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Population genetic structure and history of fragmented remnant populations of the New England cottontail (Sylvilagus transitionalis)

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Abstract

The New England cottontail (Sylvilagus transitionalis) has suffered from extensive loss and fragmentation of its habitat and is now a species of conservation priority in the northeastern United States. Remnant New England cottontail populations currently occur in five geographically disjunct locations: southern Maine and southeastern New Hampshire (MENH); the Merrimack Valley in central New Hampshire (NH-MV); Cape Cod, Massachusetts (CC); parts of eastern Connecticut and Rhode Island (CTRI); and western Connecticut, southeastern New York and southwestern Massachusetts (CTNY). We used microsatellite genotyping to discern patterns of population structure, genetic variability, and demographic history across the species’ range and to assess whether the observed patterns are a consequence of recent habitat loss and fragmentation. Our findings show that the geographic populations are highly differentiated (overall F ST = 0.145; P < 0.001). Using Bayesian clustering analyses, we identified five genetic clusters, which corresponded closely to the geographic populations, but grouped MENH & NH-MV together (ME/NH) and identified an isolated population in eastern Connecticut (Bluff Point). The genetic clusters showed little evidence of recent gene flow and are highly influenced by genetic drift. The CC and Bluff Point populations show signs they experienced a genetic bottleneck, whereas the ME/NH population shows evidence of ongoing decline. Populations in Bluff Point, CC, and ME/NH also show significantly reduced genetic variation relative to the other clusters (CTNY and CTRI without Bluff Point). Without immediate human intervention, the short-term persistence of New England cottontail populations in Maine, New Hampshire and Cape Cod is at great risk. Conservation efforts at this time should focus on within-population sustainability and eventually restoring connectivity among these isolated populations.

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Acknowledgments

We are grateful to the many agency biologists, volunteers, former students and technicians for their assistance with trapping and pellet collection, including, Walter Jakubas, Kate O’Brien, Kelly Boland, Steven Fuller, Howard Kilpatrick, Paul Novak, Brian Tefft, Mike Marchand, Brian Johnson, Robin Innes, Vanessa Johnson, and Jim Panaccione. Melanie Schroer, Elisha Allan, Grace Smarsh, Samantha Petren, Cynthia Sirois and Allison Citro helped with DNA extractions and species identifications. Funding for this research was provided by the United States Fish and Wildlife Service, Maine Department of Inland Fisheries and Wildlife, and the Maine Outdoor Heritage Fund. We thank Anthony Tur, Kate O’Brien and Walter Jakubas for their support. Stephanie Coster, Jennifer Walsh, Daniel Brubaker, Charlotte Gabrielsen and two anonymous reviewers provided helpful comments on earlier versions of this manuscript. Partial funding was provided by the New Hampshire Agricultural Experiment Station. This is Scientific Contribution Number 2447.

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  1. Zoology Graduate Program, University of New Hampshire, Durham, NH, 03824, USA

    Lindsey E. Fenderson & Marianne K. Litvaitis

  2. Department of Natural Resources and the Environment, University of New Hampshire, 56 College Rd, Durham, NH, 03824, USA

    Adrienne I. Kovach, John A. Litvaitis & Marianne K. Litvaitis

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  1. Lindsey E. Fenderson
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  2. Adrienne I. Kovach
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Correspondence to Adrienne I. Kovach.

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Fenderson, L.E., Kovach, A.I., Litvaitis, J.A. et al. Population genetic structure and history of fragmented remnant populations of the New England cottontail (Sylvilagus transitionalis). Conserv Genet 12, 943–958 (2011). https://doi.org/10.1007/s10592-011-0197-x

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