Testing the intrinsic mechanisms driving the dynamics of Ross River Virus across Australia.

The mechanisms driving dynamics of many epidemiologically important mosquito-borne pathogens are complex, involving combinations of vector and host factors (e.g., species composition and life-history traits), and factors associated with transmission and reporting. Understanding which intrinsic mechanisms contribute most to observed disease dynamics is important, yet often poorly understood. Ross River virus (RRV) is Australia's most important mosquito-borne disease, with variable transmission dynamics across geographic regions. We used deterministic ordinary differential equation models to test mechanisms driving RRV dynamics across major epidemic centers in Brisbane, Darwin, Mandurah, Mildura, Gippsland, Renmark, Murray Bridge, and Coorong. We considered models with up to two vector species (Aedes vigilax, Culex annulirostris, Aedes camptorhynchus, Culex globocoxitus), two reservoir hosts (macropods, possums), seasonal transmission effects, and transmission parameters. We fit models against long-term RRV surveillance data (1991-2017) and used Akaike Information Criterion to select important mechanisms. The combination of two vector species, two reservoir hosts, and seasonal transmission effects explained RRV dynamics best across sites. Estimated vector-human transmission rate (average ß = 8.04x10-4per vector per day) was similar despite different dynamics. Models estimate 43% underreporting of RRV infections. Findings enhance understanding of RRV transmission mechanisms, provide disease parameter estimates which can be used to guide future research into public health improvements and offer a basis to evaluate mitigation practices.

Coexistence in two-species competition with delayed maturation.

Inter- and intraspecific competition is most important during the immature life stage for many species of interest, such as multiple coexisting mosquito species that act as vectors of diseases. Mortality caused by competition that occurs during maturation is explicitly modelled in some alternative formulations of the Lotka-Volterra competition model. We generalise this approach by using a distributed delay for maturation time. The kernel of the distributed delay is represented by a truncated Erlang distribution. The shape and rate of the distribution, as well as the position of the truncation, are found to determine the solution at equilibrium. The resulting system of delay differential equations is transformed into a system of ordinary differential equations using the linear chain approximation. Numerical solutions are provided to demonstrate cases where competitive exclusion and coexistence occur. Stability conditions are determined using the nullclines method and local stability analysis. The introduction of a distributed delay promotes coexistence and survival of the species compared to the limiting case of a discrete delay, potentially affecting management of relevant pests and threatened species.

Spatial modelling for population replacement of mosquito vectors at continental scale.

Malaria is one of the deadliest vector-borne diseases in the world. Researchers are developing new genetic and conventional vector control strategies to attempt to limit its burden. Novel control strategies require detailed safety assessment to ensure responsible and successful deployments. Anopheles gambiae sensu stricto (s.s.) and Anopheles coluzzii, two closely related subspecies within the species complex Anopheles gambiae sensu lato (s.l.), are among the dominant malaria vectors in sub-Saharan Africa. These two subspecies readily hybridise and compete in the wild and are also known to have distinct niches, each with spatially and temporally varying carrying capacities driven by precipitation and land use factors. We model the spread and persistence of a population-modifying gene drive system in these subspecies across sub-Saharan Africa by simulating introductions of genetically modified mosquitoes across the African mainland and its offshore islands. We explore transmission of the gene drive between the two subspecies that arise from different hybridisation mechanisms, the effects of both local dispersal and potential wind-aided migration to the spread, and the development of resistance to the gene drive. Given the best current available knowledge on the subspecies' life histories, we find that an introduced gene drive system with typical characteristics can plausibly spread from even distant offshore islands to the African mainland with the aid of wind-driven migration, with resistance beginning to take over within a decade. Our model accounts for regional to continental scale mechanisms, and demonstrates a range of realistic dynamics including the effect of prevailing wind on spread and spatio-temporally varying carrying capacities for subspecies. As a result, it is well-placed to answer future questions relating to mosquito gene drives as important life history parameters become better understood.

Transferability of correlative and process-based species distribution models revisited: A response to Booth.

