Shadows over Caribbean reefs: Identification of a new invasive soft coral species, Xenia umbellata , in southwest Puerto Rico.

In October 2023, several colonies of an alien soft coral species were reported on shallow reefs in southwest Puerto Rico. The soft coral was identified as a xeniid octocoral (species undetermined), resembling the octocoral Unomia stolonifera , which has invaded and overgrown reefs in Venezuela in recent years. To conclusively characterize the species of the invading xeniid, we employed multilocus barcoding targeting four genes (ND2, mtMutS, COI, and 28S) of three separate colonies across three locations in southwest Puerto Rico. Sequence comparisons with xeniid sequences from GenBank, including those from the genera Xenia and Unomia , indicated a 100% sequence identity (>3,000 bp combined) with the species Xenia umbellata (Octocorallia : Malacalcyonacea : Xeniidae). Xenia umbellata is native to the Red Sea and to our knowledge, this represents the first confirmed case of this species as an invader on Caribbean reefs. Similar to U. stolonifera, X. umbellata is well known for its ability to rapidly overgrow substrate as well as tolerate environmental extremes. In addition, X. umbellata has recently been proposed as a model system for tissue regeneration having the ability to regenerate completely from a single tentacle. These characteristics greatly amplify X. umbellata' s potential to adversely affect any reef it invades. Our findings necessitate continued collaborative action between local management agencies and stakeholders in Puerto Rico, as well as neighboring islands, to monitor and control this invasion prior to significant ecological perturbation.

Using eDNA sampling for species-specific fish detection in tropical oceanic samples: limitations and recommendations for future use.

Background: Over the past decade, environmental DNA (eDNA) has become a resourceful tool in conservation and biomonitoring. Environmental DNA has been applied in a variety of environments, but the application to studies of marine fish, particularly at tropical latitudes, are limited. Since many commercially important Caribbean fishes are overexploited, these species are optimal candidates to explore the use of this method as a biomonitoring tool. Specifically, for many of these species, the formation of fish spawning aggregations (FSAs) marks a critical life history event where fishes will gather in large numbers for reproduction. These FSAs are ephemeral in nature, lasting only a few days, but are predictable in time and space which makes them susceptible to overfishing. Methods: In this study, we test the feasibility of using an eDNA sampling approach (water and sediment collection) to detect the presence of known FSAs off the west coast of Puerto Rico, with cytochrome c oxidase subunit 1 (CO1) and 12S rRNA (12S) primers designed to target specific species. A total of 290 eDNA samples were collected and, of those, 206 eDNA samples were processed. All eDNA samples varied in DNA concentration, both between replicates and collection methods. A total of 12 primer sets were developed and tested using traditional PCR and qPCR. Results: Despite validation of primer accuracy and sample collection during known peak spawning times, the use of traditional PCR and qPCR with both molecular markers failed to produce species-specific amplification. Thus, a trial test was conducted using the CO1 primers in which target fish DNA was 'spiked' at various concentrations into the respective eDNA samples to determine the target species DNA concentration limit of detection. Upon successful amplification of the trial, results indicated that eDNA samples were below the detection threshold of our methods, suggesting that the number of fish present at the spawning aggregations was inadequate for single-species detection methods. In addition, elements such as the unavoidable presence of non-target DNA, oceanic environmental conditions, shedding rates of target fish, among other biotic and abiotic factors could have affected DNA persistence and degradation rates at the sites. Conclusion: We provide recommendations for species-specific fish detection in lower latitudes, and suggestions for studies aiming to monitor or detect fish spawning aggregations using eDNA sampling.

The first complete mitochondrial genome of Diadema antillarum (Diadematoida, Diadematidae) / El primer genoma mitocondrial completo de Diadema antillarum (Diadematoida, Diadematidae)

The mitochondrial genome of the long-spined black sea urchin, Diadema antillarum, was sequenced using Illumina next-generation sequencing technology. The complete mitogenome is 15,708 bp in length, containing two rRNA, 22 tRNA and 13 protein-coding genes, plus a noncoding control region of 133 bp. The nucleotide composition is 18.37% G, 23.79% C, 26.84% A and 30.99% T. The A + T bias is 57.84%. Phylogenetic analysis based on 12 complete mitochondrial genomes of sea urchins, including four species of the family Diadematidae, supported familial monophyly; however, the two Diadema species, D. antillarum and D. setosum were not recovered as sister taxa.

