Comparative population genomics of manta rays has global implications for management.

Understanding population connectivity and genetic diversity is of fundamental importance to conservation. However, in globally threatened marine megafauna, challenges remain due to their elusive nature and wide-ranging distributions. As overexploitation continues to threaten biodiversity across the globe, such knowledge gaps compromise both the suitability and effectiveness of management actions. Here, we use a comparative framework to investigate genetic differentiation and diversity of manta rays, one of the most iconic yet vulnerable groups of elasmobranchs on the planet. Despite their recent divergence, we show how oceanic manta rays (Mobula birostris) display significantly higher heterozygosity than reef manta rays (Mobula alfredi) and that M. birostris populations display higher connectivity worldwide. Through inferring modes of colonization, we reveal how both contemporary and historical forces have likely influenced these patterns, with important implications for population management. Our findings highlight the potential for fisheries to disrupt population dynamics at both local and global scales and therefore have direct relevance for international conservation of marine species.

Distribution of the reef manta ray Mobula alfredi and the oceanic manta ray Mobula birostris in the Philippines: a collaborative effort for conservation.

Little is known about manta ray population size, structure and connectivity in the Philippines. In collaboration with dive operators, non-governmental organizations and authorities, sightings of manta rays were collated into a single national database. Using in-water photographs and videos gathered through citizen science and dedicated research efforts, this study compiled sightings between 2004 and 2020, showing 22 separate sites throughout the archipelago with manta rays present. A total of 392 individual reef manta rays (Mobula alfredi) and 107 oceanic manta rays (Mobula birostris) were identified from the collected footage. Four specific sites in the provinces of Masbate and Palawan together hosted 89% of all identified individuals and accounted for 95% of sightings, highlighting these areas are key aggregation sites. This study also reports the movements of M. birostris within the Philippines, based on photo-identification of three individuals moving 150 km between Cebu and Masbate. Despite the growing number of recreational divers in Daanbantayan and San Jacinto, an 80% decline in M. birostris sightings was observed at these sites. To ensure effective future conservation, it is recommended that efforts focus on the identification and protection of manta ray hotspots and migratory corridors, the creation of a sustainable tourism framework and, most important, the implementation of mitigation strategies to reduce fisheries interactions.

Donsol: an important reproductive habitat for the world's largest fish Rhincodon typus?

Little is known about the reproductive ecology of the whale shark Rhincodon typus. On 15 March 2020, a free-swimming neonate whale shark was found in the shallow, coastal waters of Donsol, Philippines. The total length of the male shark was 60 cm, falling within the species known size-at-birth. This is the third occurrence of neonatal whale sharks reported in the area, and coupled with the occurrence of juveniles and adults, and anecdotal mating and precopulatory behaviour reported herein, the importance of the site for this endangered species is highlighted.

Phylogenomics and species delimitation for effective conservation of manta and devil rays.

Practical biodiversity conservation relies on delineation of biologically meaningful units. Manta and devil rays (Mobulidae) are threatened worldwide, yet morphological similarities and a succession of recent taxonomic changes impede the development of an effective conservation strategy. Here, we generate genome-wide single nucleotide polymorphism (SNP) data from a geographically and taxonomically representative set of manta and devil ray samples to reconstruct phylogenetic relationships and evaluate species boundaries under the general lineage concept. We show that nominal species units supported by alternative data sources constitute independently evolving lineages, and find robust evidence for a putative new species of manta ray in the Gulf of Mexico. Additionally, we uncover substantial incomplete lineage sorting indicating that rapid speciation together with standing variation in ancestral populations has driven phylogenetic uncertainty within Mobulidae. Finally, we detect cryptic diversity in geographically distinct populations, demonstrating that management below the species level may be warranted in certain species. Overall, our study provides a framework for molecular genetic species delimitation that is relevant to wide-ranging taxa of conservation concern, and highlights the potential for genomic data to support effective management, conservation and law enforcement strategies.

Changes in diving behaviour and habitat use of provisioned whale sharks: implications for management.

Whale shark (Rhincodon typus) tourism is increasingly popular at predictable aggregations around the world, but only a few use provisioning to ensure close interactions. Understanding the effects of provisioning on the behaviour of this endangered species is critical to manage this growing industry. We recorded the diving behaviour and habitat use of juvenile whale sharks (n = 4) for a mean of 49.5 provisioned and 33.8 non-provisioned days using temperature-depth-recorders. We found that time spent at the surface (< 2 m) between 6 am and 1 pm increased ~ sixfold, while timing of deep dives shifted from 4-10 am to 10 am-2 pm, i.e. near or at the end of the provisioning activities. The shift might be related to a need to thermoregulate following a prolonged period of time in warmer water. These changes could have fitness implications for individuals frequently visiting the provisioning site. Based on recorded amount of time spent in warm waters and published Q10 values for ectotherms, we estimate a 7.2 ± 3.7% (range 1.3-17.8%) higher metabolic rate when sharks frequent the provisioning site. The observed behavioural, habitat use, and potential fitness shifts should be considered when developing guidelines for sustainable tourism, particularly in light of new provisioning sites developing elsewhere.

