Field ecologists in Everglades National Park know that the dynamics of water flow affect the breeding success of wading birds. A number of recent studies have suggested foraging success as the primary causal link. Data on the number and location of foraging birds are available from the Systematic Reconnaissance Flights, monthly aerial surveys of wading birds and surface water condition. A set of regression models were developed that predict the number of foraging birds observed in the Park at the beginning of May, a crucial period in the breeding season of almost all wading birds in this area. Predictor variables were obtained by converting the observations of surface water condition into three indexes that describe (1) the amount of surface water in the Park in January (near the beginning of the ‘dry’ season), (2) the rate at which it dries over the subsequent months, and (3) the amount of disruption to that drying process. An information-theoretic measure, ICOMP(IFIM), was used to choose on the basis of parsimony between the large set of possible models that incorporate these predictors. Most species were best predicted by the same few models, and the fitted model parameters were also similar, indicating that the same pattern of surface water dynamics was optimal for most species. The optimal pattern was: intermediate water levels at the beginning of the dry season, a rapid rate of drying, and no disruption in the drying process. A number of disruptions in drying since 1985 have been the result of releases of water from the flow-control structures at the northern boundary of Everglades National Park. Reducing or eliminating these unnatural hydrological events should help wading bird populations to increase.

The extant genetic variation of a population is the legacy of both long-term and recent population dynamics. Most practical methods for estimating effective population size are only able to detect recent effects on genetic variation and do not account for long-term fluctuations in species abundance. The utility of a maximum likelihood estimator of long-term effective population size based upon the coalescent theory of gene genealogies is examined for three endangered Colorado River fishes: humpback chub (Gila cypha), bonytail chub (Gila elegans) and razorback sucker (Xyrauchen texanus). Extant mitochondrial DNA (mtDNA) variation in humpback chub suggests this species has retained its historical equilibrium genetic variation despite recent declines in abundance. The mtDNA variation in razorback suckers indicates the population was quite large and expanding prior to recent declines and that rare alleles still survive in the remnant populations. The remaining mtDNA variation in bonytail chub indicates that dramatic, recent declines may have already obliterated a substantial portion of any historical variation. The results from long-term effective population size analyses are consistent with known natural history and illustrate the utility of the analysis for endangered species management.

New Zealand's native frogs (genus Leiopelma) are considered to be archaic amphibians of exceptional scientific interest that appear to have remained virtually unchanged for 160-200 million years. They are among the rarest extant amphibians and are highly restricted in distribution, confined to isolated, highly disjunct, populations on the North Island and a few small offshore islands in Cook Strait. Previous investigations have suggested, based on patterns of allozyme variation, that the Stephens Island frog (Leiopelma hamiltoni) and Archey's frog (L. archeyi) are sister taxa to the exclusion of the Maud Island frog, a species in close geographical proximity to the Stephens Island frog and previously viewed as a population of this species. As a consequence of these data, a new species, L. pakeka, the Maud Island Frog, has been described. This new species definition has dramatically enhanced the conservation status of L. hamiltoni, of which there are probably fewer than 150 individuals. In this study we re-examine the systematics of the Leiopelmatidae using mtDNA sequence analyses. Partial 12 S ribosomal RNA and cytochrome b (Cyt b) gene sequences were obtained for 57 frogs from six populations representing all four extant Leiopelma species. Contrary to previous reports we find L. pakeka and L. hamiltoni to be monophyletic. The amount of variation evident between these present species (<1% for Cyt b) is comparable to that seen between populations of L. archeyi. Based on these data, classification of L. pakeka and L. hamiltoni as separate species appears to be unwarranted, but they may be sufficiently distinct to warrant classification as evolutionarily significant units.

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.

