RAD-tag sequencing is a promising method for conducting genome-wide evolutionary studies. However... more RAD-tag sequencing is a promising method for conducting genome-wide evolutionary studies. However, to date, only a handful of studies empirically tested its applicability above the species level. In this communication, we use RAD tags to contribute to the delimitation of species within a diverse genus of deep-sea octocorals, Chrysogorgia, for which few classical genetic markers have proved informative. Previous studies have hypothesized that single mitochondrial haplotypes can be used to delimit Chrysogorgia species. On the basis of two lanes of Illumina sequencing, we inferred phylogenetic relationships among 12 putative species that were delimited using mitochondrial data, comparing two RAD analysis pipelines (Stacks and PyRAD). The number of homologous RAD loci decreased dramatically with increasing divergence, as >70% of loci are lost when comparing specimens separated by two mutations on the 700-nt long mitochondrial phylogeny. Species delimitation hypotheses based on the mitochondrial mtMutS gene are largely supported, as six out of nine putative species represented by more than one colony were recovered as discrete, well-supported clades. Significant genetic structure (correlating with geography) was detected within one putative species, suggesting that individuals characterized by the same mtMutS haplotype may belong to distinct species. Conversely, three mtMutS haplotypes formed one well-supported clade within which no population structure was detected, also suggesting that intraspecific variation exists at mtMutS in Chrysogorgia. Despite an impressive decrease in the number of homologous loci across clades, RAD data helped us to fine-tune our interpretations of classical mitochondrial markers used in octocoral species delimitation, and discover previously undetected diversity
This dataset contains oceanographic data collected along the continental slope submarine canyons,... more This dataset contains oceanographic data collected along the continental slope submarine canyons, en route to and returning from the North Atlantic Seamount Chain. ROV operations were conducted on the seamounts both inside and outside the U.S. EEZ. Operations focused on areas of high potential for discovery and of interest to the management community. ROV dives were conducted mostly during the day, while CTD casts and acoustic mapping occurred when the ROV was on deck. Data acquisition from shipboard sensors includes navigation data, meteorological data (wind, air temperature, relative humidity, barometric pressure), and oceanographic data (thermosalinograph, remote temperature probe, sound velocity probe, bathythermograph).
This dataset contains oceanographic data collected in the deep waters in and around Papahanaumoku... more This dataset contains oceanographic data collected in the deep waters in and around Papahanaumokuakea Marine National Monument (PMNM) in the Northwestern Hawaiian Islands and Johnston Atoll. The primary goal for this cruise was to collect baseline data and information to support priority NOAA science and management needs. The expedition is part of a three-year Campaign of Expeditions (Campaign to Address Pacific monument Science, Technology, and Ocean NEeds or CAPSTONE) focused on exploring deepwater marine protected areas in the Pacific. Operations for this cruise included the 24-hour collection of ship navigation data and scientific computing system data, which comprises of meteorological and oceanographic sensor data, as well as water column profile data. The ship also conducted daytime ROV dives that focused in depths between 250 and 6,000 meters, and included high-resolution visual surveys and biological/geological sample collections. Opportunistic CTD rosette operations were c...
... Western North Atlantic, Cape Hatteras to Florida Straits, Antilles Lusitanian-Mediterranean ... more ... Western North Atlantic, Cape Hatteras to Florida Straits, Antilles Lusitanian-Mediterranean Stoloniferous forms Clavulariidae Anthelia borealis (Koren and Danielssen, 1883) XX Antheliafallax Broch, 1912 XX Clavularia alba (Grieg, 1888) XX Clavularia griegii Madsen, 1944 ...
The diversity, ubiquity and prevalence in deep waters of the octocoral family Chrysogorgiidae Ver... more The diversity, ubiquity and prevalence in deep waters of the octocoral family Chrysogorgiidae Verrill, 1883 make it noteworthy as a model system to study radiation and diversification in the deep sea. Here we provide the first comprehensive phylogenetic analysis of the Chrysogorgiidae, and compare phylogeny and depth distribution. Phylogenetic relationships among 10 of 14 currently-described Chrysogorgiidae genera were inferred based on mitochondrial (mtMutS, cox1) and nuclear (18S) markers. Bathymetric distribution was estimated from multiple sources, including museum records, a literature review, and our own sampling records (985 stations, 2345 specimens). Genetic analyses suggest that the Chrysogorgiidae as currently described is a polyphyletic family. Shallow-water genera, and two of eight deep-water genera, appear more closely related to other octocoral families than to the remainder of the monophyletic, deep-water chrysogorgiid genera. Monophyletic chrysogorgiids are composed of strictly (Iridogorgia Verrill, 1883, Metallogorgia Versluys, 1902, Radicipes Stearns, 1883, Pseudochrysogorgia Pante & France, 2010) and predominantly (Chrysogorgia Duchassaing & Michelotti, 1864) deep-sea genera that diversified in situ. This group is sister to gold corals (Primnoidae Milne Edwards, 1857) and deep-sea bamboo corals (Keratoisidinae Gray, 1870), whose diversity also peaks in the deep sea. Nine species of Chrysogorgia that were described from depths shallower than 200 m, and mtMutS haplotypes sequenced from specimens sampled as shallow as 101 m, suggest a shallow-water emergence of some Chrysogorgia species.
