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 largescale 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). Benthic 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.

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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.

Phoronid larvae, actinotrochs, are beautiful and complicated organisms which have attracted as much, if not more, attention than their adult forms. We collected actinotrochs from the waters of the Pacific and Caribbean coasts of Panama, and used DNA barcoding of mtCOI, as well as 16S and 18S sequences, to estimate the diversity of phoronids in the region. We discovered three operational taxonomic units (OTUs) in the Bay of Panama on the Pacific coast and four OTUs in Bocas del Toro on the Caribbean coast. Not only did all OTUs differ from each other by >10% pairwise distance in COI, but they also differed from all phoronid sequences in GenBank, including the four species for which adults have been reported for the Pacific of Panama, Phoronopsis harmeri, Phoronis psammophila, Phoronis muelleri, and Phoronis hippocrepia. In each ocean region, one common OTU was more abundant and occurred more frequently than other OTUs in our samples. The other five OTUs were relatively rare, with only one to three individuals collected during the entire project. Species accumulation curves were relatively flat but suggest that at least one more species is likely to be present at each site. Actinotrochs from the seven sequenced OTUs had morphologies typical of species with non‐brooded planktotrophic development and, in some cases, may be distinguished by differences in pigmentation and the arrangement of blood masses. We found one larva with morphology typical of brooded planktotrophic larvae for which sequencing failed, bringing the total number of potential species detected to eight and representing >50% of the adult species currently recognized globally.

Lingulids and discinids are the only brachiopods that exhibit life histories that include a feeding planktonic stage usually referred to as a “larva”. 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 >20% for COI, >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.

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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.

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.