A previously recognized north-south mitochondrial DNA (mtDNA) break in populations of deer mice, Peromyscus maniculatus, was investigated in Western North America. A 383-bp fragment of the mtDNA control region was analyzed from 107 tissue samples in the unstudied Warner Mountains of northeastern California. To determine if this north-south mtDNA break was also reflected in morphology, six cranial and mandibular measurements were taken from 72 deer mice. Using multivariate analysis of variance (MANOVA), it was determined that cranial characters did not vary significantly between the two mtDNA haplogroups, and discriminant function analysis (DFA) was unable to discriminate between the two haplogroups. Neutrality statistics and mismatch distribution analyses were performed on both mitochondrial haplotypes to test for recent demographic expansion. The analyses suggest that during Pleistocene glaciations, P. maniculatus persisted south of the glacial leading edge and in Pacific Northwest refugia. Upon retreat of the glaciers, refugial mice expanded from their glacial refuges, while populations south of the glaciers remained fairly stable
