Predicting extinction risks for plants: environmental stochasticity can save declining populations

An emerging generalization from theoretical and empirical studies on conservation biology is that high levels of environmental stochasticity increase the likelihood of population extinction. However, coexistence theory has illustrated that there are circumstances under which environmental stochasticity can increase the chance of population persistence. These theoretical studies have shown that the sign of the effect of environmental stochasticity on population persistence is determined by interactions between life history and environmental stochasticity. These interactions mean that the stochastic and deterministic rates of population growth might differ fundamentally. Although difficult to demonstrate in real systems, observed life histories and variance in the vital rates of populations suggest that this phenomenon is likely to be common, and is therefore of much relevance to conservation biologists.     

An Assessment of the Annual Mortality Rate and Population Demographics Status in Birds Based on Ring-Recovery Data

A new method for assessing the annual mortality rate in bird populations is described. Ring recoveries from birds that died from various causes serve as the basis for such an assessment. The commonly accepted technique for such an assessment performed with the help of MARK software is laborious, yet fails to ensure a highly precise assessment. To calculate the mortality rate, we propose an exponential demographic model that is based on the geometric progression of a decrease in the annual numbers in some arbitrarily selected set of birds in a population. The equation of the model allows calculating the annual mortality rate of a bird population or even a species in a simple way, if the ringing data covers a vast area, for example, the territory of Russia. In addition, the proposed equation permits producing “a mortality pattern,” namely, to present a chart of interrelations between the theoretical and real rates of the decrease in numbers in a given cohort of birds. The interrelations between the theoretical and real annual mortality rates allow understanding the status of a bird population each year during a period of ringing and recovery collecting: this makes it possible to reveal the population trend about whether the population is stable or decreasing or increasing in numbers.     

INVITED REVIEW: What is a population? An empirical evaluation of some genetic methods for identifying the number of gene pools and their degree of connectivity

We review commonly used population definitions under both the ecological paradigm (which emphasizes demographic cohesion) and the evolutionary paradigm (which emphasizes reproductive cohesion) and find that none are truly operational. We suggest several quantitative criteria that might be used to determine when groups of individuals are different enough to be considered 'populations'. Units for these criteria are migration rate (m) for the ecological paradigm and migrants per generation (Nm) for the evolutionary paradigm. These criteria are then evaluated by applying analytical methods to simulated genetic data for a finite island model. Under the standard parameter set that includes L = 20 High mutation (microsatellite-like) loci and samples of S = 50 individuals from each of n = 4 subpopulations, power to detect departures from panmixia was very high ( approximately 100%; P < 0.001) even with high gene flow (Nm = 25). A new method, comparing the number of correct population assignments with the random expectation, performed as well as a multilocus contingency test and warrants further consideration. Use of Low mutation (allozyme-like) markers reduced power more than did halving S or L. Under the standard parameter set, power to detect restricted gene flow below a certain level X (H(0): Nm < X) can also be high, provided that true Nm < or = 0.5X. Developing the appropriate test criterion, however, requires assumptions about several key parameters that are difficult to estimate in most natural populations. Methods that cluster individuals without using a priori sampling information detected the true number of populations only under conditions of moderate or low gene flow (Nm < or = 5), and power dropped sharply with smaller samples of loci and individuals. A simple algorithm based on a multilocus contingency test of allele frequencies in pairs of samples has high power to detect the true number of populations even with Nm = 25 but requires more rigorous statistical evaluation. The ecological paradigm remains challenging for evaluations using genetic markers, because the transition from demographic dependence to independence occurs in a region of high migration where genetic methods have relatively little power. Some recent theoretical developments and continued advances in computational power provide hope that this situation may change in the future.     