El genoma mitocondrial del erizo de mar negro de espinas largas, Diadema antillarum, se secuenció utilizando la tecnología de secuenciación de nueva generación de Illumina. El mitogenoma completo tiene un tamaño de 15,708 pb, que contiene dos ARNr, 22 ARNt y 13 genes codificadores de proteínas, además de una región de control no codificante de 133 pb. La composición de nucleótidos es 18.37% G, 23.79% C, 26.84% A y 30.99% T. El sesgo A+T es del 57.84%. El análisis filogenético basado en 12 genomas mitocondriales completos de erizos de mar, incluyendo cuatro especies de la familia Diadematidae, apoya la monofilia familiar. Sin embargo,  las dos especies de Diadema en este estudio,  D. antillarum y D. setosum no fueron identificadas como taxones hermanos.

Fine scale population structure of Acropora palmata and Acropora cervicornis in the Colombian Caribbean.

Using a standardized SNP array, we identified two populations of Acropora cervicornis and one population of A. palmata in the Caribbean coast of Colombia. San Andrés was the most genetically differentiated location for both species. An average pairwise FST value of 0.131 and 0.050 between San Andrés and neighboring collection sites was estimated, for A. cervicornis and A. palmata, respectively. Based on population patterns of both acroporid species, we inferred that Magdalena River is not a barrier of genetic connectivity among Colombian populations. Genetic comparisons between the Colombian coast of Caribbean with other Caribbean locations agree with previous studies for both species, where four populations were identified in A. cervicornis and three in A. palmata. Our results support published bio-physical model predictions and highlight the Panama-Colombia gyre as a possible isolating mechanism within the western Caribbean. However, the genetic diversity in both species was about half (mean HE per site = 0.321 in A. palmata and 0.369 in A. cervicornis) than previous estimates in acroporid populations in the Caribbean. The lower genetic diversity as well their relative isolation and high levels of reef degradation may be of particular conservation concern that may require species-specific management coupled with science-based restoration efforts.

The first complete mitochondrial genome of Diadema antillarum (Diadematoida, Diadematidae).

The mitochondrial genome of the long-spined black sea urchin, Diadema antillarum, was sequenced using Illumina next-generation sequencing technology. The complete mitogenome is 15,708 bp in length, containing two rRNA, 22 tRNA and 13 protein-coding genes, plus a noncoding control region of 133 bp. The nucleotide composition is 18.37% G, 23.79% C, 26.84% A and 30.99% T. The A + T bias is 57.84%. Phylogenetic analysis based on 12 complete mitochondrial genomes of sea urchins, including four species of the family Diadematidae, supported familial monophyly; however, the two Diadema species, D. antillarum and D. setosum were not recovered as sister taxa.

Description of four Millepora spp. transcriptomes and their potential to delimit the Caribbean fire coral species.

Millepora is a relatively species-rich genus of hydrocorals, with 16 species distributed around the globe. It is considered an important reef building cnidarian. The current diversity of Caribbean Millepora species consists of Millepora complanata, M. alcicornis, M. squarrosa and M. striata. Here, we report the de novo transcriptome assembly and phylotranscriptomic analysis of M. alcicornis, M. complanata, M. squarrosa and a undescribed morphotype (Millepora sp.) found in exposed Thalassia beds and mangrove areas in southwest Puerto Rico. Over 345 million sequence reads were obtained for the analysis of the Millepora transcriptomes (Illumina HiSeq4000; 2x150bp). The analysis pipeline consisted of assembly with Trinity, BUSCO, RSEM and ORFs calling for each transcriptome, followed by ontology (Blast2GO) and phylogenetic analysis. The phylogenetic analysis was performed after selecting homologous genes among the transcriptomes, resulting in 10,596 sequences. Concatenation analysis (Maximum Likelihood and Bayesian inference) and a coalescence-based analysis were performed to the dataset too. Concatenation analysis yielded a topology supporting a clade of M. complanata and M. alcicornis, with Millepora sp. outside this clade and M. squarrosa as an outgroup. The coalescence-based tree estimation analysis (ASTRAL-II), presented a different topology placing M. alcicornis and Millepora sp. as sister taxa, rather than grouping with M. alcicornis with M. complanata. Our coalescence analysis indicated that there is a high degree of incomplete lineage sorting, suggesting a very recent time of species emergence among three out of the four Caribbean Millepora species. Calculations of ABBA-BABA statistics derived from transcriptome-wide SNP data indicate the possible presence of introgression between Millepora complanata and M. alcicornis.

