Reintroductions of captive-managed animals are a vital tool for the conservation of populations and species extinct in the wild. Because genetic diversity may impact population persistence, the genetic composition of reintroduced and captive populations is critical. For captive-managed species with known pedigrees, individual animals can be selected to create reintroduced populations with specific genetic compositions. Five genetic and demographic strategies for selecting animals were tested on four species. Selection strategies were based on criteria identified in field and theoretical studies. Simulated reintroductions of animals from captive-breeding programmes created a genetic conflict. Among the different strategies, increases in the genetic diversity of one subpopulation were negatively correlated with changes in the genetic diversity of the other subpopulation. For example, the release of genetically over-represented animals was the most beneficial strategy for a captive-breeding programme, but provided the least genetic diversity for the reintroduced population. However, gains and losses in genetic diversity between populations varied with different selection criteria and different population structures. Because captive-breeding histories vary for each species, changes in genetic composition cannot be accurately predicted and no one strategy is universally optimal. Thus, genetic trade-offs must be assessed for each population relative to specific programme goals.

The extent of inbreeding and outbreeding depression is thought to be a fundamental factor influencing the long term persistence of an endangered species. However, there have been no comprehensive examinations of either factor in an endangered species, except for a mouse species. Here we examined both the extent of inbreeding and outbreeding depression for five traits related to fitness in populations from the four watersheds in which the endangered Gila topminnow (Poeciliopsis o. occidentalis) still exists in the USA by making experimental matings with replicate samples and simultaneous controls. There was generally high survival, similar body size, and little bilateral asymmetry for all the inbred and outbred matings for all populations, i.e. there was no evidence of either inbreeding or outbreeding depression for these traits. Similarly there was no evidence of inbreeding or outbreeding effects for fecundity or sex ratio except for the sample from Monkey Spring, which had highly skewed (female-biased) sex ratios after one generation of inbreeding. In addition, brood sizes for Sharp Spring declined over time in inbred lines maintained by full-sib mating. These results further support the suggestion, based on molecular genetic analysis and considerations of habitat differences, that Monkey Spring be considered an evolutionarily significant unit, distinct from the remainder of existing populations. Potential explanations for the results and their implications for conservation are discussed.

A field-validated metapopulation model of patch occupancy was used to examine the persistence of greater gliders (Petauroides volans) in patches of remnant native eucalypt forest in south-eastern Australia. The model was based on a system of eucalypt patches embedded within a plantation forest of exotic radiata pine (Pinus radiata) at Buccleuch State Forest, New South Wales. The probability of local extinction in occupied patches was a function of patch size. The probability of colonization of empty patches was a function of the size and proximity of occupied patches. The results of the simulations suggested that suitable habitat should occupy approximately 10% (or more) of the total landscape to ensure the persistence of greater gliders. Rates of patch occupancy were maximized when suitable habitat was clustered into larger patches. Patches <3 ha in area were predicted to be of limited value as habitat for greater gliders. The predictions of the model are consistent with the observed persistence of greater gliders in the eucalypt patch system. The system of unlogged eucalypt patches within the pine plantation is a useful model of a network of small to medium-sized conservation reserves. Principles of reserve design can have value even in somewhat degraded and highly modified landscapes. The results demonstrate that reserved patches of native forest embedded within intensively logged forest can have significant conservation value, with important implications for the design and establishment of new softwood plantations.

The range of the tammar wallaby (Macropus eugenii) has decreased substantially in Australia in recent times. Because two introduced populations in New Zealand may have descended from a now-extinct Australian population(s), we investigated their origins using a novel approach. We combined data from seven highly polymorphic microsatellite markers with simulation modelling to infer the history and conservation value of the New Zealand populations. The microsatellite alleles in one New Zealand population (Rotorua) are merely a subset of those in the other (Kawau Is.), suggesting Rotorua had no immigrants from an independent source. However, in the Kawau Is. population (sample size 33–37), 37 alleles were absent that were present in the Kangaroo Is. (South Australia) population at frequencies ranging from 1–40%. The probability of those alleles being lost during a founding event from Kangaroo Is. was investigated using a program that simulates the genetic consequences of population size bottlenecks. Use of realistic bottleneck parameters resulted in probabilities approaching zero that the observed allele deficiencies in the Kawau population could have occurred randomly, identifying the New Zealand tammar wallabies as descendants of a distinct taxon that is no longer extant in Australia.

