Extinction Threshold Research Articles

Threshold extinction in food webs

Food web response to species loss has been investigated in several ways in the previous years. In binary food webs, species go secondarily extinct if no resource item remains to be exploited. In this work, we considered that species can go extinct before the complete loss of their resources and we introduced thresholds of minimum energy requirement for species survival. According to this approach, extinction of a node occurs whenever an initial extinction event eliminates its incoming links so it is left with an overall energy intake lower than the threshold value. We tested the robustness of 18 real food webs by removing species from most to least connected and considering different scenarios defined by increasing the extinction threshold. Increasing energy requirement threshold negatively affects food web robustness. We found that a very small increase of the energy requirement substantially increases system fragility. In addition, above a certain value of energy requirement threshold we found no relationship between the robustness and the connectance of the web. Further, food webs with more species showed higher fragility with increasing energy threshold. This suggests that the shape of the robustness–complexity relationship of a food web depends on the sensitivity of consumers to loss of prey.

Ecological and anthropogenic drivers of rabies exposure in vampire bats: implications for transmission and control.

Despite extensive culling of common vampire bats in Latin America, lethal human rabies outbreaks transmitted by this species are increasingly recognized, and livestock rabies occurs with striking frequency. To identify the individual and population-level factors driving rabies virus (RV) transmission in vampire bats, we conducted a longitudinal capture-recapture study in 20 vampire bat colonies spanning four regions of Peru. Serology demonstrated the circulation of RV in vampire bats from all regions in all years. Seroprevalence ranged from 3 to 28 per cent and was highest in juvenile and sub-adult bats. RV exposure was independent of bat colony size, consistent with an absence of population density thresholds for viral invasion and extinction. Culling campaigns implemented during our study failed to reduce seroprevalence and were perhaps counterproductive for disease control owing to the targeted removal of adults, but potentially greater importance of juvenile and sub-adult bats for transmission. These findings provide new insights into the mechanisms of RV maintenance in vampire bats and highlight the need for ecologically informed approaches to rabies prevention in Latin America.

HIV-1 genome is often defective in PBMCs and rectal tissues after long-term HAART as a result of APOBEC3 editing and correlates with the size of reservoirs

Precise characterization of viruses present in reservoirs in long-term pretreated patients will be a major issue to consider in the context of viral eradication. We assessed the frequency of defective viruses present in cellular reservoirs. Peripheral blood mononuclear cells (PBMCs) and rectal biopsy samples were compared between five patients on successful long-term highly active antiretroviral therapy (HAART) (>7 years without blips) and five untreated patients. Molecular cloning and sequencing of the reverse transcriptase region were used to detect the presence of and quantify in-frame stop codons in HIV quasi-species. The relationship between the size of the reservoir and the frequency of defective genomes was assessed. Defective genomes were systematically detected in all patients on long-term HAART in both compartments (PBMCs and rectal tissues), with a higher level of defective genomes per sample compared with PBMCs of untreated patients. A high level of defective genomes was correlated with a small size of HIV proviral DNA. Regarding the nucleotide context, guanine (G) to adenine (A) substitution at tryptophan positions was responsible for the appearance of 89% of all in-frame stop codons in the context of G-to-A hypermutation, likely reflecting APOBEC3 footprints on the viral genome. We propose a scenario whereby defective genomes accumulate during HAART treatment, eventually reaching a viral extinction threshold. In the context of viral eradication, measurement of the relative amounts of defective and non-defective viruses (by molecular cloning and ultradeep sequencing) should be used as a new criterion for eradicating HIV.

From Molecular Genetics to Phylodynamics: Evolutionary Relevance of Mutation Rates Across Viruses

Although evolution is a multifactorial process, theory posits that the speed of molecular evolution should be directly determined by the rate at which spontaneous mutations appear. To what extent these two biochemical and population-scale processes are related in nature, however, is largely unknown. Viruses are an ideal system for addressing this question because their evolution is fast enough to be observed in real time, and experimentally-determined mutation rates are abundant. This article provides statistically supported evidence that the mutation rate determines molecular evolution across all types of viruses. Properties of the viral genome such as its size and chemical composition are identified as major determinants of these rates. Furthermore, a quantitative analysis reveals that, as expected, evolution rates increase linearly with mutation rates for slowly mutating viruses. However, this relationship plateaus for fast mutating viruses. A model is proposed in which deleterious mutations impose an evolutionary speed limit and set an extinction threshold in nature. The model is consistent with data from replication kinetics, selection strength and chemical mutagenesis studies.

