The evolutionary history of the order Antipatharia (Cnidaria: Anthozoa: Hexacorallia) as inferred from mitochondrial and nuclear DNA: implications for black coral taxonomy and systematics

Unveiling the early evolution of black corals

Black corals, primarily deep-sea cnidarians (Anthozoa: Antipatharia), are inferred to have originated either in the Ediacaran or Cambrian based on molecular clock estimates. However, only the fossil family Sinopathidae, comprising Sinopathes and Sterictopathes, from the Early Ordovician of Hubei, China, has been recorded in the fossil record. The affinity of this family has been questioned because of morphological inconsistencies between fossil and extant species. Here we describe two transitional species of Sterictopathes from the Middle Ordovician of Shaanxi, China, bridging the fossil gaps and thereby elevating the genus Sterictopathes to a new family, Sterictopathidae fam. nov. The hypothesized evolutionary trend toward regularity in the axial skeleton from the Ordovician to modern Antipatharia is highlighted by reduced ridges and longitudinal fusion of networks. This discovery and confirmation of Ordovician black corals paves the way for future fossil findings and offers new insights into the early evolution of Hexacorallia.

Whip black corals (Antipatharia: Antipathidae: Stichopathes) of the Mesophotic Coral Ecosystem of Mo'orea (French Polynesia), with the description of a new species

Black corals are key species of marine ecosystems. They can be found in dense aggregations worldwide, but some parts of the world remain totally unexplored. This is the case of the Mesophotic Coral Ecosystem of Mo'orea where the Under the Pole scientific expedition explored mesophotic ecosystems between 60 and 120 m depth and focused on whip black corals. A total of 64 specimens were analyzed morphologically and genetically, and all belonged to the genus Stichopathes. Among them, we describe the new species Stichopathes desaturata sp. nov. It is characterized by an unbranched corallum, irregularly sinuous, with a basal diameter not exceeding 1 mm, reaching a dozen of cm in height. The polyps measure 0.50-1.0 mm in transverse diameter, the interpolypar space is well defined and up to 0.50 mm, with 6-8 polyps per cm. The polypar spines are taller than abpolypar spines, reaching 0.13 mm, perpendicular to the corallum, and conical with a pointed tip, with round and/or elongated papillae on two thirds of the spine. The abpolypar spines are conical to triangular, inclined upwards, with the same ornamentation as the polypar spines. We also identified specimens assigned as Stichopathes cf. contorta and four other putative species. Genetic analyses showed that Mo'orea specimens grouped in three different clades. Analyses of endosymbionts showed that the association with Symbiodiniaceae was likely not involved in the process of host species delineation.

Skimming genomes for systematics and DNA barcodes of corals

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.

Alternatipathes longispina sp. nov. and Bathypathes longicaulis sp. nov., two black corals (Antipatharia, Schizopathidae) from seamounts in the Western Pacific

Members of the order Antipatharia Milne-Edwards & Haime, 1857 are important structural components of hard bottom communities in the shallow and deep seas. However, their diversity in the Western Pacific is poorly known. Here we describe two new species of black corals within the family Schizopathidae Brook, 1889 from the tropical Western Pacific seamounts: Alternatipathes longispina sp. nov. and Bathypathes longicaulis sp. nov. The new species Alternatipathes longispina is characterized by a monopodial and unbranched corallum with the maximum width nearly two times as long as the height, the lower unpinnulated section of stem slightly shorter than the upper pinnulated one, the pinnules decreasing in length from the lowermost ones to the uppermost, and the prominent polypar spines ranging from 0.29 mm to 0.58 mm high, such a feature make the species differ from all congeners. Bathypathes longicaulis sp. nov. is characterized by a monopodial and unbranched corallum with a much longer unpinnulated stem and alternately arranged pinnules along the upper part of stem. It can be distinguished from congeners by its much longer unpinnulated stem, the alternately arranged pinnules, and the number of pinnules. Phylogenetic analyses based on the nuclear internal transcribed spacer region (ITS1-5.8S-ITS2) and three mitochondrial fragments cox3-IGR-cox1, trnW-IGR-nad2 and nad5-IGR-nad1 shows that A. longispina sp. nov. clusters with the type species A. bipinnata, and the genus Alternatipathes is closely related to Umbellapathes. The present phylogenetic trees confirm the polyphyly of Bathypathes and show that B. longicaulis sp. nov. is sister to Telopathes cf. magna MacIsaac & Best, 2013.

