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This document provides information on the discovery of a female squid in the deep sea carrying large eggs. The squid was found in the Gulf of California at a depth of 2566m and is believed to be from the Gonatidae family. The size of the eggs is larger than what is typically found in other squid species. The document also discusses the reproductive strategies of squids and the potential advantages of producing large eggs. Overall, this research offers valuable insights into the reproductive biology of deep-sea cephalopods. Additionally, the document explores the development and characteristics of deep-sea cephalopod eggs, with a focus on giant gonatid squid eggs. The stable and predictable environmental conditions in the deep water column allow for fewer, larger eggs and advanced hatchlings. However, the cold waters of the deep sea result in long development times for these eggs. The document also highlights the limited knowledge about the development of large cephalopod eggs at low temperatures and the possibility of extensive multiyear brooding of giant eggs when predation pressure is low. The authors suggest that further exploration of the deep water column is necessary to gain a better understanding of the biology of these mysterious oceanic creatures. [Extracted from the article]

Gelatinous zooplankton are increasingly recognized as key components of pelagic ecosystems, and there have been many recent insights into their ecology and roles in food webs. To examine the trophic ecology of siphonophores (Cnidaria, Hydrozoa), we used bulk (carbon and nitrogen) and compound‐specific (nitrogen) isotope analysis of individual amino acids (CSIA‐AA). We collected samples of 15 siphonophore genera using blue‐water diving, midwater trawls, and remotely operated vehicles in the California Current Ecosystem, from 0 to 3000 m. We examined the basal resources supporting siphonophore nutrition by comparing their isotope values to those of contemporaneously collected sinking and suspended particles (0–500 m). Stable isotope values provided novel insights into siphonophore trophic ecology, indicating considerable niche overlap between calycophoran and physonect siphonophores. However, there were clear relationships between siphonophore trophic positions and phylogeny, and the highest siphonophore trophic positions were restricted to physonects. Bulk and source amino acid nitrogen isotope (δ15N) values of siphonophores and suspended particles all increased significantly with increasing collection depth. In contrast, siphonophore trophic positions did not increase with increasing collection depth. This suggests that microbially reworked, deep, suspended particles with higher δ15N values than surface particles, likely indirectly support deep‐pelagic siphonophores. Siphonophores feed upon a range of prey, from small crustaceans to fishes, and we show that their measured trophic positions reflect this trophic diversity, spanning 1.5 trophic levels (range 2.4–4.0). Further, we demonstrate that CSIA‐AA can elucidate the feeding ecology of gelatinous zooplankton and distinguish between nutritional resources across vertical habitats. These findings improve our understanding of the functional roles of gelatinous zooplankton and energy flow through pelagic food webs. [ABSTRACT FROM AUTHOR]

Bioluminescence is the production of visible light by an organism. This phenomenon is particularly widespread in marine animals, especially in the deep sea. While the luminescent status of numerous marine animals has been recently clarified thanks to advancements in deep-sea exploration technologies and phylogenetics, that of others has become more obscure due to dramatic changes in systematics (themselves triggered by molecular phylogenies). Here, we combined a comprehensive literature review with unpublished data to establish a catalogue of marine luminescent animals. Inventoried animals were identified to species level in over 97% of the cases and were associated with a score reflecting the robustness of their luminescence record. While luminescence capability has been established in 695 genera of marine animals, luminescence reports from 99 additional genera need further confirmation. Altogether, these luminescent and potentially luminescent genera encompass 9405 species, of which 2781 are luminescent, 136 are potentially luminescent (e.g., suggested luminescence in those species needs further confirmation), 99 are non-luminescent, and 6389 have an unknown luminescent status. Comparative analyses reveal new insights into the occurrence of luminescence among marine animal groups and highlight promising research areas. This work will provide a solid foundation for future studies related to the field of marine bioluminescence. [ABSTRACT FROM AUTHOR]

Siphonophores (Cnidaria: Hydrozoa) are abundant predators found throughout the ocean and are important constituents of the global zooplankton community. They range in length from a few centimeters to tens of meters. They are gelatinous, fragile, and difficult to collect, so many aspects of the biology of these roughly 200 species remain poorly understood. To survey siphonophore genome diversity, we performed Illumina sequencing of 32 species sampled broadly across the phylogeny. Sequencing depth was sufficient to estimate nuclear genome size from k -mer spectra in six specimens, ranging from 0.7 to 2.3 Gb, with heterozygosity estimates between 0.69% and 2.32%. Incremental k -mer counting indicates k -mer peaks can be absent with nearly 20× read coverage, suggesting minimum genome sizes range from 1.4 to 5.6 Gb in the 25 samples without peaks in the k -mer spectra. This work confirms most siphonophore nuclear genomes are large relative to the genomes of other cnidarians, but also identifies several with reduced size that are tractable targets for future siphonophore nuclear genome assembly projects. We also assembled complete mitochondrial genomes for 33 specimens from these new data, indicating a conserved gene order shared among nonsiphonophore hydrozoans, Cystonectae, and some Physonectae, revealing the ancestral mitochondrial gene order of siphonophores. Our results also suggest extensive rearrangement of mitochondrial genomes within other Physonectae and in Calycophorae. Though siphonophores comprise a small fraction of cnidarian species, this survey greatly expands our understanding of cnidarian genome diversity. This study further illustrates both the importance of deep phylogenetic sampling and the utility of k -mer–based genome skimming in understanding the genomic diversity of a clade. [ABSTRACT FROM AUTHOR]

The study of evolution and speciation in non-model systems provides us with an opportunity to expand our understanding of biodiversity in nature. Connectivity studies generally focus on species with obvious boundaries to gene flow, but in open-ocean environments, such boundaries are difficult to identify. Due to the lack of obvious boundaries, speciation and population subdivision in the pelagic environment remain largely unexplained. Comb jellies (Phylum Ctenophora) are mostly planktonic gelatinous invertebrates, many of which are considered to have freely interbreeding distributionsworldwide. It is thought that the lobate ctenophore Bolinopsis infundibulum is distributed throughout cooler northern latitudes and B. vitrea warmer. Here, we examined the global population structure for species of Bolinopsis with genetic and morphological data. We found distinct evolutionary patterns within the genus, where B. infundibulum had a broad distribution from northern Pacific to Atlantic waters despite many physical barriers, while other species were geographically segregated despite few barriers. Divergent patterns of speciation within the genus suggest that oceanic currents, sea-level, and geological changes over time can act as either barriers or aids to dispersal in the pelagic environment. Further, we used population genomic data to examine evolution in the open ocean of a distinct lineage of Bolinopsis ctenophores from the North Eastern Pacific. Genetic information and morphological observations validated this as a separate species, Bolinopsis microptera, which was previously described but has recently been called B. infundibulum. We found that populations of B. microptera from California were in cytonuclear discordance, which indicates a secondary contact zone for previously isolated populations. Discordance at this scale is rare, especially in a continuous setting. [ABSTRACT FROM AUTHOR]

