Variations in species occurrence and distribution across the landscape over time provide fundamental information concerning population dynamics. How this relates to habitat characteristics at multiple scales can elucidate the process of habitat selection. I evaluated these processes for a montane fir (Abies) forest specialist, Bicknell’s Thrush (Catharus bicknelli) in Vermont. This species is threatened by a suite of anthropogenic disturbances on its breeding grounds and quantifying the effects of environmental change at the population level for this songbird has not been addressed. The naturally fragmented breeding habitat of varying size, quality, and connectivity warranted a metapopulation approach and a robust occupancy analysis. Detection/non-detection data was collected for Bicknell’s Thrush across 88 sites during the breeding seasons in 2006 and 2007. Local habitat characteristics were measured for each site and landscape-level features were calculated using a predictive habitat model. The six local habitat variables were combined using a principal component analysis. Principal component 1 (PC1) described a gradient of increasing coniferous shrub density and proportion of coniferous dominated forest with decreasing canopy height. The landscape covariate was calculated by dividing patch size by patch isolation creating a continuum of small, isolated patches to large, less isolated patches. Thus each site was characterized by a single local habitat (PC1) and landscape metric. From these data, 67 models considering all combinations of landscape and local habitat scores (univariate, additive and interaction) were evaluated for individual estimates of the following parameters: (1) probability of detection, (2) probability of initial site occupancy, (3) probability of site colonization, and (4) probability of local site extinction. AIC model selection techniques were used to rank the models, which represented ecologically plausible hypotheses that compared the strength of local habitat characteristics to large-scale landscape features. Models within 4 AICc points of the top model were considered plausible. The top eight models were all plausible. Landscape characteristics alone were not significant in driving population dynamics. The relative importance of landscape + local habitat was highest for both probability of initial occupancy and local site extinction. Probability of occupancy increased and extinction decreased with the combination of increased patch size and decreased patch isolation (landscape) and increased coniferous shrub density, proportion of coniferous dominated forest and decreased canopy height (local habitat). Probability of site colonization was driven mainly by local habitat features and increased with increasing habitat quality. These results indicate a complex system with intricate links between landscape and local scales. Preserving large tracts of habitat may not be sufficient in assuring future species persistence, but could minimize local extinction risk. Careful consideration should be given to local habitat features within habitat fragments, particularly to maintain adequate colonization rates. Because important features from both scales are correlated, in intact montane forest patches, landscape-scale attributes alone may serve as a surrogate for identifying quality breeding habitat, assuming processes of natural disturbance can be maintained.

The Lower Keys marsh rabbit (LKMR, Sylvilagus palustris hefneri), a subspecies of marsh rabbit endemic to the Lower Keys, Florida, is threatened with extinction due to extensive coastal development of salt marsh habitats. LKMR recovery is limited by habitat loss and degradation from brush encroachment, predation by freeroaming cats (Felis catus) and raccoons (Procyon lotor), sea-level rise, and hurricanes. This study sought to determine local and landscape factors that influence LKMR metapopulation ecology and dynamics and to evaluate strategies for their recovery. I evaluated the influence of patch and landscape characteristics on LKMR densities, extinction, and colonization rates following Hurricane Wilma, and the response of LKMRs and salt marsh habitats to prescribed fire. I used estimates of population change based on annual monitoring data to validate vital rates, constructed a spatially explicit demographic model to evaluate various levels and spatial configurations of recovery scenarios implemented throughout the LKMRs range, and validated expected changes in parameter estimates using measures of habitat degradation and raccoon activity from known LKMR populations. I found LKMR densities were higher in patches with greater numbers of bunchgrasses and forbs and less edge and lower in patches with higher measures of raccoon activity. In response to a hurricane, I found the distance between LKMR patches and the coast had a negative influence on extinction probability; the distance between an extirpated and occupied LKMR patch had a negative influence on colonization probability and patch size had a positive influence. Adult LKMRs increased as woody cover <0.5 m decreased, herbaceous cover <0.5 m increased, and food availability increased in at least one site following prescribed fire. Model results indicated habitat management actions that improve carrying capacity of local rabbit populations and juvenile survival and control raccoon populations to increase rabbit reproductive rates are effective population recovery strategies. In total, my results provide a conservation planning tool that can be used to select recovery strategies and locations that will maximize benefits to LKMRs, thus improving their viability and recovery.

