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Numerous genomic methods developed over the past two decades have enabled the discovery and extraction of orthologous loci to help resolve phylogenetic relationships across various taxa and scales. Genome skimming (or low‐coverage genome sequencing) is a promising method to not only extract high‐copy loci but also 100s to 1000s of phylogenetically informative nuclear loci (e.g., ultraconserved elements [UCEs] and exons) from contemporary and museum samples. The subphylum Anthozoa, including important ecosystem engineers (e.g., stony corals, black corals, anemones, and octocorals) in the marine environment, is in critical need of phylogenetic resolution and thus might benefit from a genome‐skimming approach. We conducted genome skimming on 242 anthozoan corals collected from 1886 to 2022. Using existing target‐capture baitsets, we bioinformatically obtained UCEs and exons from the genome‐skimming data and incorporated them with data from previously published target‐capture studies. The mean number of UCE and exon loci extracted from the genome skimming data was 1837 ± 662 SD for octocorals and 1379 ± 476 SD loci for hexacorals. Phylogenetic relationships were well resolved within each class. A mean of 1422 ± 720 loci was obtained from the historical specimens, with 1253 loci recovered from the oldest specimen collected in 1886. We also obtained partial to whole mitogenomes and nuclear rRNA genes from >95% of samples. Bioinformatically pulling UCEs, exons, mitochondrial genomes, and nuclear rRNA genes from genome skimming data is a viable and low‐cost option for phylogenetic studies. This approach can be used to review and support taxonomic revisions and reconstruct evolutionary histories, including historical museum and type specimens. [ABSTRACT FROM AUTHOR]

Deep-sea lineages are generally thought to arise from shallow-water ancestors, but this hypothesis is based on a relatively small number of taxonomic groups. Anthozoans, which include corals and sea anemones, are significant contributors to the faunal diversity of the deep sea, but the timing and mechanisms of their invasion into this biome remain elusive. Here, we reconstruct a fully resolved, time-calibrated phylogeny of 83 species in the order Antipatharia (black coral) to investigate their bathymetric evolutionary history. Our reconstruction indicates that extant black coral lineages first diversified in continental slope depths (∼250–3000 m) during the early Silurian (∼437 millions of years ago (Ma)) and subsequently radiated into, and diversified within, both continental shelf (less than 250 m) and abyssal (greater than 3000 m) habitats. Ancestral state reconstruction analysis suggests that the appearance of morphological features that enhanced the ability of black corals to acquire nutrients coincided with their invasion of novel depths. Our findings have important conservation implications for anthozoan lineages, as the loss of 'source' slope lineages could threaten millions of years of evolutionary history and confound future invasion events, thereby warranting protection. [ABSTRACT FROM AUTHOR]

Whole mitochondrial genomes are often used in phylogenetic reconstruction. However, discordant patterns in species relationships between mitochondrial and nuclear phylogenies are commonly observed. Within Anthozoa (Phylum Cnidaria), mitochondrial (mt)-nuclear discordance has not yet been examined using a large and comparable dataset. Here, we used data obtained from target-capture enrichment sequencing to assemble and annotate mt genomes and reconstruct phylogenies for comparisons to phylogenies inferred from hundreds of nuclear loci obtained from the same samples. The datasets comprised 108 hexacorals and 94 octocorals representing all orders and > 50% of extant families. Results indicated rampant discordance between datasets at every taxonomic level. This discordance is not attributable to substitution saturation, but rather likely caused by introgressive hybridization and unique properties of mt genomes, including slow rates of evolution driven by strong purifying selection and substitution rate variation. Strong purifying selection across the mt genomes caution their use in analyses that rely on assumptions of neutrality. Furthermore, unique properties of the mt genomes were noted, including genome rearrangements and the presence of nad5 introns. Specifically, we note the presence of the homing endonuclease in ceriantharians. This large dataset of mitochondrial genomes further demonstrates the utility of off-target reads generated from target-capture data for mt genome assembly and adds to the growing knowledge of anthozoan evolution. [ABSTRACT FROM AUTHOR]

Anthozoan cnidarians (corals and sea anemones) include some of the world's most important foundation species, capable of building massive reef complexes that support entire ecosystems. Although previous molecular phylogenetic analyses have revealed widespread homoplasy of the morphological characters traditionally used to define orders and families of anthozoans, analyses using mitochondrial genes or rDNA have failed to resolve many key nodes in the phylogeny. With a fully resolved, time-calibrated phylogeny for 234 species constructed from hundreds of ultraconserved elements and exon loci, we explore the evolutionary origins of the major clades of Anthozoa and some of their salient morphological features. The phylogeny supports reciprocally monophyletic Hexacorallia and Octocorallia, with Ceriantharia as the earliest diverging hexacorals; two reciprocally monophyletic clades of Octocorallia; and monophyly of all hexacoral orders with the exception of the enigmatic sea anemone Relicanthus daphneae. Divergence dating analyses place Anthozoa in the Cryogenian to Tonian periods (648–894 Ma), older than has been suggested by previous studies. Ancestral state reconstructions indicate that the ancestral anthozoan was a solitary polyp that had bilateral symmetry and lacked a skeleton. Colonial growth forms and the ability to precipitate calcium carbonate evolved in the Ediacaran (578 Ma) and Cambrian (503 Ma) respectively; these hallmarks of reef-building species have subsequently arisen multiple times independently in different orders. Anthozoans formed associations with photosymbionts by the Devonian (383 Ma), and photosymbioses have been gained and lost repeatedly in all orders. Together, these results have profound implications for the interpretation of the Precambrian environment and the early evolution of metazoans.[Bilateral symmetry; coloniality; coral; early metazoans; exon capture; Hexacorallia; Octocorallia photosymbiosis; sea anemone; ultraconserved elements.] [ABSTRACT FROM AUTHOR]

In August 2007, October 2008 and September–October 2010, 241 Tucker trawl and plankton net tows were conducted at the surface to depths of 1377 m at six locations in the northern and eastern Gulf of Mexico (GOM) to document leptocephalus diversity and determine how assemblage structure, larval size, abundance and isotopic signatures differ across the region and with depth. Overall, 2696 leptocephali representing 59 distinct taxa from 10 families were collected. Five families accounted for 96% of the total catch with Congridae and Ophichthidae being the most abundant. The top four most abundant species composed 59% of the total catch and included: Ariosoma balearicum, Paraconger caudilimbatus, Rhynchoconger flavus and Ophichthus gomesii. Four anguilliform species not previously documented in the GOM as adults or leptocephali were collected in this study, including Monopenchelys acuta, Quassiremus ascensionis, Saurenchelys stylura and one leptocephalus only known from its larval stage, Leptocephalus proboscideus. Leptocephalus catches were significantly greater at night than during the day. Catches at night were concentrated in the upper 200 m of the water column and significantly declined with increasing depth. Leptocephali abundances and assemblages were significantly different between sites on the upper continental slope (c. 500 m depth) and sites on the middle to lower continental slope (c. 1500–2300 m). Sites on the lower continental slope had a mixture of deep‐sea demersal, bathypelagic and coastal species, whereas upper‐slope sites contained several numerically dominant species (e.g., A. balearicum, P. caudilimbatus) that probably spawn over the continental shelf and upper slope of the GOM. Standard lengths of the four dominant species differed between sites and years, indicating heterochronic reproduction and potential larval source pools within and outside of the GOM. Stable‐isotope analyses (δ13C and δ15N) conducted on 185 specimens from six families revealed that leptocephali had a wide range of isotopic values at the family and size‐class levels. Species in the families Muraenidae, Congridae and Ophichthidae had similar δ15N values compared with the broad range of δ15N values seen in the deep‐sea families Nemichthyidae, Nettastomatidae and Synaphobranchidae. Stable‐isotope values were variably related to length, with δ15N values being positively size correlated in ophichthids and δ13C values being negatively size correlated in A. balearicum and P. caudilimbatus. Results suggest that leptocephali feed in various water depths and masses, and on different components of POM, which could lead to niche partitioning. Ecological aspects of these important members of the plankton community provide insight into larval connectivity in the GOM as well as the early life history of Anguilliformes. [ABSTRACT FROM AUTHOR]

