In order to better understand the dynamic of molecular decay of genes that are most likely useless for
cavefishes living in total darkness, we analysed the distribution of putative loss-of-function (LoF) mutations
in light processing genes of several cavefish species. Only one LoF mutation was found in the Astyanax
mexicanus population of blind fish from the Pachón cave. This LoF mutation is in the gene pde6b, it is very
recent, specific to this cave and it did not yet reach fixation, in accordance with a very recent origin of this
cave population, most likely during the late Pleistocene. We also found two large deletions that lead to the
loss of 3 opsins in several cave populations. In the tetraploid genus Sinocyclocheilus, the eyed species S.
grahami has accumulated LoF mutations but less so than the small-eyed S. rhinocerous which accumulated
less LoF mutations than the blind S. anshuiensis, in accordance with cumulative effect of polyploidization
and cave adaptation on the rate of gene decay. In the genus Lucifuga, more LoF mutations were also found
in the blind L. dentata than the small-eyed Lucifuga sp. (Holguin). The distribution of the number of LoF
mutations per gene in L. dentata suggests that the whole set of genes analysed is dispensable in caves
whereas most genes are still under selection to maintain them functional in Lucifuga sp. (Holguin).
Molecular dating based on the number of pseudogenes shows that L. dentata evolved in the cave
environment during the Pleistocene but much earlier than A. mexicanus