Implications of past and present genetic connectivity for management of the saltwater crocodile ( Crocodylus porosus )

Effective management of protected species requires information on appropriate evolutionary and geographic population boundaries and knowledge of how the physical environment and life-history traits combine to shape the population structure and connectivity. Saltwater crocodiles (Crocodylus porosus) are the largest and most widely distributed of living crocodilians, extending from Sri Lanka to Southeast Asia and down to northern Australia. Given the long-distance movement capabilities reported for C. porosus, management units are hypothesised to be highly connected by migration. However, the magnitude, scale, and consistency of connection across managed populations are not fully understood. Here we used an efficient genotyping method that combines DArTseq and sequence capture to survey ≈ 3000 high-quality genome-wide single nucleotide polymorphisms from 1176 C. porosus sampled across nearly the entire range of the species in Queensland, Australia. We investigated historical and present-day connectivity patterns using fixation and diversity indices coupled with clustering methods and the spatial distribution of kin pairs. We inferred kinship using forward simulation coupled with a kinship estimation method that is robust to unspecified population structure. The results demonstrated that the C. porosus population has substantial genetic structure with six broad populations correlated with geographical location. The rate of gene flow was highly correlated with spatial distance, with greater differentiation along the east coast compared to the west. Kinship analyses revealed evidence of reproductive philopatry and limited dispersal, with approximately 90% of reported first and second-degree relatives showing a pairwise distance of <50 km between sampling locations. Given the limited dispersal, lack of suitable habitat, low densities of crocodiles and the high proportion of immature animals in the population, future management and conservation interventions should be considered at regional and state-wide scales.

Co-evolution assists geographic dispersal: the case of Madagascar

Interspecific associations may limit the dispersal of individual species, but may also facilitate it when entire co-evolved systems expand their geographic ranges. We tested the recent proposal that episodic land bridges linked Africa and Madagascar at three stages during the Cenozoic by comparing divergence estimates of Madagascar’s angiosperm taxa with their dispersal mechanisms. Plants that rely on gravity for seed dispersal indicate at least two episodes of land connection between Africa and Madagascar, in the Early Palaeocene and Early Oligocene. Seed dispersal by strepsirrhine primates possibly evolved in the Palaeocene, with the divergence of at least one endemic Malagasy angiosperm genus, Burasaia (Menispermaceae). This genus may have facilitated the lemur colonization of Madagascar. Frugivory, nectarivory and gummivory probably generalized in the Oligocene, with the co-evolution of modern lemurs and at least 10 new Malagasy angiosperm families. In the Late Miocene, more angiosperms were probably brought from Africa by birds via a discontinuous land connection, and radiated on Madagascar in diffuse association with birds (asities) and dwarf nocturnal lemurs (cheirogaleids). During the same connective episode, Madagascar was probably colonized by hippopotamuses, which both followed and re-seeded a variety of plants, forming the grassy Uapaca ‘tapia’ forest and ericoid ‘savoka’ thicket.

Dietary shifts may underpin the recovery of a large carnivore population

Supporting the recovery of large carnivores is a popular yet challenging endeavour. Estuarine crocodiles in Australia are a large carnivore conservation success story, with the population having extensively recovered from past heavy exploitation. Here, we explored if dietary changes had accompanied this large population recovery by comparing the isotopes δ¹³C and δ¹⁵N in bones of crocodiles sampled 40 to 55 years ago (small population) with bones from contemporary individuals (large population). We found that δ¹³C and δ¹⁵N values were significantly lower in contemporary crocodiles than in the historical cohort, inferring a shift in prey preference away from marine and into terrestrial food webs. We propose that an increase in intraspecific competition within the recovering crocodile population, alongside an increased abundance of feral ungulates occupying the floodplains, may have resulted in the crocodile population shifting to feed predominantly upon terrestrial food sources. The number of feral pigs consumed to sustain and grow crocodile biomass may help suppress pig population growth and increase the flow of terrestrially derived nutrients into aquatic ecosystems. The study highlights the significance of prey availability in contributing to large carnivore population recovery.