Assessment of the Power Balance at a Copper Cathode Submitted to an Electric Arc by Surface Temperature Measurements and Numerical Modelling

The aim of this work is to improve the understanding of the heating of copper cathodes under the action of a nonstationary electric arc in air. An experimental method is proposed for the measurement of the surface temperature distribution just after a very fast arc-controlled arc extinction. The arc current intensity is about 60-70 A, and the arc duration is in the range of 2.5-5 ms. Different kinds of surface temperature distributions have been observed depending on the arc root behavior. The measurement of the temperature decrease after the arc extinction was used to estimate the cathode surface temperature just at the moment of arc extinction. Two-dimensional thermal modeling taking into account phase changes is used to estimate the power balance at the cathode surface and to propose a second estimation of the surface temperature at the point of arc extinction. The comparisons between experimental results and thermal modeling lead in the present experimental conditions to a volt equivalent at the cathode in the range 6.7-10.7 V, to a surface power density in the range0.6 × 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">9</sup> - 2.5 × 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">9</sup> W/m <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> and to a maximum surface temperature in the range 850°C-1300 °C .

Investigation into the use of rapid (alternative) microbial detection methods to determine bioburden of NHS pharmacy-manufactured non-sterile medicines†

BackgroundRapid microbiological methods (RMMs) have been shown to improve aseptic NHS QA activities. This study investigates the potential to use these new rapid qualitative technologies for quantitative bioburden testing. The...

Predator-prey dynamics in a uniform medium lead to directed percolation and wave-train propagation

The dynamics of birth-death processes with extinction points that are unstable in the deterministic average description has been extensively studied, mainly in the context of the stochastic transition from the mean-field attracting fixed point to the absorbing state. Here we study the opposite case of a small perturbation from the zero-population absorbing state. We show that such perturbations can grow beyond the mean-field attracting fixed point and then can collapse back into the absorbing state. Such dynamics can represent, for example, the fast growth of a pathogen and then its destruction by the immune system. We show that when the prey perturbation extinction probability is high, the loss of synchronization between the prey densities in different regions in space leads to two possible dynamic regimes: (a) a directed percolation regime based on the balance between regions escaping the absorbing state and regions absorbed into it, and (b) wave trains representing the transition of the entire space to the mean-field stable positive fixed point.

Extinction thresholds in deterministic and stochastic epidemic models

The basic reproduction number, ℛ0, one of the most well-known thresholds in deterministic epidemic theory, predicts a disease outbreak if ℛ0>1. In stochastic epidemic theory, there are also thresholds that predict a major outbreak. In the case of a single infectious group, if ℛ0>1 and i infectious individuals are introduced into a susceptible population, then the probability of a major outbreak is approximately 1−(1/ℛ0) i . With multiple infectious groups from which the disease could emerge, this result no longer holds. Stochastic thresholds for multiple groups depend on the number of individuals within each group, i j , j=1, …, n, and on the probability of disease extinction for each group, q j . It follows from multitype branching processes that the probability of a major outbreak is approximately . In this investigation, we summarize some of the deterministic and stochastic threshold theory, illustrate how to calculate the stochastic thresholds, and derive some new relationships between the deterministic and stochastic thresholds.

Ignition and extinction in perfectly stirred reactors with detailed chemistry

Ignition and extinction of steady state combustion are known to be associated with the lower and upper turning points on the “S”-curves. In the present study, this concept is further investigated with eigen-analysis on the Jacobian matrix for oxidation of methane and dimethyl ether (DME), respectively, in perfectly stirred reactors (PSRs). It was found that there can be multiple ignition and extinction turning points on the “S”-curves for DME–air due to negative temperature coefficient (NTC) behaviors. Furthermore, the physical extinction points for DME–air obtained from flame stability analysis can be different from the turning points on the “S”-curves although there is no differential diffusion or heat loss in PSR. Physically unstable segments were observed on the branches of an “S”-curve for DME–air corresponding to both strong and cool flames. A rigorous definition of ignition and extinction of steady state combustion based on eigen-analysis of the Jacobian matrix is proposed for practical fuels in the present study.

Species and global change-assessing the extinction point of albacore stocks

Global change determines the environmental condition and leads to decide the carrying capacity. While carrying capacity determines the extinction of the species, it is an important issue to estimate the extinction point of the species, the minimal carrying capacity, or the tolerant limitation of the species. If it is possible to estimate the tolerant limitation of the species, it will be possible to control the global change. Applied the above idea to the albacore stocks, it revealed that extinction point was about 0.0018% of the present status. From these results, it implies that this method may also suitable to other species for estimating their carrying capacities.

