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Biodiversity assessments are critical for setting conservation priorities, understanding ecosystem function and establishing a baseline to monitor change. Surveys of marine biodiversity that rely almost entirely on sampling adult organisms underestimate diversity because they tend to be limited to habitat types and individuals that can be easily surveyed. Many marine animals have planktonic larvae that can be sampled from the water column at shallow depths. This life stage often is overlooked in surveys but can be used to relatively rapidly document diversity, especially for the many species that are rare or live cryptically as adults. Using DNA barcode data from samples of nemertean worms collected in three biogeographical regions—Northeastern Pacific, the Caribbean Sea and Eastern Tropical Pacific—we found that most species were collected as either benthic adults or planktonic larvae but seldom in both stages. Randomization tests show that this deficit of operational taxonomic units collected as both adults and larvae is extremely unlikely if larvae and adults were drawn from the same pool of species. This effect persists even in well-studied faunas. These results suggest that sampling planktonic larvae offers access to a different subset of species and thus significantly increases estimates of biodiversity compared to sampling adults alone. Spanish abstract is available in the electronic supplementary material.

The identity of wild cloning sea star larvae has been a mystery since they were first documented in the Caribbean. The most commonly collected cloning species was thought to belong to the Oreasteridae, on the basis of similarity with sequences from

DNA barcoding is a useful tool to identify the components of mixed or bulk samples, as well as to determine individuals that lack morphologically diagnostic features. However, the reference database of DNA barcode sequences is particularly sparsely populated for marine invertebrates and for tropical taxa. We used samples collected as part of two field courses, focused on graduate training in taxonomy and systematics, to generate DNA sequences of the barcode fragments of cytochrome c oxidase subunit I (COI) and mitochondrial ribosomal 16S genes for 447 individuals, representing at least 129 morphospecies of decapod crustaceans. COI sequences for 36% (51/140) of the species and 16S sequences for 26% (37/140) of the species were new to GenBank. Automatic Barcode Gap Discovery identified 140 operational taxonomic units (OTUs) which largely coincided with the morphospecies delimitations. Barcode identifications (i.e. matches to identified sequences) were especially useful for OTUs within Synalpheus, a group that is notoriously difficult to identify and rife with cryptic species, a number of which we could not identify to species, based on morphology. Non-concordance between morphospecies and barcode OTUs also occurred in a few cases of suspected cryptic species. As mitochondrial pseudogenes are particularly common in decapods, we investigate the potential for this dataset to include pseudogenes and discuss the utility of these sequences as species identifiers (i.e. barcodes). These results demonstrate that material collected and identified during training activities can provide useful incidental barcode reference samples for under-studied taxa.

The diversity of tropical marine invertebrates is poorly documented, especially those groups for which collecting adults is difficult. We collected the planktonic tornaria larvae of hemichordates (acorn worms) to assess their hidden diversity in the Neotropics. Larvae were retrieved in plankton tows from waters of the Pacific and Caribbean coasts of Panama, followed by DNA barcoding of mitochondrial cytochrome c oxidase subunit I (COI) and 16S ribosomal DNA to estimate their diversity in the region. With moderate sampling efforts, we discovered six operational taxonomic units (OTUs) in the Bay of Panama on the Pacific coast, in contrast to the single species previously recorded for the entire Tropical Eastern Pacific. We found eight OTUs in Bocas del Toro province on the Caribbean coast, compared to seven species documented from adults in the entire Caribbean. All OTUs differed from each other and from named acorn worm sequences in GenBank by >10% pairwise distance in COI and >2% in 16S. Two of our OTUs matched 16S hemichordate sequences in GenBank: one was an unidentified or unnamed Balanoglossus from the Caribbean of Panama, and the other was an unidentified ptychoderid larva from the Bahamas. The species accumulation curves suggest that nearly all the species have been collected and only one more species might still remain undetected in the Pacific. In contrast, the Caribbean species accumulation curve suggests that further sampling could yield more than 10 additional OTUs. Tornaria from the 14 OTUs exhibited typical planktotrophic morphologies, and, in some cases, may be distinguished by differences in pigmentation and by the number of telotrochal ciliary bands, but in general, few diagnostic differences were detected.

