DOI: 10.5061/dryad.3j9kd51vn
title: Supplementary data: The molecular evolution of cancer associated genes in mammals

description: Cancer is a disease that many multicellular organisms have faced for
 millions of years, and species have evolved various tumour suppression
 mechanisms to control oncogenesis. Although cancer occurs across the tree
 of life, cancer related mortality risks vary across mammalian orders, with
 Carnivorans particularly affected. Evolutionary theory predicts different
 selection pressures on genes associated with cancer progression and
 suppression, including oncogenes, tumour suppressor genes and immune
 genes. Therefore, we investigated the evolutionary history of cancer
 associated gene sequences across 384 mammalian taxa, to detect signatures
 of selection across categories of oncogenes (GRB2, FGL2 and CDC42), tumour
 suppressors (LITAF, Casp8 and BRCA2) and immune genes (IL2, CD274 and
 B2M). This approach allowed us to conduct a fine scale analysis of gene
 wide and site-specific signatures of selection across mammalian lineages
 under the lens of cancer susceptibility. Phylogenetic analyses revealed
 that for most species the evolution of cancer associated genes follows the
 species’ evolution. The gene wide selection analyses revealed oncogenes
 being the most conserved, tumour suppressor and immune genes having
 similar amounts of episodic diversifying selection. Despite BRCA2’s status
 as a key caretaker gene, episodic diversifying selection was detected
 across mammals. The site-specific selection analyses revealed that the two
 apoptosis associated domains of the Casp8 gene of bats (Chiroptera) are
 under opposing forces of selection (positive and negative respectively),
 highlighting the importance of site-specific selection analyses to
 understand the evolution of highly complex gene families. Our results
 highlighted the need to critically assess different types of selection
 pressure on cancer associated genes when investigating evolutionary
 adaptations to cancer across the tree of life. This study provides an
 extensive assessment of cancer associated genes in mammals with highly
 representative, and substantially large sample size for a comparative
 genomic analysis in the field and identifies various avenues for future
 research into the mechanisms of cancer resistance and susceptibility in
 mammals.
description: For information on sampling and analysis see:
 https://doi.org/10.1038/s41598-024-62425-0
description: # Supplementary data: The molecular evolution of cancer associated genes
 in mammals \[Access this dataset on Dryad](Dataset DOI link) The dataset
 contains supplementary files for the comparative genomic analysis
 conducted in our study. Analysis was conducted on 9 cancer associated
 genes across 868 mammalian species. Data files include sequence
 alignments, phylogenetic trees and values generated from analyses
 conducted on the data monkey webserver
 ([https://www.datamonkey.org/](https://www.datamonkey.org/)): MEME and
 FUBAR. Genes: Based on their roles associated with cancer development and
 progression, nine genes were selected for in depth analyses. Three
 oncogenes; Growth factor receptor-bound protein 2 (GRB2), Fibrinogen like
 protein 2 (FGL2) and Cell Division Control protein 42 homolog (CDC42) and
 three tumour suppressors; Lipopolysaccharide Induced Tumour Necrosis
 Factor (LITAF), Caspase 8 (Casp8) and Breast Cancer gene 2 (BRCA2), and
 three immune genes; Interleukin-2 (IL2), Cluster Differentiation 274
 (CD274), and Beta-2-Microglobin (B2M) ## Gene Sequence Alignments
 Sequences were obtained from the NCBI genomic data based and manually
 aligned. The alignments were used as input to generate the phylogenetic
 trees and as input into the MEME and FUBAR analyses. Files are saved in
 the FASTA format. They can be viewed in alignment editing tools such as
 MEGA, Bioedit, Geneious, ect. Fasta files can also be viewed in text
 editors, e.g. notepad or Nano ### Files: B2M_Alignment.fas
 BRCA2_Alignment.fas Casp8_Alignment.fas CD274_Alignment.fas
 CDC42_Alignment.fas FGL2_Alignment.fas GRB2_Alignment.fas
 IL2_Alignment.fas LITAF_Alignment.fas ## Phylogenetic trees Phylogenetic
 trees were generated for each gene using MEGAX. Input for the trees are
 the sequence alignment FASTA files found in the "Gene Sequence
 Alignments" folder. Files are stored as netwicks. Files following the
 naming format of Gene_Tree_Netwick. The trees can be viewed using tools
 such as iTOL ([https://itol.embl.de/](https://itol.embl.de/)) or Figtree
 ([https://tree.bio.ed.ac.uk/software/figtree/](https://tree.bio.ed.ac.uk/software/figtree/)). ### Files: B2M_Tree_Tree_Netwick BRCA2_Tree_Netwick Casp8_Tree_Netwick CD274_Tree_Netwick FGL2_Tree_Netwick GRB2_Tree_Netwick IL2_Tree_netwick LITAF_Tree_Netwick ## Data monkey This folder contains results from two analyses conducted using the Datamonkey webserver. Each excel file follows the naming format of "Gene_FUBAR/MEME_Results" Descriptions for each data column is taken directly from the Datamonkey webserver description for the data columns. #### MEME (Mixed Effects Model of Evolution) Site: Refers to the nucleotide in the gene sequence the data is for Partition α : Synonymous substitution rate at a site β<sup>-</sup> : Non-synonymous substitution rate at a site for the negative/neutral evolution component p<sup>-</sup> : Mixture distribution weight allocated to β<sup>+</sup>; loosely -- the proportion of the tree evolving neutrally or under negative selection β<sup>+</sup> : Non-synonymous substitution rate at a site for the positive/neutral evolution component p<sup>+</sup> : Mixture distribution weight allocated to β<sup>+</sup>; loosely -- the proportion of the tree evolving neutrally or under positive selection LRT : Asymptotic p-value for episodic diversification, i.e., p<sup>+</sup> 0 andbeta<sup>+</sup> &gt; alpha p-value : Likelihood ratio test statistic for episodic diversification. i.e., p<sup>+</sup> 0 andbeta<sup>+</sup> &gt;alpha branches under selection : A rough estimate of the number of branches (here branches is either a single species or group of species) that have been under selection at this site. i.e. had an empirical bayes factor of 100 or more for the beta<sup>+</sup> rate ### Files: B2M_MEME_Results.xlsx BRCA2_MEME_Results.xlsx Casp8_MEME_Results.xlsx CD274_MEME_Results.xlsx CDC42_MEME_Results.xlsx FGL2_MEME_Results.xlsx GRB2_MEME_Results.xlsx IL2_MEME_Results.xlsx #### FUBAR (Fast, UnconstrainedBayesian AppRoximation) Site: Refers to the nucleotide in the gene sequence the data is for Partition: α : Mean posterior synonymous substitution rate at a site β : Mean posterior non-synonymous substitution rate at a site β-α : Mean posterior beta - alpha Prob[α&gt;β] : Posterior probability of negative selection at a site Prob[α&lt;β] : Posterior probability of positive selection at a site BayesFactor[α&lt;β] : Empirical Bayes Factor for positive selection at a site ### Files: B2M_FUBAR_Results.xlsx BRCA2_FUBAR_Results.xlsx CASP8_FUBAR_Results.xlsx CD274_FUBAR_Results.xlsx CDC42_FUBAR_Results.xlsx FGL2_FUBAR_Results.xlsx GRB2_FUBAR_Results.xlsx IL2_FUBAR_Results.xlsx LITAF_FUBAR_Results.xlsx