Whale sharks Rhincodon typus get cleaned by the blue-streak cleaner wrasse Labroides dimidiatus and the moon wrasse Thalassoma lunare in the Philippines.

Cleaning interactions are essential for healthy marine ecosystem communities. This study reports the first documentation of the whale shark Rhincodon typus cleaning behaviour in the Indo-West Pacific by two wrasse species, the blue-streak cleaner wrasse Labroides dimidiatus and the moon wrasse Thalassoma lunare in Cebu, Philippines. This study documented 36 cleaning interactions with 14 individual whale sharks. The cleaning interactions appear opportunistic rather than targeted by the sharks, unlike that observed in other species of elasmobranchs. Further work should focus on understanding the drivers of these unique cleaning interactions.

In-water observations highlight the effects of provisioning on whale shark behaviour at the world's largest whale shark tourism destination.

The whale shark is the world's largest fish that forms predictable aggregations across its range, many of which support tourism industries. The largest non-captive provisioned whale shark destination globally is at Oslob, Philippines, where more than 500 000 tourists visit yearly. There, the sharks are provisioned daily, year-round, allowing the human-shark interaction in nearshore waters. We used in-water behavioural observations of whale sharks between 2015 and 2017 to understand the relationship between external stimuli and shark behaviour, whether frequency of visits at the site can act as a predictor of behaviour, and the tourist compliance to the code of conduct. Mixed effects models revealed that the number of previous visits at the site was a strong predictor of whale shark behaviour, and that provisioned sharks were less likely to exhibit avoidance. Compliance was poor, with 93% of surveys having people less than 2 m from the animal, highlighting overcrowding of whale sharks at Oslob. Given the behavioural implications to whale sharks highlighted here and the local community's reliance on the tourism industry, it is imperative to improve management strategies to increase tourist compliance and strive for sustainable tourism practices.

Photo-ID and telemetry highlight a global whale shark hotspot in Palawan, Philippines.

The Philippines is home to the second largest known population of whale sharks in the world. The species is listed as endangered due to continued population declines in the Indo-Pacific. Knowledge about the connectivity within Southeast Asia remains poor, and thus international management is difficult. Here, we employed pop-up archival tags, data mining and dedicated effort to understand an aggregation of whale sharks at Honda Bay, Palawan, Philippines, and its role in the species' conservation. Between Apr and Oct 2018, we conducted 159 surveys identifying 117 individual whale sharks through their unique spot patterns (96.5% male, mean 4.5 m). A further 66 individual whale sharks were identified from local operators, and data mined on social media platforms. The satellite telemetry data showed that the whale sharks moved broadly, with one individual moving to Sabah, Malaysia, before returning to the site <1 year later. Similarly, another tagged whale shark returned to the site at a similar periodicity after reaching the Malay-Filipino border. One individual whale shark first identified in East Kalimantan, Indonesia by a citizen scientist was resighted in Honda Bay ~3.5 years later. Honda Bay is a globally important site for the endangered whale shark with connectivity to two neighbouring countries, highlighting the need for international cooperation to manage the species.

DNA metabarcoding assays reveal a diverse prey assemblage for Mobula rays in the Bohol Sea, Philippines.

Diet studies provide base understanding of trophic structure and are a valuable initial step for many fields of marine ecology, including conservation and fisheries biology. Considerable complexity in marine trophic structure can exist due to the presence of highly mobile species with long life spans. Mobula rays are highly mobile, large, planktivorous elasmobranchs that are frequently caught either directly or as bycatch in fisheries, which, combined with their conservative life history strategy, makes their populations susceptible to decline in intensely fished regions. Effective management of these iconic and vulnerable species requires an understanding of the diets that sustain them, which can be difficult to determine using conventional sampling methods. We use three DNA metabarcode assays to identify 44 distinct taxa from the stomachs (n = 101) of four sympatric Mobula ray species (Mobula birostris, Mobula tarapacana, Mobula japanica, and Mobula thurstoni) caught over 3 years (2013-2015) in a direct fishery off Bohol in the Philippines. The diversity and incidence of bony fishes observed in ray diets were unprecedented. Nevertheless, rays showed dietary overlap, with krill (Euphausia) dominating their diet. Our results provide a more detailed assessment of sympatric ray diets than was previously described and reveal the complexity that can exist in food webs at critical foraging habitats.

