Andrea E. Byrom

Density Estimation by Spatially Explicit Capture–Recapture: Likelihood-Based Methods

Population density is a key ecological variable, and it has recently been shown how captures on an array of traps over several closely-spaced time intervals may be modelled to provide estimates of population density (Borchers and Efford 2007). Specifics of the model depend on the properties of the traps (more generally ‘detectors’). We provide a concise description of the newly developed likelihood-based methods and extend them to include ‘proximity detectors’ that do not restrict the movements of animals after detection. This class of detector includes passive DNA sampling and camera traps. The probability model for spatial detection histories comprises a submodel for the distribution of home-range centres (e.g. 2-D Poisson) and a detection submodel (e.g. halfnormal function of distance between a range centre and a trap). The model may be fitted by maximising either the full likelihood or the likelihood conditional on the number of animals observed. A wide variety of other effects on detection probability may be included in the likelihood using covariates or mixture models, and differences in density between sites or between times may also be modelled. We apply the method to data on stoats Mustela erminea in a New Zealand beech forest identified by microsatellite DNA from hair samples. The method assumes that multiple individuals may be recorded at a detector on one occasion. Formal extension to ‘single-catch’ traps is difficult, but in our simulations the ‘multi-catch’ model yielded nearly unbiased estimates of density for moderate levels of trap saturation (≤ 86% traps occupied), even when animals were clustered or the traps spanned a gradient in density.

Of mast and mean: differential-temperature cue makes mast seeding insensitive to climate change.

Mast-seeding plants often produce high seed crops the year after a warm spring or summer, but the warm-temperature model has inconsistent predictive ability. Here, we show for 26 long-term data sets from five plant families that the temperature difference between the two previous summers (ΔT) better predicts seed crops. This discovery explains how masting species tailor their flowering patterns to sites across altitudinal temperature gradients; predicts that masting will be unaffected by increasing mean temperatures under climate change; improves prediction of impacts on seed consumers; demonstrates that strongly masting species are hypersensitive to climate; explains the rarity of consecutive high-seed years without invoking resource constraints; and generates hypotheses about physiological mechanisms in plants and insect seed predators. For plants, ΔT has many attributes of an ideal cue. This temperature-difference model clarifies our understanding of mast seeding under environmental change, and could also be applied to other cues, such as rainfall.

Incorporating Genotype Uncertainty into Mark–Recapture-Type Models For Estimating Abundance Using DNA Samples

Sampling DNA noninvasively has advantages for identifying animals for uses such as mark-recapture modeling that require unique identification of animals in samples. Although it is possible to generate large amounts of data from noninvasive sources of DNA, a challenge is overcoming genotyping errors that can lead to incorrect identification of individuals. A major source of error is allelic dropout, which is failure of DNA amplification at one or more loci. This has the effect of heterozygous individuals being scored as homozygotes at those loci as only one allele is detected. If errors go undetected and the genotypes are naively used in mark-recapture models, significant overestimates of population size can occur. To avoid this it is common to reject low-quality samples but this may lead to the elimination of large amounts of data. It is preferable to retain these low-quality samples as they still contain usable information in the form of partial genotypes. Rather than trying to minimize error or discarding error-prone samples we model dropout in our analysis. We describe a method based on data augmentation that allows us to model data from samples that include uncertain genotypes. Application is illustrated using data from the European badger (Meles meles).

Connectivity and invasive species management: towards an integrated landscape approach

Invasive plants and animals are a major cause of global biodiversity loss. Invasive Species Management (ISM) helps conserve localized populations and ecosystems, but rarely have its potential benefits been explored at the landscape scale. We explore how ISM can enhance landscape connectivity, and how its incorporation into conservation planning algorithms could help design optimal reserve networks. Conversely, conservation planning and connectivity modelling can optimize targeting of ISM, achieving benefits for a wider range of taxa and ecological processes, without the need for additional resources. Empirical research must investigate the spatial pattern of benefits from ISM, and when to target priority conservation sites or the areas (matrix) between them. By bolstering populations within—and increasing connectivity between—focal patches, ISM should move beyond conserving individual sites to creating functionally connected networks of conservation areas.

Invasive mammals and habitat modification interact to generate unforeseen outcomes for indigenous fauna.

