  The family Nymphalidae is the largest family within the true butterflies and
has been used to develop hypotheses explaining evolutionary interactions
between plants and insects. Theories of insect and hostplant dynamics predict
accelerated diversification in some scenarios. We investigated whether
phylogenetic uncertainty affects a commonly used method (MEDUSA, modelling
evolutionary diversity using stepwise AIC) for estimating shifts in
diversification rates in lineages of the family Nymphalidae, by extending the
method to run across a random sample of phylogenetic trees from the posterior
distribution of a Bayesian run. We found that phylogenetic uncertainty greatly
affects diversification rate estimates. Different trees from the posterior
distribution can give diversification rates ranging from high values to almost
zero for the same clade, and for some clades both significant rate increase and
decrease were estimated. Only three out of 13 significant shifts found on the
maximum credibility tree were consistent across more than 95% of the trees from
the posterior: (i) accelerated diversification for Solanaceae feeders in the
tribe Ithomiini; (ii) accelerated diversification in the genus Charaxes, and
(iii) deceleration in the Danaina. By using the binary speciation and
extinction model (BISSE), we found that a hostplant shift to Solanaceae or a
codistributed character is responsible for the increase in diversification rate
in Ithomiini, and the result is congruent with the diffuse cospeciation
hypothesis. A shift to Apocynaceae is not responsible for the slowdown of
diversification in Danaina. Our results show that taking phylogenetic
uncertainty into account when estimating diversification rate shifts is of
great importance, and relying on the maximum credibility tree alone potentially
can give erroneous results.
