Development on the island of Key Largo, Florida, has isolated the Key Largo woodrat (KLWR, Neotoma floridana smalli) on approximately 850 ha of remaining habitat. The KLWR was listed as a federally endangered species in 1984, yet there is still only a limited amount of knowledge about its ecology and population dynamics. The objective of this study was to produce reliable information on KLWR ecology to aid in its management and recovery. Specifically, the study examined (1) the trend and status of the KLWR population, (2) KLWR habitat and nesting preferences, (3) the potential of a fatal disease on KLWR, (4) the movements and ranges of the KLWR, and (5) the viability of the KLWR population. I trapped on 60 (1-ha) grids from March to September 2002 and 10 (1-ha) grids in October 2002 and January, April, and July 2003. Additionally I radio-collared 17 KLWRs and tracked them from March to November 2002. I estimated the current population of KLWR to be between 26 and 106 individuals. I found KLWR selected young hammock (disturbed > 1971) over medium (disturbed between 1940-1971) and old hammock (disturbed < 1940). KLWRs selected garbage and rock piles in the young hammock for nesting sites. From the analysis of 64 raccoon (Procyon lotor) fecal samples, I have no evidence that the potentially fatal raccoon roundworm parasite (Baylisascaris procyonis) was present on Key Largo or had negative impact on the KLWR. Telemetry data indicated males have larger ranges than females. Females appear socially tolerant of one another and have significantly smaller ranges than males during the spring and summer breeding season. Results of a population viability analysis (PVA) using demographic parameters from previous studies and my study projected a high risk of extinction for the KLWR within the next 10 years. I recommend the creation of large continuous blocks of young (disturbed > 1971) habitat and the creation of nesting habitat for the KLWR within these areas. I would also advocate a large-scale captive breeding and augmentation of the population along with continued research on the limiting factors that are driving the KLWR toward extinction.

Development on the island of Key Largo, Florida, has isolated the Key Largo woodrat (KLWR, Neotoma floridana smalli) on approximately 850 ha of remaining habitat. The KLWR was listed as a federally endangered species in 1984, yet there is still only a limited amount of knowledge about its ecology and population dynamics. The objective of this study was to produce reliable information on KLWR ecology to aid in its management and recovery. Specifically, the study examined (1) the trend and status of the KLWR population, (2) KLWR habitat and nesting preferences, (3) the potential of a fatal disease on KLWR, (4) the movements and ranges of the KLWR, and (5) the viability of the KLWR population. I trapped on 60 (1-ha) grids from March to September 2002 and 10 (1-ha) grids in October 2002 and January, April, and July 2003. Additionally I radio-collared 17 KLWRs and tracked them from March to November 2002. I estimated the current population of KLWR to be between 26 and 106 individuals. I found KLWR selected young hammock (disturbed > 1971) over medium (disturbed between 1940-1971) and old hammock (disturbed < 1940). KLWRs selected garbage and rock piles in the young hammock for nesting sites. From the analysis of 64 raccoon (Procyon lotor) fecal samples, I have no evidence that the potentially fatal raccoon roundworm parasite (Baylisascaris procyonis) was present on Key Largo or had negative impact on the KLWR. Telemetry data indicated males have larger ranges than females. Females appear socially tolerant of one another and have significantly smaller ranges than males during the spring and summer breeding season. Results of a population viability analysis (PVA) using demographic parameters from previous studies and my study projected a high risk of extinction for the KLWR within the next 10 years. I recommend the creation of large continuous blocks of young (disturbed > 1971) habitat and the creation of nesting habitat for the KLWR within these areas. I would also advocate a large-scale captive breeding and augmentation of the population along with continued research on the limiting factors that are driving the KLWR toward extinction.

Woodrats (Neotoma spp.) are imperiled in the north-central and north eastern United States. In Illinois, eastern woodrats (N. floridana) experienced range reductions and population bottlenecks over the past century. Hypothesized reasons for the decline of many woodrat populations that inhabit rock outcrops in the eastern United States include parasitism by raccoon roundworms (Baylisascaris procyonis), hard mast shortages, owl predation, and reductions in crevice availability for nest construction. During 2004-2005, the isolated remnant populations along the Mississippi bluffs in southwestern Illinois were genetically augmented with 47 eastern woodrats from Arkansas and Missouri resulting in 40% admixture within the largest population. In 2009, a strong windstorm created canopy gaps and woody debris throughout this area, potentially improving habitat for eastern woodrats. During 2003–2009, 422 eastern woodrats were reintroduced to 5 sites in the southeastern Illinois, and 172 eastern woodrats to 2 southern Illinois state parks during 2013–2014. These reintroductions are the only woodrat reintroductions to date with >50 individuals released per site. Most previous woodrat reintroduction attempts have released small numbers of individuals (10–15 per site and 10–54 total) and either failed to establish populations or required frequent management for populations to persist. My objectives were to (1) investigate the status of augmented eastern woodrat populations in southwestern Illinois, (2) evaluate the success of the southern Illinois reintroductions, (3) investigate whether eastern woodrats demographics within a reintroduced metapopulation could be predicted by factors underlying hypothesized reasons for woodrat declines, and (4) develop and evaluate noninvasive alternatives to live-trapping and sign surveys for monitoring woodrat populations.

