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      Pantanodontidae (Teleostei, Cyprinodontiformes), the sister group to all other cyprinodontoid killifishes as inferred by molecular data

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      Zoosystematics and Evolution

      Pensoft Publishers

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          Abstract

          Pantanodon, containing two African extant species and four European fossil species, for a long time had an uncertain position among the Cyprinodontiformes due to its peculiar morphology. In the last decades, Pantanodon has been considered closely related to African lamp-eyes of the Procatopodinae clade, which is contained in the Poeciliidae, a teleost fish family with a broad geographical distribution in Africa and the Americas. However, recent molecular studies have challenged the monophyly of the Poeciliidae, but the position of Pantanodon remained uncertain. We analysed one mitochondrial (COI) and five nuclear loci (GLYT1, MYH6, SH3PX3, RAG1, ENC1), a total of 5,083 bp, for 27 cyprinodontiform taxa and 6 outgroups, obtaining a well-supported phylogeny, in which the monophyly of Poeciliidae, as supported by morphological data is refuted. Pantanodon stuhlmanni, the type species of the genus, is recovered as the most basal cyprinodontoid lineage and other African taxa formerly placed in Poeciliidae are highly supported as more closely related to European non-poeciliid cyprinodontoid genera than to other taxa. Since the present tree topology is not compatible with the present classification of the Cyprinodontoidei, a new classification using available family group names is provided: Pantanodontidae is used for Pantanodon; Procatopodidae, for the African lamp-eye clade; and Fluviphylacidae, for the South American genus Fluviphylax. Poeciliidae is restricted to the American livebearers, hence restoring the classification generally used prior to 1981.

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          Most cited references 13

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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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            The Tree of Life and a New Classification of Bony Fishes

            The tree of life of fishes is in a state of flux because we still lack a comprehensive phylogeny that includes all major groups. The situation is most critical for a large clade of spiny-finned fishes, traditionally referred to as percomorphs, whose uncertain relationships have plagued ichthyologists for over a century. Most of what we know about the higher-level relationships among fish lineages has been based on morphology, but rapid influx of molecular studies is changing many established systematic concepts. We report a comprehensive molecular phylogeny for bony fishes that includes representatives of all major lineages. DNA sequence data for 21 molecular markers (one mitochondrial and 20 nuclear genes) were collected for 1410 bony fish taxa, plus four tetrapod species and two chondrichthyan outgroups (total 1416 terminals). Bony fish diversity is represented by 1093 genera, 369 families, and all traditionally recognized orders. The maximum likelihood tree provides unprecedented resolution and high bootstrap support for most backbone nodes, defining for the first time a global phylogeny of fishes. The general structure of the tree is in agreement with expectations from previous morphological and molecular studies, but significant new clades arise. Most interestingly, the high degree of uncertainty among percomorphs is now resolved into nine well-supported supraordinal groups. The order Perciformes, considered by many a polyphyletic taxonomic waste basket, is defined for the first time as a monophyletic group in the global phylogeny. A new classification that reflects our phylogenetic hypothesis is proposed to facilitate communication about the newly found structure of the tree of life of fishes. Finally, the molecular phylogeny is calibrated using 60 fossil constraints to produce a comprehensive time tree. The new time-calibrated phylogeny will provide the basis for and stimulate new comparative studies to better understand the evolution of the amazing diversity of fishes.
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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
                February 09 2018
                February 09 2018
                : 94
                : 1
                : 137-145
                Article
                10.3897/zse.94.22173
                © 2018

                http://creativecommons.org/licenses/by/4.0/

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