Search

A central question in evolutionary biology is whether sponges or ctenophores (comb jellies) are the sister group to all other animals. These alternative phylogenetic hypotheses imply different scenarios for the evolution of complex neural systems and other animal-specific traits1–6. Conventional phylogenetic approaches based on morphological characters and increasingly extensive gene sequence collections have not been able to definitively answer this question7–11. Here we develop chromosome-scale gene linkage, also known as synteny, as a phylogenetic character for resolving this question12. We report new chromosome-scale genomes for a ctenophore and two marine sponges, and for three unicellular relatives of animals (a choanoflagellate, a filasterean amoeba and an ichthyosporean) that serve as outgroups for phylogenetic analysis. We find ancient syntenies that are conserved between animals and their close unicellular relatives. Ctenophores and unicellular eukaryotes share ancestral metazoan patterns, whereas sponges, bilaterians, and cnidarians share derived chromosomal rearrangements. Conserved syntenic characters unite sponges with bilaterians, cnidarians, and placozoans in a monophyletic clade to the exclusion of ctenophores, placing ctenophores as the sister group to all other animals. The patterns of synteny shared by sponges, bilaterians, and cnidarians are the result of rare and irreversible chromosome fusion-and-mixing events that provide robust and unambiguous phylogenetic support for the ctenophore-sister hypothesis. These findings provide a new framework for resolving deep, recalcitrant phylogenetic problems and have implications for our understanding of animal evolution.

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.

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.

Animals are known to regulate the composition of their cell membranes to maintain key biophysical properties in response to changes in temperature. For deep-sea marine organisms, high hydrostatic pressure represents an additional, yet much more poorly understood, perturbant of cell membrane structure. Previous studies in fish and marine microbes have reported correlations with temperature and depth of membrane-fluidizing lipid components, such as polyunsaturated fatty acids. Because little has been done to isolate the separate effects of temperature and pressure on the lipid pool, it is still not understood whether these two environmental factors elicit independent or overlapping biochemical adaptive responses. Here, we use the taxonomic and habitat diversity of the phylum Ctenophora to test whether distinct low-temperature and high-pressure signatures can be detected in fatty acid profiles. We measured the fatty acid composition of 105 individual ctenophores, representing 21 species, from deep and shallow Arctic, temperate, and tropical sampling locales (sea surface temperature, −2° to 28°C). In tropical and temperate regions, remotely operated submersibles (ROVs) enabled sampling down to 4000 m. We found that among specimens with body temperatures 7.5°C or colder, depth predicted fatty acid unsaturation levels. In contrast, in the upper 200 m of the water column, temperature predicted fatty acid chain lengths. Taken together, our findings suggest that lipid metabolism may be specialized with respect to multiple physical variables in diverse marine environments. Largely distinct modes of adaptation to depth and cold imply that polar marine invertebrates may not find a ready refugium from climate change in the deep., Summary: Global sampling of comb jellies reveals distinct fatty acid compositions in cold versus deep habitats, suggesting that high hydrostatic pressure requires specialized adaptation of lipid membranes.

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.

Sönke Johnsen and Steve Haddock introduce the remarkable deep-sea fish Macropinna microstoma whose transparent head and rotating tubular eyes are two novel adaptations that allow it to see and hunt at depth.

