Loss-of-function genetic variation is often seen as sources of maladaptive phenotypes. However, loss-of-function per se should not necessarily result in loss of adaptive potential, particularly if a given gene function becomes itself maladaptive under a new environment—making its dispensation the optimal strategy (e.g. the "less-is-more” hypothesis; Olson, 1999).

Like other animal species living in caves and similar habitats, different populations of the Mexican tetra (Astyanax mexicanus) have independently evolved in their dark dwellings by foregoing their pigmentation, eye function, and circadian rhythm regulation (Figure 1). This pervasive loss-of-function across multiple traits in cave species is frequently described as a textbook example of how relaxed selection allows deleterious mutations to erode gene function. However, is this classic view a correct representation of their evolutionary history?

Figure 1. In the Mexican tetra (Astyanax mexicanus) cave-dwelling populations have evolved independently at least twice, associated with typical cave animal phenotypes such as loss of pigmentation and visual function (Credit: Daniel Castranova, NICHD/NIH).

In a new study in Molecular Biology and Evolution, a team led by Emma Y. Roback and Suzanne E. McGaugh (University of Minnesota, United States) took advantage of the multiple surface and cave-dwelling populations of Mexican tetra to investigate these questions (Roback et al., 2025). After sequencing the genomes of 138 Mexican tetras from 12 populations in central Mexico, as well as gene expression data, researchers focused on a specific type of genetic variant—premature termination codons (PTCs). These were important because they were simultaneously easier to genotype, and likely indicative of gene loss-of-function due to the expression of non-functional truncated transcripts.

By focusing on the distribution of high-frequency PTCs in each population, the researchers found that this type of variant was, as expected, much more prevalent in the cave populations. To illustrate this, in some populations as many as 30% of all PTCs were high-frequency, compared to a maximum of less than 2% in surface populations. When looking at patterns of sequence evolution, cave populations had, in genes containing PTCs, signatures of relaxed selection (increased genetic diversity and differentiation), likely associated with pseudogenization. Modeling approaches and comparisons between PTCs and previously described quantitative trait loci for cavefish traits seem to confirm that, as a whole, relaxation of selection plays a major role in the accumulation of putative loss-of-function mutations.

Does this mean a blow to the “less-is-more” hypothesis of adaptive evolution? Not quite. Roback and McGaugh's team produced a curated list of putative phenotypes linked to genes with PTCs, and identified candidate genes of interest. These genes defied the general trend by showing localized signatures of selection, and some of them had signatures of convergent evolution (independent mutations in different populations), suggesting an adaptive role.

Strikingly, one of those genes was pde6c, whose homologs were convergently disrupted by PTCs in subterranean mammals and implicated in photoreception in zebrafishes. To evaluate if pde6c is involved with vision in Mexican tetras, the team used CRISPR-Cas9 gene editing on surface fish—relative to non-edited siblings, CRISPants had smaller eye size and reduced optomotor response. While this experiment by itself does not necessarily demonstrate functional change is being driven by adaptation, it is nevertheless a strong suggestion of PTC-mediated functional change that is directly relevant to the darker cave environment. This is potentially adaptive since previous studies suggest eye reduction confers fitness advantages through reduced energy expenditure (Moran et al., 2015).

Molecular data from natural populations showcase the myriad, complementary ways through which populations leverage genetic variation throughout evolution. Confirming classical expectations, neutral processes largely govern trait degeneration when natural selection becomes relaxed, but detailed functional exploration of key traits illuminates the complex paths through which natural populations adapt to environmental change.

Want to learn more about trait loss in cavefish? Check the new article by Roback et al. in Genome Biology and Evolution:

Roback EY, Ferrufino E, Moran RL, Shennard D, Mulliniks C, Gallop J, Weagley J, Miller J, Fily Y, Ornelas-García CP, Rohner N. Population genomics of premature termination codons in cavefish with substantial trait loss. Mol Biol Evol. 2025:42(2):msaf012. https://doi.org/10.1093/molbev/msaf012

References

Moran D, Softley R, Warrant EJ. The energetic cost of vision and the evolution of eyeless Mexican cavefish. Science advances. 2015:11;1(8):e1500363. https://doi.org/10.1126/sciadv.1500363

Olson MV. When less is more: gene loss as an engine of evolutionary change. The American Journal of Human Genetics. 1999:1;64(1):18-23. https://doi.org/10.1086/302219