Gastrointestinal parasites of the New England cottontail rabbit (Sylvilagus transitionalis) and eastern cottontail rabbit (Sylvilagus floridanus) in the Hudson Valley, New York


The New England cottontail rabbit (NEC, Sylvilagus transitionalis) population has decreased dramatically in New York, USA, and the role of parasites in limiting the population has never been examined. The closely related and sympatric eastern cottontail rabbit (EC, Sylvilagus floridanus) was introduced into the range of NEC by humans and is currently thriving. This study aimed to investigate gastrointestinal parasites of the NEC and the EC and compare their parasite communities. Fecal pellets from 195 NEC and 125 EC were collected from the Hudson Valley, New York, in the winter of 2013–2014. Centrifugal fecal floats were performed in Sheather’s sugar solution, and parasite ova and cysts were examined microscopically to identify gastrointestinal parasites present. For all pellets combined (n = 320), 91% were found to harbor at least 1 parasite species, with Eimeria species being the most common. Genetic analysis of pellets using microsatellite DNA identified 248 individual rabbits, with parasite prevalence (94%) similar to the prevalence estimate based on all pellets (91%). EC samples had a significantly higher (p < 0.05) parasite species richness (1.73, range 0–4) than NEC (1.20, range 0–3). EC and NEC shared 3 moderate to high (9–89%) prevalence parasites, in which EC prevalence was consistently higher. One parasite species was only found in NEC, and two were only found in EC, but the majority of these were of low abundance, precluding further statistical analyses.

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Special thanks to A. Cheeseman who helped with collections and coordination of sampling efforts. Thanks to A. Bloomfield, J. Decotis, M. delPuerto, K. Deweese, K. Farrell, J. Jaycox, P. Novak, E. Underwood, and G. Walters, who aided with pellet collection. Thanks to K.A.W Lindsay, C. Michaud, S. Page, and M. Wilson who assisted with lab work. Thanks to A. Bielecki who assisted with data entry.


The New York Department of Environmental Conservation provided funding and logistical support.

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Correspondence to Christopher M. Whipps.

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Although there was no handling of live animals as a direct component of the research reported here, this work was part of a larger project which was conducted with approval of the SUNY-ESF Institutional Animal Care and Use Committee (protocol #120801).

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The authors declare that there is no conflict of interest.

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This study represents the first parasitological study of cottontail rabbits in New York.

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Whipps, C.M., Gavard, E.J., Cohen, J. et al. Gastrointestinal parasites of the New England cottontail rabbit (Sylvilagus transitionalis) and eastern cottontail rabbit (Sylvilagus floridanus) in the Hudson Valley, New York. Parasitol Res 118, 2257–2262 (2019).

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  • Sylvilagus transitionalis
  • Sylvilagus floridanus
  • New England cottontail
  • Non-invasive genetics
  • Eimeria