Los sifonóforos son cnidarios hidrozoos coloniales depredadores que habitan todas las regiones pelágicas del océano. Las téntilas (ramificaciones laterales de los tentáculos) de los sifonóforos son estructuras biológicas dedicadas a la captura de presas. Las téntilas se componen de una matriz compleja de cnidocitos (células urticantes) portadores de diferentes tipos de nematocistes (cápsulas urticantes) y estructuras auxiliares. Las téntilas presenta una extensa diversidad morfológica y funcional en las diferentes especies de sifonóforo. Las relaciones entre la forma de las téntilas y las dietas de los sifonóforos has sido estudiadas previamente, sin embargo, la historia evolutiva que dio lugar a esta diversidad morfológica no ha sido explorada apenas. En este estudio examinamos las adquisiciones y pérdidas evolutivas de las subestructuras de la téntila y los tipos de nematocisto utilizando la filogenia molecular más reciente de los sifonóforos. Las téntilas presentan un mecanismo de disparo a alta velocidad, sincronizando las diferentes subestructuras con gran precisión, durante el cual se la téntila de desenrolla mientras los nematocistes se disparan sobre la presa. En este estudio caracterizamos la diversidad cinemática de estas reacciones para la captura de presas utilizando video de alta velocidad, y describimos su relación con los caracteres morfológicos. Dado que la descarga de las téntilas ocurre en sincronía en toda su diversidad morfológica, hemos evaluado cómo la evolución con integración fenotípica mantiene las correlaciones entre los caracteres morfológicos a través del tiempo. Hallamos que el morfo-espacio de las téntilas tiene baja dimensionalidad, encontramos casos de heterocronía y convergencia morfológica, y generamos hipótesis sobre las dietas de especies de sifonóforo poco estudiadas. Nuestros hallazgos indican que las téntilas de los sifonóforos son estructuras con fenotipos integrados y con una historia evolutiva compleja que ha dado lugar a una diversidad filogenéticamente estructurada de formas asociadas a diferentes rendimientos cinemáticos y hábitos alimenticios.

The high seas—marine areas beyond national jurisdiction (1)—cover nearly half of Earth's surface (2). The high seas support our planet in countless ways, from regulating the climate, to feeding millions of people, to supporting industries that contribute billions of dollars to the global economy (3). Even so, less than 1% of the high seas are fully protected (4), and the current patchwork of management and lack of oversight leaves them vulnerable to abuse. In 2017, the United Nations resolved to develop an international treaty for the conservation and sustainable use of the high seas. Negotiations are set to end this year. We must ensure that the forthcoming framework conserves high-seas biodiversity and promotes sustainable and equitable use.

Although members of the Rhopalonematidae family (Cnidaria, Hydrozoa, Trachymedusae) are known to exhibit unusually powerful jet swimming in addition to their more normal slow swimming behaviour, for the most part, reports are rare and anecdotal. Many species are found globally at depths of 600–2000 m, and so observation and collection depend on using remotely operated submersible vehicles. With a combination of in situ video footage and laboratory measurements, we have quantified kinematic aspects of this dual swimming motion and its electrophysiology. The species included are from two Rhopalonematidae clades; they are Colobonema sericeum, Pantachogon haeckeli, Crossota millsae and two species of Benthocodon. Comparison is made with Aglantha digitale, a species from a third Rhopalonematidae clade brought to the surface by natural water movement. We find that although all Rhopalonematidae appear to have two swimming modes, there are marked differences in their neural anatomy, kinematics and physiology. Giant motor axons, known to conduct impulses during fast swimming in A. digitale, are absent from C. sericeum and P. haeckeli. Slow swimming is also different; in C. sericeum and its relatives it is driven by contractions restricted to the base of the bell, whereas in A. digitale it is driven by contractions in the mid-bell region. These behavioural differences are related to the position of the different clades on a ribosomal DNA-based phylogenetic tree. This finding allows us to pinpoint the phylogenetic branch point leading to the appearance of giant motor axons and escape swimming. They place the remarkable dual swimming behaviour of members of the Rhopalonematidae family into an evolutionary context., Summary: 18S ribosomal DNA data support anatomical, kinematic and electrophysiological evidence that identifies the phylogenetic branch point giving rise to giant-axon-based fast and slow swimming in the Rhopalonematidae.

Significance Predatory specialization is often associated with the evolution of modifications in the morphology of the prey-capture apparatus. Specialization has been considered an evolutionary “dead end” due to the constraints associated with these morphological changes. However, in predators like siphonophores, armed with modular structures used exclusively for prey capture, this assumption is challenged. Our results show that siphonophores can evolve generalism and new prey-type specializations by modifying the morphological states, modes of evolution, and evolutionary correlations between the parts of their prey-capture apparatus. These findings demonstrate how studying open-ocean nonbilaterian predators can reveal novel patterns and mechanisms in the evolution of specialization. Understanding these evolutionary processes is fundamental to the study of food web structure and complexity., 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 armed with nematocysts) exclusively for prey capture. Here we 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.

