Contrasting gene decay in subterranean vertebrates: insights from cavefishes and fossorial mammals,Molecular Biology and Evolution

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Contrasting gene decay in subterranean vertebrates: insights from cavefishes and fossorial mammals
Molecular Biology and Evolution ( IF 11.0 ) Pub Date : 2020-09-28 , DOI: 10.1093/molbev/msaa249
Maxime Policarpo ₁ , Julien Fumey ₁ , Philippe Lafargeas ₁ , Delphine Naquin ₂ , Claude Thermes ₂ , Magali Naville ₃ , Corentin Dechaud ₃ , Jean-Nicolas Volff ₃ , Cedric Cabau ₄ , Christophe Klopp ₅ , Peter Rask Møller ₆ , Louis Bernatchez ₇ , Erik García-Machado _{7,

8} , Sylvie Rétaux ₉ , Didier Casane _{1,

10}

Affiliation

CNRS, IRD, UMR Évolution, Génomes, Comportement et Écologie, Université Paris-Saclay, Gif-sur-Yvette, France.
Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France.
Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, CNRS UMR 5242, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, Lyon, France.
SIGENAE, GenPhySE, INRAE, ENVT, Université de Toulouse, Castanet Tolosan, France.
INRAE, SIGENAE, Genotoul Bioinfo, MIAT UR875, Castanet Tolosan, France.
Natural History Museum of Denmark, University of Copenhagen, Copenhagen Ø, Denmark.
Department of Biology, Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec City, QC, Canada.
Centro de Investigaciones Marinas, Universidad de La Habana, La Habana, Cuba.
CNRS, Institut des Neurosciences Paris-Saclay, Université Paris-Saclay, Gif-sur-Yvette, France.
UFR Sciences du Vivant, Université de Paris, Paris, France.

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.

更新日期：2020-09-28

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