Complete genome sequence of Brachybacterium sp. GU-2 (Actinomycetota), isolated from the massive coral Porites lobata

Brachybacterium sp. GU-2 was isolated from the hard coral Porites lobata found in Apra Harbor, Guam, Micronesia. This genome sequence will be beneficial to understand the role of actinomycetes in coral holobionts. The Brachybacterium genome contains several gene clusters for bioactive compounds, including antibiotics.

Animal evolution at the ocean's water-air interface

Innovation is a key to evolutionary success and entrance into novel ecosystems.1 Species that float freely at the ocean's surface, termed obligate neuston (also called pleuston, here referred to simply as neuston), include highly specialized taxa from distinct evolutionary lineages that evolved floating morphologies.2 In 1958, Soviet scientist, A.I. Savilov,3 stated that floating animal species are derived from benthic ancestors, rather than species from the adjacent pelagic zone, and that floating morphologies are homologous to benthic attachment structures. To test Savilov's hypothesis, we constructed molecular phylogenies and ancestral states for all major floating groups for which molecular data were available. Our results reveal that four of the five clades examined arose directly from a substrate-attached ancestor, although that substrate was not necessarily the benthos, as Savilov stated, and instead included epibiotic and rafting ancestors. Despite their diverse evolutionary origins, floating animals use gas-trapping mechanisms to remain at the surface,4,5,6 and many of these gas-trapping structures appear to be homologous to substrate attachment structures. We also reconstruct the trophic habits of floating mollusks and their sister species, revealing that prey preference remains conserved upon entering the ocean's surface ecosystem. Colonization of the ocean's surface seems to have occurred through successive evolutionary steps from the seafloor. Our results suggest that these steps often included transitions through epibiotic (where species attach to other living organisms) or rafting (where species attach to floating debris) habits. The water-air interface, despite its unique properties, may, in some ways, be just another substrate.

Rapid, high-throughput phenotypic profiling of endosymbiotic dinoflagellates (Symbiodiniaceae) using benchtop flow cytometry

Endosymbiotic dinoflagellates (Family Symbiodiniaceae) are the primary producer of energy for many cnidarians, including corals. The intricate coral-dinoflagellate symbiotic relationship is becoming increasingly important under climate change, as its breakdown leads to mass coral bleaching and often mortality. Despite methodological progress, assessing the phenotypic traits of Symbiodiniaceae in-hospite remains a complex task. Bio-optics, biochemistry, or "-omics" techniques are expensive, often inaccessible to investigators, or lack the resolution required to understand single-cell phenotypic states within endosymbiotic dinoflagellate assemblages. To help address this issue, we developed a protocol that collects information on cell autofluorescence, shape, and size to simultaneously generate phenotypic profiles for thousands of Symbiodiniaceae cells, thus revealing phenotypic variance of the Symbiodiniaceae assemblage to the resolution of single cells. As flow cytometry is adopted as a robust and efficient method for cell counting, integration of our protocol into existing workflows allows researchers to acquire a new level of resolution for studies examining the acclimation and adaptation strategies of Symbiodiniaceae assemblages.

Leveraging Public Data to Predict Global Niches and Distributions of Rhizostome Jellyfishes

