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© The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Hardenstine, R., He, S., Cochran, J., Braun, C., Cagua, E., Pierce, S., Prebble, C., Rohner, C., Saenz‐Angudelo, P., Sinclair‐Taylor, T., Skomal, G., Thorrold, S., Watts, A., Zakroff, C., & Berumen, M. Pieces in a global puzzle: population genetics at two whale shark aggregations in the western Indian Ocean. Ecology and Evolution, 12(1), (2022): e8492, https://doi.org/10.1002/ece3.8492., 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., Work in Saudi Arabia was funded in part by KAUST baseline research funds (to MLB), KAUST award nos. USA00002 and KSA 00011 (to SRT), and the U.S. National Science Foundation (OCE 0825148 to SRT and GBS).

© The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Hardenstine, R., He, S., Cochran, J., Braun, C., Cagua, E., Pierce, S., Prebble, C., Rohner, C., Saenz‐Angudelo, P., Sinclair‐Taylor, T., Skomal, G., Thorrold, S., Watts, A., Zakroff, C., & Berumen, M. Pieces in a global puzzle: population genetics at two whale shark aggregations in the western Indian Ocean. Ecology and Evolution, 12(1), (2022): e8492, https://doi.org/10.1002/ece3.8492., 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., Work in Saudi Arabia was funded in part by KAUST baseline research funds (to MLB), KAUST award nos. USA00002 and KSA 00011 (to SRT), and the U.S. National Science Foundation (OCE 0825148 to SRT and GBS).

The whale shark, Rhincodon typus, is a long-lived migratory species inhabiting tropical and warm-temperate waters worldwide. Seasonal aggregations of whale sharks in shallow coastal waters of many countries have led to the development of ecotourism industries. Whale sharks that aggregate seasonally at Ningaloo Reef in Western Australia have a migration range within Indonesian and Southeast Asian waters. However, very little is known about their behaviour, local migration patterns, or potential threats faced in this region. In this study, we investigated traditional ecological knowledge of whale sharks through interviews with Bajo and other fishers from five settlements in the Timor and Roti Islands in eastern Indonesia. We found that there are culturally driven prohibitions and customary beliefs concerning whale sharks among Bajo fishermen, who commonly sight sharks in the Timor Sea, in southern Indonesian and Timor Leste waters. Sightings are most common during the months of August to December. Interviews also indicate a low level of harvesting of whale sharks in the region. The results demonstrate the potential for combining traditional ecological knowledge and new technology to develop whale shark management strategies, and to determine the predictability of whale shark appearances as one vital factor in assessing the potential for development of small-scale whale shark ecotourism initiatives.

Seven whale sharks were tracked using satellite-linked tags from Ningaloo Reef, off northern Western Australia, following tagging in April and June 2002 and April–May 2005. We investigated how the movements of those whale shark tracks were influenced by geostrophic surface currents during sequential one-week periods by using a passive diffusion model parameterised with observed starting locations of the sharks and weekly maps of surface current velocity and direction (derived from altimetry). We compared the outputs from the passive diffusion model and maps of chlorophyll-a concentration (SeaWiFs/MODIS) and with the actual tracks of the sharks using GIS and generalized linear mixed-effects models (GLMM). The GLMM indicated very little support for passive diffusion with sea-surface ocean currents influencing whale shark distributions in the north eastern Indian Ocean. Moreover, the sharks' movements correlated only weakly with the spatial distribution of sea-surface chlorophyll-a concentrations. The seven whale sharks had average swimming speeds comparable with those recorded in other satellite tracking studies of this species. Swimming speeds of the seven sharks were similar to those reported in previous studies and up to three times greater than the maximum sea-surface current velocities that the sharks encountered while traversing into lower southerly latitudes (moving northward towards the equator). Our results indicate that whale sharks departing from Ningaloo travel actively and independently of near-surface currents where they spend most of their time despite additional metabolic costs of this behaviour.

