Data from: Mitochondrial DNA for phylogeny building: Assessing individual and grouped mtGenes as proxies for the mtGenome in Platyrrhines

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 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.