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 in creasing frequency to estimate phylogenetic relationships among animal taxa. The advantage to using DNA-sequence data is that many of the pr ocesses governing the evolution and inheritance of DNA are already und erstood. DNA data, however, do not guarantee the correct phylogenetic tree because of problems associated with shared ancestral polymorphism s 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 i ndividual genes and nucleotides. This article reviews molecular proces ses, discusses the correction of genetic distances and the weighting o f DNA data, and provides an assessment of the phylogenetic usefulness of specific mitochondrial genes. The Appendix presents a compilation o f conserved polymerase chain reaction primers that can be used to ampl ify virtually any gene in the mitochondrial genome. DNA data sets vary tremendously in degree of phylogenetic usefulness. Correction or weig hting (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 o f ribosomal genes can be problematic, whereas unconstrained sites in p rotein coding genes appear to have fewer problems. In addition, inform ation from studies of amino acid substitutions in rapidly evolving gen es may help to decipher close relationships. For intermediate levels o f divergence where silent sites contain many multiple hits, amino acid changes can be useful for construction phylogenetic relationships. Fo r 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 tax onomic categories, no sweeping generalizations can be made about the t axonomic rank at which particular genes are useful. As more DNA-sequen ce data accumulate, we will be able to gain an even better understandi ng of the way in which genes and species evolve.