Despite their abundance and ecological importance in a wide variety of shallow and deep water mar... more Despite their abundance and ecological importance in a wide variety of shallow and deep water marine communities, octocorals (soft corals, sea fans, and sea pens) are a group whose taxonomy and phylogenetic relationships remain poorly known and little studied. The group is currently divided into three orders (O: Alcyonacea, Pennatulacea, and Helioporacea); the large O. Alcyonacea (soft corals and sea fans) is further subdivided into six sub-ordinal groups on the basis of skeletal composition and colony growth form. We used 1429 bp of two mitochondrial protein-coding genes, ND2 and msh1, to construct a phylogeny for 103 octocoral genera representing 28 families. In agreement with a previous 18S rDNA phylogeny, our results support a division of Octocorallia into two major clades plus a third, minor clade. We found one large clade (Holaxonia-Alcyoniina) comprising the sea fan sub-order Holaxonia and the majority of soft corals, and a second clade (Calcaxonia-Pennatulacea) comprising sea pens (O. Pennatulacea) and the sea fan sub-order Calcaxonia. Taxa belonging to the sea fan group Scleraxonia and the soft coral family Alcyoniidae were divided among the Holaxonia-Alcyoniina clade and a third, small clade (Anthomastus-Corallium) whose relationship to the two major clades was unresolved. In contrast to the previous studies, we found sea pens to be monophyletic but nested within Calcaxonia; our analyses support the sea fan family Ellisellidae as the sister taxon to the sea pens. We are unable to reject the hypothesis that the calcaxonian and holaxonian skeletal axes each arose once and suggest that the skeletal axis of sea pens is derived from that of Calcaxonia. Topology tests rejected the monophyly of sub-ordinal groups Alcyoniina, Scleraxonia, and Stolonifera, as well as 9 of 14 families for which we sampled multiple genera. The much broader taxon sampling and better phylogenetic resolution aVorded by our study relative to the previous eVorts greatly clarify the relationships among families and subordinal groups within each of the major clades. The failure of these mitochondrial genes as well as previous 18S rDNA studies to resolve many of the deeper nodes within the tree (including its root) suggest that octocorals underwent a rapid radiation and that large amounts of sequence data will be required in order to resolve the basal relationships within the clade.
The widespread assumption that COI and other mitochondrial genes will be ineffective DNA barcodes... more The widespread assumption that COI and other mitochondrial genes will be ineffective DNA barcodes for anthozoan cnidarians has not been well tested for most anthozoans other than scleractinian corals. Here we examine the limitations of mitochondrial gene barcoding in the sub-class Octocorallia, a large, diverse, and ecologically important group of anthozoans. Pairwise genetic distance values (uncorrected p) were compared for three candidate barcoding regions: the Folmer region of COI; a fragment of the octocoral-specific mitochondrial proteincoding gene, msh1; and an extended barcode of msh1 plus COI with a short, adjacent intergenic region (igr1). Intraspecific variation was <0.5%, with most species exhibiting no variation in any of the three gene regions. Interspecific divergence was also low: 18.5% of congeneric morphospecies shared identical COI barcodes, and there was no discernible barcoding gap between intra-and interspecific p values. In a case study to assess regional octocoral biodiversity, COI and msh1 barcodes each identified 70% of morphospecies. In a second case study, a nucleotide character-based analysis correctly identified 70% of species in the temperate genus Alcyonium. Although interspecific genetic distances were 2• greater for msh1 than COI, each marker identified similar numbers of species in the two case studies, and the extended COI + igr1 + msh1 barcode more effectively discriminated sister taxa in Alcyonium. Although far from perfect for species identification, a COI + igr1 + msh1 barcode nonetheless represents a valuable addition to the depauperate set of characters available for octocoral taxonomy.