Presently, eleven western states and two Canadian provinces utilize sport hunting as the primary mechanism for managing cougar (Puma concolor) populations. However, the impacts of sustained harvest on population dynamics and demographic structure arc not well understood. Additionally, the lack of cost-effective enumeration techniques and strongly conflicting societal values complicate effective management of this species. Given these concerns, the primary goals of this study were (I) to determine the effects of sustained harvest on cougar populations, and (2) estimate the level and extent of cougar harvest statewide. I monitored cougar populations on Monroe Mountain in south-central Utah, and in the Oquirrh Mountains of north-central Utah from 1999 to 2003. Over this interval the Monroe population was subjected to heavy annual removals and was characterized demographically by a younger age structure. low survival and fecundity, and declining density. In contrast , the Oquirrh Mountain population was partially protected and exhibited an older age distribution, relatively high survival and fecundity, and static density. To examine the statewide distribution of sport hunting, I mapped the locations of all cougars legally harvested from I 996-200 I, and calculated harvest rates by watershed (# cougars killed I yr I I 00 km2) . Population trends derived on the st udy sites under known harvest regimes were used as benchmarks and compared with rates calculated for occupied cougar habitat across the state. This provided an index of where cougar populations were stable or declining as a result of hunting pressure. Results from this research suggest heavy, sustained harvest can have significant impacts on cougar population dynamics and demographics. Patterns of recruitment resemble a source-sink population structure due in part to spatially variable management strategies. Moreover, these results indicate during the later I 990s, most of the statewide population was exploited at levels equal to or surpass ing those measured on Monroe Mountain. Because cougar density and habitat characteristics vary across management units, the temporal scale of population recovery will most likely depend on the interaction of harvest regime, productivity of unexploited populations, and landscape connectivity.

Despite the two-fold advantage to asexual reproduction and its prevalence in a variety of organisms, sexual reproduction is prevalent across all taxa. The maintenance of two sexes is required to ensure genetic diversity and to prevent “evolutionary dead ends,” especially in clonal organisms. Many mechanisms have been proposed for the maintenance of two sexes, ranging from environmental variation and stochasticity, parasites and predators, and mutation rates. Spatial configuration, the size and location of populations with respect to other populations, can allow two competitors to coexist when one would normally be lost. This is especially important when the two competitors are the two sexes. In the clonal organism Marchantia inflexa, I determined that spatial configuration of populations can directly influence the maintenance of both sexes in a population and in an aggregate of populations (a metapopulation) using a combination of theoretical models and field studies. Based on field studies, population size has a significant influence on whether a subpopulation will contain both sexes, with populations smaller than 1m2 being more likely to contain only one sex while populations greater than 1m2 are more likely to contain both sexes. Based on mathematical models, the spatial arrangement of subpopulations within a metapopulation can greatly influence whether a metapopulation maintains both sexes as well as whether the metapopulation persists once one sex has been lost. Field data suggest that distance to nearest neighbor, a measurement of spatial arrangement, influences the maintenance of the sexes within subpopulations, but could affect maintenance differently depending on the metapopulation identity. In some metapopulations, both sexes are maintained when the nearest neighbor is close, while in other streams, one sex is lost when the nearest neighbor is close. When mathematical models are used to explicitly simulate natural metapopulations, the mathematical model predicts the observed sex ratios in one metapopulation, predicts the observed bias in another metapopulation, and fails to predicted observed values in two other metapopulations. Understanding spatial configuration helps us understand the maintenance and loss of sex, but other factors, such as environmental differences, may be required to accurately predict which sex will be lost.

