Find research datasets worth reusing

opencc-by-4.0Jan 2024View details →

Coral Reef Soundscapes - Lizard Island, Australia

Repository to support the publication: Unlocking the soundscapes of coral reefs with artificial intelligence. Williams et al (2024) https://doi.org/10.1101/2024.02.02.578582. If using this data please cite or acknowledge the paper. This repository contains all the raw data from the Australian coral reef soundscape dataset. Note, some site names were switched for the publication, so differ to the raw files in this repository. For conversions use: This repo -> The publication SiteA -> Site A SiteB -> Site G SiteC -> Site D SiteD -> Site E SiteE -> Site B SiteF -> Site I SiteG -> Site H SiteH -> Site L SiteI -> Site C SiteJ -> Site F SiteK -> Site J SiteL -> Site K

opencc-zeroApr 2024View details →

Symbiodiniaceae ITS2 sequences from reef corals in St. John, U.S. Virgin Islands

Monitoring coral cover can describe the ecology of reef degradation, but rarely can it reveal the proximal mechanisms of change, or achieve its full potential in informing conservation actions. Describing temporal variation in Symbiodiniaceae within corals can help address these limitations, but this is rarely a research priority. Here, we augmented an ecological time series of the coral reefs of St. John, US Virgin Islands, by describing the genetic complement of symbiotic algae in common corals. Seventy-five corals from 9 species were marked and sampled in 2017, and following hurricanes in September 2017, 41% were sampled in 2018, and 72% in 2019; 28% could not be found and were assumed to have died. Symbiodiniaceae ITS2 sequencing identified 525 distinct sequences (comprising 42 ITS2 type profiles), and symbiont diversity differed among host species and individuals, but was in most cases preserved within hosts over 3 yrs that were marked by physical disturbances from major hurricanes and the onset of stony coral tissue loss disease. While changes in symbiont communities were slight and stochastic over time within colonies, variation in the dominant symbionts among colonies was observed for all host species. Together these results indicate that declining host abundances could lead to the loss of rare algal lineages that are found in a low proportion of few coral colonies left on many reefs, especially if coral declines are symbiont-specific. These findings highlight the importance of identifying Symbiodiniaceae as part of a time series of coral communities to support holistic conservation planning. Repeated sampling of tagged corals is unlikely to be viable for this purpose, because many Caribbean corals are dying before they can be sampled multiple times. Instead, random sampling of large numbers of corals may be more effective in capturing the diversity and temporal dynamics of Symbiodiniaceae metacommunities in reef corals.

opencc-by-4.0Dec 2024View details →

Data for: The hydrodynamics of Lizard Island lagoon, Great Barrier Reef

Open the record for dataset details and reuse information.

opencc-zeroApr 2022View details →

Echolocation clicks and anthropogenic detections with neural network labels in Hawaiian Island HARP data from Kona, Kaua`i, and Pearl and Hermes Reef

This dataset consists of echolocation clicks and detections of anthropogenic signals at three sites in the Hawaiian Islands Archipelago. These sites are Hawaii/Hawaii_K, Kauai/KA, and Pearl and Hermes Reef/PHR. Echolocation clicks were grouped into 5 minute bins, for which summary data is provided. Files are in .mat format that can be read using any desired coding language using a netcdf reading script. Files are separated by site, deployment, and neural network class (i.e. sitedeployment_cbins_class or site_deployment_cbins_class). Manual labels are provided.

opencc-zeroMay 2022View details →

Host-parasite interactions between a copepod (Pharodes tortugensis) and small reef-associated gobies (Coryphopterus) in the British Virgin Islands

