Comparison of the phylogenetic performance of neodermatan mitochondrial protein-coding genes

We examined the ability of all protein-coding genes of 11 neodermatan mitochondrial genomes to recover the phylogeny of their combination. We subsampled randomly selected lengths (1-6000 bp) of contiguous sequence to consider the effect of length (100-6000 bp) on performance. All genes performed as well as randomly selected regions except ND2 (better) and ND5 (worse). All expected nodes were recovered (> 90% bootstrap) when 4.0 Kb had been sampled; 40 samples of 100 performed as well as four samples of 1000.