Examples demonstrating instances where the minimum number of mt protein-coding (PC) genes is either apparent or ambiguous.

<p>A) A phylogeny for the Cephalopoda where the number of mt protein-coding (PC) genes minimally required to infer a statistically indistinguishable topology to that of the “supergene” set (i.e., all 13 mt PC genes) is apparent. Shimodaira-Hasegawa (SH) tests indicated a minimum of four genes as being needed. The break is clearly indicated by the large decrease in Ln <i>L</i> compared to the “supergene” phylogeny when utilizing less than four genes or when utilizing four or more genes. This trend was typical for the majority of lineages examined (93.5% and 93.0% when utilizing amino acid and nucleotide data, respectively). B) A phylogeny for the Haplorrhini where the number of mt protein-coding (PC) genes minimally required to infer a statistically indistinguishable topology to that of the “supergene” topology is ambiguous. In this case, the SH tests indicated utilizing any combination other than three genes recovered the “supergene” topology, which is indicated by the large decrease in Ln <i>L</i> when just three genes are employed. In these cases, the minimum number of genes that statistically recreated the “supergene” topology was chosen (e.g., a single gene, NAD5, for Haplorrhini). This alternative trend was atypical of the data (6.5% and 7.0% of lineages when utilizing amino acid and nucleotide data, respectively). Comparisons presented in A and B are for phylogenies that utilized amino acid data and were inferred via maximum likelihood.