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The deep ocean is the largest biome on Earth and yet it is among the least studied environments of our planet. Life at great depths requires several specific adaptations; however, their molecular mechanisms remain understudied. We examined patterns of positive selection in 416 genes from four brittle star (Ophiuroidea) families displaying replicated events of deep-sea colonization (288 individuals from 216 species). We found consistent signatures of molecular convergence in functions related to protein biogenesis, including protein folding and translation. Five genes were recurrently positively selected, including chaperonin-containing TCP-1 subunit α (CCTα), which is essential for protein folding. Molecular convergence was detected at the functional and gene levels but not at the amino-acid level. Pressure-adapted proteins are expected to display higher stability to counteract the effects of denaturation. We thus examined in silico local protein stability of CCTα across the ophiuroid tree of life (967 individuals from 725 species) in a phylogenetically corrected context and found that deep-sea-adapted proteins display higher stability within and next to the substrate-binding region, which was confirmed by in silico global protein stability analyses. This suggests that CCTα displays not only structural but also functional adaptations to deep-water conditions. The CCT complex is involved in the folding of ∼10% of newly synthesized proteins and has previously been categorized as a “cold-shock” protein in numerous eukaryotes. We thus propose that adaptation mechanisms to cold and deep-sea environments may be linked and highlight that efficient protein biogenesis, including protein folding and translation, is a key metabolic deep-sea adaptation.

The deep sea represents the largest and least explored biome on the planet. Despite the iconic status of the Galapagos Islands and being considered one of the most pristine locations on earth, the deep-sea benthic ecosystems of the archipelago are virtually unexplored in comparison to their shallow-water counterparts. In 2015, we embarked on a multi-disciplinary scientific expedition to conduct the first systematic characterization of deep-sea benthic invertebrate communities of the Galapagos, across a range of habitats. We explored seven sites to depths of over 3,300 m using a two-part Remotely Operated Vehicle (ROV) system aboard the E/V Nautilus, and collected 90 biological specimens that were preserved and sent to experts around the world for analysis. Of those, 30 taxa were determined to be undescribed and new to science, including members of five new genera (2 sponges and 3 cnidarians). We also systematically analysed image frame grabs from over 85 h of ROV footage to investigate patterns of species diversity and document the presence of a range of underwater communities between depths of 290 and 3,373 m, including cold-water coral communities, extensive glass sponge and octocoral gardens, and soft-sediment faunal communities. This characterization of Galapagos deep-sea benthic invertebrate megafauna across a range of ecosystems represents a first step to study future changes that may result from anthropogenic impacts to the planet’s climate and oceans, and informed the creation of fully protected deep-water areas in the Galapagos Marine Reserve that may help preserve these unique communities in our changing planet.

Since 2012, whenOphiothelawas first described in the Atlantic, there has been no consensus regarding its identification. It has been described asO.mirabilis,O. cf.mirabilis,O.danae, or onlyOphiothelasp. In order to fill these gaps, our aim was to test if specimens from Brazil areOphiothela mirabilisand/orOphiothela danae. Syntypes from the Museum of Comparative Zoology and United States National Museum, Smithsonian Institution, were used. We examined species boundaries of the small six-rayed brittle starOphiothelausing independent character sets utilizing morphology (external morphology and morphometry) and molecular data (16S and COI). Concordance was found between the analyses indicating thatOphiothelasp. from Brazil (BR),Ophiothela mirabilisandOphiothela danaeare closely related. We suggest thatO.danaeshould be considered as a junior synonym ofO.mirabilis. A detailed description ofO.mirabilisBR is presented using external morphology and microstructural ossicles (arm plates, vertebra, dental and oral plates). This description includes new diagnostic features, particularly regarding its microstructures: (i) transspondylous articulation (first record in Ophiotrichidae); (ii) eight smooth knobs on the dorsal surface of the vertebrae (to date only inOphiothela); (iii) vertebrae with distal keel divided into two separate end processes matching the two large dorsal grooves proximally (first time in the literature); and (iv) an opening on both sides of the oral plate (as seen in other fissiparous speciesOphiactis savignyiandOphiocomella ophiactoides).

The largest and commercially appealing mineral deposits can be found in the abyssal sea floor of the Clarion-Clipperton Zone (CCZ), a polymetallic nodule province, in the NE Pacific Ocean, where experimental mining is due to take place. In anticipation of deep-sea mining impacts, it has become essential to rapidly and accurately assess biodiversity. For this reason, ophiuroid material collected during eight scientific cruises from five exploration licence areas within CCZ, one area being protected from mining (APEI3, Area of Particular Environmental Interest) in the periphery of CCZ and the DISturbance and re-COLonisation (DISCOL) Experimental Area (DEA), in the SE Pacific Ocean, was examined. Specimens were genetically analysed using a fragment of the mitochondrial cytochrome c oxidase subunit I (COI). Maximum-likelihood and neighbour-joining trees were constructed, while four tree-based and distance-based methods of species delineation (automatic barcode gap discovery, ABGD; barcode index numbers, BINs; general mixed Yule–coalescent, GMYC; multi-rate Poisson tree process, mPTP) were employed to propose secondary species hypotheses (SSHs) within the ophiuroids collected. The species delimitation analyses' concordant results revealed the presence of 43 deep-sea brittle star SSHs, revealing an unexpectedly high diversity and showing that the most conspicuous invertebrates in abyssal plains have been so far considerably underestimated. The number of SSHs found in each area varied from five (IFREMER area) to 24 (BGR (Federal Institute for Geosciences and Natural Resources, Germany) area) while 13 SSHs were represented by singletons. None of the SSHs were found to be present in all seven areas while the majority of species (44.2 %) had a single-area presence (19 SSHs). The most common species were Ophioleucidae sp. (Species 29), Amphioplus daleus (Species 2) and Ophiosphalma glabrum (Species 3), present in all areas except APEI3. The biodiversity patterns could be mainly attributed to particulate organic carbon (POC) fluxes that could explain the highest species numbers found in BGR (German contractor area) and UKSRL (UK Seabed Resources Ltd, UK contractor area) areas. The five exploration contract areas belong to a mesotrophic province, while conversely the APEI3 is located in an oligotrophic province, which could explain the lowest diversity as well as very low similarity with the other six study areas. Based on these results the representativeness and the appropriateness of APEI3 to meet its purpose of preserving the biodiversity of the CCZ fauna are questioned. Finally, this study provides the foundation for biogeographic and functional analyses that will provide insight into the drivers of species diversity and its role in ecosystem function.