South Africa's National Parks Board has opted to control African elephants (Loxodonta africana) through culling in the Kruger National Park (KNP). Killing elephants is highly controversial. The Board must balance this controversy against the probable destruction of vegetation and the consequent depletion of biological diversity that high elephant densities cause. Annual aerial counts provided the population estimates on which the culling quotas were based. For management purposes, the elephant population of the Park is divided into four sub-populations. From 1984 to 1994, the annual quota was usually taken from only one of these sub-populations during a given year. This resulted in 3 to 5 years elapsing between culls in each sub-population. We investigated the year-to-year changes in densities after culling. These changes were density dependent. Density dependence implies that immediate culls following estimated high densities may be premature. If left alone, the densities would decline naturally. Indeed, culling becomes self-reinforcing as it moves population densities towards the level where reproduction is greatest. Data confirm this intuition: at densities greater than 0.37 elephants/km2 elephant numbers generally declined without culling. Many culls were unnecessary. Culling, as implemented in the past, may have had consequences for elephants and their habitat that were different to those expected from a mere reduction in their numbers. Densities in the year immediately after a cull tended to decline – not increase as would be expected from density dependence alone. Undoubtedly, this unexpected decline was the consequence of disturbance and subsequent emigration. In following years, the densities rose as animals moved back into the sub-population. A management programme where culling will be instituted only when densities exceed 0.37 elephants/km2 in selected regions in the park for at least 1 year, may be more acceptable than the programme used up to 1995. However, we do not know if the vegetation of KNP can withstand the resulting episodic high densities. With densities presently exceeding the cut-off values calculated for both the south and the northern management regions vegetation changes there need to be monitored.

Many species are currently undergoing reductions in population size due to widespread habitat loss and expanding human activities. Because interspecific hybridization is often a consequence of population decline and fragmentation, identification of individuals or populations with hybrid ancestry is an increasingly important issue in conservation biology. In many wild cattle and bison species, the problem of natural hybridization has been compounded by indiscriminate crossbreeding with domestic cattle for the purpose of improving domesticated stocks. Therefore, a genetic test using the polymerase chain reaction was developed so that wild cattle and bison with domestic cattle mitochondrial DNA (mtDNA) haplotypes could be rapidly identified. Using this genetic test, domestic cattle mtDNA haplotypes were detected in Bos grunniens (yak), Bison bonasus (European bison), and 6 out of the 15 (40%) Bison bison (North American bison) populations tested. In total, 30 out of the 572 (5.2%) North American bison tested, were found to have domestic cattle mtDNA. The hybrid origin of these mtDNA haplotypes was verified in a phylogenetic analysis using the parametric bootstrap. These results are discussed in terms of their implications for the conservation status and future management of wild cattle and bison species.

During the past two decades, pedigree analysis has documented inbreeding depression in many captive populations. This and subsequent research has led to a recognition that inbreeding depression is a potentially important determinate of small population fitness, in both captivity and the wild. Modern captive-breeding programmes now universally avoid inbreeding. We use simulation to investigate how much traditional pedigree analysis will reveal about the effect of inbreeding in such populations. We find that pedigrees typical of breeding programmes designed to avoid inbreeding have low statistical power to detect inbreeding depression.

The Atlantic forests of South America hold a great concentration of biodiversity, but most of this habitat has been destroyed. We therefore expect many species to become extinct, and yet no bird extinctions have conclusively been recorded. There could be three explanations for this. First, birds may be able to adapt to deforested landscapes. Second, many species may have become extinct before they were known to science. Third, there may be a time-lag following deforestation before extinction occurs. We present the most complete list to date of the endemic birds of the Atlantic forests (124 forest-dependent species), and then use the species–area relationship to predict how many species we expect to become extinct through deforestation (51 species i.e. 41%). We also count how many Atlantic forest endemic birds are independently considered ‘threatened’ with ‘a high risk of extinction in the wild in the medium-term future’ (45 species i.e. 36%). We compare these totals and find that they are similar, suggesting that there is a time-lag between deforestation and extinction. We go on to test the robustness of this result by varying the parameters used to make our predictions. The only parameter that varies enough to substantially weaken predictions based on deforestation is the habitat classification of Atlantic ‘forest’ birds. If we include species that can survive in secondary and non-forest habitats then, unsurprisingly, we find that deforestation overestimates threat. Overall, not only does deforestation accurately predict threat to Atlantic forest endemic birds, but this result is robust enough to accommodate considerable variability within our data.

