Data files associated with: Evolution of the mutation spectrum across a mammalian phylogeny ...

• Main Authors: Beichman, Annabel, Robinson, Jacqueline, Lin, Meixi, Moreno-Estrada, Andrés, Nigenda-Morales, Sergio, Harris, Kelley
• Format: Dataset
• Language: English
• Published: Dryad 2023
• Subjects: Mutation; phylogeny; phylogenetic signal; Mus musculus; Mus spretus; Ursus arctos; Phocoena sinus; Balaenoptera physalus; Ursus maritimus; Pongo abelii; Pongo pygmaeus; Pan paniscus; Pan troglodytes; Canis lupus; Gorilla gorilla; mutation spectrum; polymorphism; FOS Biological sciences; Fin whale; gray wolf
• Online Access: https://dx.doi.org/10.5068/d1339f; https://datadryad.org/stash/dataset/doi:10.5068/D1339F

Although evolutionary biologists have long theorized that variation in DNA repair efficacy might explain some of the diversity of lifespan and cancer incidence across species, we have little data on the variability of normal germline mutagenesis outside of humans. Here, we shed light on the spectrum and etiology of mutagenesis across mammals by quantifying mutational sequence context biases using polymorphism data from thirteen species of mice, apes, bears, wolves, and cetaceans. After normalizing the mutation spectrum for reference genome accessibility and k-mer content, we use the Mantel test to deduce that mutation spectrum divergence is highly correlated with genetic divergence between species, whereas life history traits like reproductive age are weaker predictors of mutation spectrum divergence. Potential bioinformatic confounders are only weakly related to a small set of mutation spectrum features. We find that clocklike mutational signatures previously inferred from human cancers cannot explain the ... : Mutation spectra were generated based on publicly-available whole genome sequencing polymorphism data (VCF format) from 13 mammal species (house mouse, Algerian mouse, humans, Bornean orangutan, Sumatran orangutan, chimpanzee, gorilla, bonobo, gray wolf, polar bear, brown bear, vaquita porpoise, and fin whale). Spectra were generated for each species at the 1-mer, 3-mer, 5-mer and 7-mer level using the program mutyper and a pipeline that is described extensively in the paper's SI Methods section and on the project's GitHub repository (https://github.com/harrispopgen/mammal_mutation_spectra/). Data files are described in depth in the Dryad repository's README file. ...