KEEPING THE HEAT ON: WEIGHTED SURVEILLANCE FOR CHYTRID FUNGUS (BATRACHOCHYTRIUM DENDROBATIDIS) IN DIXIE VALLEY TOADS (ANAXYRUS [= BUFO] WILLIAMSI)

Introduced fungal pathogens have caused declines and extinctions of naïve wildlife populations across vertebrate classes. Consequences of introduced pathogens to hosts with small ranges might be especially severe because of limited redundancy to rescue populations and lower abundance that may limit the resilience of populations to perturbations like disease introduction. As a complement to biosecurity measures to prevent the spread of pathogens, surveillance programs may enable early detection of pathogens, when management actions to limit the effects of pathogens on naïve hosts might be most beneficial. We analyzed surveillance data for the endangered and narrowly endemic Dixie Valley toad (Anaxyrus [= Bufo] williamsi) from two time periods (2011-2014 and 2019-2021) to estimate the minimum detectable prevalence of the amphibian fungal pathogen Batrachochytrium dendrobatidis (Bd). We assessed if detection efficiency could be improved by using samples from both Dixie Valley toads and co-occurring introduced American bullfrogs (Lithobates catesbeianus) and literature-derived surveillance weights. We further evaluated a weighted surveillance design to increase the efficiency of surveillance efforts for Bd within the toad's small (<6 km2) range. We found that monitoring adult and larval American bullfrogs would probably detect Bd more efficiently than monitoring Dixie Valley toads alone. Given that no Bd was detected, minimum detectable prevalence of Bd was <3% in 2011-2014, and <5% (Dixie Valley toads only) and <10% (American bullfrogs only) in 2019-2021. Optimal management for Bd depends on the mechanisms underlying its apparent absence from the range of Dixie Valley toads, but a balanced surveillance scheme that includes sampling American bullfrogs to increase the likelihood of detecting Bd, and adult Dixie Valley toads to ensure broad spatial coverage where American bullfrogs do not occur, would probably result in efficient surveillance, which might permit timely management of Bd if it is detected.

Protected areas slow declines unevenly across the tetrapod tree of life

Protected areas (PAs) are the primary strategy for slowing terrestrial biodiversity loss. Although expansion of PA coverage is prioritized under the Convention on Biological Diversity, it remains unknown whether PAs mitigate declines across the tetrapod tree of life and to what extent land cover and climate change modify PA effectiveness1,2. Here we analysed rates of change in abundance of 2,239 terrestrial vertebrate populations across the globe. On average, vertebrate populations declined five times more slowly within PAs (-0.4% per year) than at similar sites lacking protection (-1.8% per year). The mitigating effects of PAs varied both within and across vertebrate classes, with amphibians and birds experiencing the greatest benefits. The benefits of PAs were lower for amphibians in areas with converted land cover and lower for reptiles in areas with rapid climate warming. By contrast, the mitigating impacts of PAs were consistently augmented by effective national governance. This study provides evidence for the effectiveness of PAs as a strategy for slowing tetrapod declines. However, optimizing the growing PA network requires targeted protection of sensitive clades and mitigation of threats beyond PA boundaries. Provided the conditions of targeted protection, adequate governance and well-managed landscapes are met, PAs can serve a critical role in safeguarding tetrapod biodiversity.

Habitat use by female desert tortoises suggests tradeoffs between resource use and risk avoidance

Animals may select habitat to maximize the benefits of foraging on growth and reproduction, while balancing competing factors like the risk of predation or mortality from other sources. Variation in the distribution of food resources may lead animals to forage at times or in places that carry greater predation risk, with individuals in poor quality habitats expected to take greater risks while foraging. We studied Mojave desert tortoises (Gopherus agassizii) in habitats with variable forage availability to determine if risk aversion in their selection of habitat relative was related to abundance of forage. As a measure of risk, we examined tortoise surface activity and mortality. We also compared tortoise body size and body condition between habitats with ample forage plants and those with less forage plants. Tortoises from low forage habitats selected areas where more annual plants were nutritious herbaceous flowering plants but did not favor areas of greater perennial shrub cover that could shelter them or their burrows. In contrast, tortoises occupying high forage habitats showed no preference for forage characteristics, but used burrows associated with more abundant and larger perennial shrubs. Tortoises in high forage habitats were larger and active above ground more often but did not have better body condition. Mortality was four times higher for females occupying low forage habitat than those in high forage habitat. Our results are consistent with the idea that tortoises may minimize mortality risk where food resources are high, but may accept some tradeoff of greater mortality risk in order to forage optimally when food resources are limiting.

Effects of Electrostatic Interactions on Kapitza Resistance in Hexagonal Boron Nitride-Water Interfaces

Electrostatic interactions in nanoscale systems can influence the heat transfer mechanism and interfacial properties. This study uses molecular dynamics simulations to investigate the impact of various electrostatic interactions on the Kapitza resistance (R_k) on a hexagonal boron nitride-water system. The Kapitza resistance at hexagonal boron nitride nanotube (hBNNT)-water interface reduces with an increase in diameter of the nanotube due to more aggregation of water molecules per unit surface area. An increase in the partial charges on boron and nitride caused the reduction in R_k. With the increase in partial charge, a better hydrogen bonding between hBNNT and water was observed, whereas the structure and order of the water molecules remain the same. Nevertheless, the addition of NaCl salt into water does not have any influence on interfacial thermal transport. R_k remains unchanged with electrolyte concentration because the cumulative Coulombic interaction between the ions and the hBNNT is significantly less when compared with water molecules. Furthermore, the effect of electric field strength on interfacial heat transfer is also investigated by providing uniform positive and negative surface charges on the outermost hBN layers. R_k is nearly independent of the practical range of applied electric fields and decreases with an increasing electric field for extreme field strengths until the electrofreezing phenomenon occurs. The ordering of water molecules toward the charged surface leads to an increase in the layering effect, causing the reduction in R_k in the presence of an electric field.

