The phylogenetic utility of cytochrome b: lessons from bufonid frogs.

The mitochondrial cytochrome b gene is widely used in systematic studies to resolve divergences of many different ages. To investigate phylogenetic relationships among frogs of the large family Bufonidae, and to explore the utility of cytochrome b for this purpose, approximately one-third of the gene was sequenced from representatives of this group. Samples were chosen to represent a range of divergence levels within Bufonidae: (1) deep (= old), among species from around the world; (2) middle, among North American species; and (3) shallow (= young), within a single species group (the Bufo boreas group). The inferred amino acid sequences of cytochrome b are highly similar in these frogs although most pairwise comparisons of the nucleotide sequences are 15-20% different. Consequently insufficient information is available to generate robust phylogenetic hypotheses for the older divergences; silent differences are saturated and yet almost no informative replacement differences exist. Among the younger divergences, silent differences are not saturated and some resolution is possible. These results show that (1) the amino acid sequence of cytochrome b evolves differently in Bufonidae than expected based on other vertebrates (2) it consequently provides surprisingly little information about old divergences in Bufonidae, and (3) phylogenetic studies applying particular genes to new groups should begin with preliminary surveys of exemplar taxa representing the range of divergence times within the group to estimate the likely phylogenetic utility of that gene in that group.