Aim Mining and petroleum industries are exploring for resources in deep seafloor environments. Lease areas are often spatially aggregated and continuous over hundreds to thousands of kilometres. Sustainable development of these resources requires an understanding of the patterns of biodiversity at similar scales, yet these data are rarely available for the deep sea. Here, we compare biodiversity metrics and assemblage composition of epibenthic megafaunal samples from deep‐sea benthic habitats from the Great Australian Bight (GAB), a petroleum exploration zone off southern Australia, to similar environments off eastern Australia. Location The Great Australian Bight (34–36°S, 129–134°E) and south‐eastern (SE) and north‐eastern (NE) Australian continental margins (23–42°S, 149–155°E) in depths of 1,900–5,000 m. Methods A species–sample matrix was constructed from invertebrate and fish megafauna collected from beam trawl samples across regions at lower bathyal (1,900–3,200 m) and abyssal (>3,200 m) depths, and analysed using multivariate, rarefaction and model‐based statistics. We modelled rank abundance distributions (RAD) against environmental factors to identify drivers of abundance, richness and evenness. Results Multivariate analyses showed regional and bathymetric assemblage structure across the region. There was an almost complete turnover of sponge fauna between the GAB and SE. SE samples had the highest total faunal abundance and species richness. RAD models linked total abundance and species richness to levels of carbon flux. Evenness was associated with seasonality of net primary production. Conclusions Significant assemblage structure at regional scales is reported for the first time at lower bathyal and abyssal depths in the southern Indo‐Pacific region along latitudinal and longitudinal gradients. The GAB fauna was distinct from other studied areas. Relatively high species richness, previously reported from the GAB continental shelf, did not occur at lower bathyal or abyssal depths. Instead, the abundance, richness and evenness of the benthic fauna are linked to surface primary production, which is elevated off SE Australia.

Bioregions are important tools for understanding and managing natural resources. Bioregions should describe locations of relatively homogenous assemblages of species occur, enabling managers to better regulate activities that might affect these assemblages. Many existing bioregionalization approaches, which rely on expert-derived, Delphic comparisons or environmental surrogates, do not explicitly include observed biological data in such analyses. We highlight that, for bioregionalizations to be useful and reliable for systems scientists and managers, the bioregionalizations need to be based on biological data; to include an easily understood assessment of uncertainty, preferably in a spatial format matching the bioregions; and to be scientifically transparent and reproducible. Statistical models provide a scientifically robust, transparent, and interpretable approach for ensuring that bioregions are formed on the basis of observed biological and physical data. Using statistically derived bioregions provides a repeatable framework for the spatial representation of biodiversity at multiple spatial scales. This results in better-informed management decisions and biodiversity conservation outcomes.

Aim: Biogeographic barriers emerged in the tropical oceans as continental masses moved with plate tectonics, and as the tropics contracted to lower latitudes from the late Eocene. These barriers have shaped tropical marine biodiversity. We characterize large-scale diversity patterns for tropical brittle stars and investigate the effect of biogeographic barriers on these in space and time. Location: Shallow-water (

Background Our knowledge of the benthic fauna at lower bathyal to abyssal (LBA, > 2000 m) depths off Eastern Australia was very limited with only a few samples having been collected from these habitats over the last 150 years. In May–June 2017, the IN2017_V03 expedition of the RV Investigator sampled LBA benthic communities along the lower slope and abyss of Australia’s eastern margin from off mid-Tasmania (42°S) to the Coral Sea (23°S), with particular emphasis on describing and analysing patterns of biodiversity that occur within a newly declared network of offshore marine parks. Methods The study design was to deploy a 4 m (metal) beam trawl and Brenke sled to collect samples on soft sediment substrata at the target seafloor depths of 2500 and 4000 m at every 1.5 degrees of latitude along the western boundary of the Tasman Sea from 42° to 23°S, traversing seven Australian Marine Parks. Results The biological sampling included 35 beam trawls, 28 Brenke sleds, 8 box cores, 20 surface meso-zooplankton tows, and 7 Deep Towed Camera transects. In total, 25,710 specimens were identified to 1084 taxonomic entities, including 847 species-level, 144 genus-level and 69 family-level and 24 higher-level taxa. Of the species-level taxa, only 457 were assigned species-level taxonomic names, which implies that up to 58% of the collected fauna is undescribed. In addition, the ranges of numerous species have been extended to include the western Tasman Sea. Conclusions The lower bathyal and abyssal fauna of soft sediment seafloors off eastern Australia has been systematically surveyed for the first time. The resultant collections will provide the foundation for much future ecological, biogeographical, phylogenetic and taxonomic research.