Population growth lags in introduced species

When introduced to new ecosystems, species'' populations often grow immediately postrelease. Some introduced species, however, maintain a low population size for years or decades before sudden, rapid population growth is observed. Because exponential population growth always starts slowly, it can be difficult to distinguish species experiencing the early phases of slow exponential population growth (inherent lags) from those with actively delayed growth rates (prolonged lags). Introduced ungulates provide an excellent system in which to examine lags, because some introduced ungulate populations have demonstrated rapid population growth immediately postintroduction, while others have not. Using studies from the literature, we investigated which exotic ungulate species and populations (n = 36) showed prolonged population growth lags by comparing the doubling time of real ungulate populations to those predicted from exponential growth models for theoretical populations. Having identified the specific populations that displayed prolonged lags, we examined the impacts of several environmental and biological variables likely to influence the length of lag period. We found that seventeen populations (47%) showed significant prolonged population growth lags. We could not, however, determine the specific factors that contributed to the length of these lag phases, suggesting that these ungulate populations'' growth is idiosyncratic and difficult to predict. Introduced species that exhibit delayed growth should be closely monitored by managers, who must be proactive in controlling their growth to minimize the impact such populations may have on their environment.     

A general modeling framework for describing spatially structured population dynamics

Variation in movement across time and space fundamentally shapes the abundance and distribution of populations. Although a variety of approaches model structured population dynamics, they are limited to specific types of spatially structured populations and lack a unifying framework. Here, we propose a unified network‐based framework sufficiently novel in its flexibility to capture a wide variety of spatiotemporal processes including metapopulations and a range of migratory patterns. It can accommodate different kinds of age structures, forms of population growth, dispersal, nomadism and migration, and alternative life‐history strategies. Our objective was to link three general elements common to all spatially structured populations (space, time and movement) under a single mathematical framework. To do this, we adopt a network modeling approach. The spatial structure of a population is represented by a weighted and directed network. Each node and each edge has a set of attributes which vary through time. The dynamics of our network‐based population is modeled with discrete time steps. Using both theoretical and real‐world examples, we show how common elements recur across species with disparate movement strategies and how they can be combined under a unified mathematical framework. We illustrate how metapopulations, various migratory patterns, and nomadism can be represented with this modeling approach. We also apply our network‐based framework to four organisms spanning a wide range of life histories, movement patterns, and carrying capacities. General computer code to implement our framework is provided, which can be applied to almost any spatially structured population. This framework contributes to our theoretical understanding of population dynamics and has practical management applications, including understanding the impact of perturbations on population size, distribution, and movement patterns. By working within a common framework, there is less chance that comparative analyses are colored by model details rather than general principles.     

Quantal Behavior of a Diffusible Factor Which Initiates Septum Formation at Potential Division Sites in Escherichia coli

Analysis of nucleated cell size in a minicell-producing strain of Escherichia coli and in its parental strain shows that the two distributions are considerably different. A model is proposed to account for this difference. The model states that: (i) in the mutant population, the cell poles are available as potential division sites in addition to the normally located division sites; (ii) the probability of a division occurring at any of the potential division sites is equal; and (iii) only enough "division factor" arises at each unit cell doubling to permit a single division. This factor is utilized entirely in the formation of a single septum. Thus, the occurrence of a polar division with the production of an anucleate minicell (which occurs only in the mutant strain) prevents the occurrence of a non-polar division, with the result that the average nucleated cell length is increased in minicell-producing strains. The model has been used to construct a theoretical population, and a number of parameters of the real and theoretical populations have been compared. The two populations are very similar in all of the parameters measured.     

When domestic cat (Felis silvestris catus) population structures interact with their viruses

Many theoretical studies have proposed different causal mechanisms by which the structure of a host population could have important implications for life history traits of pathogens. However, little information is available from real systems to test these hypotheses. The domestic cat, Felis silvestris catus, whose populations exhibit a great variability in social and spatial structure, represent an ideal case study to assess this question. In the present article, we show how cat population structure may have influenced the evolution of feline viruses and, in return, how these viruses may have modified the genetic structure of cat populations. To cite this article: D. Pontier et al., C. R. Biologies 332 (2009).     

Spatial dynamics of adaptive sex ratios

According to Fisherian sex allocation theory, parents that can adjust their offspring sex ratio in response to skews in population sex ratio will maximize their fitness over parents lacking this ability. There is good evidence that adaptive sex ratio adjustment occurs in many natural populations, but deviations from theoretical predictions have also been observed. These anomalies may be more apparent than real. When the spatial dimension of sex ratio variation is ignored, then a mismatch between empirical data and theoretical predictions based on panmictic mating is to be expected. We illustrate this with data on human sex ratio variation in 21 preindustrial populations, and with a cellular automaton model built to obey Fisherian sex allocation rules. The results from the model generally match with the data. When information about the ambient sex ratio is limited, then the sex allocation decisions may appear locally maladaptive. In general, the results indicate that Fisher's sex-ratio theory may have greater explanatory power than previously thought.     