Abstract: Anthozoans (e.g., corals, anemones) are an ecologically important and diverse group of marine metazoans that occur from shallow to deep waters worldwide. However, our understanding of the evolutionary relationships among the ~7,500 species within this class is hindered by the lack of phylogenetically informative markers that can be reliably sequenced across a diversity of taxa. We designed and tested 16,306 RNA baits to capture 720 ultraconserved element loci and 1,071 exon loci. Library preparation and target enrichment were performed on 33 taxa from all orders within the class Anthozoa. Following Illumina sequencing and Trinity assembly, we recovered 1,774 of 1,791 targeted loci. The mean number of loci recovered from each species was 638 ± 222, with more loci recovered from octocorals (783 ± 138 loci) than hexacorals (475 ± 187 loci). Parsimony informative sites ranged from 26 to 49% for alignments at differing hierarchical taxonomic levels (e.g., Anthozoa, Octocorallia, Hexacorallia). The per cent of variable sites within each of three genera (Acropora, Alcyonium, and Sinularia) for which multiple species were sequenced ranged from 4.7% to 30%. Maximum‐likelihood analyses recovered highly resolved trees with topologies matching those supported by other studies, including the monophyly of the order Scleractinia. Our results demonstrate the utility of this target‐enrichment approach to resolve phylogenetic relationships from relatively old to recent divergences. Redesigning the baits with improved affinities to capture loci within each subclass will provide a valuable toolset to address systematic questions, further our understanding of the timing of diversifications and help resolve long‐standing controversial relationships in the class Anthozoa. [ABSTRACT FROM AUTHOR]

Target‐capture approaches have facilitated a rapid growth in the field of phylogenomics but few probe sets exist for molluscs, an exceptionally rich phylum with unparalleled ecological and morphological diversity. We designed and tested the first universal probe set using Phyluce to capture ultraconserved elements (UCEs) and exon loci from the Subclass Caenogastropoda ‐ one of six major lineages of gastropods. The probe set consists of 29,441 probes designed to target 1142 UCE loci and 1933 exon loci (3075 total). In silico analyses of our probe set yielded an average of 2110 loci from genomes and 1389 loci from transcriptomes of diverse caenogastropods, from which an average of 1669 and 849 loci were retained respectively after screening to remove those that matched multiple contigs. Phylogenetic analyses of the loci extracted from transcriptomes produced well‐supported trees very similar to those published based on transcriptomic analyses. Phylogenetic relationships estimated from loci extracted from genomes recover similar phylogenetic relationships, and indicate that the loci targeted with this probe set are informative for resolving deep phylogenetic relationships. An in vitro analysis of the probe set with the Epitoniidae, a diverse caenogastropod family of uncertain affinity and with poorly resolved evolutionary relationships, recovered a total of 2850 loci. Although preliminary, the analysis of loci captured by our probe set for a small number of epitoniid taxa produced a well‐resolved tree indicating that this probe set is also able to resolve relationships at shallower hierarchical scales. Together, the in silico and in vitro analyses indicate that target‐capture enrichment with this probe set is a useful tool for reconstructing phylogenetic relationships across taxonomic levels and evolutionary time scales. [ABSTRACT FROM AUTHOR]

Recent investigations of demersal fish communities in deepwater (>50 m) habitats have considerably increased our knowledge of the factors that influence the assemblage structure of fishes across mesophotic to deep-sea depths. While different habitat types influence deepwater fish distribution, whether different types of rugged seafloor features provide functionally equivalent habitat for fishes is poorly understood. In the northeastern Caribbean, different types of rugged features (e.g., seamounts, banks, canyons) punctuate insular margins, and thus create a remarkable setting in which to compare demersal fish communities across various features. Concurrently, several water masses are vertically layered in the water column, creating strong stratification layers corresponding to specific abiotic conditions. In this study, we examined differences among fish assemblages across different features (e.g., seamount, canyon, bank/ridge) and water masses at depths ranging from 98 to 4060 m in the northeastern Caribbean. We conducted 26 remotely operated vehicle dives across 18 sites, identifying 156 species of which 42% of had not been previously recorded from particular depths or localities in the region. While rarefaction curves indicated fewer species at seamounts than at other features in the NE Caribbean, assemblage structure was similar among the different types of features. Thus, similar to seamount studies in other regions, seamounts in the Anegada Passage do not harbor distinct communities from other types of rugged features. Species assemblages, however, differed among depths, with zonation generally corresponding to water mass boundaries in the region. High species turnover occurred at depths <1200 m, and may be driven by changes in water mass characteristics including temperature (4.8–24.4 °C) and dissolved oxygen (2.2–9.5 mg per l). Our study suggests the importance of water masses in influencing community structure of benthic fauna, while considerably adding to the knowledge of mesophotic and deep-sea fish biogeography. [ABSTRACT FROM AUTHOR]

Deep-sea corals are the structural foundation of their ecosystems along continental margins worldwide, yet the factors driving their broad distribution are poorly understood. Environmental factors, especially depth-related variables including water mass properties, are thought to considerably affect the realized distribution of deep-sea corals. These factors are governed by local and regional oceanographic conditions that directly influence the dispersal of larvae, and therefore affect the ultimate distribution of adult corals. We used molecular barcoding of mitochondrial and nuclear sequences to identify species of octocorals in the genus Paramuricea collected from the Labrador Sea to the Grand Banks of Newfoundland, Canada at depths of 150–1500 m. The results of this study revealed overlapping bathymetric distributions of the Paramuricea species present off the eastern Canadian coast, including the presence of a few cryptic species previously designated as Paramuricea placomus . The distribution of Paramuricea species in the western North Atlantic differs from the Gulf of Mexico, where five Paramuricea species exhibit strong segregation by depth. The different patterns of Paramuricea species in these contrasting biogeographic regions provide insight into how water mass structure may shape species distribution. Investigating Paramuricea prevalence and distribution in conjunction with oceanographic conditions can help demonstrate the factors that generate and maintain deep-sea biodiversity. [ABSTRACT FROM AUTHOR]

The article presents the highlights of the three-leg Océano Profundo 2015 expedition that was conducted by the U.S. National Oceanic and Atmospheric Administration (NOAA) Office of Ocean Exploration and Research (OER) to study and characterize the deep waters around Puerto Rico and the U.S. Virgin Islands (USVI). Among the activities is the collection of high-resolution multibeam bathymetry, backscatter, and subbottom data of the seafloor.

The continental margin off the northeastern United States (NEUS) contains numerous, topographically complex features that increase habitat heterogeneity across the region. However, the majority of these rugged features have never been surveyed, particularly using direct observations. During summer 2013, 31 Remotely-Operated Vehicle (ROV) dives were conducted from 494 to 3271 m depth across a variety of seafloor features to document communities and to infer geological processes that produced such features. The ROV surveyed six broad-scale habitat features, consisting of shelf-breaching canyons, slope-sourced canyons, inter-canyon areas, open-slope/landslide-scar areas, hydrocarbon seeps, and Mytilus Seamount. Four previously unknown chemosynthetic communities dominated by Bathymodiolus mussels were documented. Seafloor methane hydrate was observed at two seep sites. Multivariate analyses indicated that depth and broad-scale habitat significantly influenced megafaunal coral (58 taxa), demersal fish (69 taxa), and decapod crustacean (34 taxa) assemblages. Species richness of fishes and crustaceans significantly declined with depth, while there was no relationship between coral richness and depth. Turnover in assemblage structure occurred on the middle to lower slope at the approximate boundaries of water masses found previously in the region. Coral species richness was also an important variable explaining variation in fish and crustacean assemblages. Coral diversity may serve as an indicator of habitat suitability and variation in available niche diversity for these taxonomic groups. Our surveys added 24 putative coral species and three fishes to the known regional fauna, including the black coral Telopathes magna, the octocoral Metallogorgia melanotrichos and the fishes Gaidropsarus argentatus, Guttigadus latifrons, and Lepidion guentheri. Marine litter was observed on 81% of the dives, with at least 12 coral colonies entangled in debris. While initial exploration revealed the NEUS region to be both geologically dynamic and biologically diverse, further research into the abiotic conditions and the biotic interactions that influence species abundance and distribution is needed. [ABSTRACT FROM AUTHOR]

Deep-sea communities are becoming increasingly vulnerable to anthropogenic disturbances, as fishing, hydrocarbon exploration and extraction, and mining activities extend into deeper water. Negative impacts from such activities were recently documented in the Gulf of Mexico (GoM), where the Deepwater Horizon oil spill caused substantial damage to a deep-water octocoral community. Although a faunal checklist and numerous museum records are currently available for the entire GoM, local-scale diversity and assemblage structure of octocoral communities remains unknown, particularly in deep water. On a series of recent cruises (2008–2011) using remotely operated vehicles, 435 octocorals were collected from 33 deep-water sites (250–2500 m) in the northern GoM. To elucidate species boundaries, the extended mitochondrial barcode (COI+igr1+msh) was successfully amplified and sequenced for 422 of these specimens, yielding a total of 64 haplotypes representing at least 52 species. Further, at least 29% of the species collected were either previously not known to occur in the GoM (12 species) or represent new species (at least three species). Overall, species richness at each site was fairly low (1–12 spp.). The greatest species richness occurred at the shallowest (<325 m: GC140, n=8 spp.) and the deepest (2100–2500 m: DC673, n=12 spp., DC583, n=10 spp.) sites, and minimum taxonomic and phylogenetic (Faith's Index) diversity was evident at 600–950 m. This pattern is the opposite of the typical pattern of deep-sea diversity in the GoM, which normally peaks at mid-slope depths. Sorensen's Index of taxonomic β-diversity indicated that six distinct (65–95% dissimilarity) species assemblages corresponded with five depth breaks at ~325, 425, 600, 1100, and 2100 m. Further assemblage structure was observed within certain depth zones. Of note, within the 425–600 m depth range, species assemblages at the West Florida Slope differed from the other sites, corresponding to an established biogeographic barrier. The phylogenetic approach used in this study provided important insights into the species boundaries of many taxa while demonstrating that evolutionary history plays a critical role in community structure of deep-sea octocorals. [ABSTRACT FROM AUTHOR]