Reference genome of the northwestern pond turtle, Actinemys marmorata

The northwestern pond turtle, Actinemys marmorata, and its recently recognized sister species, the southwestern pond turtle, A. pallida, are the sole aquatic testudines occurring over most of western North America, and the only living representatives of the genus Actinemys. Although it historically ranged from Washington state through central California, USA, populations of the northwestern pond turtle have been in decline for decades and the species is afforded state-level protection across its range; it is currently being considered for protection under the US Endangered Species Act. Here, we report a new, chromosome-level assembly of A. marmorata as part of the California Conservation Genomics Project (CCGP). Consistent with the reference genome strategy of the CCGP, we used Pacific Biosciences HiFi long reads and Hi-C chromatinproximity sequencing technology to produce a de novo assembled genome. The assembly comprises 198 scaffolds spanning 2,319,339,408 base pairs, has a contig N50 of 75 Mb, a scaffold N50 of 146Mb, and BUSCO complete score of 96.7%, making it the most complete testudine assembly of the 24 species from 13 families that are currently available. In combination with the A. pallida reference genome that is currently under construction through the CCGP, the A. marmorata genome will be a powerful tool for documenting landscape genomic diversity, the basis of adaptations to salt tolerance and thermal capacity, and hybridization dynamics between these recently diverged species.

Slip and stress from low shear rate nonequilibrium molecular dynamics: The transient-time correlation function technique

We derive the transient-time correlation function (TTCF) expression for the computation of phase variables of inhomogenous confined atomistic fluids undergoing boundary-driven planar shear (Couette) flow at constant pressure. Using nonequilibrium molecular dynamics simulations, we then apply the TTCF formalism to the computation of the shear stress and the slip velocity for atomistic fluids at realistic low shear rates, in systems under constant pressure and constant volume. We show that, compared to direct averaging of multiple trajectories, the TTCF method dramatically improves the accuracy of the results at low shear rates and that it is suitable to investigate the tribology and rheology of atomistically detailed confined fluids at realistic flow rates.

Divergent Genital Morphologies and Female-Male Covariation in Watersnakes

Genital evolution can be driven by diverse selective pressures. Across taxa we see evidence of covariation between males and females, as well as divergent genital morphologies between closely related species. Quantitative analyses of morphological changes in coevolving male and female genitalia have not yet been shown in vertebrates. This study uses 2D and 3D geometric morphometrics to quantitatively compare the complex shapes of vaginal pouches and hemipenes across three species of watersnakes (the sister taxa Nerodia fasciata, N. sipedon, and a close relative N. rhombifer) to address the relationship between genital morphology and divergence time in a system where sexual conflict may have driven sexually antagonistic coevolution of genital traits. Our pairwise comparisons of shape differences across species show that the sister species have male and female genitalia that are significantly different from each other, but more similar to each other than to N. rhombifer. We also determine that the main axes of shape variation are the same for males and females, with changes that relate to deeper bilobation of the vaginal pouch and hemipenes. In males, the protrusion of the region of spines at the base of the hemipene trades off with the degree of bilobation, suggesting amelioration of sexual conflict, perhaps driven by changes in the relative size of the entrance of the vaginal pouch that could have made spines less effective.

Hydrodynamic slip of alkali chloride solutions in uncharged graphene nanochannels

Using non-equilibrium molecular dynamics simulations, we demonstrate the effect of concentration and alkali cation types (K⁺, Na⁺, and Li⁺) on the hydrodynamic slip of aqueous alkali chloride solutions in an uncharged graphene nanochannel. We modeled the graphene-electrolyte interactions using the potential of Williams et al. [J. Phys. Chem. Lett. 8, 703 (2017)], which uses optimized graphene-ion Lennard-Jones interaction parameters to effectively account for surface and solvent polarizability effects on the adsorption of ions in an aqueous solution to a graphene surface. In our study, the hydrodynamic slip exhibits a decreasing trend for alkali chloride solutions with increasing salt concentration. The NaCl solution shows the highest reduction in the slip length followed by KCl and LiCl solutions, and the reduction in the slip length is very much dependent on the salt type. We also compared the slip length with that calculated using a standard unoptimized interatomic potential obtained from the Lorentz-Berthelot mixing rule for the ion-carbon interactions, which is not adjusted to account for the surface and solvent polarizability at the graphene surface. In contrast to the optimized model, the slip length of alkali chloride solutions in the unoptimized model shows only a nominal change with salt concentration and is also independent of the nature of salts. Our study shows that adoption of the computationally inexpensive optimized potential of Williams et al. for the graphene-ion interactions has a significant influence on the calculation of slip lengths for electrolyte solutions in graphene-based nanofluidic devices.

