Browse
Submit Data
Databases
API
Help

Dataset Information

29 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

DNA barcoding of reef brittle stars (Ophiuroidea, Echinodermata) from the southwestern Indian Ocean evolutionary hot spot of biodiversity.

ABSTRACT: In anticipation of the current biodiversity crisis, it has become critical to rapidly and accurately assess biodiversity. DNA barcoding has proved efficient in facilitating the discovery and description of thousands of species and also provides insight into the dynamics of biodiversity. Here, we sequenced a portion of the mitochondrial cytochrome c oxidase subunit I (COI) gene from all morphospecies of reef brittle stars collected during a large-scale biodiversity survey in the southwestern Indian Ocean (SWIO). Three methods of species delineation (Automatic Barcode Gap Discovery, Generalized Mixed Yule Coalescent model, and Bayesian Poisson Tree Processes) showed concordant results and revealed 51 shallow reef species in the region. Mean intraspecific genetic distances (0.005-0.064) and mean interspecific genetic distances within genera (0.056-0.316) were concordant with previous echinoderm studies. This study revealed that brittle-star biodiversity is underestimated by 20% within SWIO and by >40% when including specimens from the Pacific Ocean. Results are discussed in terms of endemism, diversification processes, and conservation implications for the Indo-West Pacific marine biodiversity. We emphasize the need to further our knowledge on biodiversity of invertebrate groups in peripheral areas.

SUBMITTER: Boissin E

PROVIDER: S-EPMC5743570 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

A taxonomic guide to the brittle-stars (Echinodermata, Ophiuroidea) from the State of Paraiba continental shelf, Northeastern Brazil.

Project description:We provide the first annotated checklist of ophiuroids from the continental shelf of the State of Paraíba, northeastern Brazil. Identification keys and taxonomic diagnoses for 23 species, belonging to 14 genera and 8 families, are provided. The material is deposited in the Invertebrate Collection Paulo Young, at the Federal University of Paraíba. Ophiopsila hartmeyeri represents the first record for the northeastern region of Brazil, while Ophiolepis impressa, Ophiolepis paucispina, Amphiura stimpsoni, Amphiodia riisei, Ophiactis quinqueradia, Ophiocoma wendtii and Ophionereis olivaceae are new records for the State of Paraíba. The number of species known for the state was increased from 16 to 23, representing approximately 17% of the species known for Brazil and 54% of the species known for northeastern Brazil. The recorded fauna has a large geographical and bathymetrical distribution.

| S-EPMC3689063 | biostudies-literature

Unravelling the origin of the basket stars and their allies (Echinodermata, Ophiuroidea, Euryalida).

Project description:Euryalids, which include the spectacular basket stars, form a morphologically aberrant group of brittle stars. Surprisingly, the most recent molecular work found them to be sister to ophiurid brittle stars, thus challenging the traditional dichotomy between euryalids and non-euryalids, and leaving an enormous ghost lineage of more than 100 million years between the oldest unambiguous euryalid fossils and their predicted divergence from ophiurids during the Triassic. Here we examine both previously known and newly collected fossils to explore the evolutionary history of euryalids. A morphology-based phylogenetic estimate confirms the Triassic Aspiduriella as a basal member of the euryalid clade that superficially resembles members of the living ophiurid sister clades. Furthermore, we use lateral arm plates and vertebrae to identify two new Jurassic ophiuroids, Melusinaster alissawhitegluzae and Melusinaster arcusinimicus, as early euryalids that are morphologically intermediate between Aspiduriella and extant euryalids. Our phylogenetic analysis is the first to combine data from completely preserved skeletons and from microfossils in order to bridge morphological and stratigraphical gaps between the sampled taxa. It fills a major gap in the fossil record of euryalids and sets a robust phylogenetic framework to understand the morphological transition from ophiurid-like ancestors to the typical modern euryalids better.

| S-EPMC5981468 | biostudies-literature

A New Fissiparous Brittle Star, Ophiacantha scissionis sp. nov. (Echinodermata, Ophiuroidea, Ophiacanthida), from Jeju Island, Korea.

