Drivers of habitat availability for terrestrial mammals: Unravelling the role of livestock, land conversion and intrinsic traits in the past 50 years

The global decline of terrestrial species is largely due to the degradation, loss and fragmentation of their habitats. The conversion of natural ecosystems for cropland, rangeland, forest products and human infrastructure are the primary causes of habitat deterioration. Due to the paucity of data on the past distribution of species and the scarcity of fine-scale habitat conversion maps, however, accurate assessment of the recent effects of habitat degradation, loss and fragmentation on the range of mammals has been near impossible. We aim to assess the proportions of available habitat within the lost and retained parts of mammals' distribution ranges, and to identify the drivers of habitat availability. We produced distribution maps for 475 terrestrial mammals for the range they occupied 50 years ago and compared them to current range maps. We then calculated the differences in the percentage of 'area of habitat' (habitat available to a species within its range) between the lost and retained range areas. Finally, we ran generalized linear mixed models to identify which variables were more influential in determining habitat availability in the lost and retained parts of the distribution ranges. We found that 59% of species had a lower proportion of available habitat in the lost range compared to the retained range, thus hypothesizing that habitat loss could have contributed to range declines. The most important factors negatively affecting habitat availability were the conversion of land to rangeland and high density of livestock. Significant intrinsic traits were those related to reproductive timing and output, habitat breadth and medium body size. Our findings emphasize the importance of implementing conservation strategies to mitigate the impacts caused by human activities on the habitats of mammals, and offer evidence indicating which species have the potential to reoccupy portions of their former range if other threats cease to occur.

Building use-inspired species distribution models: Using multiple data types to examine and improve model performance

Species distribution models (SDMs) are becoming an important tool for marine conservation and management. Yet while there is an increasing diversity and volume of marine biodiversity data for training SDMs, little practical guidance is available on how to leverage distinct data types to build robust models. We explored the effect of different data types on the fit, performance and predictive ability of SDMs by comparing models trained with four data types for a heavily exploited pelagic fish, the blue shark (Prionace glauca), in the Northwest Atlantic: two fishery dependent (conventional mark-recapture tags, fisheries observer records) and two fishery independent (satellite-linked electronic tags, pop-up archival tags). We found that all four data types can result in robust models, but differences among spatial predictions highlighted the need to consider ecological realism in model selection and interpretation regardless of data type. Differences among models were primarily attributed to biases in how each data type, and the associated representation of absences, sampled the environment and summarized the resulting species distributions. Outputs from model ensembles and a model trained on all pooled data both proved effective for combining inferences across data types and provided more ecologically realistic predictions than individual models. Our results provide valuable guidance for practitioners developing SDMs. With increasing access to diverse data sources, future work should further develop truly integrative modeling approaches that can explicitly leverage the strengths of individual data types while statistically accounting for limitations, such as sampling biases.

Widespread habitat loss and redistribution of marine top predators in a changing ocean

The Northwest Atlantic Ocean and Gulf of Mexico are among the fastest warming ocean regions, a trend that is expected to continue through this century with far-reaching implications for marine ecosystems. We examine the distribution of 12 highly migratory top predator species using predictive models and project expected habitat changes using downscaled climate models. Our models predict widespread losses of suitable habitat for most species, concurrent with substantial northward displacement of core habitats >500 km. These changes include up to >70% loss of suitable habitat area for some commercially and ecologically important species. We also identify predicted hot spots of multi-species habitat loss focused offshore of the U.S. Southeast and Mid-Atlantic coasts. For several species, the predicted changes are already underway, which are likely to have substantial impacts on the efficacy of static regulatory frameworks used to manage highly migratory species. The ongoing and projected effects of climate change highlight the urgent need to adaptively and proactively manage dynamic marine ecosystems.

Evaluation of thermal infrared imaging from uninhabited aerial vehicles for arboreal wildlife surveillance

An important component of wildlife management and conservation is monitoring the health and population size of wildlife species. Monitoring the population size of an animal group can inform researchers of habitat use, potential changes in habitat and resulting behavioral adaptations, individual health, and the effectiveness of conservation efforts. Arboreal monkeys are difficult to monitor as their habitat is often poorly accessible and most monkey species have some degree of camouflage, making them hard to observe in and below the tree canopy. Surveys conducted using uninhabited aerial vehicles (UAVs) equipped with thermal infrared (TIR) cameras can help overcome these limitations by flying above the canopy and using the contrast between the warm body temperature of the monkeys and the cooler background vegetation, reducing issues with impassable terrain and animal camouflage. We evaluated the technical and procedural elements associated with conducting UAV-TIR surveys for arboreal and terrestrial macaque species. Primary imaging missions and analyses were conducted over a monkey park housing approximately 160 semi-free-ranging Japanese macaques (Macaca fuscata). We demonstrate Repeat Station Imaging (RSI) procedures using co-registered TIR image pairs facilitate the use of image differencing to detect targets that were moving during rapid sequence imaging passes. We also show that 3D point clouds may be generated from highly overlapping UAV-TIR image sets in a forested setting using structure from motion (SfM) image processing techniques. A point cloud showing area-wide elevation values was generated from TIR imagery, but it lacked sufficient point density to reliably determine the 3D locations of monkeys.

