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Additional file 3. Annotation tables for species involved in this study.

Electrophoresis of amplified RT-PCR products. ;3-dimensional models of MCOX2 (A) and FCOX2 (B) in S. plana predicted by Phyre2.;Primer used to amplify the Mcox2 and Fcox2 gene regions. ;Position of predicted transmembrane helices within MCOX2;BLASTp and BLASTn hits for MCOX2's insertion complete sequence and ORFs.

Additional file 6. Partitioning and substitution model information for all eight datasets used in the Maximum Likelihood analyses.

Additional file 1. Putative secondary structures of mitochondrial tRNAs in Mimachlamys varia. Amino acids are represented by their one-letter code. (*: structure predicted by RNAfold, all other structures were predicted by MITOS2)

Additional file 5. Tandem repeats detected in pectinid mitogenomes.

Additional file 4. Common interval analysis results presented on a Bayesian tree, where each tip represents a unique gene order. Internal nodes are named as An, where n is a number between 0 and 7, and represent ancestral gene orders. C and P indicate consistency and parsimony values, respectively. The colors code consistent (green; highest level of certainty), k-consistent (yellow; intermediate level of certainty) and inconsistent (red; low level of certainty) nodes. Mutation types are indicated on corresponding branches, T: transposition, TDRL: tandem duplication and random loss. Arrows point to diagrams showing the two gene orders, and the mutation steps leading from the more ancestral to the younger node. Frames connect gene blocks affected by a rearrangement event, and parts of the mitogenome that is affected by a rearrangement event.

Additional file 2. Putative secondary structure of the Major Non-coding Region of Mimachlamys varia. There is a 100 basepair overlap kept between parts. 1: 5484���6439; 2: 6339���7805; 3: 7705���9689.

Nomenclatural note on the homonymy between the octocoral genus Dendrobrachia Brook 1889 and the entoproct phylum Dendrobrachia Xian-Guan, Bergstr��m, Xio-Ya and Jie 2006 ERIC PANTE LIENSs Laboratory, UMR 7266 CNRS-University of La Rochelle, 2 rue Olympe de Gouges, 17000 La Rochelle, France Dendrobrachia was proposed by Xian-Guan et al. (2006) as the name of a new phylum of entoproct-like animals from the Lower Cambrian (Yunnan Province, China). This name was however preoccupied by the octocoral Dendrobrachia Brook 1889, which position within the subclass Octocorallia is currently uncertain (Opresko and Bayer 1991; Berntson et al. 1999, 2001). Based on the principles of homonymy and priority (Articles 52 and 23, respectively; ICZN 1999), a substitute name for the entoproct Dendrobrachia is necessary, and I propose Dendrobrachion (based on the Greek brachion, for arm)., Published as part of Pante, Eric, 2016, Nomenclatural note on the homonymy between the octocoral genus Dendrobrachia Brook 1889 and the entoproct phylum Dendrobrachia Xian-Guan, Bergstr��m, Xio-Ya and Jie 2006, pp. 598 in Zootaxa 4107 (4) on page 598, DOI: 10.11646/zootaxa.4107.4.8, http://zenodo.org/record/263773, {"references":["Brook, G. (1889) Report on the Antipatharia. Report of the Scientific Results of the Voyage of H. M. S. Challenger, 32 (Zoology), 1 - 222, pls. 1 - 15.","Xian-Guang, H., Bergstrom, J., Xiao-Ya, M. & Jie, Z. (2006) The Lower Cambrian Phlogites Luo & Hu re-considered. GFF, 128 (1), 47 - 51.","Opresko, D. & Bayer, F. (1991) Rediscovery of the enigmatic Coelenterate Dendrobrachia (Octocorallia: Gorgonacea) with descriptions of two new species. Transactions of the Royal Society of S. Australia, 115 (1), 1 - 19.","Berntson, E. A., France S. C., Mullineaux, L. S. (1999) Phylogenetic relationships within the Class Anthozoa (Phylum Cnidaria) based on nuclear 18 s rDNA sequences. Molecular Phylogenetics and Evolution, 13 (2), 417 - 433. http: // dx. doi. org / 10.1006 / mpev. 1999.0649","Berntson, E. A., Bayer, F. M., McArthur, A. G. & France, S. C. (2001) Phylogenetic relationships within the Octocorallia (Cnidaria: Anthozoa) based on nuclear 18 s rRNA sequences. Marine Biology, 138 (2), 235 - 246. http: // dx. doi. org / 10.1007 / s 002270000457","ICZN (1999) International Code of Zoological Nomenclature. Fourth Edition. International Trust for Zoological Nomenclature, London, 306 pp."]}

International audience; Dendrobrachia was proposed by Xian-Guan et al. (2006) as the name of a new phylum of entoproct-like animals from the Lower Cambrian (Yunnan Province, China). This name was however preoccupied by the octocoral Dendrobrachia Brook 1889, which position within the subclass Octocorallia is currently uncertain (Opresko and Bayer 1991; Berntson et al. 1999, 2001). Based on the principles of homonymy and priority (Articles 52 and 23, respectively; ICZN 1999), a substitute name for the entoproct Dendrobrachia is necessary, and I propose Dendrobrachion (based on the Greek brachion, for arm).