The rare octocoral genus Isidoides Nutting, 1910 was originally placed in the Gorgonellidae (now ... more The rare octocoral genus Isidoides Nutting, 1910 was originally placed in the Gorgonellidae (now the Ellisellidae), even though it showed a remarkable similarity to the Isidae (now the Isididae). Isidoides was not classified in the Isididae mostly because the type specimen lacked skeletal nodes, a defining characteristic of that family. The genus was later assigned to the Chrysogorgiidae based on sclerite morphology. Specimens were recently collected in the south-western Pacific, providing material for genetic analysis and detailed characterisation of the morphology, and allowing us to consider the systematic placement of this taxon within the suborder Calcaxonia. A previously reported phylogeny allowed us to reject monophyly with the Chrysogorgiidae, and infer a close relationship with the Isididae subfamily Keratoisidinae. While scanning for molecular variation across mitochondrial genes, we discovered a novel gene order that is, based on available data, unique among metazoans. De...
Seamounts are undersea mountains commonly characterized by accelerated currents, exposed hard-sub... more Seamounts are undersea mountains commonly characterized by accelerated currents, exposed hard-substrates, and relatively high biomass and biodiversity. Hydrographic features associated with seamounts have led authors to hypothesize that benthic invertebrate populations from geographically separated seamounts (and the continental slope) may experience varying degrees of genetic isolation, resulting in high levels of endemism. While this hypothesis has been tested for multiple taxonomic groups in the Pacific, it has rarely been addressed in the Atlantic. We tested the null hypothesis that the geographic ranges of corals from NW Atlantic seamounts are restricted to individual seamounts. We examined 188 octocoral and 50 antipatharian colonies (representing 6 and 2 genera, respectively) from 14 seamounts, spanning 1700 km, and the adjacent continental margin and estimated their genetic variation using mitochondrial loci (msh1 for all octocorals, as well as an intergenic region for isidids, and 3 multi-gene spanning segments for antipatharians). Well-sampled haplotypes were not geographically isolated on individual seamounts, thus refuting the hypothesis of local endemism of coral fauna on the New England and Corner Seamounts. The narrow geographic distribution of rare haplotypes is most likely due to undersampling rather than endemism. Our results do not preclude that cryptic variation and endemism not revealed by mitochondrial DNA may become evident should more variable markers be developed.
Octocorals, especially gorgonians, are conspicuous on Caribbean coral reefs, but there is no cons... more Octocorals, especially gorgonians, are conspicuous on Caribbean coral reefs, but there is no consensus regarding species relationships. Mitochondrial protein-coding genes [NADH-dehydrogenase subunits 2 (ND2) and 6 (ND6), and mutS homolog (msh1), 1633 bp] from 28 shallow-water species were sequenced to develop the first molecular phylogeny for Caribbean octocorals. The specimens were collected primarily in the Caribbean or off Brazil in 1999-2001. Morphological characters (sclerites and axial ultrastructure) were also examined in order to map them onto the molecular phylogeny. Analyses of both nucleotide and amino acid substitutions using maximum parsimony and likelihood (including maximum-likelihood and Bayesian analysis) generated very similar results, with most nodes having high levels of support. These molecular results were significantly different from the generally accepted classification. Neither Plexauridae nor Gorgoniidae were monophyletic. Plexaurella spp., nominal plexaurids, were basal to the gorgoniids, sharing many morphological characters with them. This corroborates previous findings using secondary metabolites and biosynthetic pathways. The sea fans, Gorgonia spp. and Pacifigorgia spp., as well as the pinnate gorgonians, Muriceopsis flavida and Pseudopterogorgia spp., did not have sea fan or pinnate relatives, suggesting there has been convergent evolution of colony form. Caribbean plexaurids appeared more derived and/or recently evolved according to both morphological and molecular data (e.g. Eunicea spp. and Plexaura spp.). Molecular phylogenetics is a promising approach for reconstructing phylogenetic relationships among octocorals as well as to understand their complex morphology.
Using the remotely operated vehicle Deep Discoverer, we observed a large stylodactylid shrimp res... more Using the remotely operated vehicle Deep Discoverer, we observed a large stylodactylid shrimp resting on a sedimented sea floor at 4826 m in the Marianas Trench Marine National Monument. The shrimp was not collected but most closely resembled Bathystylodactylus bathyalis, known previously only from a single broken specimen. Video footage shows the shrimp facing into the current and extending its upraised and fringed first and second pereopods, presumably capturing passing particles. The video footage is the first ever to show a living deep-sea stylodactylid and constitutes the deepest record for the family. We provide a list of the deepest reports of caridean shrimps world-wide.
