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The use of parameter-rich substitution models in molecular phylogenetics has been criticized on the basis that these models can cause a reduction both in accuracy and in the ability to discriminate among competing topologies. We have explored the relationship between nucleotide substitution model complexity and nonparametric bootstrap support under maximum likelihood (ML) for six data sets for which the true relationships are known with a high degree of certainty. We also performed equally weighted maximum parsimony analyses in order to assess the effects of ignoring branch length information during tree selection. We observed that maximum parsimony gave the lowest mean estimate of bootstrap support for the correct set of nodes relative to the ML models for every data set except one. For several data sets, we established that the exact distribution used to model among-site rate variation was critical for a successful phylogenetic analysis. Site-specific rate models were shown to perform very poorly relative to gamma and invariable sites models for several of the data sets most likely because of the gross underestimation of branch lengths. The invariable sites model also performed poorly for several data sets where this model had a poor fit to the data, suggesting that addition of the gamma distribution can be critical. Estimates of bootstrap support for the correct nodes often increased under gamma and invariable sites models relative to equal rates models. Our observations are contrary to the prediction that such models cause reduced confidence in phylogenetic hypotheses. Our results raise several issues regarding the process of model selection, and we briefly discuss model selection uncertainty and the role of sensitivity analyses in molecular phylogenetics.

New Zealand's isolation, its well-studied rapidly changing landscape, and its many examples of rampant speciation make it an excellent location for studying the process of genetic differentiation. Using 1520 base pairs of mitochondrial DNA from the cytochrome oxidase subunit I, ATPase subunits 6 and 8 and tRNA(Asp) genes, we detected two well-differentiated, parapatrically distributed clades within the widespread New Zealand cicada species Maoricicada campbelli that may prove to represent two species. The situation that we uncovered is unusual in that an ancient lineage with low genetic diversity is surrounded on three sides by two recently diverged lineages. Using a relaxed molecular clock model coupled with Bayesian statistics, we dated the earliest divergence within M. campbelli at 2.3 +/- 0.55 million years. Our data suggest that geological and climatological events of the late Pliocene divided a once-widespread species into northern and southern components and that near the middle of the Pleistocene the northern lineage began moving south eventually reaching the southern clade. The southern clade seems to have moved northward to only a limited extent. We discovered five potential zones of secondary contact through mountain passes that will be examined in future work. We predict that, as in North American periodical cicadas, contact between these highly differentiated lineages will exist but will not involve gene flow.