Although the Kimberley coast situated in north-western Australia has been recognized as one of the world’s least human-impacted coastal areas, many knowledge gaps remain and the diversity and extent of marine life in the Kimberley nearshore habitats, north-west Australian remains. One region that has not been comprehensively surveyed is the King George River, far north-eastern Kimberley. Consequently, a multi-taxon biodiversity and habitat survey was conducted in 2014. The survey included 146 stations ranging from the base of the King George River twin waterfalls to the mouth of the river and 15 km offshore into the Timor Sea. The King George River region contains at least eleven habitat types. As the river bends some four and a half kilometres upstream from the mouth, there are extensive stands of mangroves. Rocky shores occur along the coast. Lesueur Islet is a low, vegetated islet surrounded by a fringing coral reef. Subtidally, the reef supports a diverse coral fauna and algal flora. Deep-water sedimentary and filter feeder communities occur offshore around and beyond Lesueur Islet. A total of 1374 animal and plant lots were collected, comprising about 3500 specimens. A total of 796 species were recorded. There were at least nine new species discovered of which five have since been named. The new species comprised five crustaceans and four echinoderms. In addition, there were eleven new records for Australia (one Cnidarian, two Echinoderms, multiple molluscs, eight crustaceans) and eighteen new records for Western Australia (all Crustaceans.) Our species accumulation curve analyses suggest true species richness may have been much higher than this and that we sampled a small area from a highly diverse community. Total richness is anticipated to be far higher. It is likely that the results are, in part, due to under sampling of hard bottom substrate in the region.

The rare ophiuroid species, Ophioleila elegans, was collected by the submersible Jiaolong from 1 660 m depth on the Caiwei Guyot located in the Magellan Seamount Chain in the Northwest Pacific Ocean. This is the first published record of this species since the types were described from similar habitat off Hawaii. We provide more detailed morphologic characteristics of arm skeleton and a phylogenetic analysis based on CO1 sequences. Both morphology and phylogeny results suggest that the genus Ophioleila is more closely related to Ophiactids than Hemieuryalids.

The Derwent River seastar, ‘Marginaster’ littoralis (Echinodermata: Asteroidea), has been assessed as critically endangered owing to its highly restricted range within one estuary in Tasmania, Australia. However, there have been concerns about the validity and status of the species. Here, we use non-invasive X-ray computed tomography to review the morphology of the holotype. This reveals the presence of internal ossicles to strengthen the disc margin, a character that requires the taxonomic transfer of this species to the family Asterinidae, genus Patiriella. The presence of relatively long marginal spinelets (0.7–0.9 mm) reliably distinguishes this species from the invasive congeneric Patiriella regularis (0.2–0.35 mm). These findings remove doubt about the validity of the species; the recorded habitat and restricted range of Patiriella littoralis are not exceptional for an asterinid seastar. The weight of evidence suggests that it is an endemic species, rather than a transient exotic introduced to Tasmania via shipping or food importation. Its known habitat has been severely impacted by urbanization, poor water quality and invasive species. Targeted surveys in 1993 and 2010 failed to find this species, and it is highly probable that the Derwent River seastar is now extinct; one of the few documented recent marine invertebrate extinctions.

The aim of the present work is to report and describe three new species of the tropical brittle-star genusOphiolepis. The new species are described herein asOphiolepis aemulatasp. nov.,Ophiolepis buitronaesp. nov. andOphiolepis crebrasp. nov. As these species were previously misidentified, morphological traits and similarities between them and other species are extensively discussed.Ophiolepis buitronaesp. nov. is widespread in tropical and warm waters of the western Atlantic from intertidal to 36 m. It has consistently been misidentified asOphiolepis impressaas these two species share a similar distribution and are found together.Ophiolepis aemulatasp. nov. is found in western Australia, as are its congenersOphiolepis superbaandOphiolepis unicolor, whileOphiolepis crebrasp. nov. is found in Australia and Indonesia. There are 25 extant species, including the three new species, which are currently referred to the genusOphiolepis.

1.Generalised Dissimilarity Modelling (GDM) is a statistical method for analysing and predicting patterns of turnover in species composition, usually in response to environmental gradients that vary in space and time. GDM is becoming widely applied in ecology and conservation science to interpret macro-ecological and biogeographical patterns, to support conservation assessment, predict changes in species distributions under climate change and prioritise biological surveys. 2.Inferential and predictive uncertainty is difficult to characterise using current implementations of GDM, reducing the utility of GDM in ecological risk assessment and conservation decision making. Current practice is to undertake permutation tests to assess the importance of variables in GDM. Permutation testing overcomes the issue of data-dependence (because dissimilarities are calculated on a smaller number of observations) but it does not give a quantification of uncertainty in predictions. Here, we address this issue by utilising the Bayesian bootstrap, so that the uncertainty in the observations is carried through the entire analysis (including into the predictions). 3.We tested our Bayesian Bootstrap GDM (BBGDM) approach on simulated datasets and two benthic species datasets. We fitted BBGDMs and GDMs to compare the differences in inference and prediction of compositional turnover that resulted from a coherent treatment of model uncertainty. We showed that our BBGDM approach correctly identified the signal within the data, resulting in an improved characterisation of uncertainty and enhanced model based inference. 4.We show that our approach gives appropriate parameter estimates while better representing the underlying uncertainty that arises when conducting inference and making predictions with GDMs. Our approach to fitting GDMs will provide more realistic insights into parameter and prediction uncertainty. This article is protected by copyright. All rights reserved.

The power and throughput of next-generation sequencing is instigating a major transformation in our understanding of evolution and classification of life on our planet. The new trees of life are robust and comprehensive. Here we provide a landmark phylogeny of the living ophiuroids and use it as the basis for a major revision of the higher classification of this class of marine invertebrates. We used an exon-capture system to generate a 1484 exon (273kbp) data-matrix from DNA extracted from ethanol-preserved museum samples. We successfully obtained an average of 90% of our target sequence from 576 species spread across the known taxonomic diversity. The topology of the major lineages was robust to taxon sampling, exon-sampling, models and methods. However, estimates of node age were much less precise, varying by about a quarter of mean age. We used a combination of phylogenetic distinctiveness and temporal-banding to guide our revision of the family-level classification. Empirically, we determined that limiting family crown age to 110±10Ma (mid Cretaceous) selected phylogenetically distinct nodes while minimising disruption to the existing taxonomy. The resulting scheme of 32 families and six orders considerably expands the number of higher taxa. The families are generally longitudinally widespread across the world's oceans, although 17 are largely confined to temperate and equatorial latitudes and six to relatively shallow water (less than 1000m depth).

