Two more Posterior Hox genes and Hox cluster dispersal in echinoderms

Background

Hox genes are key elements in patterning animal development. They are renowned for their, often, clustered organisation in the genome, with supposed mechanistic links between the organisation of the genes and their expression. The widespread distribution and comparable functions of Hox genes across the animals has led to them being a major study system for comparing the molecular bases for construction and divergence of animal morphologies. Echinoderms (including sea urchins, sea stars, sea cucumbers, feather stars and brittle stars) possess one of the most unusual body plans in the animal kingdom with pronounced pentameral symmetry in the adults. Consequently, much interest has focused on their development, evolution and the role of the Hox genes in these processes. In this context, the organisation of echinoderm Hox gene clusters is distinctive. Within the classificatory system of Duboule, echinoderms constitute one of the clearest examples of Disorganized (D) clusters (i.e. intact clusters but with a gene order or orientation rearranged relative to the ancestral state).

Results

Here we describe two Hox genes (Hox11/13d and e) that have been overlooked in most previous work and have not been considered in reconstructions of echinoderm Hox complements and cluster organisation. The two genes are related to Posterior Hox genes and are present in all classes of echinoderm. Importantly, they do not reside in the Hox cluster of any species for which genomic linkage data is available.

Conclusion

Incorporating the two neglected Posterior Hox genes into assessments of echinoderm Hox gene complements and organisation shows that these animals in fact have Split (S) Hox clusters rather than simply Disorganized (D) clusters within the Duboule classification scheme. This then has implications for how these genes are likely regulated, with them no longer covered by any potential long-range Hox cluster-wide, or multigenic sub-cluster, regulatory mechanisms.

     

Spread of bacteria of the genus Acinetobacter in the hydrobios of the Bay of Peter the Great, the Sea of Japan

The analysis of the spread of bacteria of the genus Acinetobacter among the invertebrate animals of the Bay of Peter the Great (the Sea of Japan): in bivalved mollusks, sea cucumbers and sea urchins Acinetobacter bacteria were detected more often than in cushion stars and crustaceous animals. The biological properties of 45 isolated bacteria were studied with the use of a wide variety of tests. The study revealed that 9% of Acinetobacter cultures isolated from marine animals had pronounced beta-hemolysis.     

Habitat-based submersible assessment of macro-invertebrate and groundfish assemblages at Heceta Bank, Oregon, from 1988 to 1990

Exploitation of groundfish off the U.S. Pacific coast reached maximum levels during the 1990s, resulting in severe declines in at least nine species of groundfish. From 1988 to 1990, we used the 2-man submersible Delta to make 42 dives and run replicate visual belt transects at six stations ranging from 67-360 m in depth at Heceta Bank on the outer continental shelf of Oregon. We identified four major habitats and associated benthic macroinvertebrate and groundfish assemblages: (1) shallow rock ridges and large boulders (< 100 m deep) dominated by basket stars, juvenile rockfishes, yelloweye rockfish, and lingcod; (2) mid-depth small boulder-cobbles (100-150 m) dominated by crinoids, brittle stars, rosethorn, pygmy/Puget sound, and canary rockfishes; (3) deep cobble (150-200 m) dominated by crinoids, brittle stars and various small rockfish species, and (4) deep mud slope (> 200 m) dominated by fragile urchins, sea cucumbers, shortspine thornyhead, and flatfishes. Although substantial interannual variation in groundfish abundance among seafloor types was evident in the 12 most abundant and/or commercially important fish taxa sampled, high variance resulted in statistically significant differences among years only in juvenile rockfishes. These data provide a baseline for future comparisons exploring long-term change this continental-shelf ecosystem.     

Quantification of echinoderms (Echinodermata) on Georges Bank,and the potential influence of marine protected areas on these populations

The spatiotemporal variation of the distribution of echinoderms in the Georges Bank ecosystem was examined from 2005 to 2012. Density and abundance of representatives from echinoderm classes (brittle stars, sand dollars, sea stars, and sea urchins) were estimated using a drop camera video survey of the benthos in areas open and closed to fish trawling. The influence of closed areas on these echinoderm populations relative to a suite of key environmental and biotic factors was evaluated using Canonical Correspondence Analysis (CCA). While marine protected areas appeared to influence the distribution of sand dollars and sea stars, the distribution of brittle stars and sea urchins seemed to be defined mainly by preferred habitat conditions. According to the CCA, depth, sediment stability, temperature, predator abundance, and management area were the most important factors explaining this echinoderm assemblage. On Georges Bank, echinoderms dominate the benthic biota and are present in a variety of habitats. They can alter marine communities and are preferred prey and main predators for several commercially targeted species. The detailed information presented here (on the scale of kilometers) on abundance and spatial distribution of these populations is thus valuable towards the implementation of ecosystem‐based fisheries management.     