The species–area relationship (SAR) has been applied to predict species richness declines as area is converted to human-dominated land covers.In many areas of the world, however, many species persist in human-dominated areas, including threatened species. Because SARs are decelerating nonlinear, small extents of natural habitat can be converted to human use with little expected loss of associated species, but with the addition of more species that are associated with human land uses. Decelerating SARs suggest that, as area is converted to human-dominated forms, more species will be added to the rare habitat than are lost from the common one. This should lead to a peaked relationship between richness and natural area. I found that the effect of natural area on avian richness across Ontario was consistent with the sum of SARs for natural habitat species and human-dominated habitat species, suggesting that almost half the natural area can be converted to human-dominated forms before richness declines. However, I found that this spatial relationship did not remain consistent through time: bird richness increased when natural cover was removed (up to 4%), irrespective of its original extent. The inclusion of metapopulation processes in predictive models of species presence improves predictions of diversity change through time dramatically. Variability in site occupancy was common among bird species evaluated in this study, likely resulting from local extinction-colonization dynamics. Likelihood of species presence declined when few neighbouring sites were previously occupied by the species. Site occupancy was also less likely when little suitable habitat was present. Consistent with expectations that larger habitats are easier targets for colonists, habitat area was more important for more isolated sites. Accounting for the effect of metapopulation dynamics on site occupancy predicted change in richness better than land cover change and increased the strength of the regional richness–natural area relationship to levels observed for continental richness–environment relationships suggesting that these metapopulation processes “scale up” to modify regional species richness patterns making them more difficult to predict. It is the existence of absences in otherwise suitable habitat within species’ ranges that appears to weaken regional richness–environment relationships.

The species–area relationship (SAR) has been applied to predict species richness declines as area is converted to human-dominated land covers.In many areas of the world, however, many species persist in human-dominated areas, including threatened species. Because SARs are decelerating nonlinear, small extents of natural habitat can be converted to human use with little expected loss of associated species, but with the addition of more species that are associated with human land uses. Decelerating SARs suggest that, as area is converted to human-dominated forms, more species will be added to the rare habitat than are lost from the common one. This should lead to a peaked relationship between richness and natural area. I found that the effect of natural area on avian richness across Ontario was consistent with the sum of SARs for natural habitat species and human-dominated habitat species, suggesting that almost half the natural area can be converted to human-dominated forms before richness declines. However, I found that this spatial relationship did not remain consistent through time: bird richness increased when natural cover was removed (up to 4%), irrespective of its original extent. The inclusion of metapopulation processes in predictive models of species presence improves predictions of diversity change through time dramatically. Variability in site occupancy was common among bird species evaluated in this study, likely resulting from local extinction-colonization dynamics. Likelihood of species presence declined when few neighbouring sites were previously occupied by the species. Site occupancy was also less likely when little suitable habitat was present. Consistent with expectations that larger habitats are easier targets for colonists, habitat area was more important for more isolated sites. Accounting for the effect of metapopulation dynamics on site occupancy predicted change in richness better than land cover change and increased the strength of the regional richness–natural area relationship to levels observed for continental richness–environment relationships suggesting that these metapopulation processes “scale up” to modify regional species richness patterns making them more difficult to predict. It is the existence of absences in otherwise suitable habitat within species’ ranges that appears to weaken regional richness–environment relationships.

The species–area relationship (SAR) has been applied to predict species richness declines as area is converted to human-dominated land covers.In many areas of the world, however, many species persist in human-dominated areas, including threatened species. Because SARs are decelerating nonlinear, small extents of natural habitat can be converted to human use with little expected loss of associated species, but with the addition of more species that are associated with human land uses. Decelerating SARs suggest that, as area is converted to human-dominated forms, more species will be added to the rare habitat than are lost from the common one. This should lead to a peaked relationship between richness and natural area. I found that the effect of natural area on avian richness across Ontario was consistent with the sum of SARs for natural habitat species and human-dominated habitat species, suggesting that almost half the natural area can be converted to human-dominated forms before richness declines. However, I found that this spatial relationship did not remain consistent through time: bird richness increased when natural cover was removed (up to 4%), irrespective of its original extent. The inclusion of metapopulation processes in predictive models of species presence improves predictions of diversity change through time dramatically. Variability in site occupancy was common among bird species evaluated in this study, likely resulting from local extinction-colonization dynamics. Likelihood of species presence declined when few neighbouring sites were previously occupied by the species. Site occupancy was also less likely when little suitable habitat was present. Consistent with expectations that larger habitats are easier targets for colonists, habitat area was more important for more isolated sites. Accounting for the effect of metapopulation dynamics on site occupancy predicted change in richness better than land cover change and increased the strength of the regional richness–natural area relationship to levels observed for continental richness–environment relationships suggesting that these metapopulation processes “scale up” to modify regional species richness patterns making them more difficult to predict. It is the existence of absences in otherwise suitable habitat within species’ ranges that appears to weaken regional richness–environment relationships.

