Variation in Mitochondrial DNA and the Biogeographic History of Woodrats (Neotoma) of the Eastern United States

Genetic variation in 114 woodrats (Neotoma) from 33 locations in the eastern and central United States was examined using analysis of mitochondrial DNA (mtDNA) restriction sites. Results indicate that three major lineages of Neotoma floridana (southern, western, and northern) diverged in the early Pleistocene. The southern lineage exhibits substantial mtDNA variability and population structure. The pattern of mtDNA variation in the southern lineage suggests that vicariance events, including the insularization of Florida, have been important determinants of geographic variation. The low levels of sequence variation within the northern and western lineages indicate that woodrat populations in these areas are probably the result of relatively recent (Holocene) range expansions. These conclusions are not entirely consistent with the current taxonomy of eastern woodrats and suggest that taxonomic revision is warranted. [Mitochondrial DNA; biogeography; phylogeography; cladistics; phylogenetics; Neotoma. ] The geographic distribution and genetic structure of contemporary populations are determined both by current ecology and by historical patterns of vicariance and dis? persal. The availability of DNA restriction site and sequence data has focused atten? tion on the use of gene genealogies (es? pecially mitochondrial DNA [mtDNA] ge? nealogies) to clarify recent patterns of gene flow and historical patterns of population subdivision and genetic differentiation. Empirical studies of the distribution of mtDNA haplotypes in the context of ex? plicit mtDNA phylogenies have demon? strated the value of this approach (e.g., Ber? mingham and Avise, 1986; Cann et al., 1987; Baker et al., 1990; Riddle and Honeycutt, 1990). The study of the relationship be? tween genealogy and geography has been termed "intraspecific phylogeography" (Avise et al., 1987; Avise, 1989). Analysis of animal mtDNA can be a powerful tool in the identification of phylogeographic patterns. Not only is mtDNA variation easily assessed (because of high copy number, small genome size, and sim? ple sequence organization), but maternal inheritance and apparent absence of re? combination simplify interpretation of mtDNA phylogenies (which are equiva? lent to maternal genealogies). In mammals, sequence differences appear to accumulate faster in mtDNA than in many single-copy nuclear genes (Wilson et al., 1985; Moritz et al., 1987), allowing discrimination of lin? eages that have diverged from one another relatively recently. However, because mtDNA is a set of completely linked mark? ers and because of lineage sorting (from polymorphic ancestors) and differential in? trogression, an mtDNA genealogy is not necessarily an accurate representation of organismal phylogeny (Avise et al., 1987; Harrison, 1989). We examined phylogeographic varia? tion of mtDNA haplotypes in woodrats of the eastern United States (Neotoma pon? dana) to gain insights into the recent pop? ulation history of this widespread rodent species. Our observations and conclusions are relevant to issues surrounding conser? vation and management of woodrat pop? ulations, which have experienced signifi? cant declines in several northern states. 3 Present address: Department of Forest Science, Oregon State University, Hatfield Marine Science Center, Newport, Oregon 97365, USA.