Ctenophores in the class Tentaculata are distinct from Cnidarians in that they use sticky, not stinging, tentacles to capture and subdue their prey. The structures that make these tentacles sticky are colloblasts, specialized multicellular adhesive structures for predation. Located on the tentacles, tentacle side-branches (tentilla), or oral tentilla, colloblasts are only found in comb jellies (phylum Ctenophora). To perform comparative anatomy of the diversity of ctenophore colloblasts, specimens were collected from the epi- to bathypelagic zones near the coasts of central California and the Hawaiian Islands using blue-water divers and remotely operated vehicles. Tentacle samples were immediately fixed in a 4% formalin solution at sea, and then prepared in the lab via secondary fixation in 2% OsO4 for scanning electron microscopy (SEM). Diversity of ultrastructural characteristics was observed using SEM, and the morphometrics of the collosphere, external secretion granules, and spiral filament were recorded for 20 species, within 9 families and 9 genera, including 13 undescribed species. Morphometry of colloblasts reveals that the shape of the collosphere (the organizational unit of sticky granules) falls into 3 classifications: spherical, ellipsoidal, or non-uniform. External secretion granule deposition falls into 2 categories: clustered or patterned; the cap cell membrane was either present or absent. This morphological variation is summarized graphically and will be useful to describe the functional diversity and feeding ecology of the interesting and controversial phylum Ctenophora.

Despite rapidly growing interest in deep-sea mineral exploitation, environmental research and management have focused on impacts to seafloor environments, paying little attention to pelagic ecosystems. Nonetheless, research indicates that seafloor mining will generate sediment plumes and noise at the seabed and in the water column that may have extensive ecological effects in deep midwaters (1), which can extend from an approximate depth of 200 meters to 5 kilometers. Deep midwater ecosystems represent more than 90% of the biosphere (2), contain fish biomass 100 times greater than the global annual fish catch (3), connect shallow and deep-sea ecosystems, and play key roles in carbon export (4), nutrient regeneration, and provisioning of harvestable fish stocks (5). These ecosystem services, as well as biodiversity, could be negatively affected by mining. Here we argue that deep-sea mining poses significant risks to midwater ecosystems and suggest how these risks could be evaluated more comprehensively to enable environmental resource managers and society at large to decide whether and how deep-sea mining should proceed. Midwater animal biodiversity: Squid, fish, shrimp, copepods, medusa, filter-feeding jellies, and marine worms are among the midwater creatures that could be affected by deep sea mining. Photos by E. Goetze, K. Peijnenburg, D. Perrine, Hawaii Seafood Council (B. Takenaka, J. Kaneko), S. Haddock, J. Drazen, B. Robison, DEEPEND (Dante Fenolio), and MBARI. Interest in deep-sea mining for sulfide deposits near hydrothermal vents, polymetallic nodules on the abyssal seafloor, and cobalt-rich crusts on seamounts (6) has grown substantially in the last decade. Equipment and system development are already occurring. The International Seabed Authority (ISA), the international organization created under the United Nations Convention on the Law of the Sea (UNCLOS) to manage deep-sea mining beyond national jurisdiction, is developing mineral exploitation regulations, the Mining Code. Currently, 30 ISA exploration contracts cover over 1.5 million … [↵][1]1To whom correspondence should be addressed. Email: jdrazen{at}hawaii.edu. [1]: #xref-corresp-1-1

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.

Odontosyllis undecimdonta is a marine syllid polychaete that produces bright internal and exuded bioluminescence. Despite over fifty years of biochemical investigation into Odontosyllis bioluminescence, the light-emitting small molecule substrate and catalyzing luciferase protein have remained a mystery. Here we describe the discovery of a bioluminescent protein fraction from O. undecimdonta, the identification of the luciferase using peptide and RNA sequencing, and the in vitro reconstruction of the bioluminescence reaction using highly purified O. undecimdonta luciferin and recombinant luciferase. Lastly, we found no identifiably homologous proteins in publicly available datasets. This suggests that the syllid polychaetes contain an evolutionarily unique luciferase among all characterized luminous taxa.

