Transfer learning for efficient classification of grouper sound.

A transfer learning approach is proposed to classify grouper species by their courtship-associated sounds produced during spawning aggregations. Vessel sounds are also included in order to potentially identify human interaction with spawning fish. Grouper sounds recorded during spawning aggregations were first converted to time-frequency representations. Two types of time frequency representations were used in this study: spectrograms and scalograms. These were converted to images, and then fed to pretrained deep neural network models: VGG16, VGG19, Google Net, and MobileNet. The experimental results revealed that transfer learning significantly outperformed the manually identified features approach for grouper sound classification. In addition, both time-frequency representations produced almost identical results in terms of classification accuracy.

Classification of red hind grouper call types using random ensemble of stacked autoencoders.

In this paper, a method is introduced for the classification of call types of red hind grouper, an important fishery resource in the Caribbean that produces sounds associated with reproductive behaviors during yearly spawning aggregations. For the undertaken task, two distinct call types of red hind are analyzed. An ensemble of stacked autoencoders (SAEs) is then designed by randomly selecting the hyperparameters of SAEs in the network. These hyperparameters include a number of hidden layers in each SAE and a number of nodes in each hidden layer. Spectrograms of red hind calls are used to train this randomly generated ensemble of SAEs one at a time. Once all individual SAEs are trained, this ensemble is used as a whole to classify call types of red hind. More specifically, the outputs of individual SAEs are combined with a fusion mechanism to produce a final decision on the call type of the input red hind sound. Experimental results show that the innovative approach produces superior results in comparison with those obtained by non-ensemble methods. The algorithm reliably classified red hind call types with over 90% accuracy and successfully detected some calls missed by human observers.

Enzyme-Catalyzed in situ Synthesis of Temporally and Spatially Distinct CdSe Quantum Dots in Biological Backgrounds.

The cellular machinery of metal metabolism is capable of making a wide range of inorganic nanoparticles and quantum dots. Individual enzymes from these metabolic pathways are being identified with metal reducing activity, and some have been isolated for in situ particle formation and labeling. We previously identified a glutathione reductase like metalloid reductase (GRLMR) from Pseudomonas Moravenis stanleyae with a high affinity for the bioavailable selenium thiolate selenodiglutatione, and exhibiting NADPH-dependent reduction of selenodiglutathione to Se(0); initiating the growth of pure selenium metal nanoparticles. In this study, we demonstrate that the GRLMR enzyme can further reduce selenium to a Se(2-) oxidative state, which is capable of nucleating with Cd(2+) to rapidly form CdSe quantum dots. We show that GRLMR can outcompete background sources of cellular selenium reduction (such as glutathione) and can control the kinetics of quantum dot formation in complex media. The resulting particles are smaller diameter, with a distinguishingly shifted emission spectra and superior FWHM. This study indicates that there is great potential for using GRLMR to study and design enzymes capable of controlled biosynthesis of nanoparticles and quantum dots; paving the way for cellularly assembled nanoparticle-biosensors and reporters.

Altered juvenile fish communities associated with invasive Halophila stipulacea seagrass habitats in the U.S. Virgin Islands.

Caribbean seagrass habitats provide food and protection for reef-associated juvenile fish. The invasive seagrass Halophila stipulacea is rapidly altering these seascapes. Since its arrival in the Caribbean in 2002, H. stipulacea has colonized and displaced native seagrasses, but the function of this invasive seagrass as a juvenile fish habitat remains unknown. To compare diversity, community structure, and abundance of juvenile fish between H. stipulacea and native seagrass beds, fish traps were deployed in four nearshore bays around St. Thomas, U.S. Virgin Islands. Traps were deployed in Frenchman, Lindbergh, and Sprat Bays for 24 h intervals in patches of bare sand, patches of H. stipulacea and patches of the native Caribbean seagrasses Thalassia testudinum and Syringodium filiforme. Traps were then deployed in Brewers Bay for 12 h intervals in stands of H. stipulacea and S. filiforme. Relative and total abundances of juvenile fish, identified at least to family, were compared across treatment habitats for each trap deployment period. The catch from H. stipulacea, compared to native seagrasses, comprised a greater abundance of nocturnal carnivores Lutjanus synagris (family Lutjanidae) and Haemulon flavolineatum (family Haemulidae). Additionally, the herbivore species Sparisoma aurofrenatum (family Labridae) and Acanthurus bahianus (family Acanthuridae) and the diurnal carnivore species Pseudopeneus maculatus (family Mullidae) were relatively scarce in H. stipulacea. The catch from sand was much smaller, compared to vegetated habitats, and comprised only L. synagris, H. flavolineatum, and H. aurolineatum. These results provide evidence of reduced family diversity and altered juvenile fish assemblages in H. stipulacea, driven by an abundance of some nocturnal carnivores and scarcity of herbivores and diurnal carnivores. The findings from the present work underpin the need for further investigation and mitigation of this invasion, particularly where H. stipulacea is driving seascape-alterations of key juvenile fish habitats.