Gnathia bermudensis (Crustacea, Isopoda, Gnathiidae), a new species from the mesophotic reefs of Bermuda, with a key to Gnathia from the Greater Caribbean biogeographic region.

Gnathia bermudensis sp. nov. is described from mesophotic coral ecosystems in Bermuda; it is distinguished by pronounced and pointed supraocular lobes, two superior frontolateral processes and a weak bifid mediofrontal process, pereonite 1 not fused dorsally with the cephalosome, and large eyes. This is the first record of a species of Gnathia from Bermuda. A synopsis and key to the other Gnathia species from the Greater Caribbean biogeographic region is provided.

A checklist of Pontarachnidae (Acari: Hydrachnidia) and notes on distributional patterns of the species.

A worldwide checklist of the pontarachnid mites is provided based on published reports and original data. A total of 53 valid species of pontarachnid mites have been compiled, of which the genus Pontarachna includes 30 species, while 23 species belong to the genus Litarachna. The highest number of species (n=16) is reported from the marine province Tropical West of the Pacific Ocean. A deutonymph of Litarachna triangularis is reported here from Dongsha Atoll, Taiwan. Patterns of endemism and seemingly incomplete species distributional records are the result of a lack of intensive faunistic surveys in different parts of the world. The taxonomy of Pontarachnid mites will be improved by the use of mite-specific sampling methods and the application of molecular phylogenetics.

De novo transcriptome assembly of the digitate morphotype of Briareum asbestinum (Octocorallia: Alcyonacea) from the southwest shelf of Puerto Rico.

Octocorals have now become the most visually dominant metazoan benthic taxa of most Caribbean reefs, following the precipitous decline of scleractinian corals. Yet taxonomic issues because of their extensive phenotypic plasticity are still abound. Briareum asbestinum one of the iconic octocorals of the shallow Caribbean coral reefs exhibits a biform morphology, the digitate and the encrusting one. The taxonomic status of each form has not been clarified, yet. Until recently, there were few genetic resources for non-model metazoans, however, affordable high-throughput DNA sequencing has removed this hindrance. We present the first transcriptome of the digitate form of Briareum asbestinum from southwest Puerto Rico. We used paired-end sequencing (Illumina NextSeq 500), with a total yield of 159,754,702 raw reads. De novo assembly was performed utilizing a multi-assembler approach generating 371,554 biologically true, non-redundant transcripts. Open reading frame analysis identified 102,839 putative ORFs of which 78,607 were with annotations. BUSCO analysis indicated a total of 96.4% complete orthologous genes from the metazoan dataset. The assembly presented here serves as an important new genomic reference for the Briareum genus that will facilitate future population and phylogenetic studies aiming to better understand the molecular basis of phenotypic plasticity exhibited throughout the genus.

De novo transcriptome assembly of the coral Agaricia lamarcki (Lamarck's sheet coral) from mesophotic depth in southwest Puerto Rico.

