The Greater Caribbean manatee (Trichechus manatus manatus), a subspecies of the American manatee formerly referred to as the Antillean manatee (Mignucci-Giannoni et al., 2024), is a large, endangered herbivore that inhabits the coastal and riverine brackish environments of the Caribbean, Mexico, Central America, and northern South America (O’Shea and ‘Lex’ Salisbury, 1991; Lefebvre et al., 2001; Lacommare et al., 2008; Self-Sullivan and Mignucci-Giannoni, 2012). As megaherbivores, manatees are considered “ecosystem engineers” in marine and aquatic plant-dominated environments, as they influence community dynamics and shape ecosystem characteristics in their feeding areas (Aragones et al., 2012; Bakker et al., 2016; Wirsing et al., 2022). Although historically widespread, their current distribution is variable, with several poorly studied populations existing within this geographical range (Lefebvre et al., 2001; Castelblanco-Martínez et al., 2012; Marsh, 2012). These populations are generally small, geographically isolated, and are increasingly threatened by human activities and habitat degradation. The subspecies is listed as endangered, with an estimated population of fewer than 2,500 mature individuals and a projected 20% population decline over the next two generations (Morales-Vela et al., 2024).

Central America, including Belize, Guatemala, Honduras, Nicaragua, Costa Rica, Panama, and parts of Mexico, serves as a vital stronghold for Greater Caribbean manatees. The diverse landscape of seagrass beds, mangrove-fringed lagoons, and numerous shallow coastal wetlands with abundant aquatic plants provides essential foraging and resting habitats, crucial for supporting both survival and reproduction (Mou et al., 1990; Lacommare et al., 2008; Self-Sullivan and Mignucci-Giannoni, 2012). Simultaneously, the dynamic nature of these environments requires manatees to adopt flexible movement patterns, ensuring access to optimal resources across various seasonal cycles. In this context, understanding how manatees navigate and maintain connectivity between isolated habitat patches is essential to ensure the long-term viability of their population (Deutsch et al., 2003, 2022a, 2022b).

Previous studies in Central America have revealed complex daily foraging movements interspersed with occasional long-distance migrations (Lacommare et al., 2008; Castelblanco-Martínez et al., 2012; Deutsch et al., 2022a, 2022b; Marmontel et al., 2012; Brady et al., 2023). These studies suggest that while some individuals show high site fidelity, often returning to familiar foraging and resting sites, others exhibit more nomadic behaviors, promoting genetic exchange across larger areas. Seasonal variability considerably influences movement patterns. During the dry season, as freshwater availability and seagrass productivity decrease, manatees often congregate in sheltered wetlands and near river mouths, protecting them from salinity and temperature extremes. In contrast, the wet season allows broader dispersal, with individuals traversing a network of interconnected habitats in search of more productive feeding grounds (Deutsch et al., 2003, 2022a). Such seasonal migration represents an essential survival strategy that balances the advantages of foraging in optimal areas with the need to avoid potentially hazardous conditions, including high-traffic zones or polluted waters (Castelblanco-Martínez et al., 2012; Deutsch et al., 2022a, 2022b).

The intertwined phenomena of connectivity, migration, residence time, and habitat use create a complex framework that underpins the spatial ecology of the Greater Caribbean manatees. This framework is crucial for understanding population dynamics, assessing conservation risks, and developing management strategies that address both local and regional threats (Marsh, 2012; Ordoñez-Nieto et al., 2024; Meirelles et al., 2024).