Siphonophores (Cnidaria: Hydrozoa) are abundant and diverse gelatinous predators in open-ocean ecosystems. Due to limited access to the midwater, little is known about the diets of most deep-dwelling gelatinous species, which constrains our understanding of food-web structure and nutrient flow in these vast ecosystems. Visual gut-content methods can rarely identify soft-bodied rapidly-digested prey, while observations from submersibles often overlook small prey items. These methods have been differentially applied to shallow and deep siphonophore taxa, confounding habitat and methodological biases. DNA metabarcoding can be used to assess both shallow and deep species' diets under a common methodological framework, since it can detect both small and gelatinous prey. We (1) further characterized the diets of open-ocean siphonophores using DNA metabarcoding, (2) compared the prey detected by visual and molecular methods to evaluate their technical biases, and (3) evaluated tentacle-based predictions of diet. To do this, we performed DNA metabarcoding analyses on the gut contents of 39 siphonophore species across depths to describe their diets, using six barcode regions along the 18S gene. Taxonomic identifications were assigned using public databases combined with local zooplankton sequences. We identified 55 unique prey items, including crustaceans, gelatinous animals, and fish across 47 siphonophore specimens in 24 species. We reported 29 novel predator-prey interactions, among them the first insights into the diets of nine siphonophore species, many of which were congruent with the dietary predictions based on tentilla morphology. Our analyses detected both small and gelatinous prey taxa underrepresented by visual methods in species from both shallow and deep habitats, indicating that siphonophores play similar trophic roles across depth habitats. We also reveal hidden links between siphonophores and filter-feeders near the base of the food web. This study expands our understanding of the ecological roles of siphonophores in the open ocean, their trophic roles within the 'jelly-web', and the importance of their diversity for nutrient flow and ecosystem functioning. Understanding these inconspicuous yet ubiquitous predator-prey interactions is critical to predict the impacts of climate change, overfishing, and conservation policies on oceanic ecosystems. [ABSTRACT FROM AUTHOR]

Siphonophores are a clade of understudied colonial hydrozoans (Cnidaria) that are abundant predators in oceanic ecosystems, with species present across the water column. We (1) synthesize current knowledge about siphonophore trophic ecology and predator–prey interactions, (2) analyze siphonophore‐prey networks to compare food‐web topology between shallow and deep‐pelagic habitats, (3) discuss contemporary techniques that will allow for more integrative studies of siphonophore feeding ecology, and (4) and present a vision for future research. We found distinct diet differences between siphonophore species, indicating that siphonophores occupy multiple trophic niches and prey on a diversity of taxa. Our results suggest that siphonophore‐prey networks may be more specialized in the deep pelagic than in the epipelagic, suggesting potential trophic differences between depth habitats. This study highlights niche differentiation and trophic complexity among siphonophores and demonstrates the importance of gelatinous zooplankton in shaping food web structure in pelagic ecosystems. [ABSTRACT FROM AUTHOR]

The mitochondrial gene cytochrome‐c‐oxidase subunit 1 (COI) is useful in many taxa for phylogenetics, population genetics, metabarcoding, and rapid species identifications. However, the phylum Ctenophora (comb jellies) has historically been difficult to study due to divergent mitochondrial sequences and the corresponding inability to amplify COI with degenerate and standard COI "barcoding" primers. As a result, there are very few COI sequences available for ctenophores, despite over 200 described species in the phylum. Here, we designed new primers and amplified the COI fragment from members of all major groups of ctenophores, including many undescribed species. Phylogenetic analyses of the resulting COI sequences revealed high diversity within many groups that was not evident from more conserved 18S rDNA sequences, in particular among the Lobata (Ctenophora; Tentaculata; Lobata). The COI phylogenetic results also revealed unexpected community structure within the genus Bolinopsis, suggested new species within the genus Bathocyroe, and supported the ecological and morphological differences of some species such as Lampocteis cruentiventer and similar undescribed lobates (Lampocteis sp. "V" stratified by depth, and "A" differentiated by colour). The newly designed primers reported herein provide important tools to enable researchers to illuminate the diversity of ctenophores worldwide via quick molecular identifications, improve the ability to analyse environmental DNA by improving reference libraries and amplifications, and enable a new breadth of population genetic studies. [ABSTRACT FROM AUTHOR]

We consider the opportunities and challenges associated with organizing a conference online, using a case study of a medium-sized (approx. 400 participants) international conference held virtually in August 2020. In addition, we present quantifiable evidence of the participants' experience using the results from an online post-conference questionnaire. Although the virtual meeting was not able to replicate the in-person experience in some aspects (e.g. less engagement between participants) the overwhelming majority of respondents found the meeting an enjoyable experience and would join similar events again. Notably, there was a strong desire for future in-person meetings to have at least some online component. Online attendance by lower-income researchers was higher compared with a past, similar-themed in-person meeting held in a high-income nation, but comparable to one held in an upper-middle-income nation. This indicates that online conferences are not a panacea for diversity and inclusivity, and that holding in-person meetings in developing economies can be at least as effective. Given that it is now relatively easy to stream contents of meetings online using low-cost methods, there are clear benefits in making all presented content accessible online, as well as organizing online networking events for those unable to attend in person. [ABSTRACT FROM AUTHOR]

Milky seas are a rare form of marine bioluminescence where the nocturnal ocean surface produces a widespread, uniform and steady whitish glow. Mariners have compared their appearance to a daylit snowfield that extends to all horizons. Encountered most often in remote waters of the northwest Indian Ocean and the Maritime Continent, milky seas have eluded rigorous scientific inquiry, and thus little is known about their composition, formation mechanism, and role within the marine ecosystem. The Day/Night Band (DNB), a new-generation spaceborne low-light imager, holds potential to detect milky seas, but the capability has yet to be demonstrated. Here, we show initial examples of DNB-detected milky seas based on a multi-year (2012–2021) search. The massive bodies of glowing ocean, sometimes exceeding 100,000 km2 in size, persist for days to weeks, drift within doldrums amidst the prevailing sea surface currents, and align with narrow ranges of sea surface temperature and biomass in a way that suggests water mass isolation. These findings show how spaceborne assets can now help guide research vessels toward active milky seas to learn more about them. [ABSTRACT FROM AUTHOR]

