Population Survival Probability Research Articles

Evolutionary rescue under demographic and environmental stochasticity.

Populations suffer two types of stochasticity: demographic stochasticity, from sampling error in offspring number, and environmental stochasticity, from temporal variation in the growth rate. By modelling evolution through phenotypic selection following an abrupt environmental change, we investigate how genetic and demographic dynamics, as well as effects on population survival of the genetic variance and of the strength of stabilizing selection, differ under the two types of stochasticity. We show that population survival probability declines sharply with stronger stabilizing selection under demographic stochasticity, but declines more continuously when environmental stochasticity is strengthened. However, the genetic variance that confers the highest population survival probability differs little under demographic and environmental stochasticity. Since the influence of demographic stochasticity is stronger when population size is smaller, a slow initial decline of genetic variance, which allows quicker evolution, is important for population persistence. In contrast, the influence of environmental stochasticity is population-size-independent, so higher initial fitness becomes important for survival under strong environmental stochasticity. The two types of stochasticity interact in a more than multiplicative way in reducing the population survival probability. Our work suggests the importance of explicitly distinguishing and measuring the forms of stochasticity during evolutionary rescue.

Survival probability and size of lineages in antibody affinity maturation.

Affinity maturation (AM) is the process through which the immune system is able to develop potent antibodies against new pathogens it encounters, and is at the base of the efficacy of vaccines. At its core AM is analogous to a Darwinian evolutionary process, where B cells mutate and are selected on the base of their affinity for an antigen (Ag), and Ag availability tunes the selective pressure. In cases when this selective pressure is high, the number of B cells might quickly decrease and the population might risk extinction in what is known as a population bottleneck. Here we study the probability for a B-cell lineage to survive this bottleneck scenario as a function of the progenitor affinity for the Ag. Using recursive relations and probability generating functions we derive expressions for the average extinction time and progeny size for lineages that go extinct. We then extend our results to the full population, both in the absence and presence of competition for T-cell help, and quantify the population survival probability as a function of Ag concentration and initial population size. Our study suggests the population bottleneck phenomenology might represent a limit case in the space of biologically plausible maturation scenarios, whose characterization could help guide the process of vaccine development.

Factors affecting the crop damage by wild boar (Sus scrofa) and effects of population control in the Ticino and Lake Maggiore Park (North-western Italy)

Wild boar foraging impacts the crops, pastures, and meadows causing remarkable losses to agricultural income. Protected areas located in plains, such as the Ticino Valley Natural Park, are characterized by the coexistence of important natural habitats and intensive agricultural areas. In the Park, from 2010 to 2017, 49% of the complaints report an event of damage to maize and 43% to meadows. The total expense for reimbursements of the maize amounted to € 439,341.52, with damages concentrated in May, after sowing period and between August and September, during the milky stage of maize. For meadows reimbursements amounted to € 324,768.66, with damage events concentrated in February and March. To reduce damage to crops, the Park administration carried out lethal control of the wild boar population. From 2006 to 2017, the most used control method was culling from hunting hides. In our analysis, we did not find significant relationships between the number of shot boars and the damage amount. The factors that determine the decrease of damage probability to crops are mainly related to human disturbance and the characteristics of the fields. The predictive model of damage risk built comparing damaged and undamaged fields showed a good predictive ability. The population viability analyses showed that it is impossible to obtain a drastic reduction of population with the current harvest rate. By tripling it and focusing on the females and sub-adult a numerical reduction of 50% of the population would be achievable in 7 years and the probability of population survival would be halved in 3 years.

Impacts and Potential Mitigation of Road Mortality for Hedgehogs in Europe.

