Marine biodiversity from zero to a thousand meters at Clipperton Atoll (Île de La Passion), Tropical Eastern Pacific

Biodiversity conservation relies upon accurate species taxonomy to support decision-making. Stony corals in the genus Pocillopora are critical ecosystem engineers in the Eastern Tropical Pacific (ETP); however, Pocillopora species diversity in the region is still unresolved due to high phenotypic plasticity, lack of diagnostic morphological characters, and low-resolution genetic markers used in previous studies. To address this gap, we leveraged low-coverage whole-genome sequencing for 342 Pocillopora coral samples collected from Panamá, Costa Rica, Colombia, Ecuador, and Clipperton Atoll (France). Sequence data were used to recover mitochondrial genomes and barcode loci, ultraconserved elements, and genome-wide single-nucleotide polymorphisms (SNPs) for species delimitation. Together, our data revealed the existence of four distinct Pocillopora species in the ETP, corresponding to the nominal species P. effusa (Veron, 2000), P. meandrina Dana, 1846, P. capitata Verrill, 1864, and P. lacera Verrill, 1869. Two P. capitata population subclusters with moderate genetic differentiation were separated between offshore islands and continental sites, and individual colonies with signatures of admixture between P. effusa and P. lacera were identified at Isla del Coco, Costa Rica. Additionally, Pocillopora-associated algal symbiont community profiling identified Cladocopium and Durusdinium as dominant genera that varied according to the host species, with P. lacera demonstrating higher specificity for associations with Cladocopium. This study highlights the power of genome skimming as an affordable, high-resolution approach to rapidly assess coral species diversity and algal symbiont associations, thereby empowering marine conservation.

Revillagigedo Archipelago and Clipperton atoll are oceanic islands located in the eastern tropical Pacific. The composition and trophic structure of their fish assemblages have never been characterized in detail, and the aim of this study was therefore to analyse the community structure and assess the similarity of fish assemblages between these two areas. Underwater visual fish censuses were conducted using band transects at two depth levels in three islands of the Revillagigedo Archipelago (Socorro, San Benedicto, and Roca Partida) and at Clipperton atoll. We calculated ecological indices (density, richness, Shannon diversity, Pielou evenness, and taxonomic distinctiveness) for each transect. These were compared in order to determine quantitative differences among the islands and bathymetric levels. Qualitative analyses (ANOSIM, nMDS, and SIMPER) were also performed. Finally, we analysed the trophic structure of the assemblages and the functional diversity of the four studied sites. The results showed significant differences for all indices, except diversity (H′). Roca Partida was the site with greatest abundance and richness due to the presence of pelagic species in large numbers. No significant differences were found in functional diversity, suggesting a high degree of ecological redundancy. Lower‐level carnivores with mean trophic level values of between 3.3 and 3.8 dominated both areas. The ordination analysis did not show a clear difference in fish composition among the islands, although Clipperton atoll has a particular fauna characterized by endemic species (Thalassoma robertsoni and Stegastes baldwini). In conclusion, the fish communities of the studied areas seem quite similar, but their assemblage structure differs. In particular, Clipperton is differentiated by the influence of endemic species.

The expanse of deep water between the central Pacific islands and the continental shelf of the Eastern Tropical Pacific is regarded as the world's most potent marine biogeographic barrier. During recurrent climatic fluctuations (ENSO, El Niño Southern Oscillation), however, changes in water temperature and the speed and direction of currents become favourable for trans-oceanic dispersal of larvae from central Pacific to marginal eastern Pacific reefs. Here, we investigate the population connectivity of the reef-building coral Porites lobata across the Eastern Pacific Barrier (EPB). Patterns of recent gene flow in samples (n = 1173) from the central Pacific and the Eastern Tropical Pacific (ETP) were analysed with 12 microsatellite loci. Results indicated that P. lobata from the ETP are strongly isolated from those in the central Pacific and Hawaii (F(ct) ' = 0.509; P < 0.001). However, samples from Clipperton Atoll, an oceanic island on the eastern side of the EPB, grouped with the central Pacific. Within the central Pacific, Hawaiian populations were strongly isolated from three co-occurring clusters found throughout the remainder of the central Pacific. No further substructure was evident in the ETP. Changes in oceanographic conditions during ENSO over the past several thousand years thus appear insufficient to support larval deliveries from the central Pacific to the ETP or strong postsettlement selection acts on ETP settlers from the central Pacific. Recovery of P. lobata populations in the frequently disturbed ETP thus must depend on local larval sources.

