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The reproductive biology of the whale shark (Rhincodon typus), the world’s largest fish, remains poorly understood, in large part due to the rarity of observations of neonates and of breeding behaviours. Although several regions in Indonesia, including Saleh Bay (West Nusa Tenggara Province), have been identified as aggregation and sighting sites for juvenile whale sharks (2–7 m total length, TL), smaller individuals from these potential nursery areas have not been previously documented. In August 2024, fishermen operating lift-net fishing vessels (bagans) in eastern Saleh Bay reported five separate sightings of a small whale shark estimated at 1.2–1.5 m TL and approximately four months old. Subsequently, on 6 September 2024, a male neonate measuring approximately 135–145 cm TL, estimated to be around four months old, was incidentally caught inside a bagan lift-net. These observations represent the first records of neonatal whale sharks in Indonesia and among the smallest free-swimming individuals ever documented globally, and suggest that Saleh Bay may serve as a pupping and early nursery area for whale sharks. These findings highlight the ecological significance of Saleh Bay for the early life stages of whale sharks and underscore the importance of collaborative monitoring and citizen science involving bagan fishermen in advancing the research and conservation of this endangered species.

Though a previous study in Sudan confirmed the existence of a living hybrid of an oceanic manta ray (Mobula birostris) and a reef manta ray (M. alfredi), courtship behaviors between the two closely related species have never been documented. Here we report the first observation of courtship behaviors between two male M. birostris and a female M. alfredi at a manta ray cleaning station on a shallow coral reef seamount in Misool, Raja Ampat, Indonesia. The observed courtship event lasted for approximately 45 min and involved one male oceanic manta actively chasing the mature reef manta female around the cleaning station and repeatedly bumping her on the left wing tip with his right cephalic lobe, while the second male continuously flanked the female to seemingly prevent her retreat from the cleaning station and potential evasion of the pursuing male. Notably, the female exhibited a rapid coloration change, likely indicative of courtship-related stress, transitioning from the striking pale hue she exhibited throughout the courtship activity to a normal chevron pattern once the males departed.

Despite the increased international attention to whale shark conservation, their populations remain predominantly depleted due to anthropogenic activities such as fishing, ship collisions, and marine pollution. Reports of whale shark strandings in Indonesia have been increasing in recent years, elevating concerns regarding their well-being and the potential disturbance to their population recovery. However, limited understanding of stranding patterns, trends, and the oceanographic factors potentially driving these events has resulted in efforts focusing primarily on responding to strandings rather than implementing effective mitigation strategies. Using a 13-year stranding dataset ( n  = 115) obtained from open-access databases, reports, news, and publications, we examined the characteristics of stranding cases in Indonesia, including population demographics, where hotspots occur, and whether their occurrence is related to oceanographic dynamics in the region. Our study highlights significant population-level disturbances, with 70% of stranded individuals being large juveniles (4–7 m). It also documented a positive interannual trend in stranding cases (R² = 0.67, p  < 0.01). The southern coast of Java has emerged as a stranding hotspot, with events seasonally associated with strong upwelling, likely related to the seasonal foraging activities of whale sharks in the region. Although natural events were identified as the main factors contributing to whale shark strandings, anthropogenic activities may also play an important role and require further investigation.

Coral reefs are highly threatened by ocean warming and the majority are likely to be lost in less than three decades. A first step in maximizing reef conservation through this period is to identify where coral reefs are more likely to survive rising ocean temperatures, such as locations that experience lower temperatures than surrounding regions, high temperature variability, and high food supply. Such conditions are often the result of naturally occurring internal gravity waves (IGWs), oscillatory subsurface disturbances that can entrain cooler and/or nutrient-rich subsurface waters and cause high frequency temperature fluctuations. These features usually remain undetected because they occur subsurface and at spatial scales of O (1 km) and smaller. To shed light on where IGWs are likely to impact temperature conditions within coral reef regions, we present an analysis of data from the LLC4320, a massive high resolution (1/48˚; < 2.5 km) numerical global ocean simulation. The results highlight strong regional differences in the incidence of IGW-induced temperature variability. The analysis also reveals that thermal refugia are limited to depths where high temperature variability coincides with the actual reef depth and may not persist year-round. Assuming 10-m depth as the nominal reef depth, reef regions likely to benefit from IGW-induced cooling occur in SE Asia and the Coral Triangle, the Galápagos, along the Pacific shelf of Central America, and isolated locations worldwide. Such refugia are rare within the Atlantic reef sector. An interactive global atlas showing the results of this study has been made freely available online at https://ncar.github.io/coral-viz/ .