Here, we respond to Booth's criticism of our paper, "Predictive ability of a process-based versus a correlative species distribution model." Booth argues that our usage of the MaxEnt model was flawed and that the conclusions of our paper are by implication flawed. We respond by clarifying that the error Booth implies we made was not made in our analysis, and we repeat statements from the original manuscript which anticipated such criticisms. In addition, we illustrate that using BIOCLIM variables in a MaxEnt analysis as recommended by Booth does not change the conclusions of the original analysis. That is, high performance in the training data domain did not equate to reliable predictions in novel data domains, and the process model transferred into novel data domains better than the correlative model did. We conclude by discussing a hidden implication of our study, namely, that process-based SDMs negate the need for BIOCLIM-type variables and therefore reframe the variable selection problem in species distribution modeling.

Predictive ability of a process-based versus a correlative species distribution model.

Species distribution modeling is a widely used tool in many branches of ecology and evolution. Evaluations of the transferability of species distribution models-their ability to predict the distribution of species in independent data domains-are, however, rare. In this study, we contrast the transferability of a process-based and a correlative species distribution model. Our case study uses 664 Australian eucalypt and acacia species. We estimate models for these species using data from their native Australia and then assess whether these models can predict the adventive range of these species. We find that the correlative model-MaxEnt-has a superior ability to describe the data in the training data domain (Australia) and that the process-based model-TTR-SDM-has a superior ability to predict the distribution of the study species outside of Australia. The implication of this analysis, that process-based models may be more appropriate than correlative models when making projections outside of the domain of the training data, needs to be tested in other case studies.

Links between environment and stomatal size through evolutionary time in Proteaceae.

The size of plant stomata (adjustable pores that determine the uptake of CO2 and loss of water from leaves) is considered to be evolutionarily important. This study uses fossils from the major Southern Hemisphere family Proteaceae to test whether stomatal cell size responded to Cenozoic climate change. We measured the length and abundance of guard cells (the cells forming stomata), the area of epidermal pavement cells, stomatal index and maximum stomatal conductance from a comprehensive sample of fossil cuticles of Proteaceae, and extracted published estimates of past temperature and atmospheric CO2. We developed a novel test based on stochastic modelling of trait evolution to test correlations among traits. Guard cell length increased, and stomatal density decreased significantly with decreasing palaeotemperature. However, contrary to expectations, stomata tended to be smaller and more densely packed at higher atmospheric CO2. Thus, associations between stomatal traits and palaeoclimate over the last 70 million years in Proteaceae suggest that stomatal size is significantly affected by environmental factors other than atmospheric CO2. Guard cell length, pavement cell area, stomatal density and stomatal index covaried in ways consistent with coordinated development of leaf tissues.

Modelling competition between hybridising subspecies.

The geographic niches of many species are dramatically changing as a result of environmental and anthropogenic impacts such as global climate change and the introduction of invasive species. In particular, genetically compatible subspecies that were once geographically separated are being reintroduced to one another. This is of concern for conservation, where rare or threatened subspecies could be bred out by hybridising with their more common relatives, and for commercial interests, where the stock or quality of desirable harvested species could be compromised. It is also relevant to disease ecology, where disease transmission is heterogeneous among subspecies and hybridisation may affect the rate and spatial spread of disease. We develop and investigate a mathematical model to combine competitive effects via the Lotka-Volterra model with hybridisation effects via mate choice. The species complex is structured into two classes: a subspecies of interest (named x), and other subspecies including any hybrids produced (named y). We show that in the absence of limit cycles the model has four possible equilibrium outcomes, representing every combination: total extinction, x-dominance (y extinct), y-dominance (x extinct), and at most a single coexistence equilibrium. We give conditions for which limit cycles cannot exist, then further show that the "total extinction" equilibrium is always unstable, that y-dominance is always stable, and that the other equilibria have stability depending on the model parameters. We demonstrate that both x-dominance and coexistence are achievable under a wide range of parameter values and initial conditions, which corresponds with empirical evidence of known competing-hybridising systems. We then briefly examine bifurcation behaviour. In particular, we note that a subcritical bifurcation is possible in which a "catastrophic" transition from x-dominance to y-dominance can occur, representing an invasion event. Finally, we briefly examine the common complication of time-varying carrying capacity, showing that such a case can make coexistence more likely.

A model for the treatment of environmentally transmitted sarcoptic mange in bare-nosed wombats (Vombatus ursinus).