Biotic invasions and habitat modification are two drivers of global change predicted to have detrimental impacts on the persistence of indigenous biota worldwide. Few studies have investigated how they operate synergistically to alter trophic interactions among indigenous and nonindigenous species in invaded ecosystems. We experimentally manipulated a suite of interacting invasive mammals, including top predators (cat Felis catus, ferret Mustela furo, stoat M. erminea), herbivores (rabbit Oryctolagus cuniculus, hare Lepus europaeus), and an insectivore (hedgehog Erinaceus europaeus occidentalis), and measured their effects on indigenous lizards and invertebrates and on an invasive mesopredator (house mouse Mus musculus). The work was carried out in a grassland/shrubland ecosystem that had been subjected to two types of habitat modification (widespread introduction of high-seed-producing pasture species, and areas of land use intensification by fertilization and livestock grazing). We also quantified food productivity for indigenous and invasive fauna by measuring pasture biomass, as well as seed and fruit production by grasses and shrubs. Indigenous fauna did not always increase following top-predator suppression: lizards increased on one of two sites; invertebrates did not increase on either site. Mesopredator release of mice was evident at the site where lizards did not increase, suggesting negative effects of mice on lizard populations. High mouse abundance occurred only on the predator-suppression site with regular production of pasture seed, indicating that this food resource was the main driver of mouse populations. Removal of herbivores increased pasture and seed production, which further enhanced ecological release of mice, particularly where pasture swards were overtopped by shrubs. An effect of landscape supplementation was also evident where nearby fertilized pastures boosted rabbit numbers and the associated top predators. Other studies have shown that both suppression of invasive predators and retiring land from grazing can benefit indigenous species, but our results suggest that the ensuing vegetation changes and complex interactions among invasive species can block recovery of indigenous fauna vulnerable to mesopredators. Top-down and bottom-up ecological release of mesopredators and landscape supplementation of top predators are key processes to consider when managing invaded communities in complex landscapes.

The effect of poisoned and notional vaccinated buffers on possum (Trichosurus vulpecula) movements: minimising the risk of bovine tuberculosis spread from forest to farmland

Context. Vaccination of brushtail possums (Trichosurus vulpecula) has been proposed as a cost-effective alternative to lethal control for preventing potentially bovine tuberculosis (Tb)-infected possums from crossing forested buffer zones that abut farmland. Aim. Evaluation of these two management option requires an estimation of the buffer width required to reduce the risk of disease spread to an acceptable level. Methods. The movements of two groups of adult and subadult possums were monitored for up to 12 months in the Kaimanawa Range, North Island of New Zealand, using GPS technology. One group was in untreated forest immediately adjacent to a recently poisoned forest buffer, and the second group was 2 km further into untreated forest, which mimicked a vaccinated buffer with no reduction in possum abundance. Key results. Close to the poisoned buffer, where the initial population density was 0.49–1.45 ha–1, adult possum home ranges averaged 10.2 ha in the summer immediately after control and 9.5 ha in the following winter. Two kilometres into the untreated forest, where the density was >3 ha–1, the corresponding values were only 3.5 ha and 2.8 ha. Over the first 6 months of monitoring, a ~350-m wide poisoned buffer would have contained 95% of movements by adult possums, as well as movements by most individuals, but a ~150-m wide vaccinated buffer would have been as effective. Equivalent results for the subsequent 6-month period were ~450 m and ~200 m for poisoned and vaccinated buffers, respectively. Movements by possums were not biased in the direction of the population ‘vacuum’ created by the poisoning operation. When subadult possums were included in the analysis, buffer widths of ~500–600 m for both poisoning and vaccination would be required to contain 95% of new den site locations. Conclusions and implications. Detailed data on possum movements provide a means for agencies managing Tb to specify the width of a buffer, subject to an acceptable level of risk that it could be breached by a potentially infected possum. As well as depending on the width of a treated buffer, the final cost-effectiveness of vaccination compared with poisoning will depend on the relative cost of applying the two control techniques, and the frequency of application required either to prevent Tb from establishing (in the case of vaccination) or to suppress possum density (in the case of lethal control).