Apparent Selection Intensity for the Cytochrome Oxidase Subunit I Gene Varies with Mode of Reproduction in Echinoderms

When most amino acid substitutions in protein-coding genes are slightly deleterious rather than selectively neutral, life history differences can potentially modify the effective population size or the selective regime, resulting in altered ratios of non-synonymous to synonymous substitutions among taxa. We studied substitution patterns for the mitochondrial cytochrome oxidase subunit I (COI) gene in a sea star genus (Leptasterias spp.) with an obligate brood-protecting mode of reproduction and small-scale population genetic subdivision, and compared the results to available COI sequences in nine other genera of echinoderms with pelagic larvae: three sea stars, five sea urchins and one brittle star. We predicted that this life history difference would be associated with differences in the ratio of non-synonymous (dN) to synonymous (dS) substitution rates. Leptasterias had a significantly greater dN/dS ratio (both between species and within species), a significantly smaller transition/transversion rate ratio, and a significantly lower average nucleotide diversity within species, than did the non-brooding genera. Other explanations for the results, such as altered mutation rates or selective sweeps, were not supported by the data analysis. These findings highlight the potential influence of reproductive traits and other life history factors on patterns of nucleotide substitution within and between species.     

Metaphylogeny of 82 gene families sheds a new light on chordate evolution

Achieving a better comprehension of the evolution of species has always been an important matter for evolutionary biologists. The deuterostome phylogeny has been described for many years, and three phyla are distinguishable: Echinodermata (including sea stars, sea urchins, etc...), Hemichordata (including acorn worms and pterobranchs), and Chordata (including urochordates, cephalochordates and extant vertebrates). Inside the Chordata phylum, the position of vertebrate species is quite unanimously accepted. Nonetheless, the position of urochordates in regard with vertebrates is still the subject of debate, and has even been suggested by some authors to be a separate phylum from cephalochordates and vertebrates. It was also the case for agnathans species -myxines and hagfish- for which phylogenetic evidence was recently given for a controversial monophyly. This raises the following question: which one of the cephalochordata or urochordata is the sister group of vertebrates and what are their relationships? In the present work, we analyzed 82 protein families presenting homologs between urochordata and other deuterostomes and focused on two points: 1) testing accurately the position of urochordata and cephalochordata phyla in regard with vertebrates as well as chordates monophyly, 2) performing an estimation of the rate of gene loss in the Ciona intestinalis genome. We showed that the urochordate phyla is the vertebrate sister group and that gene loss played a major role in structuring the urochordate genome.     

Responses of the black sea urchin Tetrapygus niger to its sea-star predators Heliaster helianthus and Meyenaster gelatinosus under field conditions

We ran field experiments to examine the responses of the black sea urchin Tetrapygus niger to predatory sea stars. Trials involving simulated attacks (one or several arms of a sea star being placed on top of half the urchin) showed that the urchin differentiated between the predatory sea stars, Heliaster helianthus and Meyenaster gelatinosus, and a non-predatory sea star, Stichaster striatus, and showed almost no response to a sea star mimic. We further compared the responses of the urchin to different threat levels presented by the two predatory sea stars. The highest threat level was a simulated attack, then mere contact, and subsequently sea stars being placed at different distances from the urchin. All urchins responded to simulated attacks and contact with both sea stars. The proportion responding decreased with distance and more rapidly in trials with H. helianthus (0% at a distance of 30 cm) than with M. gelatinosus (33% at a distance of 50 cm). At each of the threat levels where there was a response to both sea stars, the urchins responded more rapidly to M. gelatinosus than to H. helianthus. In a third experiment where a predatory sea star was added to a circular area (1-m diameter) in which either 4-8 or 11-19 undisturbed urchins were present, the urchins fled the area more rapidly when the added sea star was M. gelatinosus, but the rate of fleeing did not vary with density, as might occur if there was communication among urchins using alarm signals. Our observations suggest that M. gelatinosus presents a stronger predatory threat than H. helianthus. This corresponds to field observations showing that the urchins are more frequently consumed by M. gelatinosus. These are the first field experiments demonstrating distance chemodetection by a marine invertebrate under back-and-forth water flow from wave activity.     

