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1. MammalNet: A Large-scale Video Benchmark for Mammal Recognition and Behavior Understanding

Author

Chen, Jun, Hu, Ming, Coker, Darren J., Berumen, Michael L., Costelloe, Blair, Beery, Sara, Rohrbach, Anna, and Elhoseiny, Mohamed

Subjects
Computer Science - Computer Vision and Pattern Recognition
Abstract

Monitoring animal behavior can facilitate conservation efforts by providing key insights into wildlife health, population status, and ecosystem function. Automatic recognition of animals and their behaviors is critical for capitalizing on the large unlabeled datasets generated by modern video devices and for accelerating monitoring efforts at scale. However, the development of automated recognition systems is currently hindered by a lack of appropriately labeled datasets. Existing video datasets 1) do not classify animals according to established biological taxonomies; 2) are too small to facilitate large-scale behavioral studies and are often limited to a single species; and 3) do not feature temporally localized annotations and therefore do not facilitate localization of targeted behaviors within longer video sequences. Thus, we propose MammalNet, a new large-scale animal behavior dataset with taxonomy-guided annotations of mammals and their common behaviors. MammalNet contains over 18K videos totaling 539 hours, which is ~10 times larger than the largest existing animal behavior dataset. It covers 17 orders, 69 families, and 173 mammal categories for animal categorization and captures 12 high-level animal behaviors that received focus in previous animal behavior studies. We establish three benchmarks on MammalNet: standard animal and behavior recognition, compositional low-shot animal and behavior recognition, and behavior detection. Our dataset and code have been made available at: https://mammal-net.github.io., Comment: CVPR 2023 proceeding

Published
2023

3. Probiotics reshape the coral microbiome in situ without detectable off-target effects in the surrounding environment

Author

Delgadillo-Ordoñez, Nathalia, Garcias-Bonet, Neus, Raimundo, Inês, García, Francisca C., Villela, Helena, Osman, Eslam O., Santoro, Erika P., Curdia, Joao, Rosado, Joao G. D., Cardoso, Pedro, Alsaggaf, Ahmed, Barno, Adam, Antony, Chakkiath Paul, Bocanegra, Carolina, Berumen, Michael L., Voolstra, Christian R., Benzoni, Francesca, Carvalho, Susana, and Peixoto, Raquel S.

Published
2024
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5. Spatial Distribution Patterns of Clownfish in Recirculating Aquaculture Systems

Author

Aljehani, Fahad, N'Doye, Ibrahima, Justo, Micaela S., Majoris, John E., Berumen, Michael L., and Laleg-Kirati, Taous-Meriem

Subjects
Computer Science - Computer Vision and Pattern Recognition, Electrical Engineering and Systems Science - Systems and Control
Abstract

Successful aquaculture systems can reduce the pressure and help secure the most diverse and productive Red Sea coral reef ecosystem to maintain a healthy and functional ecosystem within a sustainable blue economy. Interestingly, recirculating aquaculture systems are currently emerging in fish farm production practices. On the other hand, monitoring and detecting fish behaviors provide essential information on fish welfare and contribute to an intelligent production in global aquaculture. This work proposes an efficient approach to analyze the spatial distribution status and motion patterns of juvenile clownfish \textit{(Amphiprion bicinctus)} maintained in aquaria at three stocking densities (1, 5, and 10 individuals/aquarium). The estimated displacement is crucial in assessing the dispersion and velocity to express the clownfish's spatial distribution and movement behavior in a recirculating aquaculture system. Indeed, we aim to compute the velocity, magnitude, and turning angle using an optical flow method to assist aquaculturists in efficiently monitoring and identifying fish behavior. We test the system design on a database containing two days of video streams of juvenile clownfish maintained in aquaria. The proposed displacement estimation reveals good performance in measuring clownfish's motion and dispersion characteristics leading to assessing the potential signs of stress behaviors. We demonstrate the effectiveness of the proposed technique for quantifying variation in clownfish activity levels between recordings taken in the morning and afternoon at different stocking densities. It provides practical baseline support for online predicting and monitoring feeding behavior in ornamental fish aquaculture., Comment: 14 pages, 15 figures

Published
2021

8. Fish Growth Trajectory Tracking via Reinforcement Learning in Precision Aquaculture

Author

Chahid, Abderrazak, N'Doye, Ibrahima, Majoris, John E., Berumen, Michael L., and Laleg-Kirati, Taous-Meriem

Subjects
Electrical Engineering and Systems Science - Systems and Control
Abstract

This paper studies the fish growth trajectory tracking via reinforcement learning under a representative bioenergetic growth model. Due to the complex aquaculture condition and uncertain environmental factors such as temperature, dissolved oxygen, un-ionized ammonia, and strong nonlinear couplings, including multi-inputs of the fish growth model, the growth trajectory tracking problem can not be efficiently solved by the model-based control approaches in precision aquaculture. To this purpose, we formulate the growth trajectory tracking problem as sampled-data optimal control using discrete state-action pairs Markov decision process. We propose two Q-learning algorithms that learn the optimal control policy from the sampled data of the fish growth trajectories at every stage of the fish life cycle from juveniles to the desired market weight in the aquaculture environment. The Q-learning scheme learns the optimal feeding control policy to fish growth rate cultured in cages and the optimal feeding rate control policy with an optimal temperature profile for the aquaculture fish growth rate in tanks. The simulation results demonstrate that both Q-learning strategies achieve high trajectory tracking performance with less amount feeding rates.

