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.