Full analysis and data repository for Putnam et al Evolutionary Applications 2016

All Analysis Script, Data, and Output files to reproduce results and figures for Putnam et al Evolutionary Applications 201

Characteristics of the four genes (<i>coI</i>, <i>calmodulin</i>, <i>rad24</i>, and <i>actin</i>) selected for in-depth phylogenetic analyses.

<p>Characteristics of the four genes (<i>coI</i>, <i>calmodulin</i>, <i>rad24</i>, and <i>actin</i>) selected for in-depth phylogenetic analyses.</p

Flow diagram of the step-wise procedure for molecular marker identification.

<p>Flow diagram of the step-wise procedure for molecular marker identification.</p

Description of the genomic DNAs used in this study.

a<p>Letters A to H correspond to the <i>Symbiodinium</i> clades. Species names of outgroup samples are indicated: <i>Gymnodinium simplex</i>, <i>Pelagodinium beii</i>, and <i>Polarella glacialis</i>.</p>b<p>Alpha-numeric names correspond to <i>Symbiodinium ITS-2</i> rDNA molecular taxonomy sensu <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0029816#pone.0029816-Pochon3" target="_blank">[71]</a>. Letters correspond to the <i>Symbiodinium</i> clades, and numbers correspond to a specific <i>ITS-2</i> sequence. All samples are genetically distinct, except for <i>Symbiodinium</i> A2, which was found in two distinct cultures and referred here to as A2_1 and A2_2. Sample D1.2 corresponds to the PSP1-05 sample originally isolated from the sponge <i>Haliclona koremella</i> (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0029816#pone.0029816-Pochon3" target="_blank">[71]</a> for details).</p>c<p>Culture names of DNAs extracted from <i>Symbiodinium</i> cultures. N/A = Not Available.</p><p>*Indicates new sequences.</p

Estimation of divergence rates between markers for <i>Symbiodinium</i> types C1, C15, C90, and C91.

<p>The minimum, maximum and averaged uncorrected genetic distances among clade C <i>Symbiodinium</i> types are indicated for each marker investigated. Calculations for <i>calmodulin</i>, <i>rad24</i>, and <i>actin</i> were made on sequence alignments excluding (−) and including (+) introns.</p>a<p>No sequences were obtained for <i>Symbiodinium</i> C90 and C91 so only two types were compared.</p>b<p>No sequences were obtained for <i>Symbiodinium</i> C90, so only three types were compared.</p

Seven out of eighty-four candidate genes selected for downstream analyses.

<p>Genes are sorted by decreasing level of transcript abundance in the two <i>Symbiodinium</i> EST libraries combined. Details of the EST libraries displaying hits in BLASTn are indicated for each gene by letters A, C, Ac, At, Ht, Kb, Km, and Lp, which correspond to EST libraries <i>Symbiodinium</i> A, <i>Symbiodinium</i> C, <i>Amphidinium carterae</i>, <i>Alexandrium tamarense</i>, <i>Heterocapsa triquetra</i>, <i>Karenia brevis</i>, <i>Karlodinium micrum</i>, and <i>Lingulodinium polyedrum</i>, respectively. Protein descriptions were obtained using BLASTx. The complete list of candidate genes (n = 84) identified after BLASTn comparisons of eight dinoflagellate EST libraries is presented in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0029816#pone.0029816.s006" target="_blank">Table S1</a>.</p

Topological comparison of benchmark <i>nr28S</i> and four selected candidate genes.

<p>(<b>A</b>) 71 nuclear large subunit (<i>nr28S</i>) sequences (alignment size: 915 bp) (<b>B</b>) 26 cytochrome oxidase subunit 1 (<i>coI</i>) sequences (1057 bp), (<b>C</b>) 92 <i>calmodulin</i> sequences (154 bp), (<b>D</b>) 73 <i>rad24</i> sequences (580 bp), and (<b>E</b>) 71 <i>actin</i> sequences (925 bp). The <i>nr28S</i> topology is used here as the benchmark marker, with colors corresponding to clades A (red), B (pink), C (green), D (brown), E (orange), F (dark blue), G (yellow), and H (light blue). Phylogenies are rooted using the dinoflagellates <i>Gymnodinium simplex</i>, <i>Pelagodinium beii</i>, and <i>Polarella glacialis</i>. Detailed phylogenetic reconstructions, including node support values from the ML bootstrap analyses and Bayesian posterior probabilities, as well as the GenBank accession numbers, are shown in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0029816#pone.0029816.s001" target="_blank">Figures S1</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0029816#pone.0029816.s002" target="_blank">S2</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0029816#pone.0029816.s003" target="_blank">S3</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0029816#pone.0029816.s004" target="_blank">S4</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0029816#pone.0029816.s005" target="_blank">S5</a>.</p

Intron position mapping of three intron-containing genes.

<p>Positions and numbers of coding (exons [E]; shown in green) and non-coding regions (introns [I]; shown in red) in the genes <i>calmodulin</i> (<b>A</b>), <i>rad24</i> (<b>B</b>), and <i>actin</i> (<b>C</b>). The sizes of the non-coding regions indicated here depict the maximum intron size recorded in genomic samples in each <i>Symbiodinium</i> clade. DNA alignments ranged from 1,107 bp to 3,087 bp in length and letters A to H correspond to the eight <i>Symbiodinium</i> clades.</p

Cunning_PLoSONE_Dryad_Archive

This archive file contains all data and scripts necessary to reproduce the analyses and figures presented in this manuscript

<i>Symbiodinium</i> clade composition for complete dataset.

<p>Bars represent the proportion of sequences in each sample from each clade.</p