Deep-sea origin and in-situ diversification of chrysogorgiid octocorals

Toward a revision of the bamboo corals: Part 6, Illuminating a new candelabrum genus (Octocorallia: Keratoisididae)

Observations and collections made using remotely operated vehicles (ROV) outfit with high-definition video cameras on bathyal seamounts of the North Atlantic and North Pacific have revealed a bamboo coral (Octocorallia, Keratoisididae) with consistent and recognizable colony morphology: a long unbranched "stem" from which many vertically aligned branches arise in a single plane to produce the aspect of a tall candelabrum. Additional observations encountered colonies with only 3 branches arising from the central terminal node to produce the appearance of a standing trident. Genetic analyses suggested both colony morphologies (trident and candelabrum) to be the same species at different growth stages. Herein we formally describe this taxon, Tridentisis candelabrum n. gen. n. sp., erecting a new genus to accommodate the unique and distinctive colony morphology, and discuss morphological variation observed across the documented geographic range.

Studies on western Pacific gorgonians (Anthozoa: Octocorallia, Chrysogorgiidae). Part 1: a review of the genus Chrysogorgia, with description of a new genus and three new species

Members of Chrysogorgia Duchassaing & Michelotti, 1864, known as golden corals, are distributed in the deep sea worldwide. Based on specimens obtained from the tropical western Pacific and an integrated morphological-molecular approach, we established a new genus Parachrysogorgia, which includes 13 species separated from Chrysogorgia, and described nine species of Chrysogorgia including three new species C. arboriformis sp. nov., C. cylindrata sp. nov. and C. tenuis sp. nov., and two new combinations of Parachrysogorgia. The genus differs from Chrysogorgia by possessing a bare, sclerite-free area at the base of each tentacle and eight distinct projections beneath tentacles. Chrysogorgia cylindrata sp. nov. is distinguished by a slender bottlebrush-shaped colony in adults, elongate and lobed scales in coenenchyme, and warty and thick sclerites near the polyp mouth area. Chrysogorgia arboriformis sp. nov. is characterized by a tree-shaped colony with a long unbranched stem, slender and thin scales usually with large warts in coenenchyme. Chrysogorgia tenuis sp. nov. can be separated by a broad bottlebrush-shaped colony, long interbranch distance, elongate scales with broad lobes in polyp body wall. In contrast to the intraspecific variation of colony form, branch internodes, branching sequence and polyps, the sclerite forms and arrangement in different parts can be viewed as the most important character to separate Chrysogorgia species. For convenient identification, we divided the Chrysogorgia species into 12 morphological groups and divided Parachrysogorgia into three groups based on their sclerite forms and arrangement.

Transcriptome assemblies of two deep-sea octocorals Calyptrophora lyra and Chrysogorgia stellata from West Pacific seamount, Godin Guyot

This is the first report of the transcriptome assemblies of the deep-sea octocorals Calyptrophora lyra and Chrysogorgia stellata, which were collected in a survey of the West Pacific seamounts area. We sequenced the transcriptomes of C. lyra and C. stellata using the Illumina NovaSeq 6000 System. De novo assembly and analysis of the coding regions predicted 193,796 unigenes from the total 116,441,796 reads of C. lyra and 235,513 unigenes from the total 122,031,866 reads of C. stellata. Our data are a valuable resource with which to understand the ecological and biological characteristics of the West Pacific deep-sea corals. The data will also contribute to the study of deep-sea environments as extreme and limited habitats and provide direction for future research and further insight into the organismal responses of deep-sea corals to environmental changes.