A landscape-scale framework to identify refugia from multiple stressors

From a conservation perspective, quantifying potential refugial capacity has been predominantly focused on climate refugia, which is critical for maintaining the persistence of species and ecosystems. However, protection from other stressors, such as human-induced changes in fire and hydrology, that cause habitat loss, degradation, and fragmentation is also necessary to ensure that conservation efforts focused on climate are not undermined by other threats. Thus, conceptual and methodological advances for quantifying potential refugia from multiple anthropogenic stressors are important to support conservation efforts. We devised a new conceptual approach, the domains of refugia, for assessing refugial capacity that identifies areas where exposure to multiple stressors is low. In our framework, patterns of environmental variability (e.g., increased frequency of warm summers), thresholds of resilience, and extent and intensity of stressors are used to identify areas of potential refugia from a suite of ongoing anthropogenic stressors (e.g., changes in fire regime). To demonstrate its utility, we applied the framework to a Southern California landscape. Sites with high refugial capacity (super-refugia sites) had on average 30% fewer extremely warm summers, 20% fewer fire events, 10% less exposure to altered river channels and riparian areas, and 50% fewer recreational trails than the surrounding landscape. Our results suggest that super-refugia sites (∼8200 km² ) for some natural communities are underrepresented in the existing protected area network, a finding that can inform efforts to expand protected areas. Our case study highlights how considering exposure to multiple stressors can inform planning and practice to conserve biodiversity in a changing world.

Foraging in marine habitats increases mercury concentrations in a generalist seabird

Methylmercury concentrations vary widely across geographic space and among habitat types, with marine and aquatic-feeding organisms typically exhibiting higher mercury concentrations than terrestrial-feeding organisms. However, there are few model organisms to directly compare mercury concentrations as a result of foraging in marine, estuarine, or terrestrial food webs. The ecological impacts of differential foraging may be especially important for generalist species that exhibit high plasticity in foraging habitats, locations, or diet. Here, we investigate whether foraging habitat, sex, or fidelity to a foraging area impact blood mercury concentrations in western gulls (Larus occidentalis) from three colonies on the US west coast. Cluster analyses showed that nearly 70% of western gulls foraged primarily in ocean or coastal habitats, whereas the remaining gulls foraged in terrestrial and freshwater habitats. Gulls that foraged in ocean or coastal habitats for half or more of their foraging locations had 55% higher mercury concentrations than gulls that forage in freshwater and terrestrial habitats. Ocean-foraging gulls also had lower fidelity to a specific foraging area than freshwater and terrestrial-foraging gulls, but fidelity and sex were unrelated to gull blood mercury concentrations in all models. These findings support existing research that has described elevated mercury levels in species using aquatic habitats. Our analyses also demonstrate that gulls can be used to detect differences in contaminant exposure over broad geographic scales and across coarse habitat types, a factor that may influence gull health and persistence of other populations that forage across the land-sea gradient.

Species and population specific gene expression in blood transcriptomes of marine turtles

BACKGROUND

Transcriptomic data has demonstrated utility to advance the study of physiological diversity and organisms' responses to environmental stressors. However, a lack of genomic resources and challenges associated with collecting high-quality RNA can limit its application for many wild populations. Minimally invasive blood sampling combined with de novo transcriptomic approaches has great potential to alleviate these barriers. Here, we advance these goals for marine turtles by generating high quality de novo blood transcriptome assemblies to characterize functional diversity and compare global transcriptional profiles between tissues, species, and foraging aggregations.

RESULTS

We generated high quality blood transcriptome assemblies for hawksbill (Eretmochelys imbricata), loggerhead (Caretta caretta), green (Chelonia mydas), and leatherback (Dermochelys coriacea) turtles. The functional diversity in assembled blood transcriptomes was comparable to those from more traditionally sampled tissues. A total of 31.3% of orthogroups identified were present in all four species, representing a core set of conserved genes expressed in blood and shared across marine turtle species. We observed strong species-specific expression of these genes, as well as distinct transcriptomic profiles between green turtle foraging aggregations that inhabit areas of greater or lesser anthropogenic disturbance.

CONCLUSIONS

Obtaining global gene expression data through non-lethal, minimally invasive sampling can greatly expand the applications of RNA-sequencing in protected long-lived species such as marine turtles. The distinct differences in gene expression signatures between species and foraging aggregations provide insight into the functional genomics underlying the diversity in this ancient vertebrate lineage. The transcriptomic resources generated here can be used in further studies examining the evolutionary ecology and anthropogenic impacts on marine turtles.

Using GIS and stakeholder involvement to innovate marine mammal bycatch risk assessment in data-limited fisheries

Fisheries bycatch has been identified as the greatest threat to marine mammals worldwide. Characterizing the impacts of bycatch on marine mammals is challenging because it is difficult to both observe and quantify, particularly in small-scale fisheries where data on fishing effort and marine mammal abundance and distribution are often limited. The lack of risk frameworks that can integrate and visualize existing data have hindered the ability to describe and quantify bycatch risk. Here, we describe the design of a new geographic information systems tool built specifically for the analysis of bycatch in small-scale fisheries, called Bycatch Risk Assessment (ByRA). Using marine mammals in Malaysia and Vietnam as a test case, we applied ByRA to assess the risks posed to Irrawaddy dolphins (Orcaella brevirostris) and dugongs (Dugong dugon) by five small-scale fishing gear types (hook and line, nets, longlines, pots and traps, and trawls). ByRA leverages existing data on animal distributions, fisheries effort, and estimates of interaction rates by combining expert knowledge and spatial analyses of existing data to visualize and characterize bycatch risk. By identifying areas of bycatch concern while accounting for uncertainty using graphics, maps and summary tables, we demonstrate the importance of integrating available geospatial data in an accessible format that taps into local knowledge and can be corroborated by and communicated to stakeholders of data-limited fisheries. Our methodological approach aims to meet a critical need of fisheries managers: to identify emergent interaction patterns between fishing gears and marine mammals and support the development of management actions that can lead to sustainable fisheries and mitigate bycatch risk for species of conservation concern.

