Using non-invasive techniques to examine black bear (Ursus americanus) abundance in the North Cascades Ecosystem, Washington State

Thesis (Master's)--University of Washington, 2013

Assessing range-wide habitat suitability for the Lesser Prairie-Chicken

Population declines of many wildlife species have been linked to habitat loss incurred through land-use change. Incorporation of conservation planning into development planning may mitigate these impacts. The threatened Lesser Prairie-Chicken (Tympanuchus pallidicinctus) is experiencing loss of native habitat and high levels of energy development across its multijurisdictional range. Our goal was to explore relationships of the species occurrence with landscape characteristics and anthropogenic effects influencing its distribution through evaluation of habitat suitability associated with one particular habitat usage, lekking. Lekking has been relatively well-surveyed, though not consistently, in all jurisdictions. All five states in which Lesser Prairie-Chickens occur cooperated in development of a Maxent habitat suitability model. We created two models, one with state as a factor and one without state. When state was included it was the most important predictor, followed by percent of land cover consisting of known or suspected used vegetation classes within a 5000 m area around a lek. Without state, land cover was the most important predictor of relative habitat suitability for leks. Among the anthropogenic predictors, landscape condition, a measure of human impact integrated across several factors, was most important, ranking third in importance without state. These results quantify the relative suitability of the landscape within the current occupied range of Lesser Prairie-Chickens. These models, combined with other landscape information, form the basis of a habitat assessment tool that can be used to guide siting of development projects and targeting of areas for conservation.

Rural property size drives patterns of upland and riparian forest retention in a tropical deforestation frontier

Deforestation in Brazilian Amazonia accounts for a disproportionate global scale fraction of both carbon emissions from biomass burning and biodiversity erosion through habitat loss. Here we use field- and remote-sensing data to examine the effects of private landholding size on the amount and type of forest cover retained within economically active rural properties in an aging southern Amazonian deforestation frontier. Data on both upland and riparian forest cover from a survey of 300 rural properties indicated that 49.4% (SD = 29.0%) of the total forest cover was maintained as of 2007. and that property size is a key regional-scale determinant of patterns of deforestation and land-use change. Small properties (<= 150 ha) retained a lower proportion of forest (20.7%, SD = 17.6) than did large properties (>150 ha; 55.6%, SD = 27.2). Generalized linear models showed that property size had a positive effect on remaining areas of both upland and total forest cover. Using a Landsat time-series, the age of first clear-cutting that could be mapped within the boundaries of each property had a negative effect on the proportion of upland, riparian, and total forest cover retained. Based on these data, we show contrasts in land-use strategies between smallholders and largeholders, as well as differences in compliance with legal requirements in relation to minimum forest cover set-asides within private landholdings. This suggests that property size structure must be explicitly considered in landscape-scale conservation planning initiatives guiding agro-pastoral frontier expansion into remaining areas of tropical forest. (C) 2010 Elsevier Ltd. All rights reserved.

Successful carnivore identification with faecal DNA across a fragmented Amazonian landscape

The use of scat surveys to obtain DNA has been well documented in temperate areas, where DNA preservation may be more effective than in tropical forests. Samples obtained in the tropics are often exposed to high humidity, warm temperatures, frequent rain and intense sunlight, all of which can rapidly degrade DNA. Despite these potential problems, we demonstrate successful mtDNA amplification and sequencing for faeces of carnivores collected in tropical conditions and quantify how sample condition and environmental variables influence the success of PCR amplification and species identification. Additionally, the feasibility of genotyping nuclear microsatellites from jaguar (Panthera onca) faeces was investigated. From October 2007 to December 2008, 93 faecal samples were collected in the southern Brazilian Amazon. A total of eight carnivore species was successfully identified from 71% of all samples obtained. Information theoretic analysis revealed that the number of PCR attempts before a successful sequence was an important negative predictor across all three responses (success of species identification, success of species identification from the first sequence and PCR amplification success), whereas the relative importance of the other three predictors (sample condition, season and distance from forest edge) varied between the three responses. Nuclear microsatellite amplification from jaguar faeces had lower success rates (15-44%) compared with those of the mtDNA marker. Our results show that DNA obtained from faecal samples works efficiently for carnivore species identification in the Amazon forest and also shows potential for nuclear DNA analysis, thus providing a valuable tool for genetic, ecological and conservation studies.

