VORTEX: a computer simulation model for population viability analysis
TL;DR: PVA by simulation modelling is an important tool for identifying populations at risk of extinction, determining the urgency of action, and evaluating options for management, providing opportunity for more complete analysis than is possible by other techniques.
Abstract: Population Viability Analysis (PVA) is the estimation of extinction probabilities by analyses that incorporate identifiable threats to population survival into models of the extinction process. Extrinsic forces, such as habitat loss, over-harvesting, and competition or predation by introduced species, often lead to population decline. Although the traditional methods of wildlife ecology can reveal such deterministic trends, random fluctuations that increase as populations become smaller can lead to extinction even of populations that have, on average, positive population growth when below carrying capacity. Computer simulation modelling provides a tool for exploring the viability of populations subjected to many complex, interacting deterministic and random processes. One such simulation model, VORTEX, has been used extensively by the Captive Breeding Specialist Group (Species Survival Commission, IUCN), by wildlife agencies, and by university classes. The algorithms, structure, assumptions and applications of VORTEX are described in this paper. VORTEX models population processes as discrete, sequential events, with probabilistic outcomes. VORTEX simulates birth and death processes and the transmission of genes through the generations by generating random numbers to determine whether each animal lives or dies, to determine the number of progeny produced by each female each year, and to determine which of the two alleles at a genetic locus are transmitted from each parent to each offspring. Fecundity is assumed to be independent of age after an animal reaches reproductive age. Mortality rates are specified for each pre-reproductive age-sex class and for reproductive-age animals. Inbreeding depression is modelled as a decrease in viability in inbred animals. The user has the option of modelling density dependence in reproductive rates. As a simple model of density dependence in survival, a carrying capacity is imposed by a probabilistic truncation of each age class if the population size exceeds the specified carrying capacity. VORTEX can model linear trends in the carrying capacity. VORTEX models environmental variation by sampling birth rates, death rates, and the carrying capacity from binomial or normal distributions. Catastrophes are modelled as sporadic random events that reduce survival and reproduction for one year. VORTEX also allows the user to supplement or harvest the population, and multiple subpopulations can be tracked, with user-specified migration among the units. VORTEX outputs summary statistics on population growth rates, the probability of population extinction, the time to extinction, and the mean size and genetic variation in extant populations. VORTEX necessarily makes many assumptions. The model it incorporates is most applicable to species with low fecundity and long lifespans, such as mammals, birds and reptiles. It integrates the interacting effects of many of the deterministic and stochastic processes that have an impact on the viability of small populations, providing opportunity for more complete analysis than is possible by other techniques. PVA by simulation modelling is an important tool for identifying populations at risk of extinction, determining the urgency of action, and evaluating options for management.
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TL;DR: The small-population paradigm has not yet contributed significantly to conserving endangered species in the wild because it treats an erect (smallness) as if it were a cause and hence is of scant theoretical interest.
Abstract: Conservation biology has two threads: the small-population paradigm which deals with the erect of smallness on the persistence of a population, and the declining-population paradigm which deals with the cause of smallness and its cure. The processes relevant to the small-population paradigm are amenable to theoretical examination because they generalize across species and are subsumed by an inclusive higher category: stochasticity. In contrast, the processes relevant to the declining-population paradigm are essentially humdrum, being not one but many. So far they have defied tight generalization and hence are of scant theoretical interest. The small-population paradigm has not yet contributed significantly to conserving endangered species in the wild because it treats an erect (smallness) as if it were a cause
2,110 citations
Cites background or methods from "VORTEX: a computer simulation model..."
...Note that these mistakes are not made by the writers of these programs [see Lacy (1993) for a clear exposition of the limitations of such software]....
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...Note that these mistakes are not made by the writers of these programs [see Lacy (1993) for a clear exposition of the limitations...
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...I have inferred its substance from the manual (Lacy & Kreeger 1992), from a recently published description of the program (Lacy 1993), from the 'readme' file of version 5....
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TL;DR: Application of empirical estimates of the properties of spontaneous deleterious mutations leads to the conclusion that populations with effective sizes smaller than 100 are highly vulnerable to extinction via a mutational meltdown on timescales of approximately 100 generations.
Abstract: Although extensive work has been done on the relationship between population size and the risk of extinction due to demographic and environmental stochasticity, the role of genetic deterioration in the extinction process is poorly understood. We develop a general theoretical approach for evaluating the risk of small populations to extinction via the accumulation of mildly deleterious mutations, and we support this with extensive computer simulations. Unlike previous attempts to model the genetic consequences of small population size, our approach is genetically explicit and fully accounts for the mutations inherited by a founder population as well as those introduced by subsequent mutation. Application of empirical estimates of the properties of spontaneous deleterious mutations leads to the conclusion that populations with effective sizes smaller than 100 (and actual sizes smaller than 1,000) are highly vulnerable to extinction via a mutational meltdown on timescales of approximately 100 generations. We ...
906 citations
Book•
01 Jan 1993
TL;DR: A framework for risk assessment using the Exonential model for population growth, the logistic equation and magpie geese as a model for suburban shrews, and other forms of density dependence.