Simple SummaryThe environmental impacts of transport infrastructure are attracting substantial research focus and road-induced mortality of wildlife is perhaps the most conspicuous impact of roads. Hedgehogs are a common victim of traffic collisions in Europe and several hedgehog species are showing marked population declines across their range. This review aims to consolidate current knowledge on the impacts of road mortality on the viability of populations of the five hedgehog species in Europe and identify research gaps. Previous studies have shown that roads are a major source of mortality for hedgehogs and that individuals with greater net movement, generally males, have the greatest likelihood of mortality. Road mortality also contributes to population isolation. More research is needed into how different individuals perceive, use and cross roads, as well as the efficacy of different mitigation measures (e.g., wildlife crossing structures) designed to reduce road mortality and population isolation. Assessing whether local hedgehog populations are at risk of extirpation or further declines due to road mortality is a prerequisite for effective conservation in environments affected by continuously developing road networks.Transport infrastructure is a pervasive element in modern landscapes and continues to expand to meet the demands of a growing human population and its associated resource consumption. Road-induced mortality is often thought to be a major contributor to the marked declines of European hedgehog populations. This review synthesizes available evidence on the population-level impacts of road mortality and the threat to population viability for the five hedgehog species in Europe. Local and national studies suggest that road mortality can cause significant depletions in population sizes, predominantly removing adult males. Traffic collisions are a probable cause of fragmentation effects, subsequently undermining ecological processes such as dispersal, as well as the genetic variance and fitness of isolated populations. Further studies are necessary to improve population estimates and explicitly examine the consequences of sex- and age-specific mortality rates. Hedgehogs have been reported to use crossing structures, such as road tunnels, yet evaluations of mitigation measures for population survival probability are largely absent. This highlights the need for robust studies that consider population dynamics and genetics in response to mitigation. In light of ongoing declines of hedgehog populations, it is paramount that applied research is prioritised and integrated into a holistic spatial planning process.

High mortality and small population size prevent population recovery of a reintroduced mesopredator

AbstractNorthern Australia's native mammal fauna has undergone a severe decline in recent decades. Putative factors include altered fire regimes, cat predation, poisoning by cane toads and disease. Populations of northern quolls, Dasyurus hallucatus severely declined following cane toad invasion and have not recovered. We monitored a population of northern quolls in Kakadu National Park that was supplemented with ‘toad‐smart’ individuals, to determine whether cane toad poisoning or predation was preventing population recovery. The population increased after supplementation, but crashed in March 2012, coincident with a high level of trap disturbance by canids. Canid predation was the major source of mortality for radio‐tagged quolls. We used population viability analyses (PVA) to explore how changes in mortality influenced the likelihood of extinction. With no management, the quoll population has a 48% chance of extinction over the next 20 years. Sensitivity analyses highlighted small population size and high mortality as the main reasons for the population failing to recover. We then explored whether population supplementation or reducing mortality could increase the likelihood of persistence. One year of supplementation increased the probability of population survival over 20 years from 51.6% to 81.7%. Continuing supplementation for 3 or 5 years increased the probability of population survival to 96.5% and 98.1% respectively. Similarly, a 2.5% reduction in the rate of mortality for juveniles and adult females increased the probability of population persistence over 20 years to 83.6%. Further reductions in mortality of 5% and 10% increased the probability of survival to 92.2% and 99.4% respectively. The results of the PVA suggest that small interventions could have a significant positive effect on population survival. We hypothesize that predation from food‐subsidized canids is preventing the recovery of quoll populations. Future management actions to reduce mortality, via improved fire management, or through population supplementation, are necessary to ensure the persistence of the northern quoll.

Efficient estimation in two-stage randomized clinical trials using ranked sets

ABSTRACTClinical trials designed for survival probability estimation of different treatment policies for chronic diseases like cancer, leukemia, and schizophrenia usually need randomization of treatments in two stages. Since complete remission is rare for these diseases, initially an induction therapy is given for patient’s remission. Further treatment, which is often an expensive maintenance therapy, is administered only for the patients with remission. If the maintenance therapy is so expensive that the cost of the trial inflates, only a simple random sample of patients will be treated with the expensive maintenance due to budget constraint. In this article, we have implemented a design using ranked sets instead of simple randomization in the second stage and obtained an unbiased estimator of the overall survival distribution for a particular treatment combination. Through simulation studies under different conditions, we have found that the design we developed based on ranked sets gives an unbiased estimate of the population survival probability which is more efficient than the estimate obtained by the usual design.

Genetic Allee effects and their interaction with ecological Allee effects.

