Reconstruction of the MalDH Sequence-Only Tree

The MalDH gene family was reconstructed with Silix (Miele et al. 2011). The 51 MalDH sequences were then aligned with Muscle (Edgar 2004) used in Guidance (Penn et al. 2010), which allows to trim ambiguously aligned sites owing to uncertainty in the guide tree topology. Remaining ambiguously aligned sites were removed with Gblocks (Castresana 2000). The Bayesian sequence-only tree was reconstructed using the CAT+GTR model implemented in PhyloBayes 3.3 (Lartillot et al. 2009). We ran 1,000,000 long independent MCMC chains, saving a sample each 10 cycles, and we discarded the 1,000 first samples as burnin. The chain's convergence was assessed if the tree bipartition PP differ by <0.05. The consensus sequence-only tree was then reconciled with the species tree.