Abstract
Phylogenetic trees are analytic tools used in primate studies to elucidate evolutionary relationships. Because of its relative ease to sequence and rapid evolution compared to nuclear genomes, mitochondrial DNA is frequently used for phylogeny building. This project evaluated the effectiveness of using individual or grouped mitochondrial genes (mtGenes) as a proxy for the mitochondrial genome (mtGenome) in phylogeny building within two nested primate datasets, Cebidae and Platyrrhini, with differing divergence dates. mtGene utility rankings were determined based on congruence values to the mtGenome tree. mtGenes trees were also assessed on tree resolution and ability to sort nested clades. We found that most individual mtGenes, including ribosomal genes (12S and 16S), COX genes, most ND genes, and d-Loop are not appropriate for use as proxies for the mtGenome when tree building in either the Cebidae or Platyrrhini set. On average, grouped mtGenes outperformed individual mtGenes in both sets, and mtGene and grouped mtGene rankings varied between sets. Pairing CYB and COX3 together or pairing ND2 and CYB worked well in both the Cebidae set and the Platyrrhini set. We also found that nucleotide diversity is not a predictor of mtGene performance. Instead, it may be that unique mtGene or mtGene system evolutionary history impacts mtGene performance.