Getting to the bottom of bycatch: a GIS-based toolbox to assess the risk of marine mammal bycatch

Marine mammal bycatch poses a particular challenge in developing countries, where data to document bycatch and its effects are often lacking. Using the Bycatch Risk Assessment (ByRA) toolkit, based on InVEST open-source models, we chose 4 field sites in Southeast Asia with varying amounts of data on marine mammals and fishing occurrence: Trat province in the eastern Gulf of Thailand, the Sibu-Tinggi Islands and Kuching Bay, Malaysia, and Kien Giang Biosphere Reserve in southwestern Vietnam. These field sites have similar species of coastal marine mammals, small-scale and commercial fisheries, and support for research from universities and/or management. In Thailand and Kuching, results showed changing patterns of fishing and Irrawaddy dolphin Orcaella brevirostris habitat use across seasons, showing how bycatch risk could change throughout the year. Risk maps for dugongs Dugong dugon in peninsular Malaysia highlighted patterns of bycatch risk concentrated around a mainland fishing pier, and revealed high risk in a northern subregion. In Vietnam, first maps of bycatch risk for the Irrawaddy dolphin showed the highest risk driven by intensive use of gillnets and trawling gear. ByRA pinpointed areas of spatial and seasonal bycatch exposure, and estimated the consequence of bycatch on local species, providing managers with critical information on where to focus bycatch mitigation and meet new global standards for US Marine Mammal Protection Act and other international regulation (e.g. Official Journal of the European Union 2019; Regulation 2019/1241) compliance. The toolbox, a transferable open-source tool, can be used to guide fisheries management, marine mammal conservation, spatial planning, and further research.

Tracking transcriptomic responses to endogenous and exogenous variation in cetaceans in the Southern California Bight

Marine wildlife populations are adapted to survive in highly dynamic environments. However, identifying the effects of endogenous versus exogenous variables on marine mammal physiology remains a substantial challenge in part because of the logistical constraints that limit the collection of physiological data in free-ranging animals. Measuring genome-wide gene expression is one minimally invasive method that can be used to elucidate how free-ranging cetaceans' physiological responses shift with changing environmental conditions or demographic states, i.e. reproductive status and maturity. We identified transcriptomic differences among bottlenose dolphins (Tursiops truncatus) from the Southern California Bight using RNAseq data from the skin of 75 individuals to examine gene expression associated with sex, pregnancy status, sea surface temperature, geographic location and ecotype. We identified transcriptomic variation between two genetically distinct ecotypes as well as variation related to environmental conditions among groups that exhibit little evidence of genetic divergence. Specifically, we found differential expression of genes associated with structural development, cellular starvation and immune response. Sex and pregnancy status explained a small proportion of the observed variation, in contrast to sea surface temperature, which explained a substantial amount of transcriptomic variation. However, these measured variables did not account for all of the differential expression observed between ecotypes and among geographically distinct groups. Additional research is needed to identify other endogenous or exogenous factors that may be contributing to observed transcriptomic differences among ecotypes.

Accounting for unintended consequences of resource policy: Connecting research that addresses displacement of environmental impacts

Natural resource policies enacted to protect environmental integrity play an important role in promoting sustainability. However, when resources are shared ecologically, economically, or through a common, global interest, policies implemented to protect resource sustainability in one domain can displace, and in some cases magnify, environmental degradation to other domains. Although such displacement has been recognized as a fundamental challenge to environmental and conservation policy within some resource sectors, there has been little cross-disciplinary and cross-sectoral integration to address the problem. This suggests that siloed knowledge may be impeding widespread recognition of the ubiquity of displacement and the need for mitigation. Here, we connect research across multiple disciplines to promote a broader discussion and recognition of the processes and pathways that can lead to displaced impacts that countermand or undermine resource policy and outline a number of approaches that can mitigate displacement.

Contaminant Exposure Linked to Cellular and Endocrine Biomarkers in Southern California Bottlenose Dolphins

Cetaceans in the Southern California Bight (SCB) are exposed to high levels of halogenated organic contaminants (HOCs), which have previously been linked to impaired reproductive health and immune responses. We used a combination of molecular tools to examine the potential physiological impacts of HOC exposure in two bottlenose dolphin ( Tursiops truncatus) ecotypes in the SCB. We quantified 25 HOCs in the blubber of 22 biopsies collected from males between 2012 and 2016. We then analyzed genome-wide gene expression in skin using RNA-sequencing and measured blubber testosterone to compare HOC exposure with cellular and endocrine biomarkers. We found high levels of HOCs in both ecotypes with significantly higher total polychlorinated biphenyls (PCBs), polybrominated diphenyl ethers (PBDEs), tris(4-chlorophenyl)methanol (TCPMOH), and chlordane-related compounds in the coastal ecotype versus the offshore ecotype. We found evidence of PBDE bioaccumulation in both ecotypes, however, the pattern of bioaccumulation or endocrine disruption for other HOCs was different between the ecotypes, suggesting potential endocrine disruption in the coastal ecotype. We also observed correlations between HOCs and gene coexpression networks enriched for xenobiotic metabolism, hormone metabolism, and immune response that could indicate cellular effects from HOC exposure. By integrating measurements of HOC load with both transcriptome profiling and endocrine biomarkers, our approach provides insight into HOC exposure and potential impacts on wild cetacean health in southern California.

