Alignment of group-specific primer set regions

Sequence alignment of DNA regions targeted by the four group-specific primer pairs amplifying Bird, Invertebrate and Plant (mitochondrial and chloroplastic) DNA. Target and non target species were aligned for each group-specific primer pair. Target species were chosen to be as much as possible divergent in order to highlight the potentiality of each primer pair to amplify a wide prey diversity. "N" represents unavailable nucleotide in the existing Genbank sequence, "-" indicates gap and nucleotides between brackets indicate insertions. Note that because Animals do not have chloraplastic DNA, only sequences from target species were aligned for the Plant chloroplastic primer pair

Influence of group, environment, season and size on feeding behaviour.

<p>Distribution of the three classes of feeding behaviour (invertebrate eaters in purple, omnivores in orange and diatom eaters in deep green). Stacked bar chart showing the proportions of the various feeding behaviour classes by species and zone type in <b>A</b>), by season for each syntopic zone in <b>B</b>). Probability of GutVac (<i>y</i>-axis) as predicted by the multinomial model as a function of size in <b>C)</b> in which the <i>X</i>-axis corresponds to body size in cm, and we can read for example the longer specimens are more omnivor than herbivor.</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

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

Evolutionary scenario of Thecosomata.

<p>On the right is denoted a series of fossil records. The names of the four drawn fossils are indicated by asterisks. Colors grouped fossils and living species together according to their closed morphology. The dotted lines characterize the unresolved branching:. Five paleoclimatic events mentioned in the text are also indicated and correspond to Late Paleocene Thermal Maximum (LPTM), Early Eocene Climatic Optimum (EECO), Oi-1 Glaciation (Oi-1), Late Oligocene warming (LOw) and Middle Miocene disruption (MMd) that corresponded to the Langhian/Serravalian boundary. Paleontological estimates correspond to the oldest fossils record from different studies: <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0059439#pone.0059439-Janssen2" target="_blank">[103]</a> for <i>Thilea</i>; and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0059439#pone.0059439-Hodgkinson1" target="_blank">[44]</a> for <i>Vaginella</i> Daudin, 1800 <i>Cheilocuspidata</i> Hodgkinson, 1992, <i>Loxobidens</i> Hodgkinson, 1992 and for <i>Euchilotheca</i> Fisher, 1882. See <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0059439#pone-0059439-t003" target="_blank">Table 3</a> for the others fossil references. The older <i>Styliola</i> and <i>Hyalocylis</i>-like fossil was represented by horizontal line on the branch.</p

Sampling map.

<p>Four allopatric stations (red for <i>P</i>. <i>toxostoma</i> and dark green for <i>C</i>. <i>nasus</i>) and 12 sympatric stations (the Rhône basin) were sampled. Furthermore, sympatric populations classified as allotopic stations (five; orange for <i>P</i>. <i>toxostoma</i> and light green for <i>C</i>. <i>nasus</i>) and syntopic station (blue stations; three for the Ardèche basin and four for the Durance basin). Allopatric and alltopic populations constituted the reference populations. This picture is a modified version of a copyright free picture of Daniel Dalet, available on <a href="http://www.histgeo.ac-aix-marseille.fr/" target="_blank">www.histgeo.ac-aix-marseille.fr</a>.</p

Summary of body deformations taking into account species, size, environment and their interaction.

<p>A) Ontogenic deformations f<i>or C</i>. <i>nasus</i> in reference condition, B) Ontogenic deformations f<i>or P</i>. <i>toxostoma</i> in reference condition, C) Interspecies deformations in reference condition, D) Deformation from reference condition to Durance for both species, E) Deformation from reference condition to Ardèche for both species. See <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0142592#pone.0142592.s005" target="_blank">S5 Fig</a>. for more details. The width of an arrow is positively related to the intensity of the deformation.</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

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

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