Exploring the trends of adaptation and evolution of sclerites with regards to habitat depth in sea pens

Octocorals possess sclerites, small elements comprised of calcium carbonate (CaCO₃) that are important diagnostic characters in octocoral taxonomy. Among octocorals, sea pens comprise a unique order (Pennatulacea) that live in a wide range of depths. Habitat depth is considered to be important in the diversification of octocoral species, but a lack of information on sea pens has limited studies on their adaptation and evolution across depth. Here, we aimed to reveal trends of adaptation and evolution of sclerite shapes in sea pens with regards to habitat depth via phylogenetic analyses and ancestral reconstruction analyses. Colony form of sea pens is suggested to have undergone convergent evolution and the loss of axis has occurred independently across the evolution of sea pens. Divergences of sea pen taxa and of sclerite forms are suggested to depend on habitat depths. In addition, their sclerite forms may be related to evolutionary history of the sclerite and the surrounding chemical environment as well as water temperature. Three-flanged sclerites may possess the tolerance towards the environment of the deep sea, while plate sclerites are suggested to be adapted towards shallower waters, and have evolved independently multiple times. The common ancestor form of sea pens was predicted to be deep-sea and similar to family Pseudumbellulidae in form, possessing sclerites intermediate in form to those of alcyonaceans and modern sea pens such as spindles, rods with spines, and three-flanged sclerites with serrated edges sclerites, as well as having an axis and bilateral traits.

When distant relatives look too alike: a new family, two new genera and a new species of deep-sea

Among octocorals, colonies of the deep-sea pennatulacean genus Umbellula Gray, 1870 are some of the most instantly recognisable forms. Historically however, species identification in this genus has been usually based on few morphological characters with very little knowledge of associated intraspecific variability. This fact, combined with the very limited access to these deep-sea organisms, has resulted in numerous uncertainties about the true characters that should be used in species determination and recognition of synonyms and questionable species. Recent phylogenetic analyses based on mitochondrial and nuclear DNA markers has shown to be an excellent complementary source of information to morphological examination, being able to detect incongruent taxonomic assignments in classifications based only on morphological characters. Molecular analyses can reveal the presence of paraphyletic or polyphyletic groupings of taxa that may then be the subject of further research integrating morphological and molecular techniques. This paper addresses the existence of a set of specimens initially assigned to the genus Umbellula Gray, 1870 but that have been shown to be distantly related to the type species Umbellula encrinus (Linnaeus, 1758) based on molecular phylogenetic hypotheses. Phylogenetic analyses based on four genetic markers, three mitochondrial (mtMutS, ND2, Cox1) and one nuclear (28S), validate the definition of a new family (Pseudumbellulidae fam. nov.) and two new genera (Pseudumbellula gen. nov. and Solumbellula gen. nov). These analyses also justify the segregation of some of the morphological characters previously included in the diagnosis of the genus Umbellula and the monotypic family Umbellulidae Kölliker, 1880. Moreover, a new species, Pseudumbellula scotiae sp. nov. is described and illustrated with material from the North Eastern Atlantic and compared with congeners. Additionally, the well-known but atypical species Umbellula monocephalus Pasternak, 1964 is transferred and described here as Solumbellula monocephalus (Pasternak, 1964), comb. nov., based on both molecular data and morphology.

Morphological and Molecular Characterization of Five Species Including Three New Species of Golden Gorgonians (Cnidaria: Octocorallia) from Seamounts in the Western Pacific

Members of genus Iridogorgia Verrill, 1883 are the typical deep-sea megabenthos with only seven species reported. Based on an integrated morphological-molecular approach, eight sampled specimens of Iridogorgia from seamounts in the tropical Western Pacific are identified as three new species, and two known species I. magnispiralis Watling, 2007 and I. densispicula Xu, Zhan, Li and Xu, 2020. Iridogorgia flexilis sp. nov. is unique in having a very broad polyp body base with stout and thick scales. Iridogorgia densispiralis sp. nov. can be distinguished by rods present in both polyps and coenenchyme, and I. verrucosa sp. nov. is characterized by having numerous verrucae in coenenchyme and irregular spindles and scales in the polyp body wall. Phylogenetic analysis based on the nuclear 28S rDNA indicated that I. densispiralis sp. nov. showed close relationships with I. splendens Watling, 2007 and I. verrucosa sp. nov., and I. flexilis sp. nov. formed a sister clade with I. magnispiralis. In addition, due to Rhodaniridogorgia fragilis Watling, 2007 nested into the Iridogorgia clade in mtMutS-COI trees and shared highly similar morphology to the latter, we propose to eliminate the genus Rhodaniridogorgia by establishing a new combination Iridogorgia fragilis (Watling, 2007) comb. nov. and resurrecting I. superba Nutting, 1908.

