THE USE OF RESTRICTION ENDONUCLEASES TO MEASURE MITOCHONDRIAL DNA SEQUENCE RELATEDNESS IN NATURAL POPULATIONS. I. POPULATION STRUCTURE AND EVOLUTION IN THE GENUS PEROMYSCUS

In this study we introduce to natural population analysis a molecular technique that involves the use of restriction endonucleases to compare mitochondrial DNA (mtDNA) sequences. We have examined the fragment patterns produced by six restriction endonucleases acting upon mtDNA isolated from 23 samples of three species of the rodent Peromyscus. Our observations confirm the following conclusions derived from previous experiments with laboratory animals: (1) mtDNA within an individual appears homogeneous; (2) at least the majority of mtDNA present in an individual is inherited from the female parent. Our experiments demonstrate for the first time that there is detectable heterogeneity in mtDNA sequences within and among natural geographic populations of a species and that this heterogeneity can readily be used to estimate relatedness between individuals and populations. Individuals collected within a single locale show less than 0.5% sequence divergence, while those collected from conspecific populations separated by 50 to 500 miles differ by approximately 1.5%. The mtDNAs of the closely related sibling species P. polionotus and P. mniculutus differ from each other by 13 to 17%; nonsibling species differ by more than 20%. Qualitative and quantitative approaches to analysis of digestion patterns are suggested. The results indicate that restriction analysis of mtDNA may become the most sensitive and powerful technique yet available for reconstructing evolutionary relationships among conspecific organisms.