Invasive species distribution modeling (iSDM): Are absence data and dispersal constraints needed to predict actual distributions?

Species distribution models (SDMs) based on statistical relationships between occurrence data and underlying environmental conditions are increasingly used to predict spatial patterns of biological invasions and prioritize locations for early detection and control of invasion outbreaks. However, invasive species distribution models (iSDMs) face special challenges because (i) they typically violate SDM's assumption that the organism is in equilibrium with its environment, and (ii) species absence data are often unavailable or believed to be too difficult to interpret. This often leads researchers to generate pseudo-absences for model training or utilize presence-only methods, and to confuse the distinction between predictions of potential vs. actual distribution. We examined the hypothesis that true-absence data, when accompanied by dispersal constraints, improve prediction accuracy and ecological understanding of iSDMs that aim to predict the actual distribution of biological invasions. We evaluated the impact of presence-only, true-absence and pseudo-absence data on model accuracy using an extensive dataset on the distribution of the invasive forest pathogen Phytophthora ramorum in California. Two traditional presence/absence models (generalized linear model and classification trees) and two alternative presence-only models (ecological niche factor analysis and maximum entropy) were developed based on 890 field plots of pathogen occurrence and several climatic, topographic, host vegetation and dispersal variables. The effects of all three possible types of occurrence data on model performance were evaluated with receiver operating characteristic (ROC) and omission/commission error rates. Results show that prediction of actual distribution was less accurate when we ignored true-absences and dispersal constraints. Presence-only models and models without dispersal information tended to over-predict the actual range of invasions. Models based on pseudo-absence data exhibited similar accuracies as presence-only models but produced spatially less feasible predictions. We suggest that true-absence data are a critical ingredient not only for accurate calibration but also for ecologically meaningful assessment of iSDMs that focus on predictions of actual distributions.     

Simple rules for ranking and optimally managing metapopulations

We present two ‘rules of thumb’ for metapopulation management. The first identifies an explicit formula for the persistence time of the population, and thus enables the population manager to form a priority species ranking by identifying those species most at risk of extinction. The second identifies an optimal management strategy that gives direction on how to alter the colonisation rate (creation or improvement of habitat corridors) and local extinction rate (restoring habitat quality or expanding habitat) in order to maximise the persistence time under a budgetary constraint. We employ a simple stochastic version of Levins (1969) metapopulation model, which is first calibrated to a more realistic spatial model. Our rules are tested on computer-generated patch networks and a model for malleefowl (Leipoa ocellata) in the Bakara region of South Australia.     

Determinants of reproductive potential and population size in open populations of Patella vulgata

The importance of external and internal population processes in determining variation in reproductive output and variation in population size were quantified with model simulations for open populations of the sequentially hermaphroditic limpet Patella vulgata using field data from the Isle of Man and South West Ireland. Cross-correlation analyses of model outputs and elasticity analyses show that population dynamics are dominated by the effects of large females, and that recruitment adds little to reproductive output. However, populations experiencing low but highly variable recruitment appear male limited and recruitment pulses carrying young males into the population are correlated to reproductive output with a 2–5-year lag. We conclude that pulses in recruitment can be a major structuring force in these limpet populations, but site-specific post-recruitment processes will determine the relative importance of recruitment to population dynamics and the lag between recruitment and reproductive output.     

Life-history trade-offs influence disease in changing climates: strategies of an amphibian pathogen

Life-history trade-offs allow many animals to maintain reproductive fitness across a range of climatic conditions. When used by parasites and pathogens, these strategies may influence patterns of disease in changing climates. The chytrid fungus, Batrachochytrium dendrobatidis, is linked to global declines of amphibian populations. Short-term growth in culture is maximal at 17 degrees-25 degrees C. This has been used in an argument that global warming, which increases the time that amphibians spend at these temperatures in cloud-covered montane environments, has led to extinctions. Here we show that the amphibian chytrid responds to decreasing temperatures with trade-offs that increase fecundity as maturation rate slows and increase infectivity as growth decreases. At 17 degrees-25 degrees C, infectious zoospores encyst (settle and develop a cell wall) and develop into the zoospore-producing stage (zoosporangium) faster, while at 7 degrees-10 degrees C, greater numbers of zoospores are produced per zoosporangium; these remain infectious for a longer period of time. We modeled the population growth of B. dendrobatidis through time at various temperatures using delayed differential equations and observational data for four parameters: developmental rate of thalli, fecundity, rate of zoospore encystment, and rate of zoospore survival. From the models, it is clear that life-history trade-offs allow B. dendrobatidis to maintain a relatively high long-term growth rate at low temperatures, so that it maintains high fitness across a range of temperatures. When a seven-day cold shock is simulated, the outcome is intermediate between the two constant temperature regimes, and in culture, a sudden drop in temperature induces zoospore release. These trade-offs can be ecologically important for a variety of organisms with complex life histories, including pathogenic microorganisms. The effect of temperature on amphibian mortality will depend on the interaction between fungal growth and host immune function and will be modified by host ecology, behavior, and life history. These results demonstrate that B. dendrobatidis populations can grow at high rates across a broad range of environmental temperatures and help to explain why it is so successful in cold montane environments.     

