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Background The American alligator ( Alligator mississippiensis ) displays temperature-dependent sex determination (TSD), in which incubation temperature during embryonic development determines the sexual fate of the individual. However, the molecular mechanisms governing this process remain a mystery, including the influence of initial environmental temperature on the comprehensive gonadal gene expression patterns occurring during TSD. Results Our characterization of transcriptomes during alligator TSD allowed us to identify novel candidate genes involved in TSD initiation. High-throughput RNA sequencing (RNA-seq) was performed on gonads collected from A. mississippiensis embryos incubated at both a male and a female producing temperature (33.5 °C and 30 °C, respectively) in a time series during sexual development. RNA-seq yielded 375.2 million paired-end reads, which were mapped and assembled, and used to characterize differential gene expression. Changes in the transcriptome occurring as a function of both development and sexual differentiation were extensively profiled. Forty-one differentially expressed genes were detected in response to incubation at male producing temperature, and included genes such as Wnt signaling factor WNT11, histone demethylase KDM6B , and transcription factor C/EBPA . Furthermore, comparative analysis of development- and sex-dependent differential gene expression revealed 230 candidate genes involved in alligator sex determination and differentiation, and early details of the suspected male-fate commitment were profiled. We also discovered sexually dimorphic expression of uncharacterized ncRNAs and other novel elements, such as unique expression patterns of HEMGN and ARX . Twenty-five of the differentially expressed genes identified in our analysis were putative transcriptional regulators, among which were MYBL2, MYCL, and HOXC10, in addition to conventional sex differentiation genes such as SOX9 , and FOXL2. Inferred gene regulatory network was constructed, and the gene-gene and temperature-gene interactions were predicted. Conclusions Gonadal global gene expression kinetics during sex determination has been extensively profiled for the first time in a TSD species. These findings provide insights into the genetic framework underlying TSD, and expand our current understanding of the developmental fate pathways during vertebrate sex determination.

Temperature-dependent sex determination (TSD), commonly found among reptiles, is a sex determination mode in which the incubation temperature during a critical temperature sensitive period (TSP) determines sexual fate of the individual rather than the individual’s genotypic background. In the American alligator ( Alligator mississippiensis ), eggs incubated during the TSP at 33 °C (male producing temperature: MPT) yields male offspring, whereas incubation temperatures below 30 °C (female producing temperature: FPT) lead to female offspring. However, many of the details of the underlying molecular mechanism remains elusive and the molecular link between environmental temperature and sex determination pathway is yet to be elucidated. Here we show the alligator TRPV4 ortholog (AmTRPV4) to be activated at temperatures proximate to the TSD-related temperature in alligators and using pharmacological exposure, we show that AmTRPV4 channel activity affects gene expression patterns associated with male differentiation. This is the first experimental demonstration of a link between a well-described thermo-sensory mechanism, TRPV4 channel and its potential role in regulation of TSD in vertebrates, shedding unique new light on the elusive TSD molecular mechanism.

Large-bodied, top- and apex predators (e.g., crocodilians, sharks, wolves, killer whales) can exert strong top-down effects within ecological communities through their interactions with prey. Due to inherent difficulties while studying the behavior of these often dangerous predatory species, relatively little is known regarding their feeding behaviors and activity patterns, information that is essential to understanding their role in regulating food web dynamics and ecological processes. Here we use animal-borne imaging systems (Crittercam) to study the foraging behavior and activity patterns of a cryptic, large-bodied predator, the American alligator (Alligator mississippiensis) in two estuaries of coastal Florida, USA. Using retrieved video data we examine the variation in foraging behaviors and activity patterns due to abiotic factors. We found the frequency of prey-attacks (mean = 0.49 prey attacks/hour) as well as the probability of prey-capture success (mean = 0.52 per attack) were significantly affected by time of day. Alligators attempted to capture prey most frequently during the night. Probability of prey-capture success per attack was highest during morning hours and sequentially lower during day, night, and sunset, respectively. Position in the water column also significantly affected prey-capture success, as individuals' experienced two-fold greater success when attacking prey while submerged. These estimates are the first for wild adult American alligators and one of the few examples for any crocodilian species worldwide. More broadly, these results reveal that our understandings of crocodilian foraging behaviors are biased due to previous studies containing limited observations of cryptic and nocturnal foraging interactions. Our results can be used to inform greater understanding regarding the top-down effects of American alligators in estuarine food webs. Additionally, our results highlight the importance and power of using animal-borne imaging when studying the behavior of elusive large-bodied, apex predators, as it provides critical insights into their trophic and behavioral interactions.

