Evolution, Weighting, and Phylogenetic Utility of Mitochondrial Gene Sequences and a Compilation of Conserved Polymerase Chain Reaction Primers

DNA-sequence data from the mitochondrial genome are being used with increasing frequency to estimate phylogenetic relationships among animal taxa. The advantage to using DNA-sequence data is that many of the processes governing the evolution and inheritance of DNA are already understood. DNA data, however, do not guarantee the correct phylogenetic tree because of problems associated with shared ancestral polymorphisms and multiple substitutions at single nucleotide sites. Knowledge of evolutionary processes can be used to improve estimates of patterns of relationships and can help to assess the phylogenetic usefulness of individual genes and nucleotides. This article reviews molecular processes, discusses the correction of genetic distances and the weighting of DNA data, and provides an assessment of the phylogenetic usefulness of specific mitochondrial genes. The Appendix presents a compilation of conserved polymerase chain reaction primers that can be used to amplify virtually any gene in the mitochondrial genome. DNA data sets vary tremendously in degree of phylogenetic usefulness. Correction or weighting (or both) of DNA-sequence data based on level of variability can improve results in some cases. Gene choice is of critical importance. For studies of relationships among closely related species, the use of ribosomal genes can be problematic, whereas unconstrained sites in protein coding genes appear to have fewer problems. In addition, information from studies of amino acid substitutions in rapidly evolving genes may help to decipher close relationships. For intermediate levels of divergence where silent sites contain many multiple hits, amino acid changes can be useful for construction phylogenetic relationships. For deep levels of divergence, protein coding genes may be saturated at the amino acid level and highly conserved regions of ribosomal RNA and transfer RNA genes may be useful. Because of the arbitrariness of taxonomic categories, no sweeping generalizations can be made about the taxonomic rank at which particular genes are useful. As more DNA-sequence data accumulate, we will be able to gain an even better understanding of the way in which genes and species evolve.