The species–area relationship (SAR) has been applied to predict species richness declines as area is converted to human-dominated land covers.In many areas of the world, however, many species persist in human-dominated areas, including threatened species. Because SARs are decelerating nonlinear, small extents of natural habitat can be converted to human use with little expected loss of associated species, but with the addition of more species that are associated with human land uses. Decelerating SARs suggest that, as area is converted to human-dominated forms, more species will be added to the rare habitat than are lost from the common one. This should lead to a peaked relationship between richness and natural area. I found that the effect of natural area on avian richness across Ontario was consistent with the sum of SARs for natural habitat species and human-dominated habitat species, suggesting that almost half the natural area can be converted to human-dominated forms before richness declines. However, I found that this spatial relationship did not remain consistent through time: bird richness increased when natural cover was removed (up to 4%), irrespective of its original extent. The inclusion of metapopulation processes in predictive models of species presence improves predictions of diversity change through time dramatically. Variability in site occupancy was common among bird species evaluated in this study, likely resulting from local extinction-colonization dynamics. Likelihood of species presence declined when few neighbouring sites were previously occupied by the species. Site occupancy was also less likely when little suitable habitat was present. Consistent with expectations that larger habitats are easier targets for colonists, habitat area was more important for more isolated sites. Accounting for the effect of metapopulation dynamics on site occupancy predicted change in richness better than land cover change and increased the strength of the regional richness–natural area relationship to levels observed for continental richness–environment relationships suggesting that these metapopulation processes “scale up” to modify regional species richness patterns making them more difficult to predict. It is the existence of absences in otherwise suitable habitat within species’ ranges that appears to weaken regional richness–environment relationships.

Doctor of Philosophy / Department of Biology / Keith B. Gido / Many native freshwater animals are imperiled as a result of habitat alteration, species introductions and climate-moderated changes in disturbance regimes. Native conservation and nonnative species management could benefit from greater understanding of critical factors promoting or inhibiting native and nonnative success in the absence of human-caused ecosystem change. The objectives of this dissertation were to (1) explain spatiotemporal patterns of native and nonnative success, (2) describe native and nonnative response to uncharacteristic wildfire disturbance, and (3) test the hypothesis that wildfire disturbance has differential effects on native and nonnative species. This research was conducted across six sites in three reaches (tributary, canyon, and valley) of the unfragmented and largely-unmodified upper Gila River Basin of southwestern New Mexico. Secondary production was measured to quantify success of native and nonnative fishes prior to wildfires during 2008-2011. Native fish production was greater than nonnatives across a range of environmental conditions, although nonnative fish, tadpole, and crayfish production could approach or exceed that of native macroinvertebrates and fishes in canyon habitats, a warmwater tributary, or in valley sites, respectively. The second objective was accomplished by measuring biomass changes of a warmwater native and nonnative community during 2010-2013 before and after consecutive, uncharacteristic wildfires. Several native insect and fish taxa decreased after both wildfires, whereas nonnative decreases were most pronounced for salmonids and more limited for other taxa. Finally, effects of uncharacteristic wildfires followed by extreme flooding on metapopulations of native and nonnative fishes were contrasted during 2008-2013. Wildfire and flood disturbances increased extinction probabilities of all native fishes while leaving many nonnative fishes unaffected. These findings revealed a swinging pendulum of native and nonnative success, wherein wildfire disturbance resulted in a pendulum swing in favor of nonnatives. Ensuring the pendulum swings back in favor of natives will be facilitated by management activities that decrease wildfire size and intensity and maintain inherent ecosystem resilience.