Molecular diversity of black corals from the Saudi Arabian Red Sea: a first assessment

Black corals occur as part of benthic assemblages from shallow to deep waters in all oceans. Despite the importance in many benthic ecosystems, where these act as biodiversity aggregators, antipatharians remain poorly studied, with 75% of the known species occurring below recreational SCUBA diving depth limits. Currently, information regarding the diversity and evolutionary history is limited, with most studies focusing on Hawaii and the South Pacific Ocean. Other regions of the world have received less attention, such as the Red Sea, where only two black coral families and four genera have been recorded. We provide the first analysis of the molecular diversity of black corals in the eastern Gulf of Aqaba and the northern and central Saudi Arabian Red Sea, based on a dataset of 161 antipatharian colonies collected down to 627 m deep. Based on specimen morphology, we ascribed our material to 11 genera belonging to 4 of the 7 known Antipatharia families, i.e. Antipathidae, Aphanipathidae, Myriopathidae and Schizopathidae. The genus level phylogeny of three intergenic mitochondrial regions, the trnW-IGR-nad2 (IgrW ), nad5-IGR-nad1 (IgrN ) and cox3-IGR-cox1 was reconstructed including previously published material. Overall, we recovered six molecular clades that included exclusively Red Sea sequences, with the highest diversity occurring at mesophotic depths. This study highlights that diversity of black corals in the Red Sea is much higher than previously known, with seven new generic records, suggesting that this basin may be a hotspot for antipatharian diversity as is known for other taxa. Our results recovered unresolved relationships within the order at the familial and generic levels. This emphasises the urgent need for an integration of genomic-wide data with a re-examination of informative morphological features necessary to revise the systematics of the order at all taxonomic levels.

Complete mitochondrial genomes of the black corals Alternatipathesmirabilis Opresko & Molodtsova, 2021 and Parantipatheslarix (Esper, 1788) (Cnidaria, Anthozoa, Hexacorallia, Antipatharia, Schizopathidae)

We describe the complete mitogenomes of the black corals Alternatipathesmirabilis Opresko & Molodtsova, 2021 and Parantipatheslarix (Esper, 1790) (Cnidaria, Anthozoa, Hexacorallia, Antipatharia, Schizopathidae). The analysed specimens include the holotype of Alternatipathesmirabilis, collected from Derickson Seamount (North Pacific Ocean; Gulf of Alaska) at 4,685 m depth and a potential topotype of Parantipatheslarix, collected from Secca dei Candelieri (Mediterranean Sea; Tyrrhenian Sea; Salerno Gulf; Italy) at 131 m depth. We also assemble, annotate and make available nine additional black coral mitogenomes that were included in a recent phylogeny (Quattrini et al. 2023b), but not made easily accessible on GenBank. This is the first study to present and compare two mitogenomes from the same species of black coral (Stauropathesarctica (Lütken, 1871)) and, thus, place minimum boundaries on the expected level of intraspecific variation at the mitogenome level. We also compare interspecific variation at the mitogenome-level across five different specimens of Parantipathes Brook, 1889 (representing at least two different species) from the NE Atlantic and Mediterranean Sea.