International audience; Human-induced disturbances generate strong selection pressures on the ecology and evolution of species, affecting community dynamics, ecosystem functioning, and global processes. In the marine environment, the taxonomy and distribution of most organisms are poorly known. As ecologists strive to understand increasingly complex processes, involving all species interacting within communities, reliable and accessible taxonomic tools to identify species in broad community-level datasets are needed. This study aims to document the species diversity of benthic marine communities in British Columbia, Canada, and to establish a molecular inventory including DNA barcodes to enable confident identification of species for ecological research. Results: Intertidal and subtidal sites were sampled across 700 km of BC coastline and 2000 specimens were collected. For marine shelled gastropods and brachyuran crabs, we used a high-throughput integrative taxonomic approach to generate fast and accurate species hypotheses based on the phylogenetic species concept. To date, 57 species have been delimited, including cryptic species that can cause difficulty in ecological studies because of taxonomic uncertainty. Rarefaction curves suggest 80%–100% of the actual diversity of macro-species living in sampled habitats was collected. However, the compilation of historic reports of species presence suggests that many micro and deep-sea species remain to be sampled in the North East Pacific. Overall, the four habitat types analyzed contained distinct species assemblages. Evidence of nonrandom co-occurrence patterns indicative of ecological relationships or reflecting preference for certain environmental conditions were observed in 35 species. Significance: This is the first study to assess marine species richness and ecological patterns in BC using a modernized approach to species hypotheses including the incorporation of DNA barcode data. The high-throughput taxonomic approach used should bring new opportunities for ecologists studying complex natural communities. The molecular inventory of native macro-species generated provides baseline data and will facilitate monitoring for invasive species in BC.

International audience; Integrative taxonomy was formally introduced in 2005 as a comprehensive framework to delimit and describe taxa by integrating information from different types of data and methodologies (Dayrat 2005; Will et al. 2005). Even if debate remains about the hierarchy of the types of characters and criteria to use for species delimitation (Schlick-Steiner et al., 2009; Padial et al., 2010; Yeates et al., 2011), most, if not all taxonomists agree that objectively evaluating several lines of evidence within a formalized framework is the most efficient and theoretically-grounded approach to defining robust species hypotheses (Samadi and Barberousse 2006; de Queiroz 2007).The last ten years have seen a renewal of taxonomy, illustrated by the increasing number of published articles related to species concepts, species delimitation methodology and its application.In the early 90s, many systematists began to suspect that the majority of species would remain undescribed (Costello et al. 2013a; Erwin 1982; Mora et al. 2011 – but see Costello et al. 2013b) and that some of them will probably go extinct before we have a chance to describe them (Barnosky et al., 2011; Leakey and Lewin, 1995; Pimm et al., 2006). The use of molecular data, and in particular molecular barcoding (Hebert et al., 2003), was presented as one answer to this “taxonomic impediment” (as defined in Rodman and Cody, 2003), and welcomed as such by taxonomists. It thus adds to the toolkit of taxonomy, which continues its development as a synergic discipline involving morphological taxonomists, field ecologists, naturalists, and statisticians (Knapp 2008). Integrative taxonomy, used for many decades by taxonomists but only recently formalized concomitantly with the molecular revolution, is organised following a three-step workflow (see also Evenhuis 2007): first, we need to accumulate data on numerous specimens (from various types of data: DNA, morphology, ecology…); second, we need to circumscribe groups of organisms using concepts that ensure that these groups correspond to species (this second step may be coupled with the first, as biological data are continuously accumulated and species hypotheses re-discussed); and third, we need to provide a species description, i.e. a diagnosis and a name for the species recognized as new.Naming new species is a fundamental step when describing biodiversity and is the only way to ensure that scientists are talking about the same entity, and that all the data linked to conspecific specimens but produced by different researchers (or amateurs) can be associated in a comparative analysis (Patterson et al., 2010; Satler et al., 2013; Schlick-Steiner et al., 2007). Not linking biological data (should they be molecular, morphological, or ecological) to a formal species name will result in these data losing tremendous value (Goldstein and DeSalle 2011). Indeed, when authors publish data on entities that are not defined within the framework of a referencing system (e.g. solely identified by an alphanumeric label), they make it very difficult for other authors to build on these data. The best example is the need for taxa to be named to have a chance to be listed in an endangered species list and to benefit from a conservation program: no name, no surviving (Mace 2004). Beyond the need for communication among scientists, names are also key to communicating with non-scientist audiences. While it is now widely recognized that integrating several lines of evidence is the most efficient and theoretically grounded way to delimit new species (e.g. de Queiroz, 2007; Schlick-Steiner et al., 2009; Yeates et al., 2011), the formal naming of new entities may have become decoupled from species delimitation. Indeed, we noted that in several cases new delimited species were not accompanied by formal species description (see also Goldstein and DeSalle 2011). The aim of this article is therefore to test the hypothesis that integrative taxonomy, as defined in 2005 (Dayrat 2005; Will et al. 2005), and in particular the use of molecular data, helped to alleviate the taxonomic impediment by delimiting and describing new species. We reviewed part of the “integrative taxonomy” literature of the last eight years (2006-2013) and tested if authors that delimit new species also name them. We also looked at how the number and type of characters used, across different taxa, varies across articles.

