Population genetic structure of Earth's largest fish, the whale shark (Rhincodon typus)

Large pelagic vertebrates pose special conservation challenges because their movements generally exceed the boundaries of any single jurisdiction. To assess the population structure of whale sharks (Rhincodon typus), we sequenced complete mitochondrial DNA control regions from individuals collected across a global distribution. We observed 51 single site polymorphisms and 8 regions with indels comprising 44 haplotypes in 70 individuals, with high haplotype (h = 0.974 +/- 0.008) and nucleotide diversity (pi = 0.011 +/- 0.006). The control region has the largest length variation yet reported for an elasmobranch (1143-1332 bp). Phylogenetic analyses reveal no geographical clustering of lineages and the most common haplotype was distributed globally. The absence of population structure across the Indian and Pacific basins indicates that oceanic expanses and land barriers in Southeast Asia are not impediments to whale shark dispersal. We did, however, find significant haplotype frequency differences (AMOVA, Phi(ST) = 0.107, P < 0.001) principally between the Atlantic and Indo-Pacific populations. In contrast to other recent surveys of globally distributed sharks, we find much less population subdivision and no evidence for cryptic evolutionary partitions. Discovery of the mating and pupping areas of whale sharks is key to further population genetic studies. The global pattern of shared haplotypes in whale sharks provides a compelling argument for development of broad international approaches for management and conservation of Earth's largest fish.     

Segregation and foraging ecology of whale sharks, Rhincodon typus, in the southwestern Gulf of California

Sharks segregate by sex and size, but few studies have attempted to explain such behaviors. To address this, we examined aggregations and the foraging ecology of whale sharks in Bahía de La Paz (BLP) with aerial and ship surveys and direct observation. Zooplankton abundance and composition, and hydrographic conditions were analyzed in relation to whale shark occurrence to explore underlying factors causing segregations. We observed large aggregations of juveniles (<9 m total length, TL) inshore, comprised by 60 % male individuals, and small aggregations of adults (>9 m TL) offshore, composed of 84 % females. Juvenile sharks were associated to turbid shallow waters in BLP, where they performed stationary and dynamic suction feeding on dense copepod swarms. Adults occurred in oceanic waters and fed by ram-filtering on diffuse patches of euphausiids, with no association to oceanographic conditions. Such segregation may be advantageous to juvenile R. typus utilizing shallow coastal waters to find abundant preferred prey needed for their fast growth rates. Our studies suggest that the main driving forces of whale shark segregation by sex and size in BLP may be diet preference for juveniles and habitat preference for adult sharks.     

Observations of stranded and swimming whale sharks Rhincodon typus in Khor Al-Zubair,NW Arabian Gulf and Shatt Al-Arab Estuary,Iraq

This study is the first record of a whale shark Rhincodon typus in Iraqi waters and the second record from the Arabian (Persian) Gulf portion of the north-west Indian Ocean. The stranding and sighting events were documented by photos of three individuals: the stranded specimen was 6.5 m total length (L_T) and the free-swimming individuals were c. 1–2 and 2–3 m L_T respectively_. An appeal is made for Iraqi policy makers to participate in regional and international organizations for the conservation of this endangered species.     

Seasonal trends in whale shark Rhincodon typus sightings in an established tourism site in the Gulf of California,Mexico

The number of individual whale shark Rhincodon typus sightings registered October 2015–March 2018 in Bahia de La Paz, Mexico, ranged from 73 to 129 animals per season (total 1662), with the majority of them identified as males. Density plot maps showed high correlations in sightings between sample seasons and revealed potential hotspot areas. Our study provides an essential baseline of information for the management of whale shark conservation and the associated touristic activities in the region.     

Whale shark Rhincodon typus strandings in the Gulf of California,Mexico

The present study analyses whale shark Rhincodon typus stranding in the Gulf of California, Mexico, reported by the public, scientists, authorities and artisanal fishermen. A total of 14 strandings were documented during the period 2001–2018. The total length of R. typus ranged from 350–1,102 cm, with a sex ratio of 3.5:1 (males: females). This study highlights potential stranding areas, the need for better stranding protocols to assist R. typus recovery and the importance of samples from dead animals for scientific research.     