The Keratoisidinae are a poorly known, but phenotypically diverse group of deepwater corals. Rece... more The Keratoisidinae are a poorly known, but phenotypically diverse group of deepwater corals. Recent developments in deepwater trawling in the southwest Pacific have provided many more specimens of bamboo corals. Two sub-regions of the mitochondrial genome were sequenced to test genetic relationships among specimens collected over a wide geographical range (27-50°S): a sub-region of the large-subunit rRNA (16S rRNA), characterized by a highly variable insertion/deletion (INDEL#2) region; and a non-coding region between COII and COI. Based on DNA haplotypes, 14 species of Keratoisidinae were recognized among 88 specimens from deep water in the southwest Pacific Ocean. The common haplotypes also appeared in specimens collected in the northwest Pacific Ocean and may indicate that some bamboo coral species are widespread in the Pacific, or that the mitochondrial markers are insensitive to recent speciation events. Many specimens were taken from flat bottom areas and, contrary to assumptions, the bamboo corals are not endemic to seamounts. The closure of some seamounts to trawling will protect bamboo corals from extinction, but not from local depletion.
ABSTRACT Bamboo corals (family Isididae) are among the most easily recognized deep-water octocora... more ABSTRACT Bamboo corals (family Isididae) are among the most easily recognized deep-water octocorals due to their articulated skeleton comprised of non-sclerite calcareous in-ternodes alternating with proteinaceous nodes. Most commonly encountered in the deep-sea are ...
Molecular Phylogenetics and Evolution, Mar 31, 2007
Black corals comprise a globally distributed shallow- and deep-water taxon whose phylogenetic pos... more Black corals comprise a globally distributed shallow- and deep-water taxon whose phylogenetic position within the Anthozoa has been debated. We sequenced the complete mitochondrial genome of the antipatharian Chrysopathes formosa to further evaluate its phylogenetic relationships. The circular mitochondrial genome (18,398 bp) consists of 13 energy pathway protein-coding genes and two ribosomal RNAs, but only two transfer RNA genes (trnM and trnW), as well as a group I intron within the nad5 gene that contains the only copies of nad1 and nad3. No novel genes were found in the antipatharian mitochondrial genome. Gene order and genome content are most similar to those of the sea anemone Metridium senile (subclass Hexacorallia), with differences being the relative location of three contiguous genes (cox2-nad4-nad6) and absence (from the antipatharian) of a group I intron within the cox1 gene. Phylogenetic analyses of multiple protein-coding genes support classifying the Antipatharia within the subclass Hexacorallia and not the subclass Ceriantipatharia; however, the sister-taxon relationships of black corals within Hexacorallia remain inconclusive.
A new species of the pardaliscid amphipod genus Halice, H. hesmonectes, is described from hydroth... more A new species of the pardaliscid amphipod genus Halice, H. hesmonectes, is described from hydrothermal vents in the eastern Pacific Ocean. The species occurs in large monospecific swarms in the immediate vicinity of low temperature vent openings. Halice hesmonectes differs from other members of the genus in having the following combination of characters: extremely long pereopods 5–7 (exceeding length of pereon, and nearly twice the length of pereopods 1–4); minute dactylus on pereopods 3 and 4, unique, constricted at midlength; pleopods well developed, as long or longer than pereopods 1–4; telson cleft along approximately two-thirds its length and terminating in an acute tip on each lobe; short article 3 (about 1/3 length of article 2) on mandibular palp; and accessory flagellum of first antenna with only two articles, the distal one being approximately 1/6 the length of the proximal. In addition, the body and virtually all appendages are covered by minute cuticular scales, probably present also on other pardaliscids (visible only via SEM) and known from other peracarids. Problematic taxonomy within the family Pardaliscidae is discussed.