Canopy-forming fucoid algae have an important role as ecosystem engineers on rocky intertidal shores, where they increase the abundance of species otherwise limited by exposure during low tide. The facilitative relationship betweenAscophyllum nodosumand associated organisms was explored using a frond breakage experiment (100%, 50%, 25%, 0% intact-frond treatments) in southern England, to assess the consequences of disturbance. Understorey substratum temperature was on average 3°C higher in 0% and 25% intact-frond treatments than in plots with 50% and 100% intact fronds. Light (as PAR during low tide) doubled in 0% intact-frond treatments in comparison to other treatments (which had similar light levels). Mobile invertebrate species richness declined by on average 1 species per m2in the treatments with only 25% and 0% intact fronds, and the abundance ofLittorina obtusatadeclined by 2.4–4.2 individuals per m2in the treatments with 25 and 0% intact fronds. Sessile taxa, includingOsmundea pinnatifidaand encrusting coralline algae, declined by half on average in the 0% intact-frond treatment. These results suggest that the ability ofAscophyllumto mediate environmental conditions to the understorey is the mechanism responsible for species distributed in the understorey (autogenic ecosystem engineering). The results of this study imply that a pulse disturbance resulting in a 50% breakage ofAscophyllumfronds significantly increases temperature and decreases the abundance of mobile invertebrates usually associated withAscophyllum. Sessile taxa associated withAscophyllumcan, however, withstand disturbances down to 25% intactAscophyllumfronds.

Summary The seafloor contains valuable mineral resources, including polymetallic (or manganese) nodules that form on offshore abyssal plains. The largest and most commercially attractive deposits are located in the Clarion Clipperton Fracture Zone (CCZ), in the eastern Pacific Ocean (EP) between Hawaii and Mexico, where testing of a mineral collection system is set to start soon [ 1 ]. The requirement to establish pre-mining environmental management plans has prompted numerous recent biodiversity and DNA barcoding surveys across these remote regions. Here we map DNA sequences from sampled ophiuroids (brittle stars, including post-larvae) of the CCZ and Peru Basin onto a substantial tree of life to show unprecedented levels of abyssal ophiuroid phylogenetic diversity including at least three ancient (>70 Ma), previously unknown clades. While substantial dark (unobserved) biodiversity has been reported from various microbial meta-barcoding projects [ 2 , 3 ], our data show that we have considerably under-estimated the biodiversity of even the most conspicuous mega-faunal invertebrates [ 4 ] of the EP abyssal plain.

The deep ocean is the largest biome on Earth and yet it is among the least studied environments of our planet. Life at great depths requires several specific adaptations, however their molecular mechanisms remain understudied. We examined patterns of positive selection in 416 genes from four brittle star (Ophiuroidea) families displaying replicated events of deep-sea colonization (288 individuals from 216 species). We found consistent signatures of molecular convergence in functions related to protein biogenesis, including protein folding and translation. Five genes were recurrently positively selected, including CCTα (Chaperonin Containing TCP-1 subunit α), which is essential for protein folding. Molecular convergence was detected at the functional and gene levels but not at the amino-acid level. Pressure-adapted proteins are expected to display higher stability to counteract the effects of denaturation. We thus examinedin silicolocal protein stability of CCTα across the ophiuroid tree of life (967 individuals from 725 species) in a phylogenetically-corrected context and found that deep sea-adapted proteins display higher stability within and next to the substrate-binding region, which was confirmed byin silicoglobal protein stability analyses. This suggests that CCTα not only displays structural but also functional adaptations to deep water conditions. The CCT complex is involved in the folding of ∼10% of newly synthesized proteins and has previously been categorized as ‘cold-shock’ protein in numerous eukaryotes. We thus propose that adaptation mechanisms to cold and deep-sea environments may be linked and highlight that efficient protein biogenesis, including protein folding and translation, are key metabolic deep-sea adaptations.

Intertidal fucoid algae can function as ecosystem engineers across temperate marine regions. In this investigation, we assessed the function of the alga dominating rocky reefs in temperate Australia and New Zealand, Hormosira banksii. Invertebrate and algal species assemblages were examined within areas of full H. banksii canopy, areas where it was naturally patchy or absent (within its potential range on the shore) and areas where the intact canopy was experimentally disturbed. Differences in species assemblages were detected between areas with natural variation in H. banksii cover (full, patchy, negligible), with defined species associated with areas of full cover. Differences were also detected between experimentally manipulated and naturally patchy areas of canopy cover. Species assemblages altered in response to canopy manipulations and did not recover even twelve months after initial sampling. Both light intensity and temperature were buffered by full canopies compared to patchy canopies and exposed rock. This study allows us to predict the consequences to the intertidal community due to the loss of canopy cover, which may result from a range of disturbances such as trampling, storm damage, sand burial and prolonged exposure to extreme temperature, and further allow for improved management of this key autogenic ecosystem engineer.

The deep-seafloor in the tropical Indo-Pacific harbours a rich and diverse benthic fauna with numerous palaeoendemics. Here, we describe a new species, genus and family of brittle-star (Ophiuroidea) from a single eight-armed specimen collected from a depth between 360 and 560 m on Banc Durand, a seamount east of New Caledonia. Leveraging a robust, fossil-calibrated (265 kbp DNA) phylogeny for the Ophiuroidea, we estimate the new lineage diverged from other ophiacanthid families in the Late Triassic or Jurassic (median = 187–178 Myr, 95% CI = 215–143 Myr), a period of elevated diversification for this group. We further report very similar microfossil remains from Early Jurassic (180 Myr) sediments of Normandy, France. The discovery of a new ancient lineage in the relatively well-known Ophiuroidea indicates the importance of ongoing taxonomic research in the deep-sea, an environment increasingly threatened by human activities.