Complex immune responses and molecular reactions to pathogens and disease in a desert reptile (Gopherus agassizii)

Immune function plays an important role in an animal's defense against infectious disease. In reptiles, immune responses may be complex and counterintuitive, and diagnostic tools used to identify infection, such as induced antibody responses are limited. Recent studies using gene transcription profiling in tortoises have proven useful in identifying immune responses to various intrinsic and extrinsic stressors. As part of a larger experiment with Mojave desert tortoises (Gopherus agassizii), we facilitated the transmission of the pathogenic bacteria, Mycoplasma agassizii (Myag), to naïve adults and measured innate and induced immune reactions over time. Specifically, we evaluated clinical condition, presence of Myag in the nasal/oral cavity, induced antibody responses specific to Myag, and measured molecular reactions (gene transcript profiles) in 15 captive tortoises classified as naïve, exposed, or infected and 14 wild tortoises for comparison. Myag was confirmed inside the nasal/oral cavity in exposed tortoises within 30-60 days of introduction to infected animals, yet we did not detect Myag specific induced antibody responses in these individuals until 420-595 days post exposure. Surprisingly, we found no overall differences in the gene transcript profiles between our experimental treatment groups throughout this study. This work highlights the complexities in assessing immune function and diagnosing pathogen related infections in tortoises and other reptiles.

A dynamic ocean management tool to reduce bycatch and support sustainable fisheries

Seafood is an essential source of protein for more than 3 billion people worldwide, yet bycatch of threatened species in capture fisheries remains a major impediment to fisheries sustainability. Management measures designed to reduce bycatch often result in significant economic losses and even fisheries closures. Static spatial management approaches can also be rendered ineffective by environmental variability and climate change, as productive habitats shift and introduce new interactions between human activities and protected species. We introduce a new multispecies and dynamic approach that uses daily satellite data to track ocean features and aligns scales of management, species movement, and fisheries. To accomplish this, we create species distribution models for one target species and three bycatch-sensitive species using both satellite telemetry and fisheries observer data. We then integrate species-specific probabilities of occurrence into a single predictive surface, weighing the contribution of each species by management concern. We find that dynamic closures could be 2 to 10 times smaller than existing static closures while still providing adequate protection of endangered nontarget species. Our results highlight the opportunity to implement near real-time management strategies that would both support economically viable fisheries and meet mandated conservation objectives in the face of changing ocean conditions. With recent advances in eco-informatics, dynamic management provides a new climate-ready approach to support sustainable fisheries.

Seabirds as regional biomonitors of legacy toxicants on an urbanized coastline

Seabirds are often cited as sentinels of the marine environment, but are rarely used in traditional ocean and coastal contaminant monitoring. Four classes of persistent organic pollutants (POPs, n=68) and three trace elements (mercury, selenium, and arsenic) were measured in the eggs of California least terns (Sterna antillarum browni), caspian terns (Hydroprogne caspia), double-crested cormorants (Phalacrocorax auritus), and western gulls (Larus occidentalis) that nest in the Southern California Bight. Building on a periodic five year regional monitoring program, we measured contaminant exposure and assessed the utility of seabirds as regional contaminant biomonitors. We found that the eggs of larger, more piscivorous species generally had the highest concentrations of POPs and trace elements while California least terns had the lowest concentrations, except for mercury which was higher in least terns. As expected, DDT concentrations were elevated near the Palos Verdes Superfund site. However, we also detected a previously unknown latitudinal pattern in PBDE concentrations in least terns. POP congener profiles also confirmed differences in contamination in urban least tern colonies closest to urban centers. Though toxicants were at detectable levels across species and sites, concentrations were below those known to cause adverse effects in avian taxa and are steady or declining compared to previous studies in this region. Our results suggest that regional seabird monitoring can inform site-specific remediation and support management and protection of regionally-threatened wildlife and coastal systems. Integration of seabird contaminant data with traditional sediment, water, bivalve and fish monitoring is needed to further our understanding of exposure pathways and food web contaminant transfer.

Comprehensive Screening Links Halogenated Organic Compounds with Testosterone Levels in Male Delphinus delphis from the Southern California Bight

While environmental pollutants have been associated with changes in endocrine health in cetaceans, efforts to link contaminant exposure with hormones have largely been limited to a list of known, targeted contaminants, overlooking minimally characterized or unknown compounds of emerging concern. To address this gap, we analyzed a suite of potential endocrine disrupting halogenated organic compounds (HOCs) in blubber from 16 male short-beaked common dolphins ( Delphinus delphis) with known maturity status collected from fishery bycatch in the Southern California Bight. We employed a suspect screening mass spectrometry-based method to investigate a wide range of HOCs that were previously observed in cetaceans from the same region. Potential endocrine effects were assessed through the measurement of blubber testosterone. We detected 167 HOCs, including 81 with known anthropogenic sources, 49 of unknown origin, and 37 with known natural sources. The sum of 11 anthropogenic and 4 unknown HOC classes were negatively correlated with blubber testosterone. Evidence suggests that elevated anthropogenic HOC load contributes to impaired testosterone production in mature male D. delphis. The application of this integrative analytical approach to cetacean contaminant analysis allows for inference of the biological consequences of accumulation of HOCs and prioritization of compounds for future environmental toxicology research.

Characterizing habitat suitability for a central-place forager in a dynamic marine environment

Characterizing habitat suitability for a marine predator requires an understanding of the environmental heterogeneity and variability over the range in which a population moves during a particular life cycle. Female California sea lions (Zalophus californianus) are central-place foragers and are particularly constrained while provisioning their young. During this time, habitat selection is a function of prey availability and proximity to the rookery, which has important implications for reproductive and population success. We explore how lactating females may select habitat and respond to environmental variability over broad spatial and temporal scales within the California Current System. We combine near-real-time remotely sensed satellite oceanography, animal tracking data (n = 72) from November to February over multiple years (2003-2009) and Generalized Additive Mixed Models (GAMMs) to determine the probability of sea lion occurrence based on environmental covariates. Results indicate that sea lion presence is associated with cool (<14°C), productive waters, shallow depths, increased eddy activity, and positive sea-level anomalies. Predictive habitat maps generated from these biophysical associations suggest winter foraging areas are spatially consistent in the nearshore and offshore environments, except during the 2004-2005 winter, which coincided with an El Niño event. Here, we show how a species distribution model can provide broadscale information on the distribution of female California sea lions during an important life history stage and its implications for population dynamics and spatial management.