Published
2021

9. Model Predictive Control Paradigms for Fish Growth Reference Tracking in Precision Aquaculture

Author

Chahid, Abderrazak, N'Doye, Ibrahima, Majoris, John E., Berumen, Michael L., and Laleg-Kirati, Taous-Meriem

Subjects
Electrical Engineering and Systems Science - Systems and Control
Abstract

In precision aquaculture, the primary goal is to maximize biomass production while minimizing production costs. This objective can be achieved by optimizing factors that have a strong influence on fish growth, such as the feeding rate, temperature, and dissolved oxygen. This paper provides a comparative study of three model predictive control (MPC) strategies for fish growth reference tracking under a representative bioenergetic growth model in precision aquaculture. We propose to evaluate three candidate MPC formulations for fish growth reference tracking based on the receding horizon. The first MPC formulation tracks a desired fish growth trajectory while penalizing the feed ration, temperature, and dissolved oxygen. The second MPC optimization strategy directly penalizes the feed conversion ratio (FCR), which is the ratio between food quantity and fish weight gain while minimizing the actual growth state's deviation from the given reference growth trajectory. The third MPC formulation includes a tradeoff between the growth rate trajectory tracking, the dynamic energy and the cost of food. Numerical simulations that integrate a realistic bioenergetic fish growth model of Nile tilapia (Oreochromis niloticus) are illustrated to examine the comparative performance of the three proposed optimal control strategies.

Published
2021

10. Distinct patterns of hybridization across a suture zone in a coral reef fish (Dascyllus trimaculatus)

Author

Salas, Eva, Hobbs, Jean‐Paul A, Bernal, Moisés A, Simison, W Brian, Berumen, Michael L, Bernardi, Giacomo, and Rocha, Luiz A

Subjects
Biological Sciences, Ecology, Genetics, Life Below Water, Dascyllus trimaculatus, hybrid zones, Indo-Pacific, introgression, mitochondrial DNA, phylogeography, RADSeq, Indo‐Pacific, Evolutionary Biology, Evolutionary biology, Ecological applications
Abstract

Hybrid zones are natural laboratories for investigating the dynamics of gene flow, reproductive isolation, and speciation. A predominant marine hybrid (or suture) zone encompasses Christmas Island (CHR) and Cocos (Keeling) Islands (CKE), where 15 different instances of interbreeding between closely related species from Indian and Pacific Oceans have been documented. Here, we report a case of hybridization between genetically differentiated Pacific and Indian Ocean lineages of the three-spot dascyllus, Dascyllus trimaculatus (Rüppell, 1829). Field observations indicate there are subtle color differences between Pacific and Indian Ocean lineages. Most importantly, population densities of color morphs and genetic analyses (mitochondrial DNA and SNPs obtained via RADSeq) suggest that the pattern of hybridization within the suture zone is not homogeneous. At CHR, both color morphs were present, mitochondrial haplotypes of both lineages were observed, and SNP analyses revealed both pure and hybrid genotypes. Meanwhile, in CKE, the Indian Ocean color morphs were prevalent, only Indian Ocean mitochondrial haplotypes were observed, and SNP analysis showed hybrid individuals with a large proportion (~80%) of their genotypes assigning to the Indian Ocean lineage. We conclude that CHR populations are currently receiving an influx of individuals from both ocean basins, with a greater influence from the Pacific Ocean. In contrast, geographically isolated CKE populations appear to be self-recruiting and with more influx of individuals from the Indian Ocean. Our research highlights how patterns of hybridization can be different at scales of hundreds of kilometers, due to geographic isolation and the history of interbreeding between lineages.

Published
2020

11. Ice ages and butterflyfishes: Phylogenomics elucidates the ecological and evolutionary history of reef fishes in an endemism hotspot

Author

DiBattista, Joseph D, Alfaro, Michael E, Sorenson, Laurie, Choat, John H, Hobbs, Jean‐Paul A, Sinclair‐Taylor, Tane H, Rocha, Luiz A, Chang, Jonathan, Luiz, Osmar J, Cowman, Peter F, Friedman, Matt, and Berumen, Michael L

Subjects
Biological Sciences, Ecology, Environmental Management, Genetics, Evolutionary Biology, Environmental Sciences, Life Below Water, biogeographic barriers, Chaetodon, coral reef, glaciation events, Pleistocene, ultraconserved elements, Evolutionary biology, Ecological applications
Abstract

For tropical marine species, hotspots of endemism occur in peripheral areas furthest from the center of diversity, but the evolutionary processes that lead to their origin remain elusive. We test several hypotheses related to the evolution of peripheral endemics by sequencing ultraconserved element (UCE) loci to produce a genome-scale phylogeny of 47 butterflyfish species (family Chaetodontidae) that includes all shallow water butterflyfish from the coastal waters of the Arabian Peninsula (i.e., Red Sea to Arabian Gulf) and their close relatives. Bayesian tree building methods produced a well-resolved phylogeny that elucidated the origins of butterflyfishes in this hotspots of endemism. We show that UCEs, often used to resolve deep evolutionary relationships, represent an important tool to assess the mechanisms underlying recently diverged taxa. Our analyses indicate that unique environmental conditions in the coastal waters of the Arabian Peninsula probably contributed to the formation of endemic butterflyfishes. Older endemic species are also associated with narrow versus broad depth ranges, suggesting that adaptation to deeper coral reefs in this region occurred only recently (

Published
2018

15. Comparative population genetic structure of redbelly tilapia (Coptodon zillii (Gervais, 1848)) from three different aquatic habitats in Egypt

Author

Soliman, Taha, Aly, Walid, Fahim, Reda M, Berumen, Michael L, Jenke‐Kodama, Holger, and Bernardi, Giacomo

Subjects
Biological Sciences, Ecology, Environmental Management, Genetics, Environmental Sciences, Zero Hunger, Life Below Water, aquaculture introduction, genetic diversity, mtDNA, redbelly tilapia, saltwater adaptation, Evolutionary Biology, Evolutionary biology, Ecological applications
Abstract

