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Changing climate conditions are well documented to affect species distribution patterns and migratory phenology, especially for thermally constrained species. Climate induced changes and other natural and anthropogenic factors may affect habitats heterogeneously, altering microhabitats that act as refugia. Here, we used a thermally constrained marine mammal, the West Indian manatee (Trichechus manatus), as a model species to examine how the availability of thermal microrefugia combined with climate driven increases in regional water temperatures may affect the timing and duration of occurrence at the northern margins of the species’ range. We used aerial, thermographic imaging to identify potential thermal anomalies that could act as thermal microrefugia for manatees during unfavorable cold temperatures and assessed manatee occurrence at these sites using citizen-sourced manatee sightings and stranding response data. To further understand how regional and longer-term water temperatures may affect the use of thermal microrefugia and phenology of migration, we compared spatial and temporal distributions of manatee sightings to air and sea surface temperatures on a decadal scale. Thermal anomalies were detected at various sources, and documented manatee sightings at or near these sites support use as thermal microrefugia during cold periods. Cold season manatee sightings at a known western migratory endpoint (Alabama waters) have increased during the last decade, primarily through increased sightings during the late fall and early winter (Nov–Jan) that correspond to increased regional temperatures during the same period. Manatees may use thermal microrefugia to remain at northern latitudes longer, delaying seasonal migrations or overwintering as conditions allow. Climate change is likely to have further effects on the species’ distribution and migration patterns, potentially facilitating modern range expansion that has implications for management and recovery actions for manatees across their range. Our study provides novel insight for manatees but may also be used as a model to understand how other thermally constrained species may expand their ranges into higher latitudes.

Abstract Stable isotope analysis (SIA) provides ecological data that can be safely and efficiently collected on endangered, threatened, and cryptic species. Marine mammals are an ecologically important group for which economical and logistical constraints can make data collection challenging. Stranded marine mammals are often used in research, but the causes of strandings and subsequent tissue decomposition could affect SIA. We conducted a three‐part study to test the validity of using δ13C and δ15N values from tissues of stranded bottlenose dolphins (Tursiops truncatus) and West Indian manatees (Trichechus manatus) for ecological studies. First, we quantified isotopic overlap using ellipses based on 95% of the data to compare isotope values in skin between stranded and live‐captured animals. Second, we compared stable isotope values from liver, skin, and muscle of animals that had stranded and were sampled at different decomposition stages. Third, we experimentally exposed each tissue to environmental conditions and sampled tissues as they decomposed. For both dolphins and manatees, isotopic ellipses from skin of stranded carcasses were similar to live‐captured individuals. Among individuals recovered at different decomposition stages, more advanced decomposition affected δ13C values in dolphin liver and skin but not in manatee tissues and had no effect on δ15N values in any tissue for either species. In the experimental manipulation, decomposition resulted in depleted δ13C values, enriched δ15N values, and increased C:N in liver for both species. Skin and muscle from stranded dolphins and manatees are representative of their corresponding live populations and can be used for SIA with appropriate caution. To facilitate the use of tissues from stranded animals, tissues should be dried or frozen for storage as soon as possible after sampling. We recommend liver from stranded animals only be used for SIA when researchers need tissues with short turnover times and can access fresh samples. Without consideration of decomposition effects on isotope values, ecologists may make inaccurate inferences about habitat use, diet, and community structure. Careful use of SIA on tissues from stranded animals can help researchers provide better quality information for managers and policy makers.

