The population biology of mitochondrial DNA and its phylogenetic implications

The reconstruction of evolutionary trees from mitochondrial DNA (mtDNA) data is a common tool with which to infer the relationships of living organisms. The wide use of mtDNA stems from the ease of getting new sequence data for a set of orthologus genes and from the availability of many existing mtDNA sequences for a wide array of species. In this review we argue that developing a fuller understanding of the biology of mitochondria is essential for the rigorous application of mtDNA to inferences about the evolutionary history of species or populations. Though much progress has been made in understanding the parameters that shape the evolution of mitochondria and mtDNA, many questions still remain, and a better understanding of the role this organelle plays in regulating organismal fitness is becoming increasingly critical for accurate phylogeny reconstruction. In population biology, the limited information content of one nonrecombining genetic marker can compromise evolutionary inference, and the effects of nuclear genetic variation-and environmental factors-in mtDNA fitness differences can compound these problems. In systematics, the limited gene set, biased amino acid composition, and problems of compensatory substitutions can cloud phylogenetic signal. Dissecting the functional bases of these biases offers both challenges and opportunities in comparative biology.