The physical uniformity of the deep sea suggests a lack of absolute barriers to faunal dispersal,... more The physical uniformity of the deep sea suggests a lack of absolute barriers to faunal dispersal, and thus genetic homogeneity in broadly distributed species is expected. The deep-sea amphipod Eurythenes gryllus Lichtenstein (Crustacea: Lysianassoidea) is considered a panoceanic, cold-water stenotherm, with a vertical depth distribution from 184 to 6500 m. We surveyed mtDNA sequence diversity in E. gryllus to assess
RAD-tag sequencing is a promising method for conducting genome-wide evolutionary studies. However... more RAD-tag sequencing is a promising method for conducting genome-wide evolutionary studies. However, to date, only a handful of studies empirically tested its applicability above the species level. In this communication, we use RAD tags to contribute to the delimitation of species within a diverse genus of deep-sea octocorals, Chrysogorgia, for which few classical genetic markers have proved informative. Previous studies have hypothesized that single mitochondrial haplotypes can be used to delimit Chrysogorgia species. On the basis of two lanes of Illumina sequencing, we inferred phylogenetic relationships among 12 putative species that were delimited using mitochondrial data, comparing two RAD analysis pipelines (Stacks and PyRAD). The number of homologous RAD loci decreased dramatically with increasing divergence, as >70% of loci are lost when comparing specimens separated by two mutations on the 700-nt long mitochondrial phylogeny. Species delimitation hypotheses based on the mitochondrial mtMutS gene are largely supported, as six out of nine putative species represented by more than one colony were recovered as discrete, well-supported clades. Significant genetic structure (correlating with geography) was detected within one putative species, suggesting that individuals characterized by the same mtMutS haplotype may belong to distinct species. Conversely, three mtMutS haplotypes formed one well-supported clade within which no population structure was detected, also suggesting that intraspecific variation exists at mtMutS in Chrysogorgia. Despite an impressive decrease in the number of homologous loci across clades, RAD data helped us to fine-tune our interpretations of classical mitochondrial markers used in octocoral species delimitation, and discover previously undetected diversity
This dataset contains oceanographic data collected along the continental slope submarine canyons,... more This dataset contains oceanographic data collected along the continental slope submarine canyons, en route to and returning from the North Atlantic Seamount Chain. ROV operations were conducted on the seamounts both inside and outside the U.S. EEZ. Operations focused on areas of high potential for discovery and of interest to the management community. ROV dives were conducted mostly during the day, while CTD casts and acoustic mapping occurred when the ROV was on deck. Data acquisition from shipboard sensors includes navigation data, meteorological data (wind, air temperature, relative humidity, barometric pressure), and oceanographic data (thermosalinograph, remote temperature probe, sound velocity probe, bathythermograph).
This dataset contains oceanographic data collected in the deep waters in and around Papahanaumoku... more This dataset contains oceanographic data collected in the deep waters in and around Papahanaumokuakea Marine National Monument (PMNM) in the Northwestern Hawaiian Islands and Johnston Atoll. The primary goal for this cruise was to collect baseline data and information to support priority NOAA science and management needs. The expedition is part of a three-year Campaign of Expeditions (Campaign to Address Pacific monument Science, Technology, and Ocean NEeds or CAPSTONE) focused on exploring deepwater marine protected areas in the Pacific. Operations for this cruise included the 24-hour collection of ship navigation data and scientific computing system data, which comprises of meteorological and oceanographic sensor data, as well as water column profile data. The ship also conducted daytime ROV dives that focused in depths between 250 and 6,000 meters, and included high-resolution visual surveys and biological/geological sample collections. Opportunistic CTD rosette operations were c...
... Western North Atlantic, Cape Hatteras to Florida Straits, Antilles Lusitanian-Mediterranean ... more ... Western North Atlantic, Cape Hatteras to Florida Straits, Antilles Lusitanian-Mediterranean Stoloniferous forms Clavulariidae Anthelia borealis (Koren and Danielssen, 1883) XX Antheliafallax Broch, 1912 XX Clavularia alba (Grieg, 1888) XX Clavularia griegii Madsen, 1944 ...
The diversity, ubiquity and prevalence in deep waters of the octocoral family Chrysogorgiidae Ver... more The diversity, ubiquity and prevalence in deep waters of the octocoral family Chrysogorgiidae Verrill, 1883 make it noteworthy as a model system to study radiation and diversification in the deep sea. Here we provide the first comprehensive phylogenetic analysis of the Chrysogorgiidae, and compare phylogeny and depth distribution. Phylogenetic relationships among 10 of 14 currently-described Chrysogorgiidae genera were inferred based on mitochondrial (mtMutS, cox1) and nuclear (18S) markers. Bathymetric distribution was estimated from multiple sources, including museum records, a literature review, and our own sampling records (985 stations, 2345 specimens). Genetic analyses suggest that the Chrysogorgiidae as currently described is a polyphyletic family. Shallow-water genera, and two of eight deep-water genera, appear more closely related to other octocoral families than to the remainder of the monophyletic, deep-water chrysogorgiid genera. Monophyletic chrysogorgiids are composed of strictly (Iridogorgia Verrill, 1883, Metallogorgia Versluys, 1902, Radicipes Stearns, 1883, Pseudochrysogorgia Pante & France, 2010) and predominantly (Chrysogorgia Duchassaing & Michelotti, 1864) deep-sea genera that diversified in situ. This group is sister to gold corals (Primnoidae Milne Edwards, 1857) and deep-sea bamboo corals (Keratoisidinae Gray, 1870), whose diversity also peaks in the deep sea. Nine species of Chrysogorgia that were described from depths shallower than 200 m, and mtMutS haplotypes sequenced from specimens sampled as shallow as 101 m, suggest a shallow-water emergence of some Chrysogorgia species.