Seasonal observations of whale shark abundance recorded by ecotourist operators at Ningaloo Reef, Western Australia from 1999 to 2004 were compared with weekly regional and global oceanographic and atmospheric variables, including average sea surface temperatures, along-shelf wind shear, sea level and the Southern Oscillation Index (SOI). Estimates of these physical variables were derived from either ground-based data or from remote sensing instruments. A generalised linear mixed-effects modelling (GLMM) approach with random sampling and model simulation was used to determine the relationships between the number of whale sharks and all model variants of the environmental parameters, using information-theoretic weights of evidence to rank models. SOI and wind shear had the most support for explaining the deviance in weekly whale shark abundance at Ningaloo Reef during a season. The SOI and wind shear variables positively influenced whale shark abundance such that more sharks were sighted when the Southern Oscillation was stronger and along-shelf winds were increasingly prevalent. This may reflect changes in the strength of oceanographic processes such as the Leeuwin Current (in response to the Southern Oscillation) and wind/current driven upwelling which may affect the abundance of whale sharks transported to the region and/or the availability of their prey by driving productivity changes. Crown Copyright

We document two recent beach strandings of whale sharks on both the east and west coasts of Australia and compare them to strandings of other species of shark and cetaceans. Historically, whale shark stranding is an unusual phenomenon in Australia. Although the reasons for whale shark strandings are speculative, their low frequency suggests they are unlikely to pose any considerable threat to the population viability of this species in Australia.

A dead 5.5 m long female whale shark (Rhincodon typus) was brought to shore by fishermen in Samutprakarn, Thailand. A necropsy was subsequently performed. Several isolated hemorrhages with multiple ulcers were observed in the gastric mucosa, extending into the subserosal tissue of the stomach. An extremely hard and stiff plastic drinking straw was found in the gastric lumen. The hardening of the straw was due to the reaction of stomach enzyme to plastic, which became a sharp foreign object inside the stomach. Although putrefaction and autolysis was observed, all other organ systems displayed normal findings and no competing cause of death was in evidence. Cause of death was thus suspected to be attributed to the ingestion of the drinking straw, with subsequent irritation of the stomach mucosa causing wounds and infections and may be not possible to eliminate due to the floating nature of the plastic. Since this is a very rare case, due to the fact that shark could usually eliminate the stomach content, we should not overlook the danger of plastic pollution in the marine environment., December 15-17, 2007, Royal Phuket City Hotel, Phuket, Thailand

A dead 5.5 m long female whale shark (Rhincodon typus) was brought to shore by fishermen in Samutprakarn, Thailand. A necropsy was subsequently performed. Several isolated hemorrhages with multiple ulcers were observed in the gastric mucosa, extending into the subserosal tissue of the stomach. An extremely hard and stiff plastic drinking straw was found in the gastric lumen. The hardening of the straw was due to the reaction of stomach enzyme to plastic, which became a sharp foreign object inside the stomach. Although putrefaction and autolysis was observed, all other organ systems displayed normal findings and no competing cause of death was in evidence. Cause of death was thus suspected to be attributed to the ingestion of the drinking straw, with subsequent irritation of the stomach mucosa causing wounds and infections and may be not possible to eliminate due to the floating nature of the plastic. Since this is a very rare case, due to the fact that shark could usually eliminate the stomach content, we should not overlook the danger of plastic pollution in the marine environment.

1. Precise estimates of demographic rates are key components of population models used to predict the effects of stochastic environmental processes, harvest scenarios and extinction probability. 2. We used a 12-year photographic identification library of whale sharks from Ningaloo Reef, Western Australia to construct Cormack-Jolly-Seber (CJS) model estimates of survival within a capture-mark-recapture (CMR) framework. Estimated survival rates, population structure and assumptions regarding age at maturity, longevity and reproduction frequency were combined in a series of age-classified Leslie matrices to infer the potential trajectory of the population. 3. Using data from 111 individuals, there was evidence for time variation in apparent survival (phi) and recapture probability (p). The null model gave a (phi) over cap of 0.825 (95% CI: 0.727-0.893) and (p) over cap = 0.184 (95% CI: 0.121-0.271). The model-averaged annual (phi) over cap ranged from 0.737 to 0.890. There was little evidence for a sex effect on survival. 4. Using standardized total length as a covariate in the CMR models indicated a size bias in phi. Ignoring the effects of time, a 5-m shark has a (phi) over cap = 0.59 and a 9 m shark has (phi) over cap = 0.81. 5. Of the 16 model combinations considered, 10 (63%) indicated a decreasing population (lambda < 1). For models based on age at first reproduction (alpha) of 13 years, the mean age of reproducing females at the stable age distribution ((A) over bar) ranged from 15 to 23 years, which increased to 29-37 years when alpha was assumed to be 25. 6. All model scenarios had higher total elasticities for non-reproductive female survival [E(s(nr))] compared to those for reproductive female survival [E(s(r))]. 7. Assuming relatively slow, but biologically realistic, vital rates (alpha = 25 and biennial reproduction) and size-biased survival probabilities, our results suggest that the Ningaloo Reef population of whale sharks is declining, although more