An unprecedented aggregation of whale sharks, Rhincodon typus, in Mexican coastal waters of the Caribbean Sea

Whale sharks, Rhincodon typus, are often perceived as solitary behemoths that live and feed in the open ocean. To the contrary, evidence is accumulating that they are gregarious and form seasonal aggregations in some coastal waters. One such aggregation occurs annually north of Cabo Catoche, off Isla Holbox on the Yucatán Peninsula of Mexico. Here we report a second, much denser aggregation of whale sharks (dubbed "the Afuera") that occurs east of the tip of the Yucatán Peninsula in the Caribbean Sea. The 2009 Afuera event comprised the largest aggregation of whale sharks ever reported, with up to 420 whale sharks observed in a single aerial survey, all gathered in an elliptical patch of ocean approximately 18 km(2). Plankton studies indicated that the sharks were feeding on dense homogenous patches of fish eggs, which DNA barcoding analysis identified as belonging to little tunny, Euthynnus alletteratus. This contrasts with the annual Cabo Catoche aggregation nearby, where prey consists mostly of copepods and sergestid shrimp. Increased sightings at the Afuera coincide with decreased sightings at Cabo Catoche, and both groups have the same sex ratio, implying that the same animals are likely involved in both aggregations; tagging data support this idea. With two whale shark aggregation areas, high coastal productivity and a previously-unknown scombrid spawning ground, the northeastern Yucatán marine region is a critical habitat that deserves more concerted conservation efforts.     

Distribution and feeding habitat characterization of whale sharks Rhincodon typus in a protected area in the north Caribbean Sea

The relationship between the distribution of the whale shark Rhincodon typus and hydrobiological variables in the Caribbean Sea during 2005–2009 was analysed. Monthly trips were made to the R. typus aggregation area during the months when this species is present in the region (May to September) to record sightings and hydrological data and to collect samples to determine nutrients, chlorophyll a (Chl a) and zooplankton biomass. A total of 2104 R. typus were counted and three zones of high abundance were identified: Cabo‐Catoche, Contoy (both within the Whale Shark Biosphere Reserve, WSBR) and the zone knows as Afuera. The zones of greatest R. typus density within the WSBR were characterized by high Chl a concentrations (median: 1·1 mg m^?3, interpercentile range: 0·5–1·8 mg m^?3) and high nutrient concentrations, such as ammonium (median: 2·5 µmol l^?1, interpercentile range: 0·5–6·4 µmol l^?1), due to the influence of local upwelling. A generalized additive model (GAM) was used to explore the relationship between R. typus distribution and the environmental variables inside WSBR. Zooplankton biomass was the most influential environmental variable, supporting the close relationship between R. typus distribution and biological productivity. Copepods were the dominant zooplankton group within the WSBR. In the Afuera zone, there were large R. typus aggregations (>80 individuals) associated with zooplankton dominated by fish eggs and significantly higher mean ± s.d. biomass (3356·1 ± 1960·8 mg m^?3) compared with that recorded inside the WSBR (103·5 ± 57·2 mg m^?3). The differences among zones generated changes in R. typus distribution patterns and provided opportunities to develop local management strategies for this species.     

Deep-diving behaviour of a whale shark Rhincodon typus during long-distance movement in the western Indian Ocean

A whale shark Rhincodon typus satellite tagged off the coast of Mozambique showed a highly directional movement across the Mozambique Channel and around the southern tip of Madagascar, a minimum distance of 1200 km in 87 days. Dives to depths well into the mesopelagic and bathypelagic zones (1286 m maximum depth) were recorded in a bathymetrically non-constraining habitat. The water temperature range recorded during the fish's movement was 3·4–29·9° C.     

General descriptions of the dermis structure of a juvenile whale shark Rhincodon typus from the Gulf of California

The aim of this study is to provide preliminary observations on the microanatomy of Rhincodon typus skin using histology and electron microscopy analyses. Skin biopsies were obtained from a deceased juvenile male shark (548 cm total length) stranded in La Paz, Mexico, during February 2018. The results of this study evidenced the basic structure of the dermal denticles in the epidermis of the trunk of the shark, as well as the composition of the connective tissue in the hypodermis. Histological images of the hypodermis showed a high concentration of collagen fibres, formed by a large number of fine and wavy fibres of compact shape and little intercellular substance.     