Recently, tilapia have become increasingly important in aquaculture and fisheries worldwide. They are one of the major protein sources in many African countries and are helping to combat malnutrition. Therefore, maintenance and conservation genetics of wild populations of tilapia are of great significance. In this study, we report the population genetic structure and genetic diversity of the redbelly tilapia (Coptodon zillii) in three different Egyptian aquatic environments: brackish (Lake Idku), marine (Al-Max Bay), and freshwater (Lake Nasser). The habitat differences, environmental factors, and harvesting pressures are the main characteristics of the sampling sites. Three mitochondrial DNA markers (COI: cytochrome oxidase subunit I; the D-loop; CYTB: cytochrome b) were used to assess population structure differences among the three populations. The population at Lake Nasser presented the highest genetic diversity (Hd  = 0.8116, H = 6), and the marine population of Al-Max Bay the lowest (Hd  = 0.2391, H = 4) of the combined sequences. In addition, the phylogenetic haplotype network showed private haplotypes in each environmental habitat. Results presented here will be useful in aquaculture to introduce the appropriate broodstock for future aquaculture strategies of C. zillii. In addition, evidence of population structure may contribute to the management of tilapia fisheries in Egyptian waters.

Published
2017

18. Dietary partitioning among three cryptobenthic reef fish mesopredators revealed by visual analysis, metabarcoding of gut content, and stable isotope analysis

Author

Palacios‐Narváez, Stephania, primary, Coker, Darren J., additional, Aylagas, Eva, additional, Justo, Micaela S., additional, Nunes‐Peinemann, Viktor, additional, Tietbohl, Matthew D., additional, Bocanegra, Carolina, additional, Antony, Chakkiath Paul, additional, and Berumen, Michael L., additional

Published
2024
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24. Genomic diversification of giant enteric symbionts reflects host dietary lifestyles

Author

Ngugi, David Kamanda, Miyake, Sou, Cahill, Matt, Vinu, Manikandan, Hackmann, Timothy J, Blom, Jochen, Tietbohl, Matthew D, Berumen, Michael L, and Stingl, Ulrich

Subjects
Genetics, Nutrition, Human Genome, Digestive Diseases, Animals, Bacteria, Biomass, Diet, Ecology, Fishes, Genomics, Herbivory, Host-Pathogen Interactions, Life Style, Metagenomics, Microbiota, Phaeophyta, Phylogeny, Polysaccharides, Rhodophyta, Symbiosis, piscine herbivores, marine algae, carbohydrases, giant enteric symbionts, Epulopiscium
Abstract

Herbivorous surgeonfishes are an ecologically successful group of reef fish that rely on marine algae as their principal food source. Here, we elucidated the significance of giant enteric symbionts colonizing these fishes regarding their roles in the digestive processes of hosts feeding predominantly on polysiphonous red algae and brown Turbinaria algae, which contain different polysaccharide constituents. Using metagenomics, single-cell genomics, and metatranscriptomic analyses, we provide evidence of metabolic diversification of enteric microbiota involved in the degradation of algal biomass in these fishes. The enteric microbiota is also phylogenetically and functionally simple relative to the complex lignocellulose-degrading microbiota of terrestrial herbivores. Over 90% of the enzymes for deconstructing algal polysaccharides emanate from members of a single bacterial lineage, "Candidatus Epulopiscium" and related giant bacteria. These symbionts lack cellulases but encode a distinctive and lineage-specific array of mostly intracellular carbohydrases concurrent with the unique and tractable dietary resources of their hosts. Importantly, enzymes initiating the breakdown of the abundant and complex algal polysaccharides also originate from these symbionts. These are also highly transcribed and peak according to the diel lifestyle of their host, further supporting their importance and host-symbiont cospeciation. Because of their distinctive genomic blueprint, we propose the classification of these giant bacteria into three candidate genera. Collectively, our findings show that the acquisition of metabolically distinct "Epulopiscium" symbionts in hosts feeding on compositionally varied algal diets is a key niche-partitioning driver in the nutritional ecology of herbivorous surgeonfishes.