Clipperton Atoll, one of the most isolated coral reefs worldwide, is of great scientific interest due to its geomorphology and high levels of endemism. This study explored the reef fish assemblage structure of Clipperton Atoll and its relationship with live coral cover. Nine stations were sampled at three sites and three depths (6, 12 and 20 m) around the reef, measuring fish species richness and biomass and hermatypic coral cover (at genus level). We evaluated variation in species richness, biomass and diversity of fish assemblages among sites and depths, as well as the relationship between the entire fish assemblage composition and live coral cover. The results showed that species richness and biomass were similar among sites, but differed across depths, increasing with depth. In contrast, diversity differed among sites but not among depths. Multivariate analyses indicated that fish assemblage composition differed among sites and depths in relation to changes in cover of coral of the genera Pocillopora, Porites, Pavona and Leptoseris, which dominate at different depths. The results showed that fish species richness and diversity were low at Clipperton Atoll and that, in isolated coral reefs with a low habitat heterogeneity and low human disturbance, live coral cover has a significant influence on the spatial variation of the reef fish assemblages. This study highlights the importance of coral habitat structure in shaping coral reef fish assemblages.

There is a need to understand the degree to which sharks move between islands in Marine Protected Areas (MPAs) of the Eastern Tropical Pacific (ETP). Exposure to fishing activities becomes significant when no-take zones do not cover the critical areas that sharks use. We analyzed an ultrasonic telemetry dataset to assess how Galapagos sharks (Carcharhinus galapagensis) and silky sharks (Carcharhinus falciformis) move between the islands that comprise the Revillagigedo Archipelago (RA) and how they migrate to other islands in the ETP. In total, 92 sharks of both species were tracked from January 2010 to December 2018 in the region. Particularly, 39 sharks were detected in the Revillagigedo Archipelago (RA). Of these, 27 were resident at one island (behavior type I), 10 moved between two or more islands within a MPA (type II), and 3 sharks moved between MPAs (behavior type III): a silky shark tagged at Roca Partida (RA) that moved to Clipperton Atoll (CA), another silky shark moved from Wolf, Galapagos Archipelago (GA) to CA and back again and a Galapagos shark tagged at Socorro Island (RA), detected at CA, and finally recorded in Darwin Island (GA). This excursion was one of the longest movements ever recorded for the species (3,160 km). The long-distance dispersal observed in these two species underscores the necessity for international collaboration. Such cooperation is essential to implement effective shark protection measures, including swimways or MigraVías, and other conservation tools in the ETP region.

BackgroundAcanthurus guttatus is distributed from the Maldives to the Hawaiian Archipelago and the Pitcairn Islands, and as north as Ryukyu Islands and as south as New Caledonia. The only known locality in the Eastern Tropical Pacific is Clipperton Atoll where three vagrant specimens have been observed.MethodsOn June 2016 and April 2017 small groups of A. guttatus were observed and photographed during SCUBA diving and snorkeling surveys for touristic suitability at Isla del Coco National Park, Costa Rica.ResultsSix specimens of A. guttatus were observed swimming over shallow rocky reefs at Isla del Coco, a volcanic island located in the Eastern Tropical Pacific.ConclusionsThis study represents the first record of A. guttatus at Isla del Coco, the second known location of occurrence in the Eastern Tropical Pacific, and the easternmost known range for the Whitespotted surgeonfish.

