Eugenia Sampayo - Academia.edu (original) (raw)

Papers by Eugenia Sampayo

Research paper thumbnail of Coral Spawning Database

The discovery of multi-species synchronous spawning of scleractinian corals on the Great Barrier ... more The discovery of multi-species synchronous spawning of scleractinian corals on the Great Barrier Reef in the 1980s stimulated an extraordinary effort to document spawning times in other parts of the globe. Unfortunately, most of these data remain unpublished which limits our understanding of regional and global reproductive patterns. The Coral Spawning Database (CSD) collates much of these disparate data into a single place. The CSD includes 6178 observations (3085 of which were unpublished) of the time or day of spawning for over 300 scleractinian species in 61 genera from 101 sites in the Indo-Pacific. The goal of the CSD is to provide open access to coral spawning data to accelerate our understanding of coral reproductive biology and to provide a baseline against which to evaluate any future changes in reproductive phenology.<br>

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Research paper thumbnail of Data from: Blind to morphology: genetics identifies several widespread ecologically common species and few endemics among Indo-Pacific cauliflower corals (Pocillopora, Scleractinia)

AIM: Using high-resolution genetic markers on samples gathered from across their wide distributio... more AIM: Using high-resolution genetic markers on samples gathered from across their wide distributional range, we endeavoured to delimit species diversity in reef-building Pocillopora corals. They are common, ecologically important, and widespread throughout the Indo-Pacific, but their phenotypic plasticity in response to environmental conditions and their nearly featureless microskeletal structures confound taxonomic assignments and limit an understanding of their ecology and evolution. LOCATION: Indo-Pacific, Red Sea, Arabian/Persian Gulf. METHODS: Sequence analysis of nuclear ribosomal (internal transcribed spacer 2, ITS2) and mitochondrial (open reading frame) loci were combined with population genetic data (seven microsatellite loci) for Pocillopora samples collected throughout the Indo-Pacific, Red Sea and Arabian Gulf, in order to assess the evolutionary divergence, reproductive isolation, frequency of hybridization and geographical distributions of the genus. RESULTS: Between five and eight genetically distinct lineages were identified that appear comparable to species with minimal or no hybridization. Colony morphology was generally incongruent with genetics across the full range of sampling, and the total number of species is apparently consistent with lower estimates from competing morphologically based hypotheses (c. seven or eight taxa). The most commonly occurring genetic lineages were widely distributed and exhibited high dispersal and gene flow, factors that have probably minimized allopatric speciation. Uniquely among scleractinian genera, this genus contains a monophyletic group of broadcast spawners that evolved recently from an ancestral brooder. MAIN CONCLUSIONS: The delineation of species diversity guided by genetics fundamentally advances our understanding of Pocillopora geographical distributions, ecology and evolution. Because traditional diagnostic features of colony and branch morphology are proving to be of limited utility, the identification of Pocillopora species for future ecological and experimental work should rely on genetic characters that will improve research and aid in conservation strategies for these and other reef-building corals, including the detection of real and mistaken endemic populations

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Research paper thumbnail of A genetic view of Indo-Pacific Pocillopora

Sample list including locations, ORF and ITS2 designations, microsatellite allelic data, and stru... more Sample list including locations, ORF and ITS2 designations, microsatellite allelic data, and structure input file

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Research paper thumbnail of Additional file 5 of Coral microbiome composition along the northern Red Sea suggests high plasticity of bacterial and specificity of endosymbiotic dinoflagellate communities

Additional file 5. Normalization and-beta-diversity.

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Research paper thumbnail of Additional file 6 of Coral microbiome composition along the northern Red Sea suggests high plasticity of bacterial and specificity of endosymbiotic dinoflagellate communities

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Research paper thumbnail of Additional file 4 of Coral microbiome composition along the northern Red Sea suggests high plasticity of bacterial and specificity of endosymbiotic dinoflagellate communities

Additional file 4. Core microbiome.