Passive acoustic monitoring has enabled long-term assessment of manatee populations through vocalization parameters and different analytical techniques (Merchan et al., 2019; Schneider et al., 2024). However, vocalization parameters cannot be compared across studies because recordings are obtained from captive or wild animals and under different instrumental settings. Average vocalization rates are one to two times per 5-minute period (Phillips et al., 2004). Manatees produce unique and complex vocalizations that are individually distinctive with considerable variations in various acoustic parameters, including fundamental frequency, emphasized bandwidth, frequency range, and call contour (Alicea-Pou, 2001; Sousa-Lima et al., 2002, 2008; Merchan et al., 2019; O’Shea and Poché, 2006). This distinctive acoustic characteristic, classified by Brady et al. (2020, 2022) into five wild-call categories (e.g., squeak, squeal, high squeak, chirp, and squeak-squeal) or by Schneider et al. (2024) into four captivity-specific call categories (e.g., squeak, squeal, high squeak, squeak-squeal, and mixed), is believed to support recognition, particularly in mother-calf bonding and maintaining broader social cohesion within social groups, as well as population size estimates (Sousa-Lima et al., 2002; Umeed et al., 2018; Brady et al., 2020, 2022; Schneider et al., 2024; Hodson, 2025). Research also suggests that slight variation in the frequencies of each manatee’s vocalization enables individual identification using noninvasive acoustic methods (Schneider et al., 2024), even considering age and sex differences in call categories and frequency (Williams, 2005). Furthermore, studies of visually identified wild Florida manatees have shown that some individuals’ vocalization parameters within individuals are not consistent or stable over time or may vary under conditions of alarm or noise (Williams, 2005; Miksis-Olds and Tyack, 2009). However, other acoustic features of manatees recorded over 1–3 years, 19 years, and 22 years remained stable across different time spans in 79-82%, 47%, and 33%, respectively, with some differences explained by sex and age group (Williams, 2005). Individuals recognize one another through sound, as females and their calves selectively respond to each other when reuniting with a group (O’Shea and Poché, 2006). Although age and sex may result in variations in class and rate of vocalizations (males vocalize less frequently), individual vocal patterns remain relatively stable over extended periods, sometimes lasting several years (Williams, 2005; Sousa-Lima et al., 2008; Umeed et al., 2018; Dietrich et al., 2022; Schneider et al., 2024). Acoustic monitoring represents a promising non-invasive methodology for identifying specific manatees, contributing to more accurate population estimates and home ranges (Merchan et al., 2019; Schneider et al., 2024).

The present study examined, for the first time, residence time and connectivity among a population of manatees in southern Central America (Panama and Costa Rica) using individual vocalizations of wild manatees without visual identification or captivity conditions (Williams, 2005; Dietrich et al., 2022; Schneider et al., 2024), which has been acoustically monitored since 2016 (Merchan et al., 2019, 2020, 2024). This is not an attempt to estimate population size (sensuSchneider et al., 2024). This novel approach provides a challenging quantitative alternative to long-term visual observations, which are often hindered by poor visibility and the brackish water conditions typical in tropical wetlands where manatees are year-round observed feeding and breeding (Guzman and Condit, 2017; Castelblanco-Martínez et al., 2018; Corona-Figueroa et al., 2021; Factheu et al., 2023; Merchan et al., 2024). Addressing these questions through an integrated, multidisciplinary approach provides valuable insights into the spatial strategies employed by the Greater Caribbean manatees in this region. More importantly, it highlights conservation priorities that are critical for preserving both the species and their habitats, as well as the overall integrity of Central America’s coastal ecosystems (Castelblanco-Martínez et al., 2012).

Clustering was conducted separately for the two datasets: Costa Rica, with 4,141 vocalizations, and Panama, with 26,787 vocalizations. The initial results yielded 82 clusters for Costa Rica and 141 for Panama. After merging overlapping groups and performing a global manual revision, the totals were reduced to 63 and 88 clusters, respectively. These clusters were then examined to determine the predominant call types they represented (Supplementary Table S4). In line with the criteria for residence time analyses, only those groups characterized by squeaks, hi-squeaks, or a mixture of both were retained. The latter category does not represent a hybrid vocalization but rather clusters in which both call types co-occur. On this basis, we identified 49 presumed individuals in Costa Rica (343 vocalizations) and 61 presumed individuals in Panama (1,012 vocalizations). The reduction in vocalization count primarily reflects the conservative nature of the HDBSCAN algorithm, which excludes outliers that do not form dense clusters, thereby enhancing the reliability of individual-level assignments.

As a result of the joint analysis and the application of the validation criteria, nine clusters were identified that potentially correspond to presumed individual manatees vocalizing in both Panama and Costa Rica (Supplementary Table S5). These findings provide novel insights into the potential for transboundary movements and support the hypothesis of regional population connectivity among West Indian manatees in this part of Central America.

