Cochran
Jesse E. M.
Cochran
Jesse E. M.
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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.
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ArticleGlobal collision-risk hotspots of marine traffic and the world’s largest fish, the whale shark(National Academy of Sciences, 2022-05-17) Womersley, Freya C. ; Humphries, Nicolas E. ; Queiroz, Nuno ; Vedor, Marisa ; da Costa, Ivo ; Furtado, Miguel ; Tyminski, John P. ; Abrantes, Katya ; Araujo, Gonzalo ; Bach, Steffen S. ; Barnett, Adam ; Berumen, Michael L. ; Bessudo Lion, Sandra ; Braun, Camrin D. ; Clingham, Elizabeth ; Cochran, Jesse E. M. ; de la Parra, Rafael ; Diamant, Stella ; Dove, Alistair D. M. ; Dudgeon, Christine L. ; Erdmann, Mark V. ; Espinoza, Eduardo ; Fitzpatrick, Richard ; Gonzalez Cano, Jaime ; Green, Jonathan R. ; Guzman, Hector M. ; Hardenstine, Royale ; Hasan, Abdi ; Hazin, Fabio H. V. ; Hearn, Alex R. ; Hueter, Robert ; Jaidah, Mohammed Y. ; Labaja, Jessica ; Ladino, Felipe ; Macena, Bruno C. L. ; Morris, John J. Jr. ; Norman, Bradley M. ; Penaherrera-Palma, Cesar ; Pierce, Simon J. ; Quintero, Lina M. ; Ramirez-Macias, Deni ; Reynolds, Samantha D. ; Richardson, Anthony J. ; Robinson, David P. ; Rohner, Christoph A. ; Rowat, David R. L. ; Sheaves, Marcus ; Shivji, Mahmood ; Sianipar, Abraham B. ; Skomal, Gregory B. ; Soler, German ; Syakurachman, Ismail ; Thorrold, Simon R. ; Webb, D. Harry ; Wetherbee, Bradley M. ; White, Timothy D. ; Clavelle, Tyler ; Kroodsma, David A. ; Thums, Michele ; Ferreira, Luciana C. ; Meekan, Mark G. ; Arrowsmith, Lucy M. ; Lester, Emily K. ; Meyers, Megan M. ; Peel, Lauren R. ; Sequeira, Ana M. M. ; Eguiluz, Victor M. ; Duarte, Carlos M. ; Sims, David W.Marine traffic is increasing globally yet collisions with endangered megafauna such as whales, sea turtles, and planktivorous sharks go largely undetected or unreported. Collisions leading to mortality can have population-level consequences for endangered species. Hence, identifying simultaneous space use of megafauna and shipping throughout ranges may reveal as-yet-unknown spatial targets requiring conservation. However, global studies tracking megafauna and shipping occurrences are lacking. Here we combine satellite-tracked movements of the whale shark, Rhincodon typus, and vessel activity to show that 92% of sharks’ horizontal space use and nearly 50% of vertical space use overlap with persistent large vessel (>300 gross tons) traffic. Collision-risk estimates correlated with reported whale shark mortality from ship strikes, indicating higher mortality in areas with greatest overlap. Hotspots of potential collision risk were evident in all major oceans, predominantly from overlap with cargo and tanker vessels, and were concentrated in gulf regions, where dense traffic co-occurred with seasonal shark movements. Nearly a third of whale shark hotspots overlapped with the highest collision-risk areas, with the last known locations of tracked sharks coinciding with busier shipping routes more often than expected. Depth-recording tags provided evidence for sinking, likely dead, whale sharks, suggesting substantial “cryptic” lethal ship strikes are possible, which could explain why whale shark population declines continue despite international protection and low fishing-induced mortality. Mitigation measures to reduce ship-strike risk should be considered to conserve this species and other ocean giants that are likely experiencing similar impacts from growing global vessel traffic.