The effects of parasitic copepods on free-living hosts are infrequently documented, and the copepod Pharodes tortugensis has remained virtually unstudied since described. For the first time, we document its host range in the British Virgin Islands (BVI), the prevalence and intensity of infections on wild hosts, and its impacts on host morphology and performance. Infections were observed on four benthic gobies in the BVI (Coryphopterus glaucofraenum, C. venezuelae, C. dicrus and C. eidolon) but not on other host species previously reported from other parts of the western Atlantic. Infected gobies were widespread in the BVI (detected at 33 of 52 sites, prevalence from 1–25%) but extremely rare elsewhere in the Caribbean (detected at 2 of 16 sites, prevalence <0.006%). As is typical of macroparasite infections, P. tortugensis was over-dispersed in BVI host populations (mean intensity = 4.7, range = 1–17). Infections were most common in juvenile and female hosts, and rarely found in larger male hosts. The copepods attach in the branchial chamber of the goby; female copepods show high attachment fidelity to the ventral surface of the chamber, while male copepods attached most often to the first two gill arches and in the branchial chamber adjacent to the female. Infections caused substantial damage to the host's branchial chamber and gill filaments. Parasitized gobies also had larger livers and smaller gonads than unparasitized individuals of similar length. The changes in organ mass of infected gobies were not sizeable enough to affect total body mass, and host condition (the body-length vs. body-mass relationship) was similar for gobies with and without infections. Parasitized gobies were, however, significantly smaller in body mass at a given age, reflecting slower overall growth. Effects of P. tortugensis on individual hosts were broadly similar to those of other parasitic copepods that infect fish gills and, for unknown reasons, the BVI appears to be a persistent hotspot of infections on these goby hosts.

Fig. 3 in Decadal status of Acanthaster planci (Linnaeus, 1758) along the coral reef habitat of Andaman and Nicobar Islands

Fig. 3 — Depth-wise occurrence of A. planci (CoTS) in Andaman and Nicobar Islands

Fig. 2 in Decadal status of Acanthaster planci (Linnaeus, 1758) along the coral reef habitat of Andaman and Nicobar Islands

Fig. 2 — Zone-wise occurrence map of A. planci (CoTS) in Andaman and Nicobar Islands

Fig. 1 in Decadal status of Acanthaster planci (Linnaeus, 1758) along the coral reef habitat of Andaman and Nicobar Islands

Fig. 1 — Occurrence of A. planci (CoTS) in Andaman and Nicobar Islands

Fig. 5 in Decadal status of Acanthaster planci (Linnaeus, 1758) along the coral reef habitat of Andaman and Nicobar Islands

Fig. 5 — Substrate specificity of A. planci (CoTS) in reef habitat of Andaman and Nicobar Islands

opencc-zeroJun 2024View details →

Data from: Challenging trophic position assessments in complex ecosystems: calculation method, choice of baseline, trophic enrichment factors, season and feeding guild do matter. A case study from Marquesas Islands coral reefs

Assessments of ecosystem functioning are a fundamental ecological challenge and an essential foundation for ecosystem-based management. An understanding of species trophic positions (TP) is essential to characterize food web architecture. However, despite the intuitive nature of the concept, empirically estimating TP is a challenging task due to the complexity of trophic interaction networks. Various alternative methods are proposed to assess TPs, including different approaches to account for the different sources of organic matter at the base of the food web (the "baseline"). However, it is often not clear which methodological approach and which baseline choices are the most reliable. Using an ecosystem-wide assessment of a tropical reef (Marquesas Islands, French Polynesia, with available data for 70 coral reef invertebrate and fish species), we tested whether different commonly used TP estimation methods yield similar results and, if not, whether it is possible to identify the most reliable method. We found significant differences in TP estimates of up to 1.7 TP for the same species, depending on the method and the baseline used. When using bulk stable isotope data, the choice of the baseline significantly impacted TP values. Indeed, while δ15N values of macroalgae led to consistent TP estimates, those using phytoplankton generated unrealistically low TP estimates. The use of a conventional enrichment factor (i.e. 3.4 ‰) or a "variable" enrichment factor (i.e. according to feeding guilds) also produced clear discrepancies between TP estimates. Regarding the use of different calculation methods, TPs obtained with δ15N values of source amino acids (compound specifics isotope analysis) were close to those assessed with macroalgae, but evidenced the opposite seasonal pattern, with significantly lower TPs in winter than in summer for the majority of assessed species, with particularly pronounced differences for lower TP species. We use the observed differences to discuss possible drivers of the diverging TP estimates and the potential ecological implications.

opencc-by-4.0Dec 2018View details →

Figure 2 in Are mangroves important for reef fish on Mayotte Island (Indian Ocean)?

