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

Directions in conservation biology

http://webpages.icav.up.pt/PTDC/BIA-BEC/099934/2008/papers/Frankham_2005_Biological_Conservation.pdf

Genetics and extinction

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 ...

Mutation accumulation and the extinction of small populations

▪ Abstract Inbreeding depression is of major concern in the management and conservation of endangered species. Inbreeding appears universally to reduce fitness, but its magnitude and specific effects are highly variable because they depend on the genetic constitution of the species or populations and on how these genotypes interact with the environment. Recent natural experiments are consistent with greater inbreeding depression in more stressful environments. In small populations of randomly mating individuals, such as are characteristic of many endangered species, all individuals may suffer from inbreeding depression because of the cumulative effects of genetic drift that decrease the fitness of all individuals in the population. In three recent cases, introductions into populations with low fitness appeared to restore fitness to levels similar to those before the effects of genetic drift. Inbreeding depression may potentially be reduced, or purged, by breeding related individuals. However, the Speke's ...

Inbreeding depression in conservation biology

Parasites are thought to provide a selective force capable of promoting genetic variation in natural populations. One rarely considered pathway for this action is via parasite-mediated selection against inbreeding. If parasites impose a fitness cost on their host and the offspring of close relatives have greater susceptibility to parasites due to the increased homozygosity that results from inbreeding, then parasite-mediated mortality may select against inbred individuals. This hypothesis has not yet been tested within a natural vertebrate population. Here we show that relatively inbred Soay sheep (Ovis aries), as assessed by microsatellite heterozygosity, are more susceptible to parasitism by gastrointestinal nematodes, with interactions indicating greatest susceptibility among adult sheep at high population density. During periods of high overwinter mortality on the island of Hirta, St. Kilda, Scotland, highly parasitised individuals were less likely to survive. More inbred individuals were also less likely to survive, which is due to their increased susceptibility to parasitism, because survival was random with respect to inbreeding among sheep that were experimentally cleared of their gastrointestinal parasite burden by anthelminthic treatment. As a consequence of this selection, average microsatellite heterozygosity increases with age in St. Kildan Soay sheep. We suggest that parasite-mediated selection acts to maintain genetic variation in this small island population by removing less heterozygous individuals.

Parasite-mediated selection against inbred Soay sheep in a free-living, island population

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.

VORTEX: a computer simulation model for population viability analysis

Small populations lose genetic variability because of genetic drift, and inbreeding within populations can further decrease individual variability. Lower variation depresses individual fitness, resistance to disease and parasites, and flexibility in coping with environmental challenges. Lower variation decreases mean fitness of populations (population growth rates), resilience, and long-term adaptability. Genetic drift can threaten viability of populations not just by depleting variation, but also by replacing natural selection as the predominant force driving evolutionary change. Although most genetic studies use laboratory or domesticated populations, evidence is accumulating that the effects of inbreeding are at least as severe on wild animals in natural habitats. Natural selection is expected to reduce the frequency of deleterious alleles in populations that persist through bottlenecks, but as yet there is little evidence for such purging of the genetic load in mammalian populations. No species of mammal has been shown to be unaffected by inbreeding. Genetic problems are contributing to the decline and vulnerability of at least several mammalian taxa. Genetic threats to population viability will be expressed through their effects on and interactions with demographic and ecological processes. Theoretical analyses, experimental tests, field studies, and conservation actions should recognize the fundamental interdependency of genetic and non-genetic processes affecting viability of populations.

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Importance of Genetic Variation to the Viability of Mammalian Populations

The structure of the VORTEX computer simulation model for population viability analysis is outlined. The program flow is described here in order to provide a detailed specification of the structure of a widely used population viability analysis model. VORTEX is an individual-based simulation program that models the effects of mean demographic rates, demographic stochasticity, environmental variation in demographic rates, catastrophes, inbreeding depression, harvest and supplementation, and metapop ulation structure on the viability of wildlife populations. The model facilitates analysis of density-dependent reproduction and changing habitat availability, and most demo graphic rates can optionally be specified as flexible functions of density, time, popula tion gene diversity, inbreeding, age, and sex. VORTEX projects changes in population size, age and sex structure, and genetic variation, as well as estimating probabilities and times to extinction and recolonization.

Structure of the VORTEX simulation model for population viability analysis

We conducted a field-based test of the widely available generic computer simulation model VORTEX for population viability analysis (PVA). The model was used to predict the abundance of three species of arboreal marsupials in a system of 39 remnant patches of Eucalyptus forest embedded within a 5050-ha area of exotic radiata pine (Pinus radiata) forest in southeastern Australia. The marsupial species were: greater glider (Petauroides volans), mountain brushtail possum (Trichosurus caninus), and common ringtail possum (Pseudocheirus peregrinus). Predictions were generated for scenarios in which: (1) the rate of exchange of animals between patches was varied, (2) different models for the migration of animals between habitat patches were invoked, (3) different levels of immigration (or dispersal) from a large, neighboring source area were simulated, (4) variations in habitat quality between remnant patches were incorporated in the model, and (5) the influence of the pine matrix surrounding the remnant patches...