To the human observer, the deep sea is as extreme an environment as Earth has to offer. Below about 200 metres, there is no light from the surface, the water can be frigid (-2 to 5°C), oxygen and food are scarce, and the pressure is staggering. Of course, to the countless species that inhabit the deep sea, these conditions are not so extreme, and in a statistical sense, they fall fairly close to average, since the deep comprises the planet's largest habitat by volume. Despite its expanse, we know little about how life persists in an environment so different from our own. Only in the last half-century has technology emerged that allows us to collect and study live deep-sea animals. Diversity, Evolution and EcoPhysiology of Ctenophores (DEEPC, deepc.org, a US NSF-supported research effort) is opening a window on biochemistry in the deep, and specifically on its relationship to high pressure. By determining structural constraints on enzyme function under pressure, we aim to inform models focusing on deep-sea animal colonization, and to find general patterns of protein adaptation with possible applications in protein engineering and biocatalysis.

To date, five ctenophore species’ mitochondrial genomes have been sequenced, and each contains open reading frames (ORFs) that if translated have no identifiable orthologs. ORFs with no identifiable orthologs are called unidentified reading frames (URFs). If truly protein-coding, ctenophore mitochondrial URFs represent a little understood path in early-diverging metazoan mitochondrial evolution and metabolism. We sequenced and annotated the mitochondrial genomes of three individuals of the beroid ctenophore Beroe forskalii and found that in addition to sharing the same canonical mitochondrial genes as other ctenophores, the B. forskalii mitochondrial genome contains two URFs. These URFs are conserved among the three individuals but not found in other sequenced species. We developed computational tools called pauvre and cuttlery to determine the likelihood that URFs are protein coding. There is evidence that the two URFs are under negative selection, and a novel Bayesian hypothesis test of trinucleotide frequency shows that the URFs are more similar to known coding genes than noncoding intergenic sequence. Protein structure and function prediction of all ctenophore URFs suggests that they all code for transmembrane transport proteins. These findings, along with the presence of URFs in other sequenced ctenophore mitochondrial genomes, suggest that ctenophores may have uncharacterized transmembrane proteins present in their mitochondria.

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.

Ctenophores, also known as comb jellies, live across extremely broad ranges of temperature and hydrostatic pressure in the ocean. Because various ctenophore lineages adapted independently to similar environmental conditions, Phylum Ctenophora is an ideal system for the study of protein adaptation to extreme environments in a comparative framework. We present such a study here, using a phylogenetically-informed method to compare sequences of four essential metabolic enzymes across gradients of habitat depth and temperature. This method predicts convergent adaptation to these environmental parameters at the amino acid level, providing a novel view of protein adaptation to extreme environments and demonstrating the power and relevance of phylogenetic comparison applied to multi-species transcriptomic datasets from early-diverging metazoa. Across all four enzymes analyzed, 46 amino acid sites were associated with depth-adaptation, 59 with temperature-adaptation, and 56 with both. Sites predicted to be depth- and temperature-adaptive occurred consistently near Rossmann fold cofactor binding motifs and disproportionately in solvent-exposed regions of the protein. These results suggest that the hydrophobic effect and ligand binding may mediate efficient enzyme function at different hydrostatic pressures and temperatures. Using predicted adaptive site maps, such mechanistic hypotheses can now be tested via mutagenesis.

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 armed with nematocysts) exclusively for prey capture. Here we study how siphonophore specialists and generalists evolve, and what morphological changes are associated with these transitions. To answer these questions, we: (1) measured 29 morphological characters of tentacles from 45 siphonophore species, (2) mapped these data to a phylogenetic tree, and (3) 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 genetic 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.Significance StatementPredatory specialization is often associated with the evolution of modifications in the morphology of the prey capture apparatus. Specialization has been considered an evolutionary ‘dead-end’ due to the constraints associated with these morphological changes. However, in predators like siphonophores, armed with modular structures used exclusively for prey capture, this assumption is challenged. Our results show that siphonophores can evolve generalism and new prey-type specializations by modifying the morphological states, modes of evolution, and genetic correlations between the parts of their prey capture apparatus. These findings demonstrate how studying open-ocean non-bilaterian predators can reveal novel patterns and mechanisms in the evolution of specialization. Understanding these evolutionary processes is fundamental to the study of food-web structure and complexity.