Generalized hydrodynamics of the Lennard-Jones liquid in view of hidden scale invariance

In recent years lines along which structure and dynamics are invariant to a good approximation, so-called isomorphs, have been identified in the thermodynamic phase diagrams of several model liquids and solids. This paper reports computer simulation data of the transverse and longitudinal collective dynamics at different length scales along an isomorph of the Lennard-Jones system. Our findings are compared to corresponding results along an isotherm and an isochore. Confirming the theoretical prediction, the reduced-unit dynamics of the transverse momentum density is invariant to a good approximation along the isomorph on all time and length scales. Likewise, the wave-vector dependent shear-stress autocorrelation function is found to be isomorph invariant (with minor deviations at very short times). A similar invariance is not seen along the isotherm or the isochore. Using a spatially nonlocal hydrodynamic model for the transverse momentum-density time-autocorrelation function, the macroscopic shear viscosity and its wave dependence are determined, demonstrating that the shear viscosity is isomorphic invariant on all length scales studied. This analysis implies the existence of a length scale that is isomorph invariant in reduced units, i.e., which characterizes each isomorph. The transverse sound-wave velocity, the Maxwell relaxation time, and the rigidity shear modulus are also isomorph invariant. In contrast to the isomorph invariance of all aspects of the transverse dynamics, the reduced-unit dynamics of the mass density is not invariant on length scales longer than the interparticle distance. By fitting to a generalized hydrodynamic model, we extract values for the wave-vector-dependent thermal diffusion coefficient, sound attenuation coefficient, and adiabatic sound velocity. The isomorph variation of these quantities in reduced units on long length scales can be eliminated by scaling with the density-scaling exponent, a fundamental quantity in the isomorph theory framework; this is an empirical observation that remains to be explained theoretically.

Electropumping of nanofluidic water by linear and angular momentum coupling: theoretical foundations and molecular dynamics simulations

In this article we review the relatively new phenomenon of electropumping in nanofluidic systems, in which nonzero net flow results when polar molecules are rotated by external electric fields. The flow is a consequence of coupling of the spin angular momentum of molecules with their linear streaming momentum. By devising confining surfaces that are asymmetric - specifically one surface is more hydrophobic compared to the other - unidirectional flow results and so pumping can be achieved without the use of pressure gradients. We first cover the historical background to this phenomenon and follow that with a detailed theoretical description of the governing hydrodynamics. Following that we summarise work that has applied this phenomenon to pump water confined to planar nanochannels, semi-functionalised single carbon nanotubes and concentric carbon nanotubes. We also report on the energy efficiency of this pumping technique by comparisons with traditional flows of planar Couette and Poiseuille flow, with the surprising conclusion that electropumping at the nanoscale is some 4 orders of magnitude more efficient than pumping by Poiseuille flow.

The phase space distribution of confined fluids under shear is not fractal

We analyze the phase-space compression, characteristic of all deterministic, dissipative systems for an inhomogeneous boundary-driven shear fluid via nonequilibrium molecular dynamics simulations. We find that, although the full system undergoes a phase space contraction, the marginal distribution of the fluid particles is described by a smooth, volume preserving probability density function. This is the case for most thermodynamic states of physical interest. Hence, we show that the models currently employed to investigate inhomogeneous fluids in a nonequilibrium steady state, in which only walls are thermostatted, generate a non-singular distribution for the fluid.

Nanoconfinement Effects on the Kapitza Resistance at Water-CNT Interfaces

The Kapitza resistance (R_k) at the water-carbon nanotube (CNT) interface, with water on the inside of the nanotube, was investigated using molecular dynamics simulations. We propose a new equilibrium molecular dynamics (EMD) method, also valid in the weak flow regime, to determine the Kapitza resistance in a cylindrical nanoconfinement system where nonequilibrium molecular dynamics (NEMD) methods are not suitable. The proposed method is independent of the correlation time compared to Green-Kubo-based methods, which only work in short correlation time intervals. R_k between the CNT and the confined water strongly depends on the diameter of the nanotube and is found to decrease with an increase in the CNT diameter, the opposite to what is reported in the literature when water is on the outside of the nanotube. R_k is furthermore found to converge to the planar graphene surface value as the number of water molecules per unit surface area approaches the value in the graphene surface and a higher overlap of the vibrational spectrum. A slight increase in R_k with the addition of the number of CNT walls was observed, whereas the chirality and flow do not have any impact.

Brackish Tidal Marsh Management and the Ecology of a Declining Freshwater Turtle

Water management practices in tidal marshes of the San Francisco Bay Estuary, California are often aimed at increasing suitable habitat for threatened fish species and sport fishes. However, little is known about how best to manage habitat for other sensitive status species like the semiaquatic freshwater Western Pond Turtle (Actinemys marmorata) that is declining throughout much of its range. Here, we examined the basking activity, abundance, survival, and growth of Western Pond Turtles at two brackish water study sites in Suisun Marsh, California that differed in how they were managed, with one having passive management (i.e., no active water regulation) and another having active management (i.e., water regulated for seasonal hunting). Our results revealed that basking activity was greatest when salinity, water stage, and air temperatures were low, shortwave radiation was high, and wind levels were intermediate. These preferred habitat characteristics often reflected conditions that were naturally maintained at the passively managed, muted tidal site. We also found that turtles were more abundant and had higher survival rates in the passively managed habitat compared to the actively managed habitat (201-323 turtles/km² and 96% survival versus 11-135 turtles/km² and 77% survival, respectively). Finally, characteristic growth constants from von Bertalanffy models showed that turtles grew more quickly in passively managed habitat compared to the actively managed habitat. Our results suggest that management strategies for this sensitive status species may be more effective if they protect passively managed muted tidal systems that limit or delay extreme cycles of salinity and water levels and conserve elevated terrestrial buffer zones adjacent to muted and full tidal systems.