The use of machine learning to detect foraging behaviour in whale sharks: a new tool in conservation

In this study we present the first attempt at modelling the feeding behaviour of whale sharks using a machine learning analytical method. A total of eight sharks were monitored with tri-axial accelerometers and their foraging behaviours were visually observed. Our results highlight that the random forest model is a valid and robust approach to predict the feeding behaviour of the whale shark. In conclusion this novel approach exposes the practicality of this method to serve as a conservation tool and the capability it offers in monitoring potential disturbances of the species.     

Population structure of a whale shark Rhincodon typus aggregation in the Red Sea

The presence of whale sharks Rhincodon typus were recorded around Shib Habil, a small, coastal reef off the Red Sea coast of Saudi Arabia, from 2010 to 2015. A total of 267 suitable photographs resulting in the identification of 136 individuals, were documented from 305 encounters. Sharks were divided evenly between the sexes with no evidence of temporal or spatial segregation. All individuals were immature based on size estimates and, for males, juvenile clasper morphology. Scars were reported for 57% of R. typus with 15% showing evidence of propeller trauma. Estimates of population size and patterns of residency were calculated by modelling the lagged identification rate. Multiple models were run simultaneously and compared using the Akaike information criterion. An open population model was found to best represent the data and estimates a daily abundance between 15 and 34 R. typus during the aggregation season, with local residence times ranging from 4 to 44 days. Residence times away from Shib Habil range from 15 to 156 days with a permanent emigration–death rate between 0·07 and 0·58 individuals year^?1. These results are broadly similar to those from other aggregations of R. typus, although the observed sexual parity and integration found at this site is unique for the species and needs further study.     

A new record of whale shark Rhincodon typus in Brazilian waters: a report of association with Caranx crysos

In May 2011, a Rhincodon typus was sighted on the continental shelf of the central Brazilian coast, in the vicinity of a gas platform. During the video record, an interspecific following association was observed between a Caranx crysos school and the R. typus.     

Isolation and characterization of microsatellite loci in the whale shark (Rhincodon typus)

In preparation for a study on population structure of the whale shark (Rhincodon typus), nine species-specific polymorphic microsatellite DNA markers were developed. An initial screening of 50 individuals from Holbox Island, Mexico found all nine loci to be polymorphic, with two to 17 alleles observed per locus. Observed and expected heterozygosity per locus ranged from 0.200 to 0.826 and from 0.213 to 0.857, respectively. Neither statistically significant deviations from Hardy-Weinberg expectations nor statistically significant linkage disequilibrium between loci were observed. These microsatellite loci appear suitable for examining population structure, kinship assessment and other applications.     

Seabird diversity hotspot linked to ocean productivity in the Canary Current Large Marine Ecosystem

Upwelling regions are highly productive habitats targeted by wide-ranging marine predators and industrial fisheries. In this study, we track the migratory movements of eight seabird species from across the Atlantic; quantify overlap with the Canary Current Large Marine Ecosystem (CCLME) and determine the habitat characteristics that drive this association. Our results indicate the CCLME is a biodiversity hotspot for migratory seabirds; all tracked species and more than 70% of individuals used this upwelling region. Relative species richness peaked in areas where sea surface temperature averaged between 15 and 20°C, and correlated positively with chlorophyll a, revealing the optimum conditions driving bottom-up trophic effects for seabirds. Marine vertebrates are not confined by international boundaries, making conservation challenging. However, by linking diversity to ocean productivity, our research reveals the significance of the CCLME for seabird populations from across the Atlantic, making it a priority for conservation action.     

Landings of whale sharks Rhincodon typus Smith, 1828 in Indian waters since protection in 2001 through the Indian Wildlife (Protection) Act, 1972

Since 28^th May 2001, Whale shark Rhincodon typus Smith, 1828 have received the highest protected status for an animal in India through the Indian Wildlife (Protection) Act, 1972 Schedule-1. However, landings have still been recorded off the Indian coast since 2001, mostly as incidental bycatch in commercial fishing operations, and other sightings have also been reported. In the 1990’s, a targeted whale shark fishery existed off the Gujarat coast following increased demand for the flesh in some other Asian countries. Since the ban, landings of whale sharks have decreased substantially with only 79 recorded between 2001 and 2011. Landings were recorded in each year and in each month of the year with the highest landings in January and February. Between 2001 and 2011, the smallest specimen reported from Indian waters was a 94 cm TL individual and the largest was a 13.7 m TL individual, with most individuals recorded in the 4–6 m TL size class. Small juveniles of less than 3 m TL are rarely recorded in the literature and appear to be rarely observed globally. Between 2006 and 2011, seven juveniles of less than 3 m TL were recorded from two landing sites. Despite the continued landing of whale sharks along the Indian coasts since 2001, the protection of this species appears to have substantially reduced the catches with only incidental landings and strandings now evident. The protection status of whale sharks in India is generally well understood by fishers, but still there is need for further education regarding the current national legislation and vulnerability of the species.     