To date, five ctenophore species’ mitochondrial genomes have been sequenced, and each contains open reading frames (ORFs) that if translated have no identifiable orthologs. ORFs with no identifiable orthologs are called unidentified reading frames (URFs). If truly protein-coding, ctenophore mitochondrial URFs represent a little understood path in early-diverging metazoan mitochondrial evolution and metabolism. We sequenced and annotated the mitochondrial genomes of three individuals of the beroid ctenophore Beroe forskalii and found that in addition to sharing the same canonical mitochondrial genes as other ctenophores, the B. forskalii mitochondrial genome contains two URFs. These URFs are conserved among the three individuals but not found in other sequenced species. We developed computational tools called pauvre and cuttlery to determine the likelihood that URFs are protein coding. There is evidence that the two URFs are under negative selection, and a novel Bayesian hypothesis test of trinucleotide frequency shows that the URFs are more similar to known coding genes than noncoding intergenic sequence. Protein structure and function prediction of all ctenophore URFs suggests that they all code for transmembrane transport proteins. These findings, along with the presence of URFs in other sequenced ctenophore mitochondrial genomes, suggest that ctenophores may have uncharacterized transmembrane proteins present in their mitochondria.

Ctenophores are one of the most conspicuous and frequent groups of the gelatinous zooplankton community, but their regional diversity in tropical and subtropical latitudes remains largely unknown. We provide an overview and update of the current knowledge of the diversity in Mexican seas, including ocean and coastal-neritic environments of the Gulf of Mexico, the Mexican Caribbean Sea, and the Mexican Pacific Ocean. Ctenophore records were reviewed based on the available scientific and gray literature, the Naturalista network (www.naturalista.mx), and the ctenophore species collected in the Gulf of California by the Monterey Bay Aquarium Research Institute. A total of 33 taxa (Class Nuda and Tentaculata) were found to occur in Mexican seas, of which 12 of the 33 taxa (36.4 % of the total) were recorded in the Gulf of Mexico, 7 (21.2 %) in the Mexican Caribbean Sea, 25 (75.8 %) in the Gulf of California, 11 (33.3 %) in the Eastern Tropical Pacific, and only 1 (3.0 %) are known in the Northeastern Pacific. Up to nine taxa included in our account represent first records for Mexico (i.e., Bathocyroe fosteri, Kiyohimea usagi, Lampocteis cruentiventer, Leucothea sp., Aulacoctena sp., Haeckelia beehleri, Charistephane fugiens, Bathyctena chuni, and Hormiphora californensis). Due to the lack of data on benthic ctenophores and the sparse studies on oceanic and deep-living species, it is expected that the list will grow as new surveys are performed in the deep sea. The lack of long-term studies on Mexican ctenophores have limited our capacity to draw valid conclusions on their abundance, total diversity, endemicity, and trophic ecology in Mexico. Fil: Puente Tapia, Francisco Alejandro. Instituto Nacional de Investigaciones y Desarrollo Pesquero; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina Fil: Gasca Serrano, Rebeca Adriana. El Colegio de la Frontera del Sur; México Fil: Schiariti, Agustin. Instituto Nacional de Investigaciones y Desarrollo Pesquero; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mar del Plata. Instituto de Investigaciones Marinas y Costeras. Universidad Nacional de Mar del Plata. Facultad de Ciencias Exactas y Naturales. Instituto de Investigaciones Marinas y Costeras; Argentina Fil: Haddock, S.H.D.. Monterey Bay Aquarium Research Institute ; Estados Unidos

