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      Data supporting phylogenetic reconstructions of the Neotropical clade Gymnotiformes

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          Abstract

          Data is presented in support of model-based total evidence (MBTE) phylogenetic reconstructions of the Neotropical clade of Gymnotiformes “Model-based total evidence phylogeny of Neotropical electric knifefishes (Teleostei, Gymnotiformes)” (Tagliacollo et al., 2016) [1]). The MBTE phylogenies were inferred using a comprehensive dataset comprised of six genes (5277 bp) and 223 morphological characters for an ingroup taxon sample of 120 of 218 valid species and 33 of the 34 extant genera. The data in this article include primer sequences for gene amplification and sequencing, voucher information and GenBank accession numbers, descriptions of morphological characters, morphological synapomorphies for the recognized clades of Gymnotiformes, a supermatrix comprised of concatenated molecular and morphological data, and computer scripts to replicate MBTE inferences. We also included here Maximum-likelihood and Bayesian topologies, which support two main gymnotiform clades: Gymnotidae and Sternopygoidei, the latter comprised of Rhamphichthyoidea (Rhamphichthyidae+Hypopomidae) and Sinusoidea (Sternopygidae+Apteronotidae).

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          Interrelationships of the ostariophysan fishes (Teleostei)

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            A Gateway for Phylogenetic Analysis Powered by Grid Computing Featuring GARLI 2.0

            We introduce molecularevolution.org, a publicly available gateway for high-throughput, maximum-likelihood phylogenetic analysis powered by grid computing. The gateway features a garli 2.0 web service that enables a user to quickly and easily submit thousands of maximum likelihood tree searches or bootstrap searches that are executed in parallel on distributed computing resources. The garli web service allows one to easily specify partitioned substitution models using a graphical interface, and it performs sophisticated post-processing of phylogenetic results. Although the garli web service has been used by the research community for over three years, here we formally announce the availability of the service, describe its capabilities, highlight new features and recent improvements, and provide details about how the grid system efficiently delivers high-quality phylogenetic results. [garli, gateway, grid computing, maximum likelihood, molecular evolution portal, phylogenetics, web service.]
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              Optimal data partitioning and a test case for ray-finned fishes (Actinopterygii) based on ten nuclear loci.

              Data partitioning, the combined phylogenetic analysis of homogeneous blocks of data, is a common strategy used to accommodate heterogeneities in complex multilocus data sets. Variation in evolutionary rates and substitution patterns among sites are typically addressed by partitioning data by gene, codon position, or both. Excessive partitioning of the data, however, could lead to overparameterization; therefore, it seems critical to define the minimum numbers of partitions necessary to improve the overall fit of the model. We propose a new method, based on cluster analysis, to find an optimal partitioning strategy for multilocus protein-coding data sets. A heuristic exploration of alternative partitioning schemes, based on Bayesian and maximum likelihood (ML) criteria, is shown here to produce an optimal number of partitions. We tested this method using sequence data of 10 nuclear genes collected from 52 ray-finned fish (Actinopterygii) and four tetrapods. The concatenated sequences included 7995 nucleotide sites maximally split into 30 partitions defined a priori based on gene and codon position. Our results show that a model based on only 10 partitions defined by cluster analysis performed better than partitioning by both gene and codon position. Alternative data partitioning schemes also are shown to affect the topologies resulting from phylogenetic analysis, especially when Bayesian methods are used, suggesting that overpartitioning may be of major concern. The phylogenetic relationships among the major clades of ray-finned fish were assessed using the best data-partitioning schemes under ML and Bayesian methods. Some significant results include the monophyly of "Holostei" (Amia and Lepisosteus), the sister-group relationships between (1) esociforms and salmoniforms and (2) osmeriforms and stomiiforms, the polyphyly of Perciformes, and a close relationship of cichlids and atherinomorphs.
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                Author and article information

                Contributors
                Journal
                Data Brief
                Data Brief
                Data in Brief
                Elsevier
                2352-3409
                06 February 2016
                June 2016
                06 February 2016
                : 7
                : 23-59
                Affiliations
                [a ]Universidade Estadual Paulista – UNESP, Instituto de Biociências de Botucatu, Botucatu, SP 18618-970, Brazil
                [b ]University of Louisiana at Lafayette, Department of Biology, Lafayette, LA 70504-2451, USA
                Author notes
                [* ]Corresponding author at: Universidade Federal do Tocantins - UFT, Programa de Pós-Graduação Ciências do Ambiente, Avenida NS 15, 109 Norte, Plano Diretor Norte, Palmas, TO 77001-090, Brazil (V.A. Tagliacollo). victor_tagliacollo@ 123456yahoo.com.br
                Article
                S2352-3409(16)30021-X
                10.1016/j.dib.2016.01.069
                4761620
                26955648
                2c5041ad-2348-444e-a874-97a2b7a277fd
                © 2016 The AAuthors

                This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).

                History
                : 20 November 2015
                : 26 January 2016
                : 30 January 2016
                Categories
                Data Article

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