The Effect of Alignment Uncertainty, Substitution Models and Priors in Building and Dating the Mammal Tree of Life

The CDS sequences derived from Liu et al. (2017) were processed to remove potential low-quality regions and indels. The aligned DNA sequences were trimmed and the sequences corresponding to any unusually long terminal branches were removed. Finally, the first and second codon positions (C12) were extracted from 4 sets of alignments - before trimming (BT), after trimming (AT), filtered by the protocol of Irisarri et al. (FP), and further filtered by comparing ML trees with the reference tree (FM). The extracted C12 positions of the BT, AT, FP, and FM alignment were used here to assess uncertainty of alignments and its effect on gene trees, species trees, and divergence time estimation.