Some of the most important wildlife diseases involve environmental transmission, with disease control attempted via treatments that induce temporary pathogen resistance among hosts. However, theoretical explanations of such circumstances remain few. A mathematical model is proposed and investigated to analyse the dynamics and treatment of environmentally transmitted sarcoptic mange in a population of bare-nosed wombats. The wombat population is structured into four classes representing stages of infection, in a model that consists of five non-linear differential equations including the unattached mite population. It is shown that four different epidemiological outcomes are possible. These are: (1) extinction of wombats (and mites); (2) mite-free wombat populations; (3) endemic wombats and mites coexisting, with the wombats' population reduced below the environmental carrying capacity; and (4) a stable limit cycle (sustained oscillating populations) with wombat population far below carrying capacity. Empirical evidence exists for the first two of these outcomes, with the third highly likely to occur in nature, and the fourth plausible at least until wombat populations succumb to Allee effects. These potential outcomes are examined to inform treatment programs for wombat populations. Through this theoretical exploration of a relatively well understood empirical system, this study supports general learning across environmentally transmitted wildlife pathogens, increasing understanding of how pathogen dynamics may cause crashes in some populations and not others.

Untangling the model muddle: Empirical tumour growth in Tasmanian devil facial tumour disease.

A pressing and unresolved topic in cancer research is how tumours grow in the absence of treatment. Despite advances in cancer biology, therapeutic and diagnostic technologies, there is limited knowledge regarding the fundamental growth and developmental patterns in solid tumours. In this ten year study, we estimated growth curves in Tasmanian devil facial tumours, a clonal transmissible cancer, in males and females with two different karyotypes (diploid, tetraploid) and facial locations (mucosal, dermal), using established differential equation models and model selection. Logistic growth was the most parsimonious model for diploid, tetraploid and mucosal tumours, with less model certainty for dermal tumours. Estimates of daily proportional tumour growth rate per day (95% Bayesian CIs) varied with ploidy and location [diploid 0.016 (0.014-0.020), tetraploid 0.026 (0.020-0.033), mucosal 0.013 (0.011-0.015), dermal 0.020 (0.016-0.024)]. Final tumour size (cm3) also varied, particularly the upper credible interval owing to host mortality as tumours approached maximum volume [diploid 364 (136-2,475), tetraploid 172 (100-305), dermal 226 (134-471)]. To our knowledge, these are the first empirical estimates of tumour growth in the absence of treatment in a wild population. Through this animal-cancer system our findings may enhance understanding of how tumour properties interact with growth dynamics in other types of cancer.

A comprehensive database of quality-rated fossil ages for Sahul's Quaternary vertebrates.

The study of palaeo-chronologies using fossil data provides evidence for past ecological and evolutionary processes, and is therefore useful for predicting patterns and impacts of future environmental change. However, the robustness of inferences made from fossil ages relies heavily on both the quantity and quality of available data. We compiled Quaternary non-human vertebrate fossil ages from Sahul published up to 2013. This, the FosSahul database, includes 9,302 fossil records from 363 deposits, for a total of 478 species within 215 genera, of which 27 are from extinct and extant megafaunal species (2,559 records). We also provide a rating of reliability of individual absolute age based on the dating protocols and association between the dated materials and the fossil remains. Our proposed rating system identified 2,422 records with high-quality ages (i.e., a reduction of 74%). There are many applications of the database, including disentangling the confounding influences of hypothetical extinction drivers, better spatial distribution estimates of species relative to palaeo-climates, and potentially identifying new areas for fossil discovery.

Climate change not to blame for late Quaternary megafauna extinctions in Australia.

Late Quaternary megafauna extinctions impoverished mammalian diversity worldwide. The causes of these extinctions in Australia are most controversial but essential to resolve, because this continent-wide event presaged similar losses that occurred thousands of years later on other continents. Here we apply a rigorous metadata analysis and new ensemble-hindcasting approach to 659 Australian megafauna fossil ages. When coupled with analysis of several high-resolution climate records, we show that megafaunal extinctions were broadly synchronous among genera and independent of climate aridity and variability in Australia over the last 120,000 years. Our results reject climate change as the primary driver of megafauna extinctions in the world's most controversial context, and instead estimate that the megafauna disappeared Australia-wide ∼13,500 years after human arrival, with shorter periods of coexistence in some regions. This is the first comprehensive approach to incorporate uncertainty in fossil ages, extinction timing and climatology, to quantify mechanisms of prehistorical extinctions.