Comparative Use of a Caribbean Mesophotic Coral Ecosystem and Association with Fish Spawning Aggregations by Three Species of Shark.

Understanding of species interactions within mesophotic coral ecosystems (MCEs; ~ 30-150 m) lags well behind that for shallow coral reefs. MCEs are often sites of fish spawning aggregations (FSAs) for a variety of species, including many groupers. Such reproductive fish aggregations represent temporal concentrations of potential prey that may be drivers of habitat use by predatory species, including sharks. We investigated movements of three species of sharks within a MCE and in relation to FSAs located on the shelf edge south of St. Thomas, United States Virgin Islands. Movements of 17 tiger (Galeocerdo cuvier), seven lemon (Negaprion brevirostris), and six Caribbean reef (Carcharhinus perezi) sharks tagged with acoustic transmitters were monitored within the MCE using an array of acoustic receivers spanning an area of 1,060 km2 over a five year period. Receivers were concentrated around prominent grouper FSAs to monitor movements of sharks in relation to these temporally transient aggregations. Over 130,000 detections of telemetered sharks were recorded, with four sharks tracked in excess of 3 years. All three shark species were present within the MCE over long periods of time and detected frequently at FSAs, but patterns of MCE use and orientation towards FSAs varied both spatially and temporally among species. Lemon sharks moved over a large expanse of the MCE, but concentrated their activities around FSAs during grouper spawning and were present within the MCE significantly more during grouper spawning season. Caribbean reef sharks were present within a restricted portion of the MCE for prolonged periods of time, but were also absent for long periods. Tiger sharks were detected throughout the extent of the acoustic array, with the MCE representing only portion of their habitat use, although a high degree of individual variation was observed. Our findings indicate that although patterns of use varied, all three species of sharks repeatedly utilized the MCE and as upper trophic level predators they are likely involved in a range of interactions with other members of MCEs.

Caribbean mesophotic coral ecosystems are unlikely climate change refugia.

Deeper coral reefs experience reduced temperatures and light and are often shielded from localized anthropogenic stressors such as pollution and fishing. The deep reef refugia hypothesis posits that light-dependent stony coral species at deeper depths are buffered from thermal stress and will avoid bleaching-related mass mortalities caused by increasing sea surface temperatures under climate change. This hypothesis has not been tested because data collection on deeper coral reefs is difficult. Here we show that deeper (mesophotic) reefs, 30-75 m depth, in the Caribbean are not refugia because they have lower bleaching threshold temperatures than shallow reefs. Over two thermal stress events, mesophotic reef bleaching was driven by a bleaching threshold that declines 0.26 °C every +10 m depth. Thus, the main premise of the deep reef refugia hypothesis that cooler environments are protective is incorrect; any increase in temperatures above the local mean warmest conditions can lead to thermal stress and bleaching. Thus, relatively cooler temperatures can no longer be considered a de facto refugium for corals and it is likely that many deeper coral reefs are as vulnerable to climate change as shallow water reefs.

Progress toward clonable inorganic nanoparticles.