Establishment of a neotype for Antipathes flabellum Pallas, 1766 (Anthozoa: Hexacorallia: Antipatharia)

A neotype is designated for the antipatharian coral Antipathes flabellum Pallas, 1766. The neotype was collected off Madagascar (the original type locality is given as the Oceanus Indicus). Morphologically, the neotype corresponds closely in corallum shape and skeletal spination to specimens that have traditionally been identified as Antipathes flabellum. Another specimen of A. flabellum from Madagascar, morphologically almost identical to the neotype and described here, has been sequenced using ultra conserved elements and exon nuclear loci, which showed that it falls within the family currently recognized as Antipathidae.

Bathymetric evolution of black corals through deep time

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.

Description of a new species of black coral in the family Aphanipathidae (Anthozoa, Antipatharia) from Puerto Rico

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, Aphanipathespuertoricoensissp. 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.

One of the Deepest Genera of Antipatharia: Taxonomic Position Revealed and Revised

The genus Abyssopathes Opresko, 2002, comprises deep-sea black corals known almost exclusively from lower bathyal and abyssal depths, mainly from seamounts covered by cobalt-rich crusts and areas of polymetallic nodules. The taxonomical position of the genus and its placement in the family Schizopathidae has been repeatedly questioned, but fruitlessly. Known only in extremely deep habitats, these corals have rarely been collected in a state suitable for morphological or molecular studies that could help to clarify their status. Recently, increasing attention has been paid to the study of fauna associated with deep-sea minerals. Using material of Abyssopathes lyra (Brook, 1889) sampled during these studies, we transfer the genus Abyssopathes from the family Schizopathidae to the family Cladopathidae based on morphological and molecular data. Morphological data includes six mesenteries in the polyps, a unique pinnulation pattern found only in genera within the Cladopathidae, and relatively short polyp tentacles, a feature typical of some cladopathids. Sequencing data, consisting of 626 bp from the mitochondrial cox1 gene, showed that Abyssopathes is 99% identical to Chrysopathes Opresko, 2003, Cladopathes Brook, 1889, Heteropathes Opresko, 2011, and Trissopathes Opresko, 2003 (all Cladopathidae), in this gene region.

A new species of Bathypathes (Cnidaria, Anthozoa, Antipatharia, Schizopathidae) from the Red Sea and its phylogenetic position

A black coral, Bathypathesthermophila Chimienti, sp. nov. is described from the Saudi Arabian coasts of the Gulf of Aqaba and north Red Sea (Neom area) using an integrated taxonomic approach. The morphological distinctiveness of the new species is confirmed by molecular analyses. The species thrives in warm and high salinity waters typical of the Red Sea at bathyal depths. It can form colony aggregations on muddy bottoms with scattered, small hard substrates. Colonies are monopodial, feather-like, and attached to a hard substrate through a thorny basal plate. Pinnules are simple, arranged biserially and alternately, and all the same length (up to approximately 20 cm) except for few, proximal ones. Spines are triangular, laterally compressed, subequal, smooth, and simple or rarely bifurcated. Polyps are elongated transversely, 1.5-2.0 mm in transverse diameter. Large colonies can have one or few branches, whose origin is discussed. The phylogenetic position of B.thermophila sp. nov. within the order Antipatharia, recovered using three mitochondrial markers, shows that it is nested within the family Schizopathidae. It is close to species in the genera Parantipathes, Lillipathes, Alternatipathes, and Umbellapathes rather than to the other available representatives of the genus Bathypathes, as currently defined based on morphology. In agreement with previous findings, our results question the evolutionary significance of morphological characters traditionally used to discriminate Antipatharia at higher taxonomic level.