Predator specialization has often been considered an evolutionary "dead end" due to the constraints associated with the evolution of morphological and functional optimizations throughout the organism. However, in some predators, these changes are localized in separate structures dedicated to prey capture. One of the most extreme cases of this modularity can be observed in siphonophores, a clade of pelagic colonial cnidarians that use tentilla (tentacle side branches armedwith nematocysts) exclusively for prey capture. Herewe study how siphonophore specialists and generalists evolve, and what morphological changes are associated with these transitions. To answer these questions, we: a) Measured 29 morphological characters of tentacles from 45 siphonophore species, b) mapped these data to a phylogenetic tree, and c) analyzed the evolutionary associations between morphological characters and prey-type data from the literature. Instead of a dead end, we found that siphonophore specialists can evolve into generalists, and that specialists on one prey type have directly evolved into specialists on other prey types. Our results show that siphonophore tentillum morphology has strong evolutionary associations with prey type, and suggest that shifts between prey types are linked to shifts in the morphology, mode of evolution, and evolutionary correlations of tentilla and their nematocysts. The evolutionary history of siphonophore specialization helps build a broader perspective on predatory niche diversification via morphological innovation and evolution. These findings contribute to understanding how specialization and morphological evolution have shaped present-day food webs. [ABSTRACT FROM AUTHOR]

The origin of novel traits can promote expansion into new niches and drive speciation. Ctenophores (comb jellies) are unified by their possession of a novel cell type: the colloblast, an adhesive cell found only in the tentacles. Although colloblast-laden tentacles are fundamental for prey capture among ctenophores, some species have tentacles lacking colloblasts and others have lost their tentacles completely. We used transcriptomes from 36 ctenophore species to identify gene losses that occurred specifically in lineages lacking colloblasts and tentacles. We cross-referenced these colloblast- and tentacle-specific candidate genes with temporal RNA-Seq during embryogenesis in Mnemiopsis leidyi and found that both sets of candidates are preferentially expressed during tentacle morphogenesis. We also demonstrate significant upregulation of candidates from both data sets in the tentacle bulb of adults. Both sets of candidates were enriched for an N-terminal signal peptide and protein domains associated with secretion; among tentacle candidates we also identified orthologs of cnidarian toxin proteins, presenting tantalizing evidence that ctenophore tentacles may secrete toxins along with their adhesive. Finally, using cell lineage tracing, we demonstrate that colloblasts and neurons share a common progenitor, suggesting the evolution of colloblasts involved co-option of a neurosecretory gene regulatory network. Together these data offer an initial glimpse into the genetic architecture underlying ctenophore cell-type diversity. [ABSTRACT FROM AUTHOR]

Food web linkages, or the feeding relationships between species inhabiting a shared ecosystem, are an ecological lens through which ecosystem structure and function can be assessed, and thus are fundamental to informing sustainable resource management. Empirical feeding datasets have traditionally been painstakingly generated from stomach content analysis, direct observations and from biochemical trophic markers (stable isotopes, fatty acids, molecular tools). Each approach carries inherent biases and limitations, as well as advantages. Here, using 27 years (1991-2016) of in situ feeding observations collected by remotely operated vehicles (ROVs), we quantitatively characterize the deep pelagic food web of central California within the California Current, complementing existing studies of diet and trophic interactions with a unique perspective. Seven hundred and fortythree independent feeding events were observed with ROVs from near-surface waters down to depths approaching 4000 m, involving an assemblage of 84 different predators and 82 different prey types, for a total of 242 unique feeding relationships. The greatest diversity of prey was consumed by narcomedusae, followed by physonect siphonophores, ctenophores and cephalopods. We highlight key interactions within the poorly understood 'jelly web', showing the importance of medusae, ctenophores and siphonophores as key predators, whose ecological significance is comparable to large fish and squid species within the central California deep pelagic food web. Gelatinous predators are often thought to comprise relatively inefficient trophic pathways within marine communities, but we build upon previous findings to document their substantial and integral roles in deep pelagic food webs. [ABSTRACT FROM AUTHOR]

Since its founding, the Monterey Bay Aquarium Research Institute (MBARI) has pioneered unique capabilities for accessing the deep ocean and its inhabitants through focused peer relationships between scientists and engineers. This focus has enabled breakthroughs in our understanding of life in the sea, leading to fundamental advances in describing the biology and the ecology of open-ocean and deep-sea animals. David Packard's founding principle was the application of technological advances to studying the deep ocean, in part because he recognized the critical importance of this habitat in a global context. Among other fields, MBARI's science has benefited from applying novel methodologies in molecular biology and genetics, imaging systems, and in situ observations. These technologies have allowed MBARI's bioluminescence and biodiversity laboratory and worldwide collaborators to address centuries-old questions related to the biodiversity, behavior, and bio-optical properties of organisms living in the water column, from the surface into the deep sea. Many of the most interesting of these phenomena are in the midwater domain--the vast region of ocean between the sunlit surface waters and the deep seafloor. [ABSTRACT FROM AUTHOR]

Jellyfish have become a topic of interest of many marine scientists and managers alike due to their conspicuous socio-economic and environmental impacts. However, our knowledge about their "everyday life" remains limited. While electronic tags (transmitters and loggers) have been extensively used to study marine vertebrates for the past 50 years, tagging is still in its infancy for marine invertebrates and jellyfish in particular. Progress has been hampered by the difficulty and limited knowledge of attaching tags to soft-bodied animals. We argue that there is huge potential to use tagging to gather basic information on the ecology and behaviour of these species. Here, we give an overview of what has been learned so far by deploying tags on jellyfish, and why tagging is an appropriate method to study their behaviour and ecology. We then describe different tagging techniques, their advantages, disadvantages and challenges, and the steps to ensure future successful jellyfish tagging studies. [ABSTRACT FROM AUTHOR]

Background: Fluorescent proteins are optically active proteins found across many clades in metazoans. A fluorescent protein was recently identified in a ctenophore, but this has been suggested to derive from a cnidarian, raising again the question of origins of this group of proteins. Results: Through analysis of transcriptome data from 30 ctenophores, we identified a member of an orthologous group of proteins similar to fluorescent proteins in each of them, as well as in the genome of Mnemiopsis leidyi. These orthologs lack canonical residues involved in chromophore formation, suggesting another function. Conclusions: The phylogenetic position of the ctenophore protein family among fluorescent proteins suggests that this gene was present in the common ancestor of all ctenophores and that the fluorescent protein previously found in a ctenophore actually derives from a siphonophore. [ABSTRACT FROM AUTHOR]