The International Seabed Authority (ISA) is developing regulations to control the future exploitation of deep-sea mineral resources including sulphide deposits near hydrothermal vents, polymetallic nodules on the abyssal seafloor, and cobalt crusts on seamounts. Under the UN Convention on the Law of the Sea the ISA is required to adopt are taking measures to ensure the effective protection of the marine environment from harmful effects arising from mining-related activities. Contractors are required to generate environmental baselines and assess the potential environmental consequences of deep seafloor mining. Understandably, nearly all environmental research has focused on the seafloor where the most direct mining effects will occur. However, sediment plumes and other impacts (e.g., noise) from seafloor mining are likely to be extensive in the water column. Sediment plumes created on the seafloor will affect the benthic boundary layer which extends 10s to 100s of meters above the seafloor. Separation or dewatering of ore from sediment and seawater aboard ships will require discharge of a dewatering plume at some depth in the water column. It is important to consider the potential impacts of mining on the ocean’s midwaters (depths from ~200 m to the seafloor) because they provide vital ecosystem services and harbor substantial biodiversity. The better known epipelagic or sunlit surface ocean provisions the rest of the water column through primary production and export flux (This was not the focus at this workshop as the subject was considered too large and surface discharges are unlikely). It is also home to a diverse community of organisms including commercially important fishes such as tunas, billfish, and cephalopods that contribute to the economies of many countries. The mesopelagic or twilight zone (200-1000 m) is dimly lit and home to very diverse and abundant communities of organisms. Mesopelagic plankton and small nekton form the forage base for many deep-diving marine mammals and commercially harvested epipelagic species. Furthermore, detritus from the epipelagic zone falls through the mesopelagic where it is either recycled, providing the vital process of nutrient regeneration, or sinks to greater depths sequestering carbon from short-term atmospheric cycles. The waters below the mesopelagic down to the seafloor (both the bathypelagic and abyssopelagic) are very poorly characterized but are likely large reservoirs of novel biodiversity and link the surface and benthic ecosystems. Great strides have been made in understanding the biodiversity and ecosystem function of the ocean’s midwaters, but large regions, including those containing many exploration license areas and the greater depths where mining plumes will occur, remain very poorly studied. It is clear that pelagic communities are distinct from those on the seafloor and in the benthic boundary layer. They are often sampled with different instrumentation. The fauna have relatively large biogeographic ranges and they are more apt to mix freely across stakeholder boundaries, reference areas and other spatial management zones. Pelagic organisms live in a three-dimensional habitat and their food webs and populations are vertically connected by daily or lifetime migrations and the sinking flux of detritus from the epipelagic. The fauna do not normally encounter hard surfaces, making them fragile, and difficult to capture and maintain for sensitivity or toxicity studies. Despite some existing general knowledge, ecological baselines for midwater communities and ecosystems that likely will be impacted by mining have not been documented. There is an urgent need to conduct more research and evaluate the midwater biota (microbes to fishes) in regions where mining is likely to occur. Deep-sea mining activities may affect midwater organisms in a number of ways, but it is still unclear at what scale perturbations may occur. The sediment plumes both from collectors on the seafloor and from midwater discharge will have a host of negative consequences. They may cause respiratory distress from clogged gills or respiratory surfaces. Suspension feeders, such as copepods, polychaetes, salps, and appendicularians, that filter small particles from the water and form an important basal group of the food web, may suffer from dilution of their food by inorganic sediments and/or clogging of their fragile mucous filter nets. Small particles may settle on gelatinous plankton causing buoyancy issues. Metals, including toxic elements that will enter the food web, will be released from pore waters and crushed ore materials. Sediment plumes will also absorb light and change backscatter properties, reducing visual communication and bioluminescent signaling that are very important for prey capture and reproduction in midwater animals. Noise from mining activities may alter the behaviors of marine mammals and other animals. Small particles have high surface area to volume ratios, high pelagic persistence and dispersal and as a result greater potential to result in pelagic impacts. All of these potential effects will result in mortality, migration (both horizontal and vertical), decreased fitness, and shifts in community composition. Depending on the scale and duration of these effects, there could be reduction in provisioning to commercial fish species, delivery of toxic metals to pelagic food webs and hence human seafood supply, and alterations to carbon transport and nutrient regeneration services. After four days of presentations and discussions, the workshop participants came to several conclusions and synthesized recommendations. 1. Assuming no discharge in the epipelagic zone, it is essential to minimize mining effects in the mesopelagic zone because of links to our human seafood supply as well as other ecosystem services provided by the mesopelagic fauna. This minimization could be accomplished by delivering dewatering discharge well below the mesopelagic/bathypelagic transition (below ~1000 m depth). 2. Research should be promoted by the ISA and other bodies to study the bathypelagic and abyssopelagic zones (from ~1000 m depths to just above the seafloor). It is likely that both collector plumes and dewatering plumes will be created in the bathypelagic, yet this zone is extremely understudied and contains major unknowns for evaluating mining impacts. 3. Management objectives, regulations and management actions need to prevent the creation of a persistent regional scale “haze” (enhanced suspended particle concentrations) in pelagic midwaters. Such a haze would very likely cause chronic harm to deep midwater ecosystem biodiversity, structure and function. 4. Effort is needed to craft suitable standards, thresholds, and indicators of harmful environmental effects that are appropriate to pelagic ecosystems. In particular, suspension feeders are very important ecologically and are likely to be very sensitive to sediment plumes. They are a high priority for study. 5. Particularly noisy mining activities such as ore grinding at seamounts and hydrothermal vents is of concern to deep diving marine mammals and other species. One way to minimize sound impacts would be to minimize activities in the sound-fixing-and-ranging (SOFAR) channel (typically at depths of ~1000 m) which transmits sounds over very long distances. 6. A Lagrangian (drifting) perspective is needed in monitoring and management because the pelagic ecosystem is not a fixed habitat and mining effects are likely to cross spatial management boundaries. For example, potential broad-scale impacts to pelagic ecosystems should be considered in the deliberations over preservation reference zones, the choice of stations for environmental baseline and monitoring studies and other area-based management and conservation measures. 7. Much more modeling and empirical study of realistic mining sediment plumes is needed. Plume models will help evaluate the spatial and temporal extent of pelagic (as well as benthic) ecosystem effects and help to assess risks from different technologies and mining scenarios. Plume modeling should include realistic mining scenarios (including duration) and assess the spatial-temporal scales over which particle concentrations exceed baseline levels and interfere with light transmission to elucidate potential stresses on communities and ecosystem services. Models should include both near and far field-phases, incorporating realistic near field parameters of plume generation, flocculation, particle sinking, and other processes. It is important to note that some inputs to these models such as physical oceanographic parameters are lacking and should be acquired in the near-term. Plume models need to be complemented by studies to understand effects on biological components by certain particle sizes and concentrations.