This study explores the application of small, commercially available drones to determine morphometric the measurements and record key demographic parameters of reef manta rays (Mobula alfredi) in Raja Ampat, Indonesia. DJI Mavic 2 Pro drones were used to obtain videos of surface-feeding M. alfredi with a floating, known-length PVC pipe as a reference scale—thus avoiding the need to utilize altitude readings, which are known to be unreliable in small drones, in our photogrammetry approach. Three dimensions (disc length (DL), disc width (DW), and cranial width (CW)) from 86 different individuals were measured. A hierarchical multivariate model was used to estimate the true measurements of these three dimensions and their population-level multivariate distributions. The estimated true measurements of these dimensions were highly accurate and precise, with the measurement of CW more accurate than that of DL and, especially, of DW. Each pairing of these dimensions exhibited strong linear relationships, with estimated correlation coefficients ranging from 0.98–0.99. Given these, our model allows us to accurately calculate DW (as the standard measure of body size for mobulid rays) using the more accurate CW and DL measurements. We estimate that the smallest mature M. alfredi of each sex we measured were 274.8 cm (males, n = 30) and 323.5 cm DW (females, n = 8). We conclude that small drones are useful for providing an accurate “snapshot” of the size distribution of surface-feeding M. alfredi aggregations and for determining the sex and maturity of larger individuals, all with minimal impact on this vulnerable species.

A comprehensive understanding of cetacean ecology is crucial for conservation and management. In 2018, Kaimana was identified as an Important Marine Mammal Area (IMMA) due to the regular presence of feeding aggregations of Australian humpback dolphins ( Sousa sahulensis ), Pacific bottlenose dolphins ( Tursiops aduncus ) and Bryde's whales ( Balaenoptera edeni ). Despite this, information on cetacean ecology in the Kaimana region is currently lacking. Notably, no cetacean surveys have been undertaken in Kaimana since it was officially recognized as an IMMA. We monitored food-provisioning interactions between lift-net fisheries and cetaceans from May 2021 to March 2023 to examine cetacean sightings, abundance and feeding associations. Five species were positively identified, including a new record of Killer whales ( Orcinus orca ). Our findings suggest a strong association between T. aduncus and lift-net fisheries, where they have been observed feeding on anchovies from outside the net in the morning. While other species were also observed, their presence was less frequent. Furthermore, year-round sightings of S. sahulensis , B. edeni , and T. aduncus during the study period indicate that these species are resident in this region. Our results suggest that Kaimana fulfills a second IMMA sub-criterion (small and resident populations of these three species) that was not previously noted in the original IMMA assessment.

The whale shark ( Rhincodon typus ) is an iconic species in the Bird’s Head Seascape (BHS) in eastern Indonesia, yet little is known about its population and residency patterns across the region. This study documents the population demographics of this globally Endangered species from four key regions within the BHS: Cenderawasih Bay (CB), Kaimana (KA), Raja Ampat, and Fakfak. Using 13 years of photographic identification (photo-ID) data sourced from researchers and citizen scientists, we aim to provide a better understanding of population dynamics, residency patterns, and threats to the species. From September 2010 to October 2023, a total of 1,118 sightings of 268 different individuals were recorded, almost exclusively around lift-net fishing platforms (bagans). The population was strongly male-biased (8.8:1.0), with estimated total lengths ranging from 2 to 8 m, and most individuals in the 4–5 m size class, indicating a dominance of juvenile males. Over half (52.6%) of the individuals were re-sighted at least once, with one re-sighting span lasting 10.63 years. Most sightings (97.8%) were concentrated in CB (551 sightings, 159 individuals) and KA (542 sightings, 95 individuals). Only two individuals were seen in multiple regions, suggesting limited movement and potential habitat segregation. Lagged Identification Rates showed substantially higher residency in CB (77.1 days ± 34.4 SE) than in KA (37.8 days ± 9.7 SE). Scarring was recorded in 76.9% of individuals, with minor abrasions (47.4%) and fin nicks (39.9%) being the most common, followed by amputations (15.3%) and lacerations (14.2%). Only 2.4% of scars were likely inflicted by boat propellers, and only 3.4% of injuries were recorded as bites by predators. KA had a higher proportion of scarred sharks (83.7%) compared to CB (73.7%). The long-term presence and high re-sighting rates of juvenile whale sharks in CB and KA highlight their importance as key habitats within the BHS. While most sightings of whale sharks in the BHS occurred inside marine protected areas, the relatively high percentage of individuals with injuries apparently related to negative interactions with fisheries and tourism underscore the need for improved management to ensure the well-being of this fully protected species in Indonesia.

