Sampling environmental DNA from trees and soil to detect cryptic arboreal mammals.

Environmental DNA (eDNA) approaches to monitoring biodiversity in terrestrial environments have largely focused on sampling water bodies, potentially limiting the geographic and taxonomic scope of eDNA investigations. We assessed the performance of two strictly terrestrial eDNA sampling approaches to detect arboreal mammals, a guild with many threatened and poorly studied taxa worldwide, within two central New Jersey (USA) woodlands. We evaluated species detected with metabarcoding using two eDNA collection methods (tree bark vs. soil sampling), and compared the performance of two detection methods (qPCR vs. metabarcoding) within a single species. Our survey, which included 94 sampling events at 21 trees, detected 16 species of mammals, representing over 60% of the diversity expected in the area. More DNA was found for the 8 arboreal versus 8 non-arboreal species detected (mean: 2466 vs. 289 reads/sample). Soil samples revealed a generally similar composition, but a lower diversity, of mammal species. Detection rates for big brown bat were 3.4 × higher for qPCR over metabarcoding, illustrating the enhanced sensitivity of single-species approaches. Our results suggest that sampling eDNA from on and around trees could serve as a useful new monitoring tool for cryptic arboreal mammal communities globally.

Dogs suppress a pivotal function in the food webs of sandy beaches.

Domestic dogs are the most abundant carnivore globally and have demonstrable negative impacts to wildlife; yet, little evidence regarding their functional roles in natural food webs exists. Adding dogs to food webs may result in a net loss (via suppression of naturally occurring species), net gain (via mesopredator release), or no change (via functional replacement) to ecosystem function. Scavenging is a pivotal function in ecosystems, particularly those that are energetically supported by carrion. Dogs also scavenge on animal carcasses, but whether scavenging by dogs influences the structural and functional properties of food webs remains unclear. Here we used camera traps baited with carrion to test the effect of dogs on the composition and diversity of the vertebrate scavenger guild, as well as carrion detection and consumption rates. We conducted this work in sandy beach ecosystems, which rely on the import of marine organic matter (i.e. stranding of dead marine animals). Diversity of the scavenger community was similar on beaches without dogs. Dogs increased the time it took for carcasses to be detected and decreased the proportion of carrion consumed. This 'dog suppression effect' on scavenging was stronger for nocturnal mammalian scavengers, presumably being driven by indirect trait-mediated effects, which raises further questions about the broader ecological consequences of domestic dogs in natural systems.

Host gene expression in wildlife disease: making sense of species-level responses.

Emerging infectious diseases are significant threats to wildlife conservation, yet the impacts of pathogen exposure and infection can vary widely among host species. As such, conservation biologists and disease ecologists have increasingly aimed to understand species-specific host susceptibility using molecular methods. In particular, comparative gene expression assays have been used to contrast the transcriptomic responses of disease-resistant and disease-susceptible hosts to pathogen exposure. This work usually assumes that the gene expression responses of disease-resistant species will reveal the activation of molecular pathways contributing to host defence. However, results often show that disease-resistant hosts undergo little gene expression change following pathogen challenge. Here, we discuss the mechanistic implications of these "null" findings and offer methodological suggestions for future molecular studies of wildlife disease. First, we highlight that muted transcriptomic responses with minimal immune system recruitment may indeed be protective for nonsusceptible hosts if they limit immunopathology and promote pathogen tolerance in systems where susceptible hosts suffer from genetic dysregulation. Second, we argue that overly narrow investigation of responses to pathogen exposure may overlook important, constitutively active molecular pathways that underlie species-specific defences. Finally, we outline alternative study designs and approaches that complement interspecific transcriptomic comparisons, including intraspecific gene expression studies and genomic methods to detect signatures of selection. Collectively, these insights will help ecologists extract maximal information from conservation-relevant transcriptomic data sets, leading to a deeper understanding of host defences and, ultimately, the implementation of successful conservation interventions.

Genomic signatures of selection in bats surviving white-nose syndrome.