ABSTRACT Vibrio cholerae is the etiological agent of the illness cholera. However, there are non-O1/non-O139 V. cholerae (NOVC) strains that generally lack the toxin gene (ctx) and colonization factors that cause cholera. These NOVC strains are autochthonous members of estuarine environments and a significant cause of seafood-borne gastroenteritis in the United States. The objective of this study was to identify environmental parameters that correlate with NOVC prevalence in oysters, water, and sediment at three ecologically diverse locations in Mobile Bay, AL, including Dog River (DR), Fowl River (FR), and Cedar Point (CP). Oyster, water, and sediment samples were collected twice a month when conditions were favorable for NOVC growth and once a month when they were not. A most probable number (MPN)/real-time PCR assay was used to determine NOVC abundances. Environmental parameters were measured during sampling to determine their relationship, if any, with NOVC at each site. NOVC abundances in oysters at DR, FR, and CP were 0.87, 0.87, and −0.13 log MPN/g, respectively. In water, the median NOVC levels at DR, FR, and CP were 1.18, −0.13, and −0.82 log MPN/mL, and in sediment, the levels were 1.48, 1.87, and −0.03 log MPN/g, respectively. Correlations of NOVC abundances in oyster, water, and sediment samples with environmental parameters were largely site specific. For example, the levels of NOVC in oysters at DR had a positive correlation with temperature but a negative correlation with dissolved oxygen (DO) and nutrient concentrations, NO2−, NO3−, dissolved inorganic nitrogen (DIN), total dissolved nitrogen (TDN), and dissolved inorganic phosphorus (DIP). At FR, however, the levels of NOVC in oysters displayed only a negative correlation with NO2−. When grouping NOVC abundances by temperature, the main driving factor for prevalence, additional correlations with salinity, total cell counts, dissolved organic nitrogen (DON), and dissolved organic carbon (DOC) became evident regardless of the site. IMPORTANCE NOVC can cause gastrointestinal illness in humans, which typically occurs after the consumption of raw or undercooked seafood. Incidence rates of NOVC gastroenteritis have increased during the past decade. In this study, NOVC was enumerated from oysters, sediment, and water collected at three sites in Mobile Bay, with environmental parameters measured concurrently over the course of a year, to identify potential environmental drivers of NOVC abundances. The data from this study, from an area lacking in V. cholerae research, provide a useful baseline for risk analysis of V. cholerae infections. Defining correlations between NOVC and environmental attributes at different sites and temperatures within a dynamic system such as Mobile Bay provides valuable data to better understand the occurrence and proliferation of V. cholerae in the environment.

Abstract Mobile, apex predators are commonly assumed to stabilize food webs through trophic coupling across spatially distinct habitats. The assumption that trophic coupling is common remains largely untested, despite evidence that individual behaviors might limit trophic coupling. We used stable isotope data from common bottlenose dolphins across the Gulf of Mexico to determine if these apex predators coupled estuarine and adjacent, nearshore marine habitats. δ13C values differed among the sites, likely driven by environmental factors that varied at each site, such as freshwater input and seagrass cover. Within most sites, δ13C values differed such that dolphins sampled in the upper reaches of embayments had values indicative of estuarine habitats while those sampled outside or in lower reaches of embayments had values indicative of marine habitats. δ15N values were more similar among and within sites than δ13C values. Data from multiple tissues within individuals corroborated that most dolphins consistently used a narrow range of habitats but fed at similar trophic levels in estuarine and marine habitats. Because these dolphins exhibited individual habitat specialization, they likely do not contribute to trophic coupling between estuarine and adjacent marine habitats at a regional scale, suggesting that not all mobile, apex predators trophically couple adjacent habitats.

