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24 results for “coral reef biodiversity”
MCR LTER: Coral Reef: 3D photogrammetry improves measurement of growth and biodiversity patterns in branching corals; data for Curtis 2023, Coral Reefs
These data and code were generated in support of the manuscript: Curtis JS, Galvan JW, Primo A, Osenberg CW, and AC Stier, Coral Reefs. We collected manual and photogrammetry-based measurements of coral size and volume to examine which method best described short-term coral growth and links between coral habitat and biodiversity of CAFI (coral-associated fishes and invertebrates). This study was completed between August and December 2019 on an experimental array located in the back reef off the south shore of Moorea, French Polynesia. These data were published in Coral Reefs, analyses and full methods descriptions of this model can be found in the manuscript “3D photogrammetry improves measurement of growth and biodiversity patterns in branching corals”. This manuscript uses data collected by the U.S. National Science Foundation's (NSF) Moorea Coral Reef Long Term Ecological Research (MCR LTER) site under Grant No. OCE 2224354 (and earlier awards). Additional financial support to the MCR LTER site was provided through a generous gift from the Gordon and Betty Moore Foundation. Research was completed under permits issued by the French Polynesian Government (Délégation à la Recherche) and the Haut-commissariat de la République en Polynésie Francaise (DTRT) (Protocole d'Accueil 2005-2023).
MCR LTER: Coral Reef: Biodiversity has a positive but saturating effect on imperiled coral reefs; data for Clements and Hay 2021, Science Advances
Species loss threatens ecosystems worldwide, but the ecological processes and thresholds that underpin positive biodiversity effects among critically important foundation species, such as corals on tropical reefs, remain inadequately understood. In field experiments, we manipulated coral species richness and intraspecific density to test whether, and how, biodiversity affects coral productivity and survival. Corals performed better in mixed species assemblages. Improved performance was unexplained by competition theory alone, suggesting that positive effects exceeded agonistic interactions during our experiments. Peak coral performance occurred at intermediate species richness and declined thereafter. Positive effects of coral diversity suggest that species’ losses on degraded reefs make recovery more difficult and further decline more likely. Harnessing these positive interactions may improve ecosystem conservation and restoration in a changing ocean. This material is based upon work supported by the U.S. National Science Foundation under Grant No. OCE 16-37396 (and earlier awards) as well as a generous gift from the Gordon and Betty Moore Foundation. Research was completed under permits issued by the French Polynesian Government (Délégation à la Recherche) and the Haut-commissariat de la République en Polynésie Francaise (DTRT) (Protocole d'Accueil 2005-2022). This work represents a contribution of the Moorea Coral Reef (MCR) LTER Site. Datasets used in this study are available online from the BCO-DMO data system. Data for this paper can be found at (https://www.bco-dmo.org/project/837802).
Hierarchical drivers of cryptic biodiversity on coral reefs
<p>Declines in habitat structural complexity have marked ecological outcomes, as currently observed in many of the world's ecosystems. Coral reefs have provided a model for such changes in marine ecosystems, but our understanding has been centred on corals and fishes at broad spatial scales when metazoan diversity on coral reefs is dominated by small cryptic taxa (herein: 'cryptofauna'). Given the paucity of studies and high taxonomic complexity of the cryptofauna, both of which limit a priori hypotheses, we asked whether hierarchical structuring theory provides a compelling framework to impose order and quantify pattern. In general terms, we explored whether cryptic communities are sufficiently described by broad seascape parameters or limited by a set of processes operating at their distinctly nested microhabitat scale. To address this theory and gaps in knowledge for the cryptofauna, we characterised community structure in coral rubble, an eroded coral condition where biodiversity proliferates. Rubble was sampled along a depth and exposure gradient at Heron Island on the Great Barrier Reef, Australia, to parameterise environmental and morphological indicators of sessile taxa and motile cryptofauna communities. We employed a hierarchical study framework from microhabitat to seascape scales, which were evaluated using non-structured multivariate analyses and Bayesian structural equation modelling. While the non-structured analyses showed the effects of seascape on the cryptobenthos and its community, this approach overlooked the finer hierarchical patterns in rubble ecology revealed only in the structured model. Seascape parameters (exposure and depth) influenced microhabitat complexity (i.e., rubble branchiness), which determined the cover of sessile organisms on rubble pieces, which shaped the motile cryptofauna community. Rubble is likely to be increasingly prevalent on coral reefs in the Anthropocene and is typically associated with low seascape-level complexity and reduced macrofaunal richness. Parallel with hierarchical structuring theory, we show a similar response operating at the microhabitat scale whereby low rubble complexity (i.e., branchiness) reduces cryptobenthic structure, diversity and size spectra. We expect there may be an initial increase in biodiversity and trophodynamic processes derived from branching rubble, but a delay in ecosystem-scale outcomes if coral, and thus rubble, generation and complexity cannot be sustained in a future ocean.</p>
Hierarchical drivers of cryptic biodiversity on coral reefs