Realized Sampling Variances of Estimates of Genetic Parameters and the Difference between Genetic and Phenotypic Correlations

A data set of 1572 heritability estimates and 1015 pairs of genetic and phenotypic correlation estimates, constructed from a survey of published beef cattle genetic parameter estimates, provided a rare opportunity to study realized sampling variances of genetic parameter estimates. The distribution of both heritability estimates and genetic correlation estimates, when plotted against estimated accuracy, was consistent with random error variance being some three times the sampling variance predicted from standard formulae. This result was consistent with the observation that the variance of estimates of heritabilities and genetic correlations between populations were about four times the predicted sampling variance, suggesting few real differences in genetic parameters between populations. Except where there was a strong biological or statistical expectation of a difference, there was little evidence for differences between genetic and phenotypic correlations for most trait combinations or for differences in genetic correlations between populations. These results suggest that, even for controlled populations, estimating genetic parameters specific to a given population is less useful than commonly believed. A serendipitous discovery was that, in the standard formula for theoretical standard error of a genetic correlation estimate, the heritabilities refer to the estimated values and not, as seems generally assumed, the true population values.     

Prediction of the human life expectancy

We have simulated demographic changes in the human population using the Penna microscopic model, based on the simple Monte Carlo method. The results of simulations have shown that during a few generations changes in the genetic pool of a population are negligible, while improving the methods of compensation of genetic defects or genetically determined proneness to many disorders drastically affects the average life span of organisms. Age distribution and mortality of the simulated populations correspond very well to real demographic data available from different countries. Basing on the comparison of structures of real human populations and the results of simulations it is possible to predict changes in the age structure of populations in the future.     

Linkage Disequilibrium Decay and Past Population History in the Human Genome

The fluctuation of population size has not been well studied in the previous studies of theoretical linkage disequilibrium (LD) expectation. In this study, an improved theoretical prediction of LD decay was derived to account for the effects of changes in effective population sizes. The equation was used to estimate effective population size (N_e) assuming a constant N_e and LD at equilibrium, and these N_e estimates implied the past changes of N_e for a certain number of generations until equilibrium, which differed based on recombination rate. As the influence of recent population history on the N_e estimates is larger than old population history, recent changes in population size can be inferred more accurately than old changes. The theoretical predictions based on this improved expression showed accurate agreement with the simulated values. When applied to human genome data, the detailed recent history of human populations was obtained. The inferred past population history of each population showed good correspondence with historical studies. Specifically, four populations (three African ancestries and one Mexican ancestry) showed population growth that was significantly less than that of other populations, and two populations originated from China showed prominent exponential growth. During the examination of overall LD decay in the human genome, a selection pressure on chromosome 14, the gephyrin gene, was observed in all populations.     

Spatial genetic structure in continuous and fragmented populations of Pinus pinaster Aiton

Habitat fragmentation, i.e., the reduction of populations into small isolated remnants, is expected to increase spatial genetic structure (SGS) in plant populations through nonrandom mating, lower population densities and potential aggregation of reproductive individuals. We investigated the effects of population size reduction and genetic isolation on SGS in maritime pine ( Pinus pinaster Aiton) using a combined experimental and simulation approach. Maritime pine is a wind-pollinated conifer which has a scattered distribution in the Iberian Peninsula as a result of forest fires and habitat fragmentation. Five highly polymorphic nuclear microsatellites were genotyped in a total of 394 individuals from two population pairs from the Iberian Peninsula, formed by one continuous and one fragmented population each. In agreement with predictions, SGS was significant and stronger in fragments ( Sp  = 0.020 and Sp  = 0.026) than in continuous populations, where significant SGS was detected for one population only ( Sp  = 0.010). Simulations suggested that under fat-tailed dispersal, small population size is a stronger determinant of SGS than genetic isolation, while under normal dispersal, genetic isolation has a stronger effect. SGS was always stronger in real populations than in simulations, except if unrealistically narrow dispersal and/or high variance of reproductive success were modelled (even when accounting for potential overestimation of SGS in real populations as a result of short-distance sampling). This suggests that factors such as nonrandom mating or selection not considered in the simulations were additionally operating on SGS in Iberian maritime pine populations.     

