Phylogeny_of_Typhlocharina_RAxML_BestTree

ML trees were obtained using RAxML 7.2.7 (Stamatakis 2006). Data sets were partitioned by gene and the protein-coding genes (cox1-a and cox1-b fragments) were additionally partitioned by separating the third codon positions (Andújar et al. 2012). An independent GTR + G model was applied to each data partition. The best scoring ML tree was selected among 200 searches on the original alignment with different randomized parsimony starting trees. Support values were obtained with 1000 bootstrap replicates (Felsenstein 1985). BI was run in MrBayes 3.2.3 (Huelsenbeck et al. 2001) on the concatenated data, partitioned by gene and codon as before, and for each partition the optimal substitution model was selected using the Akaike information criterion (AIC) in jModelTest 2.1.7 (Darriba et al. 2012).