Fit to predict? Eco-informatics for predicting the catchability of a pelagic fish in near real time

The ocean is a dynamic environment inhabited by a diverse array of highly migratory species, many of which are under direct exploitation in targeted fisheries. The timescales of variability in the marine realm coupled with the extreme mobility of ocean-wandering species such as tuna and billfish complicates fisheries management. Developing eco-informatics solutions that allow for near real-time prediction of the distributions of highly mobile marine species is an important step towards the maturation of dynamic ocean management and ecological forecasting. Using 25 yr (1990-2014) of NOAA fisheries' observer data from the California drift gillnet fishery, we model relative probability of occurrence (presence-absence) and catchability (total catch per gillnet set) of broadbill swordfish Xiphias gladius in the California Current System. Using freely available environmental data sets and open source software, we explore the physical drivers of regional swordfish distribution. Comparing models built upon remotely sensed data sets with those built upon a data-assimilative configuration of the Regional Ocean Modelling System (ROMS), we explore trade-offs in model construction, and address how physical data can affect predictive performance and operational capacity. Swordfish catchability was found to be highest in deeper waters (>1,500 m) with surface temperatures in the 14-20°C range, isothermal layer depth (ILD) of 20-40 m, positive sea surface height (SSH) anomalies, and during the new moon (<20% lunar illumination). We observed a greater influence of mesoscale variability (SSH, wind speed, isothermal layer depth, eddy kinetic energy) in driving swordfish catchability (total catch) than was evident in predicting the relative probability of presence (presence-absence), confirming the utility of generating spatiotemporally dynamic predictions. Data-assimilative ROMS circumvent the limitations of satellite remote sensing in providing physical data fields for species distribution models (e.g., cloud cover, variable resolution, subsurface data), and facilitate broad-scale prediction of dynamic species distributions in near real time.

Natal foraging philopatry in eastern Pacific hawksbill turtles

The complex processes involved with animal migration have long been a subject of biological interest, and broad-scale movement patterns of many marine turtle populations still remain unresolved. While it is widely accepted that once marine turtles reach sexual maturity they home to natal areas for nesting or reproduction, the role of philopatry to natal areas during other life stages has received less scrutiny, despite widespread evidence across the taxa. Here we report on genetic research that indicates that juvenile hawksbill turtles (Eretmochelys imbricata) in the eastern Pacific Ocean use foraging grounds in the region of their natal beaches, a pattern we term natal foraging philopatry. Our findings confirm that traditional views of natal homing solely for reproduction are incomplete and that many marine turtle species exhibit philopatry to natal areas to forage. Our results have important implications for life-history research and conservation of marine turtles and may extend to other wide-ranging marine vertebrates that demonstrate natal philopatry.

Coupling gene-based and classic veterinary diagnostics improves interpretation of health and immune function in the Agassiz's desert tortoise (Gopherus agassizii)

The analysis of blood constituents is a widely used tool to aid in monitoring of animal health and disease. However, classic blood diagnostics (i.e. hematologic and plasma biochemical values) often do not provide sufficient information to determine the state of an animal's health. Field studies on wild tortoises and other reptiles have had limited success in drawing significant inferences between blood diagnostics and physiological and immunological condition. However, recent research using gene transcription profiling in the threatened Mojave desert tortoise (Gopherus agassizii) has proved useful in identifying immune or physiologic responses and overall health. To improve our understanding of health and immune function in tortoises, we evaluated both standard blood diagnostic (body condition, hematologic, plasma biochemistry values, trace elements, plasma proteins, vitamin A levels) and gene transcription profiles in 21 adult tortoises (11 clinically abnormal; 10 clinically normal) from Clark County, NV, USA. Necropsy and histology evaluations from clinically abnormal tortoises revealed multiple physiological complications, with moderate to severe rhinitis or pneumonia being the primary cause of morbidity in all but one of the examined animals. Clinically abnormal tortoises had increased transcription for four genes (SOD, MyD88, CL and Lep), increased lymphocyte production, biochemical enzymes and organics, trace elements of copper, and decreased numbers of leukocytes. We found significant positive correlations between increased transcription for SOD and increased trace elements for copper, as well as genes MyD88 and Lep with increased inflammation and microbial insults. Improved methods for health assessments are an important element of monitoring tortoise population recovery and can support the development of more robust diagnostic measures for ill animals, or individuals directly impacted by disturbance.

