Phylogeography, colouration, and cryptic speciation across the Indo-Pacific in the sea urchin genus Echinothrix.

The sea urchins Echinothrix calamaris and Echinothrix diadema have sympatric distributions throughout the Indo-Pacific. Diverse colour variation is reported in both species. To reconstruct the phylogeny of the genus and assess gene flow across the Indo-Pacific we sequenced mitochondrial 16S rDNA, ATPase-6, and ATPase-8, and nuclear 28S rDNA and the Calpain-7 intron. Our analyses revealed that E. diadema formed a single trans-Indo-Pacific clade, but E. calamaris contained three discrete clades. One clade was endemic to the Red Sea and the Gulf of Oman. A second clade occurred from Malaysia in the West to Moorea in the East. A third clade of E. calamaris was distributed across the entire Indo-Pacific biogeographic region. A fossil calibrated phylogeny revealed that the ancestor of E. diadema diverged from the ancestor of E. calamaris ~ 16.8 million years ago (Ma), and that the ancestor of the trans-Indo-Pacific clade and Red Sea and Gulf of Oman clade split from the western and central Pacific clade ~ 9.8 Ma. Time since divergence and genetic distances suggested species level differentiation among clades of E. calamaris. Colour variation was extensive in E. calamaris, but not clade or locality specific. There was little colour polymorphism in E. diadema.

A new species and comparative morphology of Philippine sea biscuits (Echinoidea: Clypeaster/).

A new species of clypeasterid sea biscuit, Clypeaster brigitteae n. sp., is described from material collected in the Philippines at depths between 100 and 200 m. The new taxon increases the number of Clypeaster species recorded from the Philippines to nine, representing nearly a quarter of the world's diversity of the genus. Other Philippine species include: C. annandalei Koehler, 1922; C. fervens Koehler, 1922; C. humilis (Leske, 1778); C. japonicus Döderlein, 1885; C. latissimus (Lamarck, 1816); C. pateriformis Mortensen, 1948; C. reticulatus (Linnaeus, 1758); and C. virescens Döderlein, 1885. Using type material where available, each of these species is compared and contrasted with C. brigitteae n. sp. in tables consisting of new data derived from general test shape and size, petal structure, food grooves, plate architecture, internal structure, and morphology of spines, pedicellariae, and tube feet.

Spinochrome Identification and Quantification in Pacific Sea Urchin Shells, Coelomic Fluid and Eggs Using HPLC-DAD-MS.

The high-performance liquid chromatography method coupled with diode array and mass spectrometric detector (HPLC-DAD-MS) method for quinonoid pigment identification and quantification in sea urchin samples was developed and validated. The composition and quantitative ratio of the quinonoid pigments of the shells of 16 species of sea urchins, collected in the temperate (Sea of Japan) and tropical (South-China Sea) climatic zones of the Pacific Ocean over several years, were studied. The compositions of the quinonoid pigments of sea urchins Maretia planulata, Scaphechinus griseus, Laganum decagonale and Phyllacanthus imperialis were studied for the first time. A study of the composition of the quinonoid pigments of the coelomic fluid of ten species of sea urchins was conducted. The composition of quinonoid pigments of Echinarachnius parma jelly-like egg membrane, of Scaphechinus mirabilis developing embryos and pluteus, was reported for the first time. In the case of Scaphechinus mirabilis, we have shown that the compositions of pigment granules of the shell epidermis, coelomic fluid, egg membrane, developing embryos and pluteus are different, which should enable a fuller understanding of the functions of pigments at different stages of life.

Functional properties of gonad protein isolates from three species of sea urchin: a comparative study.