Species in the genus Paramuricea are among the most common corals in deep waters (>200 m) of the Gulf of Mexico. Paramuricea spp. increase habitat heterogeneity and provide substrate for numerous faunal associates, including ophiuroids that occur on the majority of coral colonies. In light of the Deepwater Horizon oil spill in the Gulf of Mexico, it has become apparent that there is a critical need for data on population dynamics within this genus. To date, at least one species of Paramuricea (P. biscaya) is known to be negatively impacted by the spill. Using remotely operated vehicles from 2009 to 2011, we documented the density and size frequency distributions of Paramuricea across 21 sites at depths of 250–2500 m. Molecular barcoding (mtCOI+igr+MutS) was used to delineate species boundaries among the specimens collected. Results suggested that seven haplotypes are present in the Gulf, and appear to be partially segregated by depth [(type H: <260 m) (type E: 278–445 m) (type A: 443–541 m) (types B1–B3: 800–2600 m)]. Densities of Paramuricea spp. determined by ROV surveys were mapped onto high-resolution bathymetric data, which confirmed the corals' preference for topographic highs composed of hard substrata. At any one site, densities ranged from 0.043±0.01 (VK906, 380 m) to 1.18±0.81 colonies/m2 (GC852, 1410 m). Mortality and recruitment rates were estimated from size-frequency data combined with estimated growth rates. Mortality rate decreased with size, from approximately 20% and 70% in new recruits of Paramuricea B3 and P. biscaya respectively, to less than 10% in colonies over 40 cm in both species. Recruitment rates were estimated from less than one to over 30 individuals per year per site, but patterns in size-frequency histograms suggest that this process is highly variable at the different sites and at different times. These data illustrate that populations of the slow-growing Paramuricea species are sparsely distributed and exhibit low recruitment rates, making them highly susceptible to anthropogenic threats. [ABSTRACT FROM AUTHOR]

Environmental variables that are correlated with depth have been suggested to be among the major forces underlying speciation in the deep sea. This study incorporated phylogenetics and ecological niche models ( ENM) to examine whether congeneric species of Callogorgia (Octocorallia: Primnoidae) occupy different ecological niches across the continental slope of the Gulf of Mexico (GoM) and whether this niche divergence could be important in the evolution of these closely related species. Callogorgia americana americana, Callogorgia americana delta and Callogorgia gracilis were documented at 13 sites in the GoM (250-1000 m) from specimen collections and extensive video observations. On a first order, these species were separated by depth, with C. gracilis occurring at the shallowest sites, C. a. americana at mid-depths and C. a. delta at the deepest sites. Callogorgia a. delta was associated with areas of increased seep activity, whereas C. gracilis and C. a. americana were associated with narrow, yet warmer, temperature ranges and did not occur near cold seeps. ENM background and identity tests revealed little to no overlap in ecological niches between species. Temporal calibration of the phylogeny revealed the formation of the Isthmus of Panama was a vicariance event that may explain some of the patterns of speciation within this genus. These results elucidate the potential mechanisms for speciation in the deep sea, emphasizing both bathymetric speciation and vicariance events in the evolution of a genus across multiple regions. [ABSTRACT FROM AUTHOR]

Abstract: Midwater fish faunas over three cold seep habitats >1000m (AC601, GC852, AT340) and over a cold-water coral bank (VK826, <1000m) in the north-central Gulf of Mexico (GOM) are described and compared. Day and night discrete-depth sampling was accomplished at each study site, 9–29 August 2007, using an opening–closing Tucker trawl towed at depth for 30min. The 159 Tucker trawl stations yielded 9802 individuals and at least 126 species (30 families) of juvenile and adult midwater fishes. Myctophidae (38 species, 28% of the total catch), Stomiidae (17 species, 1.4%), Gonostomatidae (12 species, 56%), Sternoptychidae (10 species, 6%), and Phosichthyidae (5 species, 6%) dominated catches at all sites. Thirty-one species (8 families) comprised about 90% of the overall abundance of fishes across the four sites. Despite the wide separation of study sites and some differences in physical oceanography, geographic and temporal patterns in mesopelagic fish assemblages were not evident (ANOSIM, Global R=0.20, p=0.1%, pairwise R values <0.3). However, station groupings were related mostly to similarities in sampled depths (SIMPROF, p<1.5%). Upper water-column station groups (<400m) were typified by Lepidophanes guentheri, Diaphus dumerilii, Vinciguerria nimbaria, Vinciguerria poweriae, Valenciennellus tripunctulatus, Argyropelecus aculeatus, Notolychnus valdiviae, Benthosema suborbitale, Gonostoma elongatum, and Hygophum taaningi. Deeper station groups (mean depth=609m) were typified by Cyclothone alba, Cyclothone acclinidens, Cyclothone braueri, Cyclothone obscura, Cyclothone pallida, Cyclothone pseudopallida, V. tripunctulatus, and Hygophum benoiti. Depth, diel, and size distributions were also analyzed for abundant species. For example, Cyclothone spp., abundant at all sites except VK826, usually occurred in deeper waters (>130m), especially during daylight hours (>335m). Most Cyclothone individuals were captured at night at GC852, whereas catches were more evenly distributed across times at AT340 and VK826. Cyclothone spp. individuals occurred in the deeper parts of the sampled depth range at AT340 and VK826 at all times compared with GC852, where they appeared to undergo a diel migration. The two most abundant Cyclothone spp., C. pallida and C. pseudopallida, had the broadest depth ranges (150–1377m) and exhibited a trend for larger specimens to occur deeper at GC852. Most V. tripunctulatus were captured at night and tended to have larger mean sizes in deeper waters. This species did not exhibit strong diel patterns of vertical distribution. Shallower depths were occupied at night by some individuals at all sites, but most individuals remained somewhat deeper at night at VK826 (350–450m at night and 200–350m by day) and AT340 (200–600m at night and 300–500m by day) compared with GC852 (150–450m at night and 750 and 1000m by day). Nearly all Vinciguerria poweriae were caught at night, and no clear trend of size with depth was apparent. This species occupied a wider depth range at night, with most in the upper 200m. Most myctophids, the strongest diel migrators, were captured at night at the offshore stations. The dominant myctophid, N. valdiviae, was most abundant at GC852 (550–1050m by day and 50–750m at night), but diel movement was more distinct at AT340 (<200m at night and 350–500m by day). No size-related trends with depth were apparent at any site for N. valdiviae, and size distributions were similar among sites. This study and others support the hypothesis that there is a geographically similar mesopelagic fish fauna throughout the GOM. However, the fauna does vary by depth, with some species remaining in deep waters at all times (e.g., Cyclothone spp.) and others occurring at mid-depths and exhibiting varying degrees of diel migration (e.g., many myctophids). Even though faunal composition is similar across the GOM, some species exhibit different movement behaviors at different locations. Such variances could be related to differences in physical or chemical factors, food resources, lunar phase, or bottom depth. [Copyright &y& Elsevier]

Deep-water coral habitats are scattered throughout slope depths (360–800 m) off the Southeastern United States (SEUS, Cape Lookout, North Carolina, to Cape Canaveral, Florida), contributing substantial structure and diversity to bottom habitats. In some areas ( e.g. off North Carolina) deep corals form nearly monotypic ( Lophelia pertusa) high profile mounds, and in other areas ( e.g. off Florida) many species may colonize hard substrata. Deep coral and hard substrata ecosystems off the SEUS support a unique fish assemblage. Using the Johnson-Sea-Link submersible (in 2000–2005, 65 dives), and a remotely operated vehicle (in 2003, five dives), fishes were surveyed in nine deep reef study areas along the SEUS slope. Forty-two benthic reef fish species occurred in deep reef habitats in these study areas. Species richness was greatest on the two coral banks off Cape Lookout, North Carolina (n = 23 and 27 species) and lowest on the two sites off Cape Canaveral, Florida (n = 7 and 8 species). Fish assemblages exhibited significantly (ANOSIM, Global R = 0.69, P = 0.001) different patterns among sites. Stations sampled off North Carolina (three study areas) formed a distinct group that differed from all dives conducted to the south. Although several species defined the fish assemblages at the North Carolina sites, Laemonema barbatulum, Laemonema melanurum, and Helicolenus dactylopterus generally had the most influence on the definition of the North Carolina group. Fish assemblages at three sites within the central survey area on the Blake Plateau were also similar to each other, and were dominated by Nezumia sclerorhynchus and L. melanurum. Synaphobranchus spp. and Neaumia sclerorhynchus differentiated the two southern sites off Cape Canaveral, Florida, from the other station groups. Combinations of depth and habitat type had the most influence on these station groups; however, explicit mechanisms contributing to the organization of these assemblages remain unclear. [ABSTRACT FROM AUTHOR]