Movement upscaled – the importance of individual foraging movement for community response to habitat loss

Habitat loss poses a severe threat to biodiversity. While many studies yield valuable information on how specific species cope with such environmental modification, the mechanistic understanding of how interacting species or whole communities are affected by habitat loss is still poor. Individual movement plays a crucial role for the space use characteristics of species, since it determines how individuals perceive and use their heterogeneous environment. At the community level, it is therefore essential to include individual movement and how it is influenced by resource sharing into the investigation of consequences of habitat loss. To elucidate the effects of foraging movement on communities in face of habitat loss, we here apply a recently published spatially‐explicit and individual‐based model of home range formation. This approach allows predicting the individual size distribution (ISD) of mammal communities in simulation landscapes that vary in the amount of suitable habitat. We apply three fundamentally different foraging movement approaches (central place forager (CPF), patrolling forager (PF) and body mass dependent nomadic forager (BNF)). Results show that the efficiency of the different foraging strategies depends on body mass, which again affects community structure in face of habitat loss. CPF is only efficient for small animals, and therefore yields steep ISD exponents on which habitat loss has little effect (due to a movement limitation of body mass). PF and particularly BNF are more efficient for larger animals, resulting in less steep ISDs with higher mass maxima, both showing a threshold behaviour with regard to loss of suitable habitat. These findings represent a new way of explaining observed ‘extinction thresholds’, and therefore indicate the importance of individual space use characterized by physiology and behaviour, i.e. foraging movement, for communities and their response to habitat loss. Findings also indicate the necessity to incorporate the crucial role of movement into future conservation efforts of terrestrial communities.

BISTABILITY AND LONG-TERM CURE IN A WITHIN-HOST MODEL OF HEPATITIS C

Treatment of hepatitis C virus (HCV) is lengthy, expensive and fraught with side-effects, succeeding in only 50% of treated patients. In clinical settings, short-term treatment response (so-called sustained virological response (SVR)) is used to predict prolonged viral suppression. Although ordinary differential equation (ODE) models for within-host HCV infection have illuminated the mechanisms underlying treatment with interferon (IFN) and ribavirin (RBV), they have difficulty producing SVR without the introduction of an external extinction threshold. Here we show that bistability in an existing ODE model of HCV, which occurs when infected hepatocytes proliferate sufficiently faster than uninfected hepatocytes, can produce SVR without an external extinction threshold under biologically relevant conditions. The model can produce all clinically observed patient profiles for realistic parameter values; it can also be used to estimate the efficacy and/or duration of treatment that will ensure permanent cure for a particular patient.

Studies on the bionomics of male Anopheles gambiae Giles and male Anopheles funestus Giles from southern Mozambique

Little is known about the fitness of wild male mosquitoes, the females of which are vectors of malaria. The problem of studying male biology has been exacerbated by difficulties associated with catching them. In southern Mozambique, however, almost the entire adult population of An. funestus and An. gambiae s.l. rest inside houses. They leave in a dusk exodus, which makes them easy to collect. In 8,348 exit collections from a village from 2003 to 2009, 567,195 male An. funestus and 34,591 male An. gambiae s.l. were collected. During the study, numbers of An. funestus increased but numbers of An. gambiae s.l. declined to the point of extinction. Overall numbers of An. gambiae s.l. were positively correlated with temperature, whilst the relationship between temperature and numbers of An. funestus changed from an initially positive one in the first three years of the study to a negative one in the last three years. Marked males were recaptured up to 300 m from the release site, with most recaptures occurring within 150 m. Estimated mean daily survival of male An. funestus was 0.86 (95% C.I. 0.869-0.850). For the years 2003-2007, estimated mean daily survival of male An gambiae s.l. was 0.660 (95% C.I. 0.682-0.638). For either species, there was no relationship between mean weekly temperature and estimated daily survival. These results imply that males of An. funestus live as long as females but have a relatively short flight range. They are discussed in the light of possible release strategies of sterile or genetically modified mosquitoes.

Immigration rates in fragmented landscapes--empirical evidence for the importance of habitat amount for species persistence.