The qualification of orthology is a significant challenge when developing large, multiloci phylogenetic data sets from assembled transcripts. Transcriptome assemblies have various attributes, such as fragmentation, frameshifts and mis-indexing, which pose problems to automated methods of orthology assessment. Here, we identify a set of orthologous single-copy genes from transcriptome assemblies for the land snails and slugs (Eupulmonata) using a thorough approach to orthology determination involving manual alignment curation, gene tree assessment and sequencing from genomic DNA. We qualified the orthology of 500 nuclear, protein-coding genes from the transcriptome assemblies of 21 eupulmonate species to produce the most complete phylogenetic data matrix for a major molluscan lineage to date, both in terms of taxon and character completeness. Exon capture targeting 490 of the 500 genes (those with at least one exon >120 bp) from 22 species of Australian Camaenidae successfully captured sequences of 2825 exons (representing all targeted genes), with only a 3.7% reduction in the data matrix due to the presence of putative paralogs or pseudogenes. The automated pipeline Agalma retrieved the majority of the manually qualified 500 single-copy gene set and identified a further 375 putative single-copy genes, although it failed to account for fragmented transcripts resulting in lower data matrix completeness when considering the original 500 genes. This could potentially explain the minor inconsistencies we observed in the supported topologies for the 21 eupulmonate species between the manually curated and 'Agalma-equivalent' data set (sharing 458 genes). Overall, our study confirms the utility of the 500 gene set to resolve phylogenetic relationships at a range of evolutionary depths and highlights the importance of addressing fragmentation at the homolog alignment stage for probe design.

The deep ocean is the largest and least-explored ecosystem on Earth, and a uniquely energy-poor environment. The distribution, drivers and origins of deep-sea biodiversity remain unknown at global scales. Here we analyse a database of more than 165,000 distribution records of Ophiuroidea (brittle stars), a dominant component of sea-floor fauna, and find patterns of biodiversity unlike known terrestrial or coastal marine realms. Both patterns and environmental predictors of deep-sea (2,000-6,500 m) species richness fundamentally differ from those found in coastal (0-20 m), continental shelf (20-200 m), and upper-slope (200-2,000 m) waters. Continental shelf to upper-slope richness consistently peaks in tropical Indo-west Pacific and Caribbean (0-30°) latitudes, and is well explained by variations in water temperature. In contrast, deep-sea species show maximum richness at higher latitudes (30-50°), concentrated in areas of high carbon export flux and regions close to continental margins. We reconcile this structuring of oceanic biodiversity using a species-energy framework, with kinetic energy predicting shallow-water richness, while chemical energy (export productivity) and proximity to slope habitats drive deep-sea diversity. Our findings provide a global baseline for conservation efforts across the sea floor, and demonstrate that deep-sea ecosystems show a biodiversity pattern consistent with ecological theory, despite being different from other planetary-scale habitats.

The biogeography of the deep-sea benthic fauna is uncertain due to the vast size and incomplete exploration of these environments. While shallow water assemblages are differentiated into tropical, temperate and polar faunas, it is unknown whether these units extend to lower depths. Here we use model-based and multivariate statistics to analyse megafaunal benthic samples along a 2300 km transect off the eastern Australian continental margin. We show that a temperate-tropical transition between 33-30°S occurs at both lower bathyal (~2500 m) and abyssal (~4000 m) depths. This transition occurs despite almost uniform temperature, salinity and dissolved oxygen concentrations occurring across latitudes at these depths. Conversely, the patterns are consistent with the flux of organic matter to the seafloor, which varies from being relatively high in the productive temperate off SE Australia to low levels in more-oligotrophic tropical waters. Biodiversity is not uniform across the deep-sea and regional-scale heterogeneity needs to be incorporated into marine park designs.

Background The Great Australian Bight (GAB) comprises the majority of Australia’s southern coastline, but to date its deep water fauna has remained almost unknown. Recent issuing of oil and gas leases in the region has highlighted this lack of baseline biological data and established a pressing need to characterise benthic abyssal fauna. Methods From 2013 to 2017, six large-scale systematic surveys of the GAB were conducted from 200 to 5000 m depth, constituting the deepest systematic biological sampling in Australia. Sampling was conducted on soft sediment and hard substrates, both at pre-determined depth intervals along north-south transect lines and at sites of interest identified by multibeam sonar. Results A total of 66,721 invertebrate specimens were collected, comprising 1267 species, with 401 species (32%) new to science. In addition to the novelty of the fauna, there was a high degree of rarity, with 31% of species known only from single specimens. Conclusions In this paper, we provide an annotated checklist of the benthic invertebrate fauna of the deep GAB, supplemented with colour photos of live specimens and commentary on taxonomy, diversity and distributions. This work represents an important addition to knowledge of Australia’s deep sea fauna, and will provide the foundation for further ecological, biogeographical and systematic research.

Caves are a useful system for testing evolutionary and biogeographic hypotheses, as they are isolated, and their environmental conditions have resulted in adaptive selection across different taxa. Although in recent years many more cave species have been discovered, cave-dwelling members of the class Ophiuroidea (brittle stars) remain scarce. Out of the more than two thousand species of brittle stars described to date, only three are regarded as true cave-dwellers. These occurrences represent rare colonising events, compared to other groups that are known to have successfully diversified in these systems. A third species from an anchihaline cave system in the Yucatan Peninsula, Mexico, has been previously identified from cytochrome oxidase I (COI) barcodes. In this study, we reassess the species boundaries of this putative cave species using a phylogenomic dataset (20 specimens in 13 species, 100 exons, 18.7 kbp). We perform species delimitation analyses using robust full-coalescent methods for discovery and validation of hypotheses on species boundaries, as well as infer its phylogenetic relationships with species distributed in adjacent marine regions, in order to investigate the origin of this cave-adapted species. We assess which hypotheses on the origin of subterranean taxa can be applied to this species by taking into account its placement within the genus Ophionereis and its demographic history. We provide a detailed description of Ophionereis commutabilis n. sp., and evaluate its morphological characters in the light of its successful adaptation to life in caves.