The plating coral, Agaricia lamarcki is a widely distributed species inhabiting reefs across the Caribbean basin and Florida. This species is of interest since it is considered a depth-generalist, found from 10 to 70 m. Given the scope of contemporary studies on this coral's population dynamics and physiology, as well as, the potential of mesophotic reefs to be refuge habitats for deteriorated shallow water reefs, we present the first de novo transcriptome assembly of an important mesophotic coral. Using next-generation paired-end sequencing (Illumina Hiseq4000; 2 × 150 bp), we obtained a total of 82,506,058 raw reads. The novel transcriptome assembly strategy included the recently developed National Center for Genome Analysis Support de novo transcriptome assembly pipeline. Assembly produced a total of 101,322 biologically true, non-redundant transcripts with an average contig length of 959 and N50 of 1830. EvidentialGene and TransDecoder were used to identify open reading frames (ORFs) with homology insight provided by the UniProtKb and PFAM databases. ORF prediction resulted in 38,517 putative ORFs of which 12,107 ORFs were annotated as genes dealing with molecular function, 1266 with biological processes and 416 with cellular components.

Traditional and confocal descriptions of a new genus and two new species of deep water Cerviniinae Sars, 1903 from the Southern Atlantic and the Norwegian Sea: with a discussion on the use of digital media in taxonomy (Copepoda, Harpacticoida, Aegisthidae).

Aegisthidae is one of the most abundant and diverse families of harpacticoid copepods living in deep-sea benthos, and the phylogenetic relationships within the family are in state of flux. Females of two new deep-water species of harpacticoid copepods belonging to the Hasegen. n. (Aegisthidae: Cerviniinae) are described. The first taxonomic description of marine copepod species based on the combined use of interference and confocal microscopy for the study of the habitus and dissected appendages is presented here. CLSM (Confocal Laser Scanning Microscopy) is a non-destructive method, comparable in quality to SEM (scanning electron microscopy) at the same magnifications. To observe and reconstruct in detail the habitus and dissected appendages, whole specimens and dissected parts were stained with Congo Red, mounted on slides with glycerine for CLSM and scanned under three visible-light lasers. Hase lagomorphicusgen. et sp. n. and Hase talpamorphicusgen. et sp. n. were collected from the sediments of the Southern Atlantic and the Norwegian Sea, from 2270 m and 5468 m depths, respectively. Hasegen. n. is included within Cerviniinae based on the caudal rami which are relatively divergent. Hasegen. n. is the sister taxon of Cerviniella based on the following synapomorphies: sturdy body, exopodites 1-3 of pereopods 1-3 heavily built, transformed into digging limbs, with strong outer and distal spines/setae, two-segmented endopod on the pereopods 2 and 3, and a reduced pereopod 5. Compared to Cerviniella, Hasegen. n. exhibits a more developed armature on the pereopod 1, which has outer and distal elements transformed into strong and long spines vs. stiff setae on Cerviniella.Hasegen. n. has one or two strong and long spines on the inner margin of the exopodite 3 of pereopod 4 and pereopod 5 is fused to the somite, ornamented with three distal setae. The telson of Hasegen. n. is subquadratic, and the furca is among the shortest yet described for Aegisthidae. The new species differ in a number of diagnostic characters, three of which are: a) the somite bearing pereopods 3 and 4 with latero-distal spiniform processes in H. talpamorphicusgen. et sp. n. but smooth in H. lagomorphicusgen. et sp. n., b) antenna is armed with three stout spines on the lateral inner margin of the exopod in H. talpamorphicusgen. et sp. n. and two proximal setae in H. lagomorphicusgen. et sp. n., and c) pereopod 4 exopodite 3 has two long and strong spines on the inner margin in H. lagomorphicusgen. et sp. n. and one spine in H. talpamorphicusgen. et sp. n. The high quality of CLSM images should foster discussion about the use of high quality digital images as type or as part of the type series in zoological studies, especially when studying rare and small macrofaunal and meiofaunal taxa.

Effective Dispersal of Caribbean Reef Fish is Smaller than Current Spacing Among Marine Protected Areas.

The oceans are deteriorating at a fast pace. Conservation measures, such as Marine Protected Areas, are being implemented to relieve areas from local stressors and allow populations to restore to natural levels. Successful networks of MPAs operate if the space among MPAs is smaller than the dispersal capacity of the species under protection. We studied connectivity patterns across populations in a series of MPAs in the common yellowhead Jawfish, Opistognathus aurifrons. Using the power of genome-wide variation, we estimated that the maximum effective dispersal is 8.3 km. We found that MPAs exchange migrants likely via intermediate unprotected habitats through stepping stone dispersal. At scales >50 km such connectivity is decreased, particularly across the Mona Passage. The MPA network studied would be unable to maintain connectivity of these small benthic fishes if habitat in between them is extirpated. Our study highlights the power of SNPs to derive effective dispersal distance and the ability of SNPs to make inferences from single individuals. Given that overall reef fish diversity is driven by species with life histories similar to that of the yellowhead jawfish, managers face a challenge to develop strategies that allow connectivity and avoid isolation of populations and their possible extinction.