The population structure of south-central Bougainville

The technique of population structure analysis is described and then applied to blood polymorphic, anthropometric, and demographic data collected from residents of south-central Bougainville Island, Territory of New Guinea. The results from these various analyses are relatively consistent, and support the idea that this theoretical model can be applied successfully to real sets of biological data and that valid conclusions concerning the breeding structure of human populations can be reached. A comparison of breeding structures from various parts of the world reveals how sharply subdivided the breeding structure in Melanesia is, and how relatively rapidly the coefficient of kinship declines over distance in that area.     

THE EFFECTS OF POPULATION BOTTLENECKS ON CLONAL INTERFERENCE, AND THE ADAPTATION EFFECTIVE POPULATION SIZE

Clonal interference refers to the competition that arises in asexual populations when multiple beneficial mutations segregate simultaneously. A large body of theoretical and experimental work now addresses this issue. Although much of the experimental work is performed in populations that grow exponentially between periodic population bottlenecks, the theoretical work to date has addressed only populations of a constant size. We derive an analytical approximation for the rate of adaptation in the presence of both clonal interference and bottlenecks, and compare this prediction to the results of an individual-based simulation, showing excellent agreement in the parameter regime in which clonal interference prevails. We also derive an appropriate definition for the effective population size for adaptive evolution experiments in the presence of population bottlenecks. This "adaptation effective population size" allows for a good approximation of the expected rate of adaptation, either in the strong-selection weak-mutation regime, or when clonal interference comes into play. In the multiple mutation regime, when the product of the population size and mutation rate is extremely large, these results no longer hold.     

The use of agent-based modelling of genetics in conservation genetics studies

Animal Landscape and Man Simulation System a genetically explicit agent-based model was used to obtain measures for the genetic and demographic status of simulated populations. This investigation aimed to test the applicability of this approach for assessing the effect of environmental perturbations on populations’ temporal and spatial dynamics. This was achieved by assessing how three simple scenarios with increasing degree of environmental disturbance, simulated by populations bottlenecks repeated at different intervals, affected the genetic and demographic characteristics of the simulated population. Model outputs from a simplified landscape scenario concurred with theoretical expectations validating the model in a qualitative way. Differences in medians, means and coefficient of variation of the observed (H_o) and expected heterozygosity (H_e), population census size (N), effective population size (N_e), inbreeding coefficient (F) and N_e/N ratio were observed for simulated populations. Impacts occurred rapidly after simulated bottleneck events and genetic estimates were less variable, and therefore more reliable, than demographic estimates. Precise genetic consequences of the bottlenecks repeated at different intervals, and resulting population perturbations, are a complex balance between effects on population sub-structure, size and founding events. Agent-based models are appropriate tools to simulate these interactions, being sufficiently flexible to mimic real population processes under a range of environmental conditions. Such models incorporating explicit genetics provide a promising new approach to evaluate the impact of environmental changes on genetic composition of populations.     

Quantifying the extinction vortex

We developed a database of 10 wild vertebrate populations whose declines to extinction were monitored over at least 12 years. We quantitatively characterized the final declines of these well-monitored populations and tested key theoretical predictions about the process of extinction, obtaining two primary results. First, we found evidence of logarithmic scaling of time-to-extinction as a function of population size for each of the 10 populations. Second, two lines of evidence suggested that these extinction-bound populations collectively exhibited dynamics akin to those theoretically proposed to occur in extinction vortices. Specifically, retrospective analyses suggested that a population size of n individuals within a decade of extinction was somehow less valuable to persistence than the same population size was earlier. Likewise, both year-to-year rates of decline and year-to-year variability increased as the time-to-extinction decreased. Together, these results provide key empirical insights into extinction dynamics, an important topic that has received extensive theoretical attention.     

