Red environmental noise and the appearance of delayed density dependence in age-structured populations

Previous work suggests that red environmental noise can lead to the spurious appearance of delayed density dependence (DDD) in unstructured populations regulated only by direct density dependence. We analysed the effect of noise reddening on the pattern of spurious DDD in several variants of the density-dependent age-structured population model. We found patterns of spurious DDD in structured populations with either density-dependent fertility or density-dependent survival of the first age class, inconsistent with predictions from unstructured population models. Moreover, we found that nonspurious negative DDD always emerges in populations with deterministic chaotic dynamics, regardless of population structure or the type of environmental noise. The effect of noise reddening in generating spurious DDD is often negligible in the chaotic region of population deterministic dynamics. Our findings suggest that differences in species' life histories may exhibit different patterns of spurious DDD (owing to noise reddening) than predicted by unstructured models.     

Allele frequency covariance among cohorts and its use in estimating effective size of age-structured populations

A general expression for the covariance of allele frequencies among cohorts in age-structured populations is derived. The expression is used to extend the so-called temporal method for estimating effective population size from allele frequency shifts among samples from cohorts born any number of years apart. Computer simulations are used to check on the accuracy and precision of the method, and an application to coastal Atlantic cod is presented.     

Hunting to extinction: biology and regional economy influence extinction risk and the impact of hunting in artiodactyls

Half of all artiodactyls (even-toed hoofed mammals) are threatened with extinction, around double the mammalian average. Here, using a complete species-level phylogeny, we construct a multivariate model to assess for the first time which intrinsic (biological) and extrinsic (anthropogenic and environmental) factors influence variation in extinction risk in artiodactyls. Globally artiodactyls at greatest risk live in economically less developed areas, have older weaning ages and smaller geographical ranges. Our findings suggest that identifying predictors of threat is complicated by interactions between both biological and anthropogenic factors, resulting in differential responses to threatening processes. Artiodactyl species that experience unregulated hunting live in significantly less economically developed areas than those that are not hunted; however, hunted species are more susceptible to extinction if they have slower reproductive rates (older weaning ages). In contrast, risk in non-hunted artiodactyls is unrelated to reproductive rate and more closely associated with the economic development of the region in which they live.     

Phylogenetic,spatial and environmental components of extinction risk in carnivores

Aim Extinction risk is non‐randomly distributed across phylogeny and space and is influenced by environmental conditions. We quantified the relative contribution of these factors to extinction risk to unveil the underlying macroecological processes and derive predictive models. Location Global. Methods Based on the IUCN global assessments, we divided 192 carnivore species into two dichotomous classes representing different levels of extinction risk. We used spatial proximity, phylogenetic relationship and environmental variables together with phylogenetic eigenvector regression and spatial eigenvector filters to model and predict threat status. Results Our full models explained between 57% and 96% of the variance in extinction risk. Phylogeny and spatial proximity roughly explained between 21% and 70% of the total variation in all analyses, while the explanatory power of environmental conditions was relatively weaker (up to 15%). Phylogeny and spatial proximity contributed equally to the explained variance in the lower threat level, while spatial proximity was the most important factor in the models of the higher threat level. Prediction of threat status achieved 97% correct assignments. Main conclusions Our approach differs fundamentally from current studies of extinction risk because it does not necessarily rely on life‐history information. We clearly show that instead of treating phylogenetic inertia and spatial signal as statistical nuisances, space and phylogeny should be viewed as very useful in explaining a wide range of phenomena in comparative studies.     

Stochastic epidemics in dynamic populations: quasi-stationarity and extinction

Empirical evidence shows that childhood diseases persist in large communities whereas in smaller communities the epidemic goes extinct (and is later reintroduced by immigration). The present paper treats a stochastic model describing the spread of an infectious disease giving life-long immunity, in a community where individuals die and new individuals are born. The time to extinction of the disease starting in quasi-stationarity (conditional on non-extinction) is exponentially distributed. As the population size grows the epidemic process converges to a diffusion process. Properties of the limiting diffusion are used to obtain an approximate expression for τ, the mean-parameter in the exponential distribution of the time to extinction for the finite population. The expression is used to study how τ depends on the community size but also on certain properties of the disease/community: the basic reproduction number and the means and variances of the latency period, infectious period and life-length. Effects of introducing a vaccination program are also discussed as is the notion of the critical community size, defined as the size which distinguishes between the two qualitatively different behaviours. Received: 14 February 2000 / Revised version: 5 June 2000 / Published online: 24 November 2000     

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.     