Sea urchin Mesocentrotus nudus, Glyptocidaris crenularis, and Strongylocentrotus intermedius gonad protein isolates (mnGPIs, gcGPIs, and siGPIs) were extracted by isoelectric solubilization/precipitation (ISP) from the defatted gonads, and their functional properties were compared. Sodium dodecyl sulfate polyacrylamide gel electrophoresis results showed the similar protein pattern between each protein isolate and defatted gonad, indicating the high efficiency of ISP processing for protein recovery. Amino acid profileconfirmed that the mnGPIs and siGPIs could be potential sources of essential amino acid in nature. As regard to functional properties, mnGPIs showed higher water- and oil- holding capacities followed bysiGPIs and gcGPIs and all protein isolates presented great foaming property. As for emulsifying activity index (EAI), mnGPIs, gcGPIs, and siGPIs showed the minimum solubility and EAI at pH 5, 3, and 4, respectively, and behaved a pH-dependent manner. The gcGPIs revealed the highest EAI from pH 6 to 8 among the samples. In addition, circular dichroism showed increased content of ß-sheet at the expense of α-helix and ß-turn, suggesting the structure denaturation of the protein isolates. Indeed, no statistical difference was observed between secondary structure of mnGPIs and siGPIs. Moreover, ISP processing increased free sulfhydryl content of sea urchin protein isolates, but no difference was observed among the samples. Furthermore, siGPIs revealed the highest amount of total sulfhydryl and disulfide bonds, whereas both defatted gonads and protein isolates from G. crenularis presented the maximum surface hydrophobicity. These results suggest that gonad protein isolates from three species of sea urchin possess various functionalities and therefore can be potentially applied in food system. PRACTICAL APPLICATION: Sea urchin M. nudus, G. crenularis, and S. intermedius gonads are edible, whereas the functional properties of protein isolates from sea urchin gonad remain unknown. In this case, the extraction and comparison of three species of sea urchin gonad protein isolates will not only confirm functional properties but also screen food ingredients with suitable functions. In this study, functionalities of protein isolates derived from M. nudus, G. crenularis, and S. intermedius gonads would provide potential application in bakery food and meat products or as emulsifier candidates in food system.

The first complete mitochondrial genome of the sand dollar Sinaechinocyamus mai (Echinoidea: Clypeasteroida).

Morphologic and molecular data often lead to different hypotheses of phylogenetic relationships. Such incongruence has been found in the echinoderm class Echinoidea. In particular, the phylogenetic status of the order Clypeasteroida is not well resolved. Complete mitochondrial genomes are currently available for 29 echinoid species, but no clypeasteroid had been sequenced to date. DNA extracted from a single live individual of Sinaechinocyamus mai was sequenced with 10× Genomics technology. This first complete mitochondrial genome (mitogenome) for the order Clypeasteroida is 15,756 base pairs in length. Phylogenomic analysis based on 34 ingroup taxa belonging to nine orders of the class Echinoidea show congruence between our new genetic inference and published trees based on morphologic characters, but also includes some intriguing differences that imply the need for additional investigation.

MITF: an evolutionarily conserved transcription factor in the sea urchin Paracentrotus lividus.

Microphthalmia-associated transcription factor (MITF) is a member of MYC superfamily, associated with melanocyte cells, as it was discovered in depigmented mice. However, over the last years it was found to be involved in many cellular signaling pathways, among which oncogenesis, osteoclast differentiation, and stress response. In mammals, Mitf gene mutations can cause diverse syndromes affecting pigmentation of eyes or skin, bone defects and melanomas. As MITF protein homologs were also found in some invertebrates, we have isolated and characterized the MITF cDNAs from the sea urchin Paracentrotus lividus, referred to as Pl-Mitf. The in silico study of the secondary and tertiary structure of Pl-Mitf protein showed high conserved regions mostly lying in the DNA binding domain. To understand the degree of evolutionary conservation of MITF, a phylogenetic analysis was performed comparing the Pl-Mitf deduced protein with proteins from different animal species. Moreover, the analysis of temporal and spatial expression pattern of Pl-Mitf mRNA showed that it was expressed from the onset of gastrulation of the sea urchin embryo to the pluteus larva, specifically in primary mesenchymes cells (PMCs), the sea urchin skeletogenic cells, and in the forming archenteron, the larval gut precursor. In silico protein-protein interactions analysis was used to understand the association of MITF with other proteins. Our results put in evidence the conservation of the MITF protein among vertebrates and invertebrates and may provide new perspectives on the pathways underlying sea urchin development, even if further functional analyses are needed.

Possible cooption of a VEGF-driven tubulogenesis program for biomineralization in echinoderms.

