NOAA National Systematics Laboratory

Abstract. The deep sea, the largest biome on Earth, has a series of characteristics that make this environment both distinct from other marine and land ecosystems and unique for the entire planet. This review describes these patterns and processes, from geological settings to biological processes, biodiversity and biogeographical patterns. It concludes with a brief discussion of current threats from anthropogenic activities to deep-sea habitats and their fauna. Investigations of deep-sea habitats and their fauna began in the late 19th century. In the intervening years, technological developments and stimulating discoveries have promoted deep-sea research and changed our way of understanding life on the planet. Nevertheless, the deep sea is still mostly unknown and current discovery rates of both habitats and species remain high. The geological, physical and geochemical settings of the deep-sea floor and the water column form a series of different habitats with unique characteristics that support specific faunal communities. Since 1840, 28 new habitats/ecosystems have been discovered from the shelf break to the deep trenches and discoveries of new habitats are still happening in the early 21st century. However, for most of these habitats the global area covered is unknown or has been only very roughly estimated; an even smaller – indeed, minimal – proportion has actually been sampled and investigated. We currently perceive most of the deep-sea ecosystems as heterotrophic, depending ultimately on the flux on organic matter produced in the overlying surface ocean through photosynthesis. The resulting strong food limitation thus shapes deep-sea biota and communities, with exceptions only in reducing ecosystems such as inter alia hydrothermal vents or cold seeps. Here, chemoautolithotrophic bacteria play the role of primary producers fuelled by chemical energy sources rather than sunlight. Other ecosystems, such as seamounts, canyons or cold-water corals have an increased productivity through specific physical processes, such as topographic modification of currents and enhanced transport of particles and detrital matter. Because of its unique abiotic attributes, the deep sea hosts a specialized fauna. Although there are no phyla unique to deep waters, at lower taxonomic levels the composition of the fauna is distinct from that found in the upper ocean. Amongst other characteristic patterns, deep-sea species may exhibit either gigantism or dwarfism, related to the decrease in food availability with depth. Food limitation on the seafloor and water column is also reflected in the trophic structure of heterotrophic deep-sea communities, which are adapted to low energy availability. In most of these heterotrophic habitats, the dominant megafauna is composed of detritivores, while filter feeders are abundant in habitats with hard substrata (e.g. mid-ocean ridges, seamounts, canyon walls and coral reefs). Chemoautotrophy through symbiotic relationships is dominant in reducing habitats. Deep-sea biodiversity is among of the highest on the planet, mainly composed of macro and meiofauna, with high evenness. This is true for most of the continental margins and abyssal plains with hot spots of diversity such as seamounts or cold-water corals. However, in some ecosystems with particularly "extreme" physicochemical processes (e.g. hydrothermal vents), biodiversity is low but abundance and biomass are high and the communities are dominated by a few species. Two large-scale diversity patterns have been discussed for deep-sea benthic communities. First, a unimodal relationship between diversity and depth is observed, with a peak at intermediate depths (2000–3000 m), although this is not universal and particular abiotic processes can modify the trend. Secondly, a poleward trend of decreasing diversity has been discussed, but this remains controversial and studies with larger and more robust data sets are needed. Because of the paucity in our knowledge of habitat coverage and species composition, biogeographic studies are mostly based on regional data or on specific taxonomic groups. Recently, global biogeographic provinces for the pelagic and benthic deep ocean have been described, using environmental and, where data were available, taxonomic information. This classification described 30 pelagic provinces and 38 benthic provinces divided into 4 depth ranges, as well as 10 hydrothermal vent provinces. One of the major issues faced by deep-sea biodiversity and biogeographical studies is related to the high number of species new to science that are collected regularly, together with the slow description rates for these new species. Taxonomic coordination at the global scale is particularly difficult, but is essential if we are to analyse large diversity and biogeographic trends.

Submarine canyons are major geomorphic features of continental margins around the world. Several recent multidisciplinary projects focused on the study of canyons have considerably increased our understanding of their ecological role, the goods and services they provide to human populations, and the impacts that human activities have on their overall ecological condition. Pressures from human activities include fishing, dumping of land-based mine tailings, and oil and gas extraction. Moreover, hydrodynamic processes of canyons enhance the down-canyon transport of litter. The effects of climate change may modify the intensity of currents. This potential hydrographic change is predicted to impact the structure and functioning of canyon communities as well as affect nutrient supply to the deep-ocean ecosystem. This review not only identifies the ecological status of canyons, and current and future issues for canyon conservation, but also highlights the need for a better understanding of anthropogenic impacts on canyon ecosystems and proposes other research required to inform management measures to protect canyon ecosystems.