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Research paper thumbnail of Additional file 3 of Coral microbiome composition along the northern Red Sea suggests high plasticity of bacterial and specificity of endosymbiotic dinoflagellate communities

Additional file 3. Bacterial OTU table.

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Research paper thumbnail of Additional file 1 of Coral microbiome composition along the northern Red Sea suggests high plasticity of bacterial and specificity of endosymbiotic dinoflagellate communities

Additional file 1. Novel ITS2 Sequances.

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Research paper thumbnail of Reef Corals Reveals Both Site- and Species-Specificity of Common Bacterial Associates

All in-text references underlined in blue are linked to publications on ResearchGate, letting you... more All in-text references underlined in blue are linked to publications on ResearchGate, letting you access and read them immediately.

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Research paper thumbnail of Local endemicity and high diversity characterise high-latitude coral–Symbiodinium partnerships

Coral Reefs, 2010

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Research paper thumbnail of Additional file 2 of Coral microbiome composition along the northern Red Sea suggests high plasticity of bacterial and specificity of endosymbiotic dinoflagellate communities

Additional file 2: Supplementary methods, figures and tables.

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Research paper thumbnail of Symbiodinium diversity on the Great Barrier Reef

Many reef invertebrates live in an obligate symbiotic relationship with dinoflagellate protists (... more Many reef invertebrates live in an obligate symbiotic relationship with dinoflagellate protists (genus Symbiodinium), also referred to as ‘zooxanthellae’. The symbiotic dinoflagellates reside within the endodermal layers of their host and provide an important proportion of their daily energy requirement (Muscatine 1990). The range of hosts that harbour Symbiodinium includes reef building corals, anemones, soft corals, gorgonians, sponges, clams, hydroids, and even other protists such as foraminiferans and ciliates (e.g. LaJeunesse et al. 2003; Pochon et al. 2006; van Oppen et al. 2001). Certain environmental conditions, such as increased sea surface temperature, increased irradiance or salinity changes, disrupt the finely balanced symbiosis whereupon the dinoflagellate symbionts are lost from the host tissue (e.g. Egana and Di Salvo 1982; Lesser et al. 1990; Glynn and D’Croz 1990). Sea surface temperature anomalies have been indicated as the predominant factor causing the loss of sy...

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Research paper thumbnail of Diversity and ecology of Symbiodinium in pocilloporid corals

The decline of coral reefs is well documented, yet a detailed understanding of the processes invo... more The decline of coral reefs is well documented, yet a detailed understanding of the processes involved in the establishment, persistence, and ecology of the coral-dinoflagellate associations still remains largely unknown. The advent of molecular techniques has resulted in significant advances in understanding the molecular diversity present of symbiotic dinoflagellates from the genus Symbiodinium, but information concerning the functional, ecological, and biogeographical significance of this expanding symbiont diversity remains limited. This thesis therefore used molecular methodologies to uncover Symbiodinium diversity in Stylophora pistillata, Pocillopora damicornis, and Seriatopora hystrix at ecological scales, in response to thermal stress, and to long-term environmental shifts. In addition, all the molecular methods currently used in Symbiodinium research are critically reviewed to provide an important baseline for future studies. The application of ITS2-DGGE coupled with the in...

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Research paper thumbnail of Macro‐ and micro‐scale adaptations allow distinct Stylophora pistillata‐symbiodiniaceae holobionts to optimize performance across a broad light habitat

Journal of Phycology

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Research paper thumbnail of An Indo-Pacific coral spawning database

Scientific Data

The discovery of multi-species synchronous spawning of scleractinian corals on the Great Barrier ... more The discovery of multi-species synchronous spawning of scleractinian corals on the Great Barrier Reef in the 1980s stimulated an extraordinary effort to document spawning times in other parts of the globe. Unfortunately, most of these data remain unpublished which limits our understanding of regional and global reproductive patterns. The Coral Spawning Database (CSD) collates much of these disparate data into a single place. The CSD includes 6178 observations (3085 of which were unpublished) of the time or day of spawning for over 300 scleractinian species in 61 genera from 101 sites in the Indo-Pacific. The goal of the CSD is to provide open access to coral spawning data to accelerate our understanding of coral reproductive biology and to provide a baseline against which to evaluate any future changes in reproductive phenology.