During embryonic development, organisms are sensitive to changes in thyroid hormone signaling which can reset the hypothalamic-pituitary-thyroid axis. It has been hypothesized that this developmental programming is a 'predictive adaptive response', a physiological adjustment in accordance with the embryonic environment that will best aid an individual's survival in a similar postnatal environment. When the embryonic environment is a poor predictor of the external environment, the developmental changes are no longer adaptive and can result in disease states. We predicted that endocrine disrupting chemicals (EDCs) and environmentally-based iodide imbalance could lead to developmental changes to the thyroid axis. To explore whether iodide or EDCs could alter developmental programming, we collected American alligator eggs from an estuarine environment with high iodide availability and elevated thyroid-specific EDCs, a freshwater environment contaminated with elevated agriculturally derived EDCs, and a reference freshwater environment. We then incubated them under identical conditions. We examined plasma thyroxine and triiodothyronine concentrations, thyroid gland histology, plasma inorganic iodide, and somatic growth at one week (before external nutrition) and ten months after hatching (on identical diets). Neonates from the estuarine environment were thyrotoxic, expressing follicular cell hyperplasia (p = 0.01) and elevated plasma triiodothyronine concentrations (p = 0.0006) closely tied to plasma iodide concentrations (p = 0.003). Neonates from the freshwater contaminated site were hypothyroid, expressing thyroid follicular cell hyperplasia (p = 0.01) and depressed plasma thyroxine concentrations (p = 0.008). Following a ten month growth period under identical conditions, thyroid histology (hyperplasia p = 0.04; colloid depletion p = 0.01) and somatic growth (body mass p<0.0001; length p = 0.02) remained altered among the contaminated sites. This work supports the hypothesis that embryonic EDC exposure or iodide imbalance could induce adult metabolic disease states, thereby stressing the need to consider the multiple environmental variables present during development.

Species displaying temperature-dependent sex determination (TSD) are especially vulnerable to the effects of a rapidly changing global climate due to their profound sensitivity to thermal cues during development. Predicting the consequences of climate change for these species, including skewed offspring sex ratios, depends on understanding how climatic factors interface with features of maternal nesting behaviour to shape the developmental environment. Here, we measure thermal profiles in 86 nests at two geographically distinct sites in the northern and southern regions of the American alligator’s (Alligator mississippiensis) geographical range, and examine the influence of both climatic factors and maternally driven nest characteristics on nest temperature variation. Changes in daily maximum air temperatures drive annual trends in nest temperatures, while variation in individual nest temperatures is also related to local habitat factors and microclimate characteristics. Without any compensatory nesting behaviours, nest temperatures are projected to increase by 1.6–3.7°C by the year 2100, and these changes are predicted to have dramatic consequences for offspring sex ratios. Exact sex ratio outcomes vary widely depending on site and emission scenario as a function of the unique temperature-by-sex reaction norm exhibited by all crocodilians. By revealing the ecological drivers of nest temperature variation in the American alligator, this study provides important insights into the potential consequences of climate change for crocodilian species, many of which are already threatened by extinction.

Individual niche specialization (INS) is increasingly recognized as an important component of ecological and evolutionary dynamics. However, most studies that have investigated INS have focused on the effects of niche width and inter- and intraspecific competition on INS in small-bodied species for short time periods, with less attention paid to INS in large-bodied reptilian predators and the effects of available prey types on INS. We investigated the prevalence, causes, and consequences of INS in foraging behaviors across different populations of American alligators (Alligator mississippiensis), the dominant aquatic apex predator across the southeast US, using stomach contents and stable isotopes. Gut contents revealed that, over the short term, although alligator populations occupied wide ranges of the INS spectrum, general patterns were apparent. Alligator populations inhabiting lakes exhibited lower INS than coastal populations, likely driven by variation in habitat type and available prey types. Stable isotopes revealed that over longer time spans alligators exhibited remarkably consistent use of variable mixtures of carbon pools (e.g., marine and freshwater food webs). We conclude that INS in large-bodied reptilian predator populations is likely affected by variation in available prey types and habitat heterogeneity, and that INS should be incorporated into management strategies to efficiently meet intended goals. Also, ecological models, which typically do not consider behavioral variability, should include INS to increase model realism and applicability.