BackgroundThe total amount of native vegetation is an important property of fragmented landscapes and is known to exert a strong influence on population and metapopulation dynamics. As the relationship between habitat loss and local patch and gap characteristics is strongly non-linear, theoretical models predict that immigration rates should decrease dramatically at low levels of remaining native vegetation cover, leading to patch-area effects and the existence of species extinction thresholds across fragmented landscapes with different proportions of remaining native vegetation. Although empirical patterns of species distribution and richness give support to these models, direct measurements of immigration rates across fragmented landscapes are still lacking.Methodology/Principal FindingsUsing the Brazilian Atlantic forest marsupial Gray Slender Mouse Opossum (Marmosops incanus) as a model species and estimating demographic parameters of populations in patches situated in three landscapes differing in the total amount of remaining forest, we tested the hypotheses that patch-area effects on population density are apparent only at intermediate levels of forest cover, and that immigration rates into forest patches are defined primarily by landscape context surrounding patches. As expected, we observed a positive patch-area effect on M. incanus density only within the landscape with intermediate forest cover. Density was independent of patch size in the most forested landscape and the species was absent from the most deforested landscape. Specifically, the mean estimated numbers of immigrants into small patches were lower in the landscape with intermediate forest cover compared to the most forested landscape.Conclusions/SignificanceOur results reveal the crucial importance of the total amount of remaining native vegetation for species persistence in fragmented landscapes, and specifically as to the role of variable immigration rates in providing the underlying mechanism that drives both patch-area effects and species extinction thresholds.

Parasitoids and ecological risk assessment: Can toxicity data developed for one species be used to protect an entire guild?

Parasitoid wasps are important control agents for a suite of economically important arthropod pests. However, it is well known that hymenoptera in general are highly vulnerable to the effects of chemical pesticides, and so represent an opportunity to better understand the compatibility of biological and chemical control of pests. Closely related species are often used in trials aimed at assessing the effects of different chemical toxicants on hymenoptera. Most of these tests focus on acute toxicity, with few exploring longer-term population outcomes. Here, using a simple mathematical framework, we quantify the relative vulnerability of a suite of parasitoid species to the sublethal effects of a toxicant acting on fecundity. Using an equation that describes a critical extinction threshold, we calculate levels of reduction in fecundity above which parasitoid species important for biological control are driven to local extinction. We apply this framework to four economically important braconid biological control agents ( Diachasmimorpha longicaudata, Psyttalia fletcheri, Fopius arisanus, and Diaeretiella rapae), and find that threshold levels vary widely among them. In particular, we find that D. rapae is far more robust to pesticide exposure than the other three species, suggesting that these four species are not interchangeable in terms of risk assessment. Our findings imply that caution should be exercised in assuming species even within the same functional guild may be used as surrogate species for one another.

Stochastic population oscillations in spatial predator-prey models

It is well-established that including spatial structure and stochastic noise in models for predator-prey interactions invalidates the classical deterministic Lotka–Volterra picture of neutral population cycles. In contrast, stochastic models yield long-lived, but ultimately decaying erratic population oscillations, which can be understood through a resonant amplification mechanism for density fluctuations. In Monte Carlo simulations of spatial stochastic predator-prey systems, one observes striking complex spatio-temporal structures. These spreading activity fronts induce persistent correlations between predators and prey. In the presence of local particle density restrictions (finite prey carrying capacity), there exists an extinction threshold for the predator population. The accompanying continuous non-equilibrium phase transition is governed by the directed-percolation universality class. We employ field-theoretic methods based on the Doi–Peliti representation of the master equation for stochastic particle interaction models to (i) map the ensuing action in the vicinity of the absorbing state phase transition to Reggeon field theory, and (ii) to quantitatively address fluctuation-induced renormalizations of the population oscillation frequency, damping, and diffusion coefficients in the species coexistence phase.

The spatial structure of hunter access determines the local abundance of forest elephants (Loxodonta africana cyclotis)

In many previously remote regions in the world, increasing and often unregulated access is leading to dramatic increases in hunting pressure and declines in the densities of prey species, sometimes to the point of local extinction. Not surprisingly, numerous studies have found a correlation between the distance to the closest access point and prey densities. Here we hypothesized that, for many wide-ranging species, local abundances are reduced by hunting associated with multiple access points as opposed to just the closest access points. We also hypothesized that the distribution of hunter access determines both patterns of occupancy and abundance in occupied areas and that these two patterns (occupancy and abundance) respond to access at different spatial scales. Using data on the distribution of abundances of African forest elephant (Loxodonta africana cyclotis) in and around five national parks in Central Africa, we tested these hypotheses using a model comparison framework. We found that models including an index based on the distance to multiple roads outperformed models including other access-based covariates, including a model based on distance to the closest road only. We also found that models that allowed us to model occupancy and abundance separately outperformed simpler models. Occupancy responds to access at the same scale as previous estimates of average maximum displacement in the subspecies, while the scale of the response of abundance is more ambiguous, but appears to be greater. Lastly, we show that incorporating indices based on multiple access points and modeling abundance and occupancy has important practical consequences for our understanding of overall regional abundances and the distribution of abundances within regions.