Potential for thermal tolerance to mediate climate change effects on three members of a cool temperate lizard genus, Niveoscincus.

Climatic changes are predicted to be greater in higher latitude and mountainous regions but species specific impacts are difficult to predict. This is partly due to inter-specific variance in the physiological traits which mediate environmental temperature effects at the organismal level. We examined variation in the critical thermal minimum (CTmin), critical thermal maximum (CTmax) and evaporative water loss rates (EWL) of a widespread lowland (Niveoscincus ocellatus) and two range restricted highland (N. microlepidotus and N. greeni) members of a cool temperate Tasmanian lizard genus. The widespread lowland species had significantly higher CTmin and CTmax and significantly lower EWL than both highland species. Implications of inter-specific variation in thermal tolerance for activity were examined under contemporary and future climate change scenarios. Instances of air temperatures below CTmin were predicted to decline in frequency for the widespread lowland and both highland species. Air temperatures of high altitude sites were not predicted to exceed the CTmax of either highland species throughout the 21st century. In contrast, the widespread lowland species is predicted to experience air temperatures in excess of CTmax on 1 or 2 days by three of six global circulation models from 2068-2096. To estimate climate change effects on activity we reran the thermal tolerance models using minimum and maximum temperatures selected for activity. A net gain in available activity time was predicted under climate change for all three species; while air temperatures were predicted to exceed maximum temperatures selected for activity with increasing frequency, the change was not as great as the predicted decline in air temperatures below minimum temperatures selected for activity. We hypothesise that the major effect of rising air temperatures under climate change is an increase in available activity period for both the widespread lowland and highland species. The consequences of a greater available activity period will depend on the extent to which changes in climate alters other related factors, such as the nature and level of competition between the respective species.

Adaptive responses to cool climate promotes persistence of a non-native lizard.

Successful establishment and range expansion of non-native species often require rapid accommodation of novel environments. Here, we use common-garden experiments to demonstrate parallel adaptive evolutionary response to a cool climate in populations of wall lizards (Podarcis muralis) introduced from southern Europe into England. Low soil temperatures in the introduced range delay hatching, which generates directional selection for a shorter incubation period. Non-native lizards from two separate lineages have responded to this selection by retaining their embryos for longer before oviposition--hence reducing the time needed to complete embryogenesis in the nest--and by an increased developmental rate at low temperatures. This divergence mirrors local adaptation across latitudes and altitudes within widely distributed species and suggests that evolutionary responses to climate can be very rapid. When extrapolated to soil temperatures encountered in nests within the introduced range, embryo retention and faster developmental rate result in one to several weeks earlier emergence compared with the ancestral state. We show that this difference translates into substantial survival benefits for offspring. This should promote short- and long-term persistence of non-native populations, and ultimately enable expansion into areas that would be unattainable with incubation duration representative of the native range.

A tool for simulating and communicating uncertainty when modelling species distributions under future climates.

Tools for exploring and communicating the impact of uncertainty on spatial prediction are urgently needed, particularly when projecting species distributions to future conditions.We provide a tool for simulating uncertainty, focusing on uncertainty due to data quality. We illustrate the use of the tool using a Tasmanian endemic species as a case study. Our simulations provide probabilistic, spatially explicit illustrations of the impact of uncertainty on model projections. We also illustrate differences in model projections using six different global climate models and two contrasting emissions scenarios.Our case study results illustrate how different sources of uncertainty have different impacts on model output and how the geographic distribution of uncertainty can vary.Synthesis and applications: We provide a conceptual framework for understanding sources of uncertainty based on a review of potential sources of uncertainty in species distribution modelling; a tool for simulating uncertainty in species distribution models; and protocols for dealing with uncertainty due to climate models and emissions scenarios. Our tool provides a step forward in understanding and communicating the impacts of uncertainty on species distribution models under future climates which will be particularly helpful for informing discussions between researchers, policy makers, and conservation practitioners.