Cnidaria, the sister group to Bilateria, is a highly diverse group of animals in terms of morphology, lifecycles, ecology, and development. How this diversity originated and evolved is not well understood because phylogenetic relationships among major cnidarian lineages are unclear, and recent studies present contrasting phylogenetic hypotheses. Here, we use transcriptome data from 15 newly-sequenced species in combination with 26 publicly available genomes and transcriptomes to assess phylogenetic relationships among major cnidarian lineages. Phylogenetic analyses using different partition schemes and models of molecular evolution, as well as topology tests for alternative phylogenetic relationships, support the monophyly of Medusozoa, Anthozoa, Octocorallia, Hydrozoa, and a clade consisting of Staurozoa, Cubozoa, and Scyphozoa. Support for the monophyly of Hexacorallia is weak due to the equivocal position of Ceriantharia. Taken together, these results further resolve deep cnidarian relationships, largely support traditional phylogenetic views on relationships, and provide a historical framework for studying the evolutionary processes involved in one of the most ancient animal radiations. [ABSTRACT FROM AUTHOR]

The biosynthesis of the luciferin coelenterazine has remained a mystery for decades. While not all organisms that use coelenterazine appear to make it themselves, it is thought that ctenophores are a likely producer. Here we analyze the transcriptome data of 24 species of ctenophores, two of which have published genomes. The natural precursors of coelenterazine have been shown to be the amino acids L-tyrosine and L-phenylalanine, with the most likely biosynthetic pathway involving cyclization and further modification of the tripeptide Phe-Tyr-Tyr (“FYY”). Therefore, we searched the ctenophore transcriptome data for genes with the short peptide “FYY” as part of their coding sequence. We recovered a group of candidate genes for coelenterazine biosynthesis in the luminous species which encode a set of highly conserved non-heme iron oxidases similar to isopenicillin-N-synthase. These genes were absent in the transcriptomes and genome of the two non-luminous species. Pairwise identities and substitution rates reveal an unusually high degree of identity even between the most unrelated species. Additionally, two related groups of non-heme iron oxidases were found across all ctenophores, including those which are non-luminous, arguing against the involvement of these two gene groups in luminescence. Important residues for iron-binding are conserved across all proteins in the three groups, suggesting this function is still present. Given the known functions of other members of this protein superfamily are involved in heterocycle formation, we consider these genes to be top candidates for laboratory characterization or gene knockouts in the investigation of coelenterazine biosynthesis. [ABSTRACT FROM AUTHOR]

Background: Siphonophores (Hydrozoa) have unparalleled colony-level complexity, precision of colony organization, and functional specialization between zooids (i.e., the units that make up colonies). Previous work has shown that, unlike other colonial animals, most growth in siphonophores is restricted to one or two well-defined growth zones that are the sites of both elongation and zooid budding. It remained unknown, however, how this unique colony growth and development is realized at the cellular level. Results: To understand the colony-level growth and development of siphonophores at the cellular level, we characterize the distribution of proliferating cells and interstitial stem cells (i-cells) in the siphonophore Nanomia bijuga. Within the colony, we find evidence that i-cells are present at the tip of the horn, the structure within the growth zone that gives rise to new zooids. Co-localized gene expression of vasa-1, pl10, piwi, nanos-1, and nanos-2 suggests that i-cells persist in the youngest zooid buds and that i-cells become progressively restricted to specific regions within the zooids until they are mostly absent from the oldest zooids. The examined genes remain expressed in gametogenic regions. No evidence for i-cells is found in the stem between maturing zooids. Domains of high cell proliferation include regions where the examined genes are expressed, but also include some areas in which the examined genes were not expressed such as the stem within the growth zones. Cell proliferation in regions devoid of vasa-1, pl10, piwi, nanos-1, and nanos-2 expression indicates the presence of mitotically active epithelial cell lineages and, potentially, progenitor cell populations. Conclusions: We provide the first evidence for i-cells in a siphonophore. Our findings suggest maintenance of i-cell populations at the sites of growth zones and that these sites are the main source of i-cells. This restriction of stem cells to particular regions in the colony, in combination with localized budding and spatial patterning during pro-bud subdivision, may play a major role in facilitating the precision of siphonophore growth. Spatially restricted maintenance of i-cells in mature zooids and absence of i-cells along the stem may explain the reduced developmental plasticity in older parts of the colony. [ABSTRACT FROM AUTHOR]

Tomopteris is a cosmopolitan genus of polychaetes. Many species produce yellow luminescence in the parapodia when stimulated. Yellow bioluminescence is rare in the ocean, and the components of this luminescent reaction have not been identified. Only a brief description, half a century ago, noted fluorescence in the parapodia with a remarkably similar spectrum to the bioluminescence, which suggested that it may be the luciferin or terminal light-emitter. Here, we report the isolation of the fluorescent yellow-orange pigment found in the luminous exudate and in the body of the animals. Liquid chromatography-mass spectrometry revealed the mass to be 270 m/z with a molecular formula of C15H10O5, which ultimately was shown to be aloe-emodin, an anthraquinone previously found in plants. We speculate that aloe-emodin could be a factor for resonant-energy transfer or the oxyluciferin for Tomopteris bioluminescence. [ABSTRACT FROM AUTHOR]

: We describe a set of best practices for scientific software development, based on research and experience, that will improve scientists' productivity and the reliability of their software. [ABSTRACT FROM AUTHOR]

A correction is presented to the article "Moving conferences online: lessons learned from an international virtual meeting."

Simple Summary: This paper describes an unusually large and distinctive deep-sea red medusa with coiled tentacles in the family Atollidae. This family is monogeneric with ten presently accepted species in the genus Atolla. The new medusa is molecularly and morphologically distinct from the five species that we have been able to sample and morphologically distinct from all ten previously described species. We have also observed and collected samples from another two potentially new species. The ocean provides over 98% of the available living space on our planet and we still do not know who is living there or how they interact with one another. This paper adds to the increasing number of new deep-sea species being described as we increase our exploration, and as advances in undersea technology and genetic sequencing become more available. We have observed and collected unusual specimens of what we recognize as undescribed types of the genus Atolla over the past 15 years. Of these, there appear to be three potentially different types. One of these has now been genetically sequenced and compared both morphologically and molecularly with five other Atolla species that have been found in the eastern Pacific. This new variant is so morphologically distinct from other previously described Atolla species that we believe it can be described as a new species, Atolla reynoldsi sp. nov. This species along with two additional types may comprise a new genus. It is also clear that a more accurate and diagnostic morphological key for the genus Atolla needs to be developed. This paper will also provide some potential starting points for a new key to the genus. [ABSTRACT FROM AUTHOR]

