Molecular identification of three sympatric lagomorphs in the Northeastern United States

The New England cottontail (Sylvilagus transitionalis) is the focus of extensive efforts to conserve the species. A major component of their conservation program is the collection of faecal samples to determine their distribution and abundance throughout their range. In parts of their range, New England cottontail is sympatric with a non-native eastern cottontail (S. floridanus) and snowshoe hare (Lepus americanus). Because faecal samples from all three lagomorphs are indistinguishable, a reliable molecular genetic method for specimen identification is necessary. We tested the efficacy of a diagnostic character method by analyzing sequence data from 1770 faecal, blood, and tissue samples collected from five states in the Northeastern United States. The method amplified a portion of the mitochondrial DNA control region and identified numerous diagnostic characters for each species. Two suspected nuclear mitochondrial DNA sequences (NUMTs) also were identified when a universal primer was used in the polymerase chain reaction. Our study could be the first evidence of a NUMT in a lagomorph and highlights the importance of using taxon-specific primers for species identification.