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ProtTest: selection of best-fit models of protein evolution
TLDR
This work has built a tool for the selection of the best-fit model of evolution, among a set of candidate models, for a given protein sequence alignment in order to study protein evolution and phylogenetic inference.
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Molecular Evidence on the Evolutionary and Biogeographical Patterns of European Cyprinids
TLDR
The existence of a Mediterranean realm independent of the central European route seems plausible based on the molecular evidence, and the new biogeographical scenario proposed here might apply to other primary freshwater European animals with low dispersal abilities, including fish, amphibians, and invertebrates.
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TranslatorX: multiple alignment of nucleotide sequences guided by amino acid translations
TLDR
TranslatorX is presented, a web server designed to align protein-coding nucleotide sequences based on their corresponding amino acid translations, with 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.
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Initial Diversification of Living Amphibians Predated the Breakup of Pangaea
TLDR
A robust molecular phylogeny based on the nuclear RAG1 gene as well as results from a variety of alternative independent molecular clock calibrations suggest that the origin and early divergence of the three living amphibian orders dates back to the Palaeozoic or early Mesozoic, before the breakup of Pangaea, and soon after the divergence from lobe‐finned fishes.
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Evolution of gastropod mitochondrial genome arrangements
TLDR
The gene order of the Vetigastropoda might represent the ancestral mitochondrial gene order for Gastropoda and it is proposed that at least three major rearrangements have taken place in the evolution of gastropods.
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Phylogeny of caecilian amphibians (Gymnophiona) based on complete mitochondrial genomes and nuclear RAG1.
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Phylogeny and evolution of the major intrinsic protein family
TLDR
This work states that with the recent increase in genomic projects, there is a considerable increase in the quantity and taxonomic range of MIPs in molecular databases.
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LRRC8 proteins share a common ancestor with pannexins, and may form hexameric channels involved in cell‐cell communication
TLDR
It is proposed that, like pannexins, LRRC8 proteins form hexameric channels, which participate in cell‐cell communication processes, and according to the inferred topological model, the six LRR domains are located in the cytoplasm, and could participate in the organisation of signalling cascades.
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Evolutionary conservation of microsatellite flanking regions and their use in resolving the phylogeny of cichlid fishes (Pisces: Perciformes)
TLDR
The design of phylogenetically highly versatile MFR-primers will be of use not only for phylogeny reconstruction among families of perciform fishes, but also for population-level work in the thousands of species belonging to this highly species-rich suborder of fishes.
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A hotspot of gene order rearrangement by tandem duplication and random loss in the vertebrate mitochondrial genome.
TLDR
New derived mt gene orders in the vertebrate "WANCY" region of four closely related caecilian amphibians are reported and the novel arrangements found, including the presence of pseudogenes, and positions of intergenic spacers fully satisfy predictions from the TDRL model.
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