Ivory poaching has been a serious problem in Asian elephant (Elephas maximus) populations. Reliable records of elephants killed and ivory harvested are generally unavailable. We have used a simulation modelling approach to estimate the numbers of male elephants killed and the quantities of ivory harvested over a 20 year period (1974–94) in the Periyar Reserve of southern India. The age-structured Leslie matrix projection model was modified for this purpose by considering three segments (female, tusked male and tuskless male), relating fecundity to adult sex ratio and iteratively simulating tusked male mortality rates so as to match the observed elephant population structure at Periyar. Four different scenarios of poaching all gave very similar results. We estimate conservatively that 336–388 tuskers have been poached and 3256–3334 kg of ivory harvested by poachers over the 20 year period. The maximum harvest came from the 10–20 year age class. Trends in various demographic parameters such as population numbers, tusked male to tuskless male ratios and female fecundity are described. The implications of ivory poaching and the extremely skewed sex ratios for the conservation and management of the elephant population at Periyar are discussed.

White Sands pupfish (Cyprinodon tularosa) are endemic to southern New Mexico and occur in only four localities: Malpais Spring, Salt Creek, Mound Spring and Lost River. Recently reported historical accounts indicate that the latter two populations were derived from translocations. Their limited distribution and complicated history suggest that knowledge of population genetic structure would be useful for the development of a sound conservation strategy. Mitochondrial DNA (mtDNA) sequences for a segment of the control region showed little variation. Variation was observed for microsatellite and allozyme loci with 37% attributable to divergence among populations. The mean genetic distance between Malpais Spring and the other three populations was high (allozymes: Darc = 0.541; microsatellites: Rst = 0.684) compared with the mean distance among the other three populations (Darc= 0.161, Rst = −0.016). There were fixed or nearly fixed differences in allele frequency between the Malpais Spring population and the other three populations at one allozyme locus (hexokinase) and two microsatellite loci (WSP-02 and WSP-11). We suggest the recognition of two evolutionarily significant units (ESUs) for the White Sands pupfish: Malpais Spring and Salt Creek. Our data indicate that the Lost River and Mound Spring populations descended from translocations from the Salt Creek population. Therefore, conservation efforts should focus on the Malpais Spring population.

Percentage canopy cover data derived from Landsat Enhanced Thematic Mapper (ETM+) sensor data, validated with field measurements, provide a useful tool for delineating Myanmar's Eld's deer (Cervus eldi) habitat. The current extent and condition of remaining Eld's deer habitat is unknown, but the species prefers dry dipterocarp forest. This habitat type has widely varying canopy cover and cannot be accurately delineated with traditional remote sensing techniques. New maps based on estimates of percentage canopy cover represent the variability of dry dipterocarp forests more accurately than maps of strict classes of habitat. Over 500 field measurements of canopy cover were used to train Landsat ETM+ data that were analysed with regression-tree analysis. The resulting satellite-based estimates of canopy cover were compared with an independent set of field validation points (r=0.539, P<0.001, n=114). The satellite-based estimates also showed potential for predicting the presence of Eld's deer (r=0.636, P<0.01, n=14). The results from the predictive maps are in accordance with previous field studies demonstrating the species' preference for dense, dry dipterocarp forest. Patterns of percentage tree-canopy cover across the study area were negatively correlated with human population density (r=-0.307, P<0.001, n=223), suggesting potential further threats to Eld's deer populations if the human population continues to grow.

The archaeological record indicates that guanacos inhabited the Patagonia of Chile and Argentina about 13,600 years ago, but were unable to migrate further south owing to the presence of glacial and water barriers that covered much of southern South America including the island of Tierra del Fuego. As environmental and ecological conditions improved, guanacos, along with other large mammals including horses, colonized the area. As a result of continued world-wide glacial melting, ocean levels rose and Tierra del Fuego became isolated from the mainland approximately 8000 years ago. Although island populations generally exhibit lower levels of genetic variation than their counterpart mainland populations, it is difficult to predict how much less variation island populations will exhibit. An analysis of mitochondrial cytochrome b and ATPase-8 sequences and 15 nuclear microsatellite loci revealed that both populations retained appreciable genetic diversity. The island population, however, exhibited much less variation than the mainland population. Measures of genetic variation revealed modest, but significant genetic differentiation, consistent with separation of the two populations approximately 8000 years ago. The assessment of levels of genetic diversity and population differentiation among populations of the wild South American camelids is becoming increasingly important as interest mounts in their utilization as a renewable resource.