Estimating population sizes and genetic diversity are key factors to understand and predict population dynamics. Marine species have been a difficult challenge in that respect, due to the difficulty in assessing population sizes and the open nature of such populations. Small, isolated islands with endemic species offer an opportunity to groundtruth population size estimates with empirical data and investigate the genetic consequences of such small populations. Here we focus on two endemic species of reef fish, the Clipperton damselfish, Stegastes baldwini, and the Clipperton angelfish, Holacanthus limbaughi, on Clipperton Atoll, tropical eastern Pacific. Visual surveys, performed over almost two decades and four expeditions, and genetic surveys based on genomic RAD sequences, allowed us to estimate kinship and genetic diversity, as well as to compare population size estimates based on visual surveys with effective population sizes based on genetics. We found that genetic and visual estimates of population numbers were remarkably similar. S. baldwini and H. limbaughi had population sizes of approximately 800,000 and 60,000, respectively. Relatively small population sizes resulted in low genetic diversity and the presence of apparent kinship. This study emphasizes the importance of small isolated islands as models to study population dynamics of marine organisms.

One hundred and fifteen species of fishes (14 oceanic, plus 101 shore and nearshore species) are known from Clipperton Island, a small, remote coral atoll in the tropical eastern Pacific (TEP). This fish fauna includes only ∼ 14% of the region's shallow-water species, and also is depauperate relative to the fish faunas of other isolated tropical islands. The island's isolation, small size, reduced habitat diversity, and oceanic environment contribute to this paucity of species. Fifty-two species at Clipperton can be identified as TEP; these include 37 widespread species, six species shared only with the Revillagigedo Islands [the nearest (950 km) offshore shoals], and eight endemic to Clipperton. Endemics species apparently have a mix of west and east Pacific origins. Sixty-three species are transpacific; they include three new records (of Naso surgeonfishes) that maybe vagrants recruited > 4,000 km from Oceania. Clipperton is situated at the juncture between the TEP and Oceania. Its fish fauna contains about equal numbers of TEP and transpacific species. This faunal structure reflects the relative influence of surface currents from Oceania and the TEP. Although most of Clipperton's transpacific shorefishes are widespread in eastern Oceania, the Clipperton fauna has specific affinities to the fauna of the Line Islands, which are located within the main eastbound current from Oceania. Clipperton may therefore be a major stepping stone for dispersal between Oceania and the remainder of the TEP. About 50% of the non-oceanic, tropical transpacific fishes occur there, and at least 75 % of those species apparently have resident populations at the island.

The tropical eastern Pacific (TEP) is a biogeographic region with a substantial set of isolated oceanic islands and mainland shoreline habitat barriers, as well as complex oceanographic dynamics due to major ocean currents, upwelling areas, eddies, and thermal instabilities. These characteristics have shaped spatial patterns of biodiversity between and within species of reef and shore fishes of the region, which has a very high rate of endemism. Scorpaenodes xyris, a small ecologically cryptic reef-dwelling scorpionfish, is widely distributed throughout the TEP, including all the mainland reef areas and all the oceanic islands. This wide distribution and its ecological characteristics make this species a good model to study the evolutionary history of this type of reef fish across the breadth of a tropical biogeographical region. Our evaluation of geographic patterns of genetic (mitochondrial and nuclear) variation shows that S. xyris comprises two highly differentiated clades (A and B), one of which contains four independent evolutionary subunits. Clade A includes four sub-clades: 1. The Cortez mainland Province; 2. The Revillagigedo Islands; 3. Clipperton Atoll; and 4. The Galapagos Islands. Clade B, in contrast, comprises a single unit that includes the Mexican and Panamic mainland provinces, plus Cocos Island. This geographical arrangement largely corresponds to previously indicated regionalization of the TEP. Oceanic distances isolating the islands have produced much of that evolutionary pattern, although oceanographic processes likely have also contributed.