The advancement of metabarcoding techniques, declining costs of high-throughput sequencing and development of systematic sampling devices, such as autonomous reef monitoring structures (ARMS), have provided the means to gather a vast amount of diversity data from cryptic marine communities. However, such increased capability could also lead to analytical challenges if the methods used to examine these communities across local and global scales are not standardized. Here we compare and assess the underlying biases of four ARMS field processing methods, preservation media, and current bioinformatic pipelines in evaluating diversity from cytochrome c oxidase I metabarcoding data. Illustrating the ability of ARMS-based metabarcoding to capture a wide spectrum of biodiversity, 3,372 OTUs and twenty-eight phyla, including 17 of 33 marine metazoan phyla, were detected from 3 ARMS (2.607 m2 area) collected on coral reefs in Mo'orea, French Polynesia. Significant differences were found between processing and preservation methods, demonstrating the need to standardize methods for biodiversity comparisons. We recommend the use of a standardized protocol (NOAA method) combined with DMSO preservation of tissues for sessile macroorganisms because it gave a more accurate representation of the underlying communities, is cost effective and removes chemical restrictions associated with sample transportation. We found that sequences identified at ≥ 97% similarity increased more than 7-fold (5.1% to 38.6%) using a geographically local barcode inventory, highlighting the importance of local species inventories. Phylogenetic approaches that assign higher taxonomic ranks accrued phylum identification errors (9.7%) due to sparse taxonomic coverage of the understudied cryptic coral reef community in public databases. However, a ≥ 85% sequence identity cut-off provided more accurate results (0.7% errors) and enabled phylum level identifications of 86.3% of the sequence reads. With over 1600 ARMS deployed, standardizing methods and improving databases are imperative to provide unprecedented global baseline assessments of understudied cryptic marine species in a rapidly changing world.

BACKGROUND: Anthozoa, Endocnidozoa, and Medusozoa are the 3 major clades of Cnidaria. Medusozoa is further divided into 4 clades, Hydrozoa, Staurozoa, Cubozoa, and Scyphozoa-the latter 3 lineages make up the clade Acraspeda. Acraspeda encompasses extraordinary diversity in terms of life history, numerous nuisance species, taxa with complex eyes rivaling other animals, and some of the most venomous organisms on the planet. Genomes have recently become available within Scyphozoa and Cubozoa, but there are currently no published genomes within Staurozoa and Cubozoa. FINDINGS: Here we present 3 new draft genomes of Calvadosia cruxmelitensis (Staurozoa), Alatina alata (Cubozoa), and Cassiopea xamachana (Scyphozoa) for which we provide a preliminary orthology analysis that includes an inventory of their respective venom-related genes. Additionally, we identify synteny between POU and Hox genes that had previously been reported in a hydrozoan, suggesting this linkage is highly conserved, possibly dating back to at least the last common ancestor of Medusozoa, yet likely independent of vertebrate POU-Hox linkages. CONCLUSIONS: These draft genomes provide a valuable resource for studying the evolutionary history and biology of these extraordinary animals, and for identifying genomic features underlying venom, vision, and life history traits in Acraspeda.

Reliable estimation of phylogeny is central to avoid inaccuracy in downstream macroevolutionary inferences. However, limitations exist in the implementation of concatenated and summary coalescent approaches, and Bayesian and full coalescent inference methods may not yet be feasible for computation of phylogeny using complicated models and large data sets. Here, we explored methodological (e.g., optimality criteria, character sampling, model selection) and biological (e.g., heterotachy, branch length heterogeneity) sources of systematic error that can result in biased or incorrect parameter estimates when reconstructing phylogeny by using the gadiform fishes as a model clade. Gadiformes include some of the most economically important fishes in the world (e.g., Cods, Hakes, and Rattails). Despite many attempts, a robust higher-level phylogenetic framework was lacking due to limited character and taxonomic sampling, particularly from several species-poor families that have been recalcitrant to phylogenetic placement. We compiled the first phylogenomic data set, including 14,208 loci ($>$2.8 M bp) from 58 species representing all recognized gadiform families, to infer a time-calibrated phylogeny for the group. Data were generated with a gene-capture approach targeting coding DNA sequences from single-copy protein-coding genes. Species-tree and concatenated maximum-likelihood (ML) analyses resolved all family-level relationships within Gadiformes. While there were a few differences between topologies produced by the DNA and the amino acid data sets, most of the historically unresolved relationships among gadiform lineages were consistently well resolved with high support in our analyses regardless of the methodological and biological approaches used. However, at deeper levels, we observed inconsistency in branch support estimates between bootstrap and gene and site coefficient factors (gCF, sCF). Despite numerous short internodes, all relationships received unequivocal bootstrap support while gCF and sCF had very little support, reflecting hidden conflict across loci. Most of the gene-tree and species-tree discordance in our study is a result of short divergence times, and consequent lack of informative characters at deep levels, rather than incomplete lineage sorting. We use this phylogeny to establish a new higher-level classification of Gadiformes as a way of clarifying the evolutionary diversification of the order. We recognize 17 families in five suborders: Bregmacerotoidei, Gadoidei, Ranicipitoidei, Merluccioidei, and Macrouroidei (including two subclades). A time-calibrated analysis using 15 fossil taxa suggests that Gadiformes evolved $\sim $79.5 Ma in the late Cretaceous, but that most extant lineages diverged after the Cretaceous-Paleogene (K-Pg) mass extinction (66 Ma). Our results reiterate the importance of examining phylogenomic analyses for evidence of systematic error that can emerge as a result of unsuitable modeling of biological factors and/or methodological issues, even when data sets are large and yield high support for phylogenetic relationships. [Branch length heterogeneity; Codfishes; commercial fish species; Cretaceous-Paleogene (K-Pg); heterotachy; systematic error; target enrichment.].

