Two trees among extant Echinodermata as deduced from the order of protein-coding, ribosomal RNA(rRNA) and transfer RNA (tRNA) mitochondrial genes.

<p>(A) One tree solution for the whole Echinodermata group calculated with mitochondrial genes (including tRNA genes). Among the 25 necessary steps, more than 6 involved the mitochondrial protein-coding and rRNA genes. (B) Tree solution calculated with mitochondrial protein-coding and rRNA genes with <i>Asterina pectinifera</i> as Ur-echinodermata (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0194334#pone.0194334.g002" target="_blank">Fig 2B</a>) on which 20 necessary rearrangements of tRNA genes have been added <i>a posteriori</i>. Among the 26 steps, 6 involved the mitochondrial protein-coding and rRNA genes.</p

The two most parsimonious trees for deuterostomes (12 evolutionary steps) deduced from the order of protein-coding and ribosomal RNA mitochondrial (mt) genes.

<p>The maximum parsimony rearrangement events among the trees are indicated by different lines (blue dashed line, inversion; green dashed line, transposition; purple solid line, reverse transposition). Hypothetical ancestral mtDNAs (HTUs) are indicated by grey shaded dots. Grey-circled white dots indicate HTUs that correspond to ground patterns of clades. Ur-echinodermata is represented by the mtDNA of either <i>Strongylocentrotus purpuratus</i> (A) or <i>Asterina pectinifera</i> (B). Grey-shaded boxes on diagrammatic representations of hypothetical ancestral mtDNAs (HTU#1a to 3b) highlight genes transcribed from the opposite strand.</p

The six most parsimonious trees deduced from the order of protein-coding and ribosomal RNA mitochondrial (mt) genes in bilaterians.

<p>The rearrangements are indicated by different lines (blue dashed line, inversion; green dashed line, transposition; purple solid line, reverse transposition). Hypothetical ancestral mtDNAs (HTUs) are indicated at each node of the trees by grey shaded dots. Grey-circled white dots indicate HTUs that correspond to ground patterns of deuterostomes, ecdysozoans and lophotrochozoans. Gene orders of HTUs are indicated in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0194334#pone.0194334.t002" target="_blank">Table 2</a>.</p

Species, systematic position, and accession number of mitochondrial genomes used for gene order comparisons.

<p><i>Cucumaria miniata</i> has the same order of protein-coding and ribosomal RNA genes as <i>Strongylocentrotus purpuratus</i> and is only used for comparisons including the transfer RNA genes.</p

A complete logical approach to resolve the evolution and dynamics of mitochondrial genome in bilaterians - Fig 1

<p><b>Diagram of three possible transpositions (top) and two possible inversions (bottom) in a circular genome leading to the same gene order. A.</b> Because of the circularity of the genome, there are always three possible transpositions leading to a similar gene order ([<i>B A C</i>] = [<i>A C B</i>] = [<i>C B A</i>]) from a given gene order ([<i>A B C</i>]). Thus, it is not possible to determine which block of genes is concerned by a transposition. <b>B.</b> Similarly, there are always two possible inversions leading to a similar gene order ([-<i>A B</i>] = [<i>A</i> -<i>B</i>]) from a given gene order ([<i>A B</i>]). Thus, it is not possible to determine which block of genes is inverted (<i>A</i> or <i>B</i>). In each example, the transposed or inverted block is underlined. The black arrowheads indicate where the transposed block is inserted. By convention, the circular genomes are read clockwise.</p

Origins of the specimens of the molecular analysis.

<p>The samples and mission correspondence are indicated as Ind. Oc.: Indian Ocean. N. Ind. Oc: North Indian Ocean. S. Atl. Oc.: South Atlantic Ocean. E. SW. Atl. Oc.: South West Atlantic ocean. S. E. Pac. Oc.: South East Pacific Ocean. Ant. Oc.: Antarctic Ocean. Med.: East Mediterranean Sea. St Number corresponds to the TARA station reference.</p

Supplementary molecular data from genbank and the Bar Coding of Life Database.

<p>Supplementary molecular data from genbank and the Bar Coding of Life Database.</p

Cladistical analysis of morphological data.

<p>Majority rule consensus tree of 74,840 equally parsimonious tree (CI = 0.816; RI = 0.854). Majority rule consensus values and bootsrap values are respectively shown above internal branches (only values ≥50% are shown). Only synapomorphies presenting a consistency index  = 1 are shown on the branches. Black bars represent the synapomorphy characterized by the corresponding morphological character number and the character state change respectively above and below. Characters coding is presented in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0059439#pone.0059439.s005" target="_blank">Table S1</a>.</p

Different phylogenetic hypothesis of Euthecosomata.

<p>A) The left topology is deduced from Rampal studies which considered two straight shell species groups: Creseidae (<i>Creseis, Hyalocylis, Styliola</i>) and Cavoliniidae composed of two sub families, the Cavoliniinae (<i>Cavolinia Clio and Diacria</i>) and the Cuvierininae (<i>Cuvierina</i>) B) The right topology is deduced from the works of Spoel <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0059439#pone.0059439-Spoel1" target="_blank">[13]</a>, and Bé & Gilmer <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0059439#pone.0059439-B1" target="_blank">[67]</a> which group all the straight shell species in Cavoliniidae, which is composed of three sub-families Clionae (<i>Clio, Creseis, Hyalocylis, Styliola</i>), Cuvierininae (<i>Cuvierina</i>) and Cavoliniinae (<i>Cavolinia, Diacria</i>). Family and sub-family taxa are indicated by symbols: diamond for Limacinidae; down triangle for Cavoliniidae; square for Creseidae; up triangle for Clionae; hexagon for Cavoliniinae; round for Cuvierininae.</p

Comparison of paleontological records, pairwise genetic distance based-method and relaxed molecular clock analysis (with/without “noisy” sites) for estimating time divergence.

<p>The table showed the time divergence estimation of 7 putative split episodes that occurred during Thecosomata evolution. Paleontological estimates correspond to the oldest fossils record found by different authors: a = <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0059439#pone.0059439-Watelet1" target="_blank">[104]</a>, b =  <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0059439#pone.0059439-Cahuzac1" target="_blank">[47]</a>, c =  <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0059439#pone.0059439-Curry1" target="_blank">[43]</a>, d =  <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0059439#pone.0059439-Hodgkinson1" target="_blank">[44]</a>, e = <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0059439#pone.0059439-Grs1" target="_blank">[79]</a>, f = <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0059439#pone.0059439-Ujihara1" target="_blank">[69]</a>. The time divergence of Event 1 is estimated at 59.1 [46.9, 114.2] Ma, the event 2 at 37.7 [23.8, 46.9] Ma, the event 3 at 19.74 [8.1, 23.8] Ma and the event 4 at 2.4 [0,8. 1] Ma. The two values presented for the relaxed clock analysis correspond respectively to the values obtained with complete data set (with “noisy” sites) and partial data set (without “noisy” sites).</p