Environmental resistance and habitat quality influence dispersal of the saltwater crocodile

Landscape genetics commonly focuses on the effects of environmental resistance on animal dispersal patterns, but there is an emerging focus on testing environmental effects on emigration and settlement choices. In this study, we used landscape genetics approaches to quantify dispersal patterns in the world's largest crocodilian, the saltwater crocodile (Crocodylus porosus), and demonstrated environmental influences on three processes that comprise dispersal: emigration, movement and settlement. We found that both environmental resistance and properties of the source and destination catchments (proportion of breeding habitat) were important factors influencing observed dispersal events. Our habitat quality variables related to hypotheses about resource competition and represented the ratio of breeding habitat (which limits carrying capacity), suggesting that competition for habitat influences emigration and settlement choices, together with the strong effect of environmental resistance to movement (where high-quality habitat was associated with greatest environmental permeability). Approximately 42% of crocodiles were migrants from populations other than their sampling locations and some outstandingly productive populations had a much higher proportion of emigration rather than immigration. The distance most commonly travelled between source and destination was 150-200 km although a few travelled much longer distances, up to 600-700 km. Given the extensive dispersal range, individual catchments or hydrographic regions that combine two or three adjacent catchments are an appropriate scale for population management.

From the river to the ocean: mitochondrial DNA analyses provide evidence of spectacled caimans (Caiman crocodilus Linnaeus 1758) mainland–insular dispersal

There are few studies that have investigated the evolutionary history of large vertebrates on islands off the Caribbean coast of South America. Here we use the spectacled caiman (Caiman crocodilus) to investigate among- and within-population patterns of genetic diversity to understand connectivity between island and mainland populations. The spectacled caiman is naturally distributed across Central and South America including the islands of Trinidad and Tobago, which are considered to have the only natural insular populations of the species. Because of this apparent isolation, we sought to determine whether caimans on Trinidad and Tobago comprise a unique lineage and have reduced genetic diversity compared to mainland caimans. We test these hypotheses by using mitochondrial DNA variation to assess the phylogenetic and phylogeographical relationships of the C. crocodilus populations inhabiting these islands within the evolutionary context of the entire spectacled caiman complex. Phylogenetic analyses placed the Trinidad and Tobago samples together with samples from Colombia, Venezuela and Brazil into one well-supported clade, which corresponds to the defined Orinoco/upper Negro lineage. Interestingly, the majority of sequences from Trinidad and Tobago are similar or identical to haplotypes reported from Venezuela and Colombia, supporting the idea of a dispersal process from the Orinoco River to these islands. We discuss the implications of our findings for systematics and the conservation of the species and how these dispersal movements could shape the current phylogeographical structure depicted for C. crocodilus.

Diving in hot water: a meta-analytic review of how diving vertebrate ectotherms will fare in a warmer world

Diving ectothermic vertebrates are an important component of many aquatic ecosystems, but the threat of climate warming is particularly salient to this group. Dive durations typically decrease as water temperatures rise; yet, we lack an understanding of whether this trend is apparent in all diving ectotherms and how this group will fare under climate warming. We compiled data from 27 studies on 20 ectothermic vertebrate species to quantify the effect of temperature on dive durations. Using meta-analytic approaches, we show that, on average, dive durations decreased by 11% with every 1°C increase in water temperature. Larger increases in temperature (e.g. +3°C versus +8-9°C) exerted stronger effects on dive durations. Although species that respire bimodally are projected to be more resilient to the effects of temperature on dive durations than purely aerial breathers, we found no significant difference between these groups. Body mass had a weak impact on mean dive durations, with smaller divers being impacted by temperature more strongly. Few studies have examined thermal phenotypic plasticity (N=4) in diving ectotherms, and all report limited plasticity. Average water temperatures in marine and freshwater habitats are projected to increase between 1.5 and 4°C in the next century, and our data suggest that this magnitude of warming could translate to substantial decreases in dive durations, by approximately 16-44%. Together, these data shed light on an overlooked threat to diving ectothermic vertebrates and suggest that time available for underwater activities, such as predator avoidance and foraging, may be shortened under future warming.

