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The performance of DNA metabarcoding approaches for characterizing biodiversity can be influenced by multiple factors. Here, we used morphological assessment of taxa in zooplankton samples to develop a large barcode database and to assess the congruence of taxonomic identification with metabarcoding under different conditions. We analysed taxonomic assignment of metabarcoded samples using two genetic markers (COI, 18S V1–2), two types of clustering into molecular operational taxonomic units (OTUs, ZOTUs), and three methods for taxonomic assignment (RDP Classifier, BLASTn to GenBank, BLASTn to a local barcode database). The local database includes 1042 COI and 1108 18S (SSU) barcode sequences, and we added new high-quality sequences to GenBank for both markers, including 109 contributions at the species level. The number of phyla detected and the number of taxa identified to phylum varied between a genetic marker and among the three methods used for taxonomic assignments. Blasting the metabarcodes to the local database generated multiple unique contributions to identify OTUs and ZOTUs. We argue that a multi-marker approach combined with taxonomic expertise to develop a curated, vouchered, local barcode database increases taxon detection with metabarcoding, and its potential as a tool for zooplankton biodiversity surveys.

Vision in the midwater of the open ocean requires animals to perform visual tasks quite unlike those of any other environment. These tasks consist of detecting small, low contrast objects and point sources against a relatively dim and uniform background. Deep-sea animals have evolved many extraordinary visual adaptations to perform these tasks. Linking eye anatomy to specific selective pressures, however, is challenging, not least because of the many difficulties of studying deep-sea animals. Computational modelling of vision, based on detailed morphological reconstructions of animal eyes, along with underwater optics, offers a chance to understand the specific visual capabilities of individual visual systems. Prior to the work presented here, comprehensive models for apposition compound eyes in the mesopelagic, the dominant eye form of crustaceans, were lacking. We adapted a model developed for single-lens eyes and used it to examine how different parameters affect the model’s ability to detect point sources and extended objects. This new model also allowed us to examine spatial summation as a means to improve visual performance. Our results identify a trade-off between increased depth range over which eyes function effectively and increased distance at which extended objects can be detected. This trade-off is driven by the size of the ommatidial acceptance angle. We also show that if neighbouring ommatidia have overlapping receptive fields, spatial summation helps with all detection tasks, including the detection of bioluminescent point sources. By applying our model to the apposition compound eyes of Phronima, a mesopelagic hyperiid amphipod, we show that the specialisations of the large medial eyes of Phronima improve both the detection of point sources and of extended objects. The medial eyes outperformed the lateral eyes at every modelled detection task. We suggest that the small visual field size of Phronima’s medial eyes and the strong asymmetry between the medial and lateral eyes reflect Phronima’s need for effective vision across a large depth range and its habit of living inside a barrel. The barrel’s narrow aperture limits the usefulness of a large visual field and has allowed a strong asymmetry between the medial and lateral eyes. The model provides a useful tool for future investigations into the visual abilities of apposition compound eyes in the deep sea.

Gelatinous zooplankton are increasingly acknowledged to contribute significantly to the carbon cycle worldwide, yet many taxa within this diverse group remain poorly studied. Here, we investigate the pelagic tunicate Pyrosoma atlanticum in the waters surrounding the Cabo Verde Archipelago. By using a combination of pelagic and benthic in situ observations, sampling, and molecular genetic analyses (barcoding, eDNA), we reveal that: P. atlanticum abundance is most likely driven by local island-induced productivity, that it substantially contributes to the organic carbon export flux and is part of a diverse range of biological interactions. Downward migrating pyrosomes actively transported an estimated 13% of their fecal pellets below the mixed layer, equaling a carbon flux of 1.96–64.55 mg C m−2 day−1. We show that analysis of eDNA can detect pyrosome material beyond their migration range, suggesting that pyrosomes have ecological impacts below the upper water column. Moribund P. atlanticum colonies contributed an average of 15.09 ± 17.89 (s.d.) mg C m−2 to the carbon flux reaching the island benthic slopes. Our pelagic in situ observations further show that P. atlanticum formed an abundant substrate in the water column (reaching up to 0.28 m2 substrate area per m2), with animals using pyrosomes for settlement, as a shelter and/or a food source. In total, twelve taxa from four phyla were observed to interact with pyrosomes in the midwater and on the benthos.

