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The globally endangered oceanic manta ray Mobula birostris is believed to spend significantly more time in the open ocean than in coastal areas. Nonetheless, the Bird's Head Seascape (BHS) in eastern Indonesia hosts a large population of this species (over 850 individuals), frequently sighted at coral reef cleaning stations and forming a vital asset for marine tourism in the region. Despite this, detailed understanding of the movements and habitat use of this wide-ranging species within shallow (< 30 m) coral reef ecosystems remains limited. Addressing this knowledge gap is urgently required for the sustainable management of oceanic manta ray-focused tourism in the region. Here, we report the results of an initial passive acoustic telemetry study investigating the use of coral reef cleaning stations by oceanic manta rays. Forty-one rays were acoustically tracked from February 2016 to August 2019 in an array of 28 acoustic receivers deployed at known cleaning stations and hypothesized transit points across the BHS (including the regions of Raja Ampat, Fakfak, and Kaimana). A total of 5,822 detections were recorded by 16 of the 28 receivers from all tagged individuals, and 421 visitation events were documented from 37 out of the 41 tagged individuals, providing valuable insights into their visitation patterns at cleaning stations. Tagged individuals were detected at receiver stations for durations ranging from 0.2 to 427.0 min (mean ± SD = 48 ± 64 min). Notably, 94% of detections were recorded during daylight hours (reaching a peak at noon), underscoring an apparent diurnal pattern in time spent around cleaning stations. The study documented frequent short-range movements between adjacent receivers (5–12 km apart), with two-thirds of all 191 tracked movements occurring between neighboring stations in southern Raja Ampat. Notably, tagged individuals were detected repeatedly at three cleaning stations which were previously only known for hosting reef manta rays, suggesting oceanic manta rays likely also utilize these cleaning stations. Our study provides important insights into the visitations and local movements of oceanic manta rays between coral reef cleaning stations, which will inform effective oceanic manta ray conservation efforts and tourism management in the BHS.

The reef manta ray Mobula alfredi is present throughout most island groups that form the Raja Ampat archipelago, Indonesia. The species is protected regionally and nationally and is currently managed as a single homogeneous population within the 6.7 million ha archipelago. However, scientific evidence is currently lacking regarding the spatial connectivity and population structure of M. alfredi within this archipelago. Using network analysis and an array of 34 acoustic receivers deployed throughout Raja Ampat between February 2016 and September 2021, we examined the movements of 72 subadult and adult M. alfredi tagged in seven regions of Raja Ampat. A total of 1094 M. alfredi movements were recorded and were primarily concentrated between nearby receiver stations, highlighting frequent local movements within, and limited long-distance movements between regional acoustic receiver arrays. Network analysis revealed highly connected nodes acting as hubs important for M. alfredi movements. A community detection algorithm further indicated clusters within the network. Our results suggest the existence of a metapopulation comprising three demographically and geographically distinct subpopulations within the archipelago. They also reveal the importance of Eagle Rock as a critical node in the M. alfredi movement network, justifying the urgent inclusion of this site within the Raja Ampat marine protected area network.

The 6.7-million-hectare Raja Ampat archipelago is home to Indonesia’s largest reef manta ray (Mobula alfredi) population and a representative network of nine marine protected areas (MPAs). However, the population dynamics of M. alfredi in the region are still largely unknown. Using our photo-identification database, we fitted modified POPAN mark-recapture models with transience and per capita recruitment parameters to estimate key demographic characteristics of M. alfredi from two of Raja Ampat’s largest MPAs: Dampier Strait and South East (SE) Misool. A total of 1,041 unique individuals were photo-identified over an 11-year period (2009–2019) from Dampier Strait (n = 515) and SE Misool (n = 536). In our models, apparent survival probabilities and per capita recruitment rates were strongly linked with El Niño–Southern Oscillation (ENSO) events. Our models also estimated high apparent survival probabilities and significant increases in (sub)population sizes in both MPAs over a decade. In Dampier Strait, the estimated population size increased significantly (p = 0.018) from 226 (95% CI: 161, 283) to 317 (280, 355) individuals. Likewise, the estimated population size in SE Misool increased significantly (p = 0.008) from 210 (137, 308) to 511 (393, 618) individuals. Regardless of variation in the percentage change in population size between years throughout the study, the estimated overall population change shows a compound growth of 3.9% (0.7, 8.6) per annum in Dampier Strait and 10.7% (4.3, 16.1) per annum in SE Misool. Despite the global decline in oceanic sharks and rays due to fishing pressure in the last five decades, our study demonstrates the positive impact of a suite of long-term conservation efforts, coupled with the influence of ENSO events, on increasing M. alfredi abundance in Raja Ampat MPAs. Our study also underscores the importance of long-term monitoring to evaluate the effectiveness of conservation management measures on manta ray populations. Our modification of the standard POPAN model by incorporating per capita recruitment and transience parameters represents an important advance in mark-recapture modelling that should prove useful when examining other manta ray populations and other highly migratory species that are likely to have a substantial percentage of transient individuals.