Kapitza resistance at water-graphene interfaces

Heat transfer across fluid-solid interfaces in nanoconfinement has received significant attention due to its relevance in nanoscale systems. In this study, we investigate the Kapitza resistance at the water-graphene interface with the help of classical molecular dynamics simulation techniques in conjunction with our recently proposed equilibrium molecular dynamics (EMD) method [S. Alosious et al., J. Chem. Phys. 151, 194502 (2019)]. The size effect of the Kapitza resistance on different factors such as the number of graphene layers, the cross-sectional area, and the width of the water block was studied. The Kapitza resistance decreases slightly with an increase in the number of layers, while the influence of the cross-sectional area and the width of the water block is negligible. The variation in the Kapitza resistance as a function of the number of graphene layers is attributed to the large phonon mean free path along the graphene cross-plane. An optimum water-graphene system, which is independent of size effects, was selected, and the same was used to determine the Kapitza resistance using the predicted EMD method. The values obtained from both the EMD and the non-equilibrium molecular dynamics (NEMD) methods were compared for different potentials and water models, and the results are shown to be in good agreement. Our method allows us to compute the Kapitza resistance using EMD simulations, which obviates the need to create a large temperature gradient required for the NEMD method.

Efficiency of Electropumping in Nanochannels

Electropumping has been shown to be an effective means of inducing a net positive flow in fluids confined within planar nanochannels and carbon nanotubes. In this Letter, we investigate the efficiency of electropumping relative to Couette and Poiseuille flows. We apply a spatially uniform rotating electric field to a fluid confined in a functionalized nanochannel that couples the water's permanent dipole moment resulting in a net positive flow. We then induce a net positive flow in nanochannels for Couette and Poiseuille flows, matching volume flow rates to allow a direct comparison of average power dissipation per unit volume between all flow types. We show that while electropumping is less efficient than Couette flow, it is 4 orders of magnitude more efficient than Poiseuille flow. This suggests that, rather than being a mere novelty, electropumping is a far more energetically efficient means of transporting water compared to conventional pressure driven pumping.

Prediction of Kapitza resistance at fluid-solid interfaces

Understanding the interfacial heat transfer and thermal resistance at an interface between two dissimilar materials is of great importance in the development of nanoscale systems. This paper introduces a new and reliable linear response method for calculating the interfacial thermal resistance or Kapitza resistance in fluid-solid interfaces with the use of equilibrium molecular dynamics (EMD) simulations. The theoretical predictions are validated against classical molecular dynamics (MD) simulations. MD simulations are carried out in a Lennard-Jones (L-J) system with fluid confined between two solid slabs. Different types of interfaces are tested by varying the fluid-solid interactions (wetting coefficient) at the interface. It is observed that the Kapitza length decreases monotonically with an increasing wetting coefficient as expected. The theory is further validated by simulating under different conditions such as channel width, density, and temperature. Our method allows us to directly determine the Kapitza length from EMD simulations by considering the temperature fluctuation and heat flux fluctuations at the interface. The predicted Kapitza length shows an excellent agreement with the results obtained from both EMD and non-equilibrium MD simulations.

Inducing a Net Positive Flow of Water in Functionalized Concentric Carbon Nanotubes Using Rotating Electric Fields

Electropumping has shown great potential as an effective means of inducing a net positive flow of water in confined channels. In this paper we present the first nonequilibrium molecular dynamics study and continuum based numerical solutions that demonstrate an effective net positive flow between concentric carbon nanotubes (CNT) using electropumping. We apply a spatially uniform rotating electric field that couples to the water's permanent dipole moment. Taking advantage of the coupling between the spin angular momentum and the linear momentum we break the symmetry of the channel radius by functionalizing the inner CNT's outer surface with carboxyl groups to induce a net positive flow. We also show that our results for concentric nanotubes are consistent with our previous work where we demonstrated that an increase in functionalization beyond an optimal point in a single walled carbon nanotube resulted in a decrease in positive net flow. We then numerically solve the coupled hydrodynamic momentum equations to show that the nonequilibrium molecular dynamics results are consistent with the continuum theory.

Computation of the equilibrium three-particle entropy for dense atomic fluids by molecular dynamics simulation

We have computed the two- and three-particle contribution to the entropy of a Weeks-Chandler-Andersen fluid via molecular dynamics simulations. The three-particle correlation function and entropy were computed with a new method which simplified the calculation. Results are qualitatively similar to Lennard-Jones systems. We observed a numerical instability in the three-particle contribution. This phenomenon has been previously detected when the traditional method is used; thus, it is likely to be intrinsic in the computation. While the effect of statistical fluctuations can be removed through an extrapolation procedure, the discretization error due to the finite bin size is more difficult to characterize. With a correct choice of the bin size, a good estimate of the three-particle entropy contribution can be achieved at any state, even close to the freezing point. We observed that, despite the fact that the magnitude of the three-particle contribution increases significantly compared to that of the two-particle contribution as freezing is approached, the error induced from overestimation of the excess entropy by the two- and three-body terms exceeds that induced by approximating the excess entropy with the two body term alone.

Physiological consequences of rising water salinity for a declining freshwater turtle

Sea-level rise, drought and water diversion can all lead to rapid salinization of freshwater habitats, especially in coastal areas. Increased water salinities can in turn alter the geographic distribution and ecology of freshwater species including turtles. The physiological consequences of salinization for freshwater turtles, however, are poorly known. Here, we compared the osmoregulatory response of two geographically separate populations of the freshwater Western Pond Turtle (Actinemys marmorata)-a species declining across its range in western North America-to three constant salinities: 0.4 ppt, 10 ppt and 15 ppt over 2 weeks. We found that turtles from a coastal estuarine marsh population regulated their plasma osmolality at lower levels than their conspecifics from an inland freshwater creek population 45 km away. Plasma osmolalities were consistently lower in estuarine marsh turtles than the freshwater creek turtles over the entire 2-week exposure to 10 ppt and 15 ppt water. Furthermore, estuarine marsh turtles maintained plasma osmolalities within 1 SD of their mean field osmolalities over the 2-week exposure, whereas freshwater creek turtles exceeded their field values within the first few days after exposure to elevated salinities. However, individuals from both populations exhibited body mass loss in 15 ppt water, with significantly greater loss in estuarine turtles. We speculate that the greater ability to osmoregulate by the estuarine marsh turtles may be explained by their reduced feeding and drinking in elevated salinities that was not exhibited by the freshwater creek population. However, due to mass loss in both populations, physiological and behavioural responses exhibited by estuarine marsh turtles may only be effective adaptations for short-term exposures to elevated salinities, such as those from tides and when traversing saline habitats, and are unlikely to be effective for long-term exposure to elevated salinity as is expected under sea-level rise.