Lying at the southernmost point of the Lucayan Archipelago, the Turks and Caicos Islands are amongst the better studied localities for anchialine cave biodiversity. For nearly five decades, novel invertebrate fauna, comprised primarily of crustaceans, have been collected from these tidally influenced pools – but new findings are always on the horizon. Herein we present new records of crustaceans and annelids from anchialine blue holes and horizontal caves of the Turks and Caicos. These findings include two potentially new species of meiofaunal annelids and a new species of remipede collected from a shallow water cave pool. Our 2019 expedition additionally expands known faunal distributions for several taxa across the Caicos islands, and raises the biodiversity of the region to 35 species, 13 of them considered endemic. This is the first comprehensive faunal list for the anchialine systems in the Caicos Bank.

Summary Transparent zooplankton and nekton are often nearly invisible when viewed under ambient light in the pelagic zone [1–3]. However, in this environment, where the light field is directional (and thus likely to cause reflections), and under the bioluminescent searchlights of potential predators, animals may be revealed by reflections from their body surface [4–7]. We investigated the cuticle surfaces of seven species of hyperiids (Crustacea; Amphipoda) using scanning electron microscopy and found two undocumented features that may reduce reflectance. We found that the legs of Cystisoma spp. (n = 5) are covered with an ordered array of nanoprotuberances 200 ± 20 nm SD in height that function optically as a gradient refractive index material [6, 8, 9]. Additionally, we observed that Cystisoma and six other species of hyperiids are covered with a monolayer of homogenous spheres (diameters ranging from 52 ± 7 nm SD on Cystisoma spp. to 320 ± 15 nm SD on Phronima spp.). Optical modeling using effective medium theory and transfer matrix methods demonstrated that both the nanoprotuberances and the monolayers reduce reflectance by as much as 100-fold, depending on the wavelength and angle of the incident light and the thickness of the gradient layer. Even though we only consider surface reflectance and not internal light scattering, our study demonstrates that these nanoprotuberances and spheres can improve crypsis in a featureless habitat where the smallest reflection can render an animal vulnerable to visual predation.

Pteropods are a widespread group of holoplanktonic gastropod molluscs and are uniquely suitable for study of long-term evolutionary processes in the open ocean because they are the only living metazoan plankton with a good fossil record. Pteropods have been proposed as bioindicators to monitor the impacts of ocean acidification and in consequence have attracted considerable research interest, however, a robust evolutionary framework for the group is still lacking. Here we reconstruct their phylogenetic relationships and examine the evolutionary history of pteropods based on combined analyses of Cytochrome Oxidase I, 28S, and 18S ribosomal rRNA sequences and a molecular clock calibrated using fossils and the estimated timing of the formation of the Isthmus of Panama. Euthecosomes with uncoiled shells were monophyletic with Creseis as the earliest diverging lineage, estimated at 41–38 million years ago (mya). The coiled euthecosomes (Limacina, Heliconoides, Thielea) were not monophyletic contrary to the accepted morphology-based taxonomy; however, due to their high rate heterogeneity no firm conclusions can be drawn. We found strong support for monophyly of most euthecosome genera, but Clio appeared as a polyphyletic group, and Diacavolinia grouped within Cavolinia, making the latter genus paraphyletic. The highest evolutionary rates were observed in Heliconoides inflatus and Limacina bulimoides for both 28S and 18S partitions. Using a fossil-calibrated phylogeny that sets the first occurrence of coiled euthecosomes at 79–66 mya, we estimate that uncoiled euthecosomes evolved 51–42 mya and that most extant uncoiled genera originated 40–15 mya. These findings are congruent with a molecular clock analysis using the Isthmus of Panama formation as an independent calibration. Although not all phylogenetic relationships could be resolved based on three molecular markers, this study provides a useful resource to study pteropod diversity and provides general insight into the processes that generate and maintain their diversity in the open ocean.

Sphaerodoridae (Annelida) is a seeming uncommon and minimally diverse group of polychaetes in the northwestern Atlantic, with only seven species reported from the United States, and none from the eastern coast of Canada, before the present study. Review of the large Smithsonian collection (National Museum of Natural History, Washington) revealed the presence of two morphologically extraordinary undescribed species and added a new record to the north-western Atlantic region. Euritmia carolensis sp. n. is characterised by bearing approximately 20 sessile spherical papillae arranged in three transverse rows per segment, ventrum with 4–6 larger papillae near the parapodial bases and parapodia without papillae; bearing 4–5 simple chaetae that are enlarged subdistally. Sphaerephesia amphorata sp. n. is distinguished from other congeners in the presence of four longitudinal rows of sessile, bottle-shaped macrotubercles with exceptionally long digitiform terminal papilla, and parapodia with four rounded and small papillae, bearing 4–7 compound chaetae, with blades 7–11 times as long as wide. Other encountered species are also herein re-described, including intraspecific variation and updated iconography. Comparison of material also allowed some systematic changes in the group, including the synonymisation of the genus Amacrodorum with Euritmia, and the transfer of Ephesiopsis shivae to Ephesiella. A key to the species reported from the Northwestern Atlantic is provided., SEMs were taken in Museo Nacional de Ciencias Naturales de Madrid during a European Commission Taxonomic Initiative SYNTHESYS (ESTAF-2839)

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.