Biomineralization is the process by which living organisms use minerals to form hard structures that protect and support them. Biomineralization is believed to have evolved rapidly and independently in different phyla utilizing preexisting components. The mechanistic understanding of the regulatory networks that drive biomineralization and their evolution is far from clear. Sea urchin skeletogenesis is an excellent model system for studying both gene regulation and mineral uptake and deposition. The sea urchin calcite spicules are formed within a tubular cavity generated by the skeletogenic cells controlled by vascular endothelial growth factor (VEGF) signaling. The VEGF pathway is essential for biomineralization in echinoderms, while in many other phyla, across metazoans, it controls tubulogenesis and vascularization. Despite the critical role of VEGF signaling in sea urchin spiculogenesis, the downstream program it activates was largely unknown. Here we study the cellular and molecular machinery activated by the VEGF pathway during sea urchin spiculogenesis and reveal multiple parallels to the regulation of vertebrate vascularization. Human VEGF rescues sea urchin VEGF knockdown, vesicle deposition into an internal cavity plays a significant role in both systems, and sea urchin VEGF signaling activates hundreds of genes, including biomineralization and interestingly, vascularization genes. Moreover, five upstream transcription factors and three signaling genes that drive spiculogenesis are homologous to vertebrate factors that control vascularization. Overall, our findings suggest that sea urchin spiculogenesis and vertebrate vascularization diverged from a common ancestral tubulogenesis program, broadly adapted for vascularization and specifically coopted for biomineralization in the echinoderm phylum.

A new ophiocistioid with soft-tissue preservation from the Silurian Herefordshire Lagerstätte, and the evolution of the holothurian body plan.

Reconstructing the evolutionary assembly of animal body plans is challenging when there are large morphological gaps between extant sister taxa, as in the case of echinozoans (echinoids and holothurians). However, the inclusion of extinct taxa can help bridge these gaps. Here we describe a new species of echinozoan, Sollasina cthulhu, from the Silurian Herefordshire Lagerstätte, UK. Sollasina cthulhu belongs to the ophiocistioids, an extinct group that shares characters with both echinoids and holothurians. Using physical-optical tomography and computer reconstruction, we visualize the internal anatomy of S. cthulhu in three dimensions, revealing inner soft tissues that we interpret as the ring canal, a key part of the water vascular system that was previously unknown in fossil echinozoans. Phylogenetic analyses strongly suggest that Sollasina and other ophiocistioids represent a paraphyletic group of stem holothurians, as previously hypothesized. This allows us to reconstruct the stepwise reduction of the skeleton during the assembly of the holothurian body plan, which may have been controlled by changes in the expression of biomineralization genes.

A phylogenomic resolution of the sea urchin tree of life.

BACKGROUND: Echinoidea is a clade of marine animals including sea urchins, heart urchins, sand dollars and sea biscuits. Found in benthic habitats across all latitudes, echinoids are key components of marine communities such as coral reefs and kelp forests. A little over 1000 species inhabit the oceans today, a diversity that traces its roots back at least to the Permian. Although much effort has been devoted to elucidating the echinoid tree of life using a variety of morphological data, molecular attempts have relied on only a handful of genes. Both of these approaches have had limited success at resolving the deepest nodes of the tree, and their disagreement over the positions of a number of clades remains unresolved. RESULTS: We performed de novo sequencing and assembly of 17 transcriptomes to complement available genomic resources of sea urchins and produce the first phylogenomic analysis of the clade. Multiple methods of probabilistic inference recovered identical topologies, with virtually all nodes showing maximum support. In contrast, the coalescent-based method ASTRAL-II resolved one node differently, a result apparently driven by gene tree error induced by evolutionary rate heterogeneity. Regardless of the method employed, our phylogenetic structure deviates from the currently accepted classification of echinoids, with neither Acroechinoidea (all euechinoids except echinothurioids), nor Clypeasteroida (sand dollars and sea biscuits) being monophyletic as currently defined. We show that phylogenetic signal for novel resolutions of these lineages is strong and distributed throughout the genome, and fail to recover systematic biases as drivers of our results. CONCLUSIONS: Our investigation substantially augments the molecular resources available for sea urchins, providing the first transcriptomes for many of its main lineages. Using this expanded genomic dataset, we resolve the position of several clades in agreement with early molecular analyses but in disagreement with morphological data. Our efforts settle multiple phylogenetic uncertainties, including the position of the enigmatic deep-sea echinothurioids and the identity of the sister clade to sand dollars. We offer a detailed assessment of evolutionary scenarios that could reconcile our findings with morphological evidence, opening up new lines of research into the development and evolutionary history of this ancient clade.