Florida manatees ( Trichechus manatus latirostris ) are challenged by human alteration of landscapes and waterways. Coastal eutrophication has increased the frequency and intensity of Indian River Lagoon (IRL) algal blooms, promoting seagrass die-offs in areas that once consistently provided manatee forage. For decades the densest aggregations of manatees in Florida, outside of warm-water sites in winter, occurred in the northern Banana River (NBR) at Kennedy Space Center. Historically, the nearby Mosquito Lagoon (ML) had low numbers. Beginning in 2011, several catastrophic algal blooms caused the die-off of nearly 60% of the areal extent of all IRL seagrasses. Most severe impacts were in the Indian River and Banana River with lesser impacts in ML. This study evaluated several decades of manatee aerial survey data using statistical models to identify the environmental and temporal factors influencing manatee abundance, behavior and habitat use in the NBR (1990–2024) and ML (2016–2024). Using a Bayesian hierarchical model, we evaluated how manatee counts were affected by season, water clarity, and coastwide trends in manatee population size. Manatee abundance was evaluated across four distinct IRL seagrass Die-Off periods: Pre-Die-Off, Initial Die-Off (2011-2015), Secondary Die-Off (2016-2022), and Post-Die-Off (2023-2024). NBR manatee abundance increased well into the Initial Die-Off and then declined sharply until reaching historic lows in 2019. Beginning in 2016, only the ML maintained high seagrass coverage and a notable surge in manatee counts indicated aggregations shifted to ML. The Boosted Regression Tree Analysis top two predictors of abundance were seagrass Die-Offs periods and season. Optimized Hotspot Analysis of NBR manatee spatial distribution was compared to seagrass distribution and revealed that during the Pre-Die-Off, manatee hotspots occurred along deep-water resting areas adjacent to seagrass. Starting in the Initial Die-Off, manatee hotspots shifted toward ever shallower waters presumably to access the receding seagrass beds. The proportion of calves observed also declined dramatically after the Initial Die-Off period. These findings demonstrate that manatees aggregate in traditional areas with extreme fidelity but need to shift to “other pastures” during localized seagrass die-offs. Future shifts from habitat degradation will require best practices and adaptive management to safeguard manatees.

The food habits and predatory interactions of Alligator mississippiensis (American Alligator) have been thoroughly studied within populations inhabiting inland freshwater ecosystems; however, it is increasingly evident that coastal populations habitually forage in estuarine and nearshore marine ecosystems inhabited by other top predators. While few studies have been performed, data reported thus far from marine-foraging populations indicate individuals chiefly consume small-bodied prey such as crustaceans, fish, and wading birds. Nonetheless, capture and consumption of large-bodied marine prey such as multiple species of sea turtles and a single species of Elasmobranchii (sharks and rays) have been documented. Here, we examine evidence regarding reciprocal intraguild predation between American Alligators and elasmobranchs. We provide the first evidence of American Alligator depredation of 4 Elasmobranchii species and review putative evidence for Elasmobranchii depredation of American Alligators. We discuss the ecological significance of these interactions, draw comparisons to similar interactions experienced by other crocodilians, and recommend further avenues for research on the subject.

The post-occipital sinus of the spinal vein is often used for the collection of blood samples from crocodilians. Although this sampling method has been reported for several crocodilian species, the technique and associated anatomy has not been described in detail in any crocodilian, including the Nile crocodile (Crocodylus niloticus). The anatomy of the cranial neck region was investigated macroscopically, microscopically, radiographically and by means of computed tomography. Latex was injected into the spinal vein and spinal venous sinus of crocodiles to visualise the regional vasculature. The spinal vein ran within the vertebral canal, dorsal to and closely associated with the spinal cord and changed into a venous sinus cranially in the post-occipital region. For blood collection, the spinal venous sinus was accessed through the interarcuate space between the atlas and axis (C1 and C2) by inserting a needle angled just off the perpendicular in the midline through the craniodorsal cervical skin, just cranial to the cranial borders of the first cervical osteoderms. The most convenient method of blood collection was with a syringe and hypodermic needle. In addition, the suitability of the spinal venous sinus for intravenous injections and infusions in live crocodiles was evaluated. The internal diameter of the commercial human epidural catheters used during these investigations was relatively small, resulting in very slow infusion rates. Care should be taken not to puncture the spinal cord or to lacerate the blood vessel wall using this route for blood collection or intravenous infusions.

Acoustic telemetry was employed to resolve seasonal and daily movement patterns of adult red drum (Sciaenops ocellatus) in the northern Indian River Lagoon system, Florida. From May 2006 to September 2008, 44 tagged fish were tracked within an array of 34 autonomous receivers with individuals detected for up to 654 days. Most red drum exhibited strong site fidelity from winter through early summer with movement rates increasing significantly during fall spawning months. While some fish migrated to the nearest ocean inlet at this time, the majority remained within the lagoon year-round suggesting that true estuarine reproduction, a behavior uncommon or poorly documented elsewhere is the dominant life history strategy locally. Diel movement patterns were also pronounced and indicated changing depth preferences over a 24 h period. Despite a harvest prohibition on large red drum, long-term estuarine residency coupled with high angling pressure (41% recapture rate in 50 months) suggest that post-release angling mortality and sub-lethal effects to growth and reproduction may strongly influence the strength of adult size classes.