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ArticleHome sweet home: spatiotemporal distribution and site fidelity of the reef manta ray (Mobula alfredi) in Dungonab Bay, Sudan(BMC, 2022-04-28) Knochel, Anna M. ; Hussey, Nigel E. ; Kessel, Steven T. ; Braun, Camrin D. ; Cochran, Jesse E. M. ; Hill, Graham ; Klaus, Rebecca ; Checkchak, Tarik ; Elamin El Hassen, Nasereldin M. ; Younnis, Mohammed ; Berumen, Michael L.Background Reef manta ray (Mobula alfredi) populations along the Northeastern African coastline are poorly studied. Identifying critical habitats for this species is essential for future research and conservation efforts. Dungonab Bay and Mukkawar Island National Park (DMNP), a component of a UNESCO World Heritage Site in Sudan, hosts the largest known M. alfredi aggregation in the Red Sea. Methods A total of 19 individuals were tagged using surgically implanted acoustic tags and tracked within DMNP on an array of 15 strategically placed acoustic receivers in addition to two offshore receivers. Two of these acoustically monitored M. alfredi were also equipped with satellite linked archival tags and one individual was fitted with a satellite transmitting tag. Together, these data are used to describe approximately two years of residency and seasonal shifts in habitat use. Results Tagged individuals were detected within the array on 96% of monitored days and recorded an average residence index of 0.39 across all receivers. Detections were recorded throughout the year, though some individuals were absent from the receiver array for weeks or months at a time, and generalized additive mixed models showed a clear seasonal pattern in presence with the highest probabilities of detection occurring in boreal fall. The models indicated that M. alfredi presence was highly correlated with increasing chlorophyll-a levels and weakly correlated with the full moon. Modeled biological factors, including sex and wingspan, had no influence on animal presence. Despite the high residency suggested by acoustic telemetry, satellite tag data and offshore acoustic detections in Sanganeb Atoll and Suedi Pass recorded individuals moving up to 125 km from the Bay. However, all these individuals were subsequently detected in the Bay, suggesting a strong degree of site fidelity at this location. Conclusions The current study adds to growing evidence that M. alfredi are highly resident and site-attached to coastal bays and lagoons but display seasonal shifts in habitat use that are likely driven by resource availability. This information can be used to assist in managing and supporting sustainable ecotourism within the DMNP, part of a recently designated UNESCO World Heritage Site.
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ArticleMovement patterns of juvenile whale sharks tagged at an aggregation site in the Red Sea(Public Library of Science, 2014-07-30) Berumen, Michael L. ; Braun, Camrin D. ; Cochran, Jesse E. M. ; Skomal, Gregory B. ; Thorrold, Simon R.Conservation efforts aimed at the whale shark, Rhincodon typus, remain limited by a lack of basic information on most aspects of its ecology, including global population structure, population sizes and movement patterns. Here we report on the movements of 47 Red Sea whale sharks fitted with three types of satellite transmitting tags from 2009–2011. Most of these sharks were tagged at a single aggregation site near Al-Lith, on the central coast of the Saudi Arabian Red Sea. Individuals encountered at this site were all juveniles based on size estimates ranging from 2.5–7 m total length with a sex ratio of approximately 1:1. All other known aggregation sites for juvenile whale sharks are dominated by males. Results from tagging efforts showed that most individuals remained in the southern Red Sea and that some sharks returned to the same location in subsequent years. Diving data were recorded by 37 tags, revealing frequent deep dives to at least 500 m and as deep as 1360 m. The unique temperature-depth profiles of the Red Sea confirmed that several whale sharks moved out of the Red Sea while tagged. The wide-ranging horizontal movements of these individuals highlight the need for multinational, cooperative efforts to conserve R. typus populations in the Red Sea and Indian Ocean.
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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.
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PreprintThe status of coral reef ecology research in the Red Sea( 2013-05) Berumen, Michael L. ; Hoey, Andrew S. ; Bass, W. H. ; Bouwmeester, J. ; Catania, D. ; Cochran, Jesse E. M. ; Khalil, M. T. ; Miyake, S. ; Mughal, M. R. ; Spaet, J. L. Y. ; Saenz-Agudelo, PabloThe Red Sea has long been recognized as a region of high biodiversity and endemism. Despite this diversity and early history of scientific work, our understanding of the ecology of coral reefs in the Red Sea has lagged behind that of other large coral reef systems. We carried out a quantitative assessment of ISI-listed research published from the Red Sea in eight specific topics (apex predators, connectivity, coral bleaching, coral reproductive biology, herbivory, marine protected areas, non-coral invertebrates and reef associated bacteria) and compared the amount of research conducted in the Red Sea to that of the Australia’s Great Barrier Reef (GBR) and the Caribbean. On average, for these eight topics, the Red Sea had 1/6th the amount of research compared to the GBR and about 1/8th the amount of the Caribbean. Further, more than 50% of the published research from the Red Sea originated from the Gulf of Aqaba, a small area (< 2% of the area of the Red Sea) in the far northern Red Sea. We summarize the general state of knowledge in these eight topics and highlight areas of future research priorities for the Red Sea region. Notably, data that could inform science-based management approaches is badly lacking in most Red Sea countries. The Red Sea, as a geologically “young” sea located in one of the warmest regions of the world, has the potential to provide insight to pressing topics such as speciation processes as well as the capacity of reef systems and organisms to adapt to global climate change. As one of the world’s most biodiverse coral reef regions, the Red Sea may yet have a significant role to play in our understanding of coral reef ecology at a global scale.