Rapid evolution of advantageous traits following abrupt environmental change can help populations recover from demographic decline. However, for many introduced diseases affecting longer-lived, slower reproducing hosts, mortality is likely to outpace the acquisition of adaptive de novo mutations. Adaptive alleles must therefore be selected from standing genetic variation, a process that leaves few detectable genomic signatures. Here, we present whole genome evidence for selection in bat populations that are recovering from white-nose syndrome (WNS). We collected samples both during and after a WNS-induced mass mortality event in two little brown bat populations that are beginning to show signs of recovery and found signatures of soft sweeps from standing genetic variation at multiple loci throughout the genome. We identified one locus putatively under selection in a gene associated with the immune system. Multiple loci putatively under selection were located within genes previously linked to host response to WNS as well as to changes in metabolism during hibernation. Results from two additional populations suggested that loci under selection may differ somewhat among populations. Through these findings, we suggest that WNS-induced selection may contribute to genetic resistance in this slowly reproducing species threatened with extinction.

Optimizing conservation benefits for threatened beach fauna following severe natural disturbances.

Wildlife on sandy beaches is often constrained by transformation of natural areas for human use, and opportunities for acquiring or restoring new habitat are rare. Storms can often force changes in land use naturally by re-shaping coastal landforms, thereby creating high quality habitat; yet, wildlife requirements are seldom considered in post-storm recovery planning, and conservation practitioners lack suitable evidence to argue for the protection of habitats freshly formed by storms. Here we used a maximum-likelihood spatial modeling approach to quantify impacts of Hurricane Sandy (mid-Atlantic United States, October 2012) on nesting habitat of four bird species of conservation concern: American oystercatchers, black skimmers, least terns and piping plovers. We calculated the immediate storm-created changes (loss, persisting, gained) in nesting habitat under two levels of conservation protections: the current regulatory framework, and a scenario in which all potential habitats were under conservation protection. Hurricane Sandy resulted in apparent large gains for least terns (+181 ha) and piping plovers (+289 ha). However, actual gains were reduced to 16 ha for plovers and reversed for least terns (net loss of 6.4 ha) because newly formed habitat occurred outside existing reserve boundaries. Similarly, under the current management framework, black skimmer nesting habitat decreased by ~164 ha. We also tested whether birds benefited from newly created nesting habitat by identifying nest and colony locations for three years following Hurricane Sandy. All species overwhelmingly nested in habitat that existed prior the storm (76-98% of all nests/colonies); only a small percentage (≤17% for all species) occupied newly created habitat. We conclude that static spatial conservation efforts fail to capitalize on potentially large gains resulting from storms for several species and recommend flexible spatial conservation investments as a key input in post-storm recovery planning.

Managing birds of conservation concern on sandy shores: How much room for future conservation actions is there?

Resource limitations often prevent the active management required to maintain habitat quality in protected areas. Because restrictions in access or allowable public activities are the sole conservation measure in these locations, an important question to consider is whether species of conservation concern truly benefit from parcels that are shielded from human disturbance. Here, we assess the conservation benefit of protecting birds from human recreation on over 204 km of sandy beaches by (a) estimating the total area of beach-nesting bird habitat that has been created by conservation protections; (b) quantifying the change in nesting habitat extent should further conservation protections be implemented; and (c) providing data to inform future protected area expansion. We use a maximum entropy species distribution modeling approach to estimate the extent and quality of suitable habitat for four beach-nesting bird species of conservation concern under the existing management regime and compare it to scenarios in which the entire study area is either unprotected of fully protected from human disturbance. Managing humans has dramatic conservation returns for least terns and piping plovers, creating extensive nesting habitat that otherwise would not exist. There is considerable scope for conservation gains, potentially tripling the extent of nesting areas. Expanding conservation footprints for American oystercatchers and black skimmers is predicted to enhance the quality of existing nesting areas. The work demonstrates the utility of modeling changes in habitat suitability to inform protected area expansion on ocean beaches and coastal dunes.

Functional plasticity in vertebrate scavenger assemblages in the presence of introduced competitors.

Introduced species may suppress or enhance ecological functions, or they may have neutral effects in ecosystems where they replace or complement native species. Few studies, however, have explicitly tested for these trajectories, and for the effect these might have for native species. In this study, we experimentally test the trajectory and scale of change in the function of 'carrion removal' at different carrion loads along ocean beaches in Eastern Australia that have different numbers of introduced red foxes (Vulpes vulpes) and several species of native raptors. We hypothesized that the 'positive' effect of foxes on carrion removal would be greatest at high carrion loads, because competition for resources between native and introduced species is lower. Scavenger abundance, fox occurrences, and carrion consumption by these species differed widely between locations and times. Despite distinct spatial differences in the structure of vertebrate scavenger assemblages, total carrion consumption was not significantly different between locations at any carrion load. This lack of variation in functional rates indicates potential functional plasticity in the scavenger assemblage and possible functional accommodation of red foxes. Neutral fox effects on ecological functions or the ecosystem more broadly are, however, very unlikely to extend beyond carrion consumption.