Published
2017

25. Reply to: Shark mortality cannot be assessed by fishery overlap alone

Author

Queiroz, Nuno, Humphries, Nicolas E., Couto, Ana, Vedor, Marisa, da Costa, Ivo, Sequeira, Ana M. M., Mucientes, Gonzalo, Santos, António M., Abascal, Francisco J., Abercrombie, Debra L., Abrantes, Katya, Acuña-Marrero, David, Afonso, André S., Afonso, Pedro, Anders, Darrell, Araujo, Gonzalo, Arauz, Randall, Bach, Pascal, Barnett, Adam, Bernal, Diego, Berumen, Michael L., Lion, Sandra Bessudo, Bezerra, Natalia P. A., Blaison, Antonin V., Block, Barbara A., Bond, Mark E., Bonfil, Ramon, Bradford, Russell W., Braun, Camrin D., Brooks, Edward J., Brooks, Annabelle, Brown, Judith, Bruce, Barry D., Byrne, Michael E., Campana, Steven E., Carlisle, Aaron B., Chapman, Demian D., Chapple, Taylor K., Chisholm, John, Clarke, Christopher R., Clua, Eric G., Cochran, Jesse E. M., Crochelet, Estelle C., Dagorn, Laurent, Daly, Ryan, Cortés, Daniel Devia, Doyle, Thomas K., Drew, Michael, Duffy, Clinton A. J., Erikson, Thor, Espinoza, Eduardo, Ferreira, Luciana C., Ferretti, Francesco, Filmalter, John D., Fischer, G. Chris, Fitzpatrick, Richard, Fontes, Jorge, Forget, Fabien, Fowler, Mark, Francis, Malcolm P., Gallagher, Austin J., Gennari, Enrico, Goldsworthy, Simon D., Gollock, Matthew J., Green, Jonathan R., Gustafson, Johan A., Guttridge, Tristan L., Guzman, Hector M., Hammerschlag, Neil, Harman, Luke, Hazin, Fábio H. V., Heard, Matthew, Hearn, Alex R., Holdsworth, John C., Holmes, Bonnie J., Howey, Lucy A., Hoyos, Mauricio, Hueter, Robert E., Hussey, Nigel E., Huveneers, Charlie, Irion, Dylan T., Jacoby, David M. P., Jewell, Oliver J. D., Johnson, Ryan, Jordan, Lance K. B., Joyce, Warren, Keating Daly, Clare A., Ketchum, James T., Klimley, A. Peter, Kock, Alison A., Koen, Pieter, Ladino, Felipe, Lana, Fernanda O., Lea, James S. E., Llewellyn, Fiona, Lyon, Warrick S., MacDonnell, Anna, Macena, Bruno C. L., Marshall, Heather, McAllister, Jaime D., Meÿer, Michael A., Morris, John J., Nelson, Emily R., Papastamatiou, Yannis P., Peñaherrera-Palma, Cesar, Pierce, Simon J., Poisson, Francois, Quintero, Lina Maria, Richardson, Andrew J., Rogers, Paul J., Rohner, Christoph A., Rowat, David R. L., Samoilys, Melita, Semmens, Jayson M., Sheaves, Marcus, Shillinger, George, Shivji, Mahmood, Singh, Sarika, Skomal, Gregory B., Smale, Malcolm J., Snyders, Laurenne B., Soler, German, Soria, Marc, Stehfest, Kilian M., Thorrold, Simon R., Tolotti, Mariana T., Towner, Alison, Travassos, Paulo, Tyminski, John P., Vandeperre, Frederic, Vaudo, Jeremy J., Watanabe, Yuuki Y., Weber, Sam B., Wetherbee, Bradley M., White, Timothy D., Williams, Sean, Zárate, Patricia M., Harcourt, Robert, Hays, Graeme C., Meekan, Mark G., Thums, Michele, Irigoien, Xabier, Eguiluz, Victor M., Duarte, Carlos M., Sousa, Lara L., Simpson, Samantha J., Southall, Emily J., and Sims, David W.

Published
2021
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26. Reply to: Caution over the use of ecological big data for conservation

Author

Queiroz, Nuno, Humphries, Nicolas E., Couto, Ana, Vedor, Marisa, da Costa, Ivo, Sequeira, Ana M. M., Mucientes, Gonzalo, Santos, António M., Abascal, Francisco J., Abercrombie, Debra L., Abrantes, Katya, Acuña-Marrero, David, Afonso, André S., Afonso, Pedro, Anders, Darrell, Araujo, Gonzalo, Arauz, Randall, Bach, Pascal, Barnett, Adam, Bernal, Diego, Berumen, Michael L., Lion, Sandra Bessudo, Bezerra, Natalia P. A., Blaison, Antonin V., Block, Barbara A., Bond, Mark E., Bonfil, Ramon, Braun, Camrin D., Brooks, Edward J., Brooks, Annabelle, Brown, Judith, Byrne, Michael E., Campana, Steven E., Carlisle, Aaron B., Chapman, Demian D., Chapple, Taylor K., Chisholm, John, Clarke, Christopher R., Clua, Eric G., Cochran, Jesse E. M., Crochelet, Estelle C., Dagorn, Laurent, Daly, Ryan, Cortés, Daniel Devia, Doyle, Thomas K., Drew, Michael, Duffy, Clinton A. J., Erikson, Thor, Espinoza, Eduardo, Ferreira, Luciana C., Ferretti, Francesco, Filmalter, John D., Fischer, G. Chris, Fitzpatrick, Richard, Fontes, Jorge, Forget, Fabien, Fowler, Mark, Francis, Malcolm P., Gallagher, Austin J., Gennari, Enrico, Goldsworthy, Simon D., Gollock, Matthew J., Green, Jonathan R., Gustafson, Johan A., Guttridge, Tristan L., Guzman, Hector M., Hammerschlag, Neil, Harman, Luke, Hazin, Fábio H. V., Heard, Matthew, Hearn, Alex R., Holdsworth, John C., Holmes, Bonnie J., Howey, Lucy A., Hoyos, Mauricio, Hueter, Robert E., Hussey, Nigel E., Huveneers, Charlie, Irion, Dylan T., Jacoby, David M. P., Jewell, Oliver J. D., Johnson, Ryan, Jordan, Lance K. B., Joyce, Warren, Keating Daly, Clare A., Ketchum, James T., Klimley, A. Peter, Kock, Alison A., Koen, Pieter, Ladino, Felipe, Lana, Fernanda O., Lea, James S. E., Llewellyn, Fiona, Lyon, Warrick S., MacDonnell, Anna, Macena, Bruno C. L., Marshall, Heather, McAllister, Jaime D., Meÿer, Michael A., Morris, John J., Nelson, Emily R., Papastamatiou, Yannis P., Peñaherrera-Palma, Cesar, Pierce, Simon J., Poisson, Francois, Quintero, Lina Maria, Richardson, Andrew J., Rogers, Paul J., Rohner, Christoph A., Rowat, David R. L., Samoilys, Melita, Semmens, Jayson M., Sheaves, Marcus, Shillinger, George, Shivji, Mahmood, Singh, Sarika, Skomal, Gregory B., Smale, Malcolm J., Snyders, Laurenne B., Soler, German, Soria, Marc, Stehfest, Kilian M., Thorrold, Simon R., Tolotti, Mariana T., Towner, Alison, Travassos, Paulo, Tyminski, John P., Vandeperre, Frederic, Vaudo, Jeremy J., Watanabe, Yuuki Y., Weber, Sam B., Wetherbee, Bradley M., White, Timothy D., Williams, Sean, Zárate, Patricia M., Harcourt, Robert, Hays, Graeme C., Meekan, Mark G., Thums, Michele, Irigoien, Xabier, Eguiluz, Victor M., Duarte, Carlos M., Sousa, Lara L., Simpson, Samantha J., Southall, Emily J., and Sims, David W.

