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In Molecular biology and evolution

Evolution sometimes proceeds by loss, especially when structures and genes become dispensable after an environmental shift relaxes functional constraints. Subterranean vertebrates are outstanding models to analyze this process, and gene decay can serve as a readout. We sought to understand some general principles on the extent and tempo of the decay of genes involved in vision, circadian clock and pigmentation in cavefishes. The analysis of the genomes of two Cuban species belonging to the genus Lucifuga provided evidence for the largest loss of eye-specific genes and non-visual opsin genes reported so far in cavefishes. Comparisons with a recently evolved cave population of Astyanax mexicanus and three species belonging to the Chinese tetraploid genus Sinocyclocheilus revealed the combined effects of the level of eye regression, time and genome ploidy on eye-specific gene pseudogenization. The limited extent of gene decay in all these cavefishes and the very small number of loss of function (LoF) mutations per pseudogene suggest that their eye degeneration may not be very ancient, ranging from early to late Pleistocene. This is in sharp contrast with the identification of several vision genes carrying many LoF mutations in ancient fossorial mammals, further suggesting that blind fishes cannot thrive more than a few million years in cave ecosystems.

Policarpo Maxime, Fumey Julien, Lafargeas Philippe, Naquin Delphine, Thermes Claude, Naville Magali, Dechaud Corentin, Volff Jean-Nicolas, Cabau Cedric, Klopp Christophe, Møller Peter Rask, Bernatchez Louis, García-Machado Erik, Rétaux Sylvie, Casane Didier


cavefishes, eye-specific genes, machine learning, molecular dating, pseudogenization, relaxed selection