Elevated sea surface temperatures are causing an increase in coral bleaching events worldwide, and represent an existential threat to coral reefs. Early studies of Mesophotic Coral Ecosystems (MCEs) highlighted their potential as thermal refuges for shallow-water coral species in the face of predicted 21st century warming. However, recent genetic evidence implies that limited ecological connectivity between shallow- and deep-water coral communities inhibits their effectiveness as refugia; instead MCEs host distinct endemic communities that are ecologically significant in and of themselves. In either scenario, understanding the response of MCEs to climate change is critical given their ecological significance and widespread global distribution. Such an understanding has so far eluded the community, however, because of the challenges associated with long-term field monitoring, the stochastic nature of climatic events that drive bleaching, and the paucity of deep-water observations. Here we document the first observed cold-water bleaching of a mesophotic coral reef at Clipperton Atoll, a remote Eastern Tropical Pacific (ETP) atoll with high coral cover and a well-developed MCE. The severe bleaching (>70 % partially or fully bleached coral cover at 32 m depth) was driven by an anomalously shallow thermocline, and highlights a significant and previously unreported challenge for MCEs. Prompted by these observations, we compiled published cold-water bleaching events for the ETP, and demonstrate that the timing of past cold-water bleaching events in the ETP coincides with decadal oscillations in mean zonal wind strength and thermocline depth. The latter observation suggests any future intensification of easterly winds in the Pacific could be a significant concern for its MCEs. Our observations, in combination with recent reports of warm-water bleaching of Red Sea and Indian Ocean MCEs, highlight that 21st century MCEs in the Eastern Pacific face a two-pronged challenge: warm-water bleaching from above, and cold-water bleaching from below.

The genus Pavona includes massive to submassive hermatypic corals and represents one of the main reef builders of the coral reefs in the Eastern Tropical Pacific (ETP). However, its development and specific ecological role, particularly on offshore reefs (e.g., oceanic Atolls), remain poorly understood. This study aims to determine the sclerochronological characteristics of the four Pavona species (Pavona duerdeni, Pavona clavus, Pavona maldivensis, and Pavona varians) in Clipperton Atoll, and their contributions to reef maintenance. Using the optical densitometry technique, Pavona annual growth parameters were obtained, showing that skeletal density (1.26 ± 0.23 g cm−3), extension rate (0.94 ± 0.31 cm year−1), and calcification rate (1.17 ± 0.36 g cm−2 year−1) were consistent with previous data from the ETP. However, differences at the species level showed that P. duerdeni, P. varians, and P. maldivensis invested their calcification resources into building denser skeletons, demonstrating the morphological plasticity of the genus, likely driven by local factors, such as strong hydrodynamics and depth, rather than regional conditions (e.g., El Niño-Southern Oscillation events). Pavona’s growth strategies contribute to the preservation potential on a geological timescale of Clipperton Atoll, highlighting their importance as one of the main reef builders at a massive coral-dominated reef.

Isolated coral reef habitats are unique systems to study the natural dynamics of coral traits and their natural acclimatization, adaptation, and recovery from global-scale stressors such as thermally induced bleaching events. This study evaluates the spatial and temporal changes in coral community attributes (diversity, live cover, and coral assemblage structure) over 14 years (2005–2019) at Clipperton, an extremely remote Eastern Tropical Pacific (ETP) atoll. The atoll exhibited overall high coral cover (~ 50–60%) dominated by massive species (Porites spp.), yet we observed large variation (44–56%) in coral community attributes among survey years (2005, 2016, 2019) with depth explaining most of the variation. Live coral cover increased in 2019 after a severe thermal stress event (El Niño, 2015–2016) and many tropical cyclones, which also caused a shift in assemblage structure from branching Pocillopora to massive Porites in the shallower reef zones, resulting in a less well-defined depth gradient. These changes in coral assemblage structure may have long-term effects on the configuration of the physical reef framework of the well-conserved coral reef ecosystems at Clipperton and consequently may alter the ecological functionality of one of the most important biogeographic stepping stones in the central Pacific and ETP regions.