Brittlestars in the family Ophiocomidae are large and colourful inhabitants of tropical shallow water habitats across the globe. Here we use targeted capture and next-generation sequencing to generate robust phylogenomic trees for 39 of the 43 species in order to test the monophyly of existing genera. The large genus Ophiocoma, as currently constituted, is paraphyletic on our trees and required revision. Four genera are recognised herein: an expanded Ophiomastix (now including Ophiocoma wendtii, O. occidentalis, O. endeani, O. macroplaca, and Ophiarthrum spp), Ophiocomella (now including the non-fissiparous Ophiocoma pumila, aethiops and valenciae) and Breviturma (now including Ophiocoma pica, O. pusilla, O. paucigranulata and O. longispina) and a restricted Ophiocoma. The resulting junior homonym Ophiomastix elegans is renamed O. brocki. The genus Ophiomastix exhibits relatively high rates of morphological disparity compared to other lineages. Ophiomastix flaccida and O. (formerly Ophiarthrum) pictum have divergent mitochondrial genomes, characterised by gene-order rearrangements, strand recoding, enriched GT base composition, and a corresponding divergence of nuclear mitochondrial protein genes. The new phylogeny indicates that larval and developmental transitions occurred rarely. Larval culture trials show that species with abbreviated lecithotrophic larval development occur only within Ophiomastix, although the possible monophyly of these species is obscured by the rapid early radiation within this genus. Asexual reproduction by fission is limited to one species-complex within Ophiocomella, also characterised by elevated levels of allelic heterozygosity, and which has achieved a relatively rapid global distribution. The crown ages of the new genera considerably predate the closure of the Tethyan seaway and all four are distributed in both the Atlantic and Indo-Pacific Oceans. Two species pairs appear to reflect the closure of the Panama Seaway, although their fossil-calibrated node ages (12–14 ± 6 my), derived from both concatenated sequence and multispecies coalescent analyses, considerably predate the terminal closure event. Ophiocoma erinaceus has crossed the East Pacific barrier and is recorded from Clipperton Island, SW of Mexico.

A new classification of Ophiuroidea, considering family rank and above, is presented. The new family and superfamily taxa in O’Hara et al. (2017) were proposed to ensure a better readability of the new phylogeny but are unavailable under the provisions of the ICZN. Here, the morphological diagnoses to all 33 families and five superfamilies are provided. Ten new families, Ophiosphalmidae fam. nov., Ophiomusaidae fam. nov., Ophiocamacidae fam. nov., Ophiopteridae fam. nov., Clarkcomidae fam. nov., Ophiopezidae fam. nov., Ophiernidae fam. nov., Amphilimnidae fam. nov., Ophiothamnidae fam. nov. and Ophiopholidae fam. nov., are described. The family Ophiobyrsidae Matsumoto, 1915, not yet discovered in the previous publication, is added, based on new molecular data. A new phylogenetic reconstruction is presented. Definitions of difficult-to-apply morphological characters are given.

Our knowledge of the distribution and evolution of deep-sea life is limited, impeding our ability to identify priority areas for conservation1. Here we analyse large integrated phylogenomic and distributional datasets of seafloor fauna from the sea surface to the abyss and from equator to pole of the Southern Hemisphere for an entire class of invertebrates (Ophiuroidea). We find that latitudinal diversity gradients are assembled through contrasting evolutionary processes for shallow (0-200 m) and deep (>200 m) seas. The shallow-water tropical-temperate realm broadly reflects a tropical diversification-driven process that shows exchange of lineages in both directions. Diversification rates are reversed for the realm that contains the deep sea and Antarctica; the diversification rates are highest at polar and lowest at tropical latitudes, and net exchange occurs from high to low latitudes. The tropical upper bathyal (200-700 m deep), with its rich ancient phylodiversity, is characterized by relatively low diversification and moderate immigration rates. Conversely, the young, specialized Antarctic fauna is inferred to be rebounding from regional extinctions that are associated with the rapid cooling of polar waters during the mid-Cenozoic era.

O’Hara, T.D. and Harding, C. 2015. Enigmatic ophiuroids from the New Caledonian region. Memoirs of Museum

Background There is growing interest in mining polymetallic nodules from the abyssal Clarion-Clipperton Zone (CCZ) in the tropical Pacific Ocean. Despite being the focus of environmental studies for decades, the benthic megafauna of the CCZ remain poorly known. In order to predict and manage the environmental impacts of mining in the CCZ, baseline knowledge of the megafauna is essential. The ABYSSLINE Project has conducted benthic biological baseline surveys in the UK Seabed Resources Ltd polymetallic-nodule exploration contract area (UK-1). Prior to these research cruises in 2013 and 2015, no biological studies had been done in this area of the eastern CCZ. New information Using a Remotely Operated Vehicle and Autonomous Underwater Vehicle, the megafauna within the UKSRL exploration contract area (UK-1) and at a site ~250 km east of the UK-1 area were surveyed, allowing us to make the first estimates of megafaunal morphospecies richness from the imagery collected. Here, we present an atlas of the abyssal echinoderm megafauna observed and collected during the ABYSSLINE cruises to the UK-1 polymetallic-nodule exploration contract area in the CCZ. There appear to be at least 62 distinct morphospecies (13 Asteroidea, 5 Crinoidea, 9 Echinoidea, 29 Holothuroidea and 6 Ophiuroidea) identified mostly by imagery but also using molecular barcoding for a limited number of animals that were collected. This atlas will aid the synthesis of megafaunal presence/absence data collected by contractors, scientists and other stakeholders undertaking work in the CCZ, ultimately helping to decipher the biogeography of the megafauna in this threatened habitat.