Traditional trapping methods outperform eDNA sampling for introduced semi-aquatic snakes

Given limited resources for managing invasive species, traditional survey methods may not be feasible to implement at a regional scale. Environmental DNA (eDNA) sampling has proven to be an effective method for detecting some invasive species, but comparisons between the detection probability of eDNA and traditional survey methods using modern occupancy modeling methods are rare. We developed a qPCR assay to detect two species of watersnake (Nerodia fasciata and Nerodia sipedon) introduced to California, USA, and we compared the efficacy of eDNA and aquatic trapping. We tested 3–9 water samples each from 30 sites near the known range of N. fasciata, and 61 sites near the known range of N. sipedon. We also deployed aquatic funnel traps at a subset of sites for each species. We detected N. fasciata eDNA in three of nine water samples from just one site, but captured N. fasciata in traps at three of ten sites. We detected N. sipedon eDNA in five of six water samples from one site, which was also the only site of nine at which this species was captured in traps. Traditional trapping surveys had a higher probability of detecting watersnakes than eDNA surveys, and both survey methods had higher detection probability for N. sipedon than N. fasciata. Occupancy models that integrated both trapping and eDNA surveys estimated that 5 sites (95% Credible Interval: 4–10) of 91 were occupied by watersnakes (both species combined), although snakes were only detected at four sites (three for N. fasciata, one for N. sipedon). Our study shows that despite the many successes of eDNA surveys, traditional sampling methods can have higher detection probability for some species. We recommend those tasked with managing species invasions explicitly compare eDNA and traditional survey methods in an occupancy framework to inform their choice of the best method for detecting nascent populations.

Measuring heat flux beyond Fourier's law

We use nonequilibrium molecular dynamics to explore the effect of shear flow on heat flux. By simulating a simple fluid in a channel bounded by tethered atoms, the heat flux is computed for two systems: a temperature driven one with no flow and a wall driven, Couette flow system. The results for the temperature driven system give Fourier's law thermal conductivity, which is shown to agree well with experiments. Through comparison of the two systems, we quantify the additional components of the heat flux parallel and normal to the walls due to shear flow. To compute the heat flux in the flow direction, the Irving-Kirkwood equations are integrated over a volume, giving the so-called volume average form, and they are also manipulated to get expressions for the surface averaged and method of planes forms. The method of planes and volume average forms are shown to give equivalent results for the heat flux when using small volumes. The heat flux in the flow direction is obtained consistently over a range of simulations, and it is shown to vary linearly with strain rate, as predicted by theory. The additional strain rate dependent component of the heat flux normal to the wall is obtained by fitting the strain rate dependence of the heat flux to the expected form. As a result, the additional terms in the thermal conductivity tensor quantified in this work should be experimentally testable.

Gene expression differs in susceptible and resistant amphibians exposed to Batrachochytrium dendrobatidis

Chytridiomycosis, the disease caused by the fungal pathogen Batrachochytrium dendrobatidis (Bd), has devastated global amphibian biodiversity. Nevertheless, some hosts avoid disease after Bd exposure even as others experience near-complete extirpation. It remains unclear whether the amphibian adaptive immune system plays a role in Bd defence. Here, we describe gene expression in two host species-one susceptible to chytridiomycosis and one resistant-following exposure to two Bd isolates that differ in virulence. Susceptible wood frogs (Rana sylvatica) had high infection loads and mortality when exposed to the more virulent Bd isolate but lower infection loads and no fatal disease when exposed to the less virulent isolate. Resistant American bullfrogs (R. catesbeiana) had high survival across treatments and rapidly cleared Bd infection or avoided infection entirely. We found widespread upregulation of adaptive immune genes and downregulation of important metabolic and cellular maintenance components in wood frogs after Bd exposure, whereas American bullfrogs showed little gene expression change and no evidence of an adaptive immune response. Wood frog responses suggest that adaptive immune defences may be ineffective against virulent Bd isolates that can cause rapid physiological dysfunction. By contrast, American bullfrogs exhibited robust resistance to Bd that is likely attributable, at least in part, to their continued upkeep of metabolic and skin integrity pathways as well as greater antimicrobial peptide expression compared to wood frogs, regardless of exposure. Greater understanding of these defences will ultimately help conservationists manage chytridiomycosis.

Thermal biology mediates responses of amphibians and reptiles to habitat modification

Human activities often replace native forests with warmer, modified habitats that represent novel thermal environments for biodiversity. Reducing biodiversity loss hinges upon identifying which species are most sensitive to the environmental conditions that result from habitat modification. Drawing on case studies and a meta-analysis, we examined whether observed and modelled thermal traits, including heat tolerances, variation in body temperatures, and evaporative water loss, explained variation in sensitivity of ectotherms to habitat modification. Low heat tolerances of lizards and amphibians and high evaporative water loss of amphibians were associated with increased sensitivity to habitat modification, often explaining more variation than non-thermal traits. Heat tolerances alone explained 24-66% (mean = 38%) of the variation in species responses, and these trends were largely consistent across geographic locations and spatial scales. As habitat modification alters local microclimates, the thermal biology of species will likely play a key role in the reassembly of terrestrial communities.