Revision of the genus Plexaurella Kölliker, 1865 (Anthozoa: Octocorallia) and resurrection of Plexaurellidae Verrill, 1912 new rank

The current knowledge on the diversity of the genus Plexaurella is based on a series of dated revisions, often with no examination of types. Although being common octocorals in western Atlantic reefs, there is no consensus on an exact number of valid species. Furthermore, phylogenetic reconstructions do not support the current classification of Plexaurella within the family Plexauridae. Thus, this study reviews the genus based on examination of available types and assesses monophyly using mitochondrial (COI+igr, mtMutS) and nuclear (28S) markers, mostly from available molecular data. Until now, up to six species were considered valid. Our results show that the group is composed of at least seven previously described species: P. dichotoma, P. nutans, P. grisea, P. teres, P. grandiflora, P. regia and P. obesa; and one new species: Plexaurella rastrera sp. nov. An illustrated key to the valid species and a list of all available names are provided and the current classification of the genus is discussed. Based on congruent phylogenetic reconstructions and genetic distances, we propose the elevation of the former plexaurid subfamily Plexaurellinae to family level. Finally, based on examination of types, we propose the synonymy between Pseudoplexaura crucis and Plexaurella tenuis under Pseudoplexaura tenuis new comb.

Morphology and phylogenetic analysis of five deep-sea golden gorgonians (Cnidaria, Octocorallia, Chrysogorgiidae) in the Western Pacific Ocean, with the description of a new species

Explorations of seamounts in the Western Pacific Ocean and South China Sea resulted in collecting 18 specimens of golden gorgonians. Based on the morphology and the genetic analysis of mtMutS, they are described as one new species, Chrysogorgiacarolinensissp. nov., and four known species, including Chrysogorgiadendritica Xu, Zhan & Xu, 2020, Metallogorgiamelanotrichos (Wright & Studer, 1889), Metallogorgiamacrospina Kükenthal, 1919, and Pseudochrysogorgiabellona Pante & France, 2010. Chrysogorgiacarolinensis belongs to the Chrysogorgia “group A, Spiculosae” with rods or spindles distributed in the polyp-body wall and tentacles, and differs from all of its congeners except C.dendritica by the 1/3L branching sequence and amoeba-shaped sclerites at the basal polyp body. The mtMutS sequence of C.carolinensissp. nov. has six deletion mutations compared to those of its congeners, supporting the establishment of the new species. Although no genetic variability was observed between the closely related species C.dendritica and C.abludo Pante & Watling, 2012, the former is different from the latter by the apparently irregular sclerites in the polyp body wall. The two specimens of Metallogorgiamelanotrichos match well with the original description except for relatively larger polyps, while the M.macrospina specimens have slightly smaller polyps than the holotype. The juvenile of Metallogorgia has an obvious morphological difference with the adults in the colony shape and branches, but they can be unified by the same polyps and sclerites as well as mitochondrial MutS sequences. Thus, the generic diagnosis of Metallogorgia is slightly extended to include the morphology of juveniles. The morphology of Pseudochrysogorgiabellona Pante & France, 2010, as a new record for the South China Sea, matches well with that of the original description. In the phylogenetic trees, the Chrysogorgia species are separated into two clades, and while Metallogorgia and Pseudochrysogorgia formed a sister clade.