Population genetic structure and dispersal in white-lipped peccaries (Tayassu pecari) from the Brazilian Pantanal

In many mammals social organization promotes genetic structuring, which can be influenced by the dispersal pattern of the species. We analyzed the population genetic structure and dispersal of white-lipped peccaries (Tayassu pecan) from the Pantanal, Brazil. We genotyped 100 individuals at 7 microsatellite loci from 2 adjacent locations with no obvious geographic barrier between them. We found a significant but low F(ST) value, and the Bayesian analysis indicated a unique cluster. No significant differences were observed between mean assignment indices of resident males and females from both locations, and the probability of being born at the location sampled of > 30% of the individuals analyzed was lower than average. Mean relatedness between resident female, male, and opposite-sex pairs was not statistically different in both locations. These results suggest a low degree of genetic differentiation between the locations analyzed, and dispersal by both sexes (contrary to the predicted male-biased dispersal of most mammalian species).

Nest-tree selection by the threatened brush-tailed phascogale (phascogale tapoatafa) (marsupialia: dasyuridae) in a highly fragmented agricultural landscape

The conservation of roosting and nesting resources is of critical concern for many hollow-dependent species around the world. We investigated the nest-tree requirements of the threatened brush-tailed phascogale (Phascogale tapoatafa) in a highly cleared agricultural landscape in south-eastern Australia. We documented the physical characteristics of selected nest trees and describe the spatial and temporal patterns of nest-tree use as revealed by radio-tracking. Nine phascogales (seven females, two males) were radio-tracked between March and July 1999 in an area where most woodland habitat is confined to linear strips along roads and streams or small patches and scattered trees in cleared farmland. Female phascogales were monitored for 13–35 days over periods of 5–15 weeks and two males were monitored for 2 and 9 days respectively. A total of 185 nest-tree fixes was collected and all nests occupied by phascogales were in standing trees. Eighty-three nest trees were identified, ranging in diameter at breast height (dbh) from 25 to 171 cm, with a mean dbh for the trees used by each individual phascogale of >80 cm. Phascogales did not discriminate between canopy tree species in selecting nest trees, but showed highly significant selection for trees in the largest size class. All individuals used multiple nest trees, with the seven females occupying an average of 11.4 nest trees from a mean of 25 diurnal locations. The number of nest trees continued to increase throughout the study, suggesting that more would be identified during a longer or more intensive study. Occupied nest trees were located throughout each individual’s home range, highlighting the importance of a continuous spatial distribution of suitable nest trees across the landscape. Nest trees were also located in adjacent farmland up to 225 m from roadside vegetation, demonstrating the value that scattered clumps and even single trees in farmland can have for wildlife conservation.

Succession of small mammal communities after fire and reintroduction of the swamp antechinus 'Antechinus minimus'

This thesis is involved with changes that have occurred to small mammal populations following a major disturbance in the Anglesea region as a result of the 1983 Ash Wednesday fires. Fire, with its effects on spatial and temporal heterogeneity, was found to be an important factor in the maintenance of vegetation and small mammal community structure and diversity in the region. Successional changes in vegetation and small mammal communities were described by multivariate analyses, using data collected annually from 22 study sites. The use of factor analysis techniques, in reducing the annual capture data content, enabled long-term changes in the structure of mammal communities to be interpreted. The small mammal communities in the coastal heath and forest vegetation in the Anglesea region show evidence of a general resilience, (the degree and speed of recovery), to disturbance. Two phases of successional response to fire by mammal species have been proposed; a ‘re-establishment’ phase which occurs in the initial 5-6 years post-fire and is accompanied by rapid increase in species’ abundance, and a subsequent ‘maintenance’ phase accompanied by relatively minor changes in abundance. Habitat Suitability Indices were produced relating to these phases. Vertical density measures of understorey shrubs and herb layers showed significant relationships with small mammal species abundance at the study sites. Long term studies following major disturbances are needed to distinguish between short term recovery of plant and animal species and long term changes in these species. Studies extending over a number of years enable a better directional view of changes in small mammal communities than can be determined from . observations made over a short period. As a part of the investigation into temporal change, it was proposed to undertake trial reintroductions of the Swamp antechinus, Ant echinus minimus, a marsupial dasyurid species which was trapped in the area prior to the 1983 fire, but rarely subsequently. Other more commonly observed native small mammal species (e.g. Rattus fuscipes,R. lutreolus, Antechinus stuartii, Sminthopsis leucopus) had re-invaded the proposed reintroduction site after this fire. Failure of A. minimus to re-establish may have been due to spatial separation of the pre-fire populations coupled with the extensive area burnt in 1983, A source population of the species was located about 100km to the west and habitat utilization and interspecific and niche relationships between the species making the small mammal community explored. Discriminant analysis revealed some spatial separation of species within a habitat based on structural vegetation factors rather than floristic factors. Temporal separation of species was observed, asA. minimus were more active than Rattus species during daylight periods. There was evidence of micro-habitat selection by species, and structural vegetation factors were most commonly identified in statistical analyses as contributing towards selection by small mammal species. Following a theoretical modelling study three reintroduction trials were carried out near Anglesea during 1992-94. Individuals were subsequently radio tracked, and habitat relationships between the species in the small mammal community investigated. Although successful breeding of A, minimus occurred during the latter two trials, the subsequent fate of offspring was not determined. Invasive techniques required to adequately monitor young animals were considered potentially too damaging. Telemetry studies indicated a preference of A. minimus for short, wet heath vegetation. Structural vegetation factors were identified as being significant in discriminating between capture locations of species. Small scale and inexpensive trial reintroductions have yielded valuable additional data on this species and may be viewed as a useful tool in the conservation of other small native mammals.

