Phylogenetic Reconstruction

For phylogenetic reconstruction from the cytochrome b sequences, three methods were employed - maximum parsimony (MP), maximum likelihood (ML), and Bayesian inference of phylogeny (BI). MP and ML analyzes were used as implemented in the program Paup 4.0b10 (Swofford 2002). Bayesian phylogenetic analysis was performed using the program MrBayes 3.0b4 (Huelsenbeck and Ronquist 2001). Because prior analyzes have shown that saturation effects are negligible in our data set, all characters were equally weighted in the parsimony analysis. ML trees were calculated using the models selected under the Akaike Information Criterion (AIC) in Modeltest 3.06 (Posada and Crandall 1998), using heuristic searches with tree-bisection-reconnection branch swapping and ten random addition sequence replicates. Bayesian analysis was performed in four chains for 1-2 millions of generations with the same parameter settings as for the ML calculation.

Support for clades from both data sets was assessed by bootstrapping (Felsenstein 1985). Bootstrap analyzes for neighbor joining and MP were performed with 1,000 replicates and under the same parameter settings as for the original trees. Under the ML criterion, bootstrap analyzes were performed with 100 replicates and without branch swapping to save computation time.

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