Consequently, a total of 61 manatees were recorded along the Caribbean coast of Panama between December 25, 2015, and August 4, 2024, while 49 individuals were acoustically detected in Costa Rica between May 12, 2021, and August 28, 2024. Among these, nine presumed individuals were identified as cross-border animals and were detected in both countries after traveling approximately 200 km at different times. To facilitate cross-site comparisons, these individuals were labeled B1 through B9, each representing a match between a detection in Costa Rica (CR ID) and the corresponding detection in Panama (P ID). The details of all detected individuals, including the matched IDs for cross-border cases, are provided in Supplementary Table S5.

Accurately grouping manatee vocalizations poses a major challenge due to natural variability in call structure within and across individuals. To address this, we applied the clustering framework developed in Merchan et al. (2024), which had previously been validated on a dataset of 23 individuals recorded in the San San River under semi-controlled conditions. That validation showed the method’s capacity to handle intra-individual variability, particularly for squeaks and hi-squeaks, making it well-suited for application to the broader datasets analyzed here.

During the validation phase, each manatee was temporarily held in a floating cage for approximately eight hours, while free-ranging conspecifics often vocalized outside the cage (Merchan et al., 2024). This enriched the dataset by incorporating calls influenced by natural acoustic and social interactions. Although such recordings may not capture the complete vocal repertoire of each individual, the algorithm effectively grouped vocalizations—such as squeaks and hi-squeaks—that exhibited moderate variation in spectral contour when produced by the same animal. Examples of these intra-individual variations, successfully grouped by the algorithm, are shown in Figure 2. This performance stems from the combination of SWT representations, edge-based image descriptors, and the non-linear mapping provided by PaCMAP, which together preserve within-individual variation while enhancing between-individual separability. HDBSCAN further refined the results by discarding outliers and enforcing density-based clustering, yielding more conservative and reliable estimates.

Given the demonstrated ability of the Merchan et al. (2024) method to group acoustically diverse vocalizations produced by the same presumed individual, all call types were preliminarily included in the clustering process. Examination of the resulting clusters confirmed the method’s capacity to group calls with moderate acoustic variation. As illustrated in Figure 2, some clusters contained both squeaks and hi-squeaks that shared correlated contour shapes and occurred in close temporal proximity, suggesting they were likely emitted by the same individual.

For the residency analysis, however, we adopted a more conservative selection strategy. Following visual inspection, only clusters predominantly composed of squeaks, hi-squeaks, or a combination of both were retained. This decision contrasts with the approach of Schneider et al. (2024), who restricted their analysis exclusively to squeaks on account of their abundance and acoustic consistency. While such a conservative restriction reduces variability, it also omits hi-squeaks, which have been consistently reported as types of individual vocal signatures in manatees (Williams, 2005; Dietrich et al., 2022; O’Shea and Poché, 2006) and are particularly frequent among calves and juveniles (Brady et al., 2020; Umeed et al., 2023). By retaining both squeaks and hi-squeaks, our analysis preserved a wider set of biologically relevant signals, enhancing the potential for individual identification across diverse acoustic contexts. Nonetheless, occasional clustering errors remain possible—for instance, duplicate clusters for a single individual or merges of acoustically similar calls from different individuals—highlighting the need for cautious interpretation.

Despite these strengths, we recognize the inherent challenges in applying clustering methods to complex bioacoustic datasets derived from long-term recordings of wild manatees. Subtle intra-individual variability in spectral components and contour shapes can lead the same animal to produce acoustically diverse calls, while individuals with similar demographic or environmental characteristics may exhibit overlapping acoustic features. Such overlap increases the risk of misclassifications, including merges of distinct individuals’ vocalizations or duplications of clusters representing the same animal. The key challenge for clustering algorithms is to balance intra-individual variability with inter-individual separation. Non-linear dimensionality reduction techniques such as PaCMAP, when applied to SWT-based time–frequency representations, have shown promise in enhancing this separation (Merchan et al., 2024). Nonetheless, occasional duplications or merges remain possible, and these limitations must be carefully considered when interpreting individual identification results obtained through unsupervised clustering.