As climate change progresses rapidly, biodiversity declines, and ecosystems shift, it is becoming increasingly difficult to document dynamic populations, track fluctuations, and predict responses to climate change. Concurrently, publicly available databases and tools are improving scientific accessibility, increasing collaboration, and generating more data than ever before. One of the most successful projects is iNaturalist, an AI-driven social network doubling as a public database designed to allow citizen scientists to report personal biodiversity reports with accuracy. iNaturalist is especially useful for the research of rare, dangerous, and charismatic organisms, but requires better integration into the marine system. Despite their abundance and ecological relevance, there are few long-term, high-sample datasets for jellyfish, which makes management difficult. To provide some high-sample datasets and demonstrate the utility of publicly collected data, we synthesized two global datasets for ten genera of jellyfishes in the order Rhizostomeae containing 8412 curated datapoints from both iNaturalist (n = 7807) and the published literature (n = 605). We then used these reports in conjunction with publicly available environmental data to predict global niche partitioning and distributions. Initial niche models inferred that only two of ten genera have distinct niche spaces; however, the application of machine learning-based random forest models suggests genus-specific variation in the relevance of abiotic environmental variables used to predict jellyfish occurrence. Our approach to incorporating reports from the literature with iNaturalist data helped evaluate the quality of the models and, more importantly, the quality of the underlying data. We find that free, accessible online data is valuable, yet subject to biases through limited taxonomic, geographic, and environmental resolution. To improve data resolution, and in turn its informative power, we recommend increasing global participation through collaboration with experts, public figures, and hobbyists in underrepresented regions capable of implementing regionally coordinated projects.

Ancient endosymbiont-mediated transmission of a selfish gene provides a model for overcoming barriers to gene transfer into animal mitochondrial genomes

In contrast to bilaterian animals, non-bilaterian mitochondrial genomes contain atypical genes, often attributed to horizontal gene transfer (HGT) as an ad hoc explanation. Although prevalent in plants, HGT into animal mitochondrial genomes is rare, lacking suitable explanatory models for their occurrence. HGT of the mismatch DNA repair gene (mtMutS) from giant viruses to octocoral (soft corals and their kin) mitochondrial genomes provides a model for how barriers to HGT to animal mitochondria may be overcome. A review of the available literature suggests that this HGT was mediated by an alveolate endosymbiont infected with a lysogenic phycodnavirus that enabled insertion of the homing endonuclease containing mtMutS into octocoral mitochondrial genomes. We posit that homing endonuclease domains and similar selfish elements play a crucial role in such inter-domain gene transfers. Understanding the role of selfish genetic elements in HGT has the potential to aid development of tools for manipulating animal mitochondrial DNA.

Calcium homeostasis disruption initiates rapid growth after micro-fragmentation in the scleractinian coral Porites lobata

Coral reefs are ecosystems under increasing threat from global climate change. Coral restoration is a tool for preserving the biological and ecological function of coral reefs by mitigating coral loss and maintaining the structural integrity and complexity of reefs. To generate the necessary stock for coral restoration, larger coral colonies are usually fragmented to generate smaller specimens for outplanting, taking advantage of the high regenerative ability of corals. In this study, we utilized RNA-seq technology to understand the physiological responses of Porites lobata colonies to physical fragmentation and outplanting, which have thus far not been characterized. Our results demonstrate that P. lobata fragments undergoing physical injury recover through two distinct phases: rapid wound regeneration of the cut margins, followed by a slower growth phase that cements the colony to the substrate. Our study found rapid physiological responses to acute physical injury and outplanting in the coral host that involved significantly increased energy production, calcium homeostasis disruption, and endoplasmic reticulum (ER) stress leading to increased antioxidant expression and rates of protein turnover. Our results suggest that phosphoinositide-mediated acute calcium homeostasis disruption stimulates wound recovery processes in response to physical injury. Symbiont gene expression revealed extremely low gene differences in response to fragmentation, growth, and outplanting. These results provide insight into the physiological mechanisms that allow for rapid wound healing and stabilization in response to physical injury in corals.

Tackling the phylogenetic conundrum of Hydroidolina (Cnidaria: Medusozoa: Hydrozoa) by assessing competing tree topologies with targeted high-throughput sequencing