Bindin from a sea star

SUMMARY The genetic basis for the evolution of development includes genes that encode proteins expressed on the surfaces of sperm and eggs. Previous studies of the sperm acrosomal protein bindin have helped to characterize the adaptive evolution of gamete compatibility and speciation in sea urchins. The absence of evidence for bindin expression in taxa other than the Echinoidea has limited such studies to sea urchins, and led to the suggestion that bindin might be a sea urchin-specific molecule. Here we characterize the gene that encodes bindin in a broadcast-spawning asterinid sea star ( Patiria miniata ). We describe the sequence and domain structure of a full-length bindin cDNA and its single intron. In comparison with sea urchins, P. miniata bindin is larger but the two molecules share several general features of their domain structure and some sequence features of two domains. Our results extend the known evolutionary history of bindin from the Mesozoic (among the crown group sea urchins) into the early Paleozoic (and the common ancestor of eleutherozoans), and present new opportunities for understanding the role of bindin molecular evolution in sexual selection, life history evolution, and speciation among sea stars.     

Lineage-Specific Evolution of Echinoderm Mitochondrial ATP Synthase Subunit 8

Peculiar evolutionary properties of the subunit 8 of mitochondrial ATP synthase (ATPase8) are revealed by comparative analyses carried out between both closely and distantly related species of echinoderms. The analysis of nucleotide substitution in the three echinoids demonstrated a relaxation of amino acid functional constraints. The deduced protein sequences display a well conserved domain at the N-terminus, while the central part is very variable. At the C-terminus, the broad distribution of positively charged amino acids, which is typical of other organisms, is not conserved in the two different echinoderm classes of the sea urchins and of the sea stars. Instead, a motif of three amino acids, so far not described elsewhere, is conserved in sea urchins and is found to be very similar to the motif present in the sea stars. Our results indicate that the N-terminal region seems to follow the same evolutionary pattern in different organisms, while the maintenance of the C-terminal part in a phylum-specific manner may reflect the co-evolution of mitochondrial and nuclear genes.     

Heterochronic activation of VEGF signaling and the evolution of the skeleton in echinoderm pluteus larvae

The evolution of the echinoderm larval skeleton was examined from the aspect of interactions between skeletogenic mesenchyme cells and surrounding epithelium. We focused on vascular endothelial growth factor (VEGF) signaling, which was reported to be essential for skeletogenesis in sea urchin larvae. Here, we examined the expression patterns of vegf and vegfr in starfish and brittle stars. During starfish embryogenesis, no expression of either vegfr or vegf was detected, which contrast with previous reports on the expression of starfish homologs of sea urchin skeletogenic genes, including Ets, Tbr, and Dri. In later stages, when adult skeletogenesis commenced, vegfr and vegf expression were upregulated in skeletogenic cells and in the adjacent epidermis, respectively. These expression patterns suggest that heterochronic activation of VEGF signaling is one of the key molecular evolutionary steps in the evolution of the larval skeleton. The absence of vegf or vegfr expression during early embryogenesis in starfish suggests that the evolution of the larval skeleton requires distinct evolutionary changes, both in mesoderm cells (activation of vegfr expression) and in epidermal cells (activation of vegf expression). In brittle stars, which have well‐organized skeletons like the sea urchin, vegfr and vegf were expressed in the skeletogenic mesenchyme and the overlying epidermis, respectively, in the same manner as in sea urchins. Therefore, the distinct activation of vegfr and vegf may have occurred in two lineages, sea urchins and brittle stars.     

The impact of mitochondrial genome analyses on the understanding of deuterostome phylogeny

Deuterostomia, one of the three major lineages of Bilateria, comprises many well-known animals such as vertebrates, sea squirts, sea stars and sea urchins. Whereas monophyly of Deuterostomia and several subtaxa is well supported, the relationships of these to each other and, hence, deuterostome relationships are still uncertain. To address these issues in deuterostome phylogeny we analyzed datasets comprising more than 300 complete deuterostome mitochondrial genomes. Based on sequence information, the results revealed support for several relationships such as a basal position of Xenoturbella within Deuterostomia or for taxa like Craniota or Ambulacraria, but yielded also problems in some taxa, e.g. Tunicata, Pterobranchia and Ophiuroidea, due to long-branch artifacts. However, within tunicates the relationships are well supported. Variation in the genetic code was also informative and, e.g., supported the taxon Ambulacraria including Pterobranchia.     

Discovery and cross-amplification of microsatellite polymorphisms in asterinid sea stars

Variation in tandem repeats of two- to six-base nucleotide motifs (microsatellites) can be used to obtain inexpensive and highly informative multi-locus data on population genetics.We developed and tested a large set of cross-amplifiable sea star (Asterinidae) microsatellite markers from a mixed pool of genomic DNA from eight species. We describe cloned sequences, primers, and PCR conditions, and characterize population-level variation for some species and markers. A few clones containing microsatellites showed considerable similarity to sequences (including genes of known function) in other sea stars and in sea urchins (from the Strongylocentrotus purpuratus complete genome). The pooled genomic DNA method was an efficient way to sample microsatellites from many species: we cloned 2-10 microsatellites from each of eight species, and most could be cross-amplified in 1-7 other species. At 12 loci in two species, we found 1-10 alleles per microsatellite, with a broad range of inbreeding coefficients. Measures of polymorphism were negatively correlated with the extent of cross-amplification.     