Background: The lack of genomic resources can present challenges for studies of non-model organisms. Transcriptome sequencing offers an attractive method to gather information about genes and gene expression without the need for a reference genome. However, it is unclear what sequencing depth is adequate to assemble the transcriptome de novo for these purposes. Results: We assembled transcriptomes of animals from six different phyla (Annelids, Arthropods, Chordates, Cnidarians, Ctenophores, and Molluscs) at regular increments of reads using Velvet/Oases and Trinity to determine how read count affects the assembly. This included an assembly of mouse heart reads because we could compare those against the reference genome that is available. We found qualitative differences in the assemblies of whole-animals versus tissues. With increasing reads, whole-animal assemblies show rapid increase of transcripts and discovery of conserved genes, while single-tissue assemblies show a slower discovery of conserved genes though the assembled transcripts were often longer. A deeper examination of the mouse assemblies shows that with more reads, assembly errors become more frequent but such errors can be mitigated with more stringent assembly parameters. Conclusions: These assembly trends suggest that representative assemblies are generated with as few as 20 million reads for tissue samples and 30 million reads for whole-animals for RNA-level coverage. These depths provide a good balance between coverage and noise. Beyond 60 million reads, the discovery of new genes is low and sequencing errors of highly-expressed genes are likely to accumulate. Finally, siphonophores (polymorphic Cnidarians) are an exception and possibly require alternate assembly strategies. [ABSTRACT FROM AUTHOR]

A perceived recent increase in global jellyfish abundance has been portrayed as a symptom of degraded oceans. This perception is based primarily on a few case studies and anecdotal evidence, but a formal analysis of global temporal trends in jellyfish populations has been missing. Here, we analyze all available long-term datasets on changes in jellyfish abundance across multiple coastal stations, using linear and logistic mixed models and effect-size analysis to show that there is no robust evidence for a global increase in jellyfish. Although there has been a small linear increase in jellyfish since the 1970s, this trend was unsubstantiated by effect-size analysis that showed no difference in the proportion of increasing vs. decreasing jellyfish populations over all time periods examined. Rather, the strongest nonrandom trend indicated jellyfish populations undergo larger, worldwide oscillations with an approximate 20-y periodicity, including a rising phase during the 1990s that contributed to the perception of a global increase in jellyfish abundance. Sustained monitoring is required over the next decade to elucidate with statistical confidence whether the weak increasing linear trend in jellyfish after 1970 is an actual shift in the baseline or part of an oscillation. Irrespective of the nature of increase, given the potential damage posed by jellyfish blooms to fisheries, tourism, and other human industries, our findings foretell recurrent phases of rise and fall in jellyfish populations that society should be prepared to face. [ABSTRACT FROM AUTHOR]

Bioluminescence is common and well studied in mesopelagic species. However, the extent of bioluminescence in benthic sites of similar depths is far less studied, although the relatively large eyes of benthic fish, crustaceans and cephalopods at bathyal depths suggest the presence of significant biogenic light. Using the Johnson-Sea-Link submersible, we collected numerous species of cnidarians, echinoderms, crustaceans, cephalopods and sponges, as well as one annelid from three sites in the northern Bahamas (500-1000 m depth). Using mechanical and chemical stimulation, we tested the collected species for light emission, and photographed and measured the spectra of the emitted light. In addition, in situ intensified video and still photos were taken of different benthic habitats. Surprisingly, bioluminescence in benthic animals at these sites was far less common than in mesopelagic animals from similar depths, with less than 20% of the collected species emitting light. Bioluminescent taxa comprised two species of anemone (Actinaria), a new genus and species of flabeilate Parazoanthidae (formerly Gerardia sp.) (Zoanthidea), three sea pens (Pennatulacea), three bamboo corals (Alcyonacea), the chrysogorgiid coral Chrysogorgia desbonni (Alcyonacea), the caridean shrimp Parapandaius sp. and Heterocarpus ensifer (Decapoda), two holothuroids (Elasipodida and Aspidochirota) and the ophiuroid Ophiochiton ternispinus (Ophiurida). Except for the ophiuroid and the two shrimp, which emitted blue light (peak wavelengths 470 and 455 nm), all the species produced greener light than that measured in most mesopelagic taxa, with the emissions of the pennatulaceans being strongly shifted towards longer wavelengths. In situ observations suggested that bioluminescence associated with these sites was due primarily to light emitted by bioluminescent planktonic species as they struck filter feeders that extended into the water column. [ABSTRACT FROM AUTHOR]

Background: Calcium-activated photoproteins are luciferase variants found in photocyte cells of bioluminescent jellyfish (Phylum Cnidaria) and comb jellies (Phylum Ctenophora). The complete genomic sequence from the ctenophore Mnemiopsis leidyi, a representative of the earliest branch of animals that emit light, provided an opportunity to examine the genome of an organism that uses this class of luciferase for bioluminescence and to look for genes involved in light reception. To determine when photoprotein genes first arose, we examined the genomic sequence from other early-branching taxa. We combined our genomic survey with gene trees, developmental expression patterns, and functional protein assays of photoproteins and opsins to provide a comprehensive view of light production and light reception in Mnemiopsis. Results: The Mnemiopsis genome has 10 full-length photoprotein genes situated within two genomic clusters with high sequence conservation that are maintained due to strong purifying selection and concerted evolution. Photoprotein-like genes were also identified in the genomes of the non-luminescent sponge Amphimedon queenslandica and the non-luminescent cnidarian Nematostella vectensis, and phylogenomic analysis demonstrated that photoprotein genes arose at the base of all animals. Photoprotein gene expression in Mnemiopsis embryos begins during gastrulation in migrating precursors to photocytes and persists throughout development in the canals where photocytes reside. We identified three putative opsin genes in the Mnemiopsis genome and show that they do not group with well-known bilaterian opsin subfamilies. Interestingly, photoprotein transcripts are coexpressed with two of the putative opsins in developing photocytes. Opsin expression is also seen in the apical sensory organ. We present evidence that one opsin functions as a photopigment in vitro, absorbing light at wavelengths that overlap with peak photoprotein light emission, raising the hypothesis that light production and light reception may be functionally connected in ctenophore photocytes. We also present genomic evidence of a complete ciliary phototransduction cascade in Mnemiopsis. Conclusions: This study elucidates the genomic organization, evolutionary history, and developmental expression of photoprotein and opsin genes in the ctenophore Mnemiopsis leidyi, introduces a novel dual role for ctenophore photocytes in both bioluminescence and phototransduction, and raises the possibility that light production and light reception are linked in this early-branching non-bilaterian animal. [ABSTRACT FROM AUTHOR]

During the past several decades, high numbers of gelatinous zooplankton species have been reported in many estuarine and coastal ecosystems. Coupled with media-driven public perception, a paradigm has evolved in which the global ocean ecosystems are thought to be heading toward being dominated by "nuisance" jellyfish. We question this current paradigm by presenting a broad overview of gelatinous zooplankton in a historical context to develop the hypothesis that population changes reflect the human-mediated alteration of global ocean ecosystems. To this end, we synthesize information related to the evolutionary context of contemporary gelatinous zooplankton blooms, the human frame of reference for changes in gelatinous zooplankton populations, and whether sufficient data are available to have established the paradigm. We conclude that the current paradigm in which it is believed that there has been a global increase in gelatinous zooplankton is unsubstantiated, and we develop a strategy for addressing the critical questions about long-term, human-related changes in the sea as they relate to gelatinous zooplankton blooms. [ABSTRACT FROM AUTHOR]

