Application of Genetic Bottleneck Testing to the Investigation of Amphibian Declines: a Case Study with Natterjack Toads

Abstract: Declines of amphibians are causing widespread concern and in some cases have been explained by factors such as climate change and the spread of microbial pathogens. A problem remains, however, in the unequivocal demonstration of decline in situations where populations may be undergoing natural fluctuations in abundance. We describe the application of a genetic test for bottlenecks ( Cornuet & Luikart 1996 ) that should distinguish between natural oscillations and true population declines. British natterjack toads (   Bufo calamita  ) provide examples of populations that have not declined in recent decades, populations that have declined, and populations in which trends are unclear. Microsatellite allele frequency data from these populations were tested for heterozygote excess and shifts in allele frequency distributions, and inferences from these computations about bottlenecks (i.e., persistently smaller population sizes than the recent means) were compared with demographic information. The genetic test correctly identified bottlenecks and should therefore prove useful in demonstrating whether amphibian declines have occurred where long-term demographic time series are not available.     

Characterization and optimization of an online system for the simultaneous measurement of atmospheric water-soluble constituents in the gas and particle phases

In this work we present the results of extensive characterization and optimization of the Ambient Ion Monitor-Ion Chromatograph (AIM-IC) system, an instrument developed by URG Corp. and Dionex Inc. for simultaneous hourly measurements of the water-soluble chemical composition of atmospheric fine particulate matter (PM(2.5)) and associated precursor gases. The sampling assembly of the AIM-IC consists of an inertial particle size-selection assembly, a parallel-plate wet denuder (PPWD) for the collection of soluble gases, and a particle supersaturation chamber (PSSC) for collection of particles, in series. The analytical assembly of the AIM-IC consists of anion and cation IC units. The system detection limits were determined to be 41 ppt, 5 ppt, and 65 ppt for gas phase NH(3(g)), SO(2(g)), and HNO(3(g)) and 29 ng m(-3), 3 ng m(-3), and 45 ng m(-3) for particle phase NH(4)(+), SO(4)(2-), and NO(3)(-) respectively. From external trace gas calibrations with permeation sources, we determined that the AIM-IC is biased low for NH(3(g)) (11%), SO(2(g)) (19%), and HNO(3(g)) (12%). The collection efficiency of SO(2(g)) was found to strongly depend on the composition of the denuder solution and was found to be the most quantitative with 5 mM H(2)O(2) solution for mixing ratios as high as 107 ppb. Using a cellulose membrane in the PPWD, the system responded to changes in SO(2(g)) and HNO(3(g)) within an hour, however for NH(3(g)), the timescale can be closer to 20 h. With a nylon membrane, the instrument response time for NH(3(g)) was significantly improved, becoming comparable to the responses for SO(2(g)) and HNO(3(g)). Performance of the AIM-IC for collection and analysis of PM(2.5) was evaluated by generating known number concentrations of ammonium sulfate and ammonium nitrate particles (with an aerodynamic diameter of 300 nm) under laboratory conditions and by comparing AIM-IC measurements to measurements from a collocated Aerosol Mass Spectrometer (AMS) during a field-sampling campaign. On average, the AIM-IC and AMS measurements agreed well and captured rapid ambient concentration changes at the same time. In this work we also present a novel inlet configuration and plumbing for the AIM-IC which minimizes sampling inlet losses, reduces peak smearing due to sample carryover, and allows for tower-height sampling from the base of a research tower.     

Effect on herbicide adsorption of organic forestry waste products used for soil remediation

Organic soil amendments can be useful for improving degraded soil, but this increase in organic matter (OM) may influence adsorption of herbicides subsequently applied to the treated soil, even though the particle size of amendments and their nature differ from typical soil OM. In this study, a batch equilibrium method was used to measure adsorption of five herbicides following application to two organic media, wood pulp and sawdust, comparing these with two cropping soils. Herbicide adsorption, quantified by distribution coefficients (k_d), was much higher in the two organic media than in the cropping soils. The increases in adsorption were strongly correlated to the percentage of organic carbon. When the k_d was normalized to adsorption coefficients corrected for OM content (k_oc), variation in results between the media was greatly reduced, indicating that OM is an important factor influencing adsorption in these media. The results of this study suggest that herbicides will be less effective when applied to soils in which sawdust and wood pulp have been added. Using organic amendments to remediate soil will increase adsorption of pesticides, reducing their bio-availability and efficacy, but also reducing their tendency to leach into root zones of deep-rooted crops and into groundwater.     

