Although capture–recapture techniques are often used to estimate population size, these approaches are difficult to implement for a wide variety of species. Highly polymorphic microsatellite markers are useful in individual identification, and these ‘molecular tags’ can be collected without having to capture or trap the individual. However, several sources of error associated with molecular identification techniques, including failure to identify individuals with the same genotype for these markers as being different, and incorrect assignment of individual genotypes, could bias population estimates. Simulations of populations sampled for the purpose of estimating population size were used to assess the extent of these potential biases. Population estimates tended to be biased downward as the likelihood of individuals sharing the same genotype increased (as measured by the probability of identity (PI) of the multi-locus genotype); this bias increased with population size. Populations of 1000 individuals were underestimated by ≥5% when the PI was as small as 1.4 × 10−7. A similar-sized bias did not occur for populations of 50 individuals until the PI had increased to approximately 2.5 × 10−5. Errors in genotype assignment resulted in overestimates of population size; this problem increased with the number of samples and loci that were genotyped. Population estimates were often >200% the size of the simulated populations when the probability of making a genotyping error was 0.05/locus and 7–10 loci were used to identify individuals. This bias was substantially reduced by decreasing genotyping error rate to 0.005. If possible, only highly polymorphic loci that are critical for the identification of the individual should be used in molecular tagging, and considerable efforts should be made to minimize errors in genotype determination.

Infectious disease is an emerging threat that conservationists are ill-equipped to manage. The threat is greatest for small populations, which can be driven to extinction by virulent pathogens; these are usually generalist pathogens that ‘spill over’ from other host species, often domestic animals. Recent attempts at disease control have taken a variety of forms, some directed at threatened hosts themselves, and others involving reservoir hosts. Thus far, few such attempts have demonstrated clear benefits of intervention, often because they were ‘crisis management’ tactics allowing no comparison with untreated controls. Design of future strategies is hampered by a lack of basic information concerning the pathogens that represent serious threats, their epidemiology in multiple-host systems, and the vaccination or treatment protocols likely to be most effective under field conditions. In general, vaccination and treatment will be most valuable in tiny populations facing very high extinction risks. However, interventions that are poorly planned or under-funded have the potential to do more harm than good. In larger populations, or over larger areas, intensive management may be inappropriate, unsustainable, or simply impractical. In these circumstances, managing population size, structure or contact between host species could offer promising alternatives to intervention.

In the early 1900s, the wolf (Canis lupus) was extirpated from France and Switzerland. There is growing evidence that the species is presently recolonizing these countries in the western Alps. By sequencing the mitochondrial DNA (mtDNA) control region of various samples mainly collected in the field (scats, hairs, regurgitates, blood or tissue; n = 292), we could (1) develop a non-invasive method enabling the unambiguous attribution of these samples to wolf, fox (Vulpes vulpes) or dog (Canis familiaris), among others; (2) demonstrate that Italian, French and Swiss wolves share the same mtDNA haplotype, a haplotype that has never been found in any other wolf population world-wide. Combined together, field and genetic data collected over 10 years corroborate the scenario of a natural expansion of wolves from the Italian source population. Furthermore, such a genetic approach is of conservation significance, since it has important consequences for management decisions. This first long-term report using non-invasive sampling demonstrates that long-distance dispersers are common, supporting the hypothesis that individuals may often attempt to colonize far from their native pack, even in the absence of suitable corridors across habitats characterized by intense human activities.

It is becoming increasingly clear that species of smaller body size tend to be less vulnerable to contemporary extinction threats than larger species, but few studies have examined the mechanisms underlying this pattern. In this paper, data for the Australian terrestrial mammal fauna are used to ask whether higher reproductive output or smaller home ranges can explain the reduced extinction risk of smaller species. Extinct and endangered species do indeed have smaller litters and larger home ranges for their body size than expected under a null model. In multiple regressions, however, only litter size is a significant predictor of extinction risk once body size and phylogeny are controlled for. Larger litters contribute to fast population growth, and are probably part of the reason that smaller species are less extinction-prone. The effect of litter size varies between the mesic coastal regions and the arid interior of Australia, indicating that the environment a species inhabits mediates the effect of biology on extinction risk. These results suggest that predicting extinction risk from biological traits is likely to be a complex task which must consider explicitly interactions between biology and environment.