Theoretical estimates of long-term minimum viable population (MVP) sizes for mammals indicate MVPs of tens of thousands, even a million. However, data to test the theoretical estimates are effectively non-existent. I here use information on distributions of primates on islands of southeast Asia to provide empirical estimates of the size of multi-millennial MVPs following the post-Pleistocene insularization in the Sunda region. Small Sunda region islands have fewer taxa than do large ones. Assuming extinction on the small islands, the MVP size is somewhere between the population size on the smallest island on which the taxon is extant and that on the largest island on which the taxon no longer exists (population size calculated as density of taxon by area of land available). Results for eight to ten genera (depending on the taxonomy) on 35 islands indicate MVPs of perhaps a few score for Nycticebus (loris) and Macaca (macaque) to several thousands, or scores of thousands, for Pongo (orang-utan) and Symphalangus (siamang). Large-bodied taxa have significantly larger MVPs than do small-bodied taxa. Only four protected areas in southeast Asia are large enough to conserve the smaller MVPs of the siamang and orang-utan.

A supplementary feeding and predator removal experiment was conducted on the hen harrier population on West Mainland, Orkney, to test whether increased predation pressure or shortage of food was responsible for the poor breeding success and potentially the decline of this population. Although numbers of crows appeared to have increased since 1983, the removal of hooded crows from breeding territories of male harriers had no detectable effect on any of the breeding parameters measured. The provision of supplementary food to male harriers significantly increased their numbers of breeding females, but had no detectable effect on either lay date, clutch size or hatching success. Results suggest that the current low levels of polygyny are a consequence of a shortage of food during the pre-lay period. Conservation management for this species should therefore be directed towards increasing the harriers' food supply, especially during the pre-lay period.

Australian mammals have one of the world's worst records of recent extinctions. A number of studies have demonstrated that red foxes (Vulpes vulpes) have a profound effect on the population biology of some species. However, not all species exposed to fox predation have declined. We studied the antipredator behaviour of a species that has not declined - the red-necked pademelon (Thylogale thetis), and contrasted it with previous studies on a species that has declined - the tammar wallaby (Macropus eugenii), to try to understand behavioural factors associated with survival. We focused on two antipredator behaviours: predator recognition and the way in which antipredator vigilance is influenced by the presence of conspecifics. We found that predator-naïve pademelons responded to the sight of certain predators, suggesting that they had some degree of innate recognition ability. However, pademelons responded similarly to a broad range of acoustic stimuli, including dingo howls, wedge-tailed eagle calls, foot-thumps - a predator-elicited sound - and a control sound, suggesting that they did not specifically recognize predator vocalizations. Unlike a number of other macropodid marsupials, including tammars, pademelons did not modify time allocated to antipredator vigilance as group size increased. Taken together, these results suggest that red-necked pademelons independently assessed and managed their predation risk whereas tammars relied more on conspecifics to assess and manage risk. We suggest that these factors may have been important determinants of species survival. More generally, we suggest that a fundamental understanding of antipredator behaviour can enlighten conservation efforts.

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.

We used the mitochondrial cytochrome b gene to study the population genetic structure of Melanosuchus niger (Brazil: Negro and Purus Rivers, Lake Janauacá; French Guiana: Kaw River swamps), and Caiman crocodilus (Brazil: Purus River, Lake Janauacá; French Guiana: Kaw River swamps). We found 10 haplotypes in M. niger and 9 haplotypes in C. crocodilus. Nested clade analysis indicated that isolation-by-distance was an important population dynamic in M. niger, but was unable to differentiate between isolation-by-distance, historical fragmentation or range expansion in C. crocodilus. Fu's Fs statistic supported the hypothesis of a demographic expansion in one out of four and two out of three sampled localities of M. niger and C. crocodilus, respectively. Populations of M. niger in central Amazonia also appeared to show differentiation that was correlated with water type. These results are compatible with the life-style of these two crocodilians; C. crocodilus is a habitat generalist and appears to disperse rapidly to newly available habitats, while M. niger is a more sedentary habitat specialist. Both species appear to be recovering from unregulated over-harvesting, however, their responses are life-history and, potentially, ecologically-dependent.