Description of a new and widely distributed species of Bathypathes (Cnidaria: Anthozoa: Antipatharia: Schizopathidae) previously misidentified as Bathypathes alternata Brook, 1889

For many years an undescribed species of the genus Bathypathes has been misidentified as Bathypathes alternata Brook, 1889 (a species currently re-assigned to the genus Alternatipathes). This new species is rather common at mid- and lower bathyal depths of the Pacific, Atlantic and Indian oceans, often in areas with high concentrations of commercially valuable cobalt-rich ferromanganese crusts, where it was observed in underwater photo and video transects to occur in high densities. Under the name B. alternata this species is recorded in several inventories and databases. There is an urgent need for a formal description of this misidentified and widely distributed species to avoid further confusion. The new species is superficially similar to A. alternata in having a monopodial corallum and simple, bilateral and alternately arranged pinnules. However, it differs from the former in that it has an upright corallum with a straight pinnulated part (vs. a horizontally bent pinnulated part), pinnules of uniform length and density (vs. decreasing regularly distally), and a constant distal angle formed by the pinnules and the stem along different parts of the corallum (vs. a decreasing distal angle near the top). The new species can therefore be easily distinguished from A. alternata in underwater imagery. We formally describe this new species in the genus Bathypathes and assign it the new name B. pseudoalternata. An extensive synonymy list with previous misidentified records is provided. To evaluate the distributional patterns of the new species we review the geographic distribution of antipatharians reported below 800 m. The majority of the hitherto described lower bathyal and abyssal species have been recorded from one biogeographic province; however, 20 species are known from more than two provinces, and only three species are widely distributed (>5 provinces), including the newly described Bathypathes pseudoalternata. Members of the family Schizopathidae, to which the new species belongs, represent the majority of the lower bathyal (50.54%) and abyssal (82.35%) species.

New species of deep-sea Antipatharians from the North Pacific (Cnidaria: Anthozoa: Antipatharia), Part 2

Five new species of deep-sea antipatharian corals are described from the North Pacific primarily collected off the coast of Alaska and on adjacent seamounts. All the species are referred to the family Schizopathidae. Described as new are: Alternatipathes mirabilis, Bathypathes ptiloides, Bathypathes tiburonae, Bathypathes alaskensis, and Parantipathes pluma. Illustrations of the type material of Bathypathes patula, B. patula var. plenispina and B. tenuis are provided for comparative proposes. Bathypathes patula var. plenispina is here recognized as a species distinct from B. patula, and B. tenuis is considered incertae sedis due to the poor condition of the type material.

Phylogenomics, Origin, and Diversification of Anthozoans (Phylum Cnidaria)

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.].

Phylogenetic Relatedness within the Internally Brooding Sea Anemones from the Arctic-Boreal Region

Phylogenetic analyses based on mitochondrial 16S rDNA, nuclear 28S rDNA, and morphological and ecological traits of Aulactinia, Urticina and Cribrinopsis sea anemones inhabiting the Arctic-boreal region indicate discordances between trees derived from molecular sequences and those based on morphological traits. Nuclear genes were more informative than mitochondrial and morphological datasets. Our findings indicate that 16S rDNA has limited applicability for phylogenetic analyses at lower taxonomic levels and can only be used for distinction of families. Although 28S rDNA allowed for the classification of distinct genera, it could not confirm that species of Urticina and Cribrinopsis, which appeared to be closely related, were correctly separated into two different genera. The nuclear tree revealed inconsistencies between specimens belonging to European Urticina crassicornis and Pacific U. crassicornis; the latter seems to be a different species. In contrast to Pacific U. crassicornis, the specimens collected from different localities in the Barents Sea are on the same tree branch. The same was observed for specimens of Aulactinia stella. Both species brood their young internally. The dispersal of sea anemones with brooding juveniles seems to be less limited than expected and might be sufficient to settle habitats more than a thousand kilometers away.