Effects of gap-based silviculture on thermal biology of a terrestrial reptile

Context Terrestrial reptiles require varied thermal environments to promote optimal physiological performance, growth, reproduction, and survival. Aims Our study was designed to determine whether gap-based silvicultural practices offer suitable thermal environments for eastern box turtles (Terrapene carolina) by examining environmental temperature variation and body temperature of eastern box turtles in, and adjacent to, canopy gaps. Methods We recorded box turtle body temperature from 20 radio-tracked turtles and environmental temperatures (canopy gaps and undisturbed habitat) using temperature loggers from June to September 2014 in a managed forest after canopy gaps (0.28–1.13 ha gap–1) were created via gap-based silviculture. Key results Over the four-month study period, gap temperatures were generally higher than adjacent undisturbed microhabitats. Box turtle body temperatures were closely correlated with environmental temperatures in undisturbed habitat in June and July. Turtle body temperatures were, however, closely correlated with environmental temperatures in canopy gaps in August and September. In addition, box turtles in our study had activity areas that overlapped canopy gaps from 0 to 65%, depending on the individual. As percentage overlap of canopy gaps increased, turtle body temperatures were increasingly correlated with canopy gap temperatures. Furthermore, as percentage overlap of canopy gaps increased, daily mean body temperature records consistently stayed within the preferred box turtle body temperature range (20.2–26.2°C). Conclusions Our study suggests that gap-based silviculture can create thermally compatible environments for box turtles depending on the time of day and year, and that box turtles use these microhabitats to thermoregulate. Implications The application of relatively small-scale silvicultural practices (≤1 ha gap–1) that provide heterogeneity in forest structure, composition, and function may be a useful alternative to clearcutting and other intensive harvesting methods that are associated with declines in terrestrial reptile populations.

Mass mortality of eastern box turtles with upper respiratory disease following atypical cold weather

Emerging infectious diseases cause population declines in many ectotherms, with outbreaks frequently punctuated by periods of mass mortality. It remains unclear, however, whether thermoregulation by ectotherms and variation in environmental temperature is associated with mortality risk and disease progression, especially in wild populations. Here, we examined environmental and body temperatures of free-ranging eastern box turtles Terrapene carolina during a mass die-off coincident with upper respiratory disease. We recorded deaths of 17 turtles that showed clinical signs of upper respiratory disease among 76 adult turtles encountered in Berea, Kentucky (USA), in 2014. Of the 17 mortalities, 11 occurred approximately 14 d after mean environmental temperature dropped 2.5 SD below the 3 mo mean. Partial genomic sequencing of the major capsid protein from 1 sick turtle identified a ranavirus isolate similar to frog virus 3. Turtles that lacked clinical signs of disease had significantly higher body temperatures (23°C) than sick turtles (21°C) during the mass mortality, but sick turtles that survived and recovered eventually warmed (measured by temperature loggers). Finally, there was a significant negative effect of daily environmental temperature deviation from the 3 mo mean on survival, suggesting that rapid decreases in environmental temperature were correlated with mortality. Our results point to a potential role for environmental temperature variation and body temperature in disease progression and mortality risk of eastern box turtles affected by upper respiratory disease. Given our findings, it is possible that colder or more variable environmental temperatures and an inability to effectively thermoregulate are associated with poorer disease outcomes in eastern box turtles.

Tropical amphibians in shifting thermal landscapes under land-use and climate change

Land-cover and climate change are both expected to alter species distributions and contribute to future biodiversity loss. However, the combined effects of land-cover and climate change on assemblages, especially at the landscape scale, remain understudied. Lowland tropical amphibians may be particularly susceptible to changes in land cover and climate warming because many species have narrow thermal safety margins resulting from air and body temperatures that are close to their critical thermal maxima (CT_max ). We examined how changing thermal landscapes may alter the area of thermally suitable habitat (TSH) for tropical amphibians. We measured microclimates in 6 land-cover types and CT_max of 16 frog species in lowland northeastern Costa Rica. We used a biophysical model to estimate core body temperatures of frogs exposed to habitat-specific microclimates while accounting for evaporative cooling and behavior. Thermally suitable habitat area was estimated as the portion of the landscape where species CT_max exceeded their habitat-specific maximum body temperatures. We projected changes in TSH area 80 years into the future as a function of land-cover change only, climate change only, and combinations of land-cover and climate-change scenarios representing low and moderate rates of change. Projected decreases in TSH area ranged from 16% under low emissions and reduced forest loss to 30% under moderate emissions and business-as-usual land-cover change. Under a moderate emissions scenario (A1B), climate change alone contributed to 1.7- to 4.5-fold greater losses in TSH area than land-cover change only, suggesting that future decreases in TSH from climate change may outpace structural habitat loss. Forest-restricted species had lower mean CT_max than species that occurred in altered habitats, indicating that thermal tolerances will likely shape assemblages in changing thermal landscapes. In the face of ongoing land-cover and climate change, it will be critical to consider changing thermal landscapes in strategies to conserve ectotherm species.