Two new species of Swima, a recently established genus of annelid worms, are introduced, one from deep water off the North American West Coast and the other from the Philippines. The acrocirrid genus now contains three named species, Swima bombiviridis, Swima fulgida sp. nov., and Swima tawitawiensis sp. nov. Swima are holopelagic, occurring only in the water column, and thus far have only been observed below 2700 m. The worms are relatively large, sometimes reaching over 30 mm in length and 5 mm in width. They have gelatinous bodies and fans of long swimming chaetae, which are flattened into paddles in S. tawitawiensis sp. nov. Members of Swima are distinguished from other swimming acrocirrids by their transparent bodies, single medial subulate branchiae, and simple nuchal organs that do not skirt the bases of lateral subulate branchiae. Swima fulgida sp. nov. is distinguished from other members of the genus by its darkly pigmented anterior gut, whereas S. tawitawiensis sp. nov. is distinguished by possessing three subulate head appendages instead of just one and by the shape of its noto- and neurochaetae. Swima species possess four pairs of elliptical, transformed segmental branchiae that produce green bioluminescence when autotomized. These 'bombs' were observed in various states of regeneration on a single individual. Swima are neutrally buoyant, often observed hanging immobile in the water column, and are active, agile swimmers. Although not previously documented in the literature, these worms are not rare in the deep water column. Since the worms were first noticed in 2001, they have been observed on more than half of the Monterey Bay Aquarium Research Institute's midwater remotely operated vehicle dives that went to sufficient depth. The discovery of Swima underscores our lack of knowledge of deep pelagic fauna. © 2011 The Linnean Society of London, Zoological Journal of the Linnean Society, 2011, 163, 663-678. [ABSTRACT FROM AUTHOR]

We investigated differential gene expression between functionally specialized feeding polyps and swimming medusae in the siphonophore Nanomia bijuga (Cnidaria) with a hybrid long-read/short-read sequencing strategy. We assembled a set of partial gene reference sequences from long-read data (Roche 454), and generated short-read sequences from replicated tissue samples that were mapped to the references to quantify expression. We collected and compared expression data with three short-read expression workflows that differ in sample preparation, sequencing technology, and mapping tools. These workflows were Illumina mRNA-Seq, which generates sequence reads from random locations along each transcript, and two tag-based approaches, SOLiD SAGE and Helicos DGE, which generate reads from particular tag sites. Differences in expression results across workflows were mostly due to the differential impact of missing data in the partial reference sequences. When all 454-derived gene reference sequences were considered, Illumina mRNA-Seq detected more than twice as many differentially expressed (DE) reference sequences as the tag-based workflows. This discrepancy was largely due to missing tag sites in the partial reference that led to false negatives in the tag-based workflows. When only the subset of reference sequences that unambiguously have tag sites was considered, we found broad congruence across workflows, and they all identified a similar set of DE sequences. Our results are promising in several regards for gene expression studies in non-model organisms. First, we demonstrate that a hybrid long-read/short-read sequencing strategy is an effective way to collect gene expression data when an annotated genome sequence is not available. Second, our replicated sampling indicates that expression profiles are highly consistent across field-collected animals in this case. Third, the impacts of partial reference sequences on the ability to detect DE can be mitigated through workflow choice and deeper reference sequencing. [ABSTRACT FROM AUTHOR]

A stable phylogenetic hypothesis for families within jellyfish class Scyphozoa has been elusive. Reasons for the lack of resolution of scyphozoan familial relationships include a dearth of morphological characters that reliably distinguish taxa and incomplete taxonomic sampling in molecular studies. Here, we address the latter issue by using maximum likelihood and Bayesian methods to reconstruct the phylogenetic relationships among all 19 currently valid scyphozoan families, using sequence data from two nuclear genes: 18S and 28S rDNA. Consistent with prior morphological hypotheses, we find strong evidence for monophyly of subclass Discomedusae, order Coronatae, rhizostome suborder Kolpophorae and superfamilies Actinomyariae, Kampylomyariae, Krikomyariae, and Scapulatae. Eleven of the 19 currently recognized scyphozoan families are robustly monophyletic, and we suggest recognition of two new families pending further analyses. In contrast to long-standing morphological hypotheses, the phylogeny shows coronate family Nausithoidae, semaeostome family Cyaneidae, and rhizostome suborder Daktyliophorae to be nonmonophyletic. Our analyses neither strongly support nor strongly refute monophyly of order Rhizostomeae, superfamily Inscapulatae, and families Ulmaridae, Catostylidae, Lychnorhizidae, and Rhizostomatidae. These taxa, as well as familial relationships within Coronatae and within rhizostome superfamily Inscapulatae, remain unclear and may be resolved by additional genomic and taxonomic sampling. In addition to clarifying some historically difficult taxonomic questions and highlighting nodes in particular need of further attention, the molecular phylogeny presented here will facilitate more robust study of phenotypic evolution in the Scyphozoa, including the evolution characters associated with mass occurrences of jellyfish. [ABSTRACT FROM AUTHOR]

Nucleotide sequence analysis of 18S ribosomal RNA gene (rRNA), internal transcribed spacer, and 5.8S rRNA was used for taxonomic identification of ctenophores collected in the northern Baltic Sea, where invasive Mnemiopsis leidyi and native Pleurobrachia pileus have been reported to occur. Contrary to previous reports, sequence analysis of 53 randomly selected specimens from seven stations revealed that none of them were M. leidyi or P. pileus. The 18S rRNA and 5.8S rRNA sequences were 100% identical to those of Mertensia ovum, a ctenophore with a broad Arctic and circumboreal distribution, which has never been reported to occur in the Baltic Sea. Polymerase chain reaction screening with primers designed to amplify all three species, and using ctenophores collected by vertically stratified sampling, confirmed that all ctenophores collected in this survey were M. ovum. The ctenophore abundance was high, up to 4500 individuals m−2, positively correlating with salinity. Our findings emphasize the utility of applying molecular tools to biological surveys and the importance of rigorous species identification. They also indicate that M. leidyi, which is a threat to the southern Baltic ecosystem, does not occur in the northern part of the sea, and call for a pan-Baltic survey to establish current distributions of ctenophores, both native and invasive. [ABSTRACT FROM AUTHOR]