The influence of drainage networks on patterns of soil respiration in a desert catchment

Hydrologic flow and connectivity act as important determinants of ecological pattern and process in heterogeneous landscapes. Here we examine how the routing of water through the drainage network of an upper Sonoran Desert basin influences landscape patterns of soil respiration (SR) at both seasonal and event-based timescales. At seasonal timescales, SR varied up to 13-fold with downstream position in the drainage network, and annual estimates of CO2 efflux ranged from 185 g C x m(-2) x yr(-1) to 1190 g C x m(-2) x yr(-1) for sites arrayed along the same flow path. Spatial patterns of SR were unrelated to the carbon and water content of surface soils, but rather tracked changes in plant size and productivity, which in turn reflect downstream increases in groundwater availability. The relative importance of precipitation and temperature as drivers of SR also changed with landscape position, with the latter becoming more important in downstream locations. At the scale of individual precipitation events, SR increased up to 30-fold upon rewetting but typically returned to background levels within 24 h, even when soil moisture remained elevated. Unlike patterns observed at seasonal scales, event-based losses of CO2 varied across the landscape as a function of the organic-matter content in surface soils. Results from labile carbon amendments confirm that CO2 losses following precipitation pulses are initially constrained by substrate availability, not soil drying. By mediating spatial patterns of vegetation structure and soil resource availability, drainage networks represent an important physical template upon which belowground processes are organized in desert basins.     

Density-dependent settlement and mortality structure the earliest life phases of a coral population

The local densities of heterospecifics and conspecifics are known to have profound effects on the dynamics of many benthic species, including rates of settlement and early post-settlement survivorship. We described the early life history of the Caribbean coral, Siderastrea radians by tracking the population dynamics from recently settled planulae to juveniles. Through three years of observation, settlement correlated with the abundance of other benthic organisms, principally turf algae (negatively) and crustose coralline algae (positively). In addition, adult density showed independent effects on coral settlement and early post-settlement survivorship. Settlement rates increased across low levels of adult cover and saturated at a maximum around 10% cover. Early post-settlement survivorship decreased with adult cover, revealing structuring density dependence in coral settlers. The earliest life stages of corals are defined by low survivorship, with survivorship increasing appreciably with colony size. However, recent settlers (one-polyp individuals, < 1-year-old) are more likely to grow into two-polyp juveniles than older single polyps (> 1-year-old) that were delayed in their development. The early benthic phase of corals is defined by a severe demographic bottleneck for S. radians, with appreciable density-dependent and density-independent effects on survivorship. For effective management and restoration of globally imperiled coral reefs, we must focus more attention on this little studied, but dynamic, early life history period of corals.     

Concentrations, sources and temporal trends in atmospheric polycyclic aromatic hydrocarbons in a major conurbation

Concentrations of atmospheric PAH were separately determined in total suspended particulate matter and associated vapour phase in ambient air in Birmingham, UK. Samples of 24 h duration were taken simultaneously at two locations (the Bristol Road Observatory Site, BROS, and the Elms Road Observatory Site, EROS) on 44 separate occasions every one to two weeks between October 1999 and January 2001. BROS was 10 m from the busy Bristol Road, 800 m from EROS that was located within the "green space" of the University of Birmingham campus. With the exception of acenaphthene, average concentrations of all measured PAH at BROS exceed those at EROS, with a paired t-test revealing these roadside increments to be significant (p < 0.05) for 9 out of the 16 target PAH, demonstrating the importance of traffic emissions of PAH. Although the declines were not statistically significant (p > 0.05) except for phenanthrene and fluoranthene, concentrations of individual PAH at EROS between July and December inclusive in 1999 and 2000 fell by between 16 and 54% compared with those during the same months in 1997. Multiple linear regression of PAH concentrations against meteorological variables confirmed the influence of the Bristol Road on BROS but not EROS. Cluster analysis of PAH contamination in individual samples showed there to be two statistically distinct groups of samples. One group contained 15 samples, all of which displayed elevated concentrations. Examination of air mass back trajectory data, revealed that these PAH pollution episodes originate due to the combined effects of meteorology and local traffic emissions, rather than as a result of long-range transport. Eighteen 12 h samples were also taken at EROS over the period of the November Bonfire Night festivals of 1999 and 2000. These revealed significantly elevated PAH concentrations on the nights when ignition of bonfires and fireworks would be anticipated to peak. These results are relevant to assessments of the impact of similar "festivals of fire" elsewhere. In particular, retene (7-isopropyl-1-methylphenanthrene) concentrations were especially elevated, indicating it has possible utility as an indicator of wood combustion emissions.     

