Genes and sites under adaptation at the phylogenetic scale also exhibit adaptation at the population-genetic scale

This Zenodo repository contains the mammalian dataset that can be used with the AdaptaPop pipeline. Scripts and instructions necessary to reproduce the empirical experiments are detailed in https://github.com/ThibaultLatrille/AdaptaPop.

The archive file OrthoMam.zip must be extracted inside the folder OrthoMam. It contains the input data at the mammalian scale(alignments, trees, annotations) and the output data (fitness profiles, estimation of ω and ω₀).

The archive file Polymorphism.zip must be extracted inside the folder Polymorphism, it contains the output data (vcf.gz and tsv.gz) for each population. Each vcf file contains SNPs for which is was possible to infer the ancestral and derived codon.

Once both OrthoMam.zip and Polymorphism.zip are extracted, it is possible to run the Snakemake inside the folder Contrasts that will contrast the rate of adaptation at the phylogenetic and population scale.

The archive file VCF.zip contains a vcf file for every population. Each vcf file contains SNPs for which is was possible to infer the ancestral and derived codon, hence to also predict its selection coefficient based on the difference in fitness between amino-acid estimated at the mammalian scale.