Carnivore translocations are usually risky and expensive, and a number of biological and non-biological factors can influence success. Biological considerations include knowledge of genetics, demographics, behavior, disease, and habitat requirements. This information is critical for determining if the translocation should be attempted, if it could be successful, and how it could be implemented in an efficient and effective manner. We stress that individual species will vary in their responses, and ideas should be tested scientifically. The technical considerations of translocation are closely related to the biological questions. They include legal framework, fiscal and intellectual resources, monitoring capacity, goals of the translocation, logistic challenges, and organizational structure of decision-making. We do not discuss socio-economic aspects of translocation because those challenges require detailed discussion in a separate paper. We suggest that because large carnivores often play key roles in regulating ecological interactions between trophic levels, restoring them is more than a single-species activity. By restoring carnivores in viable numbers, we can take a large step toward recovering ecological integrity of geographically extensive landscapes.

A stochastic dynamic programming model is presented for decision-making by the manager of a small rhino reserve facing a poaching threat, with the objective of maximizing the rhino population size in the long term. The manager decides annually what proportion of the budget to spend on dehorning as opposed to law enforcement. Poacher incentives depend on revenues from illegal horn sales, which are related to the manager's decisions through the mean horn size of the rhino population (affected by spending on dehorning). Poacher incentives also depend on hunting costs, which are related to the manager's decisions through the risk of capture and punishment (affected by spending on law enforcement). The results suggest that, at realistic parameter values, the optimal strategy is to dehorn as many rhinos as possible annually except at very low rhino population sizes, budgets or mean horn sizes. The simple strategy of dehorning annually regardless of population size or mean horn size gives very similar results to the optimal strategy. Other potential strategies (such as dehorning only half the rhinos each year) performed badly. Selling horns and reinvesting the proceeds in rhino conservation did not provide enough revenue to significantly increase rhino population sizes.

Use of a new class of molecular marker for evolutionary or conservation studies may promise improved information, but it may also call for reassessment of analytical methods and empirical limitations. We used DNA microsatellites to study population structure in Rocky Mountain bighorn sheep (Ovis canadensis canadensis) and to test the ability of microsatellites to distinguish bighorn subspecies. Genetic differentiation between bighorn populations was dramatically greater than in comparable studies of brown bears and grey wolves, and these species differences are consistent with known differences in habitat use and dispersal. In bighorn, however, statistical limitations make it difficult to distinguish between moderately and highly divergent populations. As a result, only gene flow estimates greater than about one migrant per generation (OMPG) are informative about true population relatedness. In bears and wolves, apparent differentiation is so low that migration estimates are greater than OMPG continent-wide, but factors other than high gene flow may contribute to these patterns. Despite analytical difficulties at large geographical scales and large genetic divergences, microsatellite data assist management by characterizing historical rates and patterns of dispersal on smaller scales, and by detecting population bottlenecks and regions of particularly high or low historical gene flow.

Anecdotal data gathered from many populations suggest that southern flying squirrel (SFS, Glaucomys volans) use of the endangered red-cockaded woodpecker's (RCW, Picoides borealis) nest and roost cavities may negatively affect RCW populations. We conducted a controlled experiment to determine the effects of SFSs on RCW reproductive success. During the 1994 and 1995 breeding seasons, SFSs were removed from 30 RCW clusters and 32 clusters served as controls. SFSs were the most frequently encountered occupants of RCW cavities and used 20–33% of RCW cavities in control and treatment clusters over both years. Treatment groups produced significantly more successful nests (≥ 1 fledgling) than control groups in 1994. In 1995 however, there was no difference in the number of successful nests. In both years, RCW groups nesting in treatment clusters produced significantly more fledglings than groups in control clusters in each of four experimental areas, averaging approximately 0.7 additional fledglings per nesting group. Loss of entire clutches or broods, possibly as a result of predation or abandonment, was a major factor limiting reproduction in control groups in 1994. In contrast, differences in partial brood loss appeared to be the cause of differential fledging success in 1995. Usurpation of RCW roost cavities by SFSs may have placed greater energetic demands on RCWs for cavity defence or thermoregulation, thus reducing energy available for reproduction. Our results show that SFS use of RCW cavities during the breeding season has a significant impact on RCWs and that management of RCW populations should include activities that either minimize SFS populations in RCW clusters or limit access of SFSs to RCW cavities.