Despite their abundance and ecological importance in a wide variety of shallow and deep water mar... more Despite their abundance and ecological importance in a wide variety of shallow and deep water marine communities, octocorals (soft corals, sea fans, and sea pens) are a group whose taxonomy and phylogenetic relationships remain poorly known and little studied. The group is currently divided into three orders (O: Alcyonacea, Pennatulacea, and Helioporacea); the large O. Alcyonacea (soft corals and sea fans) is further subdivided into six sub-ordinal groups on the basis of skeletal composition and colony growth form. We used 1429 bp of two mitochondrial protein-coding genes, ND2 and msh1, to construct a phylogeny for 103 octocoral genera representing 28 families. In agreement with a previous 18S rDNA phylogeny, our results support a division of Octocorallia into two major clades plus a third, minor clade. We found one large clade (Holaxonia-Alcyoniina) comprising the sea fan sub-order Holaxonia and the majority of soft corals, and a second clade (Calcaxonia-Pennatulacea) comprising sea pens (O. Pennatulacea) and the sea fan sub-order Calcaxonia. Taxa belonging to the sea fan group Scleraxonia and the soft coral family Alcyoniidae were divided among the Holaxonia-Alcyoniina clade and a third, small clade (Anthomastus-Corallium) whose relationship to the two major clades was unresolved. In contrast to the previous studies, we found sea pens to be monophyletic but nested within Calcaxonia; our analyses support the sea fan family Ellisellidae as the sister taxon to the sea pens. We are unable to reject the hypothesis that the calcaxonian and holaxonian skeletal axes each arose once and suggest that the skeletal axis of sea pens is derived from that of Calcaxonia. Topology tests rejected the monophyly of sub-ordinal groups Alcyoniina, Scleraxonia, and Stolonifera, as well as 9 of 14 families for which we sampled multiple genera. The much broader taxon sampling and better phylogenetic resolution aVorded by our study relative to the previous eVorts greatly clarify the relationships among families and subordinal groups within each of the major clades. The failure of these mitochondrial genes as well as previous 18S rDNA studies to resolve many of the deeper nodes within the tree (including its root) suggest that octocorals underwent a rapid radiation and that large amounts of sequence data will be required in order to resolve the basal relationships within the clade.
The widespread assumption that COI and other mitochondrial genes will be ineffective DNA barcodes... more The widespread assumption that COI and other mitochondrial genes will be ineffective DNA barcodes for anthozoan cnidarians has not been well tested for most anthozoans other than scleractinian corals. Here we examine the limitations of mitochondrial gene barcoding in the sub-class Octocorallia, a large, diverse, and ecologically important group of anthozoans. Pairwise genetic distance values (uncorrected p) were compared for three candidate barcoding regions: the Folmer region of COI; a fragment of the octocoral-specific mitochondrial proteincoding gene, msh1; and an extended barcode of msh1 plus COI with a short, adjacent intergenic region (igr1). Intraspecific variation was <0.5%, with most species exhibiting no variation in any of the three gene regions. Interspecific divergence was also low: 18.5% of congeneric morphospecies shared identical COI barcodes, and there was no discernible barcoding gap between intra-and interspecific p values. In a case study to assess regional octocoral biodiversity, COI and msh1 barcodes each identified 70% of morphospecies. In a second case study, a nucleotide character-based analysis correctly identified 70% of species in the temperate genus Alcyonium. Although interspecific genetic distances were 2• greater for msh1 than COI, each marker identified similar numbers of species in the two case studies, and the extended COI + igr1 + msh1 barcode more effectively discriminated sister taxa in Alcyonium. Although far from perfect for species identification, a COI + igr1 + msh1 barcode nonetheless represents a valuable addition to the depauperate set of characters available for octocoral taxonomy.