Chirosurveillance: The use of native bats to detect invasive agricultural pests.

Invasive insect pests cost the agricultural industry billions of dollars annually in crop losses. Timely detection of pests is critical for management efficiency. Innovative pest detection strategies, such as environmental DNA (eDNA) techniques, combined with efficient predators, maximize sampling resolution across space and time and may improve surveillance. We tested the hypothesis that temperate insectivorous bats can be important sentinels of agricultural insect pest surveillance. Specifically, we used a new high-sensitivity molecular assay for invasive brown marmorated stink bugs (Halyomorpha halys) to examine the extent to which big brown bats (Eptesicus fuscus) detect agricultural pests in the landscape. We documented consistent seasonal predation of stink bugs by big brown bats. Importantly, bats detected brown marmorated stink bugs 3-4 weeks earlier than the current standard monitoring tool, blacklight traps, across all sites. We highlight here the previously unrecognized potential ecosystem service of bats as agents of pest surveillance (or chirosurveillance). Additional studies examining interactions between other bat and insect pest species, coupled with comparisons of detectability among various conventional monitoring methods, are needed to verify the patterns extracted from this study. Ultimately, robust economic analyses will be needed to assess the cost-effectiveness of chirosurveillance as a standard strategy for integrated pest management.

Regional drivers of clutch loss reveal important trade-offs for beach-nesting birds.

Coastal birds are critical ecosystem constituents on sandy shores, yet are threatened by depressed reproductive success resulting from direct and indirect anthropogenic and natural pressures. Few studies examine clutch fate across the wide range of environments experienced by birds; instead, most focus at the small site scale. We examine survival of model shorebird clutches as an index of true clutch survival at a regional scale (∼200 km), encompassing a variety of geomorphologies, predator communities, and human use regimes in southeast Queensland, Australia. Of the 132 model nests deployed and monitored with cameras, 45 (34%) survived the experimental exposure period. Thirty-five (27%) were lost to flooding, 32 (24%) were depredated, nine (7%) buried by sand, seven (5%) destroyed by people, three (2%) failed by unknown causes, and one (1%) was destroyed by a dog. Clutch fate differed substantially among regions, particularly with respect to losses from flooding and predation. 'Topographic' exposure was the main driver of mortality of nests placed close to the drift line near the base of dunes, which were lost to waves (particularly during storms) and to a lesser extent depredation. Predators determined the fate of clutches not lost to waves, with the depredation probability largely influenced by region. Depredation probability declined as nests were backed by higher dunes and were placed closer to vegetation. This study emphasizes the scale at which clutch fate and survival varies within a regional context, the prominence of corvids as egg predators, the significant role of flooding as a source of nest loss, and the multiple trade-offs faced by beach-nesting birds and those that manage them.

The Early Shorebird Will Catch Fewer Invertebrates on Trampled Sandy Beaches.

Many species of birds breeding on ocean beaches and in coastal dunes are of global conservation concern. Most of these species rely on invertebrates (e.g. insects, small crustaceans) as an irreplaceable food source, foraging primarily around the strandline on the upper beach near the dunes. Sandy beaches are also prime sites for human recreation, which impacts these food resources via negative trampling effects. We quantified acute trampling impacts on assemblages of upper shore invertebrates in a controlled experiment over a range of foot traffic intensities (up to 56 steps per square metre) on a temperate beach in Victoria, Australia. Trampling significantly altered assemblage structure (species composition and density) and was correlated with significant declines in invertebrate abundance and species richness. Trampling effects were strongest for rare species. In heavily trafficked plots the abundance of sand hoppers (Amphipoda), a principal prey item of threatened Hooded Plovers breeding on this beach, was halved. In contrast to the consistently strong effects of trampling, natural habitat attributes (e.g. sediment grain size, compactness) were much less influential predictors. If acute suppression of invertebrates caused by trampling, as demonstrated here, is more widespread on beaches it may constitute a significant threat to endangered vertebrates reliant on these invertebrates. This calls for a re-thinking of conservation actions by considering active management of food resources, possibly through enhancement of wrack or direct augmentation of prey items to breeding territories.

