstruct the phylogenetic relationships among the main lineages of gastropods.ResultsComparative analyses with other mollusk mitochondrial genomes allowed us to describe molecular features and general trends in the evolution of mitochondrial genome organization in gastropods. Phylogenetic reconstruction with commonly used methods of phylogenetic inference (ME, MP, ML, BI) arrived at a single topology, which was used to reconstruct the evolution of mitochondrial gene rearrangements in the group.ConclusionFour main lineages were identified within gastropods: Caenogastropoda, Vetigastropoda, Patellogastropoda, and Heterobranchia. Caenogastropoda and Vetigastropoda are sister taxa, as well as, Patellogastropoda and Heterobranchia. This result rejects the validity of the derived clade Apogastropoda (Caenogastropoda + Heterobranchia). The position of Patellogastropoda remains unclear likely due to long-branch attraction biases. Within Heterobranchia, the most heterogeneous group of gastropods, neither Euthyneura (because of the inclusion of P. dolabrata) nor Pulmonata (polyphyletic) nor Opisthobranchia (because of the inclusion S. pectinata) were recovered as monophyletic groups. The gene order of the Vetigastropoda might represent the ancestral mitochondrial gene order for Gastropoda and we propose that at least three major rearrangements have taken place in the evolution of gastropods: one in the ancestor of Caenogastropoda, another in the ancestor of Patellogastropoda, and one more in the ancestor of Heterobranchia.

Background information. MIPs (major intrinsic proteins) form channels across biological membranes that control recruitment of water and small solutes such as glycerol and urea in all living organisms. Because of their widespread occurrence and large number, MIPs are a sound model system to understand evolutionary mechanisms underlying the generation of protein structural and functional diversity. With the recent increase in genomic projects, there is a considerable increase in the quantity and taxonomic range of MIPs in molecular databases.Results. In the present study, I compiled more than 450 non-redundant amino acid sequences of MIPs from NCBI databases. Phylogenetic analyses using Bayesian inference reconstructed a statistically robust tree that allowed the classification of members of the family into two main evolutionary groups, the GLPs (glycerol-uptake facilitators or aquaglyceroporins) and the water transport channels or AQPs (aquaporins). Separate phylogenetic analyses of each of the MIP subfamilies were performed to determine the main groups of orthology. In addition, comparative sequence analyses were conducted to identify conserved signatures in the MIP molecule.Conclusions. The earliest and major gene duplication event in the history of the MIP family led to its main functional split into GLPs and AQPs. GLPs show typically one single copy in microbes (eubacteria, archaea and fungi), up to four paralogues in vertebrates and they are absent from plants. AQPs are usually single in microbes and show their greatest numbers and diversity in angiosperms and vertebrates. Functional recruitment of NOD26-like intrinsic proteins to glycerol transport due to the absence of GLPs in plants was highly supported. Acquisition of other MIP functions such as permeability to ammonia, arsenite or CO 2 is restricted to particular MIP paralogues. Up to eight fairly conserved boxes were inferred in the primary sequence of the MIP molecule. All of them mapped on to one side of the channel except the conserved glycine residues from helices 2 and 5 that were found in the opposite side.

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