Hawksbill turtle terra incognita: conservation genetics of eastern Pacific rookeries

Prior to 2008 and the discovery of several important hawksbill turtle (Eretmochelys imbricata) nesting colonies in the EP (Eastern Pacific), the species was considered virtually absent from the region. Research since that time has yielded new insights into EP hawksbills, salient among them being the use of mangrove estuaries for nesting. These recent revelations have raised interest in the genetic characterization of hawksbills in the EP, studies of which have remained lacking to date. Between 2008 and 2014, we collected tissue samples from 269 nesting hawksbills at nine rookeries across the EP and used mitochondrial DNA sequences (766 bp) to generate the first genetic characterization of rookeries in the region. Our results inform genetic diversity, population differentiation, and phylogeography of the species. Hawksbills in the EP demonstrate low genetic diversity: We identified a total of only seven haplotypes across the region, including five new and two previously identified nesting haplotypes (pooled frequencies of 58.4% and 41.6%, respectively), the former only evident in Central American rookeries. Despite low genetic diversity, we found strong stock structure between the four principal rookeries, suggesting the existence of multiple populations and warranting their recognition as distinct management units. Furthermore, haplotypes EiIP106 and EiIP108 are unique to hawksbills that nest in mangrove estuaries, a behavior found only in hawksbills along Pacific Central America. The detected genetic differentiation supports the existence of a novel mangrove estuary "reproductive ecotype" that may warrant additional conservation attention. From a phylogeographic perspective, our research indicates hawksbills colonized the EP via the Indo-Pacific, and do not represent relict populations isolated from the Atlantic by the rising of the Panama Isthmus. Low overall genetic diversity in the EP is likely the combined result of few rookeries, extremely small reproductive populations and evolutionarily recent colonization events. Additional research with larger sample sizes and variable markers will help further genetic understanding of hawksbill turtles in the EP.

Improved estimation of intrinsic growth r(max) for long-lived species: integrating matrix models and allometry

Intrinsic population growth rate (r(max)) is an important parameter for many ecological applications, such as population risk assessment and harvest management. However, r(max) can be a difficult parameter to estimate, particularly for long-lived species, for which appropriate life table data or abundance time series are typically not obtainable. We describe a method for improving estimates of r(max) for long-lived species by integrating life-history theory (allometric models) and population-specific demographic data (life table models). Broad allometric relationships, such as those between life history traits and body size, have long been recognized by ecologists. These relationships are useful for deriving theoretical expectations for r(max), but r(max) for real populations may vary from simple allometric estimators for "archetypical" species of a given taxa or body mass. Meanwhile, life table approaches can provide population-specific estimates of r(max) from empirical data, but these may have poor precision from imprecise and missing vital rate parameter estimates. Our method borrows strength from both approaches to provide estimates that are consistent with both life-history theory and population-specific empirical data, and are likely to be more robust than estimates provided by either method alone. Our method uses an' allometric constant: the product of r(max) and the associated generation time for a stable-age population growing at this rate. We conducted a meta-analysis to estimate the mean and variance of this allometric constant across well-studied populations from three vertebrate taxa (birds, mammals, and elasmobranchs) and found that the mean was approximately 1.0 for each taxon. We used these as informative Bayesian priors that determine how much to "shrink" imprecise vital rate estimates for a data-limited population toward the allometric expectation. The approach ultimately provides estimates of r(max) (and other vital rates) that reflect a balance of information from the individual studied population, theoretical expectation, and meta-analysis of other populations. We applied the method specifically to an archetypical petrel (representing the genus Procellaria) and to white sharks (Carcharodon carcharias) in the context of estimating sustainable-fishery bycatch limits.

Using community-level metrics to monitor the effects of marine protected areas on biodiversity

Marine protected areas (MPAs) are used to protect species, communities, and their associated habitats, among other goals. Measuring MPA efficacy can be challenging, however, particularly when considering responses at the community level. We gathered 36 abundance and 14 biomass data sets on fish assemblages and used meta-analysis to evaluate the ability of 22 distinct community diversity metrics to detect differences in community structure between MPAs and nearby control sites. We also considered the effects of 6 covariates-MPA size and age, MPA size and age interaction, latitude, total species richness, and level of protection-on each metric. Some common metrics, such as species richness and Shannon diversity, did not differ consistently between MPA and control sites, whereas other metrics, such as total abundance and biomass, were consistently different across studies. Metric responses derived from the biomass data sets were more consistent than those based on the abundance data sets, suggesting that community-level biomass differs more predictably than abundance between MPA and control sites. Covariate analyses indicated that level of protection, latitude, MPA size, and the interaction between MPA size and age affect metric performance. These results highlight a handful of metrics, several of which are little known, that could be used to meet the increasing demand for community-level indicators of MPA effectiveness.

Identifying bioaccumulative halogenated organic compounds using a nontargeted analytical approach: seabirds as sentinels

Persistent organic pollutants (POPs) are typically monitored via targeted mass spectrometry, which potentially identifies only a fraction of the contaminants actually present in environmental samples. With new anthropogenic compounds continuously introduced to the environment, novel and proactive approaches that provide a comprehensive alternative to targeted methods are needed in order to more completely characterize the diversity of known and unknown compounds likely to cause adverse effects. Nontargeted mass spectrometry attempts to extensively screen for compounds, providing a feasible approach for identifying contaminants that warrant future monitoring. We employed a nontargeted analytical method using comprehensive two-dimensional gas chromatography coupled to time-of-flight mass spectrometry (GC×GC/TOF-MS) to characterize halogenated organic compounds (HOCs) in California Black skimmer (Rynchops niger) eggs. Our study identified 111 HOCs; 84 of these compounds were regularly detected via targeted approaches, while 27 were classified as typically unmonitored or unknown. Typically unmonitored compounds of note in bird eggs included tris(4-chlorophenyl)methane (TCPM), tris(4-chlorophenyl)methanol (TCPMOH), triclosan, permethrin, heptachloro-1'-methyl-1,2'-bipyrrole (MBP), as well as four halogenated unknown compounds that could not be identified through database searching or the literature. The presence of these compounds in Black skimmer eggs suggests they are persistent, bioaccumulative, potentially biomagnifying, and maternally transferring. Our results highlight the utility and importance of employing nontargeted analytical tools to assess true contaminant burdens in organisms, as well as to demonstrate the value in using environmental sentinels to proactively identify novel contaminants.