Individual identification algorithms (Stowell et al., 2019; Brady et al., 2022; Knight et al., 2024; Merchan et al., 2024) have considerably enhanced our understanding of the movement patterns and social behaviors of the Greater Caribbean manatees in this subregion. The initial detection records based on unclassified call vocalizations indicated remarkable regional presence and connectivity among manatees. In Panama, 61 individuals were recorded between December 2023 and August 2024, whereas 49 individuals were identified in Costa Rica between May 2021 and August 2024. Individual numbers used for residence time and migration assessments dropped by almost one-third when considering the three most crucial call vocalizations (e.g., squeak, hi-squeak, and a mix of squeak and hi-squeak). Notably, nine individuals were acoustically detected in both regions after a short migration of nearly 200 km, highlighting the cross-border movement and potential connectivity between these populations. Detailed individual matches (Supplementary Table S5) lay the foundation for understanding movement dynamics and can inform future research aimed at identifying factors that facilitate such connectivity. The detection of these cross-border individuals (B1–B9) suggests that manatees are likely to respond to shared ecological drivers or resource distribution patterns that transcend national boundaries. Herein, we reveal notable spatiotemporal variations in manatee detection across Costa Rica and Panama.

In Costa Rica, consistent detection throughout the monitoring period, with peaks in mid-2021, early 2022 and 2024, indicates stable habitat use, particularly at Stations S1 and S2, which recorded months with more than 12 individuals. Such consistent patterns suggest that these areas offer favorable environmental conditions or vital resources for resident manatees. Rainfall and flooding patterns in northern Costa Rica occur year-round (non-seasonal), unlike in southern Costa Rica and Panama, which experience more seasonal patterns. The region features a three-lagoonal inner system at the northwestern limit of the Barra del Colorado protected area, offering a suitable habitat for manatees year-round with minimal disturbance from transiting boats or human activities (Miksis-Olds et al., 2007; Brady et al., 2023; Slone et al., 2023). Conversely, the detection patterns in Panama were sporadic. Early detection in 2015 and 2018, interrupted by a data loss gap until December 2019, was followed by intermittent peaks, including a remarkable count of 17 individuals in April 2021. The lack of a consistent correlation between the number of detections and distinct individuals suggests variable residency and movement dynamics, again highlighting potential differences in local habitat use or transient activity with no clear response to seasonal drivers (Deutsch et al., 2022a; Factheu et al., 2023). The results indicate that all recorded manatees departed from Panama via the Changuinola River before entering Costa Rican waters. Notably, while several individuals likely accessed Costa Rica through the northern sector near Barra del Colorado, others appeared to have entered further south via the Tortuguero–Pacuare region. This pattern of diverging entry routes suggests marked individual variability and potential directional preferences along the Caribbean coastline, possibly reflecting differences in habitat suitability, resource availability, and environmental conditions as previously reported (Castelblanco-Martínez et al., 2009, 2013a, 2013b; Deutsch et al., 2022a, 2022b; Brady et al., 2023).

Analysis of residence times revealed considerable spatial variation in manatee habitat use across the transboundary region and in interannual fidelity. In Costa Rica, manatees remained at the northern sites of Barra del Colorado for an average of 546.50 days. In contrast, the southern Tortuguero-Pacuare area recorded much shorter and more variable stays (37.71 days). In Panama, the Changuinola region exhibited long-term site fidelity, with an average residence time of 1,926.31 days, in contrast to the more transient use observed in San San (191.93 days). Our data initially suggested high interannual fidelity for several individuals (Deutsch et al., 2022a). Binational comparisons revealed that specific individuals accumulated substantial residence times, averaging 2,202.22 days in Panamanian waters, before migrating to Costa Rica, where they stayed for an average of 277.05 days, with an intermediate migration period of 340 days.

KDE revealed distinct spatial patterns of vocalization density along the coasts of Costa Rica and Panama. In Costa Rica, high-density areas were concentrated near Barra del Colorado, and additional hotspots near Tortuguero and Pacuare suggest that these regions provide essential resources and preferred habitat conditions. Meanwhile, Panama exhibited broader and more intense activity centers near the Changuinola River than near the San San River. Both scenarios aligned with prior manatee habitat assessments, corroborating earlier observations of extended residency and site fidelity in this region (Castelblanco-Martínez et al., 2013a, 2013b; Deutsch et al., 2022a, 2022b). Additionally, within-site analyses revealed localized variations in habitat use. In Barra del Colorado, high- and medium-density zones accounted for 24.53% and 12.33% of the home range, respectively, indicating a concentrated spatial use pattern probably linked to the interconnected lagoonal habitats. Tortuguero presented a more uniform distribution, probably related to the lineal orography of the wetlands, whereas Pacuare was characterized by a predominantly low-density vocalization (5.95% of the area). In Panama, the distribution was notably extensive, with low-, medium-, and high-density zones comprising 39.69%, 30.72%, and 29.59% of the home range, respectively, underscoring the complex spatial utilization patterns previously documented in coastal manatee populations in Puerto Rico, Belize, and Mexico (Deutsch et al., 2003, 2022a, 2022b). Therefore, the KDE results highlight recurrent vocalization hotspots that may indicate manatees in this region of Central America are capable of long-distance travel over short periods and exhibit sedentary or high-site fidelity behaviors similar to those reported for manatees with satellite tags and photo IDs (Deutsch et al., 2022a).