Morphology and molecular phylogeny of three new deep-sea species of Chrysogorgia (Cnidaria, Octocorallia) from seamounts in the tropical Western Pacific Ocean

Three new species of Chrysogorgia were discovered from seamounts in the tropical Western Pacific Ocean. Chrysogorgia dendritica sp. nov. and Chrysogorgia fragilis sp. nov. were collected from the Kocebu Guyot of the Magellan Seamount chain with the water depth of 1,821 m and 1,279-1,321 m, respectively, and Chrysogorgia gracilis sp. nov. was collected from a seamount adjacent to the Mariana Trench with the water depth of 298 m. They all belong to the Chrysogorgia "group A, Spiculosae" with rods distributed in body wall and tentacles, and differ from all congeners except C. abludo Pante & Watling, 2012 by having a tree-shaped colony (vs. bottlebrush-shaped, planar or biflabellate). Chrysogorgia dendritica sp. nov. is unique in having a monopodial stem, the 1/3L branching sequence and the amoeba-shaped sclerites (sclerites branched toward to many directions) at the body bases of polyps. Chrysogorgia fragilis sp. nov. is most similar to C. abludo, but differs by the regular 1/3L branching sequence and elongate flat scales in coenenchyme. Chrysogorgia gracilis sp. nov. is easily separated from congeners by the 1/4L branching sequence, the absence of sclerites in the basal body wall, and the very sparse scales in coenenchyme. Based on the phylogenetic and genetic distance analyses of mtMutS gene, all the available Chrysogorgia species were separated into two main groups: one includes C. binata, C. cf. stellata and C. chryseis, which have two or more fans emerging from a short main stem (bi- or multi-flabellate colony); the other one includes all the species with the branching patterns as a single ascending spiral (clockwise or counterclockwise, bottlebrush-shaped colony), a fan (planar colony) and a bush of branches perched on top of a long straight stem (tree-shaped colony). Additionally, the tree-shaped colony represents a new branching pattern in Chrysogorgia, and therefore we extend the generic diagnosis.

Multiplexed ISSR genotyping by sequencing distinguishes two precious coral species (Anthozoa: Octocorallia: Coralliidae) that share a mitochondrial haplotype

Background

Precious corals known as coralliid corals (Anthozoa: Octocorallia) play an important role in increasing the biodiversity of the deep sea. Currently, these corals are highly threatened because of overfishing that has been brought on by an increased demand and elevated prices for them.The deep sea precious corals Pleurocorallium elatius and P. konojoi are distributed in Japanese waters and have distinct morphological features: (1) the terminal branches of the colony form of P. elatius are very fine, while those of P. konojoi are blunt and rounded, (2) the autozooids of P. elatius are arranged in approximately four rows, while those of P. konojoi are clustered in groups. However, previous genetic analysis using mtDNA and nuclear DNA did not indicate monophyly. Therefore, it is important to clarify their species status to allow for their conservation.

Methodology

We collected a total of 87 samples (60 of Corallium japonicum and 27 of P. konojoi) from around the Ryukyu Islands and Shikoku Island, which are geographically separated by approximately 1,300 km. We used a multiplexed inter-simple sequence repeat (ISSR) genotyping by sequencing (MIG-seq) and obtained 223 SNPs with which to perform STRUCTURE analysis and principle coordinate analysis (PCoA). In addition, two relatively polymorphic mtDNA regions were sequenced and compared.

Results

P. elatius and P. konojoi share a same mtDNA haplotype, which has been previously reported. However, MIG-seq analysis clearly distinguished the two species based on PCoA and STRUCTURE analysis, including 5% of species-specific fixed SNPs.

Conclusion

This study indicated that P. elatius and P. konojoi are different species and therefore both species should be conserved separately. Our findings highlight the importance of the conservation of these two species, especially P. elatius, whose population has been dramatically depleted over the last 100 years. The study also demonstrated the effectiveness and robustness of MIG-seq for defining closely related octocoral species that were otherwise indistinguishable using traditional genetic markers (mtDNA and EF).