Pseudomonas moraviensis stanleyae was recently isolated from the roots of the selenium (Se) hyperaccumulator plant Stanleya pinnata. This bacterium tolerates normally lethal concentrations of SeO3(2-) in liquid culture, where it also produces Se nanoparticles. Structure and cellular ultrastructure of the Se nanoparticles as determined by cellular electron tomography shows the nanoparticles as intracellular, of narrow dispersity, symmetrically irregular and without any observable membrane or structured protein shell. Protein mass spectrometry of a fractionated soluble cytosolic material with selenite reducing capability identified nitrite reductase and glutathione reductase homologues as NADPH dependent candidate enzymes for the reduction of selenite to zerovalent Se nanoparticles. In vitro experiments with commercially sourced glutathione reductase revealed that the enzyme can reduce SeO3(2-) (selenite) to Se nanoparticles in an NADPH-dependent process. The disappearance of the enzyme as determined by protein assay during nanoparticle formation suggests that glutathione reductase is associated with or possibly entombed in the nanoparticles whose formation it catalyzes. Chemically dissolving the nanoparticles releases the enzyme. The size of the nanoparticles varies with SeO3(2-) concentration, varying in size form 5 nm diameter when formed at 1.0 µM [SeO3(2-)] to 50 nm maximum diameter when formed at 100 µM [SeO3(2-)]. In aggregate, we suggest that glutathione reductase possesses the key attributes of a clonable nanoparticle system: ion reduction, nanoparticle retention and size control of the nanoparticle at the enzyme site.

Marine managed areas and associated fisheries in the US Caribbean.

The marine managed areas (MMAs) of the U.S. Caribbean are summarized and specific data-rich cases are examined to determine their impact upon fisheries management in the region. In this region, the productivity and connectivity of benthic habitats such as mangroves, seagrass and coral reefs is essential for many species targeted by fisheries. A minority of the 39 MMAs covering over 4000km(2) serve any detectable management or conservation function due to deficiencies in the design, objectives, compliance or enforcement. Fifty percent of the area within MMA boundaries had no-take regulations in the U.S. Virgin Islands, while Puerto Rico only had 3%. Six case studies are compared and contrasted to better understand the potential of these MMAs for fisheries management. Signs of success were associated with including sufficient areas of essential fish habitat (nursery, spawning and migration corridors), year-round no-take regulations, enforcement and isolation. These criteria have been identified as important in the conservation of marine resources, but little has been done to modify the way MMAs are designated and implemented in the region. Site-specific monitoring to measure the effects of these MMAs is needed to demonstrate the benefits to fisheries and gain local support for a greater use as a fisheries management tool.

Intraspecific variation in vertical habitat use by tiger sharks (Galeocerdo cuvier) in the western North Atlantic.

Tiger sharks (Galeocerdo cuvier) are a wide ranging, potentially keystone predator species that display a variety of horizontal movement patterns, making use of coastal and pelagic waters. Far less, however, is known about their vertical movements and use of the water column. We used pop-up satellite archival tags with two data sampling rates (high rate and standard rate tags) to investigate the vertical habitat use and diving behavior of tiger sharks tagged on the Puerto Rico-Virgin Islands platform and off Bermuda between 2008 and 2009. Useable data were received from nine of 14 sharks tagged, tracked over a total of 529 days. Sharks spent the majority of their time making yo-yo dives within the upper 50 m of the water column and considerable time within the upper 5 m of the water column. As a result, sharks typically occupied a narrow daily temperature range (∼2°C). Dives to greater than 200 m were common, and all sharks made dives to at least 250 m, with one shark reaching a depth of 828 m. Despite some similarities among individuals, a great deal of intraspecific variability in vertical habit use was observed. Four distinct depth distributions that were not related to tagging location, horizontal movements, sex, or size were detected. In addition, similar depth distributions did not necessitate similar dive patterns among sharks. Recognition of intraspecific variability in habitat use of top predators can be crucial for effective management of these species and for understanding their influence on ecosystem dynamics.

Population structure and phylogeography in Nassau grouper (Epinephelus striatus), a mass-aggregating marine fish.

To address patterns of genetic connectivity in a mass-aggregating marine fish, we analyzed genetic variation in mitochondrial DNA (mtDNA), microsatellites, and single nucleotide polymorphisms (SNPs) for Nassau grouper (Epinephelus striatus). We expected Nassau grouper to exhibit genetic differentiation among its subpopulations due to its reproductive behavior and retentive oceanographic conditions experienced across the Caribbean basin. All samples were genotyped for two mitochondrial markers and 9 microsatellite loci, and a subset of samples were genotyped for 4,234 SNPs. We found evidence of genetic differentiation in a Caribbean-wide study of this mass-aggregating marine fish using mtDNA (FST = 0.206, p<0.001), microsatellites (FST = 0.002, p = 0.004) and SNPs (FST = 0.002, p = 0.014), and identified three potential barriers to larval dispersal. Genetically isolated regions identified in our work mirror those seen for other invertebrate and fish species in the Caribbean basin. Oceanographic regimes in the Caribbean may largely explain patterns of genetic differentiation among Nassau grouper subpopulations. Regional patterns observed warrant standardization of fisheries management and conservation initiatives among countries within genetically isolated regions.

