Blind catfish evolution

About one hundred cave catfishes have been described. Most of them are found in the Americas, in particular in South America but a few species also thrive in Central and North America. No genomic approach to decipher cave associated genomic changes, nor to estimate cave colonization periods have yet been carried out, despite high quality genomes have been assembled for the Mexican blindcat Prietella phreatophila and for the Colombian blind catfish Trichomycterus rosablanca. We filled this gap, by additionally sequencing the genomes of four blind and depigmented catfishes from Peru (three Trichomycterus and one Astroblepus), as well as the genomes of four close surface relatives. We first extracted a large set of light-related genes, such as phototransduction and crystallin genes, and found contrasting decays of these sequences in different cave species, from 1% of pseudogenes in T. rosablanca to 48% in P. phreatophila. Molecular dating using the percentage of pseudogenes indicates that catfishes settled in caves at different periods, ranging from Early Pliocene to Late Pleistocene, supporting the hypothesis that surface catfishes were able to recurrently and rapidly adapt to caves and thrive during a few million years in this environment. On the other hand, genome-wide analysis of protein-coding genes shows a weaker purifying selection on mildly deleterious mutations in cavefishes, a process that is more pronounced in the oldest cave species. Thus, these highly specialized cavefish with restricted distributions may become evolutionary dead-ends after spending a few millions of years in the subterranean environment This repository contains every result files, which can be analysed using the Rscript "Silucave_mainscript_analysis.R"