Figure 2. – Relative abundance of adults and juveniles of fishes in different mangrove habitats.

opencc-by-4.0Dec 2016View details →

Figure 1 in Marine benthic diatoms in the coral reefs of Reunion and Rodrigues Islands, West Indian Ocean

Figure 1. Map showing location of Reunion and Rodrigues Islands, Indian Ocean and sampling sites.

opencc-zeroOct 2022View details →

The oceanographic isolation of the Ogasawara Islands and genetic divergence in a reef-building coral

Aim: Due to their spatial isolation, oceanic islands are natural systems to study evolutionary divergence. The Ogasawara Islands belong to the most isolated archipelagos on Earth and are well-known for their high terrestrial endemicity, however, less is known about the marine realm. Here, we analyze the degree of oceanographic isolation of the archipelago based on genetic data of a reef-building coral and a biophysical dispersal model. Location: North-Western Pacific (Ogasawara, Ryukyu, Daito Islands, Guam) Taxon: Galaxea fascicularis L. Method: Three to 15 specimens were sampled at several sites in Ogasawara and its closest potential migration sources in southern Japan and the Mariana Islands (Guam) and RAD-sequenced. 108 specimens from the common Pacific lineages 'L' (Ryukyu- and Daito Islands, Guam) and 'Ogasawara' (Ogasawara) were analyzed with population genetics and demographic modeling. Oceanographic dispersal was investigated by inverse particle tracking using a Lagrangian particle advection simulation based on ROMS and applying biological dispersal parameters of G. fascicularis. Results: The G. fascicularis population in Ogasawara is genetically highly differentiated from the next closest reefs in the region and has diverged from the Ryukyu Islands under very little, asymmetric, eastward migration. Inverse particle tracking confirmed the oceanographic isolation of Ogasawara and showed that the islands are rarely but most likely reached by settlers from the Ryukyu Islands by long-distance-dispersal of exceptionally long-lived larvae (>44 days), with no dispersal vice versa. Main conclusions: Ogasawara is a dispersal sink location and the high degree of genetic differentiation in Galaxea has resulted from strong oceanographic isolation. This research highlights how oceanographic features impact species-level genetic differentiation even in well-dispersed taxa such as broadcast-spawning corals, and they are likely even more pronounced in less vagile organisms. These findings suggest the Ogasawaran Archipelago should be considered an important priority for marine conservation, alongside its high importance for terrestrial conservation.

opencc-zeroMar 2023View details →

Mixed-species groups of herbivorous reef fish show variable responses to ecosystem perturbations in the Lakshadweep Islands, India

This dataset contains data on mixed-species groups of herbivorous reef fish and local species composition in the Lakshadweep Islands, India. Herbivorous reef fish provide a vital function in reef ecosystems by removing algae and making space available to coral recruits. The high abundance of herbivores in the reefs of the Lakshadweep islands has potentially aided in reef recovery and helped avoid a phase shift to an algal-dominated system, despite most areas having suffered massive coral losses. Mixed-species grouping in herbivores could potentially benefit both the participant species and the reef ecosystem by improving foraging efficiency. We examined the grouping propensity and species richness for three types of herbivore groups after a mass-bleaching event in 2010 and a mass recruitment event in 2015. The species richness and number of parrotfish groups, as well as the grouping propensity of common species, declined starkly across years, indicating that these groups may have formed in response to the mass-bleaching event, slowly diminishing as the reefs recovered. Conversely, large surgeonfish, which varied in richness and propensity across islands and aspect, are likely influenced by local processes. Small surgeonfish only increased in species richness and number in 2015, which may have been in response to the recruitment event. Thus, herbivorous fish may respond differently to local ecosystem perturbations and play different roles in reef recovery.

publicApr 2024View details →

Symbiodiniaceae ITS2 sequences from reef corals in St. John, U.S. Virgin Islands

Open the record for dataset details and reuse information.

publicJun 2024View details →

Data from: Challenging trophic position assessments in complex ecosystems: calculation method, choice of baseline, trophic enrichment factors, season and feeding guild do matter. A case study from Marquesas Islands coral reefs

Open the record for dataset details and reuse information.

publicDec 2022View details →

Echolocation clicks and anthropogenic detections with neural network labels in Hawaiian Island HARP data from Kona, Kaua`i, and Pearl and Hermes Reef

Open the record for dataset details and reuse information.

publicMar 2023View details →

Mixed-species groups of herbivorous reef fish show variable responses to ecosystem perturbations in the Lakshadweep Islands, India

Open the record for dataset details and reuse information.

publicNov 2022View details →

The oceanographic isolation of the Ogasawara Islands and genetic divergence in a reef-building coral

Open the record for dataset details and reuse information.