The objectives of this study were to: (1) quantify levels of genetic intermixing in remnant Illinois eastern woodrat populations augmented with Ozark woodrats, and (2) assess genetic health and population viability in remnant and reintroduced woodrat populations. This dissertation is arranged into 3 chapters. DNA extractions, microsatellite genotyping, and mtDNA haplotype sequencing were conducted for individuals from the western Shawnee National Forest (WSNF) (i.e., LaRue Pine Hills [LPH], Fountain Bluff, Horseshoe Bluff), eastern Arkansas (AR), southern Missouri (MO), and 5 locations in the eastern Shawnee National Forest (ESNF), Illinois. Genetic data provided a strong signal in STRUCTURE which confirmed MO, AR, and LPH were genetically distinct populations prior to the genetic augmentation at LPH. Following augmentation, eastern woodrats in ESNF and WSNF have experienced admixture with introduced populations, increased allelic richness, decreased inbreeding, and increased effective population size, while genetic swamping was not observed. Haplotypes from both introduced populations were observed after augmentation at LPH but neither were detected in adjacent remnant populations. Reintroduced populations in the ESNF are acting as a single population and descendants consist of primarily AR and MO individuals. Admixture was apparent in all ESNF populations and haplotypes from all source populations persisted. Effective population size was largest at Garden of the Gods but all 5 populations had similar allelic richness and heterozygosity. In the ESNF, migration is not supported between study populations and additional habitat management may be needed. Future population monitoring of the ESNF population should focus efforts in the 3 central populations which are likely source populations. Future eastern woodrat management efforts should focus on (1) connectivity between ESNF populations and (2) connectivity in the WSNF amongst remnant populations and between remnant and reintroduced populations in the central Shawnee National Forest. I recommend the establishment of migration corridors by decreasing canopy cover in the forested matrix and the establishment of artificial rock outcrops in the form of boulder piles along migration corridors. My study indicates that genetic augmentations can be a beneficial management action in isolated eastern woodrat populations having experienced loss in gene flow, while reintroductions can benefit woodrats in areas believed to have experienced local extirpation. I also recommend identifying genetic structure of source populations for genetic augmentations and reintroductions beforehand to confirm multiple source populations, genetic variation, and introduction of multiple alleles. As rodents often have short lifespans and individual reintroductions may fail to establish, genetic augmentations and reintroductions should include the relocation of multiple individuals over time via soft release.

Key Largo woodrats are an endangered subspecies with an extremely limited habitat. This study sought to understand woodrat habitat preferences in order to guide management. Woodrats build stick nests from natural and artificial materials, so nest distribution and nest occupancy were used as indicators of preference. Distribution was determined by nest surveys, and remote cameras were used to assess occupancy. Forest structure, human disturbance, nest, and animal presence metrics were also collected. More nests were found along abandoned roads than along forest transects and more artificial nests were occupied than natural nests. These findings indicate that woodrats prefer areas with human disturbance, rather than forest age and structure as previously believed. This may have consequences on woodrat management, as it suggests that man-made materials are currently needed by woodrats even in a protected natural area.

Estimates of animal abundance or density are fundamental quantities in ecology and conservation, but for many species such as rare, small mammals, obtaining robust estimates is problematic. In this thesis, I combine elements of two standard abundance estimation methods, capture-recapture and distance sampling, to develop a method called trapping point transects (TPT). In TPT, a "detection function", g(r) (i.e. the probability of capturing an animal, given it is r m from a trap when the trap is set) is estimated using a subset of animals whose locations are known prior to traps being set. Generalised linear models are used to estimate the detection function, and the model can be extended to include random effects to allow for heterogeneity in capture probabilities. Standard point transect methods are modified to estimate abundance. Two abundance estimators are available. The first estimator is based on the reciprocal of the expected probability of detecting an animal, ^P, where the expectation is over r; whereas the second estimator is the expectation of the reciprocal of ^P. Performance of the TPT method under various sampling efforts and underlying true detection probabilities of individuals in the population was investigated in a simulation study. When underlying probability of detection was high (g(0) = 0:88) and between-individual variation was small, survey effort could be surprisingly low (c. 510 trap nights) to yield low bias (c. 4%) in the two estimators; but under certain situations, the second estimator can be extremely biased. Uncertainty and relative bias in population estimates increased with decreasing detectability and increasing between-individual variation. Abundance of the Key Largo woodrat (Neotoma floridana smalli), an endangered rodent with a restricted geographic range, was estimated using TPT. The TPT method compared well to other viable methods (capture-recapture and spatially-explicit capture-recapture), in terms of both field practicality and cost. The TPT method may generally be useful in estimating animal abundance in trapping studies and variants of the TPT method are presented.