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 km2 and the extent of activity space (95% UD) between 5.3–1,195.4 km2 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.

Abstract The Bird's Head Seascape (BHS), Papua, Indonesia is located within the epicenter of global marine biodiversity and has been the focus of recent conservation efforts to protect marine resources. Here, we provide an overview of Marine Protected Areas (MPAs) progress in the BHS over the past decade, including establishment history, changes in management effectiveness and ecosystem health, as well as examining trends in tourism growth. While generally viewed as a conservation success story, we reflect on both successes and challenges in the BHS, identifying where we need to continue to improve and adapt in response to rapid economic and environmental change. As of 2020, BHS MPAs cover 5.1 million ha across 23 MPAs. As expected, management effectiveness is steadily increasing in BHS MPAs—although newer MPAs face substantial capacity gaps. Tourism is rapidly growing—with an almost 3,000% increase in tourist visits between 2007 and 2018. Overall, hard coral cover in monitored BHS MPAs remained stable at 33% from 2010 to 2019, although trends in reef fish biomass were more variable. Given continued conservation challenges in the region, BHS MPAs are successfully preventing biodiversity loss while providing ecosystem services for local communities.

Though extremely valuable to the local marine tourism industry, there is a dearth of published information on the ecology and population dynamics of reef manta rays (Mobula alfredi) in Raja Ampat, West Papua, Indonesia. Knowledge of the movement ecology in particular of this large and scattered population is urgently needed to better manage the rapidly expanding manta-focused tourism. Here we report the results of an initial passive acoustic telemetry study designed to provide local managers with the first detailed knowledge of the site use and movement patterns of reef mantas in northern Raja Ampat. A total of 39 reef mantas were tagged with Vemco V16 acoustic transmitters over a 15-month period between 27 November 2013 and 22 February 2015. To monitor their movements, VR2W acoustic receivers were deployed at eight sites corresponding to known manta cleaning and feeding aggregation sites, with receivers downloaded every six months over a two-year initial monitoring period. The duration between tag deployments and last date of detections at sites ranged from 1 to 682 days (mean ± SE = 237 ± 27). The cumulative number of days of manta detections at receiver sites by individual mantas ranged from 1 to 188 days (mean ± SE = 42 ± 7). Manta Ridge was the most visited site with 565 days of detections. The tagged mantas demonstrated strong site fidelity to the observed aggregation sites. At the same time, they also exhibited seasonal movements within an approximately 150 km long corridor between sites in the Dampier Strait and the northwest of Waigeo Island. Data analysed from a nearby array of six VR2W receivers in southern Raja Ampat (approximately 180 km to the south of the study area) confirmed that none of the tagged mantas were detected in this array, providing further evidence of strong site fidelity and limited movements within northern Raja Ampat. More than 96% of detections occurred during the daytime. The number of detections reached a peak around noon at Yefnabi Kecil and Eagle Rock and slightly earlier at Manta Ridge. These findings have been shared with the Raja Ampat Marine Protected Area Management Authority and are now being used in the formulation of a management plan for this vulnerable and economically important species to ensure the long-term health of Raja Ampat's reef mantas and the sustainability of manta tourism in the region.