The distribution of genetic variation in a species depends on both gene flow and population history. In this study, we demonstrate the utility of nested clade analysis for identifying historical factors—ignored by most traditional analyses—and provide one of the first studies to apply this approach to plants. PCR-RFLP markers were used to survey 912 bp of cpDNA in Delphinium nuttallii (Ranunculaceae), a native of the Pacific Northwest. Twelve populations located throughout the range of the species were examined, sampling five individuals per population. Sixteen polymorphisms and nine haplotypes were observed. A single most parsimonious network was found, which contained only one homoplastic trait. AMOVA, a non-historical analysis, suggested a regime of restricted gene flow to explain the pattern of genetic variation that was observed (F ST = 0.87, P < 0.0001). A simple historical approach, the exact nested contingency analysis, rejected the null hypothesis of no geographical association for all but one nesting group (P < 0.05 for these clades), but could not identify the source of these associations. The full nested clade analysis detected restricted gene flow or past fragmentation for all one-step clades, and contiguous range expansion at high cladogram levels. These inferences are supported by the biology of D. nuttallii which has no special adaptations for seed dispersal, and by the geologic history of the area. Post-Pleistocene glacial retreat would have allowed northward expansion of D. nuttallii during the last 15,000 years, and the Missoula Floods of 13,500-15,000 years ago may have permitted subsequent dispersal through the Columbia River Gorge into the western portion of its current range. For D. nuttallii, nested clade analysis detected and identified important historical factors that could not be resolved by simpler analyses employed in this study.

Key words: chloroplast DNA, Delphinium nuttallii, nested clade analysis, phylogeography