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: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 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/), 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.