The black and white ruffed lemur, Varecia variegata, which is endemic to Madagascar, is under the threat of extinction due to the loss and fragmentation of its natural habitat, a consequence of deforestation. Behavioural researchers studying a population of V. variegata inhabiting the Manombo Special Reserve, noted that over a 4-year period, none of the family groups within the reserve produced offspring while those in neighbouring populations had been reproductively successful. Inbreeding depression was postulated as the trigger for this occurrence. However, another explanation exists. A cyclone, striking the region in 1997, destroyed a large percentage of the mature fruit-producing trees that V. variegata relied upon as a food source, which is likely to have produced a nutritional deficit. A panel of 25 simple sequence repeat (SSR) markers was utilised to assess the genetic diversity within four V. variegata populations, including individuals from Manombo and three other populations in southeastern Madagascar. The data revealed that the level of genetic diversity apparent within the Manombo population is comparable to the other groups studied. Therefore, it seems probable that genetic factors are not responsible for the recent lack of reproductive success on the part of the V. variegata at Manombo Special Reserve.

Species diversity and community structure indices (richness, diversity and evenness) are typically derived from contemporary biological survey atlases to identify conservation areas or to determine macroecological-environment relationships. Surprisingly, there are few studies based on national taxa surveys that describe and measure the influence human disturbance patterns may have on these ecological measures. This study uses various spatial statistical methods to examine and model large-scale spatial structure in diversity, structure indices derived from a comprehensive bird atlas, and composite variables of environment and human land transformation. Data were derived from an atlas of South African birds and segregated into five vegetation biomes. For each sample location, environmental and land-use data were used to calculate composite environmental gradients in climate, topography and human land transformation. Semivariograms were used to detect large-scale trends and spatial scale, and Moran's I statistic correlograms to test for large-scale spatial autocorrelation in detrended diversity indices. Ordinary least squares regressions for all biomes indicated a significant positive relationship between high levels of human transformation and species diversity, whereas high transformation had a significant negative influence on evenness. These same relationships held for the majority of biomes after the effects of environmental gradients were removed. The analysis also shows that in areas with favourable environmental resource levels, diversity for birds increases. These areas also tend to contain a large proportion of highly transformed land, and evenness decreases in the woodland, grassland, Karoo and fynbos biomes. This suggests that high-intensity transformation may bring in novel resources for birds not normally found in some of the biomes, with some species adept at exploiting these changes and reaching high densities with a tendency for assemblage structure to drift towards single species dominance. The results imply that species data derived from contemporary atlases may begin to demonstrate the effects of human influence on ecological measures rather than only indicating the effects of environmental variation on community structure.

Using published IUCN red-lists for the threatened bird species of Indonesia (Stattersfield & Capper, 2000), we document that the species at risk in Indonesia are not a taxonomically random sample, consistent with patterns seen at the global scale (Purvis et al., 2000). This implies that a greater than random proportion of Indonesia's and the world's (through the loss of endemics) phylogenetic diversity (PD) is at risk (Von Euler, 2001). Using cytochrome b (Johns & Avise, 1998) and a distance-based taxonomy, we attempt to quantify this projected loss of PD in millions of years and conclude with a brief discussion of the conservation implications for Indonesia, and of the use of ‘evolutionary heritage’ as a measure for conservation at the geopolitical level.