Published
2021
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27. Dispersal patterns of sandfish (Holothuria scabra) larvae in Manus Province, Papua New Guinea.

Author

Waldie, Peter, Feary, David A., Bode, Michael, Matawai, Manuai, Harrison, Hugo B., Berumen, Michael L., Molai, Chris, Karo, Maunoa, and Hamilton, Richard J.

Subjects
LARVAL dispersal, SEA cucumbers, LARVAE, FISHERIES, GROUNDFISHES, COASTS
Abstract

In many tropical nations, coastal communities seek to manage their sea cucumber fisheries by establishing locally managed marine areas on their traditional fishing grounds. These managed areas can protect spawning stocks, however the extent to which they help to replenish nearby sea cucumber fisheries is debated, as nothing is known about the scales at which sea cucumber larvae disperse. In this study, we used genetic parentage analyses and statistical modelling to provide the first empirical measure of larval dispersal patterns for a sea cucumber species. We analysed tissue samples from 765 adult and 827 juvenile sandfish (Holothuria scabra) collected from five traditional fishing grounds of the Titan tribe, from Manus Province, Papua New Guinea. All adults were sampled from the Pere fishing grounds (the larval source area), with juveniles sampled from the Pere, Mbunai, Tawi, Timonai and Mbuke fishing grounds. Parentage analysis identified 15 juveniles that were the offspring of parents sampled from Pere fishing grounds, with six of these juveniles located in the same fishing grounds as their parents. The best-fit larval dispersal kernel predicted that the average H. scabra larvae travelled 15 km from its spawning location, with 50% of larvae settling within 6.7 km of their parents and 95% of larvae settling within 59 km of their parents. These results suggest that the Titan tribes' desire to protect their H. scabra spawning stocks by establishing a network of locally managed marine areas across 65 km of continuous coastline is a culturally appropriate strategy, which has merit from both an ecological and fisheries standpoint. [ABSTRACT FROM AUTHOR]

Published
2024
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28. Linking vertical movements of large pelagic predators with distribution patterns of biomass in the open ocean

Author

Braun, Camrin D., primary, Della Penna, Alice, additional, Arostegui, Martin C., additional, Afonso, Pedro, additional, Berumen, Michael L., additional, Block, Barbara A., additional, Brown, Craig A., additional, Fontes, Jorge, additional, Furtado, Miguel, additional, Gallagher, Austin J., additional, Gaube, Peter, additional, Golet, Walter J., additional, Kneebone, Jeff, additional, Macena, Bruno C. L., additional, Mucientes, Gonzalo, additional, Orbesen, Eric S., additional, Queiroz, Nuno, additional, Shea, Brendan D., additional, Schratwieser, Jason, additional, Sims, David W., additional, Skomal, Gregory B., additional, Snodgrass, Derke, additional, and Thorrold, Simon R., additional

Published
2023
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33. Global status and conservation potential of reef sharks

Author

MacNeil, M. Aaron, Chapman, Demian D., Heupel, Michelle, Simpfendorfer, Colin A., Heithaus, Michael, Meekan, Mark, Harvey, Euan, Goetze, Jordan, Kiszka, Jeremy, Bond, Mark E., Currey-Randall, Leanne M., Speed, Conrad W., Sherman, C. Samantha, Rees, Matthew J., Udyawer, Vinay, Flowers, Kathryn I., Clementi, Gina, Valentin-Albanese, Jasmine, Gorham, Taylor, Adam, M. Shiham, Ali, Khadeeja, Pina-Amargós, Fabián, Angulo-Valdés, Jorge A., Asher, Jacob, Barcia, Laura García, Beaufort, Océane, Benjamin, Cecilie, Bernard, Anthony T. F., Berumen, Michael L., Bierwagen, Stacy, Bonnema, Erika, Bown, Rosalind M. K., Bradley, Darcy, Brooks, Edd, Brown, J. Jed, Buddo, Dayne, Burke, Patrick, Cáceres, Camila, Cardeñosa, Diego, Carrier, Jeffrey C., Caselle, Jennifer E., Charloo, Venkatesh, Claverie, Thomas, Clua, Eric, Cochran, Jesse E. M., Cook, Neil, Cramp, Jessica, D’Alberto, Brooke, de Graaf, Martin, Dornhege, Mareike, Estep, Andy, Fanovich, Lanya, Farabaugh, Naomi F., Fernando, Daniel, Flam, Anna L., Floros, Camilla, Fourqurean, Virginia, Garla, Ricardo, Gastrich, Kirk, George, Lachlan, Graham, Rory, Guttridge, Tristan, Hardenstine, Royale S., Heck, Stephen, Henderson, Aaron C., Hertler, Heidi, Hueter, Robert, Johnson, Mohini, Jupiter, Stacy, Kasana, Devanshi, Kessel, Steven T., Kiilu, Benedict, Kirata, Taratu, Kuguru, Baraka, Kyne, Fabian, Langlois, Tim, Lédée, Elodie J. I., Lindfield, Steve, Luna-Acosta, Andrea, Maggs, Jade, Manjaji-Matsumoto, B. Mabel, Marshall, Andrea, Matich, Philip, McCombs, Erin, McLean, Dianne, Meggs, Llewelyn, Moore, Stephen, Mukherji, Sushmita, Murray, Ryan, Kaimuddin, Muslimin, Newman, Stephen J., Nogués, Josep, Obota, Clay, O’Shea, Owen, Osuka, Kennedy, Papastamatiou, Yannis P., Perera, Nishan, Peterson, Bradley, Ponzo, Alessandro, Prasetyo, Andhika, Quamar, L. M. Sjamsul, Quinlan, Jessica, Ruiz-Abierno, Alexei, Sala, Enric, Samoilys, Melita, Schärer-Umpierre, Michelle, Schlaff, Audrey, Simpson, Nikola, Smith, Adam N. H., Sparks, Lauren, Tanna, Akshay, Torres, Rubén, Travers, Michael J., van Zinnicq Bergmann, Maurits, Vigliola, Laurent, Ward, Juney, Watts, Alexandra M., Wen, Colin, Whitman, Elizabeth, Wirsing, Aaron J., Wothke, Aljoscha, Zarza-Gonzâlez, Esteban, and Cinner, Joshua E.