Allee effects, mating systems and the extinction risk in populations with two sexes

The Allee effect is one of the population consequences of sexual reproduction that has received increased attention in recent years. Due to its impact on small population dynamics, it is commonly accepted that Allee effects should render populations more extinction prone. In particular, monogamous species are considered more susceptible to the Allee effect and hence, more extinction prone, than polygamous species. Although this hypothesis has received theoretical support, there is little empirical evidence. In this study, we investigate (1) how variation in tertiary sex ratio affects the presence and intensity of the Allee effect induced by mating system, as well as (2) how this effect contributes to extinction risk. In contrast with previous predictions, we show that all mating systems are likely to experience a strong Allee effect when the operational sex ratio (OSR) is balanced. This strong Allee effect does not imply being exceptionally extinction prone because it is associated with an OSR that result in a relatively small extinction risk. As a consequence, the impact of Allee effects on overall extinction risk is buffered. Moreover, the OSR of natural populations appears to be often male biased, thus making it unlikely that they will suffer from an Allee effect induced by mating system.     

Catastrophic events and recovery from low densities in populations of otariids: implications for risk of extinction

Two key factors in a population's risk of extinction are major population declines induced by natural or anthropogenic events (catastrophes) and whether the population's rate of growth increases or decreases at very low abundance levels. These two elements should be included in any population viability analysis (PVA), but estimates of the frequency and intensity of catastrophic events and data on the dynamics of low population densities are difficult to obtain. We examined the literature on population dynamics of otariids (fur seals and sea lions), to determine how frequently populations are subjected to major population declines, and to what extent depleted populations recover from low population size. We present frequency distributions for percentage declines for otariid life‐stages (pup, juvenile, adult female and male), and describe eight examples of events leading to a population decline of 50% or greater among otariids. We found that numerous otariid populations have been reduced to very low densities by exploitation (low enough to be thought extinct) and have recovered to levels where they are no longer at risk of extinction. This suggests that the reduction in population rate of increase at low densities in otariid populations may not be strong.     

Environmental correlates of body size influence range size and extinction risk: A global study in rodents

Aim

Species-level traits, such as body and range sizes, are important correlates of extinction risk. However, both are often related and are driven by environmental factors. Here, we elucidated links between environmental factors, body size, range size and susceptibility to extinction, across the whole order of rodents.

Location

Global.

Time period

Current.

Major taxa studied

Rodents (order Rodentia).

Methods

We compiled an unprecedentedly large database of rodent morphology, phylogeny, range size, conservation status, global climate and normalized difference vegetation index (NDVI), comprising >86% of all described species. Using phylogenetic regressions, we initially explored the environmental factors driving body size. Next, we modelled the relationship between body size and range size. From this relationship, we computed and mapped (at the assemblage level) an index of relative range size, corresponding to the deviation from the expected range size of each species, given its body size. Finally, we tested whether relative range was correlated with the risk of extinction of the species derived from an assessment by the International Union for Conservation of Nature.

Results

We found that, contrary to the expectations of Bergmann's rule, the body size of rodents was mostly influenced by variation in NDVI (rather than latitude/temperature). Body size, in turn, imposed a constraint on species range size, as evidenced by a triangular relationship that was segmented at the lower bound. The relative species range size derived from this relationship highlighted four geographical regions where rodents with small relative range were concentrated globally. We demonstrated that lower relative range size was associated with increased risk of extinction.

Main conclusions

Species that, given their body size, are distributed across ranges that are smaller than expected have elevated extinction risk. Therefore, investigating the relationships between environmental drivers, body size and range size might help to detect species that could become threatened in the near future.     