New species and new records of Cumacea (Crustacea: Peracarida: Cumacea) from mesophotic reefs of Puerto Rico and U.S. Virgin Islands, Caribbean Sea.

The cumacean fauna of the Caribbean mesophotic reefs is remarkably rich but understudied. Herein, we present the description of 22 new species of the family Nannastacidae, including one from shallow reefs, 20 of them belonging to Cumella (Cumella) and two new species belonging to the subgenus Cumewingia. We have also included range extensions and new locations for ten previously known species of Cumella, two species in the genus Vaunthompsonia (family Bodotriidae) and one species in the genus Cubanocuma (family Nannastacidae). Taxonomic keys are provided for the western tropical Atlantic species of Cumella (Cumella) and Cumella (Cumewingia), separately for the adult males and females. Large sampling efforts and careful systematic studies, even in relatively well-characterized regions such as the Caribbean, can yield a surprising number of new discoveries. Our current findings emphasize our previous assertion that the mesophotic reefs are treasure troves of undiscovered benthic fauna and might be qualified as biodiversity hotspots.

Proteomic analysis of bleached and unbleached Acropora palmata, a threatened coral species of the Caribbean.

There has been an increase in the scale and frequency of coral bleaching around the world due mainly to changes in sea temperature. This may occur at large scales, often resulting in significant decline in coral coverage. In order to understand the molecular and cellular basis of the ever-increasing incidence of coral bleaching, we have undertaken a comparative proteomic approach with the endangered Caribbean coral Acropora palmata. Using a proteomic tandem mass spectrometry approach, we identified 285 and 321 expressed protein signatures in bleached and unbleached A. palmata colonies, respectively, in southwestern Puerto Rico. Overall the expression level of 38 key proteins was significantly different between bleached and unbleached corals. A wide range of proteins was detected and categorized, including transcription factors involved mainly in heat stress/UV responses, immunity, apoptosis, biomineralization, the cytoskeleton, and endo-exophagocytosis. The results suggest that for bleached A. palmata, there was an induced differential protein expression response compared with those colonies that did not bleach under the same environmental conditions.

New genus and new species of Caprellidae (Crustacea: Peracarida: Amphipoda) from the mesophotic coral ecosystems of Puerto Rico and St. Croix, Caribbean Sea.

A new genus and two new species are described based on material collected from the mesophotic coral ecosystems of the U.S. Caribbean. The new genus Borikenella can be distinguished from other related genera such as Pseudaeginella, Paradeutella, Aciconula and Deutella by the combination of the following characters: pereopods 3 and 4 three-articulate, pereopods 5-7 six-articulate, mandible molar present, palp of the mandible with a setal formula 1-x-0, abdomen without appendages. The new species Liropus gurui, can be distinguished from the closely related L. japonicus mainly by the lack of anteroventral margin extended forward in pereonite 3, the lack of cleft and serration in the propodus of gnathopod 2, the longer pereopod 3 and the larger abdominal appendages.

Genetic seascape of the threatened Caribbean elkhorn coral, Acropora palmata, on the Puerto Rico Shelf.