Fish with chips: tracking reef fish movements to evaluate size and connectivity of Caribbean marine protected areas.

Coral reefs and associated fish populations have experienced rapid decline in the Caribbean region and marine protected areas (MPAs) have been widely implemented to address this decline. The performance of no-take MPAs (i.e., marine reserves) for protecting and rebuilding fish populations is influenced by the movement of animals within and across their boundaries. Very little is known about Caribbean reef fish movements creating a critical knowledge gap that can impede effective MPA design, performance and evaluation. Using miniature implanted acoustic transmitters and a fixed acoustic receiver array, we address three key questions: How far can reef fish move? Does connectivity exist between adjacent MPAs? Does existing MPA size match the spatial scale of reef fish movements? We show that many reef fishes are capable of traveling far greater distances and in shorter duration than was previously known. Across the Puerto Rican Shelf, more than half of our 163 tagged fish (18 species of 10 families) moved distances greater than 1 km with three fish moving more than 10 km in a single day and a quarter spending time outside of MPAs. We provide direct evidence of ecological connectivity across a network of MPAs, including estimated movements of more than 40 km connecting a nearshore MPA with a shelf-edge spawning aggregation. Most tagged fish showed high fidelity to MPAs, but also spent time outside MPAs, potentially contributing to spillover. Three-quarters of our fish were capable of traveling distances that would take them beyond the protection offered by at least 40-64% of the existing eastern Caribbean MPAs. We recommend that key species movement patterns be used to inform and evaluate MPA functionality and design, particularly size and shape. A re-scaling of our perception of Caribbean reef fish mobility and habitat use is imperative, with important implications for ecology and management effectiveness.

Hurricanes benefit bleached corals.

Recent, global mass-mortalities of reef corals due to record warm sea temperatures have led researchers to consider global warming as one of the most significant threats to the persistence of coral reef ecosystems. The passage of a hurricane can alleviate thermal stress on coral reefs, highlighting the potential for hurricane-associated cooling to mitigate climate change impacts. We provide evidence that hurricane-induced cooling was responsible for the documented differences in the extent and recovery time of coral bleaching between the Florida Reef Tract and the U.S. Virgin Islands during the Caribbean-wide 2005 bleaching event. These results are the only known scenario where the effects of a hurricane can benefit a stressed marine community.

Temporal and spatial dynamics of Lutjanus cyanopterus (Pisces: Lutjanidae) and L. jocu spawning aggregations in the United States Virgin Islands / Dinámica temporal y espacial de Lutjanus cyanopterus (Pisces: Lutjanidae) y agregaciones de desove de L. jocu en las Islas Vírgenes de los Estados Unidos

The Grammanik bank is a deep reef (35-40 m) located approximately 14 km south of St. Thomas USVI, on the southern edge of the Puerto Rico shelf. The relatively narrow 1.5 km long reef annually hosts spawning aggregations of several species of groupers, snappers and jacks. Until February of 2005, when temporary seasonal protection was offered by the Caribbean Fisheries Management Council, the bank was subject to moderate or heavy exploitation from fishers. Cubera snapper (Lutjanus cyanopterus) were observed aggregating on the Grammanik bank in relatively large numbers from 2003 to 2005 and dog snapper (L. jocu) aggregations were observed in 2005. The arrival and departure of these aggregations appeared to be seasonal and to revolve around the moon phase. Cubera snapper spawning seasonality coincided with that elsewhere in the Caribbean and off south Florida. Schools of up to 1000 fish of each species were observed as well as pre-spawning behavior and milt release. Aggregations of both species showed high site fidelity within seasons but cubera snapper aggregations sites moved between seasons. The authors recommend year-round closure of the Grammanik bank based on its importance as critical fish habitat and a multi-species aggregation area. Rev. Biol. Trop. 54 (Suppl. 3): 69-78. Epub 2007 Jan. 15.

