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

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

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

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

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