A 30-year monitoring of changes in coral community structure following anthropogenic disturbances in Tolo Harbour and Channel, Hong Kong.

Coral communities in Tolo Harbour and Channel, northeastern Hong Kong, suffered from tremendous degradations in 1980s due to excessive sewage pollutions. This study examined changes in coral community structures over the last 30 years including period before, at the height of and after implementation of abatement measures of pollution impacts. Signs of coral degradations finally stopped in inner harbour and some corals started to reappear, likely due to sewage export scheme since 1998. Yet, the coral cover remained very low (<2%) in 2012. Natural recovery is limited by very low coral recruitment success other than that of Oulastrea crispata. The outer coral communities, which suffered least in 1980s, continued to decline, possibly due to new biological disturbances like sea urchin predation and bioerosion. This long-term study clearly revealed how coral communities could so easily be destroyed and yet natural recovery could be so difficult and unlikely.

Effects of Nodal inhibition on development of temnopleurid sea urchins.

Adult rudiment formation in some temnopleurids begins with the formation of a cell mass that is pinched off the left ectoderm in early larval development. The cell mass forms the adult rudiment with the left coelomic pouch of the mesodermal region. However, details of the mechanisms to establish position of the cell mass are still unknown. We analyzed the inhibiting effect of Nodal, a factor for morphogenesis of the oral region and right side, for location of the cell mass, in four temnopleurids. Pulse inhibition, at least 5 min inhibition, during coelomic pouch formation allowed a cell mass to form on both sides, whereas treatments after that period did not. These results indicate that Nodal signaling controls the oral-aboral axis before gastrulation and then affects the position of the cell mass and adult rudiment up to coelomic pouch formation. They also indicate that the position of the adult rudiment under Nodal signaling pathways is conserved in temnopleurids, as adult rudiment formation is dependent on the cell mass.

Cartilage acidic protein 1, a new member of the beta-propeller protein family with amyloid propensity.

Cartilage acidic protein1 (CRTAC1) is an extracellular matrix protein of chondrogenic tissue in humans and its presence in bacteria indicate it is of ancient origin. Structural modeling of piscine CRTAC1 reveals it belongs to the large family of beta-propeller proteins that in mammals have been associated with diseases, including amyloid diseases such as Alzheimer's. In order to characterize the structure/function evolution of this new member of the beta-propeller family we exploited the unique characteristics of piscine duplicate genes Crtac1a and Crtac1b and compared their structural and biochemical modifications with human recombinant CRTAC1. We demonstrate that CRTAC1 has a beta-propeller structure that has been conserved during evolution and easily forms high molecular weight thermo-stable aggregates. We reveal for the first time the propensity of CRTAC1 to form amyloid-like structures, and hypothesize that the aggregating property of CRTAC1 may be related to its disease-association. We further contribute to the general understating of CRTAC1's and beta-propeller family evolution and function. Proteins 2017; 85:242-255. © 2016 Wiley Periodicals, Inc.

Differences in Larval Arm Movements Correlate with the Complexity of Musculature in Two Phylogenetically Distant Echinoids, Eucidaris tribuloides (Cidaroidea) and Lytechinus variegatus (Euechinoidea).

Within a common body plan, echinoid planktotrophic larvae are morphologically diverse, with variations in overall size, the length, and number of arms and the presence or absence of epidermal structures. In this report, we are interested in variation in larval arm-flexing behavior and correlated differences in larval musculature. Larvae of the cidaroid Eucidaris tribuloides exhibit conspicuous and regular arm-flexing behavior. In contrast, Lytechinus variegatus, a representative of the euechinoid clade, does not exhibit this behavior. We hypothesized that there were differences in musculature that correlated with this behavioral contrast and compared the development and structure of larval muscles between these species. We report substantial differences in some aspects of larval musculature. In addition to previously described oral musculature, both larvae possessed polygon-shaped musculature at the basal end of the larva. However, larval musculature in E. tribuloides was larger and contained additional muscles not observed in larvae of L. variegatus. Therefore, a conspicuous larval behavior consisting of repeated flexing of the postoral and posterodorsal larval arms was correlated with a larger, more complex musculature. This simple contrast indicates that larval musculature not associated with endoderm evolves in a manner that relates to differences in larval behavior and that additional comparisons are warranted.