Tracking a voyager: mitochondrial DNA analyses reveal mainland-to-island dispersal of an American crocodile (Crocodylus acutus) across the Caribbean

Conservation efforts have allowed American crocodile (Crocodylus acutus) populations to recover to the point that dispersal movements are beginning to be documented. The environmental authority of San Andres Island in Colombia reported, for the first time, the arrival of two C. acutus from unknown localities in 2012 and 2018. The former was sacrificed, and the latter was captured and kept in captivity to determining its potential origin. We used wildlife forensics to establish the origin of the animal that arrived in 2018 based on two mitochondrial genes (COI and Cytb). Additionally, five other samples from Tayrona National Natural Park (TNNP), and Salamanca Island Road Park (SIRP) were sequenced for molecular attribution of these populations to the currently described lineages. Phylogenetic and phylogeographic analyses showed that the American crocodile found in San Andrés belongs to a continental evolutionary lineage endemic to Colombia, showing also a strong genetic similarity with animals from SIRP. Thus, the most likely origin for this individual was not the nearest continental area but somewhere around the central Colombian Caribbean, located ~700 km from the island. We discuss the implication of our findings in the systematics and conservation of the species and the potential of mitochondrial DNA analysis to identify such migrants.

Operational Protocols for the Use of Drones in Marine Animal Research

The use of drones to study marine animals shows promise for the examination of numerous aspects of their ecology, behaviour, health and movement patterns. However, the responses of some marine phyla to the presence of drones varies broadly, as do the general operational protocols used to study them. Inconsistent methodological approaches could lead to difficulties comparing studies and can call into question the repeatability of research. This review draws on current literature and researchers with a wealth of practical experience to outline the idiosyncrasies of studying various marine taxa with drones. We also outline current best practice for drone operation in marine environments based on the literature and our practical experience in the field. The protocols outlined herein will be of use to researchers interested in incorporating drones as a tool into their research on marine animals and will help form consistent approaches for drone-based studies in the future.

Alligators in the abyss: The first experimental reptilian food fall in the deep ocean

The high respiration rates of the deep-sea benthos cannot be sustained by known carbon supply pathways alone. Here, we investigate moderately-sized reptilian food falls as a potential alternative carbon pathway. Specifically, three individual carcasses of Alligator mississippiensis were deployed along the continental slope of the northern Gulf of Mexico at depths of ~2000m in early 2019. We posit the tough hide of alligators would impeded scavengers by limiting access to soft tissues of the alligator fall. However, the scavengers began consuming the food fall 43 hours post-deployment for one individual (198.2cm, 29.7kg), and the carcass of another individual (175.3 cm, 19.5kg) was completely devoid of soft tissue at 51 days post-deployment. A third individual (172.7cm, 18.5kg) was missing completely after 8 days, with only the deployment harness and weight remaining drug 8 meters away, suggesting a large elasmobranch scavenger. Additionally, bones recovered post-deployment reveal the first observations of the bone-eating Osedax in the Gulf of Mexico and are confirmed here as new to science. The findings of this study indicate the quick and successful utilization of terrestrial and aquatic-based carbon food sources in the deep marine environment, though outcome variability may be high.

