Regional Consequences of Local Population Demography and Genetics in Relation to Habitat Management in Gentiana pneumonanthe

Abstract:  A joint demographic and population genetics stage-based model for a subdivided population was applied to Gentiana pneumonanthe , an early successional perennial herb, at a regional (metapopulation) scale. We used numerical simulations to determine the optimal frequency of habitat disturbance (sod cutting) and the intensity of gene flow among populations of G. pneumonanthe to manage both population viability and genetic diversity in this species. The simulations showed that even small populations that initially had near-equal allele frequencies could, if managed properly through sod cutting every 6 to 7 years, sustain their high genetic variation over the long run without gene flow. The more the allele frequencies in the small populations are skewed, however, the higher the probability that in the absence of gene flow, some alleles will be lost and within-population genetic variation will decrease even under proper management. This implies that although local population dynamics should be the major target for management, regional dynamics become important when habitat fragmentation and decreased population size lead to the loss of local genetic diversity. The recommended strategy to improve genetic composition of small populations is the introduction of seeds or seedlings of nonlocal origin.     

Genetic differentiation among matrilines in social groups of rhesus monkeys

Summary In rhesus monkey populations, animals related by descent to some female comprise a matriline or genealogy. Data on blood protein polymorphisms in the Cayo Santiago rhesus colony indicate that allele frequency variations among matrilines in social groups are large. These variations occur despite high levels of outbreeding. Computer simulation analyses indicate that pedigree or linear effect account for much of the observed genetic differentiation among genealogies. A sampling with correlation model in which genealogy sizes and average kinship levels are parameters predicts among matriline genetic differentiation. This study indicates that substantial genetic substructure is present within rhesus social groups. Our analyses also predict that large variances in allele frequencies should be common among social or trait groups based on kinship relationships.     

Hereditary Blindness in a Captive Wolf (Canis lupus) Population: Frequency Reduction of a Deleterious Allele in Relation to Gene Conservation

Numerous cases of hereditary diseases and disorders have been reported in wild animals bred in captivity, but little attention has been paid to the particular genetic management problems that arise when such defects occur. These problems include the obstacle of eliminating the deleterious allele(s) without contemporary loss of genetic variability. In this paper we use the statistical methods of pedigree analysis to address questions regarding a previously presumed hereditary form of blindness observed in a captive wolf population bred for conservation purposes in Scandinavian zoos. The most likely mode of inheritance coincides with an autosomal recessive allele with either a full penetrance or a reduced penetrance of 0.6 (depending on the reliability of studbook records). Using these two models of inheritance, we calculate the probability of carrying the blindness allele for each living animal. Analysis of the effect of removing high-probability carriers on founder allele survival and level of inbreeding demonstrates that the frequency of the deleterious allele can be significantly reduced without seriously affecting founder allele survival or current degree of inbreeding in the wolf population.     

Inbreeding and Loss of Genetic Variation in a Reintroduced Population of Mauritius Kestrel

Abstract:  Many populations have recovered from severe bottlenecks either naturally or through intensive conservation management. In the past, however, few conservation programs have monitored the genetic health of recovering populations. We conducted a conservation genetic assessment of a small, reintroduced population of Mauritius Kestrel ( Falco punctatus ) to determine whether genetic deterioration has occurred since its reintroduction. We used pedigree analysis that partially accounted for individuals of unknown origin to document that (1) inbreeding occurred frequently (2.6% increase per generation; N _eI= 18.9), (2) 25% of breeding pairs were composed of either closely or moderately related individuals, (3) genetic diversity has been lost from the population (1.6% loss per generation; N _eV= 32.1) less rapidly than the corresponding increase in inbreeding, and (4) ignoring the contribution of unknown individuals to a pedigree will bias the metrics derived from that pedigree, ultimately obscuring the prevailing genetic dynamics. The rates of inbreeding and loss of genetic variation in the subpopulation of Mauritius Kestrel we examined were extreme and among the highest yet documented in a wild vertebrate population. Thus, genetic deterioration may affect this population's long-term viability. Remedial conservation strategies are needed to reduce the impact of inbreeding and loss of genetic variation in this species. We suggest that schemes to monitor genetic variation after reintroduction should be an integral component of endangered species recovery programs.     