Higher-level relationships of the Hydrozoan subclass Hydroidolina, which encompasses the vast majority of medusozoan cnidarian species diversity, have been elusive to confidently infer. The most widely adopted phylogenetic framework for Hydroidolina based on ribosomal RNA data received low support for several higher level relationships. To address this issue, we developed a set of RNA baits to target more than a hundred loci from the genomes of a broad taxonomic sample of Hydroidolina for high-throughput sequencing. Using these data, we inferred the relationships of Hydroidolina using maximum likelihood and Bayesian approaches. Both inference methods yielded well-supported phylogenetic hypotheses that largely agree with each other. Using maximum likelihood and Baysian hypothesis testing frameworks, we found that several alternate topological hypotheses proposed previously may be rejected in light of the genomic data generated for this study. Both the maximum likelihood and Bayesian topologies inferred herein consistently score well across testing frameworks, suggesting that their consensus represents the most likely phylogenetic hypothesis of Hydroidolina. This phylogenetic framework places Aplanulata as sister lineage to the remainder of Hydroidolina. This is a strong deviation from previous phylogenetic analyses that placed Capitata or Siphonophorae as sister group to the remainder of Hydroidolina. Considering that Aplanulata represents a lineage comprised of species that for the most part possess a life cycle involving a solitary polyp and free-swimming medusa stage, the phylogenetic hypotheses presented herein have potentially large implications for clarifying the evolution of life cycles, coloniality, and the division of labor in Hydrozoa as taxon sampling for phylogenetic analyses becomes more complete.

Lineage-specific variation in the evolutionary stability of coral photosymbiosis

More than half of reef-building corals (Scleractinia) participate in a nutritional symbiosis, known as photosymbiosis, with photosynthetic dinoflagellates that ranges from obligate to facultative dependence. Fitting hidden-rates models allowing among-lineage variation in the rate of trait evolution to supertree and molecular phylogenies of Scleractinia, we reconstruct the history of photosymbiosis within Scleractinia and characterize its evolutionary stability. We find that most lineages of scleractinians are extraordinarily stable for the trait, evincing no instances of loss, but that in some clades photosymbiosis is more labile, thus providing a framework for comparative studies to further our mechanistic understanding of the factors that shape the evolutionary fates of scleractinian photosymbiosis.

Going with the flow: How corals in high-flow environments can beat the heat

Coral reefs are experiencing unprecedented declines in health on a global scale leading to severe reductions in coral cover. One major cause of this decline is increasing sea surface temperature. However, conspecific colonies separated by even small spatial distances appear to show varying responses to this global stressor. One factor contributing to differential responses to heat stress is variability in the coral's micro-environment, such as the amount of water flow a coral experiences. High flow provides corals with a variety of health benefits, including heat stress mitigation. Here, we investigate how water flow affects coral gene expression and provides resilience to increasing temperatures. We examined host and photosymbiont gene expression of Acropora cf. pulchra colonies in discrete in situ flow environments during a natural bleaching event. In addition, we conducted controlled ex situ tank experiments where we exposed A. cf. pulchra to different flow regimes and acute heat stress. Notably, we observed distinct flow-driven transcriptomic signatures related to energy expenditure, growth, heterotrophy and a healthy coral host-photosymbiont relationship. We also observed disparate transcriptomic responses during bleaching recovery between the high- and low-flow sites. Additionally, corals exposed to high flow showed "frontloading" of specific heat-stress-related genes such as heat shock proteins, antioxidant enzymes, genes involved in apoptosis regulation, innate immunity and cell adhesion. We posit that frontloading is a result of increased oxidative metabolism generated by the increased water movement. Gene frontloading may at least partially explain the observation that colonies in high-flow environments show higher survival and/or faster recovery in response to bleaching events.

Revision of the genus Carybdea (Cnidaria: Cubozoa: Carybdeidae): clarifying the identity of its type species Carybdea marsupialis