Translocation, genetic structure and homing ability confirm geographic barriers disrupt saltwater crocodile movement and dispersal

Translocated saltwater crocodiles (Crocodylus porosus) in the Northern Territory (NT) of Australia often return to their original capture sites, which complicates management interventions aimed at reducing human-crocodile conflict. We examined the spatial events implicated in this homing ability, using ARGOS satellite tracking devices. Five large male C. porosus (3.03 m to 4.02 m TL) were shifted and released 100-320 km from their capture sites, and 3 additional ones (3.67 m to 4.23 m TL) were released at their site of capture as controls. Translocated crocodiles were more mobile than the controls, and moved at sea in the direction of their original capture site. However, they were unable or unwilling to swim around a geographic structure, Cobourg Peninsula, which prevented homing being achieved in all five cases. Two control crocodiles remained near their capture sites, but one, after the first year, made a 900km journey for six months, before returning to its original capture and release site. Genetic analysis of tissue samples from nests across the NT coast demonstrated significant genetic structure across the coast, and confirmed that Cobourg Peninsula contributes to genetic differentiation among populations along the NT coast. These results provide new insights into C. porosus movements, which have management significance for the maintenance of public safety.

Ontogenetic shifts in the nesting behaviour of female crocodiles

Body size and age are crucial factors influencing reproductive capacity and success. As females grow, their reproductive investment and success often increase due to improved overall physiological condition and experience gained through successive reproductive events. While much of this work has been conducted on birds and mammals, surprisingly little is known on how body size affects nesting decisions in other long-lived vertebrates. We monitored the movements and nesting behaviour of 57 wild female estuarine crocodiles Crocodylus porosus over a 10-year period (and across consecutive nesting seasons) using externally mounted satellite tags, implanted acoustic transmitters and a network of submerged acoustic receivers. Applying Hidden Markov models to the telemetry-derived location data revealed that female nesting behaviours could be split into three distinct states: (i) ranging movements within home ranges and at nesting sites; (ii) migrations to and from nesting sites; (iii) and nesting/nest guarding. We found that during migration events, larger females migrated further and remained away from dry season territories for longer periods than smaller individuals. Furthermore, not only were migratory movements stimulated by increases in rainfall, larger females migrated to nest sites at lower rainfall thresholds than smaller females. We provide some of the first evidence of body size influencing nesting decisions in an ectothermic vertebrate, with shifts likely resulting from an increased willingness to invest in nest protection among larger and more experienced females.

Trophic interactions between larger crocodylians and giant tortoises on Aldabra Atoll, Western Indian Ocean, during the Late Pleistocene

Today, the UNESCO World Heritage Site of Aldabra Atoll is home to about 100 000 giant tortoises, Aldabrachelys gigantea, whose fossil record goes back to the Late Pleistocene. New Late Pleistocene fossils (age ca. 90-125 000 years) from the atoll revealed some appendicular bones and numerous shell fragments of giant tortoises and cranial and postcranial elements of crocodylians. Several tortoise bones show circular holes, pits and scratch marks that are interpreted as bite marks of crocodylians. The presence of a Late Pleistocene crocodylian species, Aldabrachampsus dilophus, has been known for some time, but the recently found crocodylian remains presented herein are distinctly larger than those previously described. This indicates the presence of at least some larger crocodylians, either of the same or of a different species, on the atoll. These larger crocodylians, likely the apex predators in the Aldabra ecosystem at the time, were well capable of inflicting damage on even very large giant tortoises. We thus propose an extinct predator-prey interaction between crocodylians and giant tortoises during the Late Pleistocene, when both groups were living sympatrically on Aldabra, and we discuss scenarios for the crocodylians directly attacking the tortoises or scavenging on recently deceased animals.