Genetic Structure of Fragmented Populations of the Endangered Daisy Rutidosis leptorrhynchoides

Abstract: The endangered grassland daisy Rutidosis leptorrhynchoides has been subject to severe habitat destruction and fragmentation over the past century. Using allozyme markers, we examined the genetic diversity and structure of 16 fragmented populations. The species had high genetic variation compared to other plant species, and both polymorphism and allelic richness showed strong positive relationships with log reproductive population size, reflecting a loss of rare alleles (frequency of q < 0.1) in smaller populations. Fixation coefficients were positively related to size, due either to a lack of rare homozygotes in small populations or to Wahlund effects (owing to spatial genetic structure) in large ones. Neither gene diversity nor heterozygosity was related to population size, and other population parameters such as density, spatial contagion, and isolation had no apparent effect on genetic variation. Genetic divergence among populations was low , despite a large north-to-south break in the species' current distribution. To preserve maximum genetic variation, conservation strategies should aim to maintain the five populations larger than 5000 reproductive plants, all of which occur in the north of the range, as well as the largest southern population of 626 plants at Truganina. Only one of these is currently under formal protection. High heterozygosity in smaller populations suggests that they are unlikely to be suffering from inbreeding depression and so are also valuable for conservation. Erosion of allelic richness at self-incompatibility loci, however, may limit the reproductive capacity of populations numbering less than 20 flowering plants.     

Simulating Retention of Rare Alleles in Small Populations to Assess Management Options for Species with Different Life Histories

Preserving allelic diversity is important because it provides the capacity for adaptation and thus enables long‐term population viability. Allele retention is difficult to predict in animals with overlapping generations, so we used a new computer model to simulate retention of rare alleles in small populations of 3 species with contrasting life‐history traits: North Island Brown Kiwi (Apteryx mantelli; monogamous, long‐lived), North Island Robins (Petroica longipes; monogamous, short‐lived), and red deer (Cervus elaphus; polygynous, moderate lifespan). We simulated closed populations under various demographic scenarios and assessed the amounts of artificial immigration needed to achieve a goal of retaining 90% of selectively neutral rare alleles (frequency in the source population = 0.05) after 10 generations. The number of immigrants per generation required to meet the genetic goal ranged from 11 to 30, and there were key similarities and differences among species. None of the species met the genetic goal without immigration, and red deer lost the most allelic diversity due to reproductive skew among polygynous males. However, red deer required only a moderate rate of immigration relative to the other species to meet the genetic goal because nonterritorial breeders had a high turnover. Conversely, North Island Brown Kiwi needed the most immigration because the long lifespan of locally produced territorial breeders prevented a large proportion of immigrants from recruiting. In all species, the amount of immigration needed generally decreased with an increase in carrying capacity, survival, or reproductive output and increased as individual variation in reproductive success increased, indicating the importance of accurately quantifying these parameters to predict the effects of management. Overall, retaining rare alleles in a small, isolated population requires substantial investment of management effort. Use of simulations to explore strategies optimized for the populations in question will help maximize the value of this effort. Simulación de la Retención de Alelos Raros en Poblaciones Pequeñas para Evaluar Opciones de Manejo para Especies con Historias de Vida Diferentes     

Preserving Population Allele Frequencies in Ex Situ Conservation Programs

Abstract: Optimization of contributions of parents to progeny by minimizing the average coancestry of the progeny is an effective strategy for maintaining genetic diversity in ex situ conservation programs, but its application on the basis of molecular markers has the negative collateral effect of homogenizing the allelic frequencies at each locus. Because one of the objectives of a conservation program is to preserve the genetic composition of the original endangered population, we devised a method in which markers are used to maintain the allele frequency distribution at each locus as closely as possible to that of the native population. Contributions of parents were obtained so as to minimize changes in allele frequency for a set of molecular markers in a population of reduced size. We used computer simulations, under a range of scenarios, to assess the effectiveness of the method in comparison with methods in which contributions of minimum coancestry are sought, either making use of molecular markers or genealogical information. Our simulations indicated that the proposed method effectively maintained the original distribution of allele frequencies, particularly under strong linkage, and maintained acceptable levels of genetic diversity in the population. Nevertheless, contributions of minimum coancestry determined from pedigree information but ignoring the genealogy previous to the conservation program, was the most effective method for maintaining allelic frequencies in realistic situations.     