In most species the offspring of closely related parents have reduced fitness compared with the offspring of unrelated parents, a phenomenon known as inbreeding depression. However if parents are very distantly related, their offspring may also have reduced fitness. This pattern, outbreeding depression, has been most commonly observed in plants and only rarely in animals. Here we examine the consequences of inbreeding and outbreeding on juvenile survival of reintroduced Arabian oryx (Oryx leucoryx) in Oman, a population with a small number of founders drawn from a number of sources. Using microsatellite-based measures of inbreeding and outbreeding, there was no apparent relationship between inbreeding or outbreeding and survival when inbreeding and outbreeding were tested in separate statistical models. However when inbreeding and outbreeding were tested in the same statistical model, we found simultaneous inbreeding depression and outbreeding depression acting on juvenile survival. Outbreeding depression may be more common in vertebrates than previously supposed, and conservation strategies that seek to maximize the genetic diversity of managed populations may risk mixing lineages that are sufficiently differentiated to cause outbreeding depression among descendants.

Camera trapping has recently been introduced as an unbiased and practical method for monitoring tiger abundance. In a high density area in the Royal Bardia National Park in lowland Nepal, we tested this method by trapping very intensively within a 25 km2 area to determine the true number of animals in that area. We then tested the effect of study design by sub-sampling the data set using varying distances between trap stations and by reducing the number of trapping nights at each station. We compared these numbers with the density estimates generated by the capture–recapture models of the program CAPTURE. Both distance between traps and trapping duration greatly influenced the results. For example, increasing the inter-trap distance from 1 to 2.1 km and reducing the trapping duration per station from 15 to 10 nights reduced the number of tigers captured by 25%. A significant decrease in trapping rates during successive 5-night periods suggested that our tigers became trap-shy, probably because of the photo flash and because they detected the camera traps from cues from impression pads 50 m from the traps. A significant behavioural response was also confirmed by the program CAPTURE. The best capture–recapture model selected by the computer program (Mbh) gave precise estimates from data collected by the initial 1 km spacing of traps. However, when we omitted data from half the number of traps, thus decreasing the sampling effort to a more realistic level for monitoring purposes, the program CAPTURE underestimated the true number of tigers. Most probably, this was due to a combination of trap shyness and the way the study was designed. Within larger protected areas, total count from intensive, stratified subsampling is suggested as a complementary technique to the capture–recapture method, since it circumvents the problem of trap shyness.

Specially trained detection dogs have been used to locate faeces (scats) for faecal analyses but their effectiveness has not been quantified. We evaluated detection and accuracy rates of dogs trained to find scats of endangered San Joaquin kit foxes (Vulpes macrotis mutica). Four dogs found from 0.43 to 5.37 presumptive kit fox scats per km of transect searched in two field sites where kit foxes and coyotes (Canis latrans) but not non-native red foxes (V. vulpes) were present. The unusually low detection rate (0.43 scats per km) by one dog (probably due to excessive panting in hot weather) was still similar to the average scat detection rate of two experienced humans. DNA tests of 1298 scats showed that all dogs were 100% accurate at distinguishing kit fox scats under our field conditions. Because red foxes are sympatric with kit foxes in some areas, we also conducted controlled discrimination experiments to see if trained dogs could distinguish between scats from kit and red foxes. Four dogs were 100% accurate at choosing a kit fox scat when red fox scats were present (n = 64 trials), but were less accurate at ignoring red fox scats in trials where a kit fox scat was absent.

Umbrella species are ‘species with large area requirements, which if given sufficient protected habitat area, will bring many other species under protection’. Historically, umbrella species were employed to delineate specific reserve boundaries but are now used in two senses: (1) as aids to identifying areas of species richness at a large geographic scale; (2) as a means of encompassing populations of co-occuring species at a local scale. In the second sense, there is a dilemma as to whether to maximize the number or viability of background populations; the umbrella population itself needs to be viable as well. Determining population viability is sufficiently onerous that it could damage the use of umbrella species as a conservation shortcut. The effectiveness of using the umbrella-species concept at a local scale was investigated in the real world by examining reserves in East Africa that were gazetted some 50 years ago using large mammals as umbrella species. Populations of these species are still numerous in most protected areas although a few have declined. Populations of other, background species have in general been well protected inside reserves; for those populations that have declined, the causes are unlikely to have been averted if reserves had been set up using other conservation tools. Outside one reserve, Katavi National Park in Tanzania, background populations of edible ungulates and small carnivores are lower than inside the reserve but small rodent and insectivore abundance is higher. While we cannot compare East African reserves to others not gazetted using umbrella species, the historical record in this region suggests that umbrella species have been an effective conservation shortcut perhaps because most reserves were initially large and could encompass substantial populations of background species. It is therefore premature to discard the local-scale umbrella-species concept despite its conceptual difficulties.