Fenestraja plutonia is an abundant member of the slope community in the western North Atlantic, occurring at depths of 293-1042 m. Aspects of the reproductive biology of F plutonia were examined for specimens collected off North Carolina. in the summer fall of 2001, 2002, and 2006. Male-to-female sex ratios were not significantly different from I:I. The smallest mature male was 215 mm TL, and the smallest mature female was 230 mm TL. Length at 50% maturity was estimated at 231 mm TL for females and 233 mm TL for males, 89 and 90% of maximum TL, respectively. Deposited egg cases (n = 107: six containing embryos), three egg-bearing females, and 11 newly hatched juveniles were collected. It appears that the upper slope off Cape Lookout, NC, at the northern end of the species range, constitutes both an egg-laying area and possibly a nursery area for this species. [ABSTRACT FROM AUTHOR]

Eptatretus lopheliae, new species, is described from three specimens caught at 430-442 m depth in cold-water coral habitat off the southeastern United States. It is diagnosed by elongated tubular nostril, lack of nasal-sinus papillae, five pairs of gill pouches, 3-cusp multicusps in anterior and posterior row of teeth but with variation of 4 cusps in posterior row, 38-41 total cusp count, 19-21 prebranchial slime pores, 88-89 total pores, palatine tooth triangular, and pinkish-orange body color. Eptatretus Iopheliae is a small hagfish species observed, videotaped, and caught in close association with Lophelia pertusa reef habitat. [ABSTRACT FROM AUTHOR]

Abstract: Deep-sea or cold-water corals form substantial habitat along many continental slopes, including the southeastern United States (SEUS). Despite increasing research on deep coral systems and growing appreciation of their importance to fishes, quantitative data on fish communities occupying these ecosystems are relatively lacking. Our overall goals were to document the fish species and their relative abundances and to describe the degree of general habitat specificity of the fishes on and around deep coral habitats on the SEUS slope. From 2000 to 2006, we used the Johnson-Sea-Link (JSL) submersible (65 dives, 366–783m), supplemented with otter trawls (33 tows, 365–910m) to document fishes and habitats from off North Carolina to east-central Florida. Eight areas with high concentrations of deep-sea corals were surveyed repeatedly. Three general habitat types (prime reef, transition reef, and off reef) were defined to determine large-scale habitat use patterns. Throughout the area, at least 99 fish species were identified, many (19%) of which yielded new distributional data. Most species observed with the JSL were on prime reef (n=50) and transition reef (n=42) habitats, but the off reef habitat supported a well developed, but different fauna (n=25 species). Prime reef was characterized by Laemonema melanurum (21% of total), Nezumia sclerorhynchus (17% of total), Beryx decadactylus (14% of total), and Helicolenus dactylopterus (10% of total). The off reef areas were dominated by Fenestraja plutonia (19% of total), Laemonema barbatulum (18% of total), Myxine glutinosa (8% of total), and Chlorophthalmus agassizi (7% of total). Transition habitat exhibited a mixture of species that were also found on either prime reef or off reef habitats. Nezumia sclerorhynchus was the most abundant (25% of total) transition habitat species, followed by L. barbatulum (16% of total) and L. melanurum (14% of total). Several species (e.g., Anthias woodsi, B. decadactylus, Conger oceanicus, and Dysommina rugosa) demonstrated specificity to deep-reef habitats, while others (e.g., C. agassizi, Benthobatis marcida, F. plutonia, and Phycis chesteri) were always more common away from reefs. In addition to new distributional data, we provide behavioral and biological observations for dominant species. [Copyright &y& Elsevier]

The article focuses on the fish community data and its relation to the proposed marine protected areas (MPA) on the outer shelf in the U.S. Fish community data are limited from deeper shelf edge hardbottoms. In 2001-2004, sampling was conducted to describe habitats and fish communities within and outside of the MPA in North Carolina. Non-metric, multi-dimensional scaling showed that hardbottom fish assemblages were distinct from non-hardbottom. A total of 152 fish species were documented.

The Gulf Stream (GS) is a major oceanographic feature with potential to influence the recruitment of larval fishes to continental shelf habitats in the southeastern United States. To test the hypothesis that the GS is a source of certain larval fishes to Onslow Bay, North Carolina, we (i) classified water masses as shelf, GS, GS front (GSF), or GS/shelf mixture (GS/S); (ii) compared larval fish assemblages and concentrations among these water masses; and (iii) compared length–frequency distributions and length–concentration relationships of indicator and commercially important taxa among water masses. A total of 21,222 larvae were collected with bongo and neuston nets from April 2000 to December 2001. Non-metric multidimensional scaling analyses revealed distinct larval assemblages associated with different water masses. For bongo catches, bothids were abundant in all water masses, gobiids, callionymids, and labrids were abundant in shelf waters, and myctophids and scombrids were abundant in the GS. For neuston catches, carangids dominated in GS/S, GSF, and GS waters, whereas triglids were abundant in shelf water. Larval concentrations in neuston catches were lower in shelf waters and higher in GS and GSF waters. Concentrations of most taxa in bongo catches were low in the GS and higher in shelf waters. We used trends in myctophid (offshore/GS) and gobiid (shelf) length–concentration data as indicators of the sources of commercially important serranids. Length distributions and concentrations of larval indicator taxa suggested local, shelf spawning, and transport of larvae from offshore. [ABSTRACT FROM AUTHOR]

Along the southeastern coast of the United States, hardground systems support a high diversity of sub-tropical and tropical fishes. Many of these hardgrounds occur in deep (ca. ≥ 50 m) waters and their fauna is still poorly described; however, with concentrated sampling in these deeper areas, new records of fishes continue to emerge. In the northeastern Gulf of Mexico and off North Carolina, we used the Johnson-Sea-Link submersible, remotely operated vehicles, trawling gear, and angling gear to sample deep reef systems (38-248 m). We document five records of fishes new to continental United States waters, including Liopropoma aberrans, Parasphyraenops incisus, Lipogramma regia, Apogon gouldi, and Prognathodes guyanensis. We also report range extensions for eleven species: Gymnothorax hubbsi, Gymnothorax vicinus, Lepophidium staurophor, Cypselurus comatus, Liopropoma mowbrayi, Serranus annularis, Rypticus saponaceus, Caranx lugubris, Prognathodes aculeatus, Centropyge argi, and Canthigaster jamestyleri. [ABSTRACT FROM AUTHOR]

Once considered the most speciose mostly azooxanthellate scleractinian group, the family Caryophylliidae is found to be highly polyphyletic based on molecular data and is undergoing a process of systematic revision. High‐throughput sequencing methods coupled with morphological analyses have facilitated revision of several scleractinian lineages, including the aforementioned family. In previous studies that relied on few mitochondrial and nuclear markers, the caryophylliid genera Stephanocyathus and Vaughanella were phylogenetically recovered in separate clades from the lineage that includes the type genus of the family, Caryophyllia, which is considered the 'true' Caryophylliidae. To help untangle the relationship among taxa of this family, here a new deep‐sea scleractinian family (Stephanocyathidae Vaga, Cairns & Kitahara fam. nov.) is proposed based on phylogenomic reconstructions coupled with molecular features, specifically gene order, of the complete mitochondrial genome. Evolutionary reconstructions were based on both mitochondrial and nuclear ultraconserved elements (UCEs) and exon loci data sets and confirmed the divergent position of the genera Stephanocyathus and Vaughanella. The new family shows a specific gene transposition in the mitochondrial genome, not present in the 'true' caryophylliid lineage, but instead already observed for the species Paraconotrochus antarcticus, recovered as sister taxon of the here proposed new family. Although its phylogenetic position is unknown, the genus Ericiocyathus is also added to the new family, based on macromorphological similarities. This study represents a step forward in our understanding of deep‐sea corals relationships and provide further information (e.g., mitochondrial gene order) that will aid in future efforts of assessing the systematic of caryophylliid lineages. [ABSTRACT FROM AUTHOR]