Many jellyfish species are known to cause a painful sting, but box jellyfish (class Cubozoa) are a well-known danger to humans due to exceptionally potent venoms. Cubozoan toxicity has been attributed to the presence and abundance of cnidarian-specific pore-forming toxins called jellyfish toxins (JFTs), which are highly hemolytic and cardiotoxic. However, JFTs have also been found in other cnidarians outside of Cubozoa, and no comprehensive analysis of their phylogenetic distribution has been conducted to date. Here, we present a thorough annotation of JFTs from 147 cnidarian transcriptomes and document 111 novel putative JFTs from over 20 species within Medusozoa. Phylogenetic analyses show that JFTs form two distinct clades, which we call JFT-1 and JFT-2. JFT-1 includes all known potent cubozoan toxins, as well as hydrozoan and scyphozoan representatives, some of which were derived from medically relevant species. JFT-2 contains primarily uncharacterized JFTs. Although our analyses detected broad purifying selection across JFTs, we found that a subset of cubozoan JFT-1 sequences are influenced by gene-wide episodic positive selection compared with homologous toxins from other taxonomic groups. This suggests that duplication followed by neofunctionalization or subfunctionalization as a potential mechanism for the highly potent venom in cubozoans. Additionally, published RNA-seq data from several medusozoan species indicate that JFTs are differentially expressed, spatially and temporally, between functionally distinct tissues. Overall, our findings suggest a complex evolutionary history of JFTs involving duplication and selection that may have led to functional diversification, including variability in toxin potency and specificity.

Despite first being described from Virginia, the widely distributed brackish water hydrozoan Blackfordia virginica is often hypothesized to have been introduced from the Black Sea to the United States. However, the alternative view that B. virginica was introduced to the Black Sea also persists in the literature. This study investigates the population structure of B. virginica in the United States to assess the directionality and/or the number of introduction events. During 2009 and 2010, estuaries were sampled from Delaware to Louisiana for brackish water hydromedusae. Nineteen samples of Blackfordia virginica were collected from four localities, including a channel running between St. Catherines Island and Lake Pontchartrain, Louisiana, a region for which it had not been reported prior to this study. We PCR amplified and sequenced two mitochondrial markers (COI & 16S), and one nuclear marker (ITS1). We compared data from individuals collected on the east coast of the United States with individuals collected in California. This revealed low diversity (two haplotypes with a maximal p-difference of 0.03% for COI and just a single haplotype for 16S) and no unique haplotypes at any locality. Low genetic variability, shared haplotypes in disparate localities, and a lack of unique haplotypes in any population are consistent with a founder effect, suggesting a single introduction and subsequent spread throughout the United States.

In this study we address the diversity of the scyphozoan jellyfish genus Nausithoe Klliker, 1853 (Nausithoidae, Coronatae), questioning the feasibility of using some characters of the medusa stage to identify species and filling in gaps concerning species of the genus and their distributions. Like most scyphozoans, the vast majority of the 21 Nausithoe species have a metagenetic life cycle, but similarity of most polyps within the genus highlights the need for studying morphology of the medusa stage. By analyzing morphological features on preserved and live specimens (polyps and medusae) and comparing these data with the original descriptions, we were able to validate twenty species of the group, providing new information for some of them.

Some of the most fascinating and poorly known animals on this planet are comb jellies of the phylum Ctenophora. About one-quarter of ctenophore richness is encompassed by the benthic species of the order Platyctenida, nearly all known from shallow waters. In this work, we integrate several systematic methods to elucidate an enigmatic genus, Tjalfiella, known previously only from deep waters near the western coastline of Greenland in the North Atlantic. For the first time, we employ microCT on museum specimens-one nearly 100 years old from the type locality of the only known species of the genus, T. tristoma-of extant ctenophores to visualize and compare their anatomy. With these data, we integrate in situ videography and genetic sequence data derived from newly collected deep sea specimens observed via NOAA Ship Okeanos Explorer in 2018 and 2022 at two distant localities in the North Atlantic, near North Carolina, USA, and the Azores, Portugal. The genetic data indicate that the newly collected specimens represent closely related but distinct species of Tjalfiella. However, neither can be named at this time because neither one could be definitively differentiated from T. tristoma, given that microCT and in situ imagery reveal striking morphological similarities and only variation in color and host preference. Despite the lack of new species descriptions, this work characterizes both the morphology and genetics of the benthic ctenophore genus Tjalfiella and specimens representing species within it, advancing our understanding of a rarely observed component of the deep-sea fauna.