Novel diversity in mitochondrial genomes of deep-sea Pennatulacea (Cnidaria: Anthozoa: Octocorallia)

We present the first documented complete mitogenomes of deep-sea Pennatulacea, representing nine genera and eight families. These include one species each of the deep-sea genera Funiculina, Halipteris, Protoptilum and Distichoptilum, four species each of Umbellula and Pennatula, three species of Kophobelemnon and two species of Anthoptilum, as well as one species of the epi- and mesobenthic genus Virgularia. Seventeen circular genomes ranged from 18,513 bp (Halipteris cf. finmarchica) to 19,171 bp (Distichoptilum gracile) and contained all genes standard to octocoral mitochondrial genomes (14 protein-coding genes, two ribosomal RNA genes and one transfer RNA). We found at least three different gene orders in Pennatulacea: the ancestral gene order, the gene order found in bamboo corals (Family Isididae), and a novel gene order. The mitogenome of one species of Umbellula has a bipartite genome (∼13 kbp and ∼5 kbp), with good evidence that both parts are circular.

A phylogenetic analysis of the Primnoidae (Anthozoa: Octocorallia: Calcaxonia) with analyses of character evolution and a key to the genera and subgenera

Background

Previous phylogenetic analyses of primnoid octocorals utilizing morphological or molecular data have each recovered evolutionary relationships among genera that are largely incongruent with each other, with some exceptions. In an effort to reconcile molecular-based phylogenies with morphological characters, phylogenetic reconstructions were performed with 33 of 43 primnoid genera using four loci (mtMutS, COI, 28S and 18S), and ancestral state reconstructions were performed using 9 taxonomically relevant characters. In addition, an updated illustrated key to the current 48 genus-level (43 genera, 5 subgenera) primnoids is presented.

Results

Ancestral state reconstruction recovered the ancestral colony shape of primnoids as dichotomous planar. Convergence was detected among all 9 characters, and reversals to the character state of the common ancestor occurred in 4 characters. However, some characters were found to be informative. For example, the weak ascus scale of Metafannyella is not likely homologous to the ascus scales of Onogorgia and Fannyella, and the monophyly of two subgenera within Thouarella, which contain polyps in either whorls or an isolated arrangement, was supported. Phylogenetic analyses were generally consistent with previous studies, and resulted in the synonymy of one genus and a subgenus, the elevation of two subgenera, and the transfer of two species back to an original genus. For example, body wall ornamentation of Fanellia was re-evaluated, indicating a synonymy with Callogorgia; the utility of polyp arrangement for the subgenus Plumarella (Dicholaphis) was not supported, and is synonymized with the nominate subgenus Plumarella (Plumarella); the subgenera Plumarella (Faxiella) and Plumarella (Verticillata) are raised to generic status; and the two Plumarella species (P. diadema and P. undulata) are transferred back to Thouarella based on the homology of their marginal scales.

Conclusions

Altogether, and similar to other octocorallian groups, these results indicate that many of the morphological characters examined among primnoids, particularly colony morphology, are labile and exhibit complex evolutionary histories. However, some morphological characters such as coordination of polyps, presence of the ascus body wall scale, number of rows of body wall scales, and number of marginal scales help identify many clades, and are suitable for robust systematic assessments among primnoids.

Electronic supplementary material

The online version of this article (10.1186/s12862-018-1182-5) contains supplementary material, which is available to authorized users.

Deep-Water Octocorals (Cnidaria, Anthozoa) from the Galápagos and Cocos Islands. Part 1: Suborder Calcaxonia

Thirteen species of deep-water calcaxonian octocorals belonging to the families Primnoidae, Chrysogorgiidae, and Isididae collected from off the Galápagos and Cocos Islands are described and figured. Seven of these species are described as new; nine of the 13 are not known outside the Galápagos region. Of the four species occurring elsewhere, two also occur in the eastern Pacific, one off Hawaii, and one from off Antarctica. A key to the 22 Indo-Pacific species of Callogorgia is provided to help distinguish those species.