Human activity affects marine mammal stranding rates in two major ways; through human interaction (HI) that may lead to mortality and through search and response efforts that enable carcass detection. To better quantify the combined effects of these interacting human influences, we analyzed strandings for bottlenose dolphins (Tursiops truncatus) in the northern Gulf of Mexico (nGOM), an area of high cetacean strandings. To identify hotspots of human influence, we first determined the number of total and HI-related bottlenose dolphin strandings normalized to shoreline length in each nGOM U.S. state, which represent major response areas. To estimate the effects of response effort on stranding numbers (for HI and non-HI strandings), we used the Deepwater Horizon oil spill (DWHOS) as an established benchmark to compare periods of lower (pre-spill) and higher (post-spill) response effort. Strandings in Alabama waters were used as a case study to detail spatial and temporal variation due to human influences during the 39-year period of retrospective study. We found an increase in strandings from Louisiana through Alabama following the DWHOS. Non-oil related HI strandings increased in total number in AL, and they increased as a proportion of total strandings in Alabama (16%) and the Florida panhandle (12%). The increase in HI-related strandings in Alabama was driven by mortality of many types, but particularly fishery interactions and cases of apparent intentional harm. The Alabama case study clearly detected lower stranding numbers during periods of low or intermittent response coverage. Our findings are consistent with an overall increase in stranding numbers due to a combination of increased stranding occurrence and response effort following the DWHOS. Importantly, we provide evidence that HI-related standings increased independently from the DWHOS, with ongoing increases in at least one hotspot (Alabama). These findings provide a first step to parsing out different effects of human influences on stranding data for a common coastal cetacean. Our approach establishes baselines for future damage and recovery assessments, identifies areas where resources can be focused for management and education, and highlights the power of response and monitoring agencies to positively influence stranding datasets.

Partial migration provides a mechanism for species to shift their geographic ranges into new, environmentally favorable regions but has been poorly studied as a means to alleviate effects of climate change. Populations at the edge of their geographic range are ideal to investigate how migratory behaviors may enable range expansion as adjacent areas become more climatically favorable. We determined the contribution of partial migration to the range expansion of West Indian manatees (Trichechus manatus) using GPS data from tagged individuals that migrated between the northern Gulf of Mexico (nGoM) and primary habitat in peninsular Florida. Most of these manatees migrated to the nGoM annually and exhibited high site fidelity among years. Many individuals spent cumulatively more time in the nGoM than in peninsular Florida, indicating the nGoM is a regular part of their geographic range, and they returned to peninsular Florida to meet temperature-related physiological needs for survival. Autumn migrations most frequently terminated at Crystal River, Florida, and manatees that commenced migration late in the season stopped less frequently and had more directed movements. Spring migrations most frequently terminated at Mobile Bay, Alabama, and several manatees quickly and directly migrated from Florida to nGoM stopover sites. Migrations ranged from 10 to 133 days in length, and variation in duration was primarily driven by use of stopover sites and directedness of travel. These data confirm partial migration as an important component of manatee migratory behavior that has already enabled range shifts for manatees on the U.S.A. Gulf of Mexico coast and has potential to facilitate future responses to climate change. As the most common type of migration across the animal kingdom, partial migration may provide a global mechanism for a diverse variety of species to resist the range limiting effects of climate change.

Abstract Ecosystems are experiencing elevated levels of disturbance, and species with narrower niches are often more vulnerable to disturbances. Niche breadth is often measured in terms of either diet or habitat use but diet and spatial use are infrequently considered in tandem. These different aspects of niche breadth potentially expose species to different types of disturbances; species with narrow dietary niches may be more affected by disturbances that alter trophic relationships, while species with narrow habitat niches may be more vulnerable to habitat loss and point‐source pollutants. We examined dietary and habitat niche breadth of common bottlenose dolphins, Tursiops truncatus truncatus, from three different nearshore sites in the Gulf of Mexico (GoM). Using stable isotopes, we determined proportional contributions of different prey groups to dolphin diets at each site and through time at one site. We used satellite‐linked telemetry at two sites to determine habitat use and site fidelity. Additionally, we examined the literature on cetacean diet, habitat use, movement, and IUCN status to determine relationships between niche breadth and population status for different species. Dolphin diets varied among sites as available prey varied, but Perciformes fish were the most frequently consumed prey. At the site for which we had temporal data, dolphins consumed more cephalopods in 2015 and 2018 but otherwise consumed primarily Perciformes fish. Dolphins had small utilization distributions and exhibited high site fidelity. Data from 31 cetacean species revealed that most species with vulnerable, threatened, or endangered IUCN statuses not only have specialized diets but also exhibit high site fidelity. Dolphins had diet characteristic of flexible generalists but were habitat specialists with high site fidelity. Dolphin populations in the GoM may have altered their diets in response to environmental changes that have altered community composition and trophic dynamics. On the other hand, their high site fidelity has exposed them to point‐source pollutants, such as oil spills, persistent organic pollutants, and freshwater. Our broader analysis of cetaceans confirmed that species with specialized diets and high site fidelity were the most vulnerable to disturbances, providing a framework to predict which nearshore dolphin populations, and cetaceans in general, are most vulnerable to environmental changes.

