Molecular phylogenetics of the avian genus Pipilo and a biogeographic argument for taxonomic uncertainty.

We sequenced 1709 base pairs (bp) of mitochondrial DNA including parts of cytochrome b, ND 2, and the control region (CR I, II) for seven members of the avian genus Pipilo (towhees), Melozone kieneri (rusty-crowned ground-sparrow), and Arremonops rufivirgatus (olive sparrow). A total of 457 bp was variable and 257 bp were potentially phylogenetically informative. All gene regions were similarly variable (20.2 to 28.4%) except for CR II (38.4%); third position transitions were as common as substitutions in the CR. Tree topology was sensitive to choice of outgroup(s) and individual sequences used as exemplars. Six trees were considered viable phylogenetic hypotheses based on maximum parsimony and maximum likelihood analyses. These trees generally supported two groups of towhees (rufous-sided group, brown towhee group), a sister taxon relationship for P. aberti and P. crissalis, and a sister taxon relationship for P. ocai and P. maculatus. The occurrence of M. kiernei within Pipilo in three trees challenges the monophyly of the latter; the other species of Melozone and other outgroups require study to resolve Pipilo monophyly. The relationships of P. albicollis and P. fuscus were ambiguous, as they were with previous data sets (allozymes, mtDNA restriction sites); they could be sister species or either one could be the basal species in the brown towhee group. We suggest that this taxonomic uncertainty obtains from the contemporaneous origin of P. fuscus, P. albicollis, and the ancestor of P. aberti/P. crissalis. We favor a "star" phylogeny because species in unrelated lineages found in the same region as P. albicollis are similarly difficult to resolve phylogenetically. Synapomorphies from coding genes and the CR did not preferentially support basal and terminal nodes, and hence did not provide different windows of taxonomic resolution, which might be expected from the apparent rapid rate of CR evolution. Phylogenetic trees inferred from allozymes, restriction sites, and mtDNA sequences were congruent, suggesting that each is a useful source of phylogenetic information. Copyright 1998 Academic Press.