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 ..., This dataset includes four main categories of data: the nexus files, the Visual TreeCmp scores, the mtGenome trees for both Platyrrhini and Cebidae, and the sample info.
(1) The nexus files were generated through extraction from whole mtGenome data, some newly published in this study and available on GenBank (PP454502-PP454561). Extractions were either present in the mtGenome as annotated from previous authors, or were predicted using Geneious Prime's v. 2023.1.2 (Biomatters Ltd.) prediction and annotation feature using a reference from a close-relative annotated genome: Sapajus xanthosternos (Accession no. KC757410) for Sapajus samples, and Cebus albifrons (Accession no. AJ309866) for Cebus samples.Entire mtGenomes, rRNA genes (n = 2), and D-Loop were aligned using the Clustal Omega v.1.2.2 (Sievers et al., 2011) alignment feature. Protein coding genes (n = 13) were aligned using the Muscle v.5.1 (Edgar, 2022) multiple alignment feature. All gene alignments were additionally check..., , # Mitochondrial DNA for phylogeny building supplemental information

[https://doi.org/10.5061/dryad.q2bvq83w8](https://doi.org/10.5061/dryad.q2bvq83w8)

## Description of the data and file structure

### Files and variables

#### Alignment files: all \"mtGene\"\_\"Clade\".nex files

**Description:** Nexus files of the nucleotide alignments of all mtGenes, grouped mtGenes, and the mtGenomes. The name of the datafile indicates the mtGene (e.g. \"ND5\") or group of mtGenes (e.g. \"ND4_ND5\") followed by which analysis set (Cebidae or Platyrrhini). IDs for the newly assembled genomes use naming is consistent with the mtGenome sample code IDs, which can be found in the Sample info spreadsheet. The nexus files were generated through extraction from whole mtGenome data, some newly published in this study and available on GenBank (PP454502-PP454561). Extractions were either present in the mtGenome as annotated from previous authors, or were predicted using Geneious Prime's v. 2023.1.2 (Biomatters Ltd....,