We sampled blood from free-living spotted salamanders (Ambystoma maculatum) to test whether differences in the concentrations of a stress hormone (corticosterone) were associated with different qualities of breeding and migration habitat. Spotted salamanders are forest specialists that migrate to vernal pools to breed, and upland habitat degradation may have sub-lethal effects on animals that lead to population declines. An individual's level of physiological stress may function as a biomonitor for sub-lethal effects, and thus as a biomonitor for ecosystem quality. We compared unstressed (baseline) and stress-induced corticosterone concentrations in spotted salamanders: (1) at sites that differed in amount of forest loss; (2) during breeding migration across forest habitat versus pavement; (3) in microhabitats that varied in soil drainage and canopy cover. Removal of large amounts of terrestrial habitat surrounding a breeding pond was correlated with lower baseline (in males) and stress-induced corticosterone concentrations, which may indicate healthy individuals with a reduced ability to respond to additional stress or individuals experiencing chronic stress. Male salamanders migrating across pavement had elevated baseline corticosterone concentrations compared to animals migrating through a forest, consistent with an acute stress response. However, concentrations of corticosterone did not differ between individuals in microhabitats with canopy cover and well-drained soil versus those in microhabitats with no canopy cover and/or swampy soil. This endocrinological technique may be one useful measure of a population's health, helping to identify populations where further ecological study is recommended to evaluate conservation concerns.

Conservation practices are supposed to get refined by advancing scientific knowledge. We study this phenomenon in the context of monitoring tiger populations in India, by evaluating the ‘pugmark census method’ employed by wildlife managers for three decades. We use an analytical framework of modern animal population sampling to test the efficacy of the pugmark censuses using scientific data on tigers and our field observations. We identify three critical goals for monitoring tiger populations, in order of increasing sophistication: (1) distribution mapping, (2) tracking relative abundance, (3) estimation of absolute abundance. We demonstrate that the present census-based paradigm does not work because it ignores the first two simpler goals, and targets, but fails to achieve, the most difficult third goal. We point out the utility and ready availability of alternative monitoring paradigms that deal with the central problems of spatial sampling and observability. We propose an alternative sampling-based approach that can be tailored to meet practical needs of tiger monitoring at different levels of refinement.

Only one of the 5000 extant louse species (Phthiraptera) and no species of flea (Siphonaptera), parasitic helminth (Platyhelminthes), parasitic nematode (Nemata), mite, or tick (Acari) is listed as threatened by the IUCN, despite impassioned pleas for parasite conservation beginning more than a decade ago. Although they should be conserved for their own sake, past arguments, highlighting the intrinsic and utilitarian value of parasites, have not translated into increased attention by scientists or conservation managers, at least by the standard of listing for protection. Here, the use of estimated genealogies and population genetic patterns of parasites to illuminate their hosts' evolutionary and demographic history is advocated. Parasite DNA generally evolves more rapidly than their hosts', which renders it an underexploited resource for conservation biologists, particularly in cases where the hosts' genealogy or degree of population genetic structure is difficult to measure directly. Moreover, parasite gene flow may occur during host dispersal irrespective of host gene flow, revealing host movement through space and time. Parasite ecology and evolution may thus become another tool for the management of endangered vertebrate populations. This will result in the recognition of new host records, parasite species and cryptic lineages, which will help lift the veil of ignorance with respect to parasite biodiversity.

There is recent evidence to suggest that domestic livestock deplete the density and diversity of wild herbivores in the cold deserts of the Trans-Himalaya by imposing resource limitations. To ascertain the degree and nature of threats faced by Himalayan ibex (Capra sibirica) from seven livestock species, we studied their resource use patterns over space, habitat and food dimensions in the pastures of Pin Valley National Park in the Spiti region of the Indian Himalaya. Species diet profiles were obtained by direct observations. We assessed the similarity in habitat use and diets of ibex and livestock using Non-Metric Multidimensional Scaling. We estimated the influence of the spatial distribution of livestock on habitat and diet choice of ibex by examining their co-occurrence patterns in cells overlaid on the pastures. The observed co-occurrence of ibex and livestock in cells was compared with null-models generated through Monte Carlo simulations. The results suggest that goats and sheep impose resource limitations on ibex and exclude them from certain pastures. In the remaining suitable habitat, ibex share forage with horses. Ibex remained relatively unaffected by other livestock such as yaks, donkeys and cattle. However, most livestock removed large amounts of forage from the pastures (nearly 250 kg of dry matter/day by certain species), thereby reducing forage availability for ibex. Pertinent conservation issues are discussed in the light of multiple-use of parks and current socio-economic transitions in the region, which call for integrating social and ecological feedback into management planning.