Using citizen science data to identify the sensitivity of species to human land use

Conservation practitioners must contend with an increasing array of threats that affect biodiversity. Citizen scientists can provide timely and expansive information for addressing these threats across large scales, but their data may contain sampling biases. We used randomization procedures to account for possible sampling biases in opportunistically reported citizen science data to identify species' sensitivities to human land use. We analyzed 21,044 records of 143 native reptile and amphibian species reported to the Carolina Herp Atlas from North Carolina and South Carolina between 1 January 1990 and 12 July 2014. Sensitive species significantly associated with natural landscapes were 3.4 times more likely to be legally protected or treated as of conservation concern by state resource agencies than less sensitive species significantly associated with human-dominated landscapes. Many of the species significantly associated with natural landscapes occurred primarily in habitats that had been nearly eradicated or otherwise altered in the Carolinas, including isolated wetlands, longleaf pine savannas, and Appalachian forests. Rare species with few reports were more likely to be associated with natural landscapes and 3.2 times more likely to be legally protected or treated as of conservation concern than species with at least 20 reported occurrences. Our results suggest that opportunistically reported citizen science data can be used to identify sensitive species and that species currently restricted primarily to natural landscapes are likely at greatest risk of decline from future losses of natural habitat. Our approach demonstrates the usefulness of citizen science data in prioritizing conservation and in helping practitioners address species declines and extinctions at large extents.

Infection risk decreases with increasing mismatch in host and pathogen environmental tolerances

The fungal pathogen Batrachochytrium dendrobatidis (Bd) has caused the greatest known wildlife pandemic, infecting over 500 amphibian species. It remains unclear why some host species decline from disease-related mortality whereas others persist. We introduce a conceptual model that predicts that infection risk in ectotherms will decrease as the difference between host and pathogen environmental tolerances (i.e. tolerance mismatch) increases. We test this prediction using both local-scale data from Costa Rica and global analyses of over 11 000 Bd infection assays. We find that infection prevalence decreases with increasing thermal tolerance mismatch and with increasing host tolerance of habitat modification. The relationship between environmental tolerance mismatches and Bd infection prevalence is generalisable across multiple amphibian families and spatial scales, and the magnitude of the tolerance mismatch effect depends on environmental context. These findings may help explain patterns of amphibian declines driven by a global wildlife pandemic.

Organic contaminants in western pond turtles in remote habitat in California

Remote aquatic ecosystems are exposed to an assortment of semivolatile organic compounds (SOCs) originating from current and historic uses, of local and global origin. Here, a representative suite of 57 current- and historic-use pesticides, polychlorinated biphenyls, and polycyclic aromatic hydrocarbons were surveyed in the plasma of the western pond turtle (Emys marmorata) and their potential prey items and habitat. California study sites included Sequoia National Park, Whiskeytown National Recreation Area, and Six Rivers National Forest. Each was downstream of undeveloped watersheds and varied in distance from agricultural and urban pollution sources. SOCs were detected frequently in all sites with more found in turtle plasma and aquatic macroinvertebrates in the two sites closest to agricultural and urban sources. Summed PCBs were highest in Whiskeytown National Recreation Area turtle plasma (mean; 1.56 ng/g ww) compared to plasma from Sequoia National Park (0.16 ng/g ww; p = 0.002) and Six Rivers National Forest (0.07 ng/g ww; p = 0.001). While no current-use pesticides were detected in turtle plasma at any site, both current- and historic-use pesticides were found prominently in sediment and macroinvertebrates at the Sequoia National Park site, which is immediately downwind of Central Valley agriculture. SOC classes associated with urban and industrial pollution were found more often and at higher concentrations at Whiskeytown National Recreation Area. These findings demonstrate a range of SOC exposure in a turtle species with current and proposed conservation status and shed additional light on the fate of environmental contaminants in remote watersheds.

Effects of Confinement on the Dielectric Response of Water Extends up to Mesoscale Dimensions

The extent of confinement effects on water is not clear in the literature. While some properties are affected only within a few nanometers from the wall surface, others are affected over long length scales, but the range is not clear. In this work, we have examined the dielectric response of confined water under the influence of external electric fields along with the dipolar fluctuations at equilibrium. The confinement induces a strong anisotropic effect which is evident up to 100 nm channel width, and may extend to macroscopic dimensions. The root-mean-square fluctuations of the total orientational dipole moment in the direction perpendicular to the surfaces is 1 order of magnitude smaller than the value attained in the parallel direction and is independent of the channel width. Consequently, the isotropic condition is unlikely to be recovered until the channel width reaches macroscopic dimensions. Consistent with dipole moment fluctuations, the effect of confinement on the dielectric response also persists up to channel widths considerably beyond 100 nm. When an electric field is applied in the perpendicular direction, the orientational relaxation is 3 orders of magnitude faster than the dipolar relaxation in the parallel direction and independent of temperature.

American Bullfrogs (Lithobates catesbeianus) Resist Infection by Multiple Isolates of Batrachochytrium dendrobatidis, Including One Implicated in Wild Mass Mortality

The emerging amphibian disease chytridiomycosis varies in severity depending on host species. Within species, disease susceptibility can also be influenced by pathogen variation and environmental factors. Here, we report on experimental exposures of American bullfrogs (Lithobates catesbeianus) to three different isolates of Batrachochytrium dendrobatidis (Bd), including one implicated in causing mass mortality of wild American bullfrogs. Exposed frogs showed low infection prevalence, relatively low infection load, and lack of clinical disease. Our results suggest that environmental cofactors are likely important contributors to Bd-associated American bullfrog mortality and that this species both resists and tolerates Bd infection.