This study examined the environmental factors influencing manatee migration in tropical coastal regions, with a focus on both migratory and non-migratory periods. Migration has been described as a generally synchronized, directional movement of individuals between distinct environments (Cooke et al., 2024), often recurring and not solely driven by immediate resource availability (Dingle and Drake, 2007). Similarly, Kennedy’s classic definition, later expanded by Morais and Daverat (2016), emphasizes persistent and directed movements that differ from local displacements or dispersal. In our study system, manatees exhibit what can be considered partial or seasonal migrations, as they repeatedly move across the Costa Rica–Panama boundary in response to hydrological and climatic drivers, while also maintaining long-term site fidelity in specific lagoons and river systems. Sea surface temperature (SST) remained relatively constant throughout both periods (migratory and non-migratory periods), indicating that thermal surface conditions are unlikely to be the primary migratory trigger in these ecosystems (Deutsch et al., 2022a). However, regional differences exist, as subtropical manatee populations have been shown to retreat to warmer waters in response to temperature changes, while Costa Rican manatees prefer warmer habitats in inner lagoon systems and may spend extended periods in deeper, stratified waters (Jimenez, 2005; Marsh, 2012). Precipitation levels and air temperature anomalies were significantly higher during migration periods, suggesting a possible atmospheric cue or consequence tied to broader climatic shifts. Low precipitation and runoff may impede migration by reducing waterway accessibility, as observed in parts of Costa Rica and Panama. Sea level anomalies were consistently lower during migration, which may reflect hydrodynamic changes or freshwater influxes associated with seasonal flooding, cold fronts, or wind-driven surges (Kjerfve, 1981; Lizano, 2006; Torres and Tsimplis, 2014). Extreme wave events, particularly during the dry season or storm periods, further highlight the role of meteorological forces (Morales-Marquez et al., 2023). Although two manatees initiated migration during the dry season, the majority migrated during the rainy season, pointing to a systemic environmental driver. These findings suggest that subregional atmospheric and hydrological variables—more than SST—are strongly associated with migratory behavior. Additional research into other factors such as wind regimes, ocean currents, and storm frequency is necessary to understand how climate variability and change will continue to shape migratory patterns (Deutsch et al., 2022a; WBG, 2021a, 2021b).

In summary, this pattern of movement reinforces the need for coordinated transboundary conservation strategies, as effective management must account for the use of multiple jurisdictions by species. Conservation of the Greater Caribbean manatee, widely regarded as a sentinel species for the health of coastal ecosystems, depends on our ability to understand and protect the intricate connections between habitat use, migratory behavior, and residency patterns. This study builds on previous regional research (Mou et al., 1990; Lacommare et al., 2008; Díaz-Ferguson et al., 2017; Castelblanco-Martínez et al., 2012) and extends it by incorporating new data sources and analytical frameworks (Merchan et al., 2024) to elucidate how manatees traverse an increasingly fragmented seascape. We conclude that manatees remain in residence over the years and follow “partial migrations” by utilizing coastal areas during the rainy season, and that “manatees inhabiting flood-pulse river systems closer to the coast may exhibit seasonal movements” (Deutsch et al., 2022a). A deeper understanding of these dynamics in biodiverse and rapidly changing regions, such as Central America, is a key to developing robust, science-based conservation strategies that ensure the persistence of this endangered species. The measurement of the residence time has practical implications for conservation management. By identifying hotspots of extended manatee occupancy, resource managers can implement targeted protective measures more effectively and establish marine protected areas (MPAs) or impose temporal restrictions on human activities during periods of critical use. These approaches are crucial in areas where competing uses, such as tourism development and commercial boating, intersect with key manatee habitats. Slone et al. (2023) reported that “manatee decisions were consistent with avoiding human interactions,” underscoring the need for minimizing human interference.