Electrochemical Approach for Isolation of Chitin from the Skeleton of the Black Coral Cirrhipathes sp. (Antipatharia)

The development of novel and effective methods for the isolation of chitin, which remains one of the fundamental aminopolysaccharides within skeletal structures of diverse marine invertebrates, is still relevant. In contrast to numerous studies on chitin extraction from crustaceans, mollusks and sponges, there are only a few reports concerning its isolation from corals, and especially black corals (Antipatharia). In this work, we report the stepwise isolation and identification of chitin from Cirrhipathes sp. (Antipatharia, Antipathidae) for the first time. The proposed method, aiming at the extraction of the chitinous scaffold from the skeleton of black coral species, combined a well-known chemical treatment with in situ electrolysis, using a concentrated Na₂SO₄ aqueous solution as the electrolyte. This novel method allows the isolation of α-chitin in the form of a microporous membrane-like material. Moreover, the extracted chitinous scaffold, with a well-preserved, unique pore distribution, has been extracted in an astoundingly short time (12 h) compared to the earlier reported attempts at chitin isolation from Antipatharia corals.

Mitogenomics suggests a sister relationship of Relicanthus daphneae (Cnidaria: Anthozoa: Hexacorallia: incerti ordinis) with Actiniaria

Relicanthus daphneae (formerly Boloceroides daphneae) was first described in 2006 as a giant sea anemone based on morphology. In 2014, its classification was challenged based on molecular data: using five genes, Relicanthus was resolved sister to zoanthideans, but with mixed support. To better understand the evolutionary relationship of Relicanthus with other early-branching metazoans, we present 15 newly-sequenced sea anemone mitochondrial genomes and a mitogenome-based phylogeny including all major cnidarian groups, sponges, and placozoans. Our phylogenetic reconstruction reveals a moderately supported sister relationship between Relicanthus and the Actiniaria. Morphologically, the cnidae of Relicanthus has apical flaps, the only existing synapomorphy for sea anemones. Based on both molecular and morphological results, we propose a third suborder (Helenmonae) within the Actiniaria to accommodate Relicanthus. Although Relicanthus shares the same gene order and content with other available actiniarian mitogenomes, it is clearly distinct at the nucleotide level from anemones within the existing suborders. The phylogenetic position of Relicanthus could reflect its association with the periphery of isolated hydrothermal vents, which, although patchy and ephemeral, harbor unique chemosynthetic communities that provide a relatively stable food source to higher trophic levels over long evolutionary timescales. The ability to colonize the deep sea and the periphery of new vent systems may be facilitated by Relicanthus’ large and extremely yolky eggs.

The unexpected diversity of microbial communities associated with black corals revealed by high-throughput Illumina sequencing

The microbes associated with black corals remain poorly studied. The present study is the first attempt to investigate microbial community structure in the black corals Antipathes ceylonensis and A. dichotoma from the South China Sea by using high-throughput Illumina sequencing. A total of 52 bacterial and 3 archaeal phyla were recovered in this study, suggesting the black corals harboured highly diverse microbial communities. Among the 55 microbial phyla, Proteobacteria, Firmicutes, Bacteroidetes, Chloroflexi, Acidobacteria and Actinobacteria dominated in the two black corals from the South China Sea. Although most of the microbial phyla recovered from the two black corals have been reported in previous studies on coral-associated microbes, eight bacterial phyla including Synergistetes, Thermi, AncK6, GNO2, NKB19, NC10, WWE1 and GAL15, and the archaeal phylum Parvarchaeota are reported for the first time from corals in this study, which expands our knowledge about the diversity of coral-associated microbes. The comparison of microbial communities in the different black coral species indicated that A. ceylonensis harboured few abundant bacterial genera such as Citrobacter and Pseudomonas, whereas a high diversity of rare bacterial genera (<1% abundance), such as Winogradskyella and Rubricoccus, was detected only in A. dichotoma. These results suggested that the microbial community in black corals exhibited species-specific variation.