Stony corals in the genus Pocillopora are among the most common and widely distributed of Indo-Pacific corals and, as such, are often the subject of physiological and ecological research. In the far Tropical Eastern Pacific (TEP), they are major constituents of shallow coral communities, exhibiting considerable variability in colony shape and branch morphology and marked differences in response to thermal stress. Numerous intermediates occur between morphospecies that may relate to extensive hybridization. The diversity of the Pocillopora genus in the TEP was analysed genetically using nuclear ribosomal (ITS2) and mitochondrial (ORF) sequences, and population genetic markers (seven microsatellite loci). The resident dinoflagellate endosymbiont (Symbiodinium sp.) in each sample was also characterized using sequences of the internal transcribed spacer 2 (ITS2) rDNA and the noncoding region of the chloroplast psbA minicircle. From these analyses, three symbiotically distinct, reproductively isolated, nonhybridizing, evolutionarily divergent animal lineages were identified. Designated types 1, 2 and 3, these groupings were incongruent with traditional morphospecies classification. Type 1 was abundant and widespread throughout the TEP; type 2 was restricted to the Clipperton Atoll; and type 3 was found only in Panama and the Galapagos Islands. Each type harboured a different Symbiodinium'species lineage' in Clade C, and only type 1 associated with the 'stress-tolerant'Symbiodinium glynni (D1). The accurate delineation of species and implementation of a proper taxonomy may profoundly improve our assessment of Pocillopora's reproductive biology, biogeographic distributions, and resilience to climate warming, information that must be considered when planning for the conservation of reef corals.

Antipathes galapagensis and Myriopathes panamensis are black coral species (Order Antipatharia) distributed in the Eastern Pacific from the Gulf of California to the coasts of Peru, at depths from -10 m to -200 m for A. galapagensis and to -50 m for M. panamensis. Antipatharians have great ecological importance as engineer species and major constituents of “coral forests,” which are recognized as vulnerable marine ecosystems. Antipathes galapagensis has been a target of fisheries in several countries and has frequently been overexploited. Thus, the aim of this study was to compile a database of georeferenced records of A. galapagensis and M. panamensis, and use distribution data and environmental variables to construct habitat suitability models with Maxent software, in order to better understand black coral environmental requirements and potential distributions in the Eastern Tropical Pacific. The models showed good fit and performance (AUC > 0.9); key variables that drive the potential distribution of both species were chlorophyll a, nutrient concentration, and seawater temperature. The models did not predict occurrences beyond the recognized distribution range limits of the species; notwithstanding, they indicated that the Pacific coast of the Baja California Peninsula and the central and southern coasts of the Mexican Pacific have areas of high suitability for the presence of these corals. To our knowledge, no black coral records from these sites exist in the literature to date; thus, field validations are needed to verify the model predictions. With these results, it is possible to offer suggestions of new conservation sites for black corals based on the areas with the highest probability of occurrence of the species.

Mesophotic coral ecosystems (MCEs), at ocean depths between 40 and 150 m, have been found throughout the tropics but are different in the Eastern Tropical Pacific (ETP). This observation is based on submersible dives that have explored several ETP mesophotic areas. The ETP is characterized by a shallow thermocline (approximately 50 m depth), reduction in light availability at deeper depths due to the accumulation of particulate matter at the thermocline, cold temperatures, low oxygen concentrations, and low aragonite saturation state (Ωarag) that may explain the absence of zoothanthellate corals below 40 m. Isla del Coco is located 500 km off the Pacific coast of Costa Rica. The MCEs of this island have been explored using the DeepSee submersible. There is a sharp change in benthic fauna, in both soft and hard bottoms, at approximately 50 m depth. The combination of the shallow thermocline bringing cold and low pH waters to near the surface plus the turbidity (low light) at the thermocline leads to a situation where zooxanthellate corals do not generally thrive below about 15–25 m depth (maximum around 40 m) and do not build reefs in deeper waters. The substrate between 50 and 150 m is densely covered with red algae (down to 90 m), octocorals, black corals, azooxanthellate corals, and calcareous hydroids. This chapter is the first synthesis of mesophotic environments of any ETP site and characterizes the MCEs of Isla del Coco National Park.