Common bottlenose dolphins (Tursiops truncatus) exposed to freshwater or low salinity (

Research on marine mammal occurrence in ship channels often focuses on large cetaceans in offshore shipping routes, while nearshore research largely addresses small vessel strikes. Marine mammals, such as the West Indian manatee, that reside in or migrate through nearshore areas, have potential to travel through a wide range of channel types, encountering a greater diversity of vessels than previously recognized. We tested the extent and conditions of ship channel use by manatees along the north-central Gulf of Mexico (nGoM) coast by combining data from telemetry-tracked individuals, opportunistic citizen-sourced sightings, and environmental attributes linked to manatee movements. Manatees used both nearshore boat channels (130 and 300 m wide) and open water fairways but used nearshore channels much more frequently, consistent with habitat requirements. Satellite-tracked individuals swam faster and moved more directly in all channel types, indicating use of these channels as migratory and travel corridors. Accordingly, generalized additive models revealed that manatees used channels most often during spring/early summer and fall and at temperatures coincidental with entry to and exit from the nGoM during migration. Manatees also occurred in ship channels when freshwater discharges were low, likely because timing of peak manatee occurrence in the nGoM coincides with seasonally low discharge periods. Expanding shipping activity world-wide is likely to increase interactions between marine mammals and a variety of vessel types, and these effects may be particularly impactful to migratory animals like manatees that use nearshore habitats at the interface of recreational boating and commercial shipping. Linking near- and offshore ship channel use to migration and habitat use will better aid risk-assessment for vessel collision and other shipping related activities for migratory marine species globally.

This study provides regional-scale data on drivers of horseshoe crab (Limulus polyphemus) presence along the northcentral Gulf of Mexico coast and has implications for understanding habitat suitability for sparse horseshoe crab populations of conservation concern worldwide. To collect baseline data on the relationship between environmental factors and presence of horseshoe crabs, we surveyed four sites from the Fort Morgan peninsula of Mobile Bay, Alabama (AL) to Horn Island, Mississippi (MS). We documented number, size and sex of live animals, molts, and carcasses as metrics of horseshoe crab presence and demographics for two years. Data were compared to in situ and remotely sensed environmental attributes to assess environmental drivers of occurrence during the time of study. Overall, greater evidence of horseshoe crab presence was found at western sites (Petit Bois and Horn Islands) compared to eastern sites (Dauphin Island, Fort Morgan peninsula), mediated by a combination of distance from areas of high freshwater discharge and interannual variation in weather. Higher sex ratios also were found associated with higher occurrence, west of Mobile Bay. Land cover, particularly Bare Land and Estuarine Emergent Wetland classes that are common to western sites, was most predictive of live animal and to some extent carcass occurrence. Our findings suggest that small-scale variation in habitat quality can affect occurrence of horseshoe crabs in sparse populations where density is not a limiting factor. Data from molts and carcasses were informative to supplement live animal data and may be useful to enhance ecological assessment and support conservation and management in regions with sparse populations.