A new South American Miocene species of 'one-holed' sand dollar (Echinoidea: Clypeasteroida: Monophorasteridae).

A new species of monophorasterid sand dollar, Monophoraster telfordi n. sp., is described from the Early Miocene basal horizons of the Chenque Formation of Patagonia, Santa Cruz Province, in southern Argentina. The new taxon raises the number of known species in the family to six, and represents first unequivocal record of the genus for the Early Miocene of South America. It is therefore also the oldest member of the genus. M. telfordi is characterized by its test width to length ratio, which is much higher than for the other two described species in the genus, but less than that known for the extremely wide members of the sister taxon, Amplaster. M. telfordi is also unusual among monophorasterids in lacking broad continuity between basicoronal and post-basicoronal plates in the oral interambulacra. A key is provided to all the known species of Monophorasteridae.

A review of New Zealand and southeast Australian echinothurioids (Echinodermata: Echinothurioida)-excluding the subfamily Echinothuriinae-with a description of a new species of Tromikosoma.

An examination of a large collection of echinothurioid echinoids (excluding the subfamily Echinothuriinae Thomson) from museum collections in New Zealand and Australia has expanded the known diversity of the group in New Zealand from three species in two genera to seven species in five genera, and revealed a new species in the genus Tromikosoma Mortensen.New records for New Zealand and Australia are reported for Sperosoma obscurum Agassiz and Clark, 1907 and S. nudum Shigei, 1978 and new records for New Zealand are reported for Tromikosoma australe (Koehler, 1922) and Kamptosoma asterias (A. Agassiz, 1881). Tromikosoma rugosum sp. nov., remarkable for its unusual wrinkled appearance and exceedingly thin test, is described from deep water in the northeast of New Zealand. No evidence for the existence of Phormosoma rigidum A. Agassiz, 1881 as a species separate from P. bursarium A. Agassiz, 1881 was found, and synonymy with P. bursarium is proposed.Previous records of these echinoid species were rare, as they live mostly in deep water (>1000 m), and three species were previously known from the type material alone. Tromikosoma rugosum sp. nov. now falls into that category, but new material of the other species greatly expands both the number of known records and their geographical distribution. The majority of these new records are from the New Zealand region, with several additional records from south-east Australia.An updated key to the echinothurioids of New Zealand is provided.

A new genus of mellitid sand dollar (Echinoidea: Mellitidae) from the eastern Pacific coast of the Americas.

Lanthonia gen. nov. Coppard 2016 is a genus of clypeasteroid sand dollar whose members inhabit shallow, sandy waters from Mexico (including the Gulf of California) to Colombia in the tropical and subtropical eastern Pacific. Lanthonia includes Lanthonia longifissa (Michelin, 1858) and Lanthonia grantii (Mortensen, 1948), with L. longifissa hereby designated as the type species. Both L. longifissa and L. grantii were previously placed in the genus Mellita (L. Agassiz, 1841). However, levels of genetic divergence between a lineage containing L. longifissa and L. grantii and a lineage containing all other species of Mellita, including the type species M. quinquiesperforata (Leske, 1778), indicate genus level differentiation. The systematic interpretation of this group also supports the designation of this new genus as it allows the tree topology to be recovered from the nomenclature and clarifies the historical biogeography of these clades. This has resulted in members of both lineages today being sympatric in the eastern Pacific. Members of Lanthonia are morphologically differentiated from the type species of Mellita and all Pacific Mellita in having very narrow ambulacral regions between the food grooves and the ambulacral lunules on the oral surface, these being very broad in both M. quinquiesperforata and M. notabilis. The dentation of the bidentate pedicellariae also differentiate these genera, with small peripheral teeth present along the edge of the blade in species of Lanthonia and one to three enlarged intersecting teeth present distally in all species of Mellita.

Protaeropsis, a new replacement generic name for fossil Sphenaster Jeffery, 1999 (Echinoidea: Spatangida) nec Wilcoxon, 1970 (Protista: Haptomonada).