Studies on the population structure of common widespread macroalgae in the Gulf of Mexico (GoMx) are scarce, and this knowledge gap limits our understanding on how disturbances affect the genetic diversity of macroalgae in this basin. The latter is due to the lack of a baseline that can be compared with allele frequency surveys conducted after a major disturbance such as the 2010 Deepwater Horizon oil spill (DWH), which leaked 780,000 m3 of crude oil in the vicinity of highly diverse macroalgal communities. Fortunately, quantitative assessments of the population structure pre-DWH can be accomplished for several macroalgae with dried specimens collected from research cruises conducted before 2010 in the offshore GoMx. Based on three markers (cytochrome c oxidase subunit I, COX II-III intergenic spacer, and the RuBisCO large subunit), this study reconstructed the allele frequencies pre-DWH for a GoMx-widespread macroalga, Botryocladia occidentalis, and revealed the existence of distinct populations in each of three distant regions of the GoMx: Florida Middle Grounds (FL), Campeche Banks (CB), and offshore Louisiana (LA). Population structure was assessed with exact tests of population differentiation and Analyses of Molecular Variance. FL harbored the most differentiated and genetically diverse population due to the presence and abundance of unique haplotypes. Interestingly, FL haplotypes were not closely phylogenetically related to each other and included the most divergent lineages of the entire GoMx; this phylogeographic pattern suggests a strong influence of migrants from the Caribbean on the FL population. Additionally, likelihood ratio tests with a small sample collected post-DWH indicated that the LA population underwent strong changes, showing statistically significant differences before (LA) vs. after (L2) the disaster. Whereas the LA population had affinity to CB, L2 showed a FL haplotype that, before the disaster, had never been reported in LA or CB. Such changes may not be permanent but rather a temporary response to disturbance; also, they may not necessarily be caused by the spilled oil but by other factors associated with the DWH.

DNA barcoding is a useful tool for documenting the diversity of metazoans. The most commonly used barcode markers, 16S and COI, are not considered suitable for species identification within some "basal" phyla of metazoans. Nevertheless metabarcoding studies of bulk mixed samples commonly use these markers and may obtain sequences for "basal" phyla. We sequenced mitochondrial DNA fragments of cytochrome oxidase c subunit I (COI), 16S ribosomal RNA (16S), NADH dehydrogenase subunits 2 (16S-ND2), 6 (ND6-ND3) and 4L (ND4L-MSH) for 27 species of Caribbean octocorals to create a reference barcode dataset and to compare the utility of COI and 16S to other markers more typically used for octocorals. The most common genera (Erythropodium, Ellisella, Briareum, Plexaurella, Muriceopsis and Pterogorgia) were effectively distinguished by small differences (5 or more substitutions or indels) in COI and 16S sequences. Gorgonia and Antillogorgia were effectively distinguished from each other by unique haplotypes, but the small genetic differences make distance approaches ineffective for these taxa. Plexaura, Pseudoplexaura and Eunicea were indistinguishable from each other but were generally effectively distinguished from other genera, further supporting the idea that these genera have undergone a rapid endemic radiation in the Caribbean.

