Journal Article

Genomic analysis of the only blind Cichlid reveals extensive inactivation in eye and pigment formation genes

Aardema, M.L., Stiassny, M.L.J. and Alter, S.E.

Record Number:
Genome Biology and Evolution
Trait loss represents an intriguing evolutionary problem, particularlywhen it occurs across independent lineages. Fishes in light-poor environments often evolve “troglomorphic” traits, including reduction or loss of both pigment and eyes. Here, we investigate the genomicbasis of trait loss in ablind anddepigmentedAfricancichlid, Lamprologus lethops, andexplore evolutionary forces (selection and drift) thatmay have contributed to these losses. This species, the only known blind cichlid, is endemic to the lower Congo River. Available evidence suggests that it inhabits deep, low-light habitats. Using genome sequencing,we show that genes related to eye formation and pigmentation, as well as other traits associated with troglomorphism, accumulated inactivating mutations rapidly after speciation. A number of the genes affected in L. lethops are also implicated in troglomorphic phenotypes inMexican cavefish (Astyanaxmexicanus) and other species.Analysis ofheterozygosity patterns across thegenomeindicates that L. lethops underwent a significant population bottleneck roughly 1Ma, afterwhich effective population sizes remained low. Branch-length tests on a subset of genes with inactivating mutations show little evidence of directional selection; however, low overall heterozygosity may reduce statistical power to detect such signals. Overall, genome-wide patterns suggest that accelerated genetic drift from a severe bottleneck, perhaps aided by directional selection for the loss of physiologically expensive traits, caused inactivatingmutations to fix rapidly in this species. Key words: convergent evolution, cave fish, depigmentation, adaptation, vision genes, trait loss, troglomorphic.
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