Riparian vegetation structure and the hunting behavior of adult estuarine crocodiles

Riparian ecosystems are amongst the most biodiverse tropical habitats. They are important, and essential, ecological corridors, linking remnant forest fragments. In this study, we hypothesised that crocodile's actively select nocturnal resting locations based on increased macaque predation potential. We examined the importance of riparian vegetation structure in the maintenance of crocodile hunting behaviours. Using airborne Light Detection and Ranging (LiDAR) and GPS telemetry on animal movement, we identified the repeated use of nocturnal resting sites by adult estuarine crocodiles (Crocodylus porosus) throughout the fragmented Lower Kinabatangan Wildlife Sanctuary in Sabah, Malaysia. Crocodile resting locations were found to resemble, in terms of habitat characteristics, the sleeping sites of long-tailed macaque; positioned in an attempt to avoid predation by terrestrial predators. We found individual crocodiles were actively selecting overhanging vegetation and that the protrusion of trees from the tree line was key to site selection by crocodiles, as well as influencing both the presence and group size of sleeping macaques. Although these findings are correlational, they have broad management implications, with the suggestion that riparian corridor maintenance and quality can have implications beyond that of terrestrial fauna. We further place our findings in the context of the wider ecosystem and the maintenance of trophic interactions, and discuss how future habitat management has the potential to mitigate human-wildlife conflict.

Phylogeography of the reticulated python (Malayopython reticulatus ssp.): Conservation implications for the worlds' most traded snake species

As an important economic natural resource in Southeast Asia, reticulated pythons (Malayopython reticulatus ssp.) are primarily harvested from the wild for their skins-which are prized in the luxury leather goods industry. Trade dynamics of this CITES Appendix II listed species are complex and management approaches on the country or regional level appear obscure. Little is known about the actual geographic point-of-harvest of snakes, how genetic diversity is partitioned across the species range, how current harvest levels may affect the genetic viability of populations, and whether genetic structure could (or should) be accounted for when managing harvest quotas. As an initial survey, we use mitochondrial sequence data to define the broad-scale geographic structure of genetic diversity across a significant portion of the reticulated python's native range. Preliminary results reveal: (1) prominent phylogenetic structure across populations east and west of Huxley's modification of Wallace's line. Thirty-four haplotypes were apportioned across two geographically distinct groups, estimated to be moderately (5.2%); (2) Philippine, Bornean and Sulawesian populations appear to cluster distinctly; (3) individuals from Ambon Island suggest recent human introduction. Malayopython reticulatus is currently managed as a single taxonomic unit across Southeast Asia yet these initial results may justify special management considerations of the Philippine populations as a phylogenetically distinct unit, that warrants further examination. In Indonesia, genetic structure does not conform tightly to political boundaries and therefore we advocate the precautionary designation and use of Evolutionary Significant Units within Malayopython reticulatus, to inform and guide regional adaptive management plans.

Morphometric analysis of the Australian freshwater crocodile (Crocodylus johnstoni)

We conducted a morphometric analysis of 279 Crocodylus johnstoni, using specimens from the McKinlay River (n = 265) and Arnhem Land (n = 14), to meet the management need for predicting body size of C. johnstoni from isolated body parts. The results also allow reconstruction of C. johnstoni dimensions for comparison with other crocodilian species. We detected sexual dimorphism in some body measurements from the McKinlay River, and geographic variation in the morphology of McKinlay River and Arnhem Land populations, but differences were slight. There is pronounced allometric growth in C. johnstoni in the immediate post-hatching phase, largely due to elongation of the snout after exiting the confines of the egg. We compared the size, shape and relative growth of C. johnstoni with that of other crocodilian species for which equivalent data are available, but particularly the other Australian crocodile, Crocodylus porosus. C. porosus has a proportionately longer tail and a shorter but wider snout than C. johnstoni, and we discuss possible ecological correlates of these and other differences.