Published
2020
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34. Species delineation and hybrid identification using diagnostic nuclear markers for Mediterranean groupers Epinephelus marginatus and Mycteroperca rubra.

Author

Song He, Bariche, Michel, Pombo-Ayora, Lucía, and Berumen, Michael L.

Subjects
EPINEPHELUS, GROUPERS, SPECIES, FISHERIES, SPECIES hybridization, MARINE biodiversity, IDENTIFICATION
Abstract

Globally, groupers (Serranidae) are commercially important fish species. Hybridization within this family has been reported in captivity and natural environments, usually among congeneric species. However, intergeneric hybridization has been reported only occasionally. Given the commercial interest in these fish, artisanal or recreational fishermen easily notice "weird-looking" individuals. This is the case of an unidentified grouper noticed by a spearfisher in Lebanese Mediterranean waters. Visual comparisons raised the possibility that the observed specimen was a hybrid. Molecular analysis based on two mitochondrial and three nuclear markers was performed to investigate this potential hybrid's affinity. The discordance of the phylogenetic gene trees of the mitochondrial and nuclear markers indicates that E. marginatus and M. rubra are potential parent species of a hybrid individual in our samples. The subsequent haploweb analysis based on the S7 nuclear marker reveals the affinity of the hybrid individual to both E. marginatus and M. rubra. In this specific hybridization case, the nuclear marker S7 emerges as a valuable diagnostic tool for species delineation and hybrid detection. [ABSTRACT FROM AUTHOR]

Published
2024
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38. Using standardized fish‐specific autonomous reef monitoring structures (FARMS) to quantify cryptobenthic fish communities

Author

Brandl, Simon J., primary, Weigt, Lee A., additional, Pitassy, Diane E., additional, Coker, Darren J., additional, Patrick, Christopher J., additional, Luchese, Matheus H., additional, Berumen, Michael L., additional, Buskey, Edward J., additional, Casey, Jordan M., additional, Di Domenico, Maikon, additional, Soeth, Marcelo, additional, Topor, Zachary M., additional, Duffy, J. Emmett, additional, Baldwin, Carole C., additional, Hagedorn, Mary, additional, and Parenti, Lynne R., additional

Published
2023
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39. Phylogenetics and taxonomy of the scleractinian coral family Euphylliidae

Author

Arrigoni, Roberto, Stolarski, Jaroslaw, Terraneo, Tullia I., Hoeksema, Bert W., Berumen, Michael L., Payri, Claude, Montano, Simone, Arrigoni, Roberto, Stolarski, Jaroslaw, Terraneo, Tullia I., Hoeksema, Bert W., Berumen, Michael L., Payri, Claude, and Montano, Simone

Abstract

The family Euphylliidae consists of reef-building zooxanthellate scleractinian corals distributed across the Indo-Pacific. Seven extant genera comprising a total of 22 valid species are currently recognised. Recent studies have re-organised the taxonomy of the family at the genus level based on molecular and morphological data, including a comprehensive revision of Euphyllia and the resurrection of Fimbriaphyllia. Here, three mitochondrial loci (coi, 12S rRNA, and 16S rRNA) were sequenced and morphological examinations were conducted at three scales (macro/micromorphology and microstructure of the skeleton, and polyp morphology) to study the phylogeny and taxonomy of Euphylliidae. We analysed a total of 11 valid species collected from seven Indo-Pacific localities. The monotypic genus Coeloseris, currently in Agariciidae, was also investigated since previous molecular data suggested a close relationship with the Euphylliidae. Molecular and morphological phylogenetic trees were broadly concordant in the definition of genus-level clades. All analysed genera, i.e., Ctenella, Euphyllia, Fimbriaphyllia, Galaxea, and Gyrosmilia, were reciprocally monophyletic based on molecular results. Coeloseris was nested within the family and, therefore, is formally moved into Euphylliidae. Updated morphological diagnoses are provided for each investigated genus. This study further demonstrated that a phylogenetic classification of scleractinian corals can be achieved by applying a combined morpho-molecular approach. Finally, we encourage phylogenetic and taxonomic studies of the euphylliid taxa not yet analysed molecularly, such as the monotypic genera Montigyra and Simplastrea.

Published
2023
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40. Widespread diversity deficits of coral reef sharks and rays

