The implications of plastic pollution, including microplastics, on marine ecosystems and species are increasingly seen as an environmental disaster. Yet few reports focus on filter-feeding megafauna in regions heavily impacted by plastic pollution, such as Indonesia in the Coral Triangle, a global marine biodiversity hotspot. Here, we evaluate plastic abundance and characterize debris from feeding grounds for manta rays Mobula alfredi and whale sharks Rhincodon typus in three coastal locations in Indonesia: Nusa Penida Marine Protected Area, Komodo National Park, and Pantai Bentar, East Java. A 200 μm plankton net was used to sample the top 0.5 m of the water column (‘trawl survey’) and floating plastics were assessed along ∼440 m long transects (‘visual survey’) during the Indonesian north-west (wet) and south-east (dry) monsoon seasons during 2016–2018. Microplastics were identified visually, measured and categorized from trawl samples, and larger floating plastics were counted and categorized visually from boats. Plastic abundance ranged widely from 0.04 to 0.90 pieces m^–3 (trawl survey) and 210 to 40,844 pieces km^–2 (visual survey). Results from linear models showed significant seasonal and location differences in estimated plastic abundance for trawl and visual surveys in Nusa Penida and Komodo. Plastic abundance was up to ∼ 44 times higher in the wet than the dry season, with the largest seasonal effect observed in Nusa Penida. Overall, small pieces < 5 mm (≥ 78%), films and fragments (> 50% combined) were the most prevalent plastics. Theoretical plastic ingestion rates were calculated using estimated filtration volumes of manta rays and whale sharks and the mean plastic abundance in their feeding grounds. Upper plastic ingestion estimates for manta rays were ∼63 and 25 pieces h^–1 for Nusa Penida and Komodo locations, respectively, and ∼137 pieces h^–1 for whale sharks in Java. Analysis of manta ray egested material confirmed plastic ingestion, the consequences of which might include exposure to toxic plastic additives and adhered persistent organic pollutants. Communicating this information to communities who stand to benefit from healthy megafauna populations might help local governments as they work toward reducing plastics in the marine environment.

Manta rays (Mobula spp.) are highly valued in nature-based tourism globally. In Indonesia, although manta rays are protected, critical information is lacking on their habitat use, population dynamics and movements. We investigate the population structure and residency patterns of reef manta rays (Mobula alfredi) in the Nusa Penida Marine Protected Area (MPA). From photo-identification data logged by citizen scientists and trained observers (mantamatcher.org), we identified 624 reef manta rays from 5,913 sightings (January 2012–April 2018) based on their unique ventral coloration patterns. Year-round records were collected from two shallow (<20 m) reefs – Manta Bay (MB; n = 3,029 sightings) and Manta Point (MP; n = 3,058) – that are used frequently by tourism operators. Maximum likelihood techniques and a Markov movement analysis were used to model residency patterns and movement between these sites within the MPA. Manta rays at MB were predominantly male (64%, n = 261 individuals), with immature males (14%, n = 59) being sighted most frequently (39%, n = 1,170). In contrast, few immature individuals were sighted at MP (6%, n = 28), and they were sighted on few occasions (2%, n = 45), while mature female manta rays comprised 26% (n = 127) of the MP community and were the most frequently sighted (48%, n = 1,413). Lagged identification rates indicated high site fidelity at each location. However, 44% (n = 278) of individuals moved between the two sites and cumulative discovery curves showed a continued recruitment of individuals over the 6 years of the study. In addition, the behaviors displayed by the manta rays differed markedly between the two sites: MB appears to be a foraging ground, especially for juveniles, and potentially a nursery, while MP is used mainly for cleaning and courtship, indicating a social and reproductive site. Reproductive behavior coincided with the peak annual sightings in May. To prevent disturbance to this threatened species by tourism, regulations for the number of boats and interactions, especially during key reproductive times should be considered. Further, strict fishing regulation in the area is recommended as fishing gear entanglement was identified as a threat to this population.

Intraspecific colour polymorphisms have been the focus of numerous studies, yet processes affecting melanism in the marine environment remain poorly understood. Arguably, the most prominent example of melanism in marine species occurs in manta rays (Mobula birostrisandMobula alfredi). Here, we use long-term photo identification catalogues to document the frequency variation of melanism across Indo-Pacific manta ray populations and test for evidence of selection by predation acting on colour morph variants. We use mark–recapture modelling to compare survivorship of typical and melanistic colour morphs in threeM. alfredipopulations and assess the relationship between frequency variation and geographical distance.While there were large differences in melanism frequencies among populations of both species (0–40.70%), apparent survival estimates revealed no difference in survivorship between colour morphs. We found a significant association between phenotypic and geographical distance inM. birostris, but not inM. alfredi. Our results suggest that melanism is not under selection by predation in the testedM. alfredipopulations, and that frequency differences across populations of both species are a consequence of neutral genetic processes.As genetic colour polymorphisms are often subjected to complex selection mechanisms, our findings only begin to elucidate the underlying evolutionary processes responsible for the maintenance and frequency variation of melanism in manta ray populations.