Polybrominated diphenyl ethers (PBDEs) in fish tissue may be an indicator of plastic contamination in marine habitats

The accumulation of plastic debris in pelagic habitats of the subtropical gyres is a global phenomenon of growing concern, particularly with regard to wildlife. When animals ingest plastic debris that is associated with chemical contaminants, they are at risk of bioaccumulating hazardous pollutants. We examined the relationship between the bioaccumulation of hazardous chemicals in myctophid fish associated with plastic debris and plastic contamination in remote and previously unmonitored pelagic habitats in the South Atlantic Ocean. Using a published model, we defined three sampling zones where accumulated densities of plastic debris were predicted to differ. Contrary to model predictions, we found variable levels of plastic debris density across all stations within the sampling zones. Mesopelagic lanternfishes, sampled from each station and analyzed for bisphenol A (BPA), alkylphenols, alkylphenol ethoxylates, polychlorinated biphenyls (PCBs) and polybrominated diphenyl ethers (PBDEs), exhibited variability in contaminant levels, but this variability was not related to plastic debris density for most of the targeted compounds with the exception of PBDEs. We found that myctophid sampled at stations with greater plastic densities did have significantly larger concentrations of BDE#s 183 -209 in their tissues suggesting that higher brominated congeners of PBDEs, added to plastics as flame-retardants, are indicative of plastic contamination in the marine environment. Our results provide data on a previously unsampled pelagic gyre and highlight the challenges associated with characterizing plastic debris accumulation and associated risks to wildlife.

Shifting the life-history paradigm: discovery of novel habitat use by hawksbill turtles

Adult hawksbill turtles (Eretmochelys imbricata) are typically described as open-coast, coral reef and hard substrate dwellers. Here, we report new satellite tracking data on female hawksbills from several countries in the eastern Pacific that revealed previously undocumented behaviour for adults of the species. In contrast to patterns of habitat use exhibited by their Caribbean and Indo-Pacific counterparts, eastern Pacific hawksbills generally occupied inshore estuaries, wherein they had strong associations with mangrove saltwater forests. The use of inshore habitats and affinities with mangrove saltwater forests presents a previously unknown life-history paradigm for adult hawksbill turtles and suggests a potentially unique evolutionary trajectory for the species. Our findings highlight the variability in life-history strategies that marine turtles and other wide-ranging marine wildlife may exhibit among ocean regions, and the importance of understanding such disparities from an ecological and management perspective.

Trace metals in an urbanized estuarine sea turtle food web in San Diego Bay, CA

San Diego Bay is an anthropogenically impacted waterway that is also a critical habitat for many sensitive species such as the green sea turtle (Chelonia mydas). In this study, we quantified trace metal concentrations in sediment and organisms composing the green sea turtle diet, and identified bioaccumulation patterns for a suite of trace metals. We found Ag, Cd, Cu, Mn, Se, and Zn exhibited the highest bioaccumulation levels in this food web. Cu and Mn concentrations in resident biota displayed a strong spatial gradient from the mouth to the head of the Bay, which was different from the patterns found in the sediment itself. Sediment median concentrations followed a general pattern across the bay of Al>Mn>Cu≈Zn>Pb>As>Cd>Ag>Se>Hg. In contrast, eelgrass displayed differential patterns in the mouth versus the back of the Bay (three front Bay sites: Al>Mn>Zn>Cu>Pb>Se>Cd≈Ag>As; five back Bay sites: Mn>Al>Zn>Cu>Pb≈Se>Cd>Ag>Hg>As) with the exception of Shelter Island where levels of Zn and Cu were elevated as a result of anti-fouling paint pollution. Observed differences between sediment and biota metal patterns are likely due to complex processes related to trace metals input and bioavailability, habitat characteristics and specific metabolic functioning of the trace metals for each member of the food web. These data highlight the fact that for the San Diego Bay ecosystem, the current use of toxicity reference values scaled up from sediment and invertebrate testing ex-situ is likely to be inaccurate when transposed to the green sea turtle. Here, we illustrate how identifying spatial variability in metal exposure can improve our understanding of habitat utilization by sea turtles in highly urbanized estuaries. Monitoring contaminants directly in food webs of sensitive vertebrates may greatly improve our understanding of their direct and indirect exposure to potentially deleterious contamination, and should be considered in the future to improve traditional risk assessment approaches.

Dynamic habitat models: using telemetry data to project fisheries bycatch

Fisheries bycatch is a recognized threat to marine megafauna. Addressing bycatch of pelagic species however is challenging owing to the dynamic nature of marine environments and vagility of these organisms. In order to assess the potential for species to overlap with fisheries, we propose applying dynamic habitat models to determine relative probabilities of species occurrence for specific oceanographic conditions. We demonstrate this approach by modelling habitats for Laysan (Phoebastria immutabilis) and black-footed albatrosses (Phoebastria nigripes) using telemetry data and relating their occurrence probabilities to observations of Hawaii-based longline fisheries in 1997-2000. We found that modelled habitat preference probabilities of black-footed albatrosses were high within some areas of the fishing range of the Hawaiian fleet and such preferences were important in explaining bycatch occurrence. Conversely, modelled habitats of Laysan albatrosses overlapped little with Hawaii-based longline fisheries and did little to explain the bycatch of this species. Estimated patterns of albatross habitat overlap with the Hawaiian fleet corresponded to bycatch observations: black-footed albatrosses were more frequently caught in this fishery despite being 10 times less abundant than Laysan albatrosses. This case study demonstrates that dynamic habitat models based on telemetry data may help to project interactions with pelagic animals relative to environmental features and that such an approach can serve as a tool to guide conservation and management decisions.