International audience; High-resolution autonomous sensors routinely measure physical (temperature, salinity), chemical (oxygen, nutrients) and biological (fluorescence) parameters. However, while fluorescence provides a proxy for phyto-plankton, heterotrophic populations remain challenging to monitor in real-time and at high resolution. Bathyphotometers, sensors which measure the light emitted by bioluminescent organisms when mechanically stimulated, provide the capability to identify bioluminescent dinoflagellates and zooplankton. In the coastal ocean, highly abundant dinoflagellates emitting low-intensity flashes generate a background bioluminescence signal, while rarer zooplankton emit bright flashes that can be individually resolved by high-frequency sensors. Bathyphotometers were deployed from ships and onboard autonomous underwater vehicles (AUVs) during three field campaigns in Monterey Bay, California. Ship-based in situ water samples were simultaneously collected and the plankton communities characterized. Plankton concentrations were matched with concurrent datasets of fluorescence and bioluminescence to develop proxies for autotrophic and heterotrophic dinoflagellates, other phytoplankton such as diatoms, copepods, larvaceans (appendicularians), and small jellies. The method extracts the bioluminescence background as a proxy for dinoflagellates, and exploits differences in bioluminescence flash intensity between several types of zooplankton to identify larvaceans, copepods and small jellies. Fluorescence is used to discriminate between autotrophic and heterotrophic dinoflagellates, and to identify other autotrophic plankton. Concurrent fluorometers and bathyphotometers onboard AUVs can thus provide a novel view of plankton diversity and phytoplankton/zooplankton interactions in the sea.

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.

1AbstractOdontosyllis undecimdonta is a marine syllid polychaete that produces bright internal and exuded bioluminescence. Despite over fifty years of biochemical investigation into Odontosyllis bioluminescence, the light-emitting small molecule substrate and catalyzing luciferase protein have remained a mystery. Here we describe the discovery of a bioluminescent protein fraction from O. undecimdonta, the identification of the luciferase using peptide and RNA sequencing, and the in vitro reconstruction of the bioluminescence reaction using highly purified O. undecimdonta luciferin and recombinant luciferase. Lastly, we found no identifiably homologous proteins in publicly available datasets. This suggests that the syllid polychaetes contain an evolutionarily unique luciferase among all characterized luminous taxa.3HighlightsThe polychaete O. undecimdonta uses a luciferin-luciferase bioluminescence systemO. undecimdonta bioluminescence does not require additional cofactorsThe luciferase of the Japanese fireworm is 329 amino acids longRecombinant luciferase is not secreted when expressed in human cellsExogenous luciferin does not seem to penetrate cell membranes-only lysate luminescesThe luciferase transcript is supported by full-length cDNA reads with 5’ and 3’ UTR