Aggregations of juvenile whale sharks (<Emphasis Type="Italic">Rhincodon typus</Emphasis>) in the Gulf of Tadjoura,Djibouti

A total of 23 whale sharks were identified over a 5 d period in the Arta Bay region of the Gulf of Tadjora, Djibouti. Most of the sharks aggregating in this area were small (<4 m TL) males. Individuals were identified using photographs of distinctive scars and spot and stripe patterns on the sides of the animals. Of these, 65% had scarring that was attributable to boat or propeller strikes. Most of the whale sharks we encountered were feeding on dense accumulations of plankton in shallow water just off (10–200 m) the shoreline. This food source may account for the aggregation of sharks in this area. One 3 m male shark was tagged with an ARGOS (Splash) satellite tag for 9 d. During this time the shark traversed to the shoreline on the opposite side of the Gulf (a distance of 14 km) and then returned to the Arta Bay area before retracing his path to the other shore. The shark spent most of the daylight hours at the surface, while at night dives were more frequent, deeper and for longer durations.

Short‐term survival and movements of Atlantic sharpnose sharks captured by hook‐and‐line in the north‐east Gulf of Mexico

Ultrasonic telemetry was used to compare post‐release survival and movements of Atlantic sharpnose sharks Rhizoprionodon terraenovae in a coastal area of the north‐east Gulf of Mexico. Ten fish were caught with standardized hook‐and‐line gear during June to October 1999. Atlantic sharpnose sharks were continuously tracked after release for periods of 0·75 to 5·90 h and their positions recorded at a median interval of 9 min. Individual rate of movement was the mean of all distance and time measurements for each fish. Mean ± s.e . individual rate of movement was 0·45 ± 0·06 total lengths per second (L_T s^?1) and ranged from 0·28 to 0·92 L_T s^?1 over all fish. Movement patterns did not differ between jaw and internally hooked Atlantic sharpnose sharks. Individual rate of movement was inversely correlated with bottom water temperature at capture (r² = 0·52, P ≤ 0·05). No consistent direction in movement was detected for Atlantic sharpnose sharks after release, except that they avoided movement towards shallower areas. Capture‐release survival was high (90%), with only one fish not surviving, i.e. this particular fish stopped movement for a period of 10 min. Total rate of movement was total distance over total time (m min^?1) for each Atlantic sharpnose shark. Mean total rate of movement was significantly higher immediately after release at 21·5 m min^?1 over the first 1·5 h of tracking, then decreased to 11·2 m min^?1 over 1·5–6 h, and 7·7 m min^?1 over 3–6 h (P ≤ 0·002), which suggested initial post‐release stress but quick recovery from capture. Thus, high survival (90%) and quick recovery indicate that the practice of catch‐and‐release would be a viable method to reduce capture mortality for R. terraenovae.     

Evidence of continued hunting of whale sharks <Emphasis Type="Italic">Rhincodon typus</Emphasis> in the Maldives

Superficial dermal wounds in whale sharks are reported to heal rapidly as with many other elasmobranchs. Here observations of two wounded whale sharks (Rhincodon typus) in Maldivian waters suggest that free ranging sharks are able to recover and rapidly heal from the effects of deeper wounding on internal organs or amputations. One specimen observed impaled by a wooden harpoon shaft, was subsequently re-encountered nearly a year later. The other suffered a near severed first dorsal fin but showed signs of rapid healing. These observations illustrate that despite national bans in whale sharks fishing, the practise persists in the Maldives. Further research to increase understanding of the demography of aggregations of this species is necessary before the impact of illegal exploitation on regional population trends can be determined. National governments are encouraged to enhance marine conservation outreach and education programmes throughout their territories.