The rare octocoral genus Isidoides Nutting, 1910 was originally placed in the Gorgonellidae (now ... more The rare octocoral genus Isidoides Nutting, 1910 was originally placed in the Gorgonellidae (now the Ellisellidae), even though it showed a remarkable similarity to the Isidae (now the Isididae). Isidoides was not classified in the Isididae mostly because the type specimen lacked skeletal nodes, a defining characteristic of that family. The genus was later assigned to the Chrysogorgiidae based on sclerite morphology. Specimens were recently collected in the south-western Pacific, providing material for genetic analysis and detailed characterisation of the morphology, and allowing us to consider the systematic placement of this taxon within the suborder Calcaxonia. A previously reported phylogeny allowed us to reject monophyly with the Chrysogorgiidae, and infer a close relationship with the Isididae subfamily Keratoisidinae. While scanning for molecular variation across mitochondrial genes, we discovered a novel gene order that is, based on available data, unique among metazoans. De...
Seamounts are undersea mountains commonly characterized by accelerated currents, exposed hard-sub... more Seamounts are undersea mountains commonly characterized by accelerated currents, exposed hard-substrates, and relatively high biomass and biodiversity. Hydrographic features associated with seamounts have led authors to hypothesize that benthic invertebrate populations from geographically separated seamounts (and the continental slope) may experience varying degrees of genetic isolation, resulting in high levels of endemism. While this hypothesis has been tested for multiple taxonomic groups in the Pacific, it has rarely been addressed in the Atlantic. We tested the null hypothesis that the geographic ranges of corals from NW Atlantic seamounts are restricted to individual seamounts. We examined 188 octocoral and 50 antipatharian colonies (representing 6 and 2 genera, respectively) from 14 seamounts, spanning 1700 km, and the adjacent continental margin and estimated their genetic variation using mitochondrial loci (msh1 for all octocorals, as well as an intergenic region for isidids, and 3 multi-gene spanning segments for antipatharians). Well-sampled haplotypes were not geographically isolated on individual seamounts, thus refuting the hypothesis of local endemism of coral fauna on the New England and Corner Seamounts. The narrow geographic distribution of rare haplotypes is most likely due to undersampling rather than endemism. Our results do not preclude that cryptic variation and endemism not revealed by mitochondrial DNA may become evident should more variable markers be developed.
Octocorals, especially gorgonians, are conspicuous on Caribbean coral reefs, but there is no cons... more Octocorals, especially gorgonians, are conspicuous on Caribbean coral reefs, but there is no consensus regarding species relationships. Mitochondrial protein-coding genes [NADH-dehydrogenase subunits 2 (ND2) and 6 (ND6), and mutS homolog (msh1), 1633 bp] from 28 shallow-water species were sequenced to develop the first molecular phylogeny for Caribbean octocorals. The specimens were collected primarily in the Caribbean or off Brazil in 1999-2001. Morphological characters (sclerites and axial ultrastructure) were also examined in order to map them onto the molecular phylogeny. Analyses of both nucleotide and amino acid substitutions using maximum parsimony and likelihood (including maximum-likelihood and Bayesian analysis) generated very similar results, with most nodes having high levels of support. These molecular results were significantly different from the generally accepted classification. Neither Plexauridae nor Gorgoniidae were monophyletic. Plexaurella spp., nominal plexaurids, were basal to the gorgoniids, sharing many morphological characters with them. This corroborates previous findings using secondary metabolites and biosynthetic pathways. The sea fans, Gorgonia spp. and Pacifigorgia spp., as well as the pinnate gorgonians, Muriceopsis flavida and Pseudopterogorgia spp., did not have sea fan or pinnate relatives, suggesting there has been convergent evolution of colony form. Caribbean plexaurids appeared more derived and/or recently evolved according to both morphological and molecular data (e.g. Eunicea spp. and Plexaura spp.). Molecular phylogenetics is a promising approach for reconstructing phylogenetic relationships among octocorals as well as to understand their complex morphology.
Using the remotely operated vehicle Deep Discoverer, we observed a large stylodactylid shrimp res... more Using the remotely operated vehicle Deep Discoverer, we observed a large stylodactylid shrimp resting on a sedimented sea floor at 4826 m in the Marianas Trench Marine National Monument. The shrimp was not collected but most closely resembled Bathystylodactylus bathyalis, known previously only from a single broken specimen. Video footage shows the shrimp facing into the current and extending its upraised and fringed first and second pereopods, presumably capturing passing particles. The video footage is the first ever to show a living deep-sea stylodactylid and constitutes the deepest record for the family. We provide a list of the deepest reports of caridean shrimps world-wide.