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Research paper thumbnail of Mutualistic microalgae co-diversify with reef corals that acquire symbionts during egg development

The ISME Journal

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Research paper thumbnail of Successive marine heatwaves cause disproportionate coral bleaching during a fast phase transition from El Niño to La Niña

Science of The Total Environment

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Research paper thumbnail of Monitoring of Coral Reefs Using Artificial Intelligence: A Feasible and Cost-Effective Approach

Remote Sensing

Ecosystem monitoring is central to effective management, where rapid reporting is essential to pr... more Ecosystem monitoring is central to effective management, where rapid reporting is essential to provide timely advice. While digital imagery has greatly improved the speed of underwater data collection for monitoring benthic communities, image analysis remains a bottleneck in reporting observations. In recent years, a rapid evolution of artificial intelligence in image recognition has been evident in its broad applications in modern society, offering new opportunities for increasing the capabilities of coral reef monitoring. Here, we evaluated the performance of Deep Learning Convolutional Neural Networks for automated image analysis, using a global coral reef monitoring dataset. The study demonstrates the advantages of automated image analysis for coral reef monitoring in terms of error and repeatability of benthic abundance estimations, as well as cost and benefit. We found unbiased and high agreement between expert and automated observations (97%). Repeated surveys and comparisons...

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Research paper thumbnail of Coral microbiome composition along the northern Red Sea suggests high plasticity of bacterial and specificity of endosymbiotic dinoflagellate communities

Microbiome

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Research paper thumbnail of Refugia under threat: Mass bleaching of coral assemblages in high‐latitude eastern Australia

Global Change Biology

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Research paper thumbnail of Coral Spawning Database

The discovery of multi-species synchronous spawning of scleractinian corals on the Great Barrier ... more The discovery of multi-species synchronous spawning of scleractinian corals on the Great Barrier Reef in the 1980s stimulated an extraordinary effort to document spawning times in other parts of the globe. Unfortunately, most of these data remain unpublished which limits our understanding of regional and global reproductive patterns. The Coral Spawning Database (CSD) collates much of these disparate data into a single place. The CSD includes 6178 observations (3085 of which were unpublished) of the time or day of spawning for over 300 scleractinian species in 61 genera from 101 sites in the Indo-Pacific. The goal of the CSD is to provide open access to coral spawning data to accelerate our understanding of coral reproductive biology and to provide a baseline against which to evaluate any future changes in reproductive phenology.<br>

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Research paper thumbnail of Data from: Blind to morphology: genetics identifies several widespread ecologically common species and few endemics among Indo-Pacific cauliflower corals (Pocillopora, Scleractinia)