Author

Simpfendorfer, Colin A., Heithaus, Michael R., Heupel, Michelle R., Macneil, M.A., Meekan, Mark, Harvey, Euan, Sherman, C.S., Currey-Randall, Leanne M., Goetze, Jordan S., Kiszka, Jeremy J., Rees, Matthew J., Speed, Conrad W., Udyawer, Vinay, Bond, Mark E., Flowers, Kathryn I., Clementi, Gina M., Valentin-Albanese, Jasmine, Adam, M.S., Ali, Khadeeja, Asher, Jacob, Aylagas, Eva, Beaufort, Océane, Benjamin, Cecilie, Bernard, Anthony T.F., Berumen, Michael L., Bierwagen, Stacy, Birrell, Chico, Bonnema, Erika, Bown, Rosalind M.K., Brooks, Edward J., Brown, J.J., Buddo, Dayne, Burke, Patrick J., Cáceres, Camila, Cambra, Marta, Cardeñosa, Diego, Carrier, Jeffrey C., Casareto, Sara, Caselle, Jennifer E., Charloo, Venkatesh, Cinner, Joshua E., Claverie, Thomas, Clua, Eric E.G., Cochran, Jesse E.M., Cook, Neil, Cramp, Jessica E., d’Alberto, Brooke M., de Graaf, Martin, Dornhege, Mareike C., Espinoza, Mario, Estep, Andy, Fanovich, Lanya, Farabaugh, Naomi F., Fernando, Daniel, Ferreira, Carlos E.L., Fields, Candace Y.A., Flam, Anna L., Floros, Camilla, Fourqurean, Virginia, Gajdzik, Laura, García Barcia, Laura, Garla, Ricardo, Gastrich, Kirk, George, Lachlan, Giarrizzo, Tommaso, Graham, Rory, Guttridge, Tristan L., Hagan, Valerie, Hardenstine, Royale S., Heck, Stephen M., Henderson, Aaron C., Heithaus, Patricia, Hertler, Heidi, Hoyos Padilla, Mauricio, Hueter, Robert E., Jabado, Rima W., Joyeux, Jean-Christophe, Jaiteh, Vanessa, Johnson, Mohini, Jupiter, Stacy D., Kaimuddin, Muslimin, Kasana, Devanshi, Kelley, Megan, Kessel, Steven T., Kiilu, Benedict, Kirata, Taratau, Kuguru, Baraka, Kyne, Fabian, Langlois, Tim, Lara, Frida, Lawe, Jaedon, Lédée, Elodie J.I., Lindfield, Steve, Luna-Acosta, Andrea, Maggs, Jade Q., Manjaji-Matsumoto, B.M., Marshall, Andrea, Martin, Lucy, Mateos-Molina, Daniel, Matich, Philip, Mccombs, Erin, Mcivor, Ashlie, Mclean, Dianne, Meggs, Llewelyn, Moore, Stephen, Mukherji, Sushmita, Murray, Ryan, Newman, Stephen J., Nogués, Josep, Obota, Clay, Ochavillo, Domingo, O'Shea, Owen, Osuka, Kennedy E., Papastamatiou, Yannis P., Perera, Nishan, Peterson, Bradley, Pimentel, Caio R., Pina-Amargós, Fabián, Pinheiro, Hudson T., Ponzo, Alessandro, Prasetyo, Andhika, Quamar, L.M.S., Quinlan, Jessica R., Reis-Filho, José Amorim, Ruiz, Hector, Ruiz-Abierno, Alexei, Sala, Enric, Salinas-de-León, Pelayo, Samoilys, Melita A., Sample, William R., Schärer-Umpierre, Michelle, Schlaff, Audrey M., Schmid, Kurt, Schoen, Sara N., Simpson, Nikola, Smith, Adam N.H., Spaet, Julia L.Y., Sparks, Lauren, Stoffers, Twan, Tanna, Akshay, Torres, Rubén, Travers, Michael J., van Zinnicq Bergmann, Maurits, Vigliola, Laurent, Ward, Juney, Warren, Joseph D., Watts, Alexandra M., Wen, Colin K., Whitman, Elizabeth R., Wirsing, Aaron J., Wothke, Aljoscha, Zarza-González, Esteban, Chapman, Demian D., Simpfendorfer, Colin A., Heithaus, Michael R., Heupel, Michelle R., Macneil, M.A., Meekan, Mark, Harvey, Euan, Sherman, C.S., Currey-Randall, Leanne M., Goetze, Jordan S., Kiszka, Jeremy J., Rees, Matthew J., Speed, Conrad W., Udyawer, Vinay, Bond, Mark E., Flowers, Kathryn I., Clementi, Gina M., Valentin-Albanese, Jasmine, Adam, M.S., Ali, Khadeeja, Asher, Jacob, Aylagas, Eva, Beaufort, Océane, Benjamin, Cecilie, Bernard, Anthony T.F., Berumen, Michael L., Bierwagen, Stacy, Birrell, Chico, Bonnema, Erika, Bown, Rosalind M.K., Brooks, Edward J., Brown, J.J., Buddo, Dayne, Burke, Patrick J., Cáceres, Camila, Cambra, Marta, Cardeñosa, Diego, Carrier, Jeffrey C., Casareto, Sara, Caselle, Jennifer E., Charloo, Venkatesh, Cinner, Joshua E., Claverie, Thomas, Clua, Eric E.G., Cochran, Jesse E.M., Cook, Neil, Cramp, Jessica E., d’Alberto, Brooke M., de Graaf, Martin, Dornhege, Mareike C., Espinoza, Mario, Estep, Andy, Fanovich, Lanya, Farabaugh, Naomi F., Fernando, Daniel, Ferreira, Carlos E.L., Fields, Candace Y.A., Flam, Anna L., Floros, Camilla, Fourqurean, Virginia, Gajdzik, Laura, García Barcia, Laura, Garla, Ricardo, Gastrich, Kirk, George, Lachlan, Giarrizzo, Tommaso, Graham, Rory, Guttridge, Tristan L., Hagan, Valerie, Hardenstine, Royale S., Heck, Stephen M., Henderson, Aaron C., Heithaus, Patricia, Hertler, Heidi, Hoyos Padilla, Mauricio, Hueter, Robert E., Jabado, Rima W., Joyeux, Jean-Christophe, Jaiteh, Vanessa, Johnson, Mohini, Jupiter, Stacy D., Kaimuddin, Muslimin, Kasana, Devanshi, Kelley, Megan, Kessel, Steven T., Kiilu, Benedict, Kirata, Taratau, Kuguru, Baraka, Kyne, Fabian, Langlois, Tim, Lara, Frida, Lawe, Jaedon, Lédée, Elodie J.I., Lindfield, Steve, Luna-Acosta, Andrea, Maggs, Jade Q., Manjaji-Matsumoto, B.M., Marshall, Andrea, Martin, Lucy, Mateos-Molina, Daniel, Matich, Philip, Mccombs, Erin, Mcivor, Ashlie, Mclean, Dianne, Meggs, Llewelyn, Moore, Stephen, Mukherji, Sushmita, Murray, Ryan, Newman, Stephen J., Nogués, Josep, Obota, Clay, Ochavillo, Domingo, O'Shea, Owen, Osuka, Kennedy E., Papastamatiou, Yannis P., Perera, Nishan, Peterson, Bradley, Pimentel, Caio R., Pina-Amargós, Fabián, Pinheiro, Hudson T., Ponzo, Alessandro, Prasetyo, Andhika, Quamar, L.M.S., Quinlan, Jessica R., Reis-Filho, José Amorim, Ruiz, Hector, Ruiz-Abierno, Alexei, Sala, Enric, Salinas-de-León, Pelayo, Samoilys, Melita A., Sample, William R., Schärer-Umpierre, Michelle, Schlaff, Audrey M., Schmid, Kurt, Schoen, Sara N., Simpson, Nikola, Smith, Adam N.H., Spaet, Julia L.Y., Sparks, Lauren, Stoffers, Twan, Tanna, Akshay, Torres, Rubén, Travers, Michael J., van Zinnicq Bergmann, Maurits, Vigliola, Laurent, Ward, Juney, Warren, Joseph D., Watts, Alexandra M., Wen, Colin K., Whitman, Elizabeth R., Wirsing, Aaron J., Wothke, Aljoscha, Zarza-González, Esteban, and Chapman, Demian D.

