ABSTRACT
The tree that resulted from the likelihood analysis of the mitochondrial data set (Fig. 1.6) was markedly different from that obtained from the same data set using parsimony but was almost identical to the tree yielded by parsimony analysis of the RAG-1 nucleotide, transversion, and codon analyses (Fig. 1.2). The only difference being the placement of the carcharhiniform taxa as the sister group to the orectolobiform taxa rather than as the sister group to the Lamniformes. As discussed previously, this is likely due to the non-stationary codon usage profiles of the Orectolobiformes. Likelihood analysis of the mitochondrial transversion data yields the same topology as that of the majority of the analyses shown in Fig. 1.2 (likelihood of the combined nucleotide data set of all mitochondrial genes and RAG-1 also yielded the topology seen in Fig. 1.2).