Demographic variance in heterogeneous populations: matrix models and sensitivity analysis

The demographic consequences of stochasticity in processes such as survival and reproduction are modulated by the heterogeneity within the population. Therefore, to study effects of stochasticity on population growth and extinction risk, it is critical to use structured population models in which the most important sources of heterogeneity (e.g. age, size, developmental stage) are incorporated as i‐state variables. Demographic stochasticity in heterogeneous populations has often been studied using one of two approaches: multitype branching processes and diffusion approximations. Here, we link these approaches, through the demographic stochasticity in age‐ or stage‐structured matrix population models. We derive the demographic variance, σ²_d, which measures the per capita contribution to the variance in population growth increment, and we show how it can be decomposed into contributions from transition probabilities and fertility across ages or stages. Furthermore, using matrix calculus we derive the sensitivity of σ²_d to age‐ or stage‐specific mortality and fertility. We apply the methods to an extensive set of data from age‐classified human populations (long‐term time‐series for Sweden, Japan and the Netherlands; two hunter–gatherer populations, and the high‐fertility Hutterites), and to a size‐classified population of the herbaceous plant Calathea ovandensis. For the human populations our analysis reveals substantial temporal changes in the demographic variance as well as its main components across age. These new methods provide a powerful approach for calculating the demographic variance for any structured model, and for analyzing its main components and sensitivities. This will make possible new analyses of demographic variance across different kinds of heterogeneity in different life cycles, which will in turn improve our understanding of mechanisms underpinning extinction risk and other important biological outcomes.     

Dispossession, degradation and extinction: environmental history in arid Australia

Among the most popular media images of Australia are the outback heroes: the explorer, pioneer and pastoralist. However, there is insufficient attention paid to the role that pastoralists and their management strategies have played in the dispossession and degradation of arid Australia. A historical overview of ecology and land management suggests that the fragility of Australia's arid ecosystems was identified over 100 years ago, and despite repeated calls for reform, effective regional management schemes are still vehemently opposed by pastoralists. I argue that, until the role played by pastoralists and their management strategies in the degradation of arid Australia has been adequately communicated, pastoralists will remain a powerful political lobby capable of thwarting the implementation of sustainable land management practises.     

Mutation induced extinction in finite populations: lethal mutagenesis and lethal isolation

Reproduction is inherently risky, in part because genomic replication can introduce new mutations that are usually deleterious toward fitness. This risk is especially severe for organisms whose genomes replicate "semi-conservatively," e.g. viruses and bacteria, where no master copy of the genome is preserved. Lethal mutagenesis refers to extinction of populations due to an unbearably high mutation rate (U), and is important both theoretically and clinically, where drugs can extinguish pathogens by increasing their mutation rate. Previous theoretical models of lethal mutagenesis assume infinite population size (N). However, in addition to high U, small N can accelerate extinction by strengthening genetic drift and relaxing selection. Here, we examine how the time until extinction depends jointly on N and U. We first analytically compute the mean time until extinction (τ) in a simplistic model where all mutations are either lethal or neutral. The solution motivates the definition of two distinct regimes: a survival phase and an extinction phase, which differ dramatically in both how τ scales with N and in the coefficient of variation in time until extinction. Next, we perform stochastic population-genetics simulations on a realistic fitness landscape that both (i) features an epistatic distribution of fitness effects that agrees with experimental data on viruses and (ii) is based on the biophysics of protein folding. More specifically, we assume that mutations inflict fitness penalties proportional to the extent that they unfold proteins. We find that decreasing N can cause phase transition-like behavior from survival to extinction, which motivates the concept of "lethal isolation." Furthermore, we find that lethal mutagenesis and lethal isolation interact synergistically, which may have clinical implications for treating infections. Broadly, we conclude that stably folded proteins are only possible in ecological settings that support sufficiently large populations.     