Structural perturbations to population skeletons: transient dynamics, coexistence of attractors and the rarity of chaos

BACKGROUND: Simple models of insect populations with non-overlapping generations have been instrumental in understanding the mechanisms behind population cycles, including wild (chaotic) fluctuations. The presence of deterministic chaos in natural populations, however, has never been unequivocally accepted. Recently, it has been proposed that the application of chaos control theory can be useful in unravelling the complexity observed in real population data. This approach is based on structural perturbations to simple population models (population skeletons). The mechanism behind such perturbations to control chaotic dynamics thus far is model dependent and constant (in size and direction) through time. In addition, the outcome of such structurally perturbed models is [almost] always equilibrium type, which fails to commensurate with the patterns observed in population data. METHODOLOGY/PRINCIPAL FINDINGS: We present a proportional feedback mechanism that is independent of model formulation and capable of perturbing population skeletons in an evolutionary way, as opposed to requiring constant feedbacks. We observe the same repertoire of patterns, from equilibrium states to non-chaotic aperiodic oscillations to chaotic behaviour, across different population models, in agreement with observations in real population data. Model outputs also indicate the existence of multiple attractors in some parameter regimes and this coexistence is found to depend on initial population densities or the duration of transient dynamics. Our results suggest that such a feedback mechanism may enable a better understanding of the regulatory processes in natural populations.     

Metapopulation Dynamics Enable Persistence of Influenza A,Including A/H5N1, in Poultry

Highly pathogenic influenza A/H5N1 has persistently but sporadically caused human illness and death since 1997. Yet it is still unclear how this pathogen is able to persist globally. While wild birds seem to be a genetic reservoir for influenza A, they do not seem to be the main source of human illness. Here, we highlight the role that domestic poultry may play in maintaining A/H5N1 globally, using theoretical models of spatial population structure in poultry populations. We find that a metapopulation of moderately sized poultry flocks can sustain the pathogen in a finite poultry population for over two years. Our results suggest that it is possible that moderately intensive backyard farms could sustain the pathogen indefinitely in real systems. This fits a pattern that has been observed from many empirical systems. Rather than just employing standard culling procedures to control the disease, our model suggests ways that poultry production systems may be modified.     

Population synchrony and environmental variation: an experimental demonstration

Understanding the causes of population synchrony is an important issue for population management. Its study in field populations involves disentangling the effects of dispersal and correlated environmental noise. Here we report on an experimental investigation of the synchronizing effects of noise in closed laboratory populations of a soil mite, Sancassania berlesei . Mite life-histories are highly plastic with respect to resource availability (which is a function of food supply and population density). By varying the food supply we imposed environmental variation. We show that (a) population synchrony is a function of environmental synchrony, (b) perceived population synchrony depends on the life-history stage counted, and (c) average population synchrony tends to be lower than environmental synchrony: even when populations were supplied with food with a correlation of 1.0, the correlation between populations was 0.63 (bootstrapped 95%CI 0.54–0.71). This supports recent theoretical work suggesting that the Moran theorem (indicating that population synchrony equals environmental synchrony) generally overestimates the population synchrony of nonlinear systems.     

Modelling problems in conservation genetics using Drosophila: consequences of fluctuating population sizes

Many natural populations fluctuate widely in population size. This is predicted to reduce effective population size, genetic variation, and reproductive fitness, and to increase inbreeding. The effects of fluctuating population size were examined in small populations of Drosophila melanogaster of the same average size, but maintained using either fluctuating ( FPS ) or equal ( EPS ) population sizes.FPS lines were maintained using seven pairs and one pair in alternate generations, and EPS lines with four pairs per generation. Ten replicates of each treatment were maintained. After eight generations, FPS had a higher inbreeding coefficient than EPS (0.60 vs. 0.38), a lower average allozyme heterozygosity (0.068 vs. 0.131), and a much lower relative fitness (0.03 vs. 0.25). Estimates of effective population sizes for FPS and EPS were 3.8 and 7.9 from pedigree inbreeding, and 4.9 vs. 7.1 from changes in average heterozygosities, as compared to theoretical expectations of 3.3 vs. 8.0. Results were generally in accordance with theoretical predictions. Management strategies for populations of rare and endangered species should aim to minimize population fluctuations over generations.