Long-held ideas regarding the evolutionary relationships among animals have recently been upended by sometimes controversial hypotheses based largely on insights from molecular data. These new hypotheses include a clade of moulting animals (Ecdysozoa) and the close relationship of the lophophorates to molluscs and annelids (Lophotrochozoa). Many relationships remain disputed, including those that are required to polarize key features of character evolution, and support for deep nodes is often low. Phylogenomic approaches, which use data from many genes, have shown promise for resolving deep animal relationships, but are hindered by a lack of data from many important groups. Here we report a total of 39.9 Mb of expressed sequence tags from 29 animals belonging to 21 phyla, including 11 phyla previously lacking genomic or expressed-sequence-tag data. Analysed in combination with existing sequences, our data reinforce several previously identified clades that split deeply in the animal tree (including Protostomia, Ecdysozoa and Lophotrochozoa), unambiguously resolve multiple long-standing issues for which there was strong conflicting support in earlier studies with less data (such as velvet worms rather than tardigrades as the sister group of arthropods), and provide molecular support for the monophyly of molluscs, a group long recognized by morphologists. In addition, we find strong support for several new hypotheses. These include a clade that unites annelids (including sipunculans and echiurans) with nemerteans, phoronids and brachiopods, molluscs as sister to that assemblage, and the placement of ctenophores as the earliest diverging extant multicellular animals. A single origin of spiral cleavage (with subsequent losses) is inferred from well-supported nodes. Many relationships between a stable subset of taxa find strong support, and a diminishing number of lineages remain recalcitrant to placement on the tree. [ABSTRACT FROM AUTHOR]

The phylum Ctenophora (known as comb jellies) consists of gelatinous marine carnivores found from the surface to several thousand meters depth. Their morphology can be simple or complex, ranging from a sac-like shape with no tentacles to large lobed forms with sinuous "auricles," papillae, and two different kinds of tentacles. This diversity appears to reflect adaptations to many different diets. For example, some species can continuously "graze" on small crustaceans or larvae, others engulf larger jellies, and some are able to snare individual larger prey through a variety of strategies. Thus feeding behavior can help explain the high morphological diversity in this relatively small phylum. Because of their fragility, comb jellies are difficult to study alive and the natural histories of many types, especially those found in the deep sea, have not been examined. This account categorizes ctenophore feeding methods using published reports as well as new observations using submersibles and blue-water scuba diving. [ABSTRACT FROM AUTHOR]

Among metazoans, crustaceans display the greatest disparity between body plans and are second only to the insects in overall species diversity. Within the crustaceans, the Amphipoda rank as one of the most speciose extant orders. Amphipods have successfully invaded a variety of ecosystems, including the pelagic midwater environment. Despite their abundance in varied and dissimilar habitats, and the use of traditional morphological and systematic comparative analyses, phylogenetic relationships among amphipods remain uncertain. The pelagic amphipods, hyperiids, have highly divergent life histories and morphological attributes in comparison to more familiar benthic, nearshore, intertidal, and terrestrial amphipods. Some of these adaptations are likely correlated with their pelagic life history and include features such as hypertrophied olfactory and visual systems, duplications of the eyes, and an array of modifications to the appendages. Many of these morphological features may represent homoplasies, thus masking the true phylogenetic relationships among extant hyperiid amphipods. Here, we sample a wide range of amphipod taxa for the COI gene and present the first preliminary molecular phylogeny among the hyperiids. [ABSTRACT FROM AUTHOR]

The pelagic realm of the ocean is characterized by extremely clear water and a lack of surfaces. Adaptations to the visual ecology of this environment include transparency, fluorescence, bioluminescence, and deep red or black pigmentation. While the signals that pelagic organisms send are increasingly well-understood, the optical capabilities of their viewers, especially for predators with camera-like vision such as fish and squid, are almost unknown. Aquatic camera-like vision is characterized by a spherical lens focusing an image on the retina. Here, we measured the resolving power of the lenses of eight species of pelagic cephalopods to obtain an approximation of their visual capabilities. We did this by focusing a standard resolution target through dissected lenses and calculating their modulation transfer functions. The modulation transfer function (MTF) is the single most complete expression of the resolving capabilities of a lens. Since the optical and retinal capabilities of an eye are generally well-matched, we considered our measurements of cephalopod lens MTF to be a good proxy for their visual capabilities in vivo. In general, squid have optical capabilities comparable to other organisms generally assumed to have good vision, such as fish and birds. Surprisingly, the optical capability of the eye of Vampyroteuthis infernalis rivals that of humans. [ABSTRACT FROM AUTHOR]

Siphonophores are a group of pelagic colonial hydrozoans (Cnidaria) that have long been of general interest because of the division of labor between the polyps and medusae that make up these "superorganisms." These polyps and medusae are each homologous to free living animals but are generated by an incomplete asexual budding process that leaves them physiologically integrated. They are functionally specialized for different tasks and are precisely organized within each colony. The number of functional types of polyps and medusae varies across taxa, and different authors have used this character to construct phylogenies polarized in opposite directions, depending on whether they thought siphonophore evolution proceeded by a reduction or an increase in functional specialization.We have collected taxa across all major groups of siphonophores, many of which are found exclusively in the deep sea, using remotely operated underwater vehicles (ROVs) and by SCUBA diving from ships in the open ocean. We have used 52 siphonophores and four outgroup taxa to estimate the siphonophore phylogeny with molecular data from the nuclear small subunit ribosomal RNA gene (18S) and the mitochondrial large subunit ribosomal RNA gene (16S). Parsimony reconstructions indicate that functionally specialized polyps and medusae have been gained and lost across the phylogeny. Maximum likelihood and Bayesian analyses of morphological data suggest that the transition rate for decreased functional specialization is greater than the transition rate for increased functional specialization for three out of the four investigated categories of polyps and medusae. The present analysis also bears on several long-standing questions about siphonophore systematics. It indicates that the cystonects are sister to all other siphonophores, a group that we call the Codonophora.We also find that the Calycophorae are nested within the Physonectae, and that the Brachystelia, a historically recognized grouping of short-stemmed taxa, are polyphyletic. [Cnidaria; colonial animals; deep sea; division of labor; functional specialization; Hydrozoa; phylogenetics; Siphonophores.] [ABSTRACT FROM AUTHOR]

On many occasions over the centuries, mariners have reported witnessing surreal nocturnal displays where the surface of the sea produces an intense, uniform, and sustained glow that extends to the horizon in all directions. Although such emissions cannot be fully reconciled with the known features of any light-emitting organism, these so-called "milky seas" are hypothesized to be manifestations of unusually strong bioluminescence produced by colonies of bacteria in association with a microalgal bloom in the surface waters. Because of their ephemeral nature and the paucity of scientific observations, an explanation of milky seas has remained elusive. Here, we report the first satellite observations of the phenomenon. An ≈15,400-km² area of the northwestern Indian Ocean, roughly the size of the state of Connecticut, was observed to glow over 3 consecutive nights, corroborated on the first night by a ship-based account. This unanticipated application of satellite remote-sensing technology provides insights pertaining to the formation and scale of these poorly understood events. [ABSTRACT FROM AUTHOR]

Examines the taxonomy of Marrus claudanielis, a new species of deep-sea physonect siphonophore. Assessment of the siphomal elements, nectophoral and bracteal canals; Observation of the hook-shaped arc of enlarged ectodermal cells; Distinction of the new specie from other Marrus species by the undivided apico-lateral ridges on the nectophores.