Impact of naturally spawning captive-bred Atlantic salmon on wild populations: depressed recruitment and increased risk of climate-mediated extinction

The assessment report of the 4th International Panel on Climate Change confirms that global warming is strongly affecting biological systems and that 20–30% of species risk extinction from projected future increases in temperature. It is essential that any measures taken to conserve individual species and their constituent populations against climate-mediated declines are appropriate. The release of captive bred animals to augment wild populations is a widespread management strategy for many species but has proven controversial. Using a regression model based on a 37-year study of wild and sea ranched Atlantic salmon (Salmo salar) spawning together in the wild, we show that the escape of captive bred animals into the wild can substantially depress recruitment and more specifically disrupt the capacity of natural populations to adapt to higher winter water temperatures associated with climate variability. We speculate the mechanisms underlying this seasonal response and suggest that an explanation based on bio-energetic processes with physiological responses synchronized by photoperiod is plausible. Furthermore, we predict, by running the model forward using projected future climate scenarios, that these cultured fish substantially increase the risk of extinction for the studied population within 20 generations. In contrast, we show that positive outcomes to climate change are possible if captive bred animals are prevented from breeding in the wild. Rather than imposing an additional genetic load on wild populations by releasing maladapted captive bred animals, we propose that conservation efforts should focus on optimizing conditions for adaptation to occur by reducing exploitation and protecting critical habitats. Our findings are likely to hold true for most poikilothermic species where captive breeding programmes are used in population management.     

Parental effects influence life history traits and covary with an environmental cline in common frog populations

Oecologia - Across latitudinal clines, the juvenile developmental rates of ectotherms often covary with the length of the growing season, due to life-history trade-offs imposed by the...     

Resistance,tolerance and environmental transmission dynamics determine host extinction risk in a load‐dependent amphibian disease

While disease‐induced extinction is generally considered rare, a number of recently emerging infectious diseases with load‐dependent pathology have led to extinction in wildlife populations. Transmission is a critical factor affecting disease‐induced extinction, but the relative importance of transmission compared to load‐dependent host resistance and tolerance is currently unknown. Using a combination of models and experiments on an amphibian species suffering extirpations from the fungal pathogen Batrachochytrium dendrobatidis (Bd), we show that while transmission from an environmental Bd reservoir increased the ability of Bd to invade an amphibian population and the extinction risk of that population, Bd‐induced extinction dynamics were far more sensitive to host resistance and tolerance than to Bd transmission. We demonstrate that this is a general result for load‐dependent pathogens, where non‐linear resistance and tolerance functions can interact such that small changes in these functions lead to drastic changes in extinction dynamics.     

Preference in patchy landscapes: the influence of scale-specific intake rates and variance in reward

Understanding the responses of foragers to patchy distributionsof resources has formed a fundamental challenge in behavioralecology. Two currencies have been used to assess the patch preferencesof herbivores—intake rate maximization and risk sensitivity.We wished to understand if small mammalian foragers, collaredlemmings (Dichrostonyx groenlandicus), choose patches to maximizefood intake rate or to reduce risk of starvation in "variable"environments. Moreover, we examined the possibility that maximizingintake rate depends on the spatial scale of patchiness. We designedan experiment offering two alternative patches of food, varyingthe predictability of food rewards and the "potential intakerate" at different spatial scales. Collared lemmings did notconsistently select patches that maximized their intake rateat either scale studied. Instead, they chose patches offeringthe least variation in food reward over the course of the experiment.Collared lemmings used prior knowledge gained from previousforaging bouts to assess food variability. We interpret theseresults as evidence for risk-averse foraging strategies, whichare predicted for continuous foragers aiming to minimize riskof starvation.     

Speeding up microevolution: the effects of increasing temperature on selection and genetic variance in a wild bird population

The amount of genetic variance underlying a phenotypic trait and the strength of selection acting on that trait are two key parameters that determine any evolutionary response to selection. Despite substantial evidence that, in natural populations, both parameters may vary across environmental conditions, very little is known about the extent to which they may covary in response to environmental heterogeneity. Here we show that, in a wild population of great tits (Parus major), the strength of the directional selection gradients on timing of breeding increased with increasing spring temperatures, and that genotype-by-environment interactions also predicted an increase in additive genetic variance, and heritability, of timing of breeding with increasing spring temperature. Consequently, we therefore tested for an association between the annual selection gradients and levels of additive genetic variance expressed each year; this association was positive, but non-significant. However, there was a significant positive association between the annual selection differentials and the corresponding heritability. Such associations could potentially speed up the rate of micro-evolution and offer a largely ignored mechanism by which natural populations may adapt to environmental changes.