While records of Carybdea marsupialis in the literature suggest a worldwide distribution of this species, the validity of some of these records has been questioned recently, as has the validity of some nominal Carybdea species. We inspected material of all known species of Carybdea from multiple locations (i.e. Spain, Algeria, Tunisia, Puerto Rico, California, Hawaii, Australia, South Africa, and Japan) using morphological and genetic tools to differentiate Carybdea species as well as understand their evolutionary relationships. We observed morphological differences between adult medusae of Mediterranean and Caribbean C. marsupialis; the most obvious differences were the structure of the phacellae, the structure of the pedalial canal knee bend, and the number and structure of the velarial canals. The characters of the adult Mediterranean specimens agree with the description provided by Claus (1878) for individuals of C. marsupialis from the Adriatic Sea (Italy); specimens from the Caribbean (Puerto Rico) agreed with the description of C. xaymacana by Conant (1897). Significant differences between both species were also observed in the newly released medusa stage. Further, we resolved a discord about the undefined polyp culture originating from Puerto Rico that was long considered Carybdea marsupialis but should be referred to as C. xaymacana. Although C. marsupialis is currently considered the only species of Cubozoa to occur in the Mediterranean, specimens collected in Algeria and Tunisia suggest that species of Alatinidae may also be present in the Mediterranean. Our investigations indicate that Carybdea spp. are more restricted in their geographical distribution than has been recognized historically. These findings confirm that Carybdea arborifera Maas, 1897 from Hawaii, Carybdea branchi, Gershwin Gibbons, 2009 from South Africa, Carybdea brevipedalia Kishinouye, 1891 from Japan, Carybdea confusa Straehler-Pohl, Matsumoto Acevedo, 2017 from California, Carybdea marsupialis Linnaeus, 1758 from the European Mediterranean Sea, Carybdea rastonii Haacke, 1886 from South Australia, and Carybdea xaymacana, Conant, 1897 from the Caribbean Sea are valid names representing distinct species, rather than synonyms. A taxonomic key for all valid species is provided, and a neotype for C. marsupialis is designated.

Phylogenomics provides a robust topology of the major cnidarian lineages and insights on the origins of key organismal traits

Background

The phylogeny of Cnidaria has been a source of debate for decades, during which nearly all-possible relationships among the major lineages have been proposed. The ecological success of Cnidaria is predicated on several fascinating organismal innovations including stinging cells, symbiosis, colonial body plans and elaborate life histories. However, understanding the origins and subsequent diversification of these traits remains difficult due to persistent uncertainty surrounding the evolutionary relationships within Cnidaria. While recent phylogenomic studies have advanced our knowledge of the cnidarian tree of life, no analysis to date has included genome-scale data for each major cnidarian lineage.

Results

Here we describe a well-supported hypothesis for cnidarian phylogeny based on phylogenomic analyses of new and existing genome-scale data that includes representatives of all cnidarian classes. Our results are robust to alternative modes of phylogenetic estimation and phylogenomic dataset construction. We show that two popular phylogenomic matrix construction pipelines yield profoundly different datasets, both in the identities and in the functional classes of the loci they include, but resolve the same topology. We then leverage our phylogenetic resolution of Cnidaria to understand the character histories of several critical organismal traits. Ancestral state reconstruction analyses based on our phylogeny establish several notable organismal transitions in the evolutionary history of Cnidaria and depict the ancestral cnidarian as a solitary, non-symbiotic polyp that lacked a medusa stage. In addition, Bayes factor tests strongly suggest that symbiosis has evolved multiple times independently across the cnidarian radiation.

Conclusions

Cnidaria have experienced more than 600 million years of independent evolution and in the process generated an array of organismal innovations. Our results add significant clarification on the cnidarian tree of life and the histories of some of these innovations. Further, we confirm the existence of Acraspeda (staurozoans plus scyphozoans and cubozoans), thus reviving an evolutionary hypothesis put forward more than a century ago.

Electronic supplementary material

The online version of this article (10.1186/s12862-018-1142-0) contains supplementary material, which is available to authorized users.