Dead or Alive? Factors Affecting the Survival of Victims during Attacks by Saltwater Crocodiles (Crocodylus porosus) in Australia

Conflicts between humans and crocodilians are a widespread conservation challenge and the number of crocodile attacks is increasing worldwide. We identified the factors that most effectively decide whether a victim is injured or killed in a crocodile attack by fitting generalized linear models to a 42-year dataset of 87 attacks (27 fatal and 60 non-fatal) by saltwater crocodiles (Crocodylus porosus) in Australia. The models showed that the most influential factors were the difference in body mass between crocodile and victim, and the position of victim in relation to the water at the time of an attack. In-water position (for diving, swimming, and wading) had a higher risk than on-water (boating) or on-land (fishing, and hunting near the water's edge) positions. In the in-water position a 75 kg person would have a relatively high probability of survival (0.81) if attacked by a 300 cm crocodile, but the probability becomes much lower (0.17) with a 400 cm crocodile. If attacked by a crocodile larger than 450 cm, the survival probability would be extremely low (<0.05) regardless of the victim's size. These results indicate that the main cause of death during a crocodile attack is drowning and larger crocodiles can drag a victim more easily into deeper water. A higher risk associated with a larger crocodile in relation to victim's size is highlighted by children's vulnerability to fatal attacks. Since the first recently recorded fatal attack involving a child in 2006, six out of nine fatal attacks (66.7%) involved children, and the average body size of crocodiles responsible for these fatal attacks was considerably smaller (384 cm, 223 kg) than that of crocodiles that killed adults (450 cm, 324 kg) during the same period (2006-2014). These results suggest that culling programs targeting larger crocodiles may not be an effective management option to improve safety for children.

Genetics and infection dynamics of Paratrichosoma sp in farmed saltwater crocodiles (Crocodylus porosus)

Paratrichosoma-associated helminthiasis has been identified in saltwater crocodiles under intensive farming conditions. The development of sustainable integrated management practices is dependent on a detailed understanding of Paratrichosoma population genetics and infection dynamics. This study investigated the genetic relationships of Paratrichosoma sp in a population of commercially farmed saltwater crocodiles, Crocodylus porosus, in northern Australia. 18S ribosomal RNA gene sequence data were obtained from Paratrichosoma sp eggs present in the epidermis of infected animals. A high level of genetic diversity was distributed within the Paratrichosoma sp population (241 variable positions in the 1094 bp alignment), indicating an accelerated rate of nucleotide base-pair substitutions in this genus of nematodes. Several possible environmental correlates of the incidence and intensity of helminthiasis, including season, rainfall, and mean monthly temperature, were investigated by visual inspection of crocodile skins. Stepwise logistic regression revealed a significant negative linear relationship (P = 0.011, R (2) = 32.69 %) between mean monthly rainfall and the incidence of monthly Paratrichosoma-associated helminthiasis. Variation in the severity of Paratrichosoma-associated helminthiasis could not be explained by any of the independent environmental variables included within an ordinal regression analysis. The large genetic diversity in these nematodes indicates a high probability of anthelmintic resistant alleles occurring in the population. We discuss how the spread of these alleles may be mitigated by adopting targeted treatment protocols.

Home range utilisation and long-range movement of estuarine crocodiles during the breeding and nesting season

The estuarine crocodile (Crocodylus porosus) is the apex-predator in waterways and coastlines throughout south-east Asia and Australasia. C. porosus pose a potential risk to humans, and management strategies are implemented to control their movement and distribution. Here we used GPS-based telemetry to accurately record geographical location of adult C. porosus during the breeding and nesting season. The purpose of the study was to assess how C. porosus movement and distribution may be influenced by localised social conditions. During breeding, the females (2.92 ± 0.013 metres total length (TL), mean ± S.E., n = 4) occupied an area<1 km length of river, but to nest they travelled up to 54 km away from the breeding area. All tagged male C. porosus sustained high rates of movement (6.49 ± 0.9 km d(-1); n = 8) during the breeding and nesting period. The orientation of the daily movements differed between individuals revealing two discontinuous behavioural strategies. Five tagged male C. porosus (4.17 ± 0.14 m TL) exhibited a 'site-fidelic' strategy and moved within well-defined zones around the female home range areas. In contrast, three males (3.81 ± 0.08 m TL) exhibited 'nomadic' behaviour where they travelled continually throughout hundreds of kilometres of waterway. We argue that the 'site-fidelic' males patrolled territories around the female home ranges to maximise reproductive success, whilst the 'nomadic' males were subordinate animals that were forced to range over a far greater area in search of unguarded females. We conclude that C. porosus are highly mobile animals existing within a complex social system, and mate/con-specific interactions are likely to have a profound effect upon population density and distribution, and an individual's travel potential. We recommend that impacts on socio-spatial behaviour are considered prior to the implementation of management interventions.