KEY TO THE COMMON DEEP- SEA GENERA OF CHRYSOGORGIIDAE VERRILL, 1883 1. Colonies unbranched, flagelliform and spirally twisted................................... Radicipes — Colonies branched. Terminal branches originating directly from the main stem or after bifurcations of primary branches................................................................................ 2 2. Colonies sympodial, branches originate in a regular spiral around the main stem, or forming two parallel fans at the top of a short trunk. Axial skeleton has brilliant metallic luster; flexibility variable among species............................................................... Chrysogorgia — Colonies monopodial and not flabellate..................................................................... 3 3. Terminal branches undivided, arising from the outside of a golden, upward-spiraling main stem........................................................................................................................... 4 — Branching in multiple planes, branches subdividing dichotomously. Axis strongly calcified, with dark, metallic luster............................................................................................ 5 4. Main stem coiled, not wavy; presence of sclerites in the coenenchyme along branches depending on species................................................................................... Iridogorgia — Main stem wavy, not coiled; array of sclerite shapes wider than in Iridogorgia, sclerites consistently present in the coenenchyme along branches.................. Rhodaniridogorgia 5. Abundant, dichotomously-subdivided branches originate in an irregular or regular spiral around a tall, upright main stem. Distance between branches along the stem short (Pseudochrysogorgia n. gen. — Dichotomously-subdivided branches arising from the top of a tall, upright main stem. Juvenile colonies have additional branches arising around the main stem. In this case, distance between branches along the stem are wide ranging (up to 10 cm) and irregular. Older colonies typically bear scars of past side branches along the main stem. Sclerites in the form of rods and scales, with little ornamentation............................. Metallogorgia, Published as part of Pante, Eric & France, Scott C., 2010, Pseudochrysogorgia bellona n. gen., n. sp.: a new genus and species of chrysogorgiid octocoral (Coelenterata, Anthozoa) from the Coral Sea, pp. 595-612 in Zoosystema 32 (4) on pages 600-601

Genus Pseudochrysogorgia n. gen. TYPE SPECIES. — Pseudochrysogorgia bellona n. gen., n. sp. ETYMOLOGY. — Th e greek prefix “pseudo”, meaning “false” or “fake”, is appended to Chrysogorgia in allusion to the morphological resemblance between this new taxon and the established Chrysogorgia. Th is resemblance is reflected by the morphology-based parsimony analysis, in which Pseudochrysogorgia n. gen. appears most closely related to Chrysogorgia rather than Metallogorgia, its sister taxon based on genetics (Fig. 8). Therefore, this combination was chosen over a combination involving Metallogorgia because misidentification of this new taxon for Chrysogorgia is more likely than misidentification for Metallogorgia. Gender is feminine. DIAGNOSIS. — The colony is bottlebrush-shaped, and its main axis is monopodial, slightly zigzagging. Branches are subdividing dichotomously in multiple planes. Branch subdivision occurs at a relatively constant angle averaging 120°, resulting in hexagonal patterns. Over half of the polyps are leaning distad. Th e neck can be narrower than the head. On average, polyps are as wide as they are tall. Sclerites are slightly ornamented, in the form of plates, scales and rods. When the polyp is not leaning distad, sclerites are arranged obliquely on the polyp body. When polyps are leaning distad, sclerites are 1) mostly longitudinally arranged (parallel to the branch) on the polyp body, 2) placed obliquely in the area of the neck, and 3) longitudinally arranged on the head and along the back of the tentacles. The branch coenenchyme contains sclerites in the form of scales and plates that are mostly parallel to main branch axis., Published as part of Pante, Eric & France, Scott C., 2010, Pseudochrysogorgia bellona n. gen., n. sp.: a new genus and species of chrysogorgiid octocoral (Coelenterata, Anthozoa) from the Coral Sea, pp. 595-612 in Zoosystema 32 (4) on page 601