Loss of metagenesis and evolution of a parasitic life style in a group of open-ocean jellyfish

Loss or stark reduction of the free-swimming medusa or jellyfish stage is common in the cnidarian class Hydrozoa. In the hydrozoan clade Trachylina, however, many species do not possess a sessile polyp or hydroid stage. Trachylines inhabiting freshwater and coastal ecosystems (i.e., Limnomedusae) possess a metagenetic life cycle involving benthic, sessile polyp and free-swimming medusa. In contrast, the paradigm is that open ocean inhabiting, oceanic trachylines (in the orders Narcomedusae and Trachymedusae) develop from zygote to medusa via a free-swimming larva, forgoing the polyp stage. In some open-ocean trachylines, development includes a sessile stage that is an ecto- or endoparasite of other oceanic organisms. We expand the molecular-based phylogenetic hypothesis of trachylines significantly, increasing taxon and molecular marker sampling. Using this comprehensive phylogenetic hypothesis in conjunction with character state reconstructions we enhance understanding of the evolution of life cycles in trachyline hydrozoans. We find that the polyp stage was lost at least twice independently, concurrent with a transition to an oceanic life style. Further, a sessile, polypoid parasitic stage arose once, rather than twice as current classification would imply, in the open ocean inhabiting Narcomedusae. Our results also support the hypothesis that interstitial species of the order Actinulida are directly descended from direct developing, oceanic trachylines.

High Abundance of the Epibenthic Trachymedusa Ptychogastria polaris Allman, 1878 (Hydrozoa, Trachylina) in Subpolar Fjords along the West Antarctic Peninsula

Medusae can be conspicuous and abundant members of seafloor communities in deep-sea benthic boundary layers. The epibenthic trachymedusa, Ptychogastria polaris Allman, 1878 (Hydrozoa: Trachylina: Ptychogastriidae) occurs in the cold, high latitude systems of both the northern and southern hemispheres, with a circumpolar distribution in Arctic and sub-Arctic areas, and disjunct reports of a few individuals from Antarctica. In January-February 2010, during benthic megafaunal photosurveys in three subpolar fjords along the West Antarctic Peninsula (Andvord, Flandres and Barilari Bays), P. polaris was recorded in Antarctic Peninsula waters. The trachymedusa, identified from megacore-collected specimens, was a common component of the epifauna in the sediment floored basins at 436-725 m depths in Andvord and Flandres Bays, reaching densities up to 13 m-2, with mean densities in individual basins ranging from 0.06 to 4.19 m-2. These densities are 2 to 400-fold higher than previously reported for P. polaris in either the Arctic or Antarctic. This trachymedusa had an aggregated distribution, occurring frequently in Andvord Bay, but was often solitary in Flandres Bay, with a distribution not significantly different from random. Epibenthic individuals were similar in size, typically measuring 15-25 mm in bell diameter. A morphologically similar trachymedusa, presumably the same species, was also observed in the water column near the bottom in all three fjords. This benthopelagic form attained abundances of up to 7 m-2 of seafloor; however, most P. polaris (~ 80%), were observed on soft sediments. Our findings indicate that fjords provide a prime habitat for the development of dense populations of P. polaris, potentially resulting from high and varied food inputs to the fjord floors. Because P. polaris resides in the water column and at the seafloor, large P. polaris populations may contribute significantly to pelagic-benthic coupling in the WAP fjord ecosystems.

Insights into the transcriptional and translational mechanisms of linear organellar chromosomes in the box jellyfish Alatina alata (Cnidaria: Medusozoa: Cubozoa)

BACKGROUND

In most animals, the mitochondrial genome is characterized by its small size, organization into a single circular molecule, and a relative conservation of the number of encoded genes. In box jellyfish (Cubozoa, Cnidaria), the mitochondrial genome is organized into 8 linear mito-chromosomes harboring between one and 4 genes each, including 2 extra protein-coding genes: mt-polB and orf314. Such an organization challenges the traditional view of mitochondrial DNA (mtDNA) expression in animals. In this study, we investigate the pattern of mitochondrial gene expression in the box jellyfish Alatina alata, as well as several key nuclear-encoded molecular pathways involved in the processing of mitochondrial gene transcription.

