DOI: 10.6084/m9.figshare.91158.v4
title: Phylogenetic maximum likelihood analyses of the voltage-gated sodium channel Î± subunits

description: <strong>Phylogenetic maximum likelihood analyses of the voltage-gated sodium channel α subunit (SCNα) gene family based on amino acid sequence alignments. The sequences and alignments described in Widmark et. al. (2011)1 were used to re-analyze the phylogenetic relationships of vertebrate SCNα subtypes with more powerful methods. </strong> <br>File information<br>Alignment file 1 includes the full subset of identified SCNα sequences and was used for the phylogenetic analyses in Figs. 1 and 3. Alignment file 2 includes only the identified SCN1A, SCN4A, SCN5A and SCN8A sequences, representing each of the four chromosomes harboring SCNα genes in tetrapod genomes1, and was used for the phylogenetic analyses in Figs. 2 and 4. Alignment files are provided in the CLUSTAL format. For sequence and alignment details see Widmark et. al. (2011)1. The trees in Figs. 1 and 2 are supported by bootstrap values while trees in Figs. 3 and 4 are supported by aLRT values (see below). In all files the first three letters of the sequence names are abbreviations of the species names, followed by the chromosome assignment of the genes and the abbreviated α subunit name (full names for the human sequences).<br><br>Phylogenetic methods<br>The phylogenetic analyses were done using the PhyML 3.0 algorithm in PhyML-aBayes (3.0.1 beta)2 available from http://www.atgc-montpellier.fr/phyml with the following settings: the JTT model of amino acid substitution was chosen based on analysis of the amino acid alignments in ProtTest 1.43 (http://darwin.uvigo.es/software/prottest.html); 8 substitution rate categories; equilibrium frequencies, proportion of invariable sites and gamma shape parameters estimated from the alignment; starting tree estimated using BIONJ; NNI and SPR methods selected for tree topology improvement with both topology and branch length optimization. The trees are supported by non-parametric bootstrap analyses with 100 bootstrap replicates (Figs. 1 and 2) or non-parametric SH-like approximate likelihood ratio tests (aLTR) (Figs. 3 and 4). Statistical support values are shown at the nodes. The trees were rooted with the identified<em> Drosophila melanogaster </em>sequence.<br><br>Species abbreviations<br>Species abbreviations are applied as follows: Homo sapiens (Hsa, human), Mus musculus (Mmu, mouse), Monodelphis domestica (Mdo, opossum), Gallus gallus (Gga, chicken), Danio rerio (Dre, zebrafish), Oryzias latipes (Ola, medaka), Gasterosteus aculeatus (Gac, stickleback), Tetraodon nigroviridis (Tni, green spotted puffer), Ciona savignyi (Csa, tunicate), Branchiostoma floridae (Bfl, lancelet), Drosophila melanogaster (Dme, fruit fly). <br><br>References 1. Widmark J, Sundström G, Ocampo Daza D, Larhammar D (2011) Differential evolution of voltage-gated sodium channels in tetrapods and teleost fishes. Molecular biology and evolution 28:859-71. DOI: 10.1093/molbev/msq257. 2. Guindon S et al. (2010) New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Systematic biology 59:307-21. DOI: 10.1093/sysbio/syq010. 3. Abascal F, Zardoya R, Posada D (2005) ProtTest: selection of best-fit models of protein evolution. Bioinformatics 21:2104-5. DOI: 10.1093/bioinformatics/bti263.