Association between deep-water scale-worms (Annelida: Polynoidae) and black corals (Cnidaria: Antipatharia) in the Southwestern Atlantic

Polynoid scale-worms have been found living as commensals with deep-water antipatharians (commonly known as black corals) in the Potiguar Basin, off Rio Grande do Norte State, Northeastern Brazil. In this paper two polychaete species and four black corals species are redescribed. Benhamipolynoecf.antipathicola and Parahololepidellacf.greeffi, and the black coral Stylopathesadinocrada Opresko, 2006 are recorded for the Southwestern Atlantic. Benhamipolynoecf.antipathicola was first described from off New Zealand and the Malay Archipelago, as symbiont with the black coral Stylopathestenuispina (Silberfeld, 1909). It was later reported for the North Atlantic, off Florida, associated with Stylopathescolumnaris (Duchassaing, 1870). In our study, B.cf.antipathicola was found in association with the black coral S.adinocrada. Parahololepidellacf.greeffi was first described as a free-living from shallow waters off São Tomé and Cabo Verde Islands, West Africa, and later reported as symbiont with the black coral Tanacetipathescf.spinescens in the same location. Our data expand both the geographical distribution and the host range of this species which is reported for the first time as symbiont with Tanacetipathesbarbadensis (Brook, 1889), T.tanacetum (Pourtalès, 1880) and T.thamnea (Warner, 1981) in Brazil. The aim of this study is to discuss commensal associations between two species of scale-worm polynoids and black corals found in the Southwestern Atlantic, and also reporting their global distribution. Finally, we provided an updated list of the commensal polynoids and their black coral hosts.

Assessing population changes of historically overexploited black corals (Order: Antipatharia) in Cozumel, Mexico

Black corals (Antipatharians) are crucial structural and ecological components of many mesophotic coral ecosystems (MCEs; reefs 30-150 m depth). In Mexico, black corals are harvested for the jewellery industry, which has historically led to population depletion. Harvesting began in the early 1960s and was concentrated around Cozumel Island until 1995. Since then, harvesting permits have been granted only for the mainland coast. Here we compare Cozumel populations between 1998 and 2016 for the two black coral species targeted by the jewellery industry. We found that densities of Plumapathes pennacea in 2016 were substantially lower than in 1998. However, the 2016 P. pennacea population has shifted to be dominated by larger colonies, suggesting disproportionate juvenile mortality or recruitment failure. Low numbers of Antipathes caribbeana were recorded, and no change in population density or colony size was detected between 1998 and 2016. Despite harvesting occurring for almost 70 years in the Mexican Caribbean, no information on reproduction, recruitment and other dynamics of the targeted species is available. We advocate for harvesting permits to be based on scientific evidence, and for implementation of future restrictions to prevent total depletion of black corals in the area.

Phylogenetic relationships of Mediterranean black corals (Cnidaria : Anthozoa : Hexacorallia) and implications for classification within the order Antipatharia

The Mediterranean black coral fauna includes type species of four antipatharian genera belonging to four different families, therefore phylogenetic studies hold great potential for enhancing systematics within the order. The analysis of six Mediterranean antipatharian species by means of nuclear sequence data of internal transcribed spacer (ITS1 and ITS2) rDNA confirms the separation into different families, as was previously noted on a morphological basis, with a clear distinction of the family Leiopathidae, whose position is supported by a unique number of mesenteries and lack of spines on thicker ramifications. The position of a newly recorded black coral species for the Mediterranean basin belonging to the genus Phanopathes is discussed. Antipathes dichotoma, the type species of the genus Antipathes, on which the order Antipatharia was based, does not group with other members of the family Antipathidae. Supporting a recent finding based on mitochondrial markers, this suggests a critical need for revision of the families that will be impacted by reassignment of this nomenclaturally important taxon.