Project description:A new species of Ophiuroidea, Ophiacantha scissionis sp. nov., is described. It was collected from Munseom Island, Jeju-do, South Korea at a depth of 28-36 m, by SCUBA diving. Ophiacantha scissionis has unique and distinct morphological characteristics: small disk, densely covered by small trifid spines, radial shields completely concealed by disk spines, six arms with four arm spines proximally, fissiparous. In addition, this species is clearly distinguished from other species of Ophiacantha by mitochondrial COI. This species is usually hexamerous and reproduces asexually by fissiparity. It is the first report of fissiparous reproduction in the genus Ophiacantha.

| S-EPMC6759868 | biostudies-literature

Twinkle twinkle brittle star: the draft genome of Ophioderma brevispinum (Echinodermata: Ophiuroidea) as a resource for regeneration research.

Project description:BackgroundEchinoderms are established models in experimental and developmental biology, however genomic resources are still lacking for many species. Here, we present the draft genome of Ophioderma brevispinum, an emerging model organism in the field of regenerative biology. This new genomic resource provides a reference for experimental studies of regenerative mechanisms.ResultsWe report a de novo nuclear genome assembly for the brittle star O. brevispinum and annotation facilitated by the transcriptome assembly. The final assembly is 2.68 Gb in length and contains 146,703 predicted protein-coding gene models. We also report a mitochondrial genome for this species, which is 15,831 bp in length, and contains 13 protein-coding, 22 tRNAs, and 2 rRNAs genes, respectively. In addition, 29 genes of the Notch signaling pathway are identified to illustrate the practical utility of the assembly for studies of regeneration.ConclusionsThe sequenced and annotated genome of O. brevispinum presented here provides the first such resource for an ophiuroid model species. Considering the remarkable regenerative capacity of this species, this genome will be an essential resource in future research efforts on molecular mechanisms regulating regeneration.

| S-EPMC9367165 | biostudies-literature

Exceptional population genomic homogeneity in the black brittle star Ophiocomina nigra (Ophiuroidea, Echinodermata) along the Atlantic-Mediterranean coast.

Project description:The Atlantic-Mediterranean marine transition is characterised by strong oceanographic barriers and steep environmental gradients that generally result in connectivity breaks between populations from both basins and may lead to local adaptation. Here, we performed a population genomic study of the black brittle star, Ophiocomina nigra, covering most of its distribution range along the Atlantic-Mediterranean region. Interestingly, O. nigra is extremely variable in its coloration, with individuals ranging from black to yellow-orange, and different colour morphs inhabiting different depths and habitats. In this work, we used a fragment of the mitochondrial COI gene and 2,374 genome-wide ddRADseq-derived SNPs to explore: (a) whether the different colour morphs of O. nigra represent different evolutionary units; (b) the disruptive effects of major oceanographic fronts on its population structure; and (c) genomic signals of local adaptation to divergent environments. Our results revealed exceptional population homogeneity, barely affected by oceanographic fronts, with no signals of local adaptation nor genetic differentiation between colour morphs. This remarkable panmixia likely results from a long pelagic larval duration, a large effective population size and recent demographic expansions. Our study unveils an extraordinary phenotypic plasticity in O. nigra, opening further research questions on the ecological and molecular mechanisms underpinning coloration in Ophiuroidea.

| S-EPMC10390532 | biostudies-literature

Biodiversity hot spot on a hot spot: novel extremophile diversity in Hawaiian fumaroles.

Project description:Fumaroles (steam vents) are the most common, yet least understood, microbial habitat in terrestrial geothermal settings. Long believed too extreme for life, recent advances in sample collection and DNA extraction methods have found that fumarole deposits and subsurface waters harbor a considerable diversity of viable microbes. In this study, we applied culture-independent molecular methods to explore fumarole deposit microbial assemblages in 15 different fumaroles in four geographic locations on the Big Island of Hawai'i. Just over half of the vents yielded sufficient high-quality DNA for the construction of 16S ribosomal RNA gene sequence clone libraries. The bacterial clone libraries contained sequences belonging to 11 recognized bacterial divisions and seven other division-level phylogenetic groups. Archaeal sequences were less numerous, but similarly diverse. The taxonomic composition among fumarole deposits was highly heterogeneous. Phylogenetic analysis found cloned fumarole sequences were related to microbes identified from a broad array of globally distributed ecotypes, including hot springs, terrestrial soils, and industrial waste sites. Our results suggest that fumarole deposits function as an "extremophile collector" and may be a hot spot of novel extremophile biodiversity.

| S-EPMC4398508 | biostudies-literature

New fossils of Jurassic ophiurid brittle stars (Ophiuroidea; Ophiurida) provide evidence for early clade evolution in the deep sea.