A new genus and species of golden coral (Anthozoa, Octocorallia, Chrysogorgiidae) from the Northwest Atlantic

A new genus and species of unbranched golden coral, Flagelligorgia gracilis, is described based on several specimens collected off the southeastern coast of the United States. The genus is provisionally included in the family Chrysogorgiidae, pending molecular confirmation. Flagelligorgia morphologically resembles other unbranched chrysogorgiids, such as Distichogorgia, Chalcogorgia, Helicogorgia and Radicipes, to which it is compared. The type species is illustrated and its distribution mapped.

Exploration of the Canyon-Incised Continental Margin of the Northeastern United States Reveals Dynamic Habitats and Diverse Communities

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.

Phylogeny and systematics of deep-sea precious corals (Anthozoa: Octocorallia: Coralliidae)

The phylogeny of Coralliidae is being increasingly studied to elucidate their evolutionary history and species delimitation due to global concerns about their conservation. Previous studies on phylogenetic relationships within Coralliidae have pointed out that the two currently recognized genera are not monophyletic and the Coralliidae should be divided into three genera. In order to provide a comprehensive revision of the taxonomy of Coralliidae, we documented 110 specimens using eight mitochondrial and one nuclear loci to reconstruct their phylogeny. The morphological features of 27 type specimens were also examined. Phylogenetic relationships based on both mitochondrial and nuclear markers revealed two reciprocally monophyletic clades of Coralliidae. One of the clades was further split into two subclades with respect to sequence variation and observable morphological features. Based on the results of genealogical analyses and distinctive morphological features, the three genera classification of Coralliidae proposed by Gray (1867) was redefined. In this revised taxonomic system, Corallium, Hemicorallium, and Pleurocorallium consist of 7, 16 and 14 species, respectively. Our results also showed that the cosmopolitan Hemicorallium laauense is a species complex containing a cryptic species.

Evolutionary dynamics of a common sub-Antarctic octocoral family

Sequence data were obtained for five different loci, both mitochondrial (cox1, mtMutS, 16S) and nuclear (18S, 28S rDNA), from 64 species representing 25 genera of the common deep-sea octocoral family Primnoidae. We tested the hypothesis that Primnoidae have an Antarctic origin, as this is where they currently have high species richness, using Maximum likelihood and Bayesian inference methods of phylogenetic analysis. Using a time-calibrated molecular phylogeny we also investigated the time of species radiation in sub-Antarctic Primnoidae. Our relatively wide taxon sampling and phylogenetic analysis supported Primnoidae as a monophyletic family. The base of the well-supported phylogeny was Pacific in origin, indicating Primnoidae sub-Antarctic diversity is a secondary species radiation. There is also evidence for a subsequent range extension of sub-Antarctic lineages into deep-water areas of the Indian and Pacific Oceans. Conservative and speculative fossil-calibration analyses resulted in two differing estimations of sub-Antarctic species divergence times. Conservative analysis suggested a sub-Antarctic species radiation occurred ∼52MYA (95% HPD: 36-73MYA), potentially before the opening of the Drake Passage and Antarctic Circumpolar Current (ACC) formation (41-37MYA). Speculative analysis pushed this radiation back into the late Jurassic, 157MYA (95% HPD: 118-204MYA). Genus-level groupings were broadly supported in this analysis with some notable polyphyletic exceptions: Callogorgia, Fanellia, Primnoella, Plumarella, Thouarella. Molecular and morphological evidence supports the placement of Tauroprimnoa austasensis within Dasystenella and Fannyella kuekenthali within Metafannyella.

Use of RAD sequencing for delimiting species

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.

First glimpse into Lower Jurassic deep-sea biodiversity: in situ diversification and resilience against extinction