AIM: Using high-resolution genetic markers on samples gathered from across their wide distributio... more AIM: Using high-resolution genetic markers on samples gathered from across their wide distributional range, we endeavoured to delimit species diversity in reef-building Pocillopora corals. They are common, ecologically important, and widespread throughout the Indo-Pacific, but their phenotypic plasticity in response to environmental conditions and their nearly featureless microskeletal structures confound taxonomic assignments and limit an understanding of their ecology and evolution. LOCATION: Indo-Pacific, Red Sea, Arabian/Persian Gulf. METHODS: Sequence analysis of nuclear ribosomal (internal transcribed spacer 2, ITS2) and mitochondrial (open reading frame) loci were combined with population genetic data (seven microsatellite loci) for Pocillopora samples collected throughout the Indo-Pacific, Red Sea and Arabian Gulf, in order to assess the evolutionary divergence, reproductive isolation, frequency of hybridization and geographical distributions of the genus. RESULTS: Between five and eight genetically distinct lineages were identified that appear comparable to species with minimal or no hybridization. Colony morphology was generally incongruent with genetics across the full range of sampling, and the total number of species is apparently consistent with lower estimates from competing morphologically based hypotheses (c. seven or eight taxa). The most commonly occurring genetic lineages were widely distributed and exhibited high dispersal and gene flow, factors that have probably minimized allopatric speciation. Uniquely among scleractinian genera, this genus contains a monophyletic group of broadcast spawners that evolved recently from an ancestral brooder. MAIN CONCLUSIONS: The delineation of species diversity guided by genetics fundamentally advances our understanding of Pocillopora geographical distributions, ecology and evolution. Because traditional diagnostic features of colony and branch morphology are proving to be of limited utility, the identification of Pocillopora species for future ecological and experimental work should rely on genetic characters that will improve research and aid in conservation strategies for these and other reef-building corals, including the detection of real and mistaken endemic populations

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Research paper thumbnail of A genetic view of Indo-Pacific Pocillopora

Sample list including locations, ORF and ITS2 designations, microsatellite allelic data, and stru... more Sample list including locations, ORF and ITS2 designations, microsatellite allelic data, and structure input file

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Research paper thumbnail of Additional file 5 of Coral microbiome composition along the northern Red Sea suggests high plasticity of bacterial and specificity of endosymbiotic dinoflagellate communities

Additional file 5. Normalization and-beta-diversity.

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Research paper thumbnail of Additional file 6 of Coral microbiome composition along the northern Red Sea suggests high plasticity of bacterial and specificity of endosymbiotic dinoflagellate communities

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Research paper thumbnail of Additional file 4 of Coral microbiome composition along the northern Red Sea suggests high plasticity of bacterial and specificity of endosymbiotic dinoflagellate communities

Additional file 4. Core microbiome.

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Research paper thumbnail of Additional file 3 of Coral microbiome composition along the northern Red Sea suggests high plasticity of bacterial and specificity of endosymbiotic dinoflagellate communities

Additional file 3. Bacterial OTU table.

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Research paper thumbnail of Additional file 1 of Coral microbiome composition along the northern Red Sea suggests high plasticity of bacterial and specificity of endosymbiotic dinoflagellate communities

Additional file 1. Novel ITS2 Sequances.

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Research paper thumbnail of Reef Corals Reveals Both Site- and Species-Specificity of Common Bacterial Associates

All in-text references underlined in blue are linked to publications on ResearchGate, letting you... more All in-text references underlined in blue are linked to publications on ResearchGate, letting you access and read them immediately.

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Research paper thumbnail of Local endemicity and high diversity characterise high-latitude coral–Symbiodinium partnerships

Coral Reefs, 2010

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Research paper thumbnail of Additional file 2 of Coral microbiome composition along the northern Red Sea suggests high plasticity of bacterial and specificity of endosymbiotic dinoflagellate communities

Additional file 2: Supplementary methods, figures and tables.

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Research paper thumbnail of Symbiodinium diversity on the Great Barrier Reef

Many reef invertebrates live in an obligate symbiotic relationship with dinoflagellate protists (... more Many reef invertebrates live in an obligate symbiotic relationship with dinoflagellate protists (genus Symbiodinium), also referred to as ‘zooxanthellae’. The symbiotic dinoflagellates reside within the endodermal layers of their host and provide an important proportion of their daily energy requirement (Muscatine 1990). The range of hosts that harbour Symbiodinium includes reef building corals, anemones, soft corals, gorgonians, sponges, clams, hydroids, and even other protists such as foraminiferans and ciliates (e.g. LaJeunesse et al. 2003; Pochon et al. 2006; van Oppen et al. 2001). Certain environmental conditions, such as increased sea surface temperature, increased irradiance or salinity changes, disrupt the finely balanced symbiosis whereupon the dinoflagellate symbionts are lost from the host tissue (e.g. Egana and Di Salvo 1982; Lesser et al. 1990; Glynn and D’Croz 1990). Sea surface temperature anomalies have been indicated as the predominant factor causing the loss of sy...