<i>Ichthyology & Herpetology</i> (formerly <i>Copeia</i>) publishes work on the biology of fishes, amphibians, and reptiles, or work using those organisms as models for testing hypotheses of broad significance.

<i>Ichthyology & Herpetology</i> (formerly <i>Copeia</i>) publishes work on the biology of fishes, amphibians, and reptiles, or work using those organisms as models for testing hypotheses of broad significance.

<i>Ichthyology & Herpetology</i> (formerly <i>Copeia</i>) publishes work on the biology of fishes, amphibians, and reptiles, or work using those organisms as models for testing hypotheses of broad significance.

Striking similarities in morphological characters and significant overlap in meristic features have resulted in different hypotheses regarding the taxonomic status of several nominal species of northwestern Pacific tongue soles of the genus Cynoglossus, including C. joyneri Gnther, 1878, C. lighti Norman, 1925, C. tenuis (Oshima, 1927), and C. tshusanensis Chabanaud, 1951. Previous hypotheses have proposed that each taxon is a valid species; or that C. lighti and C. tshusanensis are junior subjective synonyms of C. joyneri; or that C. tenuis is a junior subjective synonym of either C. joyneri or C. lighti. Although several previous investigations concluded that C. lighti is a synonym of C. joyneri, names of both nominal species still appear in contemporary literature indicating that taxonomic status of these nominal species remains unresolved. To clarify the taxonomic status of these four nominal species, detailed study of morphological characters of 138 specimens collected from 22 localities in Japan and China, and re-examination of type specimens of three of these nominal species was conducted. The molecular barcodes of mitochondrial DNA from six representative specimens featuring morphological variation purportedly useful for distinguishing C. lighti from C. joyneri were also analyzed and then compared with sequences reported for C. joyneri in the literature. Lectotypes of C. joyneri and C. lighti differed in only two morphological characters (body depth and position of posterior tip of rostral hook relative to anterior margin of lower eye). However, when these two characters were examined in 138 recently collected non-type specimens, no differences were found among these nominal species. Our results do not support recognizing these as separate species. Results from genetic analyses also support recognizing only a single species among the material examined. Furthermore, overall similarities in morphological features between the holotype of C. tshusanensis and specimens of C. joyneri support recognizing C. tshusanensis as a junior subjective synonym of C. joyneri. Likewise, values for morphological features of C. joyneri examined in the present study also encompass the range of values reported in the original description of C. tenuis. This finding supports conclusions of previous studies that this nominal species is also a junior synonym of C. joyneri. Based on morphological and genetic evidence, we conclude that only a single species, C. joyneri, should be recognized among the four nominal species included in this study. Cynoglossus joyneri is re-described based on data from 492 specimens collected throughout nearly the entire range of the species.

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

Toothed whales, smaller cetaceans, seabirds, and epipelagic gamefishes rely on deep-pelagic (meso- and bathypelagic) nekton as primary or secondary prey. This trophic interaction is mediated by downward and upward vertical movements (e.g., sperm whale diving and lantern fishes migration, respectively). This interaction also links particle-feeding lower trophic levels with top predators in a manner that spans the gamut of depth domains. This is particularly important with respect to a whole-water column disturbance such as the Deepwater Horizon oil spill (DWHOS). Here we present highly resolved vertical distribution and migration data collected during a large-scale, NOAA-supported, deep-pelagic (0-1500 m) survey in 2011, along with data collected during ongoing GoMRI-supported DEEPEND consortium surveys. The deep-pelagic nekton community of the Gulf of Mexico is a complex mixture of migrating, non-migrating, and partially migrating assemblages that connect surface waters with depths in excess of 1000 m. Major patterns of vertical distribution for 400+ species of fishes, cephalopods, and macrocrustaceans, the primary prey of many important species of oceanic vertebrates living near-surface, will be summarized and quantified with the goal of highlighting potential vectors of anthropogenic contamination transfer in the deep-pelagial, the Gulf's largest ecosystem.

Preassembly of Canthigaster amboinensis (USNM 442417) based on SRA data (SRR14163830, SRR14432035), derived using SPAdes 3.15.2. All contigs less than 200 bp removed.

Preassembly of Canthigaster amboinensis (USNM 442417) based on SRA data (SRR14163830, SRR14432035), derived using SPAdes 3.15.2. All contigs less than 200 bp removed.

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