• Genomic capture methods can resolve clades that lack decades of molecular marker development. • An enhanced bait setfor Hexacorallia recovers >2400 UCE/exon loci in stony corals. • Phylogenomics resolves coral relationships at deep and shallow time scales. • Well-supported clades in Acropora are not supported by macromorphological features. Targeted enrichment of genomic DNA can profoundly increase the phylogenetic resolution of clades and inform taxonomy. Here, we redesign a custom bait set previously developed for the cnidarian class Anthozoa to more efficiently target and capture ultraconserved elements (UCEs) and exonic loci within the subclass Hexacorallia. We test this enhanced bait set (targeting 2476 loci) on 99 specimens of scleractinian corals spanning both the "complex" (Acroporidae, Agariciidae) and "robust" (Fungiidae) clades. Focused sampling in the staghorn corals (genus Acropora) highlights the ability of sequence capture to inform the taxonomy of a clade previously deficient in molecular resolution. A mean of 1850 (±298) loci were captured per taxon (955 UCEs, 894 exons), and a 75% complete concatenated alignment of 96 samples included 1792 loci (991 UCE, 801 exons) and ~1.87 million base pairs. Maximum likelihood and Bayesian analyses recovered robust molecular relationships and revealed that species-level relationships within the Acropora are incongruent with traditional morphological groupings. Both UCE and exon datasets delineated six well-supported clades within Acropora. The enhanced bait set will facilitate investigations of the evolutionary history of many important groups of reef corals, particularly where previous molecular marker development has been unsuccessful. [ABSTRACT FROM AUTHOR]

The integration of morphological and molecular lines of evidence has enabled the family Deltocyathidae to be erected to accommodate Deltocyathus species that were previously ascribed to the family Caryophylliidae. However, although displaying the same morphological characteristics as other species of Deltocyathus, molecular data suggested that D. magnificus was phylogenetically distant from Deltocyathidae, falling within the family Turbinoliidae instead. To elucidate the enigmatic evolutionary history of this species and skeletal microstructural features, the phylogenetic relationships of Deltocyathidae and Turbinoliidae were investigated using nuclear ultraconserved and exon loci and complete mitochondrial genomes. Both nuclear and mitochondrial phylogenomic reconstructions confirmed the position of D. magnificus within turbinolids. Furthermore, a novel mitochondrial gene order was uncovered for Deltocyathidae species. This gene order was not present in Turbinoliidae or in D. magnificus that both have the scleractinian canonical gene order, further indicating the taxonomic utility of mitochondrial gene order. D. magnificus is therefore formally moved to the family Turbinoliidae and accommodated in a new genus (Dennantotrochus Kitahara, Vaga & Stolarski, gen. nov.). Surprisingly, turbinolids and deltocyathids do not differ in microstructural organisation of the skeleton that consists of densely packed, individualised rapid accretion deposits and thickening deposits composed of fibres perpendicular to the skeleton surface. Therefore, although both families are clearly evolutionarily divergent, macromorphological features indicate a case of skeletal convergence while these may still share conservative biomineralisation mechanisms. [ABSTRACT FROM AUTHOR]

Background: Our ability to investigate processes shaping the evolutionary diversification of corals (Cnidaria: Anthozoa) is limited by a lack of understanding of species boundaries. Discerning species of corals has been challenging due to a multitude of factors, including homoplasious and plastic morphological characters and the use of molecular markers that are either not informative or have not completely sorted. Hybridization can also blur species boundaries by leading to incongruence between morphology and genetics. We used traditional DNA barcoding and restriction-site associated DNA sequencing combined with coalescence-based and allele-frequency methods to elucidate species boundaries and simultaneously examine the potential role of hybridization in a speciose genus of octocoral, Sinularia. Results: Species delimitations using two widely used DNA barcode markers, mtMutS and 28S rDNA, were incongruent with one another and with the morphospecies identifications. When mtMutS and 28S were concatenated, a 0.3% genetic distance threshold delimited the majority of morphospecies. In contrast, 12 of the 15 examined morphospecies formed well-supported monophyletic clades in both concatenated RAxML phylogenies and SNAPP species trees of > 6000 RADSeq loci. DAPC and Structure analyses also supported morphospecies assignments, but indicated the potential for two additional cryptic species. Three morphologically distinct species pairs could not, however, be distinguished genetically. ABBA-BABA tests demonstrated significant admixture between some of those species, suggesting that hybridization may confound species delimitation in Sinularia. Conclusions: A genomic approach can help to guide species delimitation while simultaneously elucidating the processes generating coral diversity. Results support the hypothesis that hybridization is an important mechanism in the evolution of Anthozoa, including octocorals, and future research should examine the contribution of this mechanism in generating diversity across the coral tree of life. [ABSTRACT FROM AUTHOR]

Background More than 3,000 species of octocorals (Cnidaria, Anthozoa) inhabit an expansive range of environments, from shallow tropical seas to the deep-ocean floor. They are important foundation species that create coral "forests," which provide unique niches and 3-dimensional living space for other organisms. The octocoral genus Renilla inhabits sandy, continental shelves in the subtropical and tropical Atlantic and eastern Pacific Oceans. Renilla is especially interesting because it produces secondary metabolites for defense, exhibits bioluminescence, and produces a luciferase that is widely used in dual-reporter assays in molecular biology. Although several anthozoan genomes are currently available, the majority of these are hexacorals. Here, we present a de novo assembly of an azooxanthellate shallow-water octocoral, Renilla muelleri. Findings We generated a hybrid de novo assembly using MaSuRCA v.3.2.6. The final assembly included 4,825 scaffolds and a haploid genome size of 172 megabases (Mb). A BUSCO assessment found 88% of metazoan orthologs present in the genome. An Augustus ab initio gene prediction found 23,660 genes, of which 66% (15,635) had detectable similarity to annotated genes from the starlet sea anemone, Nematostella vectensis, or to the Uniprot database. Although the R. muelleri genome may be smaller (172 Mb minimum size) than other publicly available coral genomes (256–448 Mb), the R. muelleri genome is similar to other coral genomes in terms of the number of complete metazoan BUSCOs and predicted gene models. Conclusions The R. muelleri hybrid genome provides a novel resource for researchers to investigate the evolution of genes and gene families within Octocorallia and more widely across Anthozoa. It will be a key resource for future comparative genomics with other corals and for understanding the genomic basis of coral diversity. [ABSTRACT FROM AUTHOR]

Background. Low back pain (LBP) is a widespread condition in sport; it can lead to high treatment costs, dropping out of training and competition, decreased quality of life, and limitations to performance. Moreover, a large number of sport athletes suffer from chronic low back pain (CLBP). Among equestrian athletes low back pain is accepted as a symptom immanent to the sport. Methods. The study is a cross-sectional survey conducted using an online cloud-based software among competitive Athletes members of the Italian Equestrian Sport Federation older than 18 years old (n = 40932). Results. 886 athletes participated in the survey: 21.90% were male and 78.10% were female. LBP had a prevalence of 91.6% and 74.2% for life-time and 1-year respectively, while CLBP had a prevalence of 23.9%. Prevalence of LBP is 61% in Show-jumping, 13.6% in Dressage, 6.3% in Eventing, 2.9% in Horse Country Riding and 2.2% in Reining. Weight has a positive association with LBP (O.R. 1.05 95% CI = [1.02, 1.09] p < 0.05), while age has a negative association (O.R. 0.95 95% CI = [0.94, 0.98] p < 0.05). Practicing activity more than 5-6 hours a week has a positive association with CLBP (O.R. 1.21 95% CI = [1.05, 1.4] p < 0.05). CLBP is associated with interrupted activity (p < 0.001), drugs consumption (p < 0.001) and restriction in participation (p < 0.001). Conclusions. LBP and CLBP are very common conditions in equestrian athletes and their prevalence is higher compared to general population. LBP is more frequent in show-jumping compared to other disciplines. Age and weight are associated with lifetime LBP, with, respectively, a negative and positive association. Athletes with CLBP showed more disability in activities of daily living (ADLs) and tendency to suspend sports more frequently. [ABSTRACT FROM AUTHOR]

Coral reefs are iconic ecosystems that support diverse, productive communities in both shallow and deep waters. However, our incomplete knowledge of cold-water coral (CWC) niche space limits our understanding of their distribution and precludes a complete accounting of the ecosystem services they provide. Here, we present the results of recent surveys of the CWC mound province on the Blake Plateau off the U.S. east coast, an area of intense human activity including fisheries and naval operations, and potentially energy and mineral extraction. At one site, CWC mounds are arranged in lines that total over 150 km in length, making this one of the largest reef complexes discovered in the deep ocean. This site experiences rapid and extreme shifts in temperature between 4.3 and 10.7 °C, and currents approaching 1 m s−1. Carbon is transported to depth by mesopelagic micronekton and nutrient cycling on the reef results in some of the highest nitrate concentrations recorded in the region. Predictive models reveal expanded areas of highly suitable habitat that currently remain unexplored. Multidisciplinary exploration of this new site has expanded understanding of the cold-water coral niche, improved our accounting of the ecosystem services of the reef habitat, and emphasizes the importance of properly managing these systems. [ABSTRACT FROM AUTHOR]