RESULTS

Read coverage of DNA-seq data is relatively uniform for all 8 mito-chromosomes, suggesting that each mito-chromosome is present in equimolar proportion in the mitochondrion. Comparison of DNA and RNA-seq based assemblies indicates that mito-chromosomes are transcribed into individual transcripts in which the beginning and ending are highly conserved. Expression levels for mt-polB and orf314 are similar to those of other mitochondrial-encoded genes, which provides further evidence for them having functional roles in the mitochondrion. Survey of the transcriptome suggests recognition of the mitochondrial tRNA-Met by the cytoplasmic aminoacyl-tRNA synthetase counterpart and C-to-U editing of the cytoplasmic tRNA-Trp after import into the mitochondrion. Moreover, several mitochondrial ribosomal proteins appear to be lost.

CONCLUSIONS

This study represents the first survey of mitochondrial gene expression of the linear multi-chromosomal mtDNA in box jellyfish (Cubozoa). Future exploration of small RNAs and the proteome of the mitochondrion will test the hypotheses presented herein.

Phylogenetic analysis of higher-level relationships within Hydroidolina (Cnidaria: Hydrozoa) using mitochondrial genome data and insight into their mitochondrial transcription

Hydrozoans display the most morphological diversity within the phylum Cnidaria. While recent molecular studies have provided some insights into their evolutionary history, sister group relationships remain mostly unresolved, particularly at mid-taxonomic levels. Specifically, within Hydroidolina, the most speciose hydrozoan subclass, the relationships and sometimes integrity of orders are highly unsettled. Here we obtained the near complete mitochondrial sequence of twenty-six hydroidolinan hydrozoan species from a range of sources (DNA and RNA-seq data, long-range PCR). Our analyses confirm previous inference of the evolution of mtDNA in Hydrozoa while introducing a novel genome organization. Using RNA-seq data, we propose a mechanism for the expression of mitochondrial mRNA in Hydroidolina that can be extrapolated to the other medusozoan taxa. Phylogenetic analyses using the full set of mitochondrial gene sequences provide some insights into the order-level relationships within Hydroidolina, including siphonophores as the first diverging clade, a well-supported clade comprised of Leptothecata-Filifera III-IV, and a second clade comprised of Aplanulata-Capitata s.s.-Filifera I-II. Finally, we describe our relatively inexpensive and accessible multiplexing strategy to sequence long-range PCR amplicons that can be adapted to most high-throughput sequencing platforms.

Evolutionary relatedness does not predict competition and co-occurrence in natural or experimental communities of green algae

The competition-relatedness hypothesis (CRH) predicts that the strength of competition is the strongest among closely related species and decreases as species become less related. This hypothesis is based on the assumption that common ancestry causes close relatives to share biological traits that lead to greater ecological similarity. Although intuitively appealing, the extent to which phylogeny can predict competition and co-occurrence among species has only recently been rigorously tested, with mixed results. When studies have failed to support the CRH, critics have pointed out at least three limitations: (i) the use of data poor phylogenies that provide inaccurate estimates of species relatedness, (ii) the use of inappropriate statistical models that fail to detect relationships between relatedness and species interactions amidst nonlinearities and heteroskedastic variances, and (iii) overly simplified laboratory conditions that fail to allow eco-evolutionary relationships to emerge. Here, we address these limitations and find they do not explain why evolutionary relatedness fails to predict the strength of species interactions or probabilities of coexistence among freshwater green algae. First, we construct a new data-rich, transcriptome-based phylogeny of common freshwater green algae that are commonly cultured and used for laboratory experiments. Using this new phylogeny, we re-analyse ecological data from three previously published laboratory experiments. After accounting for the possibility of nonlinearities and heterogeneity of variances across levels of relatedness, we find no relationship between phylogenetic distance and ecological traits. In addition, we show that communities of North American green algae are randomly composed with respect to their evolutionary relationships in 99% of 1077 lakes spanning the continental United States. Together, these analyses result in one of the most comprehensive case studies of how evolutionary history influences species interactions and community assembly in both natural and experimental systems. Our results challenge the generality of the CRH and suggest it may be time to re-evaluate the validity and assumptions of this hypothesis.

