Date of Award


Degree Name

Doctor of Philosophy



First Advisor

Nielsen, Clayton


Northern bobwhite (Colinus virginianus) and swamp rabbits (Sylvilagus aquaticus) are species both strongly influenced by habitat loss and fragmentation in agricultural landscapes. Population declines for the bobwhite and the paucity of information regarding swamp rabbit prevalence add uncertainty to their potential for persistence in Illinois. Research has indicated that these 2 species rarely disperse long distances. In a metapopulation context, such limitations ultimately dictate species' ability to colonize habitat, thereby affecting their persistence. Since gene flow is one of the consequences of dispersal, I employed genetic investigations of the landscape features that affect gene flow, called landscape genetics, to aid the understanding of factors influencing the persistence of the northern bobwhite and swamp rabbit in an agricultural landscape. Tissue samples were collected from hunter harvested bobwhite in central and southern Illinois during 2007-2008. Tissue from trapped swamp rabbits and fecal pellets from swamp rabbit habitat were collected during 2004-2011 in the southernmost counties of Illinois. Microsatellite genetic markers were analyzed for each species. Bayesian clustering methods were used to find interbreeding groups. Levels of gene flow were assessed with F statistics. Correlations between individual genetic distances and landscape features provided an assessment of geographical attributes affecting gene flow. Northern bobwhite expressed less genetic structure among the southern and central counties of Illinois than expected from their sedentary reputation. Genetic differentiation among pre-defined subpopulations was low (FST <0.05) but significant. Genetic clusters were not tightly linked to geography. Individual-based analysis indicated that distance impacted gene flow more than the distribution of suitable habitat or highway barriers. Additionally, the distribution of suitable habitat on the landscape had a negative affect on gene flow indicating bobwhite may disperse through unsuitable habitat more readily than through suitable habitat. These results suggest that greater area of suitable habitat and improvement of existing habitat may be more beneficial to bobwhite than its arrangement or position on the landscape. Significant genetic structure was observed in swamp rabbits in the Cache River watershed of southernmost Illinois. Bayesian clustering indicated 4 distinct genetic groups inhabited the study area. Such structuring suggests swamp rabbits in the northernmost part of their range experience low connectivity among habitat patches and are consequently at risk for extinction in Illinois. Gene flow of swamp rabbits was tied to watercourses indicating their affinity for a water source impacts their dispersal tendencies. Gene flow was negatively impacted by highway barriers, which may interrupt swamp rabbit dispersal due to their avoidance of roads or land cover associated with roads. Alterations to swamp rabbit habitat that leads to loss, increased fragmentation, or increased road density may have severe negative impacts and should be avoided. Habitat improvement focused closer to watercourses may provide a greater benefit for swamp rabbits.




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