The archaic, deep-sea cephalopod Vampyroteuthis infernalis occurs in dark, oxygen-poor waters below 600 m off Monterey Bay, California. Living specimens, collected gently with a remotely operated vehicle (ROV) and quickly transported to a laboratory ashore, have revealed two hitherto undescribed means of bioluminescent expression for the species. In the first, light is produced by a new type of organ located at the tips of all eight arms. In the second, a viscous fluid containing microscopic luminous particles is released from the arm tips to form a glowing cloud around the animal. Both modes of light production are apparently linked to anti-predation strategies. Use of the tip-lights is readily educed by contact stimuli, while fluid expulsion has a much higher triggering threshold. Coelenterazine and luciferase are the chemical precursors of light production. This paper presents observations on the structure and operation of the arm-tip light organs, the character of the luminous cloud, and how the light they produce is incorporated into behavioral patterns. [ABSTRACT FROM AUTHOR]

Bioluminescence (BL) predictability experiments (predictions of the intensity, depth, and distance offshore of the BL maximum) were conducted using an advective-diffusive tracer model with velocities and diffusivities from a fine-resolution model of the Monterey Bay, California, area. For tracer initialization, observations were assimilated into the tracer model while velocities and diffusivities were taken from the hydrodynamic model and kept unchanged during the initialization process. This dynamic initialization procedure provides an equilibrium tracer distribution that is balanced with the velocity and diffusivity fields from the hydrodynamic model. This equilibrium BL distribution was used as the initial BL field for 3 days of prognostic calculations. Two cross-shore surveys of bioluminescence data conducted at two locations (north of the bay and inside the bay) were used in four numerical experiments designed to estimate the limits of bioluminescence predictions by tracers. The cross-shore sections extended to around 25 km offshore, they were around 30 m deep, and on average they were approximately 35 km apart from each other. Bioluminescence predictability experiments demonstrated a strong utility of the tracer model (combined with limited bioluminescence observations and with the output from a circulation model) in predicting (over a 72-h period and over 25-35-km distances) the location and intensity of the BL maximum. Analysis of the model velocity fields and observed and model-predicted bioluminesence fields shows that the BL maximum is located in the frontal area representing a strong reversal of flow direction. [ABSTRACT FROM AUTHOR]

Bioluminescence, light produced by living organisms, is a common trait in the ocean. In benthic ecosystems in the deep-sea, octocorals are some of the most abundant luminous animals. Among luminous sessile organisms, the shallow-water sea pansy Renilla has been well studied for its chemistry and molecular biology. Aside from Renilla, however, little is known about the bioluminescent mechanisms of other anthozoans, especially deep-sea corals. In this study, we investigated the characteristics of bioluminescence in deep-sea anthozoans. The bioluminescent capabilities of Heteropolypus, Kophobelemnon, Paragorgia, and a hormathiid anemone are newly described. Coelenterazine, a substrate for bioluminescent reactions, was detected in extracts from octocorals. Coelenterazine-dependent luciferase activity was found in all the anthozoans. Moreover, immunoreactivity against Renilla luciferase was detected in protein extracts from the families Isididae, Alcyoniidae, Umbellulidae, Funiculinidae, Kophobelemnidae and Protoptilidae, suggesting that all luminous octocorals may share a common biochemical mechanism, which utilizes coelenterazine and Renilla-type luciferase. Our results support the hypothesis that the last common ancestor of all the octocorals was bioluminescent, and that bioluminescence evolved a minimum of six times in Cnidaria. Future studies with robust phylogenies, wide taxon sampling, and comparative transcriptome analyses could reveal the patterns of evolution of bioluminescence in octocorals and anthozoans. Our study provides fundamental observations of deep-sea corals and experimental evidence of their coelenterazine-dependent luciferase systems. [ABSTRACT FROM AUTHOR]

Bioluminescence is a prominent functional trait used for visual communication. A recent quantification showed that in pelagic ecosystems more than 75% of individual macro-planktonic organisms are categorized as able to emit light. In benthic ecosystems, only a few censuses have been done, and were based on a limited number of observations. In this study, our dataset is based on observations from remotely operated vehicle (ROV) dives conducted from 1991–2016, spanning 0–3,972 m depth. Data were collected in the greater Monterey Bay area in central California, USA and include 369,326 pelagic and 154,275 epibenthic observations at Davidson Seamount, Guide Seamount, Sur Ridge and Monterey Bay. Because direct observation of in situ bioluminescence remains a technical challenge, taxa from ROV observations were categorized based on knowledge gained from the literature to assess bioluminescence status. We found that between 30–41% of the individual observed benthic organisms were categorized as capable of emitting light, with a strong difference between benthic and pelagic ecosystems. We conclude that overall variability in the distribution of bioluminescent organisms is related to the major differences between benthic and pelagic habitats in the deep ocean. This study may serve as the basis of future investigations linking the optical properties of various habitats and the variability of bioluminescent organism distributions. [ABSTRACT FROM AUTHOR]

The capability of animals to emit light, called bioluminescence, is considered to be a major factor in ecological interactions. Because it occurs across diverse taxa, measurements of bioluminescence can be powerful to detect and quantify organisms in the ocean. In this study, 17 years of video observations were recorded by remotely operated vehicles during surveys off the California Coast, from the surface down to 3,900 m depth. More than 350,000 observations are classified for their bioluminescence capability based on literature descriptions. The organisms represented 553 phylogenetic concepts (species, genera or families, at the most precise taxonomic level defined from the images), distributed within 13 broader taxonomic categories. The importance of bioluminescent marine taxa is highlighted in the water column, as we showed that 76% of the observed individuals have bioluminescence capability. More than 97% of Cnidarians were bioluminescent, and 9 of the 13 taxonomic categories were found to be bioluminescent dominant. The percentage of bioluminescent animals is remarkably uniform over depth. Moreover, the proportion of bioluminescent and non-bioluminescent animals within taxonomic groups changes with depth for Ctenophora, Scyphozoa, Chaetognatha, and Crustacea. Given these results, bioluminescence has to be considered an important ecological trait from the surface to the deep-sea. [ABSTRACT FROM AUTHOR]