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Data from: The importance of standardization for biodiversity comparisons: a case study using Autonomous Reef Monitoring Structures (ARMS) and metabarcoding to measure cryptic diversity on Mo'orea coral reefs, French Polynesia
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Data from: Influence of the geography of speciation on current patterns of coral reef fish biodiversity across the Indo-Pacific
The role of speciation processes in shaping current biodiversity patterns represents a major scientific question for ecologists and biogeographers. Hence, numerous methods have been developed to determine the geography of speciation based on co-occurrence between sister-species. Most of these methods rely on the correlation between divergence time and several metrics based on the geographic ranges of sister-taxa (i.e. overlap, asymmetry). The relationship between divergence time and these metrics has scarcely been examined in a spatial context beyond regression curves. Mapping this relationship across spatial grids, however, may unravel how speciation processes have shaped current biodiversity patterns through space and time. This can be particularly relevant for coral reef fishes of the Indo-Pacific since the origin of the exceptional concentration of biodiversity in the Indo-Australian Archipelago (IAA) has been actively debated, with several alternative hypotheses involving species diversification and dispersal. We reconstructed the phylogenetic relationships between three species-rich families of coral reef fish (Chaetodontidae, Labridae, Pomacentridae) and calculated co-occurrence metrics between closely related lineages of those families. We demonstrated that repeated biogeographic processes can be identified in present-day species distribution by projecting co-occurrence metrics between related lineages in a geographical context. Our study also evidence that sister-species do not co-occur randomly across the Indo-Pacific, but tend to overlap their range within the IAA. We identified the imprint of two important biogeographic processes that caused this pattern in 48% of the sister-taxa considered: speciation events within the IAA and repeated divergence between the Indian and Pacific Ocean, with subsequent secondary contact in the IAA.
Data from: Coral reefs as drivers of cladogenesis: expanding coral reefs, cryptic extinction events, and the development of biodiversity hotspots
Diversification rates within four conspicuous coral reef fish families (Labridae, Chaetodontidae, Pomacentridae, Apogonidae) were estimated using Bayesian inference. Lineage through time plots revealed a possible late Eocene/early Oligocene cryptic extinction event coinciding with the collapse of the ancestral Tethyan/Arabian hotspot. Rates of diversification analysis revealed elevated cladogenesis in all families in the Oligocene/Miocene. Throughout the Miocene, lineages with a high percentage of coral reef associated taxa display significantly higher net diversification rates than expected. The development of a complex mosaic of reef habitats in the Indo-Australian Archipelago (IAA) during the Oligocene/Miocene appears to have been a significant driver of cladogenesis. Patterns of diversification suggest that coral reefs acted as a refuge from high extinction, as reef taxa are able to sustain diversification at high extinction rates. The IAA appears to support both cladogenesis and survival in associated lineages, laying the foundation for the Recent IAA marine biodiversity hotspot.
FIGURE 1 in An annotated list of fish parasites (Copepoda, Monogenea, Digenea, Cestoda and Nematoda) collected from Emperors and Emperor Bream (Lethrinidae) in New Caledonia further highlights parasite biodiversity estimates on coral reef fish
FIGURE 1. Species of Hatschekia collected from lethrinid hosts, all drawn to same scale. A. Hatschekia gracilis Yamaguti, 1954; B. Hatschekia new species 12; C. Hatschekia cf. elegans Kabata, 1991; D. Hatschekia new species 16; E. Hatschekia new species 13; F. Hatschekia new species 14, G. Hatschekia new species 15.
Host-level biodiversity shapes the dynamics and networks within the coral reef microbiome
<p>This is the repository associated with the manuscript <strong>Host-level biodiversity shapes the dynamics and networks within the coral reef microbiome</strong>. It contains all data files used for figures presented in the manuscript. The code to reproduce the files can be found on <a href="https://github.com/SushiLab/coralmicrobiome-hostbiodiversity)">GitHub</a>.</p> <p> </p> <h2>Files</h2> <p><br><code>raw_host-associated_1.asvs.tsv --> ASV table, host-associated samples</code><br><code>raw_host-associated_2.asvs.tsv --> ASV table, host-associated samples</code><br><code>raw_free-living_1.asvs.tsv --> ASV table, Sterivex samples</code><br><code>raw_free-living_2.asvs.tsv --> ASV table, Sterivex samples</code><br><code>metadata_host-associated.csv --> metadata, host-associated samples</code><br><code>metadata_free-living.csv --> ASV table, Sterivex samples</code><br><code>asv_dat_taxinfo.tsv --> taxonomy annotated using SILVA v138.1</code><br><code>asv_bctab.tsv --> square-root transformed Bray-Curtis dissimilarities </code><br><code>asv_richtab.tsv --> Hill number diversity indices</code><br><code>asv_shared.tsv --> number of shared ASVs</code><br><code>pathway_list_cat.csv --> KEGG pathway list with hand-annotated categories</code><br><code>KEGG_path_to_ko.tsv --> KEGG file mapping pathways to KOs</code></p> <p> </p>
Figure 3 in Coral reef tanaidacean assemblages along the SW and SE Gulf of Mexico: biodiversity, geographic distribution and community structure
Figure 3. Dendrograms of each sampling site and grouping of sampling sites with spatial analysis of non-metric multidimensional scaling (MDS) obtained with a dissimilarity matrix using Bray–Curtis indices. Area Natural Protegida Tuxpan–Lobos (ANPT–L), Parque Nacional Sistema Arrecifal Veracruzano (PNSAV) and Sistema Arrecifal Bajos Sisal (SABS).