As coral populations decline worldwide in the face of ongoing environmental change, documenting their distribution, diversity and conservation status is now more imperative than ever. Accurate delimitation and identification of species is a critical first step. This task, however, is not trivial as morphological variation and slowly evolving molecular markers confound species identification. New approaches to species delimitation in corals are needed to overcome these challenges. Here, we test whether target enrichment of ultraconserved elements (UCEs) and exons can be used for delimiting species boundaries and population structure within species of corals by focusing on two octocoral genera, Alcyonium and Sinularia, as exemplary case studies. We designed an updated bait set (29,181 baits) to target‐capture 3,023 UCE and exon loci, recovering a mean of 1,910 ± 168 SD per sample with a mean length of 1,055 ± 208 bp. Similar numbers of loci were recovered from Sinularia (1,946 ± 227 SD) and Alcyonium (1,863 ± 177 SD). Species‐level phylogenies were highly supported for both genera. Clustering methods based on filtered single nucleotide polymorphisms delimited species and populations that are congruent with previous allozyme, DNA barcoding, reproductive and ecological data for Alcyonium, and offered further evidence of hybridization among species. For Sinularia, results were congruent with those obtained from a previous study using restriction site associated DNA sequencing. Both case studies demonstrate the utility of target‐enrichment of UCEs and exons to address a wide range of evolutionary and taxonomic questions across deep to shallow timescales in corals. [ABSTRACT FROM AUTHOR]

Black corals (Anthozoa: Antipatharia) are an anthozoan lineage in the class Hexacorallia that occur across a wide range of habitats from the tropics to the poles and from surface waters to depths deeper than 8000 m. A new species of black coral, Aphanipathes puertoricoensis sp. nov., collected with a remotely operated vehicle 357 m deep off Puerto Rico is recognized in the family Aphanipathidae. The new species is characterized by very long and loosely coiled primary branches and up to 0.5 mm tall spines with as many as 40 or more small conical tubercles. A phylogeny composed of 13 taxa that are closely related to the new species was reconstructed from 793 nuclear loci to show their systematic relationships. Our study integrated morphological and genomic data to show that this new species is distinct from other species in the genus Aphanipathes. Furthermore, our results add to the growing knowledge of black coral diversity, while further demonstrating the need for exploration in deep waters of the Caribbean Sea. [ABSTRACT FROM AUTHOR]

The depth-differentiation hypothesis proposes that the bathyal region is a source of genetic diversity and an area where there is a high rate of species formation. Genetic differentiation should thus occur over relatively small vertical distances, particularly along the upper continental slope (200--1000 m) where oceanography varies greatly over small differences in depth. To test whether genetic differentiation within deepwater octocorals is greater over vertical rather than geographical distances, Callogorgia delta was targeted. This species commonly occurs throughout the northern Gulf of Mexico at depths ranging from 400 to 900 m. We found significant genetic differentiation (FST = 0.042) across seven sites spanning 400 km of distance and 400 m of depth. A pattern of isolation by depth emerged, but geographical distance between sites may further limit gene flow. Water mass boundaries may serve to isolate populations across depth; however, adaptive divergence with depth is also a possible scenario. Microsatellite markers also revealed significant genetic differentiation (FST = 0.434) between C. delta and a closely related species, Callogorgia americana, demonstrating the utility of microsatellites in species delimitation of octocorals. Results provided support for the depth-differentiation hypothesis, strengthening the notion that factors covarying with depth serve as isolation mechanisms in deep-sea populations. [ABSTRACT FROM AUTHOR]

Corals are a dominant benthic fauna that occur across a vast range of depths from just below the ocean's surface to the abyssopelagic zone. However, little is known about the evolutionary mechanisms that enable them to inhabit such a wide range of environments. The mitochondrial (mt) genome, which is involved in energetic pathways, may be subject to selection pressures at greater depths to meet the metabolic demands of that environment. Here, we use a phylogenomic framework combined with codon-based models to evaluate whether mt protein-coding genes (PCGs) associated with cellular energy functions are under positive selection across depth in three groups of corals: Octocorallia, Scleractinia, and Antipatharia. The results demonstrated that mt PCGs of deep- and shallow-water species of all three groups were primarily under strong purifying selection (0.0474 < ω < 0.3123), with the exception of positive selection in atp6 (ω = 1.3263) of deep-sea antipatharians. We also found evidence for positive selection at fifteen sites across cox1, mtMutS, and nad1 in deep-sea octocorals and nad3 of deep-sea antipatharians. These results contribute to our limited understanding of mt adaptations as a function of depth and provide insight into the molecular response of corals to the extreme deep-sea environment. [ABSTRACT FROM AUTHOR]

Numerous submarine canyons along the United States middle Atlantic continental margin support enhanced productivity, diverse and unique habitats, active fisheries, and are vulnerable to various anthropogenic disturbances. During two cruises (15 Aug–2 Oct 2012 and 30 Apr–27 May 2013), Baltimore and Norfolk canyons and nearby areas (including two cold seeps) were intensively surveyed to determine demersal fish distributions and habitat associations. Overall, 34 ROV dives (234–1612 m) resulted in 295 h of bottom video observations and numerous collections. These data were supplemented by 40, 30-min bottom trawl samples. Fish observations were assigned to five general habitat designations: 1) sand-mud (flat), 2) sloping sand-mud with burrows, 3) low profile gravel, rock, boulder, 4) high profile, canyon walls, rocks or ridges, and 5) seep-mixed hard and soft substrata, the later subdivided into seven habitats based on amounts of dead mussel and rock cover. The influence of corals, sponges and live mussels (seeps only) on fish distributions was also investigated. Both canyon areas supported abundant and diverse fish communities and exhibited a wide range of habitats, including extensive areas of deep-sea corals and sponges and two nearby methane seeps (380–430 m, 1455–1610 m). All methods combined yielded a total of 123 species of fishes, 12 of which are either new records for this region or have new range data. Depth was a major factor that separated the fish faunas into two zones with a boundary around 1400 m. Fishes defining the deeper zone included Lycodes sp., Dicrolene introniger, Gaidropsaurus ensis, Hydrolagus affinis, Antimora rostrata , and Aldrovandia sp. Fishes in the deep zone did not exhibit strong habitat affinities, despite the presence of a quite rugged, extensive methane seep. We propose that habitat specificity decreases with increasing depth. Fishes in the shallower zone, characterized by Laemonema sp., Phycis chesteri, Nezumia bairdii, Brosme brosme , and Helicolenus dactylopterus , exhibited a variety of habitat use patterns. In general, fish assemblages in the soft substrata areas (dominated by P. chesteri, N. bairdii, Glyptocephalus cynoglossus, Lophius americanus, Merluccius albidus ) were different from those in more complex habitats (dominated by Laemonema spp., Hoplostethus spp., B. brosme , Benthocometes robustus, L. americanus, Dysommina rugosa ). Although, when present, the dense coral and sponge cover did not statistically affect general fish assemblage patterns in hard bottom habitats, these sessile organisms markedly increased habitat complexity, and some fish species exhibited close association with them. Fish species compositions in the two canyons were not substantially different from the surrounding slopes. However, the diversity of habitats within both the canyons and seeps exerted an important influence on assemblage structure. At least for some species (e.g., B. brosme ) canyon and seep environments may be a refuge from intensive bottom fishing activities. We frequently observed evidence of commercial and recreational fishing activity (lost gear on bottom and fishing boats in the area) throughout the canyons and some resulting habitat damage. Conservation measures for the unique and more vulnerable areas (seep and coral habitats) have recently been approved. [ABSTRACT FROM AUTHOR]

Distinguishing coral species is not only crucial for physiological, ecological, and evolutionary studies but also to enable effective management of threatened reef ecosystems. However, traditional hypotheses that delineate coral species based on morphological traits from the coral skeleton are frequently at odds with tree-based molecular approaches. Additionally, a dearth of species-level molecular markers has made species delimitation particularly challenging in species-rich coral genera, leading to the widespread assumption that interspecific hybridization might be responsible for this apparent conundrum. Here, we used three lines of evidence—morphology, breeding trials, and molecular approaches—to identify species boundaries in a group of ecologically important tabular Acropora corals. In contrast to previous studies, our morphological analysis yielded groups that were congruent with experimental crosses as well as with coalescent-based and allele sharing-based multilocus approaches to species delimitation. Our results suggest that species of the genus Acropora are reproductively isolated and independently evolving units that can be distinguished morphologically. These findings not only pave the way for a taxonomic revision of coral species but also outline an approach that can provide a solid basis to address species delimitation and provide conservation support to a wide variety of keystone organisms. [ Acropora ; coral reefs; hybridization; reproductive isolation; taxonomy.] [ABSTRACT FROM AUTHOR]