The Keratoisidinae are a poorly known, but phenotypically diverse group of deepwater corals. Rece... more The Keratoisidinae are a poorly known, but phenotypically diverse group of deepwater corals. Recent developments in deepwater trawling in the southwest Pacific have provided many more specimens of bamboo corals. Two sub-regions of the mitochondrial genome were sequenced to test genetic relationships among specimens collected over a wide geographical range (27-50°S): a sub-region of the large-subunit rRNA (16S rRNA), characterized by a highly variable insertion/deletion (INDEL#2) region; and a non-coding region between COII and COI. Based on DNA haplotypes, 14 species of Keratoisidinae were recognized among 88 specimens from deep water in the southwest Pacific Ocean. The common haplotypes also appeared in specimens collected in the northwest Pacific Ocean and may indicate that some bamboo coral species are widespread in the Pacific, or that the mitochondrial markers are insensitive to recent speciation events. Many specimens were taken from flat bottom areas and, contrary to assumptions, the bamboo corals are not endemic to seamounts. The closure of some seamounts to trawling will protect bamboo corals from extinction, but not from local depletion.
ABSTRACT Bamboo corals (family Isididae) are among the most easily recognized deep-water octocora... more ABSTRACT Bamboo corals (family Isididae) are among the most easily recognized deep-water octocorals due to their articulated skeleton comprised of non-sclerite calcareous in-ternodes alternating with proteinaceous nodes. Most commonly encountered in the deep-sea are ...
Molecular Phylogenetics and Evolution, Mar 31, 2007
Black corals comprise a globally distributed shallow- and deep-water taxon whose phylogenetic pos... more Black corals comprise a globally distributed shallow- and deep-water taxon whose phylogenetic position within the Anthozoa has been debated. We sequenced the complete mitochondrial genome of the antipatharian Chrysopathes formosa to further evaluate its phylogenetic relationships. The circular mitochondrial genome (18,398 bp) consists of 13 energy pathway protein-coding genes and two ribosomal RNAs, but only two transfer RNA genes (trnM and trnW), as well as a group I intron within the nad5 gene that contains the only copies of nad1 and nad3. No novel genes were found in the antipatharian mitochondrial genome. Gene order and genome content are most similar to those of the sea anemone Metridium senile (subclass Hexacorallia), with differences being the relative location of three contiguous genes (cox2-nad4-nad6) and absence (from the antipatharian) of a group I intron within the cox1 gene. Phylogenetic analyses of multiple protein-coding genes support classifying the Antipatharia within the subclass Hexacorallia and not the subclass Ceriantipatharia; however, the sister-taxon relationships of black corals within Hexacorallia remain inconclusive.
A new species of the pardaliscid amphipod genus Halice, H. hesmonectes, is described from hydroth... more A new species of the pardaliscid amphipod genus Halice, H. hesmonectes, is described from hydrothermal vents in the eastern Pacific Ocean. The species occurs in large monospecific swarms in the immediate vicinity of low temperature vent openings. Halice hesmonectes differs from other members of the genus in having the following combination of characters: extremely long pereopods 5–7 (exceeding length of pereon, and nearly twice the length of pereopods 1–4); minute dactylus on pereopods 3 and 4, unique, constricted at midlength; pleopods well developed, as long or longer than pereopods 1–4; telson cleft along approximately two-thirds its length and terminating in an acute tip on each lobe; short article 3 (about 1/3 length of article 2) on mandibular palp; and accessory flagellum of first antenna with only two articles, the distal one being approximately 1/6 the length of the proximal. In addition, the body and virtually all appendages are covered by minute cuticular scales, probably present also on other pardaliscids (visible only via SEM) and known from other peracarids. Problematic taxonomy within the family Pardaliscidae is discussed.
The physical uniformity of the deep sea suggests a lack of absolute barriers to faunal dispersal,... more The physical uniformity of the deep sea suggests a lack of absolute barriers to faunal dispersal, and thus genetic homogeneity in broadly distributed species is expected. The deep-sea amphipod Eurythenes gryllus Lichtenstein (Crustacea: Lysianassoidea) is considered a panoceanic, cold-water stenotherm, with a vertical depth distribution from 184 to 6500 m. We surveyed mtDNA sequence diversity in E. gryllus to assess
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