Rates of biodiversity loss are clearly associated with a reduction in the extent of original habitat. The most frequently used method to derive such estimates comes from the well-known species–area relationship. We explored the relationship between habitat loss and area for the Brazilian mammal fauna on a biome level (Atlantic Forest, Cerrado and the Brazilian portion of the Amazon basin), as well as on a smaller regional scale (the Rio Doce Valley of the Atlantic Forest). Habitat loss overestimates the number of threatened species when the entire species pool is considered (endemics and wide-ranging species). Restricting the analyses to the endemic species, the predicted extinction as a function of habitat loss in the Atlantic Forest and in the Cerrado is found to be greater than the number of taxa actually listed as threatened. This relation is reversed in the Amazon. When considering only the localized species pool for the Rio Doce Valley region of the Atlantic Forest, the function accurately predicts the number of extinctions resulting from habitat loss. We suggest that there is both theoretical and empirical evidence to suggest that threat analysis will generate more accurate estimates of species loss when conducted on a more local scale, particularly for the fauna of non-insular, continental regions. Furthermore, other phenomena affecting the likelihood of extinction of certain groups of species, such as hunting, need to be taken into account in order to better understand the dynamics of biodiversity loss.

Conservation and ecological monitoring programmes often estimate animal densities over time, but in wooded and forested areas practical techniques are still poorly developed. Here I have examined five simple methods of deriving densities of large and medium-sized mammals using line transects driven through miombo woodland habitat in Africa. These methods calculated area by dividing the number of individuals seen by (i) an average of each species' sighting distances, (ii) a fixed 200 m belt width, (iii) the area visible from the centre of the transect, (iv) visible area weighted by species' vegetation preferences, and (v) by dividing the number of groups seen by area visible from the transect. Individual-based methods produced quite divergent estimates of species' densities and overall biomass with belt transects giving the lowest values. The group method and corresponding individual-based method gave similar values, however. Most of these calculations yielded considerably higher density estimates than aerial surveys conducted in the same area over a similar time period. Sightings of species were not distributed evenly across vegetation types although the majority of mammal species were observed more often in open habitat. These findings indicate that ground-based conservation monitoring programmes should set transects through several vegetation types, restrict comparisons to those studies that use the same methodology, and refrain from comparing ground and aerial surveys.

We extend an earlier population viability analysis (PVA) of the Asian elephant (Elephas maximus) conducted by Sukumar & Santiapillai (1993) in order to examine how conclusions about viability can depend upon the time frame examined. We find that there is an approximately 200 year lag period before extinction events begin to occur in slowly declining populations of E. maximus. Therefore, examining population persistence over a 100 year time frame seriously underestimates the risk of population extinction over a longer, 1000 year period. These results are supported by the use of both a species-specific model of elephant demography, ELEPHANT, and a generic PVA package, VORTEX.

For populations with long generations, a 100 year time period will often not be sufficient to evaluate demographic processes leading to extinction. These results have important implications for how investigators conduct PVAs, and for the listing of endangered species by the World Conservation Union (IUCN).

Genetic diversity within a population is a critical parameter for conservation biologists to assess. One approach for examining genetic diversity is through the determination of effective population sizes. Animal Conservation recently published a review of genetic approaches for estimating effective population sizes. We felt this review was incomplete both methodologically and conceptually. Here we extend that review to include coalescent-based approaches for estimating effective population sizes. We then discuss different kinds of effective population sizes, including inbreeding, variance and eigenvalue effective sizes.

In 1998 we wrote a paper describing DNA-based methods for estimating and monitoring both census (Nc) and effective (Ne) population sizes in natural populations (Schwartz, Tallmon & Luikart, 1998). The purposes of this paper were: (i) to review some relatively unexplored, but promising ways that multi-locus genetic data can be used to monitor and detect population declines, (ii) to encourage further development and validation of recent DNA-based Nc and Ne estimators. These approaches are urgently needed to help detect natural population declines in their early stages, so that management actions can be taken to avoid population endangerment and subsequent extinction. Crandall, Posada & Vasco (1999) have criticized the Ne portion of our review claiming that we: (i) excluded phylogenetic estimators of Ne that employ coalescent theory, (ii) did not distinguish between historical and current estimates of Ne, (iii) did not define which Ne we were estimating.