El banco Grammanik es un arrecife profundo (35-40 m) ubicado aproximadamente 14 km al Sur de St. Thomas (Islas Vírgenes EUA), en el límite sur de la plataforma de Puerto Rico. Este arrecife relativamente angosto y de 1.5 km de longitud, recibe anualmente agrupaciones de varias especies de meros, pargos y jureles, durante sus desoves. Fue objeto de explotación de moderada a alta por parte de los pescadores hasta febrero del 2005, cuando el Consejo de Pesca del Caribe le ofreció protección temporal. El pargo cubera (Lutjanus cyanopterus) fue observado en el banco Grammanik en agrupaciones numerosas entre el año 2003 y el 2005, a su vez, agrupaciones del pargo perro o pargo caucha (L. jocu) se observaron en el 2005. La llegada y partida de estos grupos parece ser estacional y estar relacionada con la fase lunar. El desove estacional del pargo cubera coincide con informes de otros sitios del Caribe y al Sur de la Florida, donde se observaron cardúmenes de hasta 1000 peces de cada especie, así como comportamientos previos al desove y liberación de esperma. Agrupaciones de ambas especies mostraron alta fidelidad al sitio en una misma estación, pero los sitios de agrupación del pargo cubera cambiaron entre estaciones. Los autores recomiendan el cierre del banco Gammanik durante todo el año, basados en su importancia como hábitat crítico para los peces y por ser un área de agrupación para múltiples especies.

Population characteristics of a recovering US Virgin Islands red hind spawning aggregation following protection.

Many species of groupers form spawning aggregations, dramatic events where 100s to 1000s of individuals gather annually at specific locations for reproduction. Spawning aggregations are often targeted by local fishermen, making them extremely vulnerable to over fishing. The Red Hind Bank Marine Conservation District located in St. Thomas, United States Virgin Islands, was closed seasonally in 1990 and closed permanently in 1999 to protect an important red hind Epinephelus guttatus spawning site. This study provides some of the first information on the population response of a spawning aggregation located within a marine protected area. Tag-and-release fishing and fish transects were used to evaluate population characteristics and habitat utilization patterns of a red hind spawning aggregation between 1999 and 2004. Compared with studies conducted before the permanent closure, the average size of red hind increased mostly during the seasonal closure period (10 cm over 12 yr), but the maximum total length of male red hind increased by nearly 7 cm following permanent closure. Average density and biomass of spawning red hind increased by over 60% following permanent closure whereas maximum spawning density more than doubled. Information from tag returns indicated that red hind departed the protected area following spawning and migrated 6 to 33 km to a ca. 500 km(2) area. Protection of the spawning aggregation site may have also contributed to an overall increase in the size of red hind caught in the commercial fishery, thus increasing the value of the grouper fishery for local fishermen.

Linking larval history to juvenile demography in the bicolor damselfish Stegastes partitus (Perciformes: Pomacentridae).

Otolith-based reconstructions of daily larval growth increments were used to examine the effect of variation in larval growth on size and age at settlement and post-settlement growth, survival and habitat preferences of juvenile bicolor damselfish (Stegastes partitus Poey). During August 1992 and 1994, newly settled S. partitus were collected from Montastraea coral heads and Porites rubble piles in Tague Bay, St. Croix, U.S. Virgin Islands (17 degrees 45'N, 64 degres 42' W). Daily lapillar otolith increments from each fish were counted and measured with Optimas image analysis software. S. partitus pelagic larval duration was 23.7 d in 1992 (n = 70) and 24.6 d in 1994 (n = 38) and larval age at settlement averaged 13.0 mm total length both years. Analysis of daily otolith increments demonstrated that variation in larval growth rates and size and age at settlement had no detectable effect on post-settlement survivorship but that larger larvae showed a preference for Montastraea coral at settlement. Late larval and early juvenile growth rates showed a significant positive relationship indicating that growth patterns established during the planktonic stage can span metamorphosis and continue into the benthic juvenile phase. Larval growth rates during the first two weeks post-hatching also had a strong effect on age to developmental competence (ability to undergo metamorphosis) in both 1992 and 1994 with the fastest growing larvae being 8 d younger and 0.8 mm smaller at settlement than the slowest growing larvae. These differential growth rates in early stage larvae established trajectories toward larval developmental competence and may prove important in biogeographical studies of larval dispersal.