Furthermore, movement ecology can elucidate local and regional patterns, particularly using satellite telemetry and acoustic tracking, which have greatly enhanced our understanding of manatee spatial behavior across various temporal scales (Cooke, 2008). Notably, these movement patterns are not uniform across the entire population. Behavioral differences have been observed among sexes, age classes, and even individual animals (Deutsch et al., 2022a, 2022b; Hodson, 2025). For instance, some studies have documented that females, particularly those with calves, tend to spend extended periods in safe, sheltered areas. In contrast, males may travel longer distances in search of new resources or mating opportunities (Lacommare et al., 2008; Deutsch et al., 2022a, 2022b). Consequently, residence time—the duration for which an individual remains within a specific habitat—is a valuable metric for inferring habitat quality and ecological stability. Extended occupancy is generally associated with locations that offer abundant resources, minimal disturbances, and favorable physical conditions. For Greater Caribbean manatees, habitats such as seagrass meadows and sheltered wetland lagoons not only provide critical foraging opportunities but also serve as refuges from human-induced disturbances and predators (Lacommare et al., 2008; Marmontel et al., 2012; Deutsch et al., 2022a, 2022b; Hodson, 2025).

In addition, integrating genetic data with movement ecology offers a promising method for quantifying and conserving the ecological corridors necessary to sustain Greater Caribbean manatee populations (Castelblanco-Martínez et al., 2012, 2019; Parr et al., 2012; Tucker et al., 2012; Díaz-Ferguson et al., 2017). Growing research evidence suggests that even geographically separated populations can remain functionally connected through intermittent gene flow and migratory movements. Genetic studies in Panama have identified shared mitochondrial haplotypes across distinct local groups, suggesting that connectivity barriers may be less absolute than previously assumed (Díaz-Ferguson et al., 2017). This connectivity is critical for maintaining genetic diversity (Vianna et al., 2006; Quintana-Rizzo and Reynolds, 2008; Hunter et al., 2010; Nourisson et al., 2011; Luna et al., 2021), which buffers populations against the harmful effects of inbreeding and small effective population sizes. In Central America, where coastal habitats are undergoing rapid environmental changes owing to urbanization and tourism, maintaining genetic corridors remains a cornerstone of long-term conservation strategies (Lefebvre et al., 2001; Flamm et al., 2005; Castleblanco-Martinez et al., 2013a; Marsh, 2012; Deutsch et al., 2022a).

Finally, we propose establishing a binational corridor to protect manatees along a transboundary area of approximately 984 km of coastline (220 km in Costa Rica and 764 km in Panama) and covering 2,631 km² (526 km² in Costa Rica and 2,015 km² in Panama), which includes coastal marine and littoral wetland ecosystems within their jurisdictional waters (Supplementary Figure S3). The coastal and littoral zones of this region serve as a feeding and breeding habitat for recently listed vulnerable species (Morales-Vela et al., 2024), with over 57 rivers extending up to the 20-meter isobath (Supplementary Figure S3). The corridor was designed to preserve functional ecological connectivity for this threatened species across both countries and between marine and coastal protected lands under various management categories, including 18 existing protected areas (eight in Costa Rica and ten in Panama) and four existing Ramsar sites: Humedal Caribe Noreste and Gandoca-Manzanillo in Costa Rica, and San San-Pond Sak and Damani-Guariviara in Panama. In Central America, where manatees inhabit a mosaic of habitats within rapidly changing wetlands, integrating multiple sources of evidence, including genetic connectivity studies, satellite telemetry, and direct habitat assessments, is crucial, to develop a comprehensive understanding of how these animals navigate their seascape. This corridor meets the requirements for long-term survival, considering the regional residence and movement patterns of the species (Flamm et al., 2005; Deutsch et al., 2022b).

Our research continues, and we have started a project using satellite telemetry (sensu Deutsch et al., 2022a) to improve our understanding of habitat use and large-scale movement patterns at a high spatial resolution in Central America. Additionally, we are analyzing our dataset to estimate the manatee population size in this area, considering the different call categories (sensu Schneider et al., 2024), and employing acoustic capture-recapture models.