Whale Shark Tourism: Impacts on Coral Reefs in the Philippines.

Reef-based tourism has been developing rapidly in recent decades yet its impacts on reef ecosystems are often overlooked. In Tan-awan, Oslob, Philippines, whale sharks are attracted to the shallow reefs where they are provisioned up to 50 tons y-1 of feed and this phenomenon in turn attracts >300,000 y-1 visitors. Given the intensive provisioning and concentrating tourism activities, we hypothesized that the whale shark tourism-impacted site (IS) will have greater impacts on reef degradation and higher anthropogenic nitrogen pollution level compared to its reference site (RS). Ecological surveys revealed that relative to the RS, the IS had 36% higher relative abundance of Pocillopora and Porites coral over other genera, >2.5-fold lower coral density, and 20% higher macroalgal cover, which we concluded are signs of reef degradation. Also, we conducted stable nitrogen isotope analysis on gorgonian skeletons to trace nitrogen sources at both sites through time. Although an average 1‰ isotope enrichment found in the IS relative to the RS could indicate anthropogenic nitrogen inputs in the IS, this enrichment was consistent over time and existed before the tourism developed. Despite that, we cautioned against the imminent threat of local eutrophication caused by the continued inputs of nitrogen derived from provisioning and tourism activities. In summary, this study provided the first documentation of the impacts of provisioned whale shark tourism on the local reefs in Tan-awan and established an ecological baseline for future comparisons. Such assessments can offer important information on reef health, coastal development, and tourism management.

Satellite tracking of juvenile whale sharks in the Sulu and Bohol Seas, Philippines.

The whale shark Rhincodon typus was uplisted to 'Endangered' in the 2016 IUCN Red List due to >50% population decline, largely caused by continued exploitation in the Indo-Pacific. Though the Philippines protected the whale shark in 1998, concerns remain due to continued take in regional waters. In light of this, understanding the movements of whale sharks in the Philippines, one of the most important hotspots for the species, is vital. We tagged 17 juvenile whale sharks with towed SPOT5 tags from three general areas in the Sulu and Bohol Seas: Panaon Island in Southern Leyte, northern Mindanao, and Tubbataha Reefs Natural Park (TRNP). The sharks all remained in Philippine waters for the duration of tracking (6-126 days, mean 64). Individuals travelled 86-2,580 km (mean 887 km) at a mean horizontal speed of 15.5 ± 13.0 SD km day-1. Whale sharks tagged in Panaon Island and Mindanao remained close to shore but still spent significant time off the shelf (>200 m). Sharks tagged at TRNP spent most of their time offshore in the Sulu Sea. Three of twelve whale sharks tagged in the Bohol Sea moved through to the Sulu Sea, whilst two others moved east through the Surigao Strait to the eastern coast of Leyte. One individual tagged at TRNP moved to northern Palawan, and subsequently to the eastern coast of Mindanao in the Pacific Ocean. Based on inferred relationships with temperature histograms, whale sharks performed most deep dives (>200 m) during the night, in contrast to results from whale sharks elsewhere. While all sharks stayed in national waters, our results highlight the high mobility of juvenile whale sharks and demonstrate their connectivity across the Sulu and Bohol Seas, highlighting the importance of the area for this endangered species.

Feeding the world's largest fish: highly variable whale shark residency patterns at a provisioning site in the Philippines.

Provisioning wildlife for tourism is a controversial yet widespread practice. We analysed the residency patterns of juvenile whale sharks (Rhincodon typus) in Oslob, Philippines, where provisioning has facilitated a large shark-watching operation since 2011. We identified 208 individual sharks over three years, with an average of 18.6 (s.d. = 7.8, range = 6-43) individuals sighted per week. Weekly shark abundance varied seasonally and peak-season abundance (approx. May-November) increased across years. Whale sharks displayed diverse individual site visitation patterns ranging from a single visit to sporadic visits, seasonal residency and year-round residency. Nine individuals became year-round residents, which represents a clear response to provisioning. The timing of the seasonal peak at Oslob did not align with known non-provisioned seasonal aggregations elsewhere in the Philippines, which could suggest that seasonal residents at Oslob exploit this food source when prey availability at alternative sites is low. Since prolonged residency equates to less time foraging naturally, provisioning could influence foraging success, alter distributions and lead to dependency in later life stages. Such impacts must be carefully weighed against the benefits of provisioning (i.e. tourism revenue in a remote community) to facilitate informed management decisions.

Mobulid rays feed on euphausiids in the Bohol Sea.