[Display omitted] • Proposition of Bathyporidae fam. nov. • Description of a new species of Madrepora. • High gene flow within Madrepora populations in the Southwestern Atlantic. Deep-water coral reefs are found worldwide and harbor biodiversity levels that are comparable to their shallow-water counterparts. However, the genetic diversity and population structure of deep-water species remain poorly explored, and historical taxonomical issues still need to be resolved. Here we used microsatellite markers as well as ultraconserved elements (UCE) and exons to shed light on the population structure, genetic diversity, and phylogenetic position of the genus Madrepora , which contains M. oculata , one of the most widespread scleractinian species. Population structure of 107 samples from three Southwestern Atlantic sedimentary basins revealed the occurrence of a cryptic species, herein named M. piresae sp. nov. (authored by Kitahara, Capel and Zilberberg), which can be found in sympatry with M. oculata. Phylogeny reconstructions based on 134 UCEs and exon regions corroborated the population genetic data, with the recovery of two well-supported groups, and reinforced the polyphyly of the family Oculinidae. In order to better accommodate the genus Madrepora , while reducing taxonomical confusion associated with the name Madreporidae, we propose the monogeneric family Bathyporidae fam. nov. (authored by Kitahara, Capel, Zilberberg and Cairns). Our findings advance the knowledge on the widespread deep-water genus Madrepora , resolve a long-standing question regarding the phylogenetic position of the genus , and highlight the need of a worldwide review of the genus. [ABSTRACT FROM AUTHOR]

The article presents a study on the reef fish community structure off the coast of New Providence Island in The Bahamas. It discusses details of the findings based on a resurvey of the community in 2006 and comparisons with baseline data from 1955 to 1973 to determine if there had been changes in diversity over the 50-year period. It highlights the importance of monitoring the areas, particularly the prevalence of the invasive lionfish, Pterois volitans.

Background: Young, trained athletes may have abnormal 12-lead electrocardiograms (ECGs) without evidence of structural cardiac disease. Whether such ECG patterns represent the initial expression of underlying cardiac disease with potential long-term adverse consequences remains unresolved. We assessed long-term clinical outcomes in athletes with ECGs characterized by marked repolarization abnormalities. Methods: From a database of 12,550 trained athletes, we identified 81 with diffusely distributed and deeply inverted T waves (≥2 mm in at least three leads) who had no apparent cardiac disease and who had undergone serial clinical, ECG, and echocardiographic studies for a mean (±SD) of 9±7 years (range, 1 to 27). Comparisons were made with 229 matched control athletes with normal ECGs from the same database. Results: Of the 81 athletes with abnormal ECGs, 5 (6%) ultimately proved to have cardiomyopathies, including one who died suddenly at the age of 24 years from clinically undetected arrhythmogenic right ventricular cardiomyopathy. Of the 80 surviving athletes, clinical and phenotypic features of hypertrophic cardiomyopathy developed in 3 after 12±5 years (at the ages of 27, 32, and 50 years), including 1 who had an aborted cardiac arrest. The fifth athlete demonstrated dilated cardiomyopathy after 9 years of follow-up. In contrast, none of the 229 athletes with normal ECGs had a cardiac event or received a diagnosis of cardiomyopathy 9±3 years after initial evaluation (P=0.001). Conclusions: Markedly abnormal ECGs in young and apparently healthy athletes may represent the initial expression of underlying cardiomyopathies that may not be evident until many years later and that may ultimately be associated with adverse outcomes. Athletes with such ECG patterns merit continued clinical surveillance. N Engl J Med 2008;358:152-61. [ABSTRACT FROM AUTHOR]

The distinctive larval stage of eels (leptocephalus) facilitates dispersal through prolonged life in the open ocean. Leptocephali are abundant and diverse off North Carolina, yet data on distributions and biology are lacking. The water column (from surface to 1,293 m) was sampled in or near the Gulf Stream off Cape Hatteras, Cape Lookout, and Cape Fear, North Carolina during summer through fall of 1999–2005, and leptocephali were collected by neuston net, plankton net, Tucker trawl, and dip net. Additional samples were collected nearly monthly from a transect across southern Onslow Bay, North Carolina (from surface to 91 m) from April 2000 to December 2001 by bongo and neuston nets, Methot frame trawl, and Tucker trawl. Overall, 584 tows were completed, and 224 of these yielded larval eels. The 1,295 eel leptocephali collected (combining all methods and areas) represented at least 63 species (nine families). Thirteen species were not known previously from the area. Dominant families for all areas were Congridae (44% of individuals, 11 species), Ophichthidae (30% of individuals, 27 species), and Muraenidae (22% of individuals, ten species). Nine taxa accounted for 70% of the overall leptocephalus catches (in order of decreasing abundance): Paraconger caudilimbatus (Poey), Gymnothorax ocellatus Agassiz complex, Ariosoma balearicum (Delaroche), Ophichthus gomesii (Castelnau), Callechelys muraena Jordan and Evermann, Letharchus aliculatus McCosker, Rhynchoconger flavus (Goode and Bean), Ophichthus cruentifer (Goode and Bean), Rhynchoconger gracilior (Ginsburg). The top three species represented 52% of the total eel larvae collected. Most leptocephali were collected at night (79%) and at depths > 45 m. Eighty percent of the eels collected in discrete depth Tucker trawls at night ranged from mean depths of 59–353 m. A substantial number (38% of discrete depth sample total) of larval eels were also collected at the surface (neuston net) at night. Daytime leptocephalus distributions were less clear partly due to low catches and lower Tucker trawl sampling effort. While net avoidance may account for some of the low daytime catches, an alternative explanation is that many species of larval eels occur during the day at depths > 350 m. Larvae of 21 taxa of typically shallow water eels were collected at depths > 350 m, but additional discrete depth diel sampling is needed to resolve leptocephalus vertical distributions. The North Carolina adult eel fauna (estuary to at least 2,000 m) consists of 51 species, 41% of which were represented in these collections. Many species of leptocephali collected are not yet known to have juveniles or adults established in the South Atlantic Bight or north of Cape Hatteras. Despite Gulf Stream transport and a prolonged larval stage, many of these eel leptocephali may not contribute to their respective populations. [ABSTRACT FROM AUTHOR]

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

Mesophotic coral ecosystems (MCEs) are recognized around the world as diverse and ecologically important habitats. In the northern Gulf of Mexico (GoMx), MCEs are rocky reefs with abundant black corals and octocorals, including the species Swiftia exserta. Surveys following the Deepwater Horizon (DWH) oil spill in 2010 revealed significant injury to these and other species, the restoration of which requires an in-depth understanding of the biology, ecology, and genetic diversity of each species. To support a larger population connectivity study of impacted octocorals in the GoMx, this study combined sequences of mtMutS and nuclear 28S rDNA to confirm the identity of Swiftia sea fans in the GoMx, compare these markers for different polyp colors in the GoMx and Atlantic, and examine the phylogeny of the genus. Two mtMutS haplotypes were identified, one seemingly endemic to the northern GoMx. Compared to other North Atlantic Swiftia, S. exserta, the type of the genus was found to be extremely divergent and distinct from the two other Swiftia at both loci, with strong evidence of polyphyly in the genus. This information refines our understanding of the geographical distribution of injured coral and highlights how little is known about MCEs. Substantial taxonomic revisions may be needed for several taxa injured by the DWH oil spill. [ABSTRACT FROM AUTHOR]

[Display omitted] • For the first time, deep nodes are resolved within the Keratoisididae, a prolific deep-sea family of octocorals. • Nuclear phylogenies built with hundreds of genes conflict with previously published single and multi-gene mitochondrial phylogenies. • Some currently recognised keratoisidid groups appear polyphyletic using nuclear phylogenies built with hundreds of markers. • Sclerite microstructure and ornamentation could be future informative taxonomic features for bamboo corals. Keratoisididae is a globally distributed, and exclusively deep-sea, family of octocorals that contains species and genera that are polyphyletic. An alphanumeric system, based on a three-gene-region phylogeny, is widely used to describe the biodiversity within this family. That phylogeny identified 12 major groups although it did not have enough signal to explore the relationships among groups. Using increased phylogenomic resolution generated from Ultraconserved Elements and exons (i.e. conserved elements), we aim to resolve deeper nodes within the family and investigate the relationships among those predefined groups. In total, 109 libraries of conserved elements were generated from individuals representing both the genetic and morphological diversity of our keratoisidids. In addition, the conserved element data of 12 individuals from previous studies were included. Our taxon sampling included 11 of the 12 keratoisidid groups. We present two phylogenies, constructed from a 75% (231 loci) and 50% (1729 loci) taxon occupancy matrix respectively, using both Maximum Likelihood and Multiple Species Coalescence methods. These trees were congruent at deep nodes. As expected, S1 keratoisidids were recovered as a well-supported sister clade to the rest of the bamboo corals. S1 corals do not share the same mitochondrial gene arrangement found in other members of Keratoisididae. All other bamboo corals were recovered within two major clades. Clade I comprises individuals assigned to alphanumeric groups B1, C1, D1&D2, F1, H1, I4, and J3 while Clade II contains representatives from A1, I1, and M1. By combining genomics with already published morphological data, we provide evidence that group H1 is not monophyletic, and that the division between other groups – D1 and D2, and A1 and M1 – needs to be reconsidered. Overall, there is a lack of robust morphological markers within Keratoisididae, but subtle characters such as sclerite microstructure and ornamentation seem to be shared within groups and warrant further investigation as taxonomically diagnostic characters. [ABSTRACT FROM AUTHOR]