Low dimensional homeochaos in coevolving host–parasitoid dimorphic populations: Extinction thresholds under local noise

A discrete time model describing the population dynamics of coevolution between host and parasitoid haploid populations with a dimorphic matching allele coupling is investigated under both determinism and stochastic population disturbances. The role of the properties of the attractors governing the survival of both populations is analyzed considering equal mutation rates and focusing on host and parasitoid growth rates involving chaos. The purely deterministic model reveals a wide range of ordered and chaotic Red Queen dynamics causing cyclic and aperiodic fluctuations of haplotypes within each species. A Ruelle–Takens–Newhouse route to chaos is identified by increasing both host and parasitoid growth rates. From the bifurcation diagram structure and from numerical stability analysis, two different types of chaotic sets are roughly differentiated according to their size in phase space and to their largest Lyapunov exponent: the Confined and Expanded attractors. Under the presence of local population noise, these two types of attractors have a crucial role in the survival of both coevolving populations. The chaotic confined attractors, which have a low largest positive Lyapunov exponent, are shown to involve a very low extinction probability under the influence of local population noise. On the contrary, the expanded chaotic sets (with a higher largest positive Lyapunov exponent) involve higher host and parasitoid extinction probabilities under the presence of noise. The asynchronies between haplotypes in the chaotic regime combined with low dimensional homeochaos tied to the confined attractors is suggested to reinforce the long-term persistence of these coevolving populations under the influence of stochastic disturbances. These ideas are also discussed in the framework of spatially-distributed host–parasitoid populations.

Habitat Loss, the Dynamics of Biodiversity, and a Perspective on Conservation

Habitat Loss, the Dynamics of Biodiversity, and a Perspective on Conservation

A Spatial Dimension of Ecology: Ilkka Hanski Crafoord Laureate in 2011

The Finnish ecologist Ilkka Hanski is awarded the Crafoord Prize in Biosciences for 2011 for his pioneering studies of how spatial variation affects the dynamics of animal and plant populations. Earlier Crafoord laureates in Biosciences include Robert L. Trivers (2007), Carl R. Woese (2003), John Maynard Smith, Ernst Mayr and George C. Williams (1999), Robert May (1996), Seymour Benzer and William T. Hamilton (1993), Paul R. Ehrlich and Edward O. Wilson (1990), Eugene P. Odum and Howard T. Odum (1987) and Daniel H. Janzen (1984). A common textbook defines ecology as the study of the mechanisms behind species abundance and distribution where each species can be characterized by the size and location of its populations. Ecological populations are rarely constant over time and space but vary due to factors both intrinsic to the system and extrinsic environmental variation. Even in a spatially homogeneous environment, populations of predator and prey may show patchy distributions due to, for example, differences in movement rates. In most cases, variation in population sizes over space (and time) is, however, a result of spatial variation in the distribution of suitable habitats, and it is in this context that Ilkka Hanski has made his major contributions. Inspired by a short paper by Richard Levins published in the late 1960s, Hanski initiated a development of both theory and empirical research that has now grown to become a major research area in ecology. Baptized as Metapopulation Ecology (Hanski 1999), this research now engages ecologists all over the world in studies in many different kinds of environments. Although animals and plants are most common, the metapopulation theories are used for all major groups of organisms. As in most scientific breakthroughs, the basic idea is quite simple. Each population is seen as an “individual”, which is born (the population is founded by colonization of a site) and ultimately dies (the population goes extinct). The likelihood of colonization is dependent on the presence of other populations in the surroundings (the isolation of the site) and the risk of extinction is dependent in the population size (the area of the site). From this simple basis of habitat area and isolation, Hanski has developed more complex theory to deal with the realism that makes ecological studies such a challenge. These extensions consider aspects such as population dynamics in local populations and stochastic variation. Along with the theoretical development, Hanski has also performed outstanding field studies, the most important being done on a butterfly (Melitaea cinxia) and its host plants in the Aland archipelago. For conservation biologists, Hanski’s studies have provided a tool box for analyzing how species are affected by habitat change and fragmentation. As habitat loss is considered as the major factor behind biodiversity decline and species extinction, the metapopulation theory has become a cornerstone of conservation biology. One major insight for conservation biology is the concept of “extinction debt” relating to the time delay between habitat loss and the extinction of a species which is particularly long when it is close to its extinction threshold. Metapopulation theory has also led to further developments of ecological theory concerned with spatial aspects of whole communities and ecosystems—metacommunityecology and meta-ecosystemecology—no doubt providing us with important new insights on the spatial dimension of the dynamics of ecological systems. In particular, metacommunity theory has developed into a rich theory studying the effects of trade-offs related to colonization and competitive ability, species-specific responses to environmental heterogeneity, stochastic demographic processes and dispersal limitation on species diversity in heterogeneous landscapes.