Abstract

A global survey of coral reefs reveals that overfishing is driving resident shark species toward extinction, causing diversity deficits in reef elasmobranch (shark and ray) assemblages. Our species-level analysis revealed global declines of 60 to 73% for five common resident reef shark species and that individual shark species were not detected at 34 to 47% of surveyed reefs. As reefs become more shark-depleted, rays begin to dominate assemblages. Shark-dominated assemblages persist in wealthy nations with strong governance and in highly protected areas, whereas poverty, weak governance, and a lack of shark management are associated with depauperate assemblages mainly composed of rays. Without action to address these diversity deficits, loss of ecological function and ecosystem services will increasingly affect human communities.

Published
2023

44. Author Correction: Global status and conservation potential of reef sharks

Author

MacNeil, M. Aaron, Chapman, Demian D., Heupel, Michelle, Simpfendorfer, Colin A., Heithaus, Michael, Meekan, Mark, Harvey, Euan, Goetze, Jordan, Kiszka, Jeremy, Bond, Mark E., Currey-Randall, Leanne M., Speed, Conrad W., Sherman, C. Samantha, Rees, Matthew J., Udyawer, Vinay, Flowers, Kathryn I., Clementi, Gina, Valentin-Albanese, Jasmine, Gorham, Taylor, Adam, M. Shiham, Ali, Khadeeja, Pina-Amargós, Fabián, Angulo-Valdés, Jorge A., Asher, Jacob, Barcia, Laura García, Beaufort, Océane, Benjamin, Cecilie, Bernard, Anthony T. F., Berumen, Michael L., Bierwagen, Stacy, Bonnema, Erika, Bown, Rosalind M. K., Bradley, Darcy, Brooks, Edd, Brown, J. Jed, Buddo, Dayne, Burke, Patrick, Cáceres, Camila, Cardeñosa, Diego, Carrier, Jeffrey C., Caselle, Jennifer E., Charloo, Venkatesh, Claverie, Thomas, Clua, Eric, Cochran, Jesse E. M., Cook, Neil, Cramp, Jessica, D’Alberto, Brooke, de Graaf, Martin, Dornhege, Mareike, Estep, Andy, Fanovich, Lanya, Farabaugh, Naomi F., Fernando, Daniel, Flam, Anna L., Floros, Camilla, Fourqurean, Virginia, Garla, Ricardo, Gastrich, Kirk, George, Lachlan, Graham, Rory, Guttridge, Tristan, Hardenstine, Royale S., Heck, Stephen, Henderson, Aaron C., Hertler, Heidi, Hueter, Robert, Johnson, Mohini, Jupiter, Stacy, Kasana, Devanshi, Kessel, Steven T., Kiilu, Benedict, Kirata, Taratu, Kuguru, Baraka, Kyne, Fabian, Langlois, Tim, Lédée, Elodie J. I., Lindfield, Steve, Luna-Acosta, Andrea, Maggs, Jade, Manjaji-Matsumoto, B. Mabel, Marshall, Andrea, Matich, Philip, McCombs, Erin, McLean, Dianne, Meggs, Llewelyn, Moore, Stephen, Mukherji, Sushmita, Murray, Ryan, Kaimuddin, Muslimin, Newman, Stephen J., Nogués, Josep, Obota, Clay, O’Shea, Owen, Osuka, Kennedy, Papastamatiou, Yannis P., Perera, Nishan, Peterson, Bradley, Ponzo, Alessandro, Prasetyo, Andhika, Quamar, L. M. Sjamsul, Quinlan, Jessica, Ruiz-Abierno, Alexei, Sala, Enric, Samoilys, Melita, Schärer-Umpierre, Michelle, Schlaff, Audrey, Simpson, Nikola, Smith, Adam N. H., Sparks, Lauren, Tanna, Akshay, Torres, Rubén, Travers, Michael J., van Zinnicq Bergmann, Maurits, Vigliola, Laurent, Ward, Juney, Watts, Alexandra M., Wen, Colin, Whitman, Elizabeth, Wirsing, Aaron J., Wothke, Aljoscha, Zarza-Gonzâlez, Esteban, and Cinner, Joshua E.

Published
2020
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