From population genetics to phylogeny: Uses and limits of mitochondrial DNA

Abstract

Mitochondrial DNA (mtDNA) is clonally and maternally inherited in all animals and in most plants. Mitochondrial gene content is similar although not identical in all eukaryotes. Because of these characteristics, mtDNA has a number of features useful to systematists for all levels of evolutionary divergence. Clonal inheritance leads to unusual confidence in constructing gene trees which are useful in population-level studies, such as in the detection of population subdivision. Maternal inheritance presents the opportunity to distinguish paternal from maternal gene flow. The clonal, or single-gene, nature of mtDNA inheritance leads to consideration of the expected convergence between gene- and species-trees. For closely related populations or species, it is desirable to use several genes to be sure that the correct species-tree is discovered; this means that, although mtDNA will be the most precise guide to the species tree because of its lower effective population size, nuclear genes should also be used in such studies. Although restriction fragment length polymorphisms dominated the field until recently, sequencing following DNA amplification using the polymerase chain reaction is now easier and opens up the use of preserved specimens to molecular systematists. Because mitochondria1 genes evolve at different rates, one of appropriate rate can be selected for almost any phylogenetic problem.