As urban areas expand, agricultural lands become increasingly important habitat for many species. Compared to some types of agricultural land-use, ranchlands provide vast expanses of minimally modified habitat that support many threatened and endangered species. Conservation biologists can promote ecologically sound management approaches by quantifying the effects of agricultural practices on resident species. I examined the effects of pasture management, cattle grazing, and landscape characteristics on both adult and larval treefrogs in a ranchland in south-central Florida. I experimentally determined optimal deployment of artificial treefrog shelters constructed of polyvinylchloride (PVC) pipe to efficiently sample adult treefrogs (Chapter 1). Seventy-two shelters were hung on oak trees (Quercus virginiana) and cabbage palm trees (Sabal palmetto) with smooth trunks or boots (residual palm fronds), at all possible combinations of three heights (2, 3, and 4 m), four compass directions (N, S, E, and W) and two water levels (with or without 10 cm). Shelter residence was completely dominated by the Squirrel Treefrog, Hyla squirella (N = 65). Significantly fewer H. squirella were found in shelters on palms with boots than on smooth palms or oak trees (0.29 ± 0.21 [mean ± 1 SE hereinafter] versus 1.3 ± 0.21 and 1.1 ± 0.21, respectively), and shelters with water had slightly more H. squirella than those without (1.5 ± 0.19 versus 0.88 ± 0.19, respectively). Orientation and height did not affect the number of treefrogs encountered; thus, the optimal protocol is to deploy shelters on either smooth palms or oak trees, with water, at 2 m height for easy sampling, and in random compass orientations. I used this protocol to sample H. squirella in woodlots surrounding twelve wetlands and examined how time, frog stage and sex, and landscape features influenced treefrog survival, recapture and site fidelity (Chapter 2). I deployed 15 shelters/ha of woodlot within a 100 m buffer around each wetland. I sampled shelters three times during the fall breeding season, removed all shelters to force frogs to overwinter in natural refugia, and replaced shelters for the final spring sampling. During sampling periods, I sexed, measured, and individually marked each frog using visual implant elastomer (VIE) tags. I used Program MARK to build linear models that included either gender group (female, male or juvenile) or life history stage (adult, juvenile) and either time (sampling interval 1, 2, or 3) or season (fall, spring). I used the most informative model as a null model to assess effects of landscape covariates on survival and recapture. Females had higher survival than either males or juveniles, for which estimates were similar (0.867 vs 0.741 and 0.783, respectively). Survival did not vary over time, although there was some support for an effect of season, with lower survival during the final over-wintering period than in the fall intervals (relative variable importance: group = 0.730; stage = 0.134; time = 0.200; season = 0.310). Adults had higher recapture rates than juveniles (average recapture 0.214 vs 0.102), and recapture for both stages varied over time, with highest recapture in sampling interval two (relative variable importance: group = 0.262; stage = 0.514; time = 0.513; season = 0.229). Hyla squirella was extremely site loyal; no individuals moved between sampling sites, and 95% of recaptured individuals were in their original shelter. Strong terrestrial site fidelity calls into question the traditional "ponds as patches" metapopulation view of treefrog population dynamics. Area of woodlot within 250 m was the most important landscape variable in explaining additional variation in both survival and recapture. Frogs had higher survival and lower recapture in larger woodlots, indicating that intact, contiguous woodlots are higher quality habitat than more fragmented woodlots. Neither survival nor recapture varied with wetland grazing treatments or between pasture types. Finally, I experimentally assessed the effects of cattle grazing and pasture management on larval H. squirella. I selected four wetlands: two in semi-natural pastures (SN) and two in intensively managed pastures (IM). One wetland in each pasture type was fenced so that it was released from cattle grazing (R). I collected three clutches of H. squirella eggs (Clutches A, B, and C) and reared tadpoles in the laboratory until Gosner stage 25. In each wetland, I deployed a total of 50 tadpoles from each clutch into 105 L pens constructed of plastic laundry baskets and mesh window screening. Clutch significantly affected tadpole survival, with Clutch A having the highest percent survival, followed by Clutch B and finally Clutch C (41.66, 32.11 - 53.95 [mean, 95% confidence limits hereinafter]; 9.00, 6.76 - 11.88; 2.89, 2.02 - 4.01, respectively). Wetland type also affected survival, with SN wetlands supporting significantly higher survival than IM wetlands (SN-R: 53.95, 32.88 - 88.13; SN-G: 18.95, 11.30 - 31.36 vs IM-R: 7.32, 4.13 - 12.49; IM-G: 1.09, 0.29 - 2.39). Genetic variation in survival confirms the potential for H. squirella to adapt to rangeland management, but extremely low survival of some clutches indicates that few clutches may be able to survive in low quality wetlands, such as IM-G wetlands. Higher survival in SN pasture wetlands suggest this is a superior habitat and future management objectives should conserve semi-natural pastures and limit further modification of intensively managed pastures, including removing woodlots near wetlands.