Cagua E. Fernando
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PreprintTopography and biological noise determine acoustic detectability on coral reefs( 2013-07) Cagua, E. Fernando ; Berumen, Michael L. ; Tyler, E. H. M.Acoustic telemetry is an increasingly common tool for studying the movement patterns, behaviour, and site fidelity of marine organisms, but to accurately interpret acoustic data, the variability, periodicity and range of detectability between acoustic tags and receivers must be understood. The relative and interactive effects of topography with biological and environmental noise have not been quantified on coral reefs. We conduct two long-term range tests (one and four months duration) on two different reef types in the central Red Sea, to determine the relative effect of distance, depth, topography, time of day, wind, lunar phase, sea surface temperature and thermocline on detection probability. Detectability, as expected, declines with increasing distance between tags and receivers, and we find average detection ranges of 530 and 120 m, using V16 and V13 tags respectively, but the topography of the reef can significantly modify this relationship, reducing the range by ~70%, even when tags and receivers are in line-of-sight. Analyses that assume a relationship between distance and detections must therefore be used with care. Nighttime detection range was consistently reduced in both locations and detections varied by lunar phase in the four month test, suggesting a strong influence of biological noise (reducing detection probability up to 30%), notably more influential than other environmental noises, including wind-driven noise, which is normally considered important in open-water environments. Analysis of detections should be corrected in consideration of the diel patterns we find, and range tests or sentinel tags should be used for more than one month to quantify potential changes due to lunar phase. Some studies assume that the most usual factor limiting detection range is weather-related noise; this cannot be extrapolated to coral reefs.
ArticlePieces in a global puzzle: population genetics at two whale shark aggregations in the western Indian Ocean(Wiley Open Access, 2022-01-25) Hardenstine, Royale S. ; He, Song ; Cochran, Jesse E. M. ; Braun, Camrin D. ; Cagua, E. Fernando ; Pierce, Simon J. ; Prebble, Clare E. M. ; Rohner, Christoph A. ; Saenz-Agudelo, Pablo ; Sinclair-Taylor, Tane H. ; Skomal, Gregory B. ; Thorrold, Simon R. ; Watts, Alexandra M. ; Zakroff, Casey ; Berumen, Michael L.The whale shark Rhincodon typus is found throughout the world's tropical and warm-temperate ocean basins. Despite their broad physical distribution, research on the species has been concentrated at a few aggregation sites. Comparing DNA sequences from sharks at different sites can provide a demographically neutral understanding of the whale shark's global ecology. Here, we created genetic profiles for 84 whale sharks from the Saudi Arabian Red Sea and 72 individuals from the coast of Tanzania using a combination of microsatellite and mitochondrial sequences. These two sites, separated by approximately 4500 km (shortest over-water distance), exhibit markedly different population demographics and behavioral ecologies. Eleven microsatellite DNA markers revealed that the two aggregation sites have similar levels of allelic richness and appear to be derived from the same source population. We sequenced the mitochondrial control region to produce multiple global haplotype networks (based on different alignment methodologies) that were broadly similar to each other in terms of population structure but suggested different demographic histories. Data from both microsatellite and mitochondrial markers demonstrated the stability of genetic diversity within the Saudi Arabian aggregation site throughout the sampling period. These results contrast previously measured declines in diversity at Ningaloo Reef, Western Australia. Mapping the geographic distribution of whale shark lineages provides insight into the species’ connectivity and can be used to direct management efforts at both local and global scales. Similarly, understanding historical fluctuations in whale shark abundance provides a baseline by which to assess current trends. Continued development of new sequencing methods and the incorporation of genomic data could lead to considerable advances in the scientific understanding of whale shark population ecology and corresponding improvements to conservation policy.
ArticleMulti-method assessment of whale shark (Rhincodon typus) residency, distribution, and dispersal behavior at an aggregation site in the Red Sea(Public Library of Science, 2019-09-09) Cochran, Jesse E. M. ; Braun, Camrin D. ; Cagua, E. Fernando ; Campbell, Michael F., Jr. ; Hardenstine, Royale S. ; Kattan, Alexander ; Priest, Mark A. ; Sinclair-Taylor, Tane H. ; Skomal, Gregory B. ; Sultan, Sahar ; Sun, Lu ; Thorrold, Simon R. ; Berumen, Michael L.Whale sharks (Rhincodon typus) are typically dispersed throughout their circumtropical range, but the species is also known to aggregate in specific coastal areas. Accurate site descriptions associated with these aggregations are essential for the conservation of R. typus, an Endangered species. Although aggregations have become valuable hubs for research, most site descriptions rely heavily on sightings data. In the present study, visual census, passive acoustic monitoring, and long range satellite telemetry were combined to track the movements of R. typus from Shib Habil, a reef-associated aggregation site in the Red Sea. An array of 63 receiver stations was used to record the presence of 84 acoustically tagged sharks (35 females, 37 males, 12 undetermined) from April 2010 to May 2016. Over the same period, identification photos were taken for 76 of these tagged individuals and 38 were fitted with satellite transmitters. In total of 37,461 acoustic detections, 210 visual encounters, and 33 satellite tracks were analyzed to describe the sharks’ movement ecology. The results demonstrate that the aggregation is seasonal, mostly concentrated on the exposed side of Shib Habil, and seems to attract sharks of both sexes in roughly equal numbers. The combined methodologies also tracked 15 interannual homing-migrations, demonstrating that many sharks leave the area before returning in later years. When compared to acoustic studies from other aggregations, these results demonstrate that R. typus exhibits diverse, site-specific ecologies across its range. Sightings-independent data from acoustic telemetry and other sources are an effective means of validating more common visual surveys.