The Multipartite Mitochondrial Genome of Enteromyxum leei (Myxozoa): Eight Fast-Evolving Megacircles

Myxozoans are a large group of poorly characterized cnidarian parasites. To gain further insight into their evolution, we sequenced the mitochondrial (mt) genome of Enteromyxum leei and reevaluate the mt genome structure of Kudoa iwatai. Although the typical animal mt genome is a compact, 13-25 kb, circular chromosome, the mt genome of E. leei was found to be fragmented into eight circular chromosomes of ∼23 kb, making it the largest described animal mt genome. Each chromosome was found to harbor a large noncoding region (∼15 kb), nearly identical between chromosomes. The protein coding genes show an unusually high rate of sequence evolution and possess little similarity to their cnidarian homologs. Only five protein coding genes could be identified and no tRNA genes. Surprisingly, the mt genome of K. iwatai was also found to be composed of two chromosomes. These observations confirm the remarkable plasticity of myxozoan mt genomes.

Potential Connectivity of Coldwater Black Coral Communities in the Northern Gulf of Mexico

The black coral Leiopathes glaberrima is a foundation species of deep-sea benthic communities but little is known of the longevity of its larvae and the timing of spawning because it inhabits environments deeper than 50 m that are logistically challenging to observe. Here, the potential connectivity of L. glaberrima in the northern Gulf of Mexico was investigated using a genetic and a physical dispersal model. The genetic analysis focused on data collected at four sites distributed to the east and west of Mississippi Canyon, provided information integrated over many (~10,000) generations and revealed low but detectable realized connectivity. The physical dispersal model simulated the circulation in the northern Gulf at a 1km horizontal resolution with transport-tracking capabilities; virtual larvae were deployed 12 times over the course of 3 years and followed over intervals of 40 days. Connectivity between sites to the east and west of the canyon was hampered by the complex bathymetry, by differences in mean circulation to the east and west of the Mississippi Canyon, and by flow instabilities at scales of a few kilometers. Further, the interannual variability of the flow field surpassed seasonal changes. Together, these results suggest that a) dispersal among sites is limited, b) any recovery in the event of a large perturbation will depend on local larvae produced by surviving individuals, and c) a competency period longer than a month is required for the simulated potential connectivity to match the connectivity from multi-locus genetic data under the hypothesis that connectivity has not changed significantly over the past 10,000 generations.

Mitochondrial group I and group II introns in the sponge orders Agelasida and Axinellida

Background

Self-splicing introns are present in the mitochondria of members of most eukaryotic lineages. They are divided into Group I and Group II introns, according to their secondary structure and splicing mechanism. Being rare in animals, self-splicing introns were only described in a few sponges, cnidarians, placozoans and one annelid species. In sponges, three types of mitochondrial Group I introns were previously described in two demosponge families (Tetillidae, and Aplysinellidae) and in the homoscleromorph family Plakinidae. These three introns differ in their insertion site, secondary structure and in the sequence of the LAGLIDADG gene they encode. Notably, no group II introns have been previously described in sponges.

Results

We report here the presence of mitochondrial introns in the cytochrome oxidase subunit 1 (COI) gene of three additional sponge species from three different families: Agelas oroides (Agelasidae, Agelasida), Cymbaxinella^pverrucosa (Hymerhabdiidae, Agelasida) and Axinella polypoides (Axinellidae, Axinellida). We show, for the first time, that sponges can also harbour Group II introns in their COI gene, whose presence in animals’ mitochondria has so far been described in only two phyla, Placozoa and Annelida. Surprisingly, two different Group II introns were discovered in the COI gene of C. verrucosa. Phylogenetic analysis indicates that the Group II introns present in C. verrucosa are related to red algae (Rhodophyta) introns.

Conclusions

The differences found among intron secondary structures and the phylogenetic inferences support the hypothesis that the introns originated from independent horizontal gene transfer events. Our results thus suggest that self-splicing introns are more diverse in the mitochondrial genome of sponges than previously anticipated.

Electronic supplementary material

The online version of this article (doi:10.1186/s12862-015-0556-1) contains supplementary material, which is available to authorized users.