Figure 1 in Coral reef tanaidacean assemblages along the SW and SE Gulf of Mexico: biodiversity, geographic distribution and community structure
Figure 1. Location of reef systems in the Gulf of Mexico. Area Natural Protegida Tuxpan–Lobos (ANPT–L), Parque Nacional Sistema Arrecifal Veracruzano (PNSAV) and Sistema Arrecifal Bajos Sisal (SABS).
Figure 3 in Depth structuring of pelagic copepod biodiversity in waters adjacent to an Eastern Indian Ocean coral reef
Figure 3. Percentage composition of the zooplankton community at LA, contrasted with that in the five depth strata sampled at CH, NE and SW. The data are pooled over all Locations and Cruises. Note that there is an order of magnitude difference in abundance from the mixed layer (<100 m) to the 300–400 m stratum (Table 1).
Figure 2 in Depth structuring of pelagic copepod biodiversity in waters adjacent to an Eastern Indian Ocean coral reef
Figure 2. Representative vertical profiles of temperature, salinity, density and chlorophyll fluorescence at SW on each of the four cruises.
Figure 5 in Depth structuring of pelagic copepod biodiversity in waters adjacent to an Eastern Indian Ocean coral reef
Figure 5. Redundancy analysis displaying relationships between zooplankton samples, locations and depths.
Figure 1 in Depth structuring of pelagic copepod biodiversity in waters adjacent to an Eastern Indian Ocean coral reef
Figure 1. Scott Reef, eastern Indian Ocean, with the location of the four stations sampled: LA, CH, NE and SW.
Matrix aggregation of species of Phyla Annelida (Polychaeta), Mollusca, Arthropoda (Decapoda, Stomatopoda, Amphipoda, and Chelicerata), and Echinodermata registered of the Caribbean Sea and Gulf of Mexico region by Ocean Biodiversity Information Systems of the research "Evaluation of the use of Autonomous Reef Monitoring Structures (ARMS) for capturing the biological diversity of two coral reefs in the Yucatán Península, México"
<p>This database consists of an aggregation matrix of species from Ocean Biodiversity Information Systems using as geographic filters the Caribbean Sea region (ID 34287) and the Gulf of Mexico region (ID 34287) nomenclature and hierarchical classification of each Phyla from World Register of Marine Species used for the calculation of average taxonomic distinction of species belonging to the Phyla Annelida (Polychaeta), Mollusca, Arthropoda (Decapoda, Stomatopoda, Amphipoda, and Chelicerata), and Echinodermata associated to Autonomous Reefs Monitoring Structures from the research “Evaluation of the use of Autonomous Reef Monitoring Structures (ARMS) to estimate cryptic diversity in two coral reefs of the Yucatan Península, México”</p> <p><strong>*Corresponding autor: </strong>edlinguerra@gmail.com</p> <p>BIS Ocean Biodiversity Information System. Available online: <a href="http://www.iobis.org/">www.iobis.org</a>.</p> <p>Horton, T.; Gofas, S.; Kroh, A.; Poore, G.C.B.; Read, G.; Rosenberg, G.; Stöhr, S.; Bailly, N.; Boury-Esnault, N.; Brandão, S.N.; et al. Improving nomenclatural consistency: A decade of experience in the World Register of Marine Species. <em>Eur. J. Taxon.</em> <strong>2017</strong>, <em>2017</em>, doi:10.5852/ejt.2017.389.</p> <p><span lang="EN-US">was produced in collaboration with the Biodiversidad Marina de Yucatán project. </span><a href="https://www.bdmy.org.mx/carteles-publicaciones/" target="_blank" rel="noopener">https://www.bdmy.org.mx/,</a> Universidad Nacional Autonoma de México and Escuela Nacional de Estudios Superiores</p>
Data from: Digging for DNA at depth: rapid universal metabarcoding surveys (RUMS) as a tool to detect coral reef biodiversity across a depth gradient
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Data from: Influence of the geography of speciation on current patterns of coral reef fish biodiversity across the Indo-Pacific
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Data from: Coral reefs as drivers of cladogenesis: expanding coral reefs, cryptic extinction events, and the development of biodiversity hotspots
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Data from: The DNA of coral reef biodiversity: predicting and protecting genetic diversity of reef assemblages
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