Complex Ancestries of Isoprenoid Synthesis in Dinoflagellates

Isoprenoid metabolism occupies a central position in the anabolic metabolism of all living cells. In plastid-bearing organisms, two pathways may be present for de novo isoprenoid synthesis, the cytosolic mevalonate pathway (MVA) and nuclear-encoded, plastid-targeted nonmevalonate pathway (DOXP). Using transcriptomic data we find that dinoflagellates apparently make exclusive use of the DOXP pathway. Using phylogenetic analyses of all DOXP genes we inferred the evolutionary origins of DOXP genes in dinoflagellates. Plastid replacements led to a DOXP pathway of multiple evolutionary origins. Dinoflagellates commonly referred to as dinotoms due to their relatively recent acquisition of a diatom plastid, express two completely redundant DOXP pathways. Dinoflagellates with a tertiary plastid of haptophyte origin, by contrast, express a hybrid pathway of dual evolutionary origin. Here, changes in the targeting motif of signal/transit peptide likely allow for targeting the new plastid by the proteins of core isoprenoid metabolism proteins. Parasitic dinoflagellates of the Amoebophyra species complex appear to have lost the DOXP pathway, suggesting that they may rely on their host for sterol synthesis.

Metatranscriptome profiling of a harmful algal bloom

Metagenomic methods provide a powerful means to investigate complex ecological phenomena. Developed originally for study of Bacteria and Archaea, the application of these methods to eukaryotic microorganisms is yet to be fully realized. Most prior environmental molecular studies of eukaryotes have relied heavily on PCR amplification with eukaryote-specific primers. Here we apply high throughput short-read sequencing of poly-A selected RNA to capture the metatranscriptome of an estuarine dinoflagellate bloom. To validate the metatranscriptome assembly process we simulated metatranscriptomic datasets using short-read sequencing data from clonal cultures of four algae of varying phylogenetic distance. We find that the proportion of chimeric transcripts reconstructed from community transcriptome sequencing is low, suggesting that metatranscriptomic sequencing can be used to accurately reconstruct the transcripts expressed by bloom-forming communities of eukaryotes. To further validate the bloom metatransciptome assembly we compared it to a transcriptomic assembly from a cultured, clonal isolate of the dominant bloom-causing alga and found that the two assemblies are highly similar. Eukaryote-wide phylogenetic analyses reveal the taxonomic composition of the bloom community, which is comprised of several dinoflagellates, ciliates, animals, and fungi. The assembled metatranscriptome reveals the functional genomic composition of a metabolically active community. Highlighting the potential power of these methods, we found that relative transcript abundance patterns suggest that the dominant dinoflagellate might be expressing toxin biosynthesis related genes at a higher level in the presence of competitors, predators and prey compared to it growing in monoculture.

Redescription of Alatina alata (Reynaud, 1830) (Cnidaria: Cubozoa) from Bonaire, Dutch Caribbean

Here we establish a neotype for Alatina alata (Reynaud, 1830) from the Dutch Caribbean island of Bonaire. The species was originally described one hundred and eighty three years ago as Carybdea alata in La Centurie Zoologique-a monograph published by René Primevère Lesson during the age of worldwide scientific exploration. While monitoring monthly reproductive swarms of A. alata medusae in Bonaire, we documented the ecology and sexual reproduction of this cubozoan species. Examination of forty six A. alata specimens and additional archived multimedia material in the collections of the National Museum of Natural History, Washington, DC revealed that A. alata is found at depths ranging from surface waters to 675 m. Additional studies have reported it at depths of up to 1607 m in the tropical and subtropical Atlantic Ocean. Herein, we resolve the taxonomic confusion long associated with A. alata due to a lack of detail in the original description and conflicting statements in the scientific literature. A new cubozoan character, the velarial lappet, is described for this taxon. The complete description provided here serves to stabilize the taxonomy of the second oldest box jellyfish species, and provide a thorough redescription of the species.