Owing to the assumed lack of deep-sea macrofossils older than the Late Cretaceous, very little is known about the geological history of deep-sea communities, and most inference-based hypotheses argue for repeated recolonizations of the deep sea from shelf habitats following major palaeoceanographic perturbations. We present a fossil deep-sea assemblage of echinoderms, gastropods, brachiopods and ostracods, from the Early Jurassic of the Glasenbach Gorge, Austria, which includes the oldest known representatives of a number of extant deep-sea groups, and thus implies that in situ diversification, in contrast to immigration from shelf habitats, played a much greater role in shaping modern deep-sea biodiversity than previously thought. A comparison with coeval shelf assemblages reveals that, at least in some of the analysed groups, significantly more extant families/superfamilies have endured in the deep sea since the Early Jurassic than in the shelf seas, which suggests that deep-sea biota are more resilient against extinction than shallow-water ones. In addition, a number of extant deep-sea families/superfamilies found in the Glasenbach assemblage lack post-Jurassic shelf occurrences, implying that if there was a complete extinction of the deep-sea fauna followed by replacement from the shelf, it must have happened before the Late Jurassic.

Explaining bathymetric diversity patterns in marine benthic invertebrates and demersal fishes: physiological contributions to adaptation of life at depth

Bathymetric biodiversity patterns of marine benthic invertebrates and demersal fishes have been identified in the extant fauna of the deep continental margins. Depth zonation is widespread and evident through a transition between shelf and slope fauna from the shelf break to 1000 m, and a transition between slope and abyssal fauna from 2000 to 3000 m; these transitions are characterised by high species turnover. A unimodal pattern of diversity with depth peaks between 1000 and 3000 m, despite the relatively low area represented by these depths. Zonation is thought to result from the colonisation of the deep sea by shallow-water organisms following multiple mass extinction events throughout the Phanerozoic. The effects of low temperature and high pressure act across hierarchical levels of biological organisation and appear sufficient to limit the distributions of such shallow-water species. Hydrostatic pressures of bathyal depths have consistently been identified experimentally as the maximum tolerated by shallow-water and upper bathyal benthic invertebrates at in situ temperatures, and adaptation appears required for passage to deeper water in both benthic invertebrates and demersal fishes. Together, this suggests that a hyperbaric and thermal physiological bottleneck at bathyal depths contributes to bathymetric zonation. The peak of the unimodal diversity-depth pattern typically occurs at these depths even though the area represented by these depths is relatively low. Although it is recognised that, over long evolutionary time scales, shallow-water diversity patterns are driven by speciation, little consideration has been given to the potential implications for species distribution patterns with depth. Molecular and morphological evidence indicates that cool bathyal waters are the primary site of adaptive radiation in the deep sea, and we hypothesise that bathymetric variation in speciation rates could drive the unimodal diversity-depth pattern over time. Thermal effects on metabolic-rate-dependent mutation and on generation times have been proposed to drive differences in speciation rates, which result in modern latitudinal biodiversity patterns over time. Clearly, this thermal mechanism alone cannot explain bathymetric patterns since temperature generally decreases with depth. We hypothesise that demonstrated physiological effects of high hydrostatic pressure and low temperature at bathyal depths, acting on shallow-water taxa invading the deep sea, may invoke a stress-evolution mechanism by increasing mutagenic activity in germ cells, by inactivating canalisation during embryonic or larval development, by releasing hidden variation or mutagenic activity, or by activating or releasing transposable elements in larvae or adults. In this scenario, increased variation at a physiological bottleneck at bathyal depths results in elevated speciation rate. Adaptation that increases tolerance to high hydrostatic pressure and low temperature allows colonisation of abyssal depths and reduces the stress-evolution response, consequently returning speciation of deeper taxa to the background rate. Over time this mechanism could contribute to the unimodal diversity-depth pattern.

Niche divergence by deep-sea octocorals in the genus Callogorgia across the continental slope of the Gulf of Mexico

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.

Molecular and morphological data support reclassification of the octocoral genus Isidoides

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. Despite these new data, the systematic placement of Isidoides is still unclear, as (1) the phylogenetic relationships among Isididae subfamilies remain poorly resolved, (2) genetic distances between mitochondrial mtMutS sequences from Isidoides and Keratoisidinae are characteristic of intra-familial distances, and (3) mitochondrial gene rearrangements may occur among confamilial genera. For these reasons, and because a revision of the Isididae is beyond the scope of this contribution, we amend the familial placement of Isidoides to incertae sedis.