Temporal Changes in Allele Frequencies and a Population's History of Severe Bottlenecks

Monitoring temporal changes in genetic variation has been suggested as a means of determining if a population has experienced a demographic bottleneck. Simulations have shown that the variance in allele frequencies over time ( F ) can provide reasonable estimates of effective population size ( N_e ). This relationship between F and N_e suggests that changes in allele frequencies may provide a way to determine the severity of recent demographic bottlenecks experienced by a population. We examined allozyme variation in experimental populations of the eastern mosquitofish ( Gambusia holbrooki ) to evaluate the relationship between the severity of demographic bottlenecks and temporal variation in allele frequencies. Estimates of F from both the fish populations and computer simulations were compared to expected rates of drift. We found that different methods for estimating F had little effect on the analysis. The variance in estimates of F was large among both experimental and simulated populations experiencing similar demographic bottlenecks. Temporal changes in allele frequencies suggested that the experimental populations had experienced bottlenecks, but there was no relationship between observed and expected values of F . Furthermore, genetic drift was likely to be underestimated in populations experiencing the most severe bottlenecks. The weak relationship between F and bottleneck severity is probably due to both sampling error associated with the number of polymorphic loci examined and the loss of alleles during the bottlenecks. For populations that may have experienced severe bottlenecks, caution should be used in making evolutionary interpretations or management recommendations based on temporal changes in allele frequencies.     

Predicted Genetic Consequences of Strong Fertility Selection Due to Pollinator Loss in an Isolated Population of Primula sieboldii

Previous studies demonstrated strong fertility selection for a self-fertile, homostyle morph due to pollinator loss in an isolated population of Primula sieboldii , an endangered heterostylous species. To predict genetic consequences of the selection we developed a deterministic genetic model based on a classical "supergene" model, and we studied the effects of pollinator availability and inbreeding depression on temporal changes of morph frequencies through model simulation. Because of the severe pollinator limitation experienced by the population, fast, irreversible loss of the thrum morph from the population was predicted, even if high inbreeding depression was assumed. To prevent the breakdown of the normal breeding system of the species, morph frequency monitoring for timely active management should be implemented. Active management should include hand pollinations and pollinator therapy—reintroduction and reestablishment of suitable pollinator populations. The method we adopted in this study to parametrize pollinator availability can be used widely in conservation modeling for a range of plant species that have multiple mating types with different degrees of self-incompatibility.     

Plant Reproductive Traits as a Function of Local, Regional, and Global Abundance

Most ecological generalizations stem from the study of common organisms, but most species are rare. There are a number of reasons to expect that rare and common species may differ consistently in their characteristics, with possible implications for conservation. Past analyses of this issue, however, have generally considered only a single measure of rarity and have not corrected analyses for the lack of independence in the traits of related species. We compared several reproductive characteristics of Mediterranean annual crucifers as a function of their global range, regional abundance, and local population density in Israel, making use of independent contrast methods to correct for the phylogenetic relationships of the species involved. We found plants growing at low local density to be disproportionately likely to be self-compatible. Petal length and floral depth (sepal length) were correlated with breeding system but showed significant interaction effects between breeding system and abundance. Floral longevity was inversely related to abundance and also showed significant interaction effects between breeding system and abundance. Overall, rare species tended to display more extreme values for floral traits than did common plants with the same breeding systems; they had unusually large and deep flowers if self-incompatible and unusually small, shallow ones if self-compatible.     