Mobulid rays have a conservative life history and are caught in direct fisheries and as by-catch. Their subsequent vulnerability to overexploitation has recently been recognized, but fisheries management can be ineffective if it ignores habitat and prey preferences and other trophic interactions of the target species. Here, we assessed the feeding ecology of four mobulids (Manta birostris, Mobula tarapacana, M. japanica, M. thurstoni) in the Bohol Sea, Philippines, using stomach contents analysis of fisheries specimens landed between November and May in 2013-2015. We show that the mobulids feed heavily on euphausiid krill while they are in the area for approximately six months of the year. We found almost no trophic separation among the mobulid species, with Euphausia diomedeae as the major prey item for all species, recorded in 81 of 89 total stomachs (91%). Mobula japanica and M. thurstoni almost exclusively had this krill in their stomach, while M. tarapacana had a squid and fish, and Ma. birostris had myctophid fishes and copepods in their stomachs in addition to E. diomedeae. This krill was larger than prey for other planktivorous elasmobranchs elsewhere and contributed a mean of 61 364 kcal per stomach (±105 032 kcal s.e., range = 0-631 167 kcal). Our results show that vertically migrating mesopelagic species can be an important food resource for large filter feeders living in tropical seas with oligotrophic surface waters. Given the conservative life history of mobulid rays, the identification of common foraging grounds that overlap with fishing activity could be used to inform future fishing effort.

Learning from a provisioning site: code of conduct compliance and behaviour of whale sharks in Oslob, Cebu, Philippines.

While shark-based tourism is a rapidly growing global industry, there is ongoing controversy about the effects of provisioning on the target species. This study investigated the effect of feeding on whale sharks (Rhincodon typus) at a provisioning site in Oslob, Cebu, in terms of arrival time, avoidance and feeding behaviour using photo-identification and focal follows. Additionally, compliance to the code of conduct in place was monitored to assess tourism pressure on the whale sharks. Newly identified sharks gradually arrived earlier to the provisioning site after their initial sighting, indicating that the animals learn to associate the site with food rewards. Whale sharks with a long resighting history showed anticipatory behaviour and were recorded at the site on average 5 min after the arrival of feeder boats. Results from a generalised linear mixed model indicated that animals with a longer resighting history were less likely to show avoidance behaviour to touches or boat contact. Similarly, sequential data on feeding behaviour was modelled using a generalised estimating equations approach, which suggested that experienced whale sharks were more likely to display vertical feeding behaviour. It was proposed that the continuous source of food provides a strong incentive for the modification of behaviours, i.e., learning, through conditioning. Whale sharks are large opportunistic filter feeders in a mainly oligotrophic environment, where the ability to use novel food sources by modifying their behaviour could be of great advantage. Non-compliance to the code of conduct in terms of minimum distance to the shark (2 m) increased from 79% in 2012 to 97% in 2014, suggesting a high tourism pressure on the whale sharks in Oslob. The long-term effects of the observed behavioural modifications along with the high tourism pressure remain unknown. However, management plans are traditionally based on the precautionary principle, which aims to take preventive actions even if data on cause and effect are still inconclusive. Hence, an improved enforcement of the code of conduct coupled with a reduction in the conditioning of the whale sharks through provisioning were proposed to minimise the impacts on whale sharks in Oslob.

Population structure and residency patterns of whale sharks, Rhincodon typus, at a provisioning site in Cebu, Philippines.

This study represents the first description of whale sharks, Rhincodon typus, occurring at a provisioning site in Oslob, Cebu, Philippines. Frequent observations of sharks are often difficult, even at tourism sites, giving rise to provisioning activities to attract them. The present study provides repeated longitudinal data at a site where daily provisioning activities took place, and whale sharks were present every day. A total of 158 individual whale sharks were photographically identified between Mar 2012 and Dec 2013, with 129 males (82%), 19 females (12%) and 10 (6%) of undetermined sex. Mean estimated total length was 5.5 m (±1.3 m S.D.). Twenty individuals were measured with laser photogrammetry to validate researchers' estimated sizes, yielding a good correlation (r (2) = 0.83). Fifty-four (34%) individuals were observed being hand-fed by local fishermen (provisioned), through in-water behavioural observations. Maximum likelihood methods were used to model mean residency time of 44.9 days (±20.6 days S.E.) for provisioned R. typus contrasting with 22.4 days (±8.9 days S.E.) for non-provisioned individuals. Propeller scars were observed in 47% of the animals. A mean of 12.7 (±4.3 S.D.) R. typus were present in the survey area daily, with a maximum of 26 individuals (Aug 10 2013) and a minimum of 2 (Dec 6 2012). Twelve (8%) individuals were seen on at least 50% of survey days (n = 621), with a maximum residency of 572 days for one individual (P-396). Twenty four individuals were photographically identified across regional hotsposts, highlighting the species' migratory nature and distribution. Extended residency and differences in lagged identification rates suggest behavioural modification on provisioned individuals, underlying the necessity for proper management of this tourism activity.