Abstract: A framework for risk assessment. A probabilistic framework. Causes of Extinction. Summary. White rhinoceros on Ndumu. Formulating a birth-and death model. Parameters and initial condition. The deterministic prediction. Adding demographic stochasticity. Introducing a population ceiling. Removing constant numbers. Environmental variation. Risk Assessment. Summary. Useful methods when data are scarce. The Exonential model for population growth. Density dependence, the logistic equation and magpie geese. Other forms of density dependence. A model for suburban shrews. More about unstructured models. Summary. Structured populations. Age structure. The Leslie matrix. Stage structure. Simulating variability. Correlation and authocorrelation. Migration and dispersal. Density and dependence. Conclusion. Summary. Spatial structure and metapopulation dynamics. Conservation of spatial structure. Occupancy models. Population dynamic model. Summary. Conservation genetics. Consequences of loss of genetic diversity. Drift, risk and genetic diversity. The effects of inbreeding on population dynamics. Stochastic model for Banksia Cunteata. The genetics of metapopulations. Summary. Extensions of risk assessment. Appendices. Reference. Index. Conclusions. Random numbers. Random events and correlated random numbers. More about sensitivity analysis. References. Index.
754 citations
TL;DR: It is found that PVA predictions were surprisingly accurate, the risk of population decline closely matched observed outcomes, there was no significant bias, and population size projections did not differ significantly from reality.
Abstract: Population viability analysis (PVA) is widely applied in conservation biology to predict extinction risks for threatened species and to compare alternative options for their management. It can also be used as a basis for listing species as endangered under World Conservation Union criteria. However, there is considerable scepticism regarding the predictive accuracy of PVA, mainly because of a lack of validation in real systems. Here we conducted a retrospective test of PVA based on 21 long-term ecological studies--the first comprehensive and replicated evaluation of the predictive powers of PVA. Parameters were estimated from the first half of each data set and the second half was used to evaluate the performance of the model. Contrary to recent criticisms, we found that PVA predictions were surprisingly accurate. The risk of population decline closely matched observed outcomes, there was no significant bias, and population size projections did not differ significantly from reality. Furthermore, the predictions of the five PVA software packages were highly concordant. We conclude that PVA is a valid and sufficiently accurate tool for categorizing and managing endangered species.
601 citations
TL;DR: It is concluded that population regulation, density dependence, resource and interference competition, the effects of environmental stress and the form of the ecological niche, are all best defined and analysed in terms of population growth rate.
Abstract: We argue that population growth rate is the key unifying variable linking the various facets of population ecology. The importance of population growth rate lies partly in its central role in forecasting future population trends; indeed if the form of density dependence were constant and known, then the future population dynamics could to some degree be predicted. We argue that population growth rate is also central to our understanding of environmental stress: environmental stressors should be defined as factors which when first applied to a population reduce population growth rate. The joint action of such stressors determines an organism's ecological niche, which should be defined as the set of environmental conditions where population growth rate is greater than zero (where population growth rate = r = log(e)(N(t+1)/N(t))). While environmental stressors have negative effects on population growth rate, the same is true of population density, the case of negative linear effects corresponding to the well-known logistic equation. Following Sinclair, we recognize population regulation as occurring when population growth rate is negatively density dependent. Surprisingly, given its fundamental importance in population ecology, only 25 studies were discovered in the literature in which population growth rate has been plotted against population density. In 12 of these the effects of density were linear; in all but two of the remainder the relationship was concave viewed from above. Alternative approaches to establishing the determinants of population growth rate are reviewed, paying special attention to the demographic and mechanistic approaches. The effects of population density on population growth rate may act through their effects on food availability and associated effects on somatic growth, fecundity and survival, according to a 'numerical response', the evidence for which is briefly reviewed. Alternatively, there may be effects on population growth rate of population density in addition to those that arise through the partitioning of food between competitors; this is 'interference competition'. The distinction is illustrated using a replicated laboratory experiment on a marine copepod, Tisbe battagliae. Application of these approaches in conservation biology, ecotoxicology and human demography is briefly considered. We conclude that population regulation, density dependence, resource and interference competition, the effects of environmental stress and the form of the ecological niche, are all best defined and analysed in terms of population growth rate.
479 citations
References
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Book•
01 Jan 1981
TL;DR: The genetic constitution of a population: Hardy-Weinberg equilibrium and changes in gene frequency: migration mutation, changes of variance, and heritability are studied.
Abstract: Part 1 Genetic constitution of a population: Hardy-Weinberg equilibrium. Part 2 Changes in gene frequency: migration mutation. Part 3 Small populations - changes in gene frequency under simplified conditions. Part 4 Small populations - less simplified conditions. Part 5 Small populations - pedigreed populations and close inbreeding. Part 6 Continuous variation. Part 7 Values and means. Part 8 Variance. Part 9 Resemblance between relatives. Part 10 Heritability. Part 11 Selection - the response and its prediction. Part 12 Selection - the results of experiments. Part 13 Selection - information from relatives. Part 14 Inbreeding and crossbreeding - changes of mean value. Part 15 Inbreeding and crossbreeding - changes of variance. Part 16 Inbreeding and crossbreeding - applications. Part 17 Scale. Part 18 Threshold characters. Part 19 Correlated characters. Part 20 Metric characters under natural selection.
20,288 citations
8,446 citations
TL;DR: An introduction to population genetics theory, An introduction to Population Genetics Theory, Population Genetics theory, Population genetics theory as discussed by the authors, Population genetics, population genetics, and population genetics theories, Population Genetic Theory
Abstract: An introduction to population genetics theory , An introduction to population genetics theory , مرکز فناوری اطلاعات و اطلاع رسانی کشاورزی
4,817 citations
Book•
01 Jan 1970
TL;DR: An introduction to population genetics theory, An introduction to Population Genetics theory, and more.
Abstract: An introduction to population genetics theory , An introduction to population genetics theory , مرکز فناوری اطلاعات و اطلاع رسانی کشاورزی
4,273 citations