DOI: 10.5061/dryad.q2bvq83w8
title: Data from: Mitochondrial DNA for phylogeny building: Assessing individual and grouped mtGenes as proxies for the mtGenome in Platyrrhines

description: 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.
description: 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<em>: Sapajus
 xanthosternos</em> (Accession no. KC757410) for <em>Sapajus
 </em>samples, and <em>Cebus albifrons</em> (Accession
 no. AJ309866) for <em>Cebus</em> 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 checked by eye and
 re-aligned if necessary. The format of the data includes whether the
 mtGene identified followed by whether the alignment comes from the
 Platyrrhini set or the Cebidae set.  (2) The Visual
 Tree CMP scores were generated using trees created from each of the
 alignments into the Visual TreeCmp online tool (https://eti.pg.edu.pl/TreeCmp/). Thus, each mtGene shows scores for all rooted metrics for both the Cebidae set and the Platyrrhini set. Additionally, some analyses have different posterior-probability thresholds (PPT) sets with corresponding metric data, where the PPT indicates the minimum posterior probability to collapse a clade into a soft polytomy. (3) The mtGenome trees were the reference trees used to evaluate the scores of the individual mtGenes. (4) Sample info is simply a collection of information about the samples that we used in each of the datasets.
description: # 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.) prediction and annotation feature using a reference from a close-relative annotated genome:S*apajus 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 checked by eye and re-aligned if necessary. The format of the data includes whether the mtGene identified followed by whether the alignment comes from the Platyrrhini set or the Cebidae set. #### File: Sample\_info.xlsx **Description**: Sample information of all of the samples used in this project. The .xlsx and .pdf (see below) have three sheets/sections. The first ('Platyrrhini info') contains information about the samples used in the Platyrrhini analysis, and the third sheet 'Cebidae info' contains information about the samples used in the Cebidae analysis. Both sheets include the Sample ID as used in the study ('Sample ID'), the Genbank identifier, Species, Latitude, and Longitude of where the samples were collected. The second sheet 'Newly assembled mtGenomes' contains information relevant to the mtGenomes that we assembled, annotated, and published to Genbank. These have more information, including 'Sample ID', or what the samples were called in the project, 'Genbank identifier', 'Species', 'Lima Alignment Identifier', which is the code used in a previous study using the same sample source (Lima 2018), mtGenome sample code, the original naming attached to the raw mtGenome reads, Latitude, Longitude, Voucher or Source, and BioSample Accession number. For Latitude and Longitude, 'Captive' indicates that the animal was captive and 'NA' indicates that the information for locality is not available. **File: Sample_info.pdf** **Description:** This is the same file as above (Sample_info.xlsx), but in an easier to read .pdf format. **File: VisualTreeCMP_scores.csv** Description: Raw incongruency scores for each set (Cebidae and Platyrrhini) across three PPTs (0.50, 0.75, 0.90). Z-scores are also included for comparison across metrics. This data was achieved using the online tool VisualTreeCMP ([https://eti.pg.edu.pl/TreeCmp/](https://eti.pg.edu.pl/TreeCmp/)), a free and accessible tool for comparing phylogenetic trees using a eighteen possible metrics (separated into rooted or unrooted tree categories). I highly recommend checking this tool out! #### File: 'mtGENOME\_PLATYRRHINE.tre' and 'mtGENOME\_CEBIDAE.tre' Description: Phylogenetic tree files generated from entire mtGenome alignments using MrBayes. **References:** Edgar, R. C. (2022). HighAccuracy Alignment Ensembles Enable Unbiased Assessments of Sequence Homology and Phylogeny. bioRxiv. . Lima, M. G. M., J. S. SilvaJnior, D. ern, et al. 2018. A Phylogenomic Perspective on the Robust Capuchin Monkey (*Sapajus*) Radiation: First Evidence for Extensive Population Admixture Across South America. Molecular Phylogenetics and Evolution 124: 137150. Sievers, F., A. Wilm, D. Dineen, et al. 2011. Fast, Scalable Generation of HighQuality Protein Multiple Sequence Alignments Using Clustal Omega. Molecular Systems Biology 7: 539. . **Code/software** Any software that can read alignments will work for the nexus (.nex) file. A free option is UGENE. Microsoft Excel can open the excel files, and .pdf bundles are also provided if excel is inaccessible. For the trees, FigTree is a commonly used free option.