It has been proposed that the elkhorn coral, Acropora palmata, is genetically separated into two distinct provinces in the Caribbean, an Eastern and a Western population admixing in western Puerto Rico and around the Mona Passage. In this study, the genetic structure of A. palmata sampled at 11 Puerto Rican localities and localities from Curaçao, the Bahamas and Guadeloupe were examined. Analyses using five microsatellite markers showed that 75% of sampled colonies had unique genotypes, the rest being clone mates. Genetic diversity among genets was high (HE = 0.761) and consistent across localities (0.685 to 0.844). FST ranged from -0.011 to 0.047 supporting low but significant genetic differentiation between localities within the previously reported Eastern and Western genetic provinces. Plots of genetic per geographic distances and significant Mantel tests supported isolation-by-distance (IBD) within Puerto Rico. Analysis with the software Structure favored a scenario with weak differentiation between two populations, assigning eastern Puerto Rican locations (Fajardo and Culebra), Guadeloupe and Curaçao to the Caribbean Eastern population and western Puerto Rican locations (west of Vega Baja and Ponce), Mona and the Bahamas to the Caribbean Western population. Vieques and San Juan area harbored admixed profiles. Standardized FSTs per 1,000 km unit further supported higher differentiation between localities belonging to different Structure populations, with IBD being stronger within Puerto Rico than on larger regional scales. This stronger genetic transition seems to separate localities between putative Eastern and Western provinces in the eastern Puerto Rican region, not around the Mona Passage.

A new species of Boca Lowry & Stoddart, 1997 (Amphipoda: Lysianassoidea: Aristiidae) from a mesophotic coral ecosystem off Puerto Rico, Caribbean Sea.

A new species of the genus Boca Lowry & Stoddart, 1997 is described from a mesophotic coral ecosystem off southwestern Puerto Rico, in the Caribbean Sea. The new species is easily recognized from the others in the genus mainly by the following characters: (1) maxilliped, inner plate with 2 long apical simple setae; palp, articles slender, subequal in length; (2) gnathopod 1, propodus slightly elongate, about 2.5 × longer than wide, and palm extremely acute, quite long and distinctly demarked by a robust seta at the palmar corner; (3) gnathopod 2, carpus slightly elongate, about 3.7 × longer than wide; (4) pereopod 5, basis widely expanded posteriorly, posterior margin rounded and smooth, and posteroventral lobe weakly developed. We also present a key to world species of Boca. This is the fifth species of Boca from world's oceans and the first record of the genus from Puerto Rico.

New records of Bodotriidae (Crustacea: Cumacea) from Puerto Rico with descriptions of three new species.

In a continuing effort to describe the cumacean fauna of Puerto Rico we describe three new species of Bodotriidae, a family that has never been reported from Puerto Rico before.  While finding and describing new microcrustacean species may not be an impossible task, if there is available taxonomic expertise, the currently described species were found in large numbers within a short distance from the Marine Laboratories of the University of Puerto Rico where the local reefs have been studied for over half a century, highlighting the large gaps that exist in our estimates of Caribbean marine diversity.  The three new species, Cyclaspis gurui sp. nov., Cyclaspis mariae sp. nov. and Vaunthompsonia budaii sp. nov. are reported from a fringing reef off La Parguera, southwest coast of Puerto Rico and Vaunthompsonia cristata Bate, 1858 represents a new record for Puerto Rico from the mesophotic reefs.

A new species of Litarachna (Acari, Hydrachnidia, Pontarachnidae) from a Caribbean mesophotic coral ecosystem.

NEW RECORDS OF PONTARACHNID MITES (ACARI: Hydrachnidia) from the Caribbean island of Puerto Rico are presented. Litarachna lopezae sp. n., from substrata collected from Bajo de Sico, a mesophotic coral reef ecosystem in Mona Passage off Puerto Rico, is described as new to science. The new species was collected from nearly 70 m depth, the greatest depth from which pontarachnid mites have been found until now. In addition, a Litarachna sp. was also found in association with the tube of the polychaete Sabellastarte magnifica (Shaw, 1800) at the shallow waters of north Puerto Rico.

Three new Nannastacidae (Crustacea: Cumacea) species from a Caribbean mesophotic ecosystem.

Examination of substrata from the mesophotic reefs of Mona Island, Puerto Rico yielded 3 new species of cumaceans, all from the family Nannastacidae: Cumella achimae sp. nov., C. victoriae sp. nov. and Nannastacus craciuni sp. nov. The 3 new species bring the total of new cumacean taxa described from the mesophotic reefs of US Caribbean to 9, highlighting the potential of mesophotic reefs as a biodiversity hotspot. For the first time we report the genus Nannastacus from the Caribbean Sea.