Cnidarians are early‐diverging metazoans, but evolutionary aspects of some taxa are still poorly understood, as in the order Zoantharia (Anthozoa: Hexacorallia). Zoantharians have been divided into two suborders based on the arrangement of the fifth septae as complete (Macrocnemina) or incomplete (Brachycnemina). Previous molecular phylogenetic analyses have indicated the need for re‐evaluation as Macrocnemina has been found to be paraphyletic. Despite many phylogenetic studies, the recovery of complete mitochondrial genomes (mt‐genomes) for systematic and evolutionary studies of zoantharians has been limited. The present study represents the first to sequence the complete mt‐genomes of members of eight of nine zoantharian families. Although all examined mt‐genomes had the same gene order arrangement, there were variations among mt‐genomes' sizes, nucleotide substitution rates, and introns. Only two species did not have the cox1 intron, which harbors a gene coding a homing endonuclease of the LAGLIDADG type. Our mitogenomic analyses also showed relatively high nucleotide diversity in mt‐DNA regions other than the standard regions traditionally considered for DNA barcoding of this group. Phylogenetic analyses using 13 mt‐genome protein‐coding genes recovered a fully resolved tree with clear separation between macrocnemic representatives. Ancestral state reconstruction analyses revealed three main transitions in arrangement of the marginal musculature through the evolutionary history of the order. An "early" transition from reticulate mesogleal to a cteniform endodermal arrangement was followed by transitions that occurred in the common ancestor of the Brachycnemina and family Hydrozoanthidae. Our results indicate the need for clarification of higher‐level phylogeny and taxonomy of Zoantharia. [ABSTRACT FROM AUTHOR]

In situ images and/or collection of seven specimens by underwater-vehicle dives at 269–609 m depth off Curaçao, Dominica, and Puerto Rico (S, E, and NE Caribbean) revealed new records and a previously unknown, distinctive color pattern for the cuskeel Neobythites unicolor (Ophidiidae). Species identification was based on detailed comparisons with earlier studied type and non-type material using morphometric, meristic, and otolith-form characters. A revised color description is provided based on images of live specimens in situ in their habitat, shortly after capture, and after preservation. Live and fresh specimens of Neobythites unicolor show a large number of distinctive, dark, rounded or irregularly shaped spots distributed dorsally on head, dorsal portion of body, and on the dorsal fin. This color pattern fades when fish are frozen, and it is completely lost during preservation over several years. The available images of fresh color patterns indicate an increase in spot size with fish size. In addition, some of the quantitatively examined morphometric and otolith characters of museum specimens show positive allometry. No geographic variation in color patterns could be detected. Although the Curaçao population is separated from all other known populations of N. unicolor by at least 650 km, the only population difference found was a slightly lower pectoral-fin ray count for the four specimens collected off Curaçao. An updated distribution map is provided correcting for an erroneous record in the inner Gulf of Mexico from which N. unicolor appears to be completely absent. While the spotted color pattern described here is unique among the 54 species of Neobythites, a similar pattern occurs in two other genera of the subfamily Neobythitinae, Sirembo and Spottobrotula. Further requirements to more fully understand the color diversity and related biology, ecology, and evolution in the species-rich genus Neobythites are emphasized. [ABSTRACT FROM AUTHOR]

Deep‐sea coral communities are key components of the Gulf of Mexico ecosystem and were adversely affected by the Deepwater Horizon (DWH) oil spill. Coral colonies exposed to oil and dispersant exhibited mortality, damage and physiological signatures of stress. Understanding how corals respond to oil and dispersant exposure at the molecular level is important to elucidate the sublethal effects of the DWH disaster and reveal broader patterns of coral stress responses. Gene expression profiles from RNAseq data were compared between corals at an impacted site and from a reference site. A total of 1,439 differentially expressed genes (≥twofold) were shared among impacted Paramuricea biscaya colonies. Genes involved in oxidative stress, immunity, wound repair, tissue regeneration and metabolism of xenobiotics were significantly differentially expressed in impacted corals. Enrichment among the overexpressed genes indicates the corals were enduring high metabolic demands associated with cellular stress responses and repair mechanisms. Underexpression of genes vital to toxin processing also suggests a diminished capacity to cope with environmental stressors. Our results provide evidence that deep‐sea corals exhibited genome‐wide cellular stress responses to oil and dispersant exposure and demonstrate the utility of next‐generation sequencing for monitoring anthropogenic impacts in deep waters. These analyses will facilitate the development of diagnostic markers for oil and dispersant exposure in deep‐sea invertebrates and inform future oil spill response efforts. [ABSTRACT FROM AUTHOR]

The development of coalescent-based and other multilocus methods for species delimitation has facilitated the identification of cryptic species complexes across the tree of life. A recent taxonomic revision of the ecologically important soft coral genus Ovabunda validated 11 morphospecies, all with type localities and overlapping geographic ranges in the Red Sea. A subsequent molecular phylogenetic analysis using mitochondrial and 28S nrDNA genes divided the genus into just two clades, with no apparent genetic distinctions among morphospecies. To further explore species boundaries among morphospecies of Ovabunda we sequenced three additional nuclear genes ( ITS , ATPS α, ATPS β), and obtained data for 1332 unlinked SNPs from restriction-site associated DNA sequencing. Both coalescent-based and allele-sharing species delimitation analyses supported four species of Ovabunda , each of which included multiple morphotypes encompassing the full range of morphological variation observed within the genus. All four species occurred over the same depth range of 5–41 m, and were sympatric at sites separated by 1100 km in the Red Sea. The only characters that have been found to distinguish three of the four species are diagnostic substitutions in the nuclear genome; the fourth differs by exhibiting polyp pulsation, a behavioral trait that can be assessed only in live colonies. The lack of any obvious morphological, life history, ecological or geographical differences among these four species begs the question of what drove the evolution and maintenance of reproductive isolating mechanisms in this cryptic species complex. [ABSTRACT FROM AUTHOR]

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

A recent phylogenetic analysis of the Myxinidae based on the 16S rRNA gene resulted in synonymization of Paramyxine with Eptatretus. This created homonymy of Paramyxine fernholmi with Eptatretus fernholmi and Paramyxine wisneri with Eptatretus wisneri. In order to resolve this nomenclatural dilemma, we made a more extensive phylogenetic assessment of the Myxinidae and examined the nomenclature of the family. We used 75 sequences (37 of which new for this study) of a 561 bp fragment of the 16S rRNA gene, representing 33 species, and 72 sequences (37 of which new for this study) of a 687 bp fragment of the cytochrome c oxidase subunit I ( COI) gene, representing 23 species, to reconstruct the phylogeny of Myxinidae. The monophyly of the subfamily Myxininae, traditionally characterized by having a single pair of external gill openings, was rejected (0.50 Bayesian posterior probability) by the 16S analysis, but supported by the COI and combined COI+ 16S analyses (0.99 and 0.81 Bpp, respectively). The monophyly of the subfamily Eptatretinae, characterized by having several pairs of external gill openings, was not supported by the 16S analysis and rejected by the COI and combined COI+ 16S analysis due to the placement of Eptatretus lopheliae as the earliest branch of Myxinidae (0.71 and 0.57 Bpp, respectively). Eptatretus lopheliae and Eptatretus rubicundus formed a monophyletic group and were allocated to a new genus, Rubicundus, characterized by the presence of an elongated tubular nostril and reddish coloration. A new monotypic subfamily, Rubicundinae, was proposed for Rubicundus. The synonymy of the genera Paramyxine and Quadratus with Eptatretus was confirmed. E. fernholmi is renamed Eptatretus luzonicus. Eptatretus wisneri was renamed Eptatretus bobwisneri. Petromyzon cirrhatus Forster, 1801, Homea banksii Fleming, 1822, and Bdellostoma forsteri Müller, 1836 are synonyms, but no type specimens are known to exist. Petromyzon cirrhatus was designated as type species of Eptatretus, conserving present usage. Gastrobranchus dombeyi Shaw, 1804 has priority over other names for Chilean myxinids. Bdellostoma stoutii was designated as type species of Polistotrema Gill. The validity of the Western Atlantic Myxine limosa as distinct from the Eastern Atlantic Myxine glutinosa was confirmed. [ABSTRACT FROM AUTHOR]