Dominance, not kinship, determines individual position within the communal roosts of a cooperatively breeding bird

Kin selection has played an important role in the evolution and maintenance of cooperative breeding behaviour in many bird species. However, although relatedness has been shown to affect the investment decisions of helpers in such systems, less is known about the role that kin discrimination plays in other contexts, such as communal roosting. Individuals that roost communally benefit from reduced overnight heat loss, but the exact benefit derived depends on an individual's position in the roost which in turn is likely to be influenced by its position in its flock's dominance hierarchy. We studied the effects of kinship and other factors (sex, age, body size and flock sex ratio) on an individual's roosting position and dominance status in captive flocks of cooperatively breeding long-tailed tits Aegithalos caudatus. We found that overall, kinship had little influence on either variable tested; kinship had no effect on a bird's position in its flock's dominance hierarchy and the effect of kinship on roosting position was dependent on the bird's size. Males were generally dominant over females and birds were more likely to occupy preferred roosting positions if they were male, old and of high status. In this context, the effect of kinship on social interactions appears to be less important than the effects of other factors, possibly due to the complex kin structure of winter flocks compared to breeding groups.     

No sympathy for the devil

Pathogens are a significant driver of biodiversity loss. We examine two wildlife disease management strategies that have seen growing use, sometimes in combination: (i) trapping-and-culling infectious animals (disease control), and (ii) trapping-and-translocating healthy animals to a reserve, with possible future reintroduction. A reserve can improve conservation when there is no disease. But, when infection exists, we show investing in the reserve may counteract disease control. We find jointly pursuing both strategies is sub-optimal when the reserve is costly to maintain. Numerically, we examine management of Devil Facial Tumor Disease, which has generated extinction risks for Tasmanian Devils. Disease control (though not eradication) is generally part of an optimal strategy, although a reserve is also optimal if it can be maintained costlessly. This implies preserving the original population by addressing in situ conservation risks, rather than translocating animals to a reserve and giving up on the original population, is generally the first-best.     

Potential Effects of a Forest Management Plan on Bachman's Sparrows (Aimophila aestivalis): Linking a Spatially Explicit Model with GIS

By combining a spatially explicit, individual-based population simulation model with a geographic information system, we have simulated the potential effects of a U.S. Forest Service management plan on the population dynamics of Bachman's Sparrow ( Aimophila aestivalis ) at the Savannah River Site, a U.S. Department of Energy facility in South Carolina. Although the Forest Service's management plan explicitly sets management goals for many species, most of the prescribed management strategy deals with the endangered Red-cockaded Woodpecker ( Picoides borealis ) because of legal requirements. We explored how a species (the sparrow) that is not the target of specific management strategies but that shares some habitat requirements with the woodpecker, would fare under the management plan. We found that the major components of the proposed management plan may allow the sparrow population to reach and exceed the minimum management goal set for this species, but only after a substantial initial decline in sparrow numbers and a prolonged transition period. In the model, the sparrow population dynamics were most sensitive to demographic variables such as adult and juvenile survivorship and to landscape variables such as the suitability of young clearcuts and mature pine stands. Using various assumptions about habitat suitability, we estimated that the 50-year probability of population extinction is at least 5% or may be much higher if juvenile survivorship is low. We believe, however, that modest changes in the management plan might greatly increase the sparrow population and presumably decrease the probability of extinction. Our results suggest that management plans focusing on one or a few endangered species may potentially threaten other species of management concern. Spatially explicit population models are a useful tool in designing modifications of management plans that can reduce the impact on nontarget species of management concern.     

No sympathy for the devil

Pathogens are a significant driver of biodiversity loss. We examine two wildlife disease management strategies that have seen growing use, sometimes in combination: (i) trapping-and-culling infectious animals (disease control), and (ii) trapping-and-translocating healthy animals to a reserve, with possible future reintroduction. A reserve can improve conservation when there is no disease. But, when infection exists, we show investing in the reserve may counteract disease control. We find jointly pursuing both strategies is sub-optimal when the reserve is costly to maintain. Numerically, we examine management of Devil Facial Tumor Disease, which has generated extinction risks for Tasmanian Devils. Disease control (though not eradication) is generally part of an optimal strategy, although a reserve is also optimal if it can be maintained costlessly. This implies preserving the original population by addressing in situ conservation risks, rather than translocating animals to a reserve and giving up on the original population, is generally the first-best.     