We investigated the habitat depth and population dynamics of mesopelagic foraminifera in Monterey Bay, California, using 12 yr of video surveys and specimens from live collections. The water column over Monterey Canyon continuously supports two distinct species of mesopelagic foraminifera, Hastigerinella digitata and a previously unknown species referred to as Hastigerina sp., with H. digitata dominating the planktonic foraminiferal assemblage at mesopelagic depths. H. digitata populations live within a narrow depth horizon that lies above the core of the regional oxygen minimum zone at a depth of 280–358 m and O2 concentrations of 1–1.3 mL L−1. Our observations provide a modern calibration for understanding fossil digitate planktonic foraminifera. We observed numerous copepods in various stages of ingestion on the spines of H. digitata and a conspicuous lack of detritus attached to the spine network, providing support for the hypothesis that H. digitata is an obligate carnivore. H. digitata populations did not show the strong two-phase seasonality that characterizes the population dynamics of many mesopelagic species that live above the Monterey Canyon, although H. digitata was generally more abundant in cooler waters on seasonal and interannual timescales.

Eulepethidae is a family of scale-bearing polychaetes. Although members of this family are common inhabitants of tropical and subtropical coastal waters, their diversity is low, with only 22 recognized species in six genera. Here we describe Eulepethus nanhaiensis sp. nov. based on 12 specimens collected from the coastal waters of the northern South China Sea. This new species can be distinguished from Eulepethus hamifer, the only previously described species in this genus, by having up to two spade-shaped lateral processes in some of the anterior elytrae, a blunt-tipped acicular chaeta in the neuropodia of segment 3, and a pair of non-overlapping elytrae in each posterior segment. Phylogenetic analysis indicates that Grubeulepis and Mexieulepis are sister genera, and these two genera form the sister clade of Eulepethus.

Enteropneusts (phylum Hemichordata), although studied extensively because of their close relationship to chordates, have long been considered shallow-water, burrowing animals. The present paper more than doubles the number of enteropneust species recorded in the deep sea based on high-resolution imaging and sampling with remotely operated vehicles. We provide direct evidence that some enteropneusts are highly mobile—using changes in posture and currents to drift between feeding sites—and are prominent members of deep, epibenthic communities. In addition, we provide ecological information for each species. We also show that despite their great morphological diversity, most deep-living enteropneusts form a single clade (the rediagnosed family Torquaratoridae) on the basis of rDNA sequences and morphology of the proboscis skeleton and stomochord. The phylogenetic position of the torquaratorids indicates that the group, after evolving from near-shore ancestors, radiated extensively in the deep sea.

An intriguing new annelid, Teuthidodrilus samae (Annelida, Cirratuliformia) gen. and sp. nov., was observed and collected during deep-water column exploration of the western Celebes Sea. The Celebes Sea is a deep pocket basin, effectively isolated from surrounding deep water, and is part of the Coral Triangle, a focal area for conservation because of its high diversity and unique geological history. Collected specimens reached 94 mm in length and possessed 10 anterior appendages that were as long or longer than the body. Two characters distinguish T. samae from other polychaetes: notochaetae forming broad, concavo-convex paddles and six pairs of free-standing, oppositely branched nuchal organs. Phylogenetic analysis of five genes and a 29-character morphological matrix showed that T. samae is an acrocirrid (primarily benthic polychaetes) belonging to the morphologically diverse swimming clade. Pelagic animals within primarily benthic clades are of particular interest in evolutionary biology, because their adaptations to life in the water column inform us of the evolutionary possibilities and constraints within the clade and indirectly of the selective pressures at work in this unfamiliar habitat. This new genus illustrates how much we have to learn about even the large, abundant inhabitants of deep-pelagic communities.

By using remotely operated vehicles, we found seven previously unknown species of swimming annelid worms below 1800 meters. Specimens were large and bore a variety of elaborate head appendages. In addition, five species have pairs of ellipsoidal organs homologous to branchiae that produce brilliant green bioluminescence when autotomized. Five genes were used to determine the evolutionary relationships of these worms within Cirratuliformia. These species form a clade within Acrocirridae and were not closely related to either of the two known pelagic cirratuliforms. Thus, this clade represents a third invasion of the pelagic realm from Cirratuliformia. This finding emphasizes the wealth of discoveries to be made in pelagic and deep demersal habitats.