Comparison of ranging behaviour in a multi-species complex of free-ranging hosts of bovine tuberculosis in relation to their use as disease sentinels

Sentinel species are increasingly used by disease managers to detect and monitor the prevalence of zoonotic diseases in wildlife populations. Characterizing home-range movements of sentinel hosts is thus important for developing improved disease surveillance methods, especially in systems where multiple host species co-exist. We studied ranging activity of major hosts of bovine tuberculosis (TB) in an upland habitat of New Zealand: we compared home-range coverage by ferrets (Mustela furo), wild deer (Cervus elaphus), feral pigs (Sus scrofa), brushtail possums (Trichosurus vulpecula) and free-ranging farmed cattle (Bos taurus). We also report in detail the proportional utilization of a seasonal (4-monthly) range area for the latter four species. Possums covered the smallest home range (<30 ha), ferrets covered ~100 ha, pigs ~4 km(2), deer and cattle both >30 km2. For any given weekly period, cattle, deer and pigs were shown to utilize 37–45% of their estimated 4-month range, while possums utilized 62% during any weekly period and 85% during any monthly period of their estimated 4-month range. We suggest that present means for estimating TB detection kernels, based on long-term range size estimates for possums and sentinel species, probably overstate the true local surveillance coverage per individual.

Asynchronous food-web pathways could buffer the response of Serengeti predators to El Niño Southern Oscillation

Understanding how entire ecosystems maintain stability in the face of climatic and human disturbance is one of the most fundamental challenges in ecology. Theory suggests that a crucial factor determining the degree of ecosystem stability is simply the degree of synchrony with which different species in ecological food webs respond to environmental stochasticity. Ecosystems in which all food-web pathways are affected similarly by external disturbance should amplify variability in top carnivore abundance over time due to population interactions, whereas ecosystems in which a large fraction of pathways are nonresponsive or even inversely responsive to external disturbance will have more constant levels of abundance at upper trophic levels. To test the mechanism underlying this hypothesis, we used over half a century of demographic data for multiple species in the Serengeti (Tanzania) ecosystem to measure the degree of synchrony to variation imposed by an external environmental driver, the El Niño Southern Oscillation (ENSO). ENSO effects were mediated largely via changes in dry-season vs. wet-season rainfall and consequent changes in vegetation availability, propagating via bottom-up effects to higher levels of the Serengeti food web to influence herbivores, predators and parasites. Some species in the Serengeti food web responded to the influence of ENSO in opposite ways, whereas other species were insensitive to variation in ENSO. Although far from conclusive, our results suggest that a diffuse mixture of herbivore responses could help buffer top carnivores, such as Serengeti lions, from variability in climate. Future global climate changes that favor some pathways over others, however, could alter the effectiveness of such processes in the future.

Predicted responses of invasive mammal communities to climate-related changes in mast frequency in forest ecosystems.

Predicting the dynamics and impacts of multiple invasive species can be complex because ecological relationships, which occur among several trophic levels, are often incompletely understood. Further, the complexity of these trophic relationships exacerbates our inability to predict climate change effects on invaded ecosystems. We explore the hypothesis that interactions between two global change drivers, invasive vertebrates and climate change, will potentially make matters worse for native biodiversity. In New Zealand beech (Nothofagus spp.) forests, a highly irruptive invasive mammal community is driven by multi-annual resource pulses of beech seed (masting). Because mast frequency is predicted to increase with climate change, we use this as a model system to explore the extent to which such effects may influence invasive vertebrate communities, and the implications of such interactions for native biodiversity and its management. We build on an established model of trophic interactions in the system, combining it with a logistic probability mast function, the parameters of which were altered to simulate either contemporary conditions or conditions of more or less frequent masting. The model predicts that increased mast frequency will lead to populations of a top predator (the stoat) and a mesopredator (the ship rat) becoming less irruptive and being maintained at appreciably higher average abundances in this forest type. In addition, the ability of both current and in-development management approaches to suppress invasive mammals is predicted to be compromised. Because invasive mammals are key drivers of native fauna extinction in New Zealand, with the additional loss of associated functions such as pollination and seed dispersal, these predictions imply potentially serious adverse impacts of climate change for the conservation of biodiversity and ecosystem function. Our study also highlights the importance of long-term monitoring data for assessing and managing future impacts of global change drivers.

Confronting the risks of large-scale invasive species control

Large-scale invasive species control initiatives are motivated by laudable desires for native species recovery and economic benefits, but they are not without risk. Management interventions and policies should include evidence-based risk-benefit assessment and mitigation planning.