Alkyl nitrate photochemistry during the tropospheric organic chemistry experiment

Alkyl nitrates (C₁–C₅) were measured at two sites (near urban and rural) in southeast England during the Tropospheric Organic Chemistry Experiment (TORCH). Methyl nitrate was the dominant species during both campaigns accounting for on average about one third of the total measured alkyl nitrates. High mixing ratios (>50 pptv) and variability of methyl nitrate were observed at the near urban site (TORCH1) that were not seen at the rural site (TORCH2) and which could not be explained by local photochemical production or direct emissions. The diurnal variation of methyl nitrate during TORCH1 showed a morning maximum that would be consistent with nighttime chemistry followed by transport to the surface by boundary layer dynamics. Similarly, elevated morning mixing ratios were also observed during TORCH2 although the magnitudes were much smaller. As a result, methyl nitrate could represent a tracer for nighttime chemistry seen at the ground the following day. At both campaigns, the dominant source of short chain alkyl nitrates and carbonyl precursor radicals (≤C₄) were from decomposition of larger compounds. The magnitude of the source increased with decreasing carbon number consistent with increasing total precursor abundance. Non-photochemical emissions of acetaldehyde and acetone could not be accounted for by automobile exhaust emissions alone and indicated that other direct sources are likely important in this environment.     

Use of opportunistic sightings and expert knowledge to predict and compare Whooping Crane stopover habitat

Predicting a species’ distribution can be helpful for evaluating management actions such as critical habitat designations under the U.S. Endangered Species Act or habitat acquisition and rehabilitation. Whooping Cranes (Grus americana) are one of the rarest birds in the world, and conservation and management of habitat is required to ensure their survival. We developed a species distribution model (SDM) that could be used to inform habitat management actions for Whooping Cranes within the state of Nebraska (U.S.A.). We collated 407 opportunistic Whooping Crane group records reported from 1988 to 2012. Most records of Whooping Cranes were contributed by the public; therefore, developing an SDM that accounted for sampling bias was essential because observations at some migration stopover locations may be under represented. An auxiliary data set, required to explore the influence of sampling bias, was derived with expert elicitation. Using our SDM, we compared an intensively managed area in the Central Platte River Valley with the Niobrara National Scenic River in northern Nebraska. Our results suggest, during the peak of migration, Whooping Crane abundance was 262.2 (90% CI 40.2?3144.2) times higher per unit area in the Central Platte River Valley relative to the Niobrara National Scenic River. Although we compared only 2 areas, our model could be used to evaluate any region within the state of Nebraska. Furthermore, our expert‐informed modeling approach could be applied to opportunistic presence‐only data when sampling bias is a concern and expert knowledge is available.     

Political transition and emergent forest‐conservation issues in Myanmar

Political and economic transitions have had substantial impacts on forest conservation. Where transitions are underway or anticipated, historical precedent and methods for systematically assessing future trends should be used to anticipate likely threats to forest conservation and design appropriate and prescient policy measures to counteract them. Myanmar is transitioning from an authoritarian, centralized state with a highly regulated economy to a more decentralized and economically liberal democracy and is working to end a long‐running civil war. With these transitions in mind, we used a horizon‐scanning approach to assess the 40 emerging issues most affecting Myanmar's forests, including internal conflict, land‐tenure insecurity, large‐scale agricultural development, demise of state timber enterprises, shortfalls in government revenue and capacity, and opening of new deforestation frontiers with new roads, mines, and hydroelectric dams. Averting these threats will require, for example, overhauling governance models, building capacity, improving infrastructure‐ and energy‐project planning, and reforming land‐tenure and environmental‐protection laws. Although challenges to conservation in Myanmar are daunting, the political transition offers an opportunity for conservationists and researchers to help shape a future that enhances Myanmar's social, economic, and environmental potential while learning and applying lessons from other countries. Our approach and results are relevant to other countries undergoing similar transitions.     

Disinfection of secondary effluents using tin oxide anodes.

Direct current applied to a tin oxide anode submersed in water has the potential to generate hydroxyl radicals, a strong chemical oxidant. Tin oxide anode systems, which may represent a viable alternative disinfectant, were investigated for the disinfection of secondary effluents. Coliform bacteria in the effluent were effectively inactivated in a bench-scale tin oxide disinfection system. The number of anodes in the tin oxide disinfection system influenced the steady-state concentration of hydroxyl radicals and, consequently, the contact time necessary to achieve a specified dose. The life expectancy of the anodes was greater than 30 days and no appreciable loss of tin was observed over a 5-day period. A preliminary estimate of the capital and operating costs of a pilot- or full-scale tin oxide disinfection system designed to meet a discharge requirement of 23 most probable number/100 mL at a 3 785-m3/d (1-mgd) facility was comparable to UV and chlorination/dechlorination facilities. Based on this preliminary assessment, tin oxide disinfection systems are a promising alternative disinfectant for secondary effluents.     

Pilot-scale constructed wetlands for petroleum-contaminated groundwater.

A pilot study was conducted to determine the feasibility of using constructed treatment wetlands to remediate recovered groundwater from the subsurface of a former refinery site. The pilot system consisted of four subsurface flow treatment cells operated in an upward vertical flow mode and equipped with subsurface aeration lines. The treatment system showed minimal capability for methyl-tert-butyl ether removal, but did effectively remove total petroleum hydrocarbons-deisel range organics and total benzene, toluene, ethylbenzene, and o-, m-, and p-xylenes (total BTEX). Effluent benzene concentrations were less than 0.05 mg/L in 70% of the samples from a treatment cell using subsurface aeration and a wetland sod amendment. Based on 1 year of operating data, cumulative mass removal approached 80% for benzene and 88% for total BTEX.