Project description:Understanding of the evolutionary history of the ophiuroids, or brittle stars, is hampered by a patchy knowledge of the fossil record. Especially, the stem members of the living clades are poorly known, resulting in blurry concepts of the early clade evolution and imprecise estimates of divergence ages. Here, we describe new ophiuroid fossil from the Lower Jurassic of France, Luxembourg and Austria and introduce the new taxa Ophiogojira labadiei gen. et sp. nov. from lower Pliensbachian shallow sublittoral deposits, Ophiogojira andreui gen. et sp. nov. from lower Toarcian shallow sublittoral deposits and Ophioduplantiera noctiluca gen. et sp. nov. from late Sinemurian to lower Pliensbachian bathyal deposits. A Bayesian morphological phylogenetic analysis shows that Ophiogojira holds a basal position within the order Ophiurida, whereas Ophioduplantiera has a more crownward position within the ophiurid family Ophiuridae. The position of Ophioduplantiera in the evolutionary tree suggests that family-level divergences within the Ophiurida must have occurred before the late Sinemurian, and that ancient slope environments played an important role in fostering early clade evolution.

| S-EPMC8371378 | biostudies-literature

Non-destructive morphological observations of the fleshy brittle star, <i>Asteronyx loveni</i> using micro-computed tomography (Echinodermata, Ophiuroidea, Euryalida).

Project description:The first morphological observation of a euryalid brittle star, Asteronyx loveni, using non-destructive X-ray micro-computed tomography (µCT) was performed. The body of euryalids is covered by thick skin, and it is very difficult to observe the ossicles without dissolving the skin. Computed tomography with micrometer resolution (approximately 4.5-15.4 µm) was used to construct 3D images of skeletal ossicles and soft tissues in the ophiuroid's body. Shape and positional arrangement of taxonomically important ossicles were clearly observed without any damage to the body. Detailed pathways inside the vertebral ossicles, lateral arm plates, and arm spines for passage of nerves and water vascular structures were observed. Inter-vertebral muscles were also observed. Forms and 3D arrangements of many important taxonomical characters of the euryalids were scrutinized by µCT in high enough resolution for taxonomic description of ophiuroids.

| S-EPMC5523172 | biostudies-literature

Barcoding pest species in a biodiversity hot-spot: the South African polyphagous broad-nosed weevils (Coleoptera, Curculionidae, Entiminae).

Project description:Polyphagous broad nosed weevils (Curculionidae: Entiminae) constitute a large and taxonomically challenging subfamily that contains economically significant agricultural pests worldwide. South Africa is a hot-spot for biodiversity and several species of indigenous and endemic genera of Entiminae have shifted on to cultivated plants, with some being phytosanitary pests. The sporadic pest status of many species (where the species has an occasional economic impact on the agricultural industry, but is not encountered often enough that is is readily recognisable by researchers and agricultural extension workers) and the presence of pest complexes and cryptic species represent an identification challenge to non-specialists. Furthermore, no comprehensive identification tools exist to identify immature stages that may be found in crops/soil. In this paper, a curated barcoding database with 70 COI sequences from 41 species (39 Entiminae, 2 Cyclominae) is initiated, to assist with the complexity of identification of species in this group.

| S-EPMC8263552 | biostudies-literature

A new ophiacanthid brittle star (Echinodermata, Ophiuroidea) from sublittoral crinoid and seagrass communities of late Maastrichtian age in the southeast Netherlands.

Project description:A new species of brittle star, Ophiomitrella floorae, is recorded from the lower two meters of the Gronsveld Member (Maastricht Formation), of late Maastrichtian age (c. 66.7 Ma). These relatively fine-grained biocalcarenites reflect shallow-water deposition in a sheltered setting with a relatively firm sea floor and clear waters, under middle sublittoral and subtropical conditions. Associated echinoderm taxa comprise more robust, sturdy-plated ophiomusaid and ophiodermatid brittle stars and numerous bourgueticrinine sea lilies. The new brittle star described herein belongs to a family whose present-day members are predominantly restricted to bathyal depths. Its small size and the exceptional preservation of a single articulated specimen partially wrapped around the stalk of a bourgueticrinine suggest that O. floorae n. sp. was probably epizoic and specifically associated with stalked crinoids.

| S-EPMC7450995 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data