Animal orientation strategies for movement in flows

For organisms that fly or swim, movement results from the combined effects of the moving medium - air or water - and the organism's own locomotion. For larger organisms, propulsion contributes significantly to progress but the flow usually still provides significant opposition or assistance, or produces lateral displacement ('drift'). Animals show a range of responses to flows, depending on the direction of the flow relative to their preferred direction, the speed of the flow relative to their own self-propelled speed, the incidence of flows in different directions and the proportion of the journey remaining. We here present a classification of responses based on the direction of the resulting movement relative to flow and preferred direction, which is applicable to a range of taxa and environments. The responses adopted in particular circumstances are related to the organisms' locomotory and sensory capacities and the environmental cues available. Advances in biologging technologies and particle tracking models are now providing a wealth of data, which often demonstrate a striking level of convergence in the strategies that very different animals living in very different environments employ when moving in a flow.

First report of a Trichinella papuae infection in a wild pig (Sus scrofa) from an Australian island in the Torres Strait region

Multiple Trichinella species are reported from the Australasian region although mainland Australia has never confirmed an indigenous case of Trichinella infection in humans or animals. Wildlife surveys in high-risk regions are essential to truly determine the presence or absence of Trichinella, but in mainland Australia are largely lacking. In this study, a survey was conducted in wild pigs from mainland Australia's Cape York Peninsula and Torres Strait region for the presence of Trichinella, given the proximity of a Trichinella papuae reservoir in nearby PNG. We report the detection of a Trichinella infection in a pig from an Australian island in the Torres Strait, a narrow waterway that separates the islands of New Guinea and continental Australia. The larvae were characterised as T. papuae (Kikori strain) by PCR and sequence analysis. No Trichinella parasites were found in any pigs from the Cape York Peninsula. These results highlight the link the Torres Strait may play in providing a passage for introduction of Trichinella parasites from the Australasian region to the Australian mainland.

Does variation in movement tactics and trophic interactions among American alligators create habitat linkages?

1. Highly mobile top predators are hypothesized to spatially and/or temporally link disparate habitats through the combination of their movement and feeding patterns, but recent studies suggest that individual specialization in habitat use and feeding could keep habitats compartmentalized. 2. We used passive acoustic telemetry and stable isotope analysis to investigate whether specialization in movement and feeding patterns of American alligators (Alligator mississippiensis) in an oligotrophic subtropical estuary created habitat linkages between marine and estuarine/freshwater food webs. 3. Individual alligators adopted one of the three relatively distinct movement tactics that were linked to variation in diets. Fifty-six per cent of alligators regularly travelled from the upstream (freshwater/mid-estuary) areas into the downstream (marine-influenced) areas where salinities exceed those typically tolerated by alligators. Thirty-one per cent of the alligators made regular trips from the mid-estuarine habitat into the upstream habitat; 13% remained in the mid-estuary zone year-round. 4. Stable isotopic analysis indicated that, unlike individuals remaining in the mid-estuary and upstream zones, alligators that used the downstream zone fed at least partially from marine food webs and likely moved to access higher prey abundance at the expense of salt stress. Therefore, 'commuting' alligators may link marine food webs with those of the estuary and marshes in the coastal Everglades and create an upstream vector for allochthonous nutrient inputs into the estuary. 5. This study lends further support to the hypothesis that large-bodied highly mobile predators faced with trade-offs are likely to exhibit individual specialization leading to habitat linkages, rather than compartmentalization. However, the conditions under which this scenario occurs require further investigation.