Potato Diversity in the Andean Center of Crop Domestication

The diversity and population structure of potato landraces ( Solanum spp.) within their center of domestication was studied using isozyme surveys of four polymorphic loci. The objective in assessing the distribution of genetic diversity was to assist in planning conservation strategies of crop genetic resources that are threatened by genetic erosion. In situ conservation methods depend on this type of analysts. Research was conducted in the region of Cusco, Peru. Eight fields spread among two microregions were randomly sampled, and 610 tubers were studied from this sample. In addition, 503 tubers were collected from markets in seven different meso-regions (provinces) surrounding the regional center of Cusco. Thirty genotypes were identified in the field sample and 82 in the regional sample. The frequency and distribution of genotypes and alleles are described. A high degree of genotype endemism was found at both the field and regional levels. Genotypes were unevenly distributed, and most of the genotypic diversity was between rather than within populations. At the allele level, however, we found that a very high percentage of the diversity was within rather than between populations. The genotype is the key unit for maintaining the population of potato landraces. Our findings suggest that collections need to be both geographically extensive and intensive. Because farmers are able to maintain most alleles on relatively small portions of their land, in situ conservation is a viable strategy.     

Translocations and the Preservation of Allelic Diversity

Translocation is a tool commonly used for the conservation of threatened and endangered fish species. Despite extensive use, the biological implications of translocation remain poorly understood. Of particular interest is the effect of translocation on genetic variability. Maintenance of genetic variability in these "refuge" populations is assumed to be important for both short- and long-term success. We examined allozyme variability at 16 loci for western mosquitofish ( Gambusia affinis ) populations with known histories of introduction. Refuge populations had significantly lower levels of heterozygosity. Refuge populations also had considerably lower levels of allelic diversity than parental populations. All losses were of relatively rare alleles (frequency less than 0.1 in parental population). These losses were probably due to an undocumented bottleneck early in the introduction history. These results were surprising because the initial transplant involved 900 fish and because mosquitofish have numerous reproductive traits that should minimize the effects of bottlenecks on genetic diversity. A literature review revealed that genetic variability is often reduced in refuge populations and that such reductions typically involve the loss of alleles. We suggest that translocated populations be examined periodically for losses of genetic variability.     

Logging Concessions Can Extend the Conservation Estate for Central African Tropical Forests

Abstract:  The management of tropical forest in timber concessions has been proposed as a solution to prevent further biodiversity loss. The effectiveness of this strategy will likely depend on species-specific, population-level responses to logging. We conducted a survey (749 line transects over 3450 km) in logging concessions (1.2 million ha) in the northern Republic of Congo to examine the impact of logging on large mammal populations, including endangered species such as the elephant ( Loxodonta africana ), gorilla ( Gorilla gorilla ), chimpanzee ( Pan troglodytes ), and bongo ( Tragelaphus eurycerus ). When we estimated species abundance without consideration of transect characteristics, species abundances in logged and unlogged forests were not different for most species. When we modeled the data with a hurdle model approach, however, analyzing species presence and conditional abundance separately with generalized additive models and then combining them to calculate the mean species abundance, species abundance varied strongly depending on transect characteristics. The mean species abundance was often related to the distance to unlogged forest, which suggests that intact forest serves as source habitat for several species. The mean species abundance responded nonlinearly to logging history, changing over 30 years as the forest recovered from logging. Finally the distance away from roads, natural forest clearings, and villages also determined the abundance of mammals. Our results suggest that logged forest can extend the conservation estate for many of Central Africa's most threatened species if managed appropriately. In addition to limiting hunting, logging concessions must be large, contain patches of unlogged forest, and include forest with different logging histories.     