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Research paper thumbnail of Diversity and ecology of Symbiodinium in pocilloporid corals

The decline of coral reefs is well documented, yet a detailed understanding of the processes invo... more The decline of coral reefs is well documented, yet a detailed understanding of the processes involved in the establishment, persistence, and ecology of the coral-dinoflagellate associations still remains largely unknown. The advent of molecular techniques has resulted in significant advances in understanding the molecular diversity present of symbiotic dinoflagellates from the genus Symbiodinium, but information concerning the functional, ecological, and biogeographical significance of this expanding symbiont diversity remains limited. This thesis therefore used molecular methodologies to uncover Symbiodinium diversity in Stylophora pistillata, Pocillopora damicornis, and Seriatopora hystrix at ecological scales, in response to thermal stress, and to long-term environmental shifts. In addition, all the molecular methods currently used in Symbiodinium research are critically reviewed to provide an important baseline for future studies. The application of ITS2-DGGE coupled with the in...

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Research paper thumbnail of Macro‐ and micro‐scale adaptations allow distinct Stylophora pistillata‐symbiodiniaceae holobionts to optimize performance across a broad light habitat

Journal of Phycology

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Research paper thumbnail of An Indo-Pacific coral spawning database

Scientific Data

The discovery of multi-species synchronous spawning of scleractinian corals on the Great Barrier ... more The discovery of multi-species synchronous spawning of scleractinian corals on the Great Barrier Reef in the 1980s stimulated an extraordinary effort to document spawning times in other parts of the globe. Unfortunately, most of these data remain unpublished which limits our understanding of regional and global reproductive patterns. The Coral Spawning Database (CSD) collates much of these disparate data into a single place. The CSD includes 6178 observations (3085 of which were unpublished) of the time or day of spawning for over 300 scleractinian species in 61 genera from 101 sites in the Indo-Pacific. The goal of the CSD is to provide open access to coral spawning data to accelerate our understanding of coral reproductive biology and to provide a baseline against which to evaluate any future changes in reproductive phenology.

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Research paper thumbnail of Mutualistic microalgae co-diversify with reef corals that acquire symbionts during egg development

The ISME Journal

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Research paper thumbnail of Successive marine heatwaves cause disproportionate coral bleaching during a fast phase transition from El Niño to La Niña

Science of The Total Environment

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Research paper thumbnail of Monitoring of Coral Reefs Using Artificial Intelligence: A Feasible and Cost-Effective Approach

Remote Sensing

Ecosystem monitoring is central to effective management, where rapid reporting is essential to pr... more Ecosystem monitoring is central to effective management, where rapid reporting is essential to provide timely advice. While digital imagery has greatly improved the speed of underwater data collection for monitoring benthic communities, image analysis remains a bottleneck in reporting observations. In recent years, a rapid evolution of artificial intelligence in image recognition has been evident in its broad applications in modern society, offering new opportunities for increasing the capabilities of coral reef monitoring. Here, we evaluated the performance of Deep Learning Convolutional Neural Networks for automated image analysis, using a global coral reef monitoring dataset. The study demonstrates the advantages of automated image analysis for coral reef monitoring in terms of error and repeatability of benthic abundance estimations, as well as cost and benefit. We found unbiased and high agreement between expert and automated observations (97%). Repeated surveys and comparisons...

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Research paper thumbnail of Coral microbiome composition along the northern Red Sea suggests high plasticity of bacterial and specificity of endosymbiotic dinoflagellate communities

Microbiome

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Research paper thumbnail of Refugia under threat: Mass bleaching of coral assemblages in high‐latitude eastern Australia

Global Change Biology

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