Date of Award

Spring 2015

Project Type


Program or Major

Natural Resources

Degree Name

Master of Science

First Advisor

Adrienne I Kovach

Second Advisor

Michael Palace

Third Advisor

Kathleen M O'Brien


Habitat connectivity is vital for dispersal and metapopulation persistence. Land use change and landscape modification alter the distribution and availability of habitat, thereby altering connectivity and impeding organisms’ dispersal abilities. Reduction of connectivity is a concern for the New England cottontail (Sylvilagus transitionalis), a species of high conservation priority that has experienced a dramatic decline of its required shrubland habitat. To better understand New England cottontail connectivity, I used a landscape genetics approach to assess the impact of landscape features on cottontail dispersal in two geographically isolated study areas, one in southern Maine-seacoast New Hampshire and the other in eastern Massachusetts on Cape Cod. I also assessed genetic diversity and structure within the Cape Cod population and compared the effectiveness of two panels of microsatellite loci for identifying polymorphism within this study area. To infer dispersal patterns, I used estimates of gene flow evaluated in relation to landscape features. I compared genetic distances calculated from microsatellite genotyping and resistance distances determined from least cost path algorithms using Mantel tests and mixed effect modeling. I tested a priori hypotheses about the influence of barrier features – roads, development, open water, forest, and fields – and facilitating features – roadsides, powerlines, scrub-shrub habitat, wetlands, pine barrens, and LiDAR-derived shrubland habitat – on cottontail dispersal. I used circuit analyses to identify long-distance movement corridors between isolated populations.

New England cottontails on Cape Cod comprised one, admixed population. I found signatures of a bottleneck, reduced genetic diversity, and low effective population sizes, as well as fine-scale spatial structuring indicating restricted dispersal in the Cape Cod cottontails. These findings suggest that the long-term persistence of this population may be at risk, without augmentation via translocation or releases of captive-bred rabbits. Unlike other specialist species that display generalist dispersal patterns, New England cottontails across all study areas were dependent upon scrub-shrub habitat for dispersal. This included both natural (scrub-shrub patches and wetlands) and anthropogenically maintained (e.g., powerlines, roadsides) scrub-shrub habitat. The relative effect of landscape features on gene flow differed among study areas according to differences in landscape composition and fragmentation levels. In general, models that were composed of barrier features were most strongly correlated with gene flow for all study areas, although models that were comprised of facilitating features influenced gene flow in more connected landscapes. These results demonstrated that fragmentation influences gene flow patterns. My results also showed that roads have dual effects as both barriers and facilitators of gene flow for early successional habitat specialists. Linear scrub-shrub elements such as roadsides and powerline right-of-ways were important features linking patches and geographically isolated populations. Given the small amount (<5%) of available scrub-shrub habitat in the landscapes occupied by New England cottontails, these anthropogenic linear features are key areas for restoring habitat and landscape connectivity. The New England Cottontail Conservation Strategy, which is focused on restoring habitat to expand remaining New England cottontail populations, can use the results of this study to identify and prioritize management areas that will improve habitat connectivity across the landscape.