Founder Effects,Inbreeding, and Loss of Genetic Diversity in Four Avian Reintroduction Programs

Abstract: The number of individuals translocated and released as part of a reintroduction is often small, as is the final established population, because the reintroduction site is typically small. Small founder and small resulting populations can result in population bottlenecks, which are associated with increased rates of inbreeding and loss of genetic diversity, both of which can affect the long‐term viability of reintroduced populations. I used information derived from pedigrees of four monogamous bird species reintroduced onto two different islands (220 and 259 ha) in New Zealand to compare the pattern of inbreeding and loss of genetic diversity among the reintroduced populations. Although reintroduced populations founded with few individuals had higher levels of inbreeding, as predicted, other factors, including biased sex ratio and skewed breeding success, contributed to high levels of inbreeding and loss of genetic diversity. Of the 10–58 individuals released, 4–25 genetic founders contributed at least one living descendent and yielded approximately 3–11 founder–genome equivalents (number of genetic founders assuming an equal contribution of offspring and no random loss of alleles across generations) after seven breeding seasons. This range is much lower than the 20 founder–genome equivalents recommended for captive‐bred populations. Although the level of inbreeding in one reintroduced population initially reached three times that of a closely related species, the long‐term estimated rate of inbreeding of this one population was approximately one‐third that of the other species due to differences in carrying capacities of the respective reintroduction sites. The increasing number of reintroductions to suitable areas that are smaller than those I examined here suggests that it might be useful to develop long‐term strategies and guidelines for reintroduction programs, which would minimize inbreeding and maintain genetic diversity.     

Molecular Genetic Consequences of a Population Bottleneck Associated with Reintroduction of the Mauna Kea Silversword (Arg yroxiphium sandwicense ssp. sandwicense [Asteraceae])

The endangered Mauna Kea silversword (Argyroxiphium sandwicense ssp. sandwicense) has experienced a severe decline in distribution and abundance because of predation by alien ungulates. By the late 1970s only a small remnant natural population persisted on the Mauna Kea volcano on the Island of Hawaii. The Hawaii Department of Land and Natural Resources, Division of Forestry and Wildlife, initiated an outplanting program in the 1970s to promote recovery of A. sandwicense ssp. sandwicense. Intermittent outplanting since 1973 has generated an outplanted population of over 450 plants on Mauna Kea, but the program has unintentionally resulted in a major population bottleneck. All plants in the outplanted population appear to be first- or subsequent-generation offspring of only two maternal founders from the natural population. Genetic variation in the natural and outplanted populations was assessed for 90 random amplified polymorphic DNA loci. Eleven loci were detectably polymorphic in the natural population, whereas only three loci were detectably polymorphic in the outplanted population. Thus, the population bottleneck has been accompanied by a 73% reduction in the level of detectable polymorphism. In addition, for eight loci, the population bottleneck has resulted in the loss of the marker allele in the outplanted population. A management strategy involving manual pollen transfer has recently been implemented to incorporate additional founders from the natural population into the outplanting program. As a supplement to the outplanting program, the strategy also includes a program promoting direct seedling establishment following manual pollen transfer. Incorporating additional founders may serve to overcome the legacy of the population bottleneck, especially if founder representation can be equalized.     

Evaluation of Central North American Prairie Management Based on Species Diversity, Life Form, and Individual Species Metrics

Abstract:  Reintroduction of fire and grazing, alone or in combination, has increasingly been recognized as central to the restoration of North American mixed-grass and tallgrass prairies. Although ecological studies of these systems are abundant, they have generally been observational, or if experimental, have focused on plant species diversity. Species diversity measures alone are not sufficient to inform management, which often has goals associated with life-form groups and individual species. We examined the effects of prescribed fire, light cattle grazing, and a combination of fire and grazing on three vegetation components: species diversity, groups of species categorized by life-form, and individual species. We evaluated how successful these three treatments were in achieving specific management goals for prairies in the Iowa Loess Hills (U.S.A.). The grazing treatment promoted the greatest overall species richness, whereas grazing and burning and grazing treatments resulted in the lowest cover by woody species. Burning alone best achieved the management goals of increasing the cover and diversity of native species and reducing exotic forb and (predominantly exotic) cool-season grass cover. Species-specific responses to treatments appeared idiosyncratic (i.e., within each treatment there existed a set of species attaining their highest frequency) and nearly half of uncommon species were present in only one treatment. Because all management goals were not achieved by any one treatment, we conclude that management in this region may need refining. We suggest that a mosaic of burning and grazing (alone and in combination) may provide the greatest landscape-level species richness; however, this strategy would also likely promote the persistence of exotic species. Our results support the need to consider multiple measures, including species-specific responses, when planning and evaluating management .