It is now widely accepted that genetic processes such as inbreeding depression and loss of genetic variation can increase the extinction risk of small populations. However, it is generally unclear whether extinction risk from genetic causes gradually increases with decreasing population size or whether there is a sharp transition around a specific threshold population size. In the ecological literature, such threshold phenomena are called 'strong Allee effects' and they can arise for example from mate limitation in small populations. In this study, we aim to (i) develop a meaningful notion of a 'strong genetic Allee effect', (ii) explore whether and under what conditions such an effect can arise from inbreeding depression due to recessive deleterious mutations, and (iii) quantify the interaction of potential genetic Allee effects with the well-known mate-finding Allee effect. We define a strong genetic Allee effect as a genetic process that causes a population's survival probability to be a sigmoid function of its initial size. The inflection point of this function defines the critical population size. To characterize survival-probability curves, we develop and analyse simple stochastic models for the ecology and genetics of small populations. Our results indicate that inbreeding depression can indeed cause a strong genetic Allee effect, but only if individuals carry sufficiently many deleterious mutations (lethal equivalents). Populations suffering from a genetic Allee effect often first grow, then decline as inbreeding depression sets in and then potentially recover as deleterious mutations are purged. Critical population sizes of ecological and genetic Allee effects appear to be often additive, but even superadditive interactions are possible. Many published estimates for the number of lethal equivalents in birds and mammals fall in the parameter range where strong genetic Allee effects are expected. Unfortunately, extinction risk due to genetic Allee effects can easily be underestimated as populations with genetic problems often grow initially, but then crash later. Also interactions between ecological and genetic Allee effects can be strong and should not be neglected when assessing the viability of endangered or introduced populations.

Massive diversification in aging colonies of Escherichia coli.

The evolutionary success of bacteria depends greatly on their capacity to continually generate phenotypic diversity. Structured environments are particularly favorable for diversification because of attenuated clonal interference, which renders selective sweeps nearly impossible and enhances opportunities for adaptive radiation. We examined at the microscale level the emergence and the spatial and temporal dynamics of phenotypic diversity and their underlying causes in Escherichia coli colonies. An important dynamic heterogeneity in the growth, metabolic activity, morphology, gene expression patterns, stress response induction, and death patterns among cells within colonies was observed. Genetic analysis indicated that the phenotypic variation resulted mostly from mutations and that indole production, oxidative stress, and the RpoS-regulated general stress response played an important role in the generation of diversity. We observed the emergence and persistence of phenotypic variants within single colonies that exhibited variable fitness compared to the parental strain. Some variants showed improved capacity to produce biofilms, whereas others were able to use different nutrients or to tolerate antibiotics or oxidative stress. Taken together, our data show that bacterial colonies provide an ecological opportunity for the generation and maintenance of vast phenotypic diversity, which may increase the probability of population survival in unpredictable environments.

Predicting population survival under future climate change: density dependence, drought and extraction in an insular bighorn sheep

1. Our understanding of the interplay between density dependence, climatic perturbations, and conservation practices on the dynamics of small populations is still limited. This can result in uninformed strategies that put endangered populations at risk. Moreover, the data available for a large number of populations in such circumstances are sparse and mined with missing data. Under the current climate change scenarios, it is essential to develop appropriate inferential methods that can make use of such data sets. 2. We studied a population of desert bighorn sheep introduced to Tiburon Island, Mexico in 1975 and subjected to irregular extractions for the last 10 years. The unique attributes of this population are absence of predation and disease, thereby permitting us to explore the combined effect of density dependence, environmental variability and extraction in a 'controlled setting.' Using a combination of nonlinear discrete models with long-term field data, we constructed three basic Bayesian state space models with increasing density dependence (DD), and the same three models with the addition of summer drought effects. 3. We subsequently used Monte Carlo simulations to evaluate the combined effect of drought, DD, and increasing extractions on the probability of population survival under two climate change scenarios (based on the Intergovernmental Panel on Climate Change predictions): (i) increase in drought variability; and (ii) increase in mean drought severity. 4. The population grew from 16 individuals introduced in 1975 to close to 700 by 1993. Our results show that the population's growth was dominated by DD, with drought having a secondary but still relevant effect on its dynamics. 5. Our predictions suggest that under climate change scenario (i), extraction dominates the fate of the population, while for scenario (ii), an increase in mean drought affects the population's probability of survival in an equivalent magnitude as extractions. Thus, for the long-term survival of the population, our results stress that a more variable environment is less threatening than one in which the mean conditions become harsher. Current climate change scenarios and their underlying uncertainty make studies such as this one crucial for understanding the dynamics of ungulate populations and their conservation.

