A CONGRUENCE TEST OF RELIABILITY USING LINKED MITOCHONDRIAL-DNA SEQUENCES

In the absence of certainty, well-corroborated hypotheses of species r elationships serve as the best estimates of the true phylogenies of gr oups. This approach was extended to linked mitochondrial DNA (mtDNA) s equences that share the same gene phylogenies because of nonrecombinat ion. This expectation of congruence forms the basis to test the reliab ility of unequal weighting for different base positions and changes of DNA sequences. The principal data for this test were the mitochondria l 12S ribosomal RNA (rRNA), 16S rRNA, and cytochrome c oxidase subunit II sequences of five pecoran species (Artiodactyla, Eutheria), as obt ained from the same plasmid clones and/or mtDNA isolations of brain, l iver, or heart. Heavy weighting for stems and first/second codon posit ions and for transversions were first evaluated against the molecular evolutionary properties of the three genes and then evaluated by congr uence, as measured in terms of both agreement and resolution. With une qual weighting, congruence was increased among the trees that result f rom separate analyses of the three genes. These results support the re liability of these weighting schemes and illustrate how phylogenetic a ccuracy can be tested with gene phylogenies for linked sequences (e.g. , of mtDNA).