Testing a simulation model for population viability analysis

We investigated the genetic and morphological status of an endemic subspecies of deer mice (  Peromyscus maniculatus anacapae) on Anacapa Island of California through mitochondrial DNA (mtDNA) analysis, morphometric discriminant function analysis, and population viability analysis. We sought to assist the development of a management plan that may include captive breeding, reintroduction, or translocation of mice following eradication of introduced rats. The genetic and morphological data were used to investigate whether the subspecies or populations on each of the three islets of Anacapa represent evolutionarily significant units for conservation. The status of the East Anacapa population was of particular concern because deer mice have recently been caught there following more than 15 years of no records of deer mice. Sequences of the mtDNA cytochrome oxidase c subunit II gene (COII ) indicated that the Anacapa subspecies had unique haplotypes not found on neighboring islands or the mainland and thus represents a distinct unit for conservation. Further, one of these haplotypes was shared among the islets, including most of the East Anacapa mice, suggesting that the East Anacapa population had either recovered from a severe bottleneck or had been recolonized by P. m. anacapae, but that it was not derived from other subspecies. Discriminant function analysis of morphological data also supported classification of the East Anacapa mice as P. m. anacapae. The mitochondrial mtDNA sequence data yielded estimates of two to seven migrants per generation among the Anacapa islets, suggesting a functioning metapopulation. Incorporating these data and information available on the life history and demographics of deer mice, we used a novel type of population viability analysis to develop a captive breeding and reintroduction plan for Anacapa deer mice should they be eradicated along with the rats. A sine wave was incorporated into the population viability analysis to simulate population size cyclicity. Our study provides baseline information needed for developing a comprehensive conservation and management plan for a threatened island endemic.




Resumen: Investigamos el estado genetico y morfologico del raton Peromyscus maniculatus anacapae de la isla Anacapa en California mediante un analisis del ADN mitocondrial, un analisis de funcion discriminante de los datos morfometricos y un analisis de viabilidad poblacional. Pretendimos colaborar con el desarrollo de un plan de manejo que podria incluir la reproduccion en cautiverio, la reintroduccion o el desplazamiento de ratones despues de la erradicacion de ratas introducidas. Los datos geneticos y morfologicos fueron utilizados para investigar si las subespecies o las poblaciones en cada una de las tres isletas de Anacapa representan unidades evolutivas significativas para la conservacion. El estado de la poblacion de Anacapa del Este fue de interes particular debido a la captura reciente de ratones, despues de 15 anos sin registros de esta especie. Las secuencias del gen citocromo oxidasa c subunidad II del ADNmt (COII ) indicaron que la subespecie de Anacapa tiene haplotipos unicos, que no se encuentran en las islas vecinas ni en tierra firme y, por lo tanto, representa una unidad unica para la conservacion. Mas aun, uno de estos haplotipos fue compartido entre las isletas, incluyendo la mayoria de los ratones de Anacapa del Este, lo que sugiere que la isla ha sido recolonizada por P. m. anacapae o que la poblacion de Anacapa del Este se ha recuperado de un cuello de botella severo pero que no ha derivado de otras subespecies. El analisis de funcion discriminante de los datos morfometricos tambien respalda la clasificacion de los ratones de Anacapa del Este como P. m. Anacapae. Los datos de secuencias del ADNmt proveen estimaciones de 2 a 7 migrantes por generacion entre las isletas Anacapa, lo que sugiere la presencia de una metapoblacion en funcionamiento. Con la incorporacion de estos datos y la informacion disponible sobre los antecedentes biologicos y la demografia del raton, se utilizo un nuevo tipo de analisis de viabilidad poblacional para desarrollar un plan de reproduccion en cautiverio y de reintroduccion del raton de Anacapa en caso de que los ratones sean exterminados junto con las ratas. Se incorporo una funcion seno al analisis de viabilidad poblacional para simular los ciclos del tamano poblacional. Nuestro estudio provee la informacion basica necesaria para desarrollar un plan de conservacion y de manejo integral para una especie endemica insular amenazada.

Robert C. Lacy

Papers

VORTEX: a computer simulation model for population viability analysis

Importance of Genetic Variation to the Viability of Mammalian Populations

Structure of the VORTEX simulation model for population viability analysis

Testing a simulation model for population viability analysis

Conservation and Management of Anacapa Island Deer Mice