Activity, feeding behaviour and diet of Ogcocephalus vespertilio in southern west Atlantic

The Brazilian batfish Ogcocephalus vespertilio is a nocturnal and early morning predator on bottom invertebrates, staying stationary and hidden in rock holes, crevices or among bottom rocks during the day. While active, it searches for prey walking along the bottom with the help of its specialized paired fins, with the illicium protracted and oscillating or exploring the substrate. The prey are either snapped up from the bottom, after visual detection, or dug out with use of the mouth and rostrum. It feeds on crustaceans (hermit crabs, true crabs, shrimps, amphipods, porcelain crabs, isopods and mysid shrimps), molluscs (snails, sea slugs and clams), polychaete worms (mostly Errantia) and echinoderms (sea urchins and brittle stars).     

The perils of single gene trees — mitochondrial versus single-copy nuclear DNA variation in white-eyes (Aves: Zosteropidae)

Phylogenetic relationships among animal populations and species commonly have been inferred from patterns of variation observed within a single gene system, most often the mitochondrial genome. Analysis of restriction site variation in the mitochondrial DNA of two species of white-eye ( Zosterops lateralis and Z. lutea ) in Australia produced a single gene tree that does not accurately represent the organismal tree. In contrast, patterns of variation at two anonymous, single-copy nuclear DNA loci revealed a phylogeography consistent with traditional classification of the species. Discordance between mitochondrial DNA and single-copy nuclear DNA variation is probably the result of past hybridization between Z. lateralis and Z. lutea , evidence of which has been lost from the nuclear genome by recombination. This study provides a clear empirical demonstration that single gene genealogies cannot be assumed to accurately represent the true phylogenies, and emphasizes the need for composite genetic analyses.     

Current Status of Echinoderm Genome Analysis - What do we Know?

Echinoderms have long served as model organisms for a variety of biological research, especially in the field of developmental biology. Although the genome of the purple sea urchin Strongylocentrotus purpuratus has been sequenced, it is the only echinoderm whose whole genome sequence has been reported. Nevertheless, data is rapidly accumulating on the chromosomes and genomic sequences of all five classes of echinoderms, including the mitochondrial genomes and Hox genes. This blossoming new data will be essential for estimating the phylogenetic relationships among echinoderms, and also to examine the underlying mechanisms by which the diverse morphologies of echinoderms have arisen.     

Identification of protein components from the mature ovary of the sea urchin Evechinus chloroticus (Echinodermata: Echinoidea)

The gonads of sea urchins are a high value seafood product, with considerable research being undertaken worldwide on the development of sea urchin aquaculture. As the best prices are obtained for specific gonad attributes, research has also focused on the development of artificial diets that enhance gonad quality and quantity. Total protein has been used as a measure of gonad quality; yet no studies to date have applied proteomics technology to diet development. Here we use a MudPIT and 2-DE approach to describe the major proteins in mature ovaries of a New Zealand sea urchin Evechinus chloroticus. This tissue, which is a target seafood product, contained 138 proteins that were identified from the recently completed sea urchin genome (Strongylocentrotus purpuratus) with high confidence. The majority of these proteins had general functions, with only 12 related to ovarian reproductive function. Eighteen proteins were located on the 2-DE; four of these were directly identified from S. purpuratus protein sequences. In combination this paper shows that the genome resources of S. purpuratus can be used to identify proteins in sea urchins from different families; describes the proteome of E. chloroticus mature ovary; and, provides proteomic tools for analysis of gonads from other edible sea urchins.     

Phylogeny and development of marine model species: strongylocentrotid sea urchins

The phylogenetic relationships of ten strongy-locentrotid sea urchin species were determined using mitochondrial DNA sequences. This phylogeny provides a backdrop for the evolutionary history of one of the most studied groups of sea urchins. Our phylogeny indicates that a major revision of this group is in order. All else remaining unchanged, it supports the inclusion of three additional species into the genus Strongylocentrotus (Hemicentrotus pulcherrimus, Allocentrotus fragilis, and Pseudocentrotus depressus). All were once thought to be closely related to this genus, but subsequent revisions separated them into other taxonomic groupings. Most strongylocentrotid species are the result of a recent burst of speciation in the North Pacific that resulted in an ecological diversification. There has been a steady reduction in the complexity of larval skeletons during the expansion of this group. Gamete attributes like egg size, on the other hand, are not correlated with phylogenetic position. In addition, our results indicate that the rate of replacement substitutions is highly variable among phylogenetic lineages. The branches leading to S. purpuratus and S. franciscanus were three to six times longer than those leading to closely related species.