The genus Sphenaster was erected by Jeffery (in Smith et al. 1999: 131) for a distinctive fossil echinoid of the Thanetian (Palaeocene) age from Spain and considered to be the most ancient element of the echinoid family Aeropsidae Clark, 1917 (Spatangida, Echinoidea). Unfortunately, up to now (Kroh 2010), it was not realized that the generic name Sphenaster is invalid, being a junior homonym of Sphenaster Wilcoxon, 1970: 80, a genus of fossil protist (Haptomonada).

Understanding trophic relationships among Caribbean sea urchins

ResumenLas especies Echinometra lucunter, Echinometra viridis, Lytechinus variegatus, Tripneustes ventricosus, and Diadema antillarum son los erizos de mar más comunes en los hábitat litorales del Caribe. Los erizos de mar T. ventricosus y L. variegatus habitan generalmente los pastos marinos mientras que las otras tres especies se encuentran asociadas a sustratos rocosos. Los hábitos alimentarios de estas especies han sido bien documentados y son reconocidas como herbívoros - omnívoros; sin embargo, pocas de estas especies han sido caracterizadas isotópicamente. Utilizamos los isótopos estables para caracterizar estas cinco especies de erizos y establecer las posiciones tróficas para las especies que cohabitan los mismos ecosistemas. También cuantificamos la contribución de los recursos alimentarios para E. lucunter. Los erizos T. ventricosus y D. antillarum mostraron los mayores valores de δ15N y valores similares de δ13C que variaron desde -11.6 ± 0.63 a -10.4 ± 0.99 %; donde el erizo E. lucunter mostró los valores más negativos con -15.40 ± 0.76 %. Las comunidades de algas no mostraron diferencias en valores promedio de δ15N (F= 1.300, df= 3, p= 0.301), pero sí mostraron variaciones en los valores de δ13C (F= 7.410, df= 3, p= 0.001). Los estudios de amplitud de elipses de nicho determinaron que las especies de los biotopos rocosos (D. antillarum, E. lucunter y E. viridis) no mostraron solapamiento de nicho. Similar resultado también se encontró en las especies de erizos que habitan en los pastos marinos. Sin embargo, la distancia entre estas dos especies fue menor respecto a la distancia entre las especies de erizos que habitan en los sustratos rocosos. Nuestros resultados muestran que las especies que habitan en los pastos marinos mostraron valores más elevados de δ13C en comparación con las especies de los sustratos rocosos. No se encontraron diferencias espaciales para E. lucunter en δ15N, pero sí en δ13C. Los modelos de mezcla bayesianos demuestran la plasticidad alimentaria de E. lucunter, especie capaz de utilizar múltiples recursos algales dependiendo de la disponibilidad por sitio. Semejanzas en δ15N entre D. antillarum y T. ventricosus parecen indicar similitudes tróficas entre ambas especies. Si bien T. ventricosus es reconocido como omnívoro, D. antillarum siempre ha sido considerado un herbívoro generalista. Finalmente, la falta de solapamiento entre las especies en los dos biotopos parece indicar una estrategia de partición de recursos para evitar la competencia de nicho entre especies concurrentes.