Animal evolution is often presented as a march toward complexity, with different living animal groups each representing grades of organization that arose through the progressive acquisition of complex traits. There are now many reasons to reject this classical hypothesis. Not only is it incompatible with recent phylogenetic analyses, but it is also an artifact of ‘hidden biology’, that is, blind spots to complex traits in non-model species. A new hypothesis of animal evolution, where many complex traits have been repeatedly gained and lost, is emerging. As we discuss here, key details of this new model hinge on a better understanding of the Porifera and Ctenophora, which have each been hypothesized to be sister to all other animals, but are poorly studied and often misrepresented.

Siphonophores are a diverse group of hydrozoans (Cnidaria) that are found at all depths of the ocean - from the surface, like the familiar Portuguese man of war, to the deep sea. Siphonophores play an important role in ocean ecosystems, and are among the most abundant gelatinous predators. A previous phylogenetic study based on two ribosomal RNA genes provided insight into the internal relationships between major siphonophore groups, however there was little support for many deep relationships within the clade Codonophora. Here, we present a new siphonophore phylogeny based on new transcriptome data from 30 siphonophore species analyzed in combination with 13 publicly available genomic and transcriptomic datasets. We use this new phylogeny to reconstruct several traits that are central to siphonophore biology, including sexual system (monoecy vs. dioecy), gain and loss of zooid types, life history traits, and habitat. The phylogenetic relationships in this study are largely consistent with the previous phylogeny, but we find strong support for new clades within Codonophora that were previously unresolved. These results have important implications for trait evolution within Siphonophora, including favoring the hypothesis that monoecy arose twice.

Species of the copepod genusSapphirinaThompson, 1829 are deemed as specialized predators of salps. There are only a few documented records of such copepods actually found within their prey. During two cruises of the R/V “Western Flyer” of MBARI (Monterey Bay Aquarium Research Institute), SCUBA diving was used to sample the zooplankton in Monterey Bay and the Gulf of California. An ovigerous female ofSapphirinairisDana, 1849 and a male ofS. sinuicaudaBrady, 1883 were collected inside aggregate zooids of the salpPegea confoederata(Forskål, 1775). Also, two adult females ofS. iriswere recorded insideP. socia(Bosc, 1802); both were lodged near the orifices they made to enter the salp’s body. This is the first documented record of the association involving these sapphirinid copepods lodged in their prey. The high number of eggs of the femaleS. irissupports the suggestion that sapphirinids have a higher fecundity than that of other planktonic copepods, an adaptive strategy related to their mode of life. The find of the maleS. sinuicaudaattached inside the salp differs from earlier observations on the behaviour of sapphirinid males.

The traditional view has been that all species of the phylum Ctenophora are capable of producing light. Our inability to elicit luminescence from members of the well-known genus Pleurobrachia, as well as a lack of published documentation, led to an effort to determine whether this genus is truly bioluminescent. Physical and chemical assays of several species from the family Pleurobrachiidae produced no evidence of bioluminescence capability, although all other species of ctenophores tested gave positive results. Some of the historical misperception that Pleurobrachia can produce light might be attributable to confusion with similar luminous genera.

Some of the most interesting and enigmatic cnidarians are classified within the hydrozoan subclass Trachylina. Despite being relatively depauperate in species richness, the clade contains four taxa typically accorded ordinal status: Actinulida, Limnomedusae, Narcomedusae and Trachymedusae. We bring molecular data (mitochondrial 16S and nuclear small and large subunit ribosomal genes) to bear on the question of phylogenetic relationships within Trachylina. Surprisingly, we find that a diminutive polyp form,Microhydrula limopsicola(classified within Limnomedusae) is actually a previously unknown life stage of a species of Stauromedusae. Our data confirm that the interstitial formHalammohydrasp. (Actinulida) is derived from holopelagic direct developing ancestors, likely within the trachymedusan family Rhopalonematidae. Trachymedusae is shown to be diphyletic, suggesting that the polyp stage has been lost independently at least two times within trachyline evolution. Narcomedusae is supported as a monophyletic group likely also arising from trachymedusan ancestors. Finally, some data, albeit limited, suggest that some trachyline species names refer to cryptic species that have yet to be sorted taxonomically.

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.