Contrasted gene decay in subterranean vertebrates

Data_Supp1. Summary of the number of genes retrieved from each species and for each gene set, along with the number of pseudogenes and the number of LoF mutations.

Data_Supp2. Sequences predicted with exonerate and ID of sequences retrieved from Ensembl.

Data_Supp3. Results obtained with different methods for dating relaxed selection on eye genes in Lucifuga dentata.

Description of Supplementary files content:
Divergence_values: Pairwise nucleotidic distances between species for each gene set.
Lucifuga_Supplementary_files_Genome: Original GFF3 file with functional annotations and scaffolds smaller than 200 bp not uploaded to NCBI.
MutPred2_Results: Raw output of MutPred2. Parsed results files to be used with the script provided in github (MutPred2_Script.R) are also provided.
Phylogenies: Gene phylogenies computed with iQTree and displayed with iTOL. The model used for each phylogeny can be found on the “Models” folder.
Concatenated_Alignments: Concatenated alignments for vision, circadian and pigmentation genes.