title: Diversity dynamics in Nymphalidae butterflies: effect of phylogenetic uncertainty on diversification rate shift estimates.
abstract: The species rich butterfly family Nymphalidae has been used to study evolutionary interactions between plants and insects. Theories of insect-hostplant dynamics predict accelerated diversification due to key innovations. In evolutionary biology, analysis of maximum credibility trees in the software MEDUSA (modelling evolutionary diversity using stepwise AIC) is a popular method for estimation of shifts in diversification rates. We investigated whether phylogenetic uncertainty can produce different results by extending the method across a random sample of trees from the posterior distribution of a Bayesian run. Using the MultiMEDUSA approach, we found that phylogenetic uncertainty greatly affects diversification rate estimates. Different trees produced diversification rates ranging from high values to almost zero for the same clade, and both significant rate increase and decrease in some clades. Only four out of 18 significant shifts found on the maximum clade credibility tree were consistent across most of the sampled trees. Among these, we found accelerated diversification for Ithomiini butterflies. We used the binary speciation and extinction model (BiSSE) and found that a hostplant shift to Solanaceae is correlated with increased net diversification rates in Ithomiini, congruent with the diffuse cospeciation hypothesis. Our results show that taking phylogenetic uncertainty into account when estimating net diversification rate shifts is of great importance, as very different results can be obtained when using the maximum clade credibility tree and other trees from the posterior distribution.
authors.affiliation: Laboratory of Genetics, Department of Biology, University of Turku, Turku, Finland.
authors.forename: Carlos
authors.initials: C
authors.lastname: Peña
authors.affiliation: Museum of Comparative Zoology, Harvard University, Cambridge, USA; Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, USA.
authors.forename: Marianne
authors.initials: M
authors.lastname: Espeland
mesh_terms: D000818:Animals; D001499:Bayes Theorem; D044822:Biodiversity; D002080:Butterflies / Q000145:classification* / Q000502:physiology; D019295:Computational Biology / Q000379:methods*; D019143:Evolution, Molecular; D008954:Models, Biological; D010802:Phylogeny; D012984:Software; D035501:Uncertainty
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