Genetic and demographic consequences of importing animals into a small population: a simulation model of the Texas State Bison Herd (USA)

The extant 40 bison ( Bison bison) constituting the Texas State Bison Herd (TSBH; USA) are directly and exclusively descended from a bison herd assembled by Charles Goodnight in the 1880s, representing a historically and genetically valuable resource. The population currently suffers from low genetic variation, low heterozygosity, high calf mortality, and low natality rates compared with other closed bison populations. Population viability analysis using the VORTEX program previously indicated a 99% chance of population extinction within the next 41 years [J. Mamm. 85 (2004) in press]. We developed a stochastic simulation model to evaluate the genetic and demographic consequences of various management scenarios for the TSBH using genotypic data from 51 microsatellite loci and demographic information recorded over a 6-year period. Our results reveal that without the introduction of new genetic variation, approximately 37% of the representative microsatellite loci will become fixed as the TSBH continues to lose genetic variation at a staggering rate of 30–40% within the next 50 years. Furthermore, if the current trends in natality and mortality rates continue, our model indicates the TSBH faces a 99% chance of extinction in the next 51 years. With the importation of unrelated male bison into the TSBH, and under the assumption of increased fitness, the probability of population survival in the next 100 years increases to 100%, and the population will reach the approximate carrying capacity of 200 bison in 15–16 years. Furthermore, our model predicts increases in genetic diversity and heterozygosity of 24.7–48.4% and 17.5–36.5%, respectively, in the next 100 years following the addition of new genetic variation. We conclude that the importation of bison into the TSBH is necessary to prevent extinction and ensure long-term population survival.

The impact of inbreeding depression on population survival depending on demographic parameters

Inbreeding depression is a critical phenomenon for conservation of small populations, especially concerning the captive breeding of endangered animals whose effective population size may be very low. In order to manage such captive populations on a long-term basis, assessment of the interactions between demographic and genetic parameters and their consequences on the population survival probability is essential. Therefore, we examined (1) the relative importance of initial population size and carrying capacity on the survival probability of a population, (2) the impact of a bottleneck in an already inbred population. For this purpose, a stochastic model taking into account the effect of genes responsible for inbreeding depression was built. It was concluded that the population survival probability is very sensitive to the carrying capacity. Moreover, in inbred populations, a large increase in the extinction rate results from a second bottleneck. With two founders, survival is high as long as the carrying capacity is not very small (above a few decades), whereas a second bottleneck has a dramatic effect, even when the carrying capacity approaches 100. Consequently, previous inbreeding should be considered in the case of reintroduction. Reason for reintroduction failure could be successive bottlenecks, with the associated deleterious effects of inbreeding.

Estimation of infant mortality and life expectancy in the time of the Roman Empire: a methodological examination

The first available written source in human history relating to the description of the life expectancy of a living population is a legal text which originates from the Roman jurist Ulpianus (murdered in AD 228). In contrast to the prevailing opinion in demography I not only do consider the text to be of `historical interest...but to be a document of inestimable worth for evaluating the population survival probability in the Roman empire. The criteria specified by Ulpianus are in line with the `pan-human survival function as described by modern model life tables when based on adulthood. Values calculated from tomb inscriptions follow the lowest level of the model life tables as well and support Ulpianus statements. The specifications by Ulpianus for the population of the Roman world empire as a whole in the `best fit with modern life tables lead to an average level of 20 years of life expectancy. As a consequence a high infant mortality rate of almost 400 [per thousand] can be concluded resulting in no more than three children at the age of five in an average family in spite of a high fertility rate. (EXCERPT) (SUMMARY IN ENG)

INCREASED PROBABILITY OF EXTINCTION DUE TO DECREASED GENETIC EFFECTIVE POPULATION SIZE: EXPERIMENTAL POPULATIONS OF CLARKIA PULCHELLA.