Application of sediment quality guidelines in the assessment and management of contaminated surficial sediments in Port Jackson (Sydney Harbour), Australia

Sediments in the Port Jackson estuary are polluted by a wide range of toxicants and concentrations are among the highest reported for any major harbor in the world. Sediment quality guidelines (SQGs), developed by the National Oceanographic and Atmospheric Administration (NOAA) in the United States are used to estimate possible adverse biological effects of sedimentary contaminants in Port Jackson to benthic animals. The NOAA guidelines indicate that Pb, Zn, DDD, and DDE are the most likely contaminants to cause adverse biological effects in Port Jackson. On an individual chemical basis, the detrimental effects due to these toxicants may occur over extensive areas of the harbor, i.e., about 40%, 30%, 15% and 50%, respectively. The NOAA SQGs can also be used to estimate the probability of sediment toxicity for contaminant mixtures by determining the number of contaminants exceeding an upper guideline value (effects range medium, or ERM), which predicts probable adverse biological effects. The exceedence approach is used in the current study to estimate the probability of sediment toxicity and to prioritize the harbour in terms of possible adverse effects on sediment-dwelling animals. Approximately 1% of the harbor is mantled with sediment containing more than ten contaminants exceeding their respective ERM concentrations and, based on NOAA data, these sediments have an 80% probability of being toxic. Sediment with six to ten contaminants exceeding their respective ERM guidelines extend over approximately 4% of the harbor and have a 57% probability of toxicity. These areas are located in the landward reaches of embayments in the upper and central harbor in proximity to the most industrialised and urbanized part of the catchment. Sediment in a further 17% of the harbor has between one and five exceedences and has a 32% probability of being toxic. The application of SQGs developed by NOAA has not been tested outside North America, and the validity of using them in Port Jackson has yet to be demonstrated. The screening approach adopted here is to use SQGs to identify contaminants of concern and to determine areas of environmental risk. The practical application and management implications of the results of this investigation are discussed.     

Exhaust temperature profiles for application of passive diesel particulate filters to solid waste collection vehicles in California

To reduce public exposure to diesel particulate matter (DPM), the California Air Resources Board has begun adoption of a series of rules to reduce these emissions from in-use heavy-duty vehicles. Passive diesel particulate filter (DPF) after-treatment technologies are a cost-effective method to reduce DPM emissions and have been used on a variety of vehicles worldwide. Two passive DPFs were interim-verified in California and approved federally for use in most 1994--2002 engine families for vehicles meeting min engine exhaust temperature requirements for successful filter regeneration. Some vehicles, however, may not be suited to passive DPFs because of lower engine exhaust temperatures. The purpose of this study was to determine the applicability of two types of passive DPFs to solid waste collection vehicles, the group of vehicles for which California recently mandated in-use DPM reductions. We selected 60 collection vehicles to represent the four main types of collection vehicle duty cycles--rolloffs, and front-end, rear, and side loaders--and collected second-by-second engine exhaust temperature readings for one week from each vehicle. As a group, the collection vehicles exhibited low engine exhaust temperatures, making the application of passive DPFs to these vehicles difficult. Only 35% of tested vehicles met the temperature requirements for one passive DPF, whereas 60% met the temperature requirements for the other. Engine exhaust temperatures varied by vehicle type. Side and front-end loaders met the engine exhaust temperature requirements in the greatest number of cases with approximately 50-90% achieving the required regeneration temperatures. Only 8-25% of the rear loader and roll-off collection vehicles met the engine exhaust temperature requirements. Solid waste collection vehicles represent a diverse fleet with a variety of duty cycles. Low engine exhaust temperatures will need to be addressed for successful use of passive DPFs in this application.     

Airborne measurements of peroxy radicals using the PERCA technique

The Peroxy Radical Chemical Amplifier (PERCA) technique is a proven method for measurement of ambient levels of peroxy radicals at ground level, but there are no published instances of the technique being used on an aerial platform. Here we describe deployment of a PERCA on the former UK Meteorological Office C-130 Hercules research aircraft. The instrument uses the established method of chemical amplification and conversion of peroxy radicals to nitrogen dioxide (NO2) by doping the sample air-flow matrix with CO and NO, subsequently measuring the NO2 yield with an improved 'Luminox' LMA-3 NO2 detector. NO2 from the amplification chemistry is distinguished from other sources of NO2 reaching the detector by periodically injecting CO approximately 1 s downstream of the NO injection point (termination mode). Chain lengths (CL's) for the amplification chemistry were typically approximately 260 (ground level) to approximately 200 (7,000 m). This variation with altitude is less than the variation associated with the 'age' of the PFA inlet material where the amplification chemistry occurs; CL's of approximately 200 with old tubing to approximately 300 with new clean tubing were typical (ground level values). The CL determinations were made in-flight using an onboard calibration unit based on the 254 nm photolysis of 7.5 to 10 parts per billion (by volume, ppbv) of CH3I in air, producing CH3O2 in a quantitative manner. The noise-equivalent detection limit for peroxy radicals (HO2 + RO2) is 2 parts per trillion (by volume, pptv) at 3,650 m when the background ambient ozone levels are stable, based on a 5 min average of five 30 s amplification cycles and five 30 s termination cycles. This detection limit is a function of several factors but is most seriously degraded when there is large variability in the ambient ozone concentration. This paper describes the instrument design, considers its performance and proposes design improvements. It concludes that the performance of an airborne PERCA in the free troposphere can be superior to that of ground-based instruments when similar sampling frequencies are compared.