Evolution of linear mitochondrial genomes in medusozoan cnidarians

In nearly all animals, mitochondrial DNA (mtDNA) consists of a single circular molecule that encodes several subunits of the protein complexes involved in oxidative phosphorylation as well as part of the machinery for their expression. By contrast, mtDNA in species belonging to Medusozoa (one of the two major lineages in the phylum Cnidaria) comprises one to several linear molecules. Many questions remain on the ubiquity of linear mtDNA in medusozoans and the mechanisms responsible for its evolution, replication, and transcription. To address some of these questions, we determined the sequences of nearly complete linear mtDNA from 24 species representing all four medusozoan classes: Cubozoa, Hydrozoa, Scyphozoa, and Staurozoa. All newly determined medusozoan mitochondrial genomes harbor the 17 genes typical for cnidarians and map as linear molecules with a high degree of gene order conservation relative to the anthozoans. In addition, two open reading frames (ORFs), polB and ORF314, are identified in cubozoan, schyphozoan, staurozoan, and trachyline hydrozoan mtDNA. polB belongs to the B-type DNA polymerase gene family, while the product of ORF314 may act as a terminal protein that binds telomeres. We posit that these two ORFs are remnants of a linear plasmid that invaded the mitochondrial genomes of the last common ancestor of Medusozoa and are responsible for its linearity. Hydroidolinan hydrozoans have lost the two ORFs and instead have duplicated cox1 at each end of their mitochondrial chromosome(s). Fragmentation of mtDNA occurred independently in Cubozoa and Hydridae (Hydrozoa, Hydroidolina). Our broad sampling allows us to reconstruct the evolutionary history of linear mtDNA in medusozoans.

Evolution of box jellyfish (Cnidaria: Cubozoa), a group of highly toxic invertebrates

Cubozoa (Cnidaria: Medusozoa) represents a small clade of approximately 50 described species, some of which cause serious human envenomations. Our understanding of the evolutionary history of Cubozoa has been limited by the lack of a sound phylogenetic hypothesis for the group. Here, we present a comprehensive cubozoan phylogeny based on ribosomal genes coding for near-complete nuclear 18S (small subunit) and 28S (large subunit) and partial mitochondrial 16S. We discuss the implications of this phylogeny for our understanding of cubozoan venom evolution, biogeography and life-history evolution. Our phylogenetic hypothesis suggests that: (i) the last common ancestor of Carybdeida probably possessed the mechanism(s) underlying Irukandji syndrome, (ii) deep divergences between Atlantic and Indo-Pacific clades may be explained by ancient vicariant events, and (iii) sexual dimorphism evolved a single time in concert with complex sexual behaviour. Furthermore, several cubozoan taxa are either para- or polyphyletic, and we address some of these taxonomic issues by designating a new family, Carukiidae, a new genus, Copula, and by redefining the families Tamoyidae and Tripedaliidae. Lastly, cubozoan species identities have long been misunderstood and the data presented here support many of the recent scientific descriptions of cubozoan species. However, the results of a phylogeographic analysis of Alatina moseri from Hawai'i and Alatina mordens from Australia indicate that these two nominal species represent a single species that has maintained metapopulation cohesion by natural or anthropogenic dispersal.

Solution to the phylogenetic enigma of Tetraplatia, a worm-shaped cnidarian

Tetraplatia is a genus containing two species of pelagic cnidarians of curious morphology. Their vermiform shape and four swimming flaps are difficult to relate to the features of other cnidarians, thus obscuring their phylogenetic affinities. Since their discovery in the mid-1800s, a number of prominent cnidarian workers have weighed in on this conundrum, some arguing that they are aberrant hydrozoans and others concluding that they are unusual scyphozoans. Current taxonomic practice conforms to the latter view. However, data presented here from the large and small subunits of the nuclear ribosome leave little doubt that Tetraplatia is in fact a hydrozoan genus. Indeed, its precise phylogenetic position is within Narcomedusae, as some authors had previously deduced based on structural characters. The distinctive body plan of Tetraplatia is remarkable because it appears to have a recent origin, in contrast to the prevailing pattern of metazoan history.