We established replicated experimental populations of the annual plant Clarkia pulchella to evaluate the existence of a causal relationship between loss of genetic variation and population survival probability. Two treatments differing in the relatedness of the founders, and thus in the genetic effective population size (Ne ), were maintained as isolated populations in a natural environment. After three generations, the low Ne treatment had significantly lower germination and survival rates than did the high Ne treatment. These lower germination and survival rates led to decreased mean fitness in the low Ne populations: estimated mean fitness in the low Ne populations was only 21% of the estimated mean fitness in the high Ne populations. This inbreeding depression led to a reduction in population survival: at the conclusion of the experiment, 75% of the high Ne populations were still extant, whereas only 31% of the low Ne populations had survived. Decreased genetic effective population size, which leads to both inbreeding and the loss of alleles by genetic drift, increased the probability of population extinction over that expected from demographic and environmental stochasticity alone. This demonstrates that the genetic effective population size can strongly affect the probability of population persistence.

Marginality: scale determined processes and the conservation of the British butterfly fauna

Marginality describes the impact that environmental and landscape factors have in decreasing the probability of population survival and persistence. It may be imposed by extreme conditions or resource scarcity. Typically, it affects populations at the range edge but can also affect populations within the core of ranges, and produces a number of symptoms: characteristically demographic, but also morphological, physiological, biochemical and genetic. In this paper, the causes and effects of marginality on British butterflies are compared in edge and centre of range populations. Issues of temporal and spatial scales are examined, as is the relevance of marginality to the conservation of single and multiple species populations. The recognition of marginality questions the appropriateness of many so-called spatially realistic models of populations and highlights areas of research which have hitherto been ignored. Projected changes in land use and climate have implications for marginality in core and peripheral populations; in view of this, current scales of mapping are found to be unsuitable for monitoring fragmentation and the increasing marginalization of butterfly species in the British landscape.

Population Viability Analysis for a Small Population of Red‐Cockaded Woodpeckers and an Evaluation of Enhancement Strategies

We performed a series of population and pedigree analyses to examine the viability of a small Red‐cockaded Woodpecker (Picoides borealis) population located at the Savannah River Site, in Barnwell and Aiken counties of South Carolina. The population’s existence and future survival are precarious. As few as four individuals, including just one breeding pair, comprised this population in 1985. Now, primarily because of experimental transformation of birds from other areas, the population has increased to 25. As of 1990, genealogy pedigree analysis showed that the respective contribution of 14 founders to the extant population has not been equal. Founder gender equivalents are low (5.4) but could reach 9.2 if poorly‐represented founders were to produce offspring. The fraction of founder gene diversity retained in the current population is 0.91. Successful recovery strategies would ensure 95% probability of population survival while maintaining 90% heterozygosity for 200 years. Viability analyses indicated that, depending on relative effects of inbreeding depression and stochastic environmental events, the Savannah River Site population has a 68–100% chance of extinction during this period. Annual translocation into the population of at least three females and two males for a 10‐year period will achieve a 96% probability of survival for 200 years. Even with translocation of numerous males and females per year (up to 50 of each), the 90% heterozygosity goal may not be achieved. We discuss recommendations for choosing individuals for translocation logistical constraints on achieving recovery objectives, and limitations of our modeling approach.

Spatial characteristics of habitat patches and population survival

The effect of the spatial arrangement of habitat patches on the survival of resident populations were considered in a stochastic model using population parameters appropriate to Peromyscus leucopus. The 34 possible arrangements of connections among five otherwise identical patches were simulated in order to determine the survival probabilities and population sizes. The main findings are that populations in completely isolated patches have lower survival probabilities than those in patches that are connected to other patches, are connected to the survival probabilities of populations in connected patches increases with the size of the largest geometric figure of which the patch is a part. The results are discussed in the context of resource management.

On the minimum size of endogamous populations.

Abstract The survival of small endogamous human populations is investigated by computer simulation. It is shown that (1) populations practicing strict monogamy with no extramarital pregnancy are less likely to survive as endogamous groups than are those in which marriage is not a prerequisite for childbearing ; (2) low fertility—low mortality populations can survive with fewer individuals than can populations subject to high fertility and mortality; (3) avoidance of close consanguinity reduces the probability of population survival, but the effect is much greater when fertility and mortality are low. In addition, an attempt is made to determine which demographic characteristics are likely to be the best predictors of potential population decline or disruption.