Date of Award

Fall 2018

Project Type


Program or Major

Natural Resources

Degree Name

Master of Science

First Advisor

Adrienne I Kovach

Second Advisor

Heidi Holman

Third Advisor

Michael Palace


Loss and fragmentation of shrubland habitat in the northeastern United States due to succession, suppression of natural disturbance regimes, and development (Cronon 1983, Litvaitis 1993) have resulted in declines of populations of shrubland specialist species, including the New England cottontail (Sylvilagus transitionalis) and shrubland birds (Litvaitis et al. 2006, Schlossberg & King 2007). The New England cottontail’s range has declined by over 86% (Litvaitis et al. 2006, Fenderson et al. 2014, Brubaker et al. 2014) and remaining populations are small and exhibit fine-scale structure, limited dispersal, and loss of metapopulation function (Fenderson 2011, 2014, Cheeseman 2017, Chapter 1). In the Northeast, declining species of shrubland birds outnumber increasing species three to one (Schlossberg & King 2007). In response to these losses, active management is ongoing to maintain and create shrubland habitat on the landscape to restore populations of specialists dependent on this habitat type. Given the extensive investments and collaboration focused on restoring shrubland habitats in New England, research is needed to monitor the effects of habitat creation on populations of shrubland specialists. Understanding how shrubland specialists are responding to ongoing habitat creation will inform additional restoration strategies in an adaptive management context, an iterative process of incorporating new information into management practices and learning from previous management outcomes.

Shrubland habitat creation and management in New England is largely focused on restoring habitat for the New England cottontail, with the idea that other species will also benefit. The New England cottontail is a highly threatened shrubland obligate requiring multiple patches of shrubland habitat within a short dispersal distance to support viable metapopulations long-term. Much of this management has been initiated by the New England Cottontail Conservation Initiative in response to the cottontail’s nine-year candidate listing status under the Endangered Species Act, and the National Fish and Wildlife Foundation Keystone Initiative. Conservation efforts implemented for the New England cottontail have included the development of a range-wide inter-agency conservation strategy, designation of focal habitat restoration areas and habitat acreage and cottontail population recovery goals, engagement with private organizations and landowners to create shrubland habitat, implementation of a range-wide cottontail occupancy monitoring protocol, and public outreach and education (Fuller & Tur 2012). Habitat management underway incorporates techniques to set back forest succession, including harvesting trees, cutting and mowing to promote shrub regrowth, planting to improve old field habitat, and controlled burning on fire-maintained habitats like pitch pine-scrub oak. Landscape-level conservation design has been initiated to identify best parcels in terms of vegetation type and patch size that can be targeted for restoration (Tash & Litvaitis 2007, Fuller et al. 2011).

Knowing how other species respond to widespread habitat management for cottontails is important to understand the full impacts and benefits of currently implemented management and to inform future management strategies. Given the resources invested in restoring shrubland habitat for cottontail populations, and the potential for other shrubland specialist species to benefit from this restoration, designating the New England cottontail a representative species could benefit strategic management for multiple species by the United States Fish and Wildlife Service. Representative species designations are a tool for strategic management to provide the greatest benefit for the most species with available resources. Research is needed to identify which additional species would benefit most from restoration to create habitat for cottontails. I investigated shrubland specialist birds as a suite of species that could benefit from habitat management for cottontails, given declining population trends for shrubland birds and their high conservation need in the Northeast.

In this thesis, I investigated the effects of habitat restoration on shrubland specialists in three case studies focused on New England cottontails and shrubland birds.

In Chapter 1, I used genetic tools to assess the population structure, genetic diversity, effective population size, and census population size of an isolated New England cottontail population in an urban landscape in Londonderry, New Hampshire. I documented attributes of small populations that pose conservation challenges, including limited dispersal and loss of metapopulation function (Chandler et al. 2015), low genetic diversity, high relatedness (Brook et al. 2002, O’Grady et al. 2006), skewed sex ratios (Tella 2001, Clout et al. 2002), and stochastic decline on isolated patches (Stacey & Taper 1992). I used a resistance surface approach to highlight areas of potential connectivity in the landscape, including powerlines, a shrub wetland, and rail corridor. I parameterized a spatially explicit individual-based simulation model that serves as a proof-of-concept for future work to compare the outcomes of alternate restoration scenarios on cottontail population size, genetic diversity, connectivity, and ability to persist in fragmented landscapes given best-case restoration scenarios.

In Chapter 2, I tracked the success of the first reintroduction effort for New England cottontails which has been ongoing at Bellamy River Wildlife Management Area since 2013. Using genetic analysis of fecal pellets collected in intensive winter surveys, I monitored survival and reproduction of founder cottontails and quantified changes in population size and genetic diversity following releases. Results indicate that reintroductions of New England cottontails can be successful. I documented successful breeding by both founders and wild-born cottontails, with some individuals reproducing and surviving over multiple years. Genetic diversity increased with the addition of breeding founders. However, I also found high post-release mortality following the first year of the reintroduction and variable survival that may be related to stochastic events, heavy snowfall, predator response, or competition for territory with established individuals. A population decline and skewed sex ratio, four years post-reintroduction, highlights the vulnerability of small reintroduced populations to stochastic decline. Key recommendations for a successful reintroduction of a small cottontail population include: 1) importantly, restoring a functional metapopulation that includes multiple occupied patches within dispersal distance and shrubland corridors connecting patches; 2) annual monitoring to track population size, sex ratios, number of breeders, and genetic diversity; and 3) repeated reintroductions over time and reintroducing large numbers of individuals, distributed spatially to avoid exceeding carrying capacity and to combat high post-release mortality (Armstrong & Seddon 2008, Hamilton et al. 2010). Additional research is needed to improve our understanding of the factors influencing founder survival and how best to supplement reintroductions after the initial release to prevent collapse of a small population.

In Chapter 3, I conducted point counts and vegetation surveys and modeled shrubland bird occupancy to determine habitat and patch-level influences on shrubland bird presence at sites occupied by or managed for New England cottontails. Of the five species of shrubland birds for which I modeled occupancy in relation to habitat covariates, Yellow Warbler and Prairie Warbler showed higher occupancy in microhabitat conditions suitable for New England cottontails. Yellow Warblers occupied wet sites with high stem densities and Prairie Warblers occupied sites with dense vegetation between 2-3 m. I also conducted indicator species analyses to identify shrubland bird specialists detected with high frequency at sites occupied by New England cottontails within the past five years and in microhabitat conditions associated with New England cottontail occupancy. Indicator species analyses identified 11 shrubland birds detected with high frequency in microhabitat conditions suitable for New England cottontail occupancy. In addition to Yellow Warbler and Prairie Warbler, which were associated with habitat covariates pertinent to New England cottontails in occupancy models, indicator species analyses identified Brown Thrasher, Field Sparrow, Blue-winged Warbler, Alder Flycatcher, Gray Catbird, Song Sparrow, Indigo Bunting, American Goldfinch, and Black-and-white Warbler as species sharing certain specific habitat requirements of New England cottontails or frequently detected on sites occupied by cottontails. Designating the New England cottontail a representative species would be an effective conservation strategy. Multiple shrubland specialist birds listed as Species of Greatest Conservation Need are associated with microhabitat conditions suitable for New England cottontail occupancy, and a suite of shrubland birds that use more open shrub habitats would benefit from habitat management before sites become suitable for cottontails.