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      Multigene analysis of the catfish genus Trichomycterus and description of a new South American trichomycterine genus (Siluriformes, Trichomycteridae)

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      Zoosystematics and Evolution

      Pensoft Publishers

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          Abstract

          Trichomycterus comprises about 170 valid species, but its monophyly has been challenged in the last decades. Bayesian Inference and Maximum Likelihood analyses comprehending mitochondrial genes COI and CYTB and nuclear genes GLYT, MYH6 and RAG2 from 71 Trichomycterinae terminal taxa and eight outgroups were performed. The analyses highly supports a clade containing Trichomycterus nigricans, the type species of the genus, and several other congeners endemic to eastern and northeastern Brazil, herein considered as the genus Trichomycterus, the sister clade the southern Brazil and adjacent areas clade; the latter clade comprises two subclades, one comprising species of the genus Scleronema and another comprising species previously placed in Trichomycterus, herein described as a new genus. Cambeva gen. n. is distinguished from all other trichomycterines by the presence of a bony flap on the channel of the maxillo-dentary ligament, the interopercle shorter than the opercle, a deep constriction on the basal portion of the antero-dorsal arm of the quadrate, absence of teeth in the coronoid process of the dentary, the maxilla shorter than the premaxilla, the cranial fontanel extending from the the medial posterior of frontal to the medial region of supraoccipital, and absence of the postorbital process of the sphenotic-prootic-pterosphenoid.

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          Most cited references 20

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          Multiple sequence alignment with the Clustal series of programs.

           R Chenna (2003)
          The Clustal series of programs are widely used in molecular biology for the multiple alignment of both nucleic acid and protein sequences and for preparing phylogenetic trees. The popularity of the programs depends on a number of factors, including not only the accuracy of the results, but also the robustness, portability and user-friendliness of the programs. New features include NEXUS and FASTA format output, printing range numbers and faster tree calculation. Although, Clustal was originally developed to run on a local computer, numerous Web servers have been set up, notably at the EBI (European Bioinformatics Institute) (http://www.ebi.ac.uk/clustalw/).
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            Fishes of the World

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              A practical approach to phylogenomics: the phylogeny of ray-finned fish (Actinopterygii) as a case study

              Background Molecular systematics occupies one of the central stages in biology in the genomic era, ushered in by unprecedented progress in DNA technology. The inference of organismal phylogeny is now based on many independent genetic loci, a widely accepted approach to assemble the tree of life. Surprisingly, this approach is hindered by lack of appropriate nuclear gene markers for many taxonomic groups especially at high taxonomic level, partially due to the lack of tools for efficiently developing new phylogenetic makers. We report here a genome-comparison strategy to identifying nuclear gene markers for phylogenetic inference and apply it to the ray-finned fishes – the largest vertebrate clade in need of phylogenetic resolution. Results A total of 154 candidate molecular markers – relatively well conserved, putatively single-copy gene fragments with long, uninterrupted exons – were obtained by comparing whole genome sequences of two model organisms, Danio rerio and Takifugu rubripes. Experimental tests of 15 of these (randomly picked) markers on 36 taxa (representing two-thirds of the ray-finned fish orders) demonstrate the feasibility of amplifying by PCR and directly sequencing most of these candidates from whole genomic DNA in a vast diversity of fish species. Preliminary phylogenetic analyses of sequence data obtained for 14 taxa and 10 markers (total of 7,872 bp for each species) are encouraging, suggesting that the markers obtained will make significant contributions to future fish phylogenetic studies. Conclusion We present a practical approach that systematically compares whole genome sequences to identify single-copy nuclear gene markers for inferring phylogeny. Our method is an improvement over traditional approaches (e.g., manually picking genes for testing) because it uses genomic information and automates the process to identify large numbers of candidate makers. This approach is shown here to be successful for fishes, but also could be applied to other groups of organisms for which two or more complete genome sequences exist, which has important implications for assembling the tree of life.
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                Author and article information

                Journal
                Zoosystematics and Evolution
                ZSE
                Pensoft Publishers
                1860-0743
                1435-1935
                November 22 2018
                November 22 2018
                : 94
                : 2
                : 557-566
                Article
                10.3897/zse.94.29872
                © 2018

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