SEARCHING FOR THE CLOSEST LIVING RELATIVE(S) OF TETRAPODS THROUGH EVOLUTIONARY ANALYSES OF MITOCHONDRIAL AND NUCLEAR-DATA

The phylogenetic relationships of the African lungfish (Protopterus do lloi) and the coelacanth (Latimeria chalumnae) with respect to tetrapo ds were analyzed using complete mitochondrial genome DNA sequences. A lungfish + coelacanth clade was favored by maximum parsimony (although this result is dependent on which transition: transversion weights ar e applied), and a lungfish + tetrapod clade was supported by neighbor- joining and maximum-likelihood analyses. These two hypotheses received the strongest statistical and bootstrap support to the exclusion of t he third alternative, the coelacanth + tetrapod sister group relations hip. All mitochondrial protein coding genes combined favor a lungfish + tetrapod grouping. We can confidently reject the hypothesis that the coelacanth is the closest living relative of tetrapods. When the comp lete mitochondrial sequence data were combined with nuclear 28S rRNA g ene data, a lungfish + coelacanth clade was supported by maximum parsi mony and maximum likelihood, but a lungfish + tetrapod clade was favor ed by neighbor-joining. The seemingly conflicting results based on dif ferent data sets and phylogenetic methods were typically not statistic ally strongly supported based on Kishino-Hasegawa and Templeton tests, although they were often supported by strong bootstrap values. Differ ences in rate of evolution of the different mitochondrial genes (slowl y evolving genes such as the cytochrome oxidase and tRNA genes favored a lungfish + coelacanth clade, whereas genes of relatively faster sub stitution rate, such as several NADH dehydrogenase genes, supported a lungfish + tetrapod grouping), as well as the rapid radiation of the l ineages back in the Devonian, rather than base compositional biases am ong taxa seem to be directly responsible for the remaining uncertainty in accepting one of the two alternate hypotheses.