How and Why Overcome the Impediments to Resolution: Lessons from rhinolophid and hipposiderid Bats

Foley, Nicole M.; Thong, Vu Dinh; Soisook, Pipat; Goodman, Steven M.; Armstrong, Kyle N.; Jacobs, David S.; Puechmaille, Sébastien J.; Teeling, Emma C.

The molecular dating analysis was carried out using the MCMCTREE program in PAML (Yang 2007) . The analysis was carried out on the exon+intron data set-outliers removed, as this represents the most optimized combined data set. MCMCTREE requires a completely bifurcating tree, and as such, the analysis was carried out on the tree resulting from the Bayesian analysis with BEAST from the same data set, because other trees contained polytomies. The analysis was run under the HKY85 model of sequence evolution, the most comprehensive model available in PAML. Analysis was carried out using both the independent and correlated rates models. The root age was set to 64-65 Ma following consistent recovery in the following articles: Eick et al. (2005) , Teeling et al. (2005) , and Miller-Butterworth et al. (2007) . The chain was run for 20,000 generations sampling every second generation, with 10% of the resulting trees discarded as burn-in. The analysis was repeated three times to check for convergence.