More biodiversity could be protected in situ if the few species that attract the most popular support (the ‘flagship’ species) had distributions that also covered the broader diversity of organisms. We studied how well different groups of mammals performed for representing the diversity of mammals and breeding birds among 1° areas of sub-Saharan Africa. We demonstrate that choosing areas of sub-Saharan Africa using either conservationists' six primary flagship mammals, or the six ‘Big Five’ mammals popular with wildlife tourists, is not significantly better for representing the diversity of mammals and birds than choosing areas at random. Furthermore, neither of these groups is significantly better for representing the diversity of mammals and birds than groups of the same number of species chosen at random. We show that in order to succeed in representing many mammals and birds in area selection, it is not sufficient for the groups used for selection to occur in many different eco-regions, they must also have low overlaps in distribution, so as to provide high ecological complementarity (a similar pattern of ecological complementarity must be shared by the larger group of species to be represented). Therefore there may be a need for an explicit policy to balance the requirements of flagship conservation and broader biodiversity conservation, which will have implications for the distribution of resources.

Risks of population decline are studied extensively in conservation biology, but are difficult to estimate because they change abruptly over a relatively narrow range of parameters. We propose that risks of decline may be usefully summarized by the expected minimum population size. This is the smallest population size that is expected to occur within a particular time period. Analytical solutions for the expected minimum population size are obtained for a stochastic population model of exponential growth. In more complex models that are analyzed by Monte Carlo simulation, the expected minimum population size may be determined by recording the smallest population size obtained in each iteration and taking the average of these values. Whereas risks of decline change abruptly with changes in parameter values, the expected minimum population size changes more gradually. The results demonstrate that the expected minimum population size provides a better indication of the propensity for decline than the risk of extinction (or risk of decline to some other small population size), especially when the risk of extinction is small.

Numbers of free-ranging dogs (Canis familiaris) have reached unprecedented levels in Zimbabwean communal lands (agropastoralist rural areas). This study examined the potential competitive interactions between dogs and wild scavengers on the boundary of Gokwe Communal Land (GCL) and the Sengwa Wildlife Research Area (SWRA) in 1995-96. Dietary studies showed that dogs were primarily scavengers of human waste and animal carcasses. Twelve experimental carcasses indicated that dogs were the most successful species in the vertebrate scavenger guild, consuming 60% of available biomass and finding 66.7% of carcasses. Dogs monopolized the supply of domestic animal carrion within GCL, but also consumed wild carrion up to 1 km within the SWRA, and were seen 3 km inside the reserve. Their principal competitors for carcasses were vultures, and to a lesser degree lions (Panthera leo), leopards (P. pardus) and spotted hyaenas (Crocuta crocuta). Dogs outcompete vultures on wildlife reserve boundaries owing to their high densities, nocturnal and diurnal activity, physical dominance and greater tolerance of human disturbance. With a population growth rate of 6.5% per annum the influence of dogs will intensify on the peripheries of reserves, exacerbating their existing threat to wild scavengers. This scenario is probably occurring in many other African countries.

The search for easy-to-use indices that substitute for direct estimation of animal density is a common theme in wildlife and conservation science, but one fraught with well-known perils (Nichols & Conroy, 1996; Yoccoz, Nichols & Boulinier, 2001; Pollock et al., 2002). To establish the utility of an index as a substitute for an estimate of density, one must: (1) demonstrate a functional relationship between the index and density that is invariant over the desired scope of inference; (2) calibrate the functional relationship by obtaining independent measures of the index and the animal density; (3) evaluate the precision of the calibration (Diefenbach et al., 1994). Carbone et al. (2001) argue that the number of camera-days per photograph is a useful index of density for large, cryptic, forest-dwelling animals, and proceed to calibrate this index for tigers (Panthera tigris). We agree that a properly calibrated index may be useful for rapid assessments in conservation planning. However, Carbone et al. (2001), who desire to use their index as a substitute for density, do not adequately address the three elements noted above. Thus, we are concerned that others may view their methods as justification for not attempting directly to estimate animal densities, without due regard for the shortcomings of their approach.