Population ecology and captive breeding of Pseudomys novaehollandiae at Anglesea

The New Holland Mouse is critically endangered within Victoria. A decline in the species abundance resulted from below average rainfall and structural changes to habitat vegetation. A captive breeding program was established as part of the species recovery plan. Induced breeding throughout the year, under controlled conditions, was limited by the species aggressive behaviour.

Effects of a fox removal program on small and medium-sized mammal population dynamics within the Anglesea Heathlands, Victoria

This thesis assessed the diet of foxes within the ALCOA lease area of Anglesea to determine which native and introduced species foxes were eating. Results showed that Swamp Wallaby was regularly eaten but many other mammals, birds, insects and reptiles were also consumed. The response of native mammals to seasonal fox removal was also determined.

Inferring activity budgets in wild animals to estimate the consequences of disturbances

Activity budgets can provide a direct link to an animal's bioenergetic budget and is thus a valuable unit of measure when assessing human-induced nonlethal effects on wildlife conservation status. However, activity budget inference can be challenging for species that are difficult to observe and require multiple observational variables. Here, we assessed whether whalewatching boat interactions could affect the activity budgets of minke whales (Balaenoptera acutorostrata). We used a stepwise modeling approach to quantitatively record, identify, and assign activity states to continuous behavioral time series data, to estimate activity budgets. First, we used multiple behavioral variables, recorded from continuous visual observations of individual animals, to quantitatively identify and define behavioral types. Activity states were then assigned to each sampling unit, using a combination of hidden and observed states. Three activity states were identified: nonfeeding, foraging, and surface feeding (SF). From the resulting time series of activity states, transition probability matrices were estimated using first-order Markov chains. We then simulated time series of activity states, using Monte Carlo methods based on the transition probability matrices, to obtain activity budgets, accounting for heterogeneity in state duration. Whalewatching interactions reduced the time whales spend foraging and SF, potentially resulting in an overall decrease in energy intake of 42%. This modeling approach thus provides a means to link short-term behavioral changes resulting from human disturbance to potential long-term bioenergetic consequences in animals. It also provides an analytical framework applicable to other species when direct observations of activity states are not possible.

Metrics to assess ecological condition, change, and impacts in sandy beach ecosystems

Complexity is increasingly the hallmark in environmental management practices of sandy shorelines. This arises primarily from meeting growing public demands (e.g., real estate, recreation) whilst reconciling economic demands with expectations of coastal users who have modern conservation ethics. Ideally, shoreline management is underpinned by empirical data, but selecting ecologically-meaningful metrics to accurately measure the condition of systems, and the ecological effects of human activities, is a complex task. Here we construct a framework for metric selection, considering six categories of issues that authorities commonly address: erosion; habitat loss; recreation; fishing; pollution (litter and chemical contaminants); and wildlife conservation. Possible metrics were scored in terms of their ability to reflect environmental change, and against criteria that are widely used for judging the performance of ecological indicators (i.e., sensitivity, practicability, costs, and public appeal). From this analysis, four types of broadly applicable metrics that also performed very well against the indicator criteria emerged: 1.) traits of bird populations and assemblages (e.g., abundance, diversity, distributions, habitat use); 2.) breeding/reproductive performance sensu lato (especially relevant for birds and turtles nesting on beaches and in dunes, but equally applicable to invertebrates and plants); 3.) population parameters and distributions of vertebrates associated primarily with dunes and the supralittoral beach zone (traditionally focused on birds and turtles, but expandable to mammals); 4.) compound measurements of the abundance/cover/biomass of biota (plants, invertebrates, vertebrates) at both the population and assemblage level. Local constraints (i.e., the absence of birds in highly degraded urban settings or lack of dunes on bluff-backed beaches) and particular issues may require alternatives. Metrics - if selected and applied correctly - provide empirical evidence of environmental condition and change, but often do not reflect deeper environmental values per se. Yet, values remain poorly articulated for many beach systems; this calls for a comprehensive identification of environmental values and the development of targeted programs to conserve these values on sandy shorelines globally.