In the northwestern Gulf of Mexico, beds of rhodoliths and unconsolidated rubble at 55–70 m depth are associated with unique offshore deep bank habitats known as salt domes or diapirs. Prior to the 2010 BP Deepwater Horizon oil spill these harbored the highest known seaweed diversity in the northern Gulf of Mexico. Six post-spill cruises led offshore Louisiana to two sites previously documented with rich algal assemblages (i.e. prespill) revealed a dramatic post-spill die-off of seaweeds at both sites, with dredged rhodoliths appearing bleached and mostly denuded of fleshy algae, or “bare” (with a few crustose genera only, e.g. Corallinales and Peyssonneliales). This rubble, brought to the laboratory and maintained in a series of ∼75 liter microcosm tanks, gradually became covered by a suite of red, green and brown seaweed germlings that to this day continue to grow to adult size, reproduce, disappear and re-emerge, and whose species composition reflects pre-spill assemblages. These experiments revealed the expression of biodiversity from alternative life stages or resting stages apparently repressed in the Gulf at the time of sampling, including new, previously overlooked diversity. The rate of algal succession was documented by biweekly photography, and species taxonomic identity is being confirmed by ongoing molecular and morphological evidence. The implications of these exciting results, namely that undetected propagules, spores and endolithic filaments collected along with the “bare” substrata and in situ seawater have been triggered to germinate, grow, and reproduce under laboratory conditions are far-reaching. We hypothesize the function of rhodoliths and rubble as marine seedbanks for biological diversity and explore the role of this ecosystem for community resilience following a major anthropogenic disaster. This is a speculative paper since we currently lack many rigorous, quantitative data. The paper is envisioned as a “first step” in approaching the dynamics of rhodoliths and associated diversity following a catastrophic anthropogenic event, from which the algal and invertebrate diversity has not recovered, as of October 2013, our last collecting expedition to Ewing Bank in the NW Gulf of Mexico.

Inhibition of early life stages of corals by benthic algae is a critical bottleneck to the recovery and resilience of corals. Increasingly frequent and severe disturbances are causing large- scale coral mortality, usually followed by colonisation and dominance by benthic algae. The capacity of corals to re-establish in such algal-dominated habitats will depend on the effects of the algae on growth and survivorship of juvenile corals. We experimentally evaluated the competition between juvenile corals Porites astreoides and algae and the effects of algae on the exposure of juvenile corals to damage by parrotfishes (family Scaridae) in a Colombian Caribbean reef. We also explored whether those effects were consistent among climatic seasons (upwelling and non-upwelling). Ben- thic algae had negative and positive effects on the juvenile corals. The removal of algal turfs and fleshy macroalgae enhanced coral growth. Unexpectedly, removal of algae from around the juvenile corals increased predation upon the corals by parrotfishes. When algae were removed, at least 50% of the corals were grazed by parrotfishes, but no bites were observed on corals with intact algae. Coral growth and parrotfish damage were not affected by season. However, damage by parrotfishes neither lessened survivorship nor resulted in negative growth for any of the grazed coral colonies. The beneficial effects of algae in protecting the juvenile corals from parrotfish damage seem to be outweighed by the negative effects of the algae on coral-algal competition. Understanding such complexities in the interactions between algae and early life stages of corals can provide insight into the roles of algae in coral reef resilience.

Lingulids and discinids are the only brachiopods that exhibit life histories that include a feeding planktonic stage usually referred to as a &ldquo, larva&rdquo, We collected planktotrophic brachiopod larvae from the Pacific and Caribbean coasts of Panama and took a DNA barcoding approach with mitochondrial cytochrome c oxidase subunit I (COI), mitochondrial ribosomal 16S, and nuclear ribosomal 18S genes to identify those larvae and to estimate their diversity in the region. We observed specimens from both coasts with distinct morphologies typical of lingulid and discinid larvae. COI and 16S were sequenced successfully for the lingulid larvae but failed consistently for all discinid larvae. 18S was sequenced successfully for larvae from both families. Sequence data from each gene revealed one lingulid operational taxonomic unit (OTU) from Bocas del Toro on the Caribbean coast, and one lingulid OTU from the Bay of Panama on the Pacific coast. These OTUs differed by &gt, 20% for COI, &gt, 10% for 16S and ~0.5% for 18S. Both OTUs clustered with GenBank sequences of Glottidia species, the only genus of lingulids in the Americas, but were distinct from G. pyramidata the only species reported for the Caribbean. Analysis of 18S sequence data for discinid larvae recovered 2 OTUs, one exclusively from the Pacific and one with a mixture of Pacific and Caribbean larvae. The 18S marker does not provide enough resolution to distinguish between species, and comparisons with GenBank sequences suggest that one OTU includes Pelagodiscus species, while the other may include Discradisca species. When compared with other marine invertebrates, our surveys of brachiopod larvae through DNA barcoding show relatively low levels of diversity for Panama.