Streamlining DNA barcoding protocols: automated DNA extraction and a new cox1 primer in arachnid systematics

Background

DNA barcoding is a popular tool in taxonomic and phylogenetic studies, but for most animal lineages protocols for obtaining the barcoding sequences—mitochondrial cytochrome C oxidase subunit I (cox1 AKA CO1)—are not standardized. Our aim was to explore an optimal strategy for arachnids, focusing on the species-richest lineage, spiders by (1) improving an automated DNA extraction protocol, (2) testing the performance of commonly used primer combinations, and (3) developing a new cox1 primer suitable for more efficient alignment and phylogenetic analyses.

Methodology

We used exemplars of 15 species from all major spider clades, processed a range of spider tissues of varying size and quality, optimized genomic DNA extraction using the MagMAX Express magnetic particle processor—an automated high throughput DNA extraction system—and tested cox1 amplification protocols emphasizing the standard barcoding region using ten routinely employed primer pairs.

Results

The best results were obtained with the commonly used Folmer primers (LCO1490/HCO2198) that capture the standard barcode region, and with the C1-J-2183/C1-N-2776 primer pair that amplifies its extension. However, C1-J-2183 is designed too close to HCO2198 for well-interpreted, continuous sequence data, and in practice the resulting sequences from the two primer pairs rarely overlap. We therefore designed a new forward primer C1-J-2123 60 base pairs upstream of the C1-J-2183 binding site. The success rate of this new primer (93%) matched that of C1-J-2183.

Conclusions

The use of C1-J-2123 allows full, indel-free overlap of sequences obtained with the standard Folmer primers and with C1-J-2123 primer pair. Our preliminary tests suggest that in addition to spiders, C1-J-2123 will also perform in other arachnids and several other invertebrates. We provide optimal PCR protocols for these primer sets, and recommend using them for systematic efforts beyond DNA barcoding.

Hidden among sea anemones: the first comprehensive phylogenetic reconstruction of the order Actiniaria (Cnidaria, Anthozoa, Hexacorallia) reveals a novel group of hexacorals

Sea anemones (order Actiniaria) are among the most diverse and successful members of the anthozoan subclass Hexacorallia, occupying benthic marine habitats across all depths and latitudes. Actiniaria comprises approximately 1,200 species of solitary and skeleton-less polyps and lacks any anatomical synapomorphy. Although monophyly is anticipated based on higher-level molecular phylogenies of Cnidaria, to date, monophyly has not been explicitly tested and at least some hypotheses on the diversification of Hexacorallia have suggested that actiniarians are para- or poly-phyletic. Published phylogenies have demonstrated the inadequacy of existing morphological-based classifications within Actiniaria. Superfamilial groups and most families and genera that have been rigorously studied are not monophyletic, indicating conflict with the current hierarchical classification. We test the monophyly of Actiniaria using two nuclear and three mitochondrial genes with multiple analytical methods. These analyses are the first to include representatives of all three currently-recognized suborders within Actiniaria. We do not recover Actiniaria as a monophyletic clade: the deep-sea anemone Boloceroides daphneae, previously included within the infraorder Boloceroidaria, is resolved outside of Actiniaria in several of the analyses. We erect a new genus and family for B. daphneae, and rank this taxon incerti ordinis. Based on our comprehensive phylogeny, we propose a new formal higher-level classification for Actiniaria composed of only two suborders, Anenthemonae and Enthemonae. Suborder Anenthemonae includes actiniarians with a unique arrangement of mesenteries (members of Edwardsiidae and former suborder Endocoelantheae). Suborder Enthemonae includes actiniarians with the typical arrangement of mesenteries for actiniarians (members of former suborders Protantheae, Ptychodacteae, and Nynantheae and subgroups therein). We also erect subgroups within these two newly-erected suborders. Although some relationships among these newly-defined groups are still ambiguous, morphological and molecular results are consistent enough to proceed with a new higher-level classification and to discuss the putative functional and evolutionary significance of several morphological attributes within Actiniaria.