Echinoderms, including feather stars, seastars, brittle stars, sea urchins and sea cucumbers, are some of the most beautiful and interesting animals in the sea. They play an important ecological role and several species of sea urchins and sea cucumbers form the basis of important fisheries. Over 1000 species live in Australian waters, from the shoreline to the depths of the abyssal plain and the tropics to Antarctic waters. Australian Echinoderms is an authoritative account of Australia’s 110 families of echinoderms. It brings together in a single volume comprehensive information on the identification, biology, evolution, ecology and management of these animals for the first time. Richly illustrated with beautiful photographs and written in an accessible style, Australian Echinoderms suits the needs of marine enthusiasts, academics and fisheries managers both in Australia and other geographical areas where echinoderms are studied. Winner of the 2018 Whitley Medal

Neuropeptides are a diverse class of intercellular signalling molecules that mediate neuronal regulation of many physiological and behavioural processes. Recent advances in genome/transcriptome sequencing are enabling identification of neuropeptide precursor proteins in species from a growing variety of animal taxa, providing new insights into the evolution of neuropeptide signalling. Here, detailed analysis of transcriptome sequence data from three brittle star species, Ophionotus victoriae , Amphiura filiformis and Ophiopsila aranea , has enabled the first comprehensive identification of neuropeptide precursors in the class Ophiuroidea of the phylum Echinodermata. Representatives of over 30 bilaterian neuropeptide precursor families were identified, some of which occur as paralogues. Furthermore, homologues of endothelin/CCHamide, eclosion hormone, neuropeptide-F/Y and nucleobinin/nesfatin were discovered here in a deuterostome/echinoderm for the first time. The majority of ophiuroid neuropeptide precursors contain a single copy of a neuropeptide, but several precursors comprise multiple copies of identical or non-identical, but structurally related, neuropeptides. Here, we performed an unprecedented investigation of the evolution of neuropeptide copy number over a period of approximately 270 Myr by analysing sequence data from over 50 ophiuroid species, with reference to a robust phylogeny. Our analysis indicates that the composition of neuropeptide ‘cocktails’ is functionally important, but with plasticity over long evolutionary time scales.

In this paper we examine the phylogeny and biogeography of the temperate genera of the Ophiocomidae (Echinodermata: Ophiuroidea) which have an interesting asymmetrical anti-tropical distribution, with two genera (Ophiocomina and Ophiopteris) previously considered to have a separate species in both the North and South hemispheres, and the third (Clarkcoma) diversifying in the southern Australian/New Zealand region. Our phylogeny, generated from one mitochondrial and two nuclear markers, revealed that Ophiopteris is sister to a mixed Ophiocomina/Clarkcoma clade. Ophiocomina was polyphyletic, with O. nigra and an undescribed species from the South Atlantic Ocean sister to a clade including Clarkcoma species and O. australis. The phylogeny also revealed a number of recently diverged lineages occurring within Clarkcoma, some of which are considered to be cryptic species due to the similarity in morphology combined with the apparent absence of interbreeding in a sympatric distribution, while the status of others is less certain. The phylogeny provides support for two transequatorial events in the group under study. A molecular clock analysis places both events in the middle to late Miocene. The analysis excludes a tectonic vicariance hypothesis for the antitropical distribution associated with the breakup of Pangaea and also excludes the hypothesis of more recent gene flow associated with Plio/Pleistocene glacial cycling.

The marine species of the southern coast of Australia have not been well studied with regard to molecular connectivity. Cryptic species are expected to be prevalent on this coastline. Here, we investigate the crinoid genus Cenolia (Echinodermata: Crinoidea: Comasteridae) using molecular methods to elucidate cryptic species and phylogenetic relationships. The genus Cenolia dominates the southern Australian crinoid fauna in shallow waters. Few studies have examined crinoids for cryptic species at a molecular level and these have been predominantly based on mitochondrial data. We employ the nuclear markers 28S rRNA and ITS-2 in addition to the mitochondrial COI. Six divergent mitochondrial clades were identified. Gene flow between confirmed clades was subsequently examined by the use of six novel microsatellite markers, showing that sympatric taxa with low mtDNA divergences (1.7% K2P) were not interbreeding in the wild. The type specimens of Cenolia benhami and C. spanoschistum were examined, as well as all six divergent clades. Morphological characters dividing taxa were refined. Due to comb pinnule morphology, the New Zealand species benhami was determined to belong to the genus Oxycomanthus (nov. comb.). Three new species of Cenolia (including the Australian "benhami") require description.

There have been comparatively few large-scale studies on spatial genetic structure of bathyal seafloor fauna, despite the importance of these data to the successful management of the world's oceans. We use a comparative analysis of mitochondrial DNA from five bathyal (200-3500 m) species of brittle-stars (Ophiuroidea) to assess phylogeographic structure along an extensive (8000 km) longitudinal gradient at temperate latitudes (28-56 degrees S) from south-west Australia (113 degrees E) to seamounts east of New Zealand (175 degrees W). We found no evidence of a genetic discontinuity between Australia and New Zealand, either across the temperate Tasman Sea or across the Southern Ocean between the South Tasman Rise and the Macquarie Ridge. However, there were latitudinal phylogeographical breaks between tropical, temperate and polar regions; longitudinal breaks across the eastern Indian Ocean; and a bathymetric break at approximately 1700 m. Although there was limited regional structure in the frequency of haplotype distributions within the major clades, and no clade appeared to be strictly panmictic, the regional structure in general was not concordant with a simple isolation-by-distance model. Demographic structure varied with three clades having a simplified haplotype network, low effective population sizes and no evidence of significant population expansion, and two clades having a high diversity of haplotypes, relatively high effective population sizes and signs of recent population expansion. These results are discussed with respect to putative dispersal strategies. We hypothesise that the 'brooding' species produce both brooded young and pelagic larvae, allowing for both the maintenance of local populations and long-distance dispersal. (C) 2013 Elsevier Ltd. All rights reserved.