Genetic variability and population structure in the endangered peregrine falcon (Falco peregrinus) were studied using DNA microsatellite markers. Special emphasis was placed on the subspecies F. p. peregrinus living in Scandinavia and Scotland. For comparative purposes, three North American peregrine subspecies (F. p. tundrius, F. p. pealei and F. p. anatum) and one Tasmanian subspecies (F. p. macropus) were included in this analysis. Twelve DNA microsatellite loci were analysed across a total of 146 individuals. The amount of genetic variation did not differ in peregrine populations for which adequate sample sizes were obtained. Within F. p. peregrinus, significant genetic differentiation was found between populations in northern and southern Scandinavia and between the Scandinavian and Scottish populations, while the populations in south-eastern Norway and south-western Sweden did not differ significantly. Analysis of cliff-nesting peregrines in northern Sweden and bog-nesting peregrines in northern Finland/Sweden suggests that the difference in nesting habitat is not associated with genetic differentiation. Population structuring in F. p. peregrinus is further supported by an assignment test, wherein simulated genotypes are correctly assigned to the northern and southern Scandinavian and Scottish populations with relatively high probabilities, and by analysis of allele-sharing among individuals. Cluster analysis of genetic distances grouped populations of peregrines in accordance with their subspecific designation, and peregrines on either side of the Atlantic Ocean were clearly separated.

Conservation planning and practice rely heavily on abundance information generated at local scales for decision-making. Unfortunately most distributional data are only provided as presence–absence records at regional or national scales and cannot be used for making local conservation decisions. To date, two methods have been proposed for estimating local abundances and area of occupancy from coarse-scale presence–absence data. Kunin (1998) proposed the use of the fractal method, which assumes that species distributions are self-similar across scales. He & Gaston (2000a), in turn, proposed the use of the negative binomial distribution (NBD) for estimating abundances from presence–absence data collected at different scales. Previously only plant data were used to test these models. In the present study, they were tested using distributional presence–absence, as well as abundance data for a selection of large herbivores that have a restricted distribution in the Kruger National Park, South Africa. The results illustrate that the fractal method tends to overestimate areas of occupancy, while the NBD method underestimates the areas of occupancy of all species. This means that there were significant differences between the predictions provided by the two methods. Both these methods rely on the relationship between the area of occupancy and the size of the area over which the survey is conducted, but describe this relationship in a different way. These techniques could prove useful in the field of conservation biology and this study illustrates that these methods can be used on large mammal species and deliver results that are consistent with previous studies on plants.

To achieve long-term viability of hunted puma (Puma concolor) populations (even at historically low densities), we propose a management plan based on the metapopulation concept that designates source areas (closed to hunting) and sink areas (open to hunting). We use 11 years of data from Idaho and Utah to demonstrate how the proposed management plan might be implemented. We use minimum and maximum densities of resident animals to calculate minimum and maximum effective population sizes, neighbourhood areas (regional management units) and usable habitat within the units. We designate sink and source areas based on their size, accessibility to hunters and juxtaposition. We show that closing 63% of puma habitat to hunting would ensure long-term puma population viability while permitting traditional hunting levels in other areas. This system could be adapted to existing state (and interstate) hunting management units, and we outline several steps by which wildlife agencies might set up a process (including public participation) to manage puma hunting.

We studied the influence of vegetation structure and tree phenology on bird communities along a gradient of tropical forest degradation in NW Madagascar. Birds were censused by point counts at Ankarafantsika, one of the largest remnants of the severely reduced dry deciduous forest. The original forest was dominated by foliage insectivores. A few years after wildfire, regrowth was dense, most forest bird species were still present and additional understorey species appeared. As a result, species richness and abundance per point count increased. In contrast, when forest was transformed into savanna, the avian assemblage became poor, dominated by granivores and aerial insectivores, with only seven species shared with the original forest. Foliage volume, grass volume and bare ground cover explained most of the bird community variation by means of canonical correspondence analysis. Birds tended to increase their habitat breadth along the forest–savanna gradient. An index of bird conservation value, including abundance, endemism and the threatened status of the species, was highest in burned forests (1.12), intermediate in unburned forests (1) and lowest in savanna (0.44). The results emphasise the urgent need to protect not only the undisturbed fragments, but also the burned dry forests, because of their high value for biodiversity.