Real-time PCR assay to detect brown marmorated stink bug, Halyomorpha halys (Stål), in environmental DNA.

BACKGROUND: Early detection before establishment and identification of key predators are time-honored strategies towards effective eradication or control of invasive species. The brown marmorated stink bug (BMSB), Halyomorpha halys, is a recent exotic pest of several important crops in North America and Europe. Resulting widespread applications of insecticides have countered years of careful integrated pest management and are leading to the resurgence of other agricultural pests. Environmental DNA (eDNA) has been used effectively to detect aquatic invasives. RESULTS: We developed a real-time PCR (qPCR) assay for BMSB in a conserved region of the ribosomal DNA interspacer 1 (ITS1). We validated this assay on worldwide populations of BMSB and tested its specificity and sensitivity against other US Pentatomidae species and on guano of big brown bat, Eptesicus fuscus, which we confirmed is a BMSB predator in New Jersey. We also detected BMSB DNA after rapid (and inexpensive) HotSHOT DNA extractions of soiled paper from cages briefly holding BMSB, as well as from discarded exuviae. CONCLUSION: Given the high sensitivity of our assay to BMSB environmental DNA (eDNA) in terrestrial samples, this tool should become a cost-effective approach for using eDNA to detect terrestrial invasive species and their key predators. © 2016 Society of Chemical Industry.

Conservation implications of ameliorating survival of little brown bats with white-nose syndrome.

Management of wildlife populations impacted by novel threats is often challenged by a lack of data on temporal changes in demographic response. Populations may suffer rapid declines from the introduction of new stressors, but how demography changes over time is critical to determining long-term outcomes for populations. White-nose syndrome (WNS), an infectious disease of hibernating bats, has caused massive and rapid population declines in several hibernating species of bats in North America since the disease was first observed on the continent in 2006. Estimating annual survival rates and demographic trends among remnant colonies of hibernating bats that experienced mass mortality from WNS is needed to determine long-term population viability of species impacted by this disease. Using mark-recapture data on infected little brown bats (Myotis lucifugus), we estimated the first apparent annual survival rates for four years following WNS detection at a site. We found strong support for an increasing trend in annual survival, which improved from 0.68 (95% CI = 0.44-0.85) to 0.75 (95% CI = 0.51-0.89) for males and 0.65 (95% CI = 0.44-0.81) to 0.70 (95% CI = 0.50-0.84) for females. These results suggest that stabilization at remnant colonies after mass mortality from WNS may be due to improved survival and not from immigration from other areas. Despite ameliorating survival, our stochastic matrix projection model predicts continued declines for little brown bat populations (λ = 0.95), raising concern for the regional persistence of this species. We conducted a vital rate sensitivity analysis and determined that adult and juvenile survival, as opposed to fecundity, are the demographic parameters most important to target to maximize recovery potential of little brown bat populations in areas impacted by WNS.

A case study of bats and white-nose syndrome demonstrating how to model population viability with evolutionary effects.

Ecological factors generally affect population viability on rapid time scales. Traditional population viability analyses (PVA) therefore focus on alleviating ecological pressures, discounting potential evolutionary impacts on individual phenotypes. Recent studies of evolutionary rescue (ER) focus on cases in which severe, environmentally induced population bottlenecks trigger a rapid evolutionary response that can potentially reverse demographic threats. ER models have focused on shifting genetics and resulting population recovery, but no one has explored how to incorporate those findings into PVA. We integrated ER into PVA to identify the critical decision interval for evolutionary rescue (DIER) under which targeted conservation action should be applied to buffer populations undergoing ER against extinction from stochastic events and to determine the most appropriate vital rate to target to promote population recovery. We applied this model to little brown bats (Myotis lucifugus) affected by white-nose syndrome (WNS), a fungal disease causing massive declines in several North American bat populations. Under the ER scenario, the model predicted that the DIER period for little brown bats was within 11 years of initial WNS emergence, after which they stabilized at a positive growth rate (λ = 1.05). By comparing our model results with population trajectories of multiple infected hibernacula across the WNS range, we concluded that ER is a potential explanation of observed little brown bat population trajectories across multiple hibernacula within the affected range. Our approach provides a tool that can be used by all managers to provide testable hypotheses regarding the occurrence of ER in declining populations, suggest empirical studies to better parameterize the population genetics and conservation-relevant vital rates, and identify the DIER period during which management strategies will be most effective for species conservation.