O'Hara, T.D. and Harding, C. 2014. A new species of Sigsbeia and additional records of ophiuroids from the Great Australian Bight. Memoirs of Museum Victoria 72: 131-140. A new species of Sigsbeia (Hemieuryalidae: Ophiuroidea) is described from south-western Australia. Previously, all species of Hemieuryalidae sensu stricto have been found in the tropical western Atlantic and eastern Pacific Oceans. Consequently, all currently recognised families of Ophiuroidea now have been collected from the Australian and New Zealand region. Additional new ophiuroid records from the Great Australian Bight include Astrotoma manilense, Ophiothrix albostriata, previously known only from the holotype, and Ophiomusium scalare. New Zealand records formerly called Astrotoma drachi are referred to A. manilense. The available name Ophiomusium aporum is synonymised with O. scalare rather than O. incertum or O. australe where it has previously been placed.

Aim Biogeographical regions are often used as a basis for management strategies, yet a challenge for biodiversity management across broad scales is establishing biogeographical regions that are robust across taxonomic groups. Methods Finite mixture models were developed to predict multiple species assemblages termed archetypes. Modelled species archetypes were developed using Decapoda, Ophiuroidea and Polychaeta species, which were grouped based on their similar responses to oceanographic and geographical gradients. Location Outer-shelf and slope (50–1200 m) of the continental margin of Western Australia (~11° S–36° S). Results Four faunal regions were defined based on cross-taxa surrogates grouped as archetypes. These faunal regions were defined by oxygen, salinity, carbon and temperature gradients across latitude and bathymetry. Two broad latitudinal bands and two bathyal regions were described. Adjacent faunal groups were not defined by abrupt geographical breaks but rather transitions. Main conclusions These results suggest that faunal distributions were less finely resolved than existing marine bioregions on the Western Australian continental margin and that environmental gradients are correlated with distributions of benthic marine invertebrates. Identifying biogeographical regions based on these methods has the potential to inform management across a broad range of environments.

The use of environmental data in biogeographic studies of the deep sea is providing greater insight into the processes underlying large-scale patterns of diversity. Recent surveys of Australia's western continental margin (~100–1100 m) provide systematic sampling of invertebrate megafauna along a gradient of 22° of latitude (13–35° S). Diversity patterns of decapod crustaceans were examined and we investigated the relative importance of environmental and spatial predictor variables on both species richness (alpha diversity) and species turnover. Distance-based linear models (DistLM) indicated a suite of variables were important in predicting species turnover, of which temperature and oxygen were the most influential. These reflected the oceanographic features that dominate distinct depth bathomes along the slope. The numbers of species within samples were highly variable; a small but significant increase in diversity towards the tropics was evident. Replicated sampling along the margin at ~100 m and ~400 m provided an opportunity to compare latitudinal patterns of diversity at different depths. On the shallow upper slope (~400 m) temperature was disassociated from latitude and the latter proved to be the best predictor of sample species richness. The predictive power of latitude over other variables indicates that proximity to the highly diverse Indo-West Pacific (IWP) may be important, especially considering that almost 40% of species in this study had a wide IWP distribution. In the management of Australia's marine environments, geomorphic surrogates have been emphasised when defining areas for protection. We found sea-floor characteristics were relatively less important in predicting richness or community composition.

The taxonomy of ophiuroids collected in 2009 and 2011, from biogenic habitats across the New Zealand continental shelf, is reviewed. Ophionereis novaezelandiae Mortensen, 1936, and its junior synonym Ophionereis terba Baker & Devaney, 1981from South-Eastern Australia, is now recognised as a distinct species, and has been removed from synonymy with Ophionereis fasciata Hutton, 1872. Ophiacantha abyssicola var. otagoensis Fell, 1958 is also recognised as a distinct spe-cies and has been removed from synonymy with Ophiacantha brachygnatha Clark H L, 1928. Amphiura eugeniae var. latisquama Mortensen, 1924 is raised to species rank and Amphioplus longirima Fell, 1952 treated as a synonym of A. latisquama . Ophiolycus farquhari McKnight, 2003 is transferred to the genus Ophiologimus . The diagnostic characters of several other species are reviewed and colour descriptions and images are included where available. The tropical species Ophiacantha longidens Lyman, 1878, Ophiotreta valenciennesi (Lyman, 1879) and Ophiobyrsa intorta (Koehler, 1922) are reported from New Zealand waters for the first time.

Dendrogramma was the iconic deep-sea animal of 2014, voted among the top-ten new species described that year [1]. The two species described are mushroom shaped animals, diploblastic, with an apparent gastrovascular system that extends from the base of the stalk to bifurcating canals that radiate through the flat disc [2]. The authors could not assign the new genus to any known animal group with certainty, leading to numerous media reports that it belonged to an entirely new phylum. Here we use phylogenomic data from newly collected specimens to show that Dendrogramma is a cnidarian, specifically a benthic siphonophore in the family Rhodaliidae. Although an entire Dendrogramma colony has not been found, we hypothesise that the mushroom-like bodies are bracts, possibly used to aid buoyancy or as defensive appendages to protect feeding gastrozooids or gonads.

Compiled as part of the Global Census of Marine Life, Biological Sampling in the Deep Sea is a comprehensive look at all major sampling techniques for the biggest habitat on earth: the deep sea. This important publication commences with introductory chapters looking at the deep sea habitat and current survey and sampling design. The major part of this new book covers all the major types of gear, each in a separate chapter. Chapters each follow a standard format and include a range of carefully-selected illustrations. The final part of the book includes chapters covering the preservation and curation of biological samples, identification of samples, information management, data analysis, applications to managing deep sea resources and biodiversity, with a final chapter looking to the future. This is considered an essential purchase for all scientists working with deep sea environments, including marine biologists, fisheries scientists, ecologists, oceanographers and environmental scientists. All universities where biological sciences, fisheries, and oceanography are studied and taught should have copies of this most important book on their shelves [Book Synopsis]