To investigate how anthropogenic activity might affect large carnivores, we studied the behaviour of spotted hyenas (Crocuta crocuta) during two time periods. From 1996 to 1998, we documented the ecological correlates of space utilization patterns exhibited by adult female hyenas defending a territory at the edge of a wildlife reserve in Kenya. Hyenas preferred areas near dense vegetation but appeared to avoid areas containing the greatest abundance of prey, perhaps because these were also the areas of most intensive livestock grazing. We then compared hyena behaviour observed in 1996-98 with that observed several years earlier and found many differences. Female hyenas in 1996-98 were found farther from dens, but closer to dense vegetation and to the edges of their territory, than in 1988-90. Recent females also had larger home ranges, travelled farther between consecutive sightings, and were more nocturnal than in 1988-90. Finally, hyenas occurred in smaller groups in 1996-98 than in 1988-90. We also found several changes in hyena demography between periods. We next attempted to explain differences observed between time periods by testing predictions of hypotheses invoking prey abundance, climate, interactions with lions, tourism and livestock grazing. Our data were consistent with the hypothesis that increased reliance on the reserve for livestock grazing was responsible for observed changes. That behavioural changes were not associated with decreased hyena population density suggests the behavioural plasticity typical of this species may protect it from extinction.

Efforts to evaluate the efficacy of translocation as a conservation tool have mostly been inadequate, particularly for reptiles and amphibians, leading many biologists to discount translocation as a viable management option. Nevertheless, with two-thirds of the world's tortoise and freshwater turtle species at risk, translocation may be one of the few remaining options for re-establishing extirpated populations and reconnecting fragmented ones. We translocated 106 gopher tortoises (Gopherus polyphemus) to a protected area within the historical range but with no resident tortoises and tested the effects of penning on site fidelity and activity area size. We assigned 38 adults and subadults to one of three penning treatments (9 months, 12 months and no penning) and radio-tracked them for 2 years. Penning significantly increased site fidelity and resulted in smaller activity areas. Our data suggest that translocation coupled with penning will improve the likelihood of establishing self-sustaining tortoise populations.

Unsustainable hunting of wildlife or bushmeat for human consumption across the tropics threatens both wildlife populations and the livelihoods of people who depend on these resources. The probability that hunting can be sustainable depends in part on ecological conditions that affect the ‘supply’ of and ‘demand’ for wildlife resources. In this study, supply is estimated across a number of tropical ecosystem types by calculating the theoretical ‘maximum sustainable offtake’ in kg/km2 for harvestable wildlife. Demand is estimated from observed harvests in kg/km2. We examine how supply and demand vary across relatively undisturbed ecosystems, indexed by annual rainfall. Supply is potentially highest in dry forests and wetter savannah grasslands and decreases in moist forests and more xeric grasslands. Demand tends to exceed supply in moist forests and xeric grasslands. Analogous to this ecological variation along the rainfall gradient is the gradient created by the conversion of tropical forests by humans. We hypothesise that the wild meat supply is greater in secondary forests and forest–farm–fallow mosaics than in undisturbed forests and test this with available data. We conclude that the probability that hunting will be sustainable varies with ecosystem type and degree of human disturbance and should influence where land is zoned for protected areas and where for wildlife harvests.

Tropical dry-deciduous forests comprise more than 45% of the tiger (Panthera tigris) habitat in India. However, in the absence of rigorously derived estimates of ecological densities of tigers in dry forests, critical baseline data for managing tiger populations are lacking. In this study tiger densities were estimated using photographic capture–recapture sampling in the dry forests of Panna Tiger Reserve in Central India. Over a 45-day survey period, 60 camera trap sites were sampled in a well-protected part of the 542-km2 reserve during 2002. A total sampling effort of 914 camera-trap-days yielded photo-captures of 11 individual tigers over 15 sampling occasions that effectively covered a 418-km2 area. The closed capture–recapture model Mh, which incorporates individual heterogeneity in capture probabilities, fitted these photographic capture history data well. The estimated capture probability/sample, $\hat{p} = 0.04$, resulted in an estimated tiger population size and standard error ($\hat{N}(S\hat{E}\hat{N}$)) of 29 (9.65), and a density ($\hat{D}(S\hat{E}\hat{D}$)) of 6.94 (3.23) tigers/100 km2. The estimated tiger density matched predictions based on prey abundance. Our results suggest that, if managed appropriately, the available dry forest habitat in India has the potential to support a population size of about 9000 wild tigers.