Nonlocal response functions for predicting shear flow of strongly inhomogeneous fluids. II. Sinusoidally driven shear and multisinusoidal inhomogeneity

We use molecular-dynamics computer simulations to investigate the density, strain-rate, and shear-pressure responses of a simple model atomic fluid to transverse and longitudinal external forces. We have previously introduced a response function formalism for describing the density, strain-rate, and shear-pressure profiles in an atomic fluid when it is perturbed by a combination of longitudinal and transverse external forces that are independent of time and have a simple sinusoidal spatial variation. In this paper, we extend the application of the previously introduced formalism to consider the case of a longitudinal force composed of multiple sinusoidal components in combination with a single-component sinusoidal transverse force. We find that additional harmonics are excited in the density, strain-rate, and shear-pressure profiles due to couplings between the force components. By analyzing the density, strain-rate, and shear-pressure profiles in Fourier space, we are able to evaluate the Fourier coefficients of the response functions, which now have additional components describing the coupling relationships. Having evaluated the Fourier coefficients of the response functions, we are then able to accurately predict the density, velocity, and shear-pressure profiles for fluids that are under the influence of a longitudinal force composed of two or three sinusoidal components combined with a single-component sinusoidal transverse force. We also find that in the case of a multisinusoidal longitudinal force, it is sufficient to include only pairwise couplings between different longitudinal force components. This means that it is unnecessary to include couplings between three or more force components in the case of a longitudinal force composed of many Fourier components, and this paves the way for a highly accurate but tractable treatment of nonlocal transport phenomena in fluids with density and strain-rate inhomogeneities on the molecular length scale.

Nonlocal response functions for predicting shear flow of strongly inhomogeneous fluids. I. Sinusoidally driven shear and sinusoidally driven inhomogeneity

We present theoretical expressions for the density, strain rate, and shear pressure profiles in strongly inhomogeneous fluids undergoing steady shear flow with periodic boundary conditions. The expressions that we obtain take the form of truncated functional expansions. In these functional expansions, the independent variables are the spatially sinusoidal longitudinal and transverse forces that we apply in nonequilibrium molecular-dynamics simulations. The longitudinal force produces strong density inhomogeneity, and the transverse force produces sinusoidal shear. The functional expansions define new material properties, the response functions, which characterize the system's nonlocal response to the longitudinal force and the transverse force. We find that the sinusoidal longitudinal force, which is mainly responsible for the generation of density inhomogeneity, also modulates the strain rate and shear pressure profiles. Likewise, we find that the sinusoidal transverse force, which is mainly responsible for the generation of sinusoidal shear flow, can also modify the density. These cross couplings between density inhomogeneity and shear flow are also characterized by nonlocal response functions. We conduct nonequilibrium molecular-dynamics simulations to calculate all of the response functions needed to describe the response of the system for weak shear flow in the presence of strong density inhomogeneity up to the third order in the functional expansion. The response functions are then substituted directly into the truncated functional expansions and used to predict the density, velocity, and shear pressure profiles. The results are compared to the directly evaluated profiles from molecular-dynamics simulations, and we find that the predicted profiles from the truncated functional expansions are in excellent agreement with the directly computed density, velocity, and shear pressure profiles.

Delimiting road-effect zones for threatened species: implications for mitigation fencing

Context Roads are a pernicious form of habitat loss for many wildlife populations because their effects often extend far beyond the roads themselves, giving rise to reduced wildlife abundance in road-effect zones. Quantifying the extent of road-effect zones more accurately portrays their impact on populations and the true extent to which habitat is lost for many species. Aim The purpose of the present study was to evaluate ways of determining the extent of road-effect zones for a model study species to better quantify the effect of roads on habitat loss. Methods We conducted road-side surveys for signs of Mojave desert tortoises (Gopherus agassizii) 0, 200, 400, 800 and 1600 m from county roads and interstates, two of the most common road types in critical habitat of this threatened species. Using data from these road-side surveys, we estimated the extent of road-effect zones using piecewise regression and modified von Bertalanffy models. Key results We found reduced abundances of tortoise sign along both county roads and interstates. Reductions extended farther from the large, high-traffic interstate than from the smaller, lower-traffic county roads (306 m versus 230 m). The increase in the abundance of tortoise signs with distance from roads approximated a negative exponential curve. Conclusions Interstate and county roads both contribute to habitat loss in road-side areas by making these habitats unsuitable to desert tortoises, presumably by removing animals via mortality from collisions with vehicles. Larger roads with greater traffic have more extensive effects. Implications Roadside mitigation fencing has been proposed as one way to reduce mortality of desert tortoises and to reclaim habitat by allowing tortoises to recolonise currently depauperate road-effect zones. Immediate mortality is more likely to be prevented by fencing county roads where tortoises occur closer to roads and are more likely to be struck by vehicles and killed. However, fencing interstate should yield more reclaimed habitat than that obtained from fencing county roads. Managers must consider balancing these goals along with other concerns when deciding where to place roadside fencing.

Porous aromatic frameworks impregnated with fullerenes for enhanced methanol/water separation

Molecular simulation techniques have revealed that the incorporation of fullerenes within porous aromatic frameworks (PAFs) remarkably enhances methanol uptake while inhibiting water uptake. The highest selectivity of methanol over water is found to be 1540 at low pressure (1 kPa) and decreases gradually with increasing pressure. The adsorption of water is very small compared to methanol, a useful material property for membrane and adsorbent-based separations. Grand canonical Monte Carlo (GCMC) simulations are utilized to calculate the pure component and mixture adsorption isotherms. The water and methanol mixture simulations show that water uptake is further inhibited above the pure component results because of the dominant methanol adsorption. Molecular dynamics (MD) simulations confirm that water diffusivity is also inhibited by strong methanol adsorption in the mixture. Overall, this study reveals profound hydrophobicity in C60@PAF materials and recommends C60@PAFs as suitable applicants for adsorbent and membrane-based separations of methanol/water mixtures and other alcohol/water separation applications.