Un Estudio de Caso sobre Murciélagos y el Síndrome de Nariz Blanca que Demuestra cómo Modelar la Viabilidad Poblacional con Efectos Evolutivos Resumen Los factores ecológicos afectan generalmente a la viabilidad poblacional en escalas rápidas de tiempo. Por esto los análisis tradicionales de viabilidad poblacional (AVP) se enfocan en aliviar las presiones ecológicas, lo que discontinúa los impactos evolutivos potenciales sobre los fenotipos individuales. Los estudios recientes del rescate evolutivo (RE) se enfocan en casos en los que cuellos de botella poblacionales inducidos por el ambiente disparan una respuesta evolutiva rápida, la que puede revertir potencialmente las amenazas demográficas. Los modelos de rescate evolutivo se han enfocado en la genética cambiante y la recuperación poblacional resultante, pero nadie ha explorado cómo incorporar estos hallazgos en los AVP. Integramos el RE a los AVP para identificar el intervalo de decisión crítica para el rescate evolutivo (IDRE), bajo el cual se deben aplicar las acciones de conservación enfocada para amortiguar a las poblaciones sometidas a RE ante la extinción por eventos estocásticos, y para determinar la tasa vital más apropiada para promover la recuperación de la población. Aplicamos este modelo a los pequeños murciélagos cafés (Myotis lucifugus) afectados por el síndrome de nariz blanca (SNB), una enfermedad micótica que causa declinaciones masivas en varias poblaciones norteamericanas de murciélagos. Bajo el escenario de RE, el modelo predijo que el periodo de IDRE para estos murciélagos estaba dentro de once años del surgimiento inicial del síndrome, después del cual se estabilizaban a una tasa positiva de crecimiento (λ = 1.05). Al comparar nuestros resultados del modelo con las trayectorias poblacionales de múltiples sitios de hibernación infectados a lo largo de la extensión del SNB, concluimos que el RE es una explicación potencial de las trayectorias observadas de pequeños murciélagos cafés a lo largo de múltiples sitios de hibernación dentro de la extensión afectada. Nuestra estrategia proporciona una herramienta que puede ser usada por todos los manejadores para proporcionar hipótesis comprobables con respecto a la aparición del RE en las poblaciones declinantes, sugerir estudios empíricos que mejoren los parámetros de la genética de poblaciones y las tasas vitales relevantes para la conservación, y para identificar el periodo IDRE durante el cual las estrategias de manejo serán más efectivas para la conservación de la especie.

Metrics to assess ecological condition, change, and impacts in sandy beach ecosystems.

Complexity is increasingly the hallmark in environmental management practices of sandy shorelines. This arises primarily from meeting growing public demands (e.g., real estate, recreation) whilst reconciling economic demands with expectations of coastal users who have modern conservation ethics. Ideally, shoreline management is underpinned by empirical data, but selecting ecologically-meaningful metrics to accurately measure the condition of systems, and the ecological effects of human activities, is a complex task. Here we construct a framework for metric selection, considering six categories of issues that authorities commonly address: erosion; habitat loss; recreation; fishing; pollution (litter and chemical contaminants); and wildlife conservation. Possible metrics were scored in terms of their ability to reflect environmental change, and against criteria that are widely used for judging the performance of ecological indicators (i.e., sensitivity, practicability, costs, and public appeal). From this analysis, four types of broadly applicable metrics that also performed very well against the indicator criteria emerged: 1.) traits of bird populations and assemblages (e.g., abundance, diversity, distributions, habitat use); 2.) breeding/reproductive performance sensu lato (especially relevant for birds and turtles nesting on beaches and in dunes, but equally applicable to invertebrates and plants); 3.) population parameters and distributions of vertebrates associated primarily with dunes and the supralittoral beach zone (traditionally focused on birds and turtles, but expandable to mammals); 4.) compound measurements of the abundance/cover/biomass of biota (plants, invertebrates, vertebrates) at both the population and assemblage level. Local constraints (i.e., the absence of birds in highly degraded urban settings or lack of dunes on bluff-backed beaches) and particular issues may require alternatives. Metrics - if selected and applied correctly - provide empirical evidence of environmental condition and change, but often do not reflect deeper environmental values per se. Yet, values remain poorly articulated for many beach systems; this calls for a comprehensive identification of environmental values and the development of targeted programs to conserve these values on sandy shorelines globally.