The behaviour and spatial use patterns of juvenile manta rays within their critical nursery habitats remain largely undocumented. Here, we report on the horizontal movements and residency of juvenile reef manta rays ( Mobula alfredi ) at a recently discovered nursery site in the Wayag lagoon, Raja Ampat, Indonesia. Using a multi-disciplinary approach, we provide further corroborative evidence that the lagoon serves as an important M. alfredi nursery. A total of 34 juvenile rays were photo-identified from 47 sightings in the sheltered nursery between 2013–2021. Five (14.7%) of these individuals were resighted for at least 486 days (~1.3 years), including two juveniles resighted after 641 and 649 days (~1.7 years), still using the nursery. Visually estimated (n=34) disc widths (DW) of juveniles using the nursery site ranged from 150–240 cm (mean ± SD: 199 ± 19), and the DW of two juveniles measured using drones were 218 and 219 cm. Five juveniles were tracked using GPS-enabled satellite transmitters for 12–69 days (mean ± SD: 37 ± 22) in 2015 and 2017, and nine juveniles were tracked using passive acoustic transmitters for 69–439 days (mean ± SD: 182 ± 109) from May 2019–September 2021. Satellite-tracked individuals exhibited restricted movements within Wayag lagoon. The minimum core activity space (50% Utilisation Distribution-UD) estimated for these five individuals ranged from 1.1–181.8 km 2 and the extent of activity space (95% UD) between 5.3–1,195.4 km 2 in area. All acoustically tagged individuals displayed high residency within the nursery area, with no acoustic detections recorded outside the lagoon in the broader Raja Ampat region. These juveniles were detected by receivers in the lagoon throughout the 24 h diel cycle, with more detections recorded at night and different patterns of spatial use of the lagoon between day and night. The observed long-term residency of juvenile M. alfredi provides further compelling evidence that the Wayag lagoon is an important nursery area for this globally vulnerable species. These important findings have been used to underpin the formulation of management strategies to specifically protect the Wayag lagoon, which will be instrumental for the survival and recovery of M. alfredi populations in Raja Ampat region.

Deep dives are performed by a range of marine megafauna, yet their function remains poorly understood. Proposed functions include foraging, predator avoidance, and navigation, but limited fine-scale data have hindered rigorous testing of these hypotheses. Here, depth time-series data from eight recovered and 16 non-recovered satellite tags deployed on oceanic manta rays ( Mobula birostris ) in Indonesia, Peru, and New Zealand were examined to characterise extreme dives and identify their potential function. From a total of 46,945 dives, 79 extreme dives (>500 m) were recorded, 11 of which were documented from recovered tags and associated high sampling frequency. Extreme dives were distinguished by rapid descents (up to 2.9 m s⁻¹), brief horizontal “steps” at depth, gradually slowing ascents, and extended periods spent near the surface both before and after diving. Unlike typical foraging dives, no substantial bottom phase was observed, and vertical oscillations—expected if feeding at depth—were absent. Extreme dives also occurred more frequently with increasing distance from the continental shelf edge as well as preceding periods of high 72h distance travelled, indicating they may inform subsequent movements. We propose that extreme dives enable oceanic manta rays to survey the properties of the water column, likely gathering environmental cues—such as temperature, dissolved oxygen, or geomagnetic gradients—to guide navigation and/or the decision to leave or remain in a general area. In open-ocean environments where external reference points are absent, such costly but infrequent dives may provide critical information for long-distance movements. Our results offer new insights into the role of extreme diving behaviour in oceanic manta rays and highlight the importance of fine-scale data for understanding deep-diving behaviours in marine megafauna.