Coral reefs are highly dependent on the mutualistic symbiosis between reef-building corals and dinoflagellates from the genus Symbiodinium. These dinoflagellates spend part of their life cycle outside the coral host and in the majority of the cases have to re-infect corals each generation. While considerable insight has been gained about Symbiodinium in corals, little is known about the ecology and biology of Symbiodinium in other reef microhabitats. This study documents Symbiodinium associating with benthic macroalgae on the southern Great Barrier Reef, including some Symbiodinium that are genetically close to the symbiotic strains from reef-building corals. It is possible that some of these Symbiodinium were in hospite, associated to soritid foraminifera or ciliates; nevertheless, the presence of Symbiodinium C3 and C15 in macroalgal microhabitats may also suggest a potential link between communities of Symbiodinium associating with both coral hosts and macroalgae.

Porites colonensis is a coral from the Caribbean Sea; colonies are foliaceous, undulated, and plate-like. Polyps are dark brown or red with small bright white or green centers; pali are present in corallites and the septal plan is bisymmetrical, conformed by three fused ventral septa, a dorsal solitary septum, and two pairs of lateral septa at each side of the dorso-ventral axis. P. colonensis is similar and can be confused with the smooth varieties of Porites astreoides and Porites branneri. There are three specimens collected from Colombia and previously identified as P. colonensis: one from Golfo de Urabá (Darién ecoregion), other from Islas del Rosario (Coralline Archipelagos ecoregion), and another from an unspecified locality, in addition to one published observation from the Golfo de Urabá without collected specimens. A recent finding of other specimens in the Tayrona National Natural Park (TNNP, Tayrona ecoregion) and the absence of a rigorous taxonomic revision for all specimens collected from Colombia showed that it was necessary to review the presence and distribution of P. colonensis in the Colombian Caribbean. A taxonomic review was done for all specimens collected from Colombia and previously identified as P. colonensis. Then, the morphologic variability of specimens that were confirmed as P. colonensis was described. Only the specimens from TNNP agreed with the holotype description of P. colonensis, while others agreed with flat varieties of P. astreoides. Thus, the presence of P. colonensis is confirmed for the first time for Colombia, but its presence in other Colombian localities outside Tayrona ecoregion could not be demonstrated. This is the only confirmed record of this species for the South American continental shelf. Furthermore, the skeletal characteristics of Colombian P. colonensis corallites showed large variability, exceeding the ranges previously described for the species.

Sedimentation is frequently associated with coral reef degradation. However, there are few experimental studies evaluating the impacts of this process on the dynamics of algal recruitment on coral reefs. In a field experiment, we manipulated the levels of sedimentation and examined the impacts on the recruitment and growth of the brown macroalgae Dictyota spp. and Lobophora variegata, in two localities (Chengue and Granate) on the Tayrona National Natural Park, Colombian Caribbean. We found considerable variability in the responses of algae to sedimentation. This variability depended on the levels of sediments used, the type of algae employed and the population parameter considered (recruitment or growth). Sediment addition generally had a negative effect on the recruitment and early growth of the alga Dictyota spp. In contrast, sediment addition did not affect the recruitment of L. variegata, while sediment removal had a negative effect on recruitment. The locality with higher sedimentation rates (Granate) generally had lower recruitment and growth of both algae than that of the other locality with lower sedimentation levels (Chengue). Our study indicates that there is substantial variability and complexity in the responses of reef algae to the effects of sedimentation. The results also suggest that the process of reef degradation can modify early population dynamics of benthic algae, with important implications for understanding the ecology of reef degradation.