The frequency and intensity of anoxic and hypoxic events are increasing worldwide, creating stress on the organisms that inhabit affected waters. To understand the effects of low dissolved oxygen stress on oysters, hatchery-reared oysters were placed in cages and deployed along with continuously recording environmental data sondes at a reef site in Mobile Bay, AL that typically experiences low oxygen conditions. To detect and measure sublethal stress, we measured growth and survival of oysters as well as expression of three biomarkers, heat shock protein 70 (HSP70), hypoxia inducible factor (HIF) and phospho-p38 MAP kinase, in tissues from juvenile and adult oysters. Survival rates were high for both juvenile and adult oysters. Expression levels of each of the 3 isoforms of HSP 70 were negatively correlated to dissolved oxygen (DO) concentrations, suggesting that HSP 70 is useful to quantify sublethal effects of DO stress. Results for HIF and phospho-p38 MAP kinase were inconclusive. Test deployments of oysters to assess expression of HSP 70 relative to environmental conditions will be useful, in addition to measuring abiotic factors, to identify appropriate sites for restoration, particularly to capture negative effects of habitat quality on biota before lethal impacts are incurred.

The explosion of the Deepwater Horizon drilling platform created the largest marine oil spill in U.S. history. As part of the Natural Resource Damage Assessment process, we applied an innovative modeling approach to obtain upper estimates for occupancy and for number of manatees in areas potentially affected by the oil spill. Our data consisted of aerial survey counts in waters of the Florida Panhandle, Alabama and Mississippi. Our method, which uses a Bayesian approach, allows for the propagation of uncertainty associated with estimates from empirical data and from the published literature. We illustrate that it is possible to derive estimates of occupancy rate and upper estimates of the number of manatees present at the time of sampling, even when no manatees were observed in our sampled plots during surveys. We estimated that fewer than 2.4% of potentially affected manatee habitat in our Florida study area may have been occupied by manatees. The upper estimate for the number of manatees present in potentially impacted areas (within our study area) was estimated with our model to be 74 (95%CI 46 to 107). This upper estimate for the number of manatees was conditioned on the upper 95%CI value of the occupancy rate. In other words, based on our estimates, it is highly probable that there were 107 or fewer manatees in our study area during the time of our surveys. Because our analyses apply to habitats considered likely manatee habitats, our inference is restricted to these sites and to the time frame of our surveys. Given that manatees may be hard to see during aerial surveys, it was important to account for imperfect detection. The approach that we described can be useful for determining the best allocation of resources for monitoring and conservation.

An unusual number of near term and neonatal bottlenose dolphin (Tursiops truncatus) mortalities occurred in the northern Gulf of Mexico (nGOM) in 2011, during the first calving season after two well documented environmental perturbations; sustained cold weather in 2010 and the Deepwater Horizon oil spill (DWHOS). Preceding the stranding event, large volumes of cold freshwater entered the nGOM due to unusually large snowmelt on the adjacent watershed, providing a third potential stressor. We consider the possibility that this extreme cold and freshwater event contributed to the pattern of perinatal dolphin strandings along the nGOM coast. During the 4-month period starting January 2011, 186 bottlenose dolphins, including 46% perinatal calves (nearly double the percentage for the same time period from 2003-2010) washed ashore from Louisiana to western Florida. Comparison of the frequency distribution of strandings to flow rates and water temperature at a monitoring buoy outside Mobile Bay, Alabama (the 4(th) largest freshwater drainage in the U.S.) and along the nGOM coast showed that dolphin strandings peaked in Julian weeks 5, 8, and 12 (February and March), following water temperature minima by 2-3 weeks. If dolphin condition was already poor due to depleted food resources, bacterial infection, or other factors, it is plausible that the spring freshet contributed to the timing and location of the unique stranding event in early 2011. These data provide strong observational evidence to assess links between the timing of the DWHOS, other local environmental stressors, and mortality of a top local predator. Targeted analyses of tissues from stranded dolphins will be essential to define a cause of death, and our findings highlight the importance of considering environmental data along with biological samples to interpret stranding patterns during and after an unusual mortality event.