Pollutants and the health of green sea turtles resident to an urbanized estuary in San Diego, CA

Rapid expansion of coastal anthropogenic development means that critical foraging and developmental habitats often occur near highly polluted and urbanized environments. Although coastal contamination is widespread, the impact this has on long-lived vertebrates like the green turtle (Chelonia mydas) is unclear because traditional experimental methods cannot be applied. We coupled minimally invasive sampling techniques with health assessments to quantify contaminant patterns in a population of green turtles resident to San Diego Bay, CA, a highly urbanized and contaminated estuary. Several chemicals were correlated with turtle size, suggesting possible differences in physiological processes or habitat utilization between life stages. With the exception of mercury, higher concentrations of carapace metals as well as 4,4'-dichlorodiphenyldichloroethylene (DDE) and γ chlordane in blood plasma relative to other sea turtle studies raises important questions about the chemical risks to turtles resident to San Diego Bay. Mercury concentrations exceeded immune function no-effects thresholds and increased carapace metal loads were correlated with higher levels of multiple health markers. These results indicate immunological and physiological effects studies are needed in this population. Our results give insight into the potential conservation risk contaminants pose to sea turtles inhabiting this contaminated coastal habitat, and highlight the need to better manage and mitigate contaminant exposure in San Diego Bay.

The impact of conservation on the status of the world's vertebrates

Using data for 25,780 species categorized on the International Union for Conservation of Nature Red List, we present an assessment of the status of the world's vertebrates. One-fifth of species are classified as Threatened, and we show that this figure is increasing: On average, 52 species of mammals, birds, and amphibians move one category closer to extinction each year. However, this overall pattern conceals the impact of conservation successes, and we show that the rate of deterioration would have been at least one-fifth again as much in the absence of these. Nonetheless, current conservation efforts remain insufficient to offset the main drivers of biodiversity loss in these groups: agricultural expansion, logging, overexploitation, and invasive alien species.

Mapping the bycatch seascape: multispecies and multi-scale spatial patterns of fisheries bycatch

Fisheries bycatch is a worldwide conservation issue. Despite a growing awareness of bycatch problems in particular ocean regions, there have been few efforts to identify spatial patterns in bycatch events. Furthermore, many studies of fisheries bycatch have been myopic, focusing on a single species or a single region. Using a range of analytical approaches to identify spatial patterns in bycatch data, we demonstrate the utility and applications of area and point pattern analyses to single and multispecies bycatch seascapes of pelagic longline fisheries in the Atlantic and Pacific Oceans. We find clear evidence of spatial clustering within bycatch species in both ocean basins, both in terms of the underlying pattern of the locations of bycatch events relative to fishing locations and for areas of high bycatch rates. Furthermore, we find significant spatial overlap in the pattern of bycatch across species relative to the spatial distribution in fishing effort and target catch. These results point to the importance of considering spatial patterns of both single and multispecies bycatch to meet the ultimate goal of reducing bycatch encounters. These analyses also highlight the importance of considering bycatch relative to target catch as a way of identifying areas where fishing effort reduction may help to reduce multispecies bycatch with minimal impact on target catch.

Comparing effectiveness of experimental and implemented bycatch reduction measures: the ideal and the real

Fishers, scientists, and resource managers have made substantial progress in reducing bycatch of sea turtles, seabirds, and marine mammals through physical modifications to fishing gear. Many bycatch-avoidance measures have been developed and tested successfully in controlled experiments, which have led to regulated implementation of modified or new fishing gear. Nevertheless, successful bycatch experiments may not translate to effective mitigation in commercial fisheries because experimental conditions are relaxed in commercial fishing operations. Such a difference between experimental results and real-world results with fishing fleets may have serious consequences for management and conservation of protected species taken as bycatch. We evaluated preimplementation experimental measures and postimplementation efficacy from primary and gray literature for three case studies: acoustic pingers that warn marine mammals of the presence of gill nets, turtle excluder devices that reduce bycatch of turtles in trawls, and various measures to reduce seabird bycatch in longlines. Three common themes to successful implementation of bycatch reduction measures are long-standing collaborations among the fishing industry, scientists, and resource managers; pre- and postimplementation monitoring; and compliance via enforcement and incentives.

Putting longline bycatch of sea turtles into perspective

Although some sea turtle populations are showing encouraging signs of recovery, others continue to decline. Reversing population declines requires an understanding of the primary factor(s) that underlie this persistent demographic trend. The list of putative factors includes direct turtle and egg harvest, egg predation, loss or degradation of nesting beach habitat, fisheries bycatch, pollution, and large-scale changes in oceanographic conditions and nutrient availability. Recently, fisheries bycatch, in particular bycatch from longline fisheries, has received increased attention and has been proposed as a primary source of turtle mortality. We reviewed the existing data on the relative impact of longline bycatch on sea turtle populations. Although bycatch rates from individual longline vessels are extremely low, the amount of gear deployed by longline vessels suggests that cumulative bycatch of turtles from older age classes is substantial. Current estimates suggest that even if pelagic longlines are not the largest single source of fisheries-related mortality, longline bycatch is high enough to warrant management actions in all fleets that encounter sea turtles. Nevertheless, preliminary data also suggest that bycatch from gillnets and trawl fisheries is equally high or higher than longline bycatch with far higher mortality rates. Until gillnet and trawl fisheries are subject to the same level of scrutiny given to pelagic longlines, our understanding of the overall impact of fisheries bycatch on vulnerable sea turtle populations will be incomplete.