AbstractThe species Echinometra lucunter, Echinometra viridis, Lytechinus variegatus, Tripneustes ventricosus, and Diadema antillarum are the most common sea urchins of littoral habitats in the Caribbean. T. ventricosus and L. variegatus are associated with seagrass beds, while the other three species usually inhabit hardground substrates. Food preferences of these species are well documented and they are commonly accepted as being primarily herbivorous-omnivorous; nevertheless, few of them have previously been characterized isotopically. We used this approach for assessing the isotopic characterization of five echinoids. We established the trophic position of two groups of co-occurring species and quantified the contribution of food resources in the diet of Echinometra lucunter, considered the most common sea urchin in the Caribbean region. The species T. ventricosus and D. antillarum showed the highest values of δ15N. Sea urchins exhibited similar values of δ13C varying from -11.6 ± 0.63 to -10.4 ± 0.99%. The echinoid E. lucunter displayed the lowest values of carbon, from -15.40 ± 0.76%. Significant differences among species were found for δ15N and δ13C. Seaweed communities exhibited no differences among sites for overall δ15N (F= 1.300, df= 3, p= 0.301), but we found spatial differences for δ13C (F= 7.410, df= 3, p= 0.001). The ellipse-based metrics of niche width analysis found that the hardground biotope species (D. antillarum, E. lucunter, and E. viridis) did not overlap each other. Similar results were obtained for the co-occurring species of the seagrass biotope; however, the distance between these species was closer than that of the hardground biotope species. The Bayesian mixing models run for E. lucunter at all four localities found differences in food resources contribution. The algae D. menstrualis, C. crassa and B. triquetrum dominated in CGD; whereas C. nitens, Gracilaria spp., and D. caribaea represented the main contributor algae to the diet of E. lucunter at LQY. In Culebra Island, no dominance of any particular algae was detected in TMD, where six of the eight species exhibited a similar contribution. Similarities in δ15N between D. antillarum and T. ventricosus may hint towards a similar trophic level for these species, although T. ventricosus is widely accepted as an omnivore, while D. antillarum is considered a generalist herbivore. The lack of overlap among species in the two biotopes seems to indicate a resource partitioning strategy to avoid niche competition among co-occurring species. Rev. Biol. Trop. 64 (2): 837-848. Epub 2016 June 01.

Ancestral state reconstruction by comparative analysis of a GRN kernel operating in echinoderms.

Diverse sampling of organisms across the five major classes in the phylum Echinodermata is beginning to reveal much about the structure and function of gene regulatory networks (GRNs) in development and evolution. Sea urchins are the most studied clade within this phylum, and recent work suggests there has been dramatic rewiring at the top of the skeletogenic GRN along the lineage leading to extant members of the euechinoid sea urchins. Such rewiring likely accounts for some of the observed developmental differences between the two major subclasses of sea urchins-cidaroids and euechinoids. To address effects of topmost rewiring on downstream GRN events, we cloned four downstream regulatory genes within the skeletogenic GRN and surveyed their spatiotemporal expression patterns in the cidaroid Eucidaris tribuloides. We performed phylogenetic analyses with homologs from other non-vertebrate deuterostomes and characterized their spatiotemporal expression by quantitative polymerase chain reaction (qPCR) and whole-mount in situ hybridization (WMISH). Our data suggest the erg-hex-tgif subcircuit, a putative GRN kernel, exhibits a mesoderm-specific expression pattern early in Eucidaris development that is directly downstream of the initial mesodermal GRN circuitry. Comparative analysis of the expression of this subcircuit in four echinoderm taxa allowed robust ancestral state reconstruction, supporting hypotheses that its ancestral function was to stabilize the mesodermal regulatory state and that it has been co-opted and deployed as a unit in mesodermal subdomains in distantly diverged echinoderms. Importantly, our study supports the notion that GRN kernels exhibit structural and functional modularity, locking down and stabilizing clade-specific, embryonic regulatory states.

EchinoDB, an application for comparative transcriptomics of deeply-sampled clades of echinoderms.

BACKGROUND: One of our goals for the echinoderm tree of life project (http://echinotol.org) is to identify orthologs suitable for phylogenetic analysis from next-generation transcriptome data. The current dataset is the largest assembled for echinoderm phylogeny and transcriptomics. We used RNA-Seq to profile adult tissues from 42 echinoderm specimens from 24 orders and 37 families. In order to achieve sampling members of clades that span key evolutionary divergence, many of our exemplars were collected from deep and polar seas. DESCRIPTION: A small fraction of the transcriptome data we produced is being used for phylogenetic reconstruction. Thus to make a larger dataset available to researchers with a wide variety of interests, we made a web-based application, EchinoDB (http://echinodb.uncc.edu). EchinoDB is a repository of orthologous transcripts from echinoderms that is searchable via keywords and sequence similarity. CONCLUSIONS: From transcripts we identified 749,397 clusters of orthologous loci. We have developed the information technology to manage and search the loci their annotations with respect to the Sea Urchin (Strongylocentrotus purpuratus) genome. Several users have already taken advantage of these data for spin-off projects in developmental biology, gene family studies, and neuroscience. We hope others will search EchinoDB to discover datasets relevant to a variety of additional questions in comparative biology.