By: Savannah Jeffrey, Julia Ciccolo, & Julia Bennett (Stonehill College, BIO323: Evolution, Spring 2025)
Overview: In many populations of cave-adapted animals, there is an increased presence of single-nucleotide premature termination codons, known as PTCs, that lead to traits losing function. PTCs are a type of mutation that cause a random stop to genetic replication processes, which can have deleterious effects on how traits are expressed. PTCs have been observed in the genetic makeup of many evolved cave species like cavefish, specifically the Mexican tetra, Astyanax mexicanus. Mexican tetras can be found in central and eastern Mexico, as well as in Texas. They originated in bodies of waters such as lakes and rivers, where eventually some Mexican tetras colonized cave systems and formed new populations. Due to these smaller population sizes in these environments, these mutations are subject to much stronger genetic drift, which occurs when alleles increase or decrease by chance in a population. This phenomenon causes traits to become more common or disappear entirely, thus making a population genetically distinct from their ancestors. Cave environments have their own unique selective pressures and allow the loss of traits to be advantageous for organisms, mainly features like eyesight, pigmentation, and circadian cycling. Allocating resources to these traits in an environment where they are not required provides no benefit to these organisms, therefore the loss of them actually positively impacts the species’ fitness, allowing them to invest in other metabolic processes. Additionally, the majority of PTCs arise in redundant genes, reducing the risk of losing genes that are vital for survival.
Research Background
This research, published in January 2025 in the journal Molecular Biology and Evolution and led by Dr. Suzanne E. McGaugh and her Ph.D. student, Emma Y. Roback, investigated the impact of PTCs on cave-derived traits in a species of cavefish called Mexican tetra, Astyanax mexicanus. In the article, Population Genomics of Premature Termination Codons in Cavefish with Substantial Trait Loss, the research team analyzed the adaptive potential of loss-of-function alleles in different lineages of these fish. When comparing different lineages of Mexican tetra, it was very apparent that the cave populations displayed higher frequencies of PTCs compared to surface populations. McGaugh, Roback, and their colleagues aimed to investigate how the presence of these gene modifications contributes to the evolution and cave adaptation within these species of cavefish. As previously mentioned, PTCs are mainly found in regions of genes that are not directly expressed as observable traits. Logistically, if the mutation is not expressed visibly, it is less susceptible to selection and overall will not hinder fitness. These types of genes are typically under less selective constraint, meaning these PTCs will not be necessarily selected against.
Methods and Results
First, DNA was taken from nine cave, three surface, and two outgroup populations and sequenced. Two of the surface populations and three of the cave populations came from the same common ancestor. The other surface population and 6 other cave populations came from a different common ancestor. Two outgroups, populations that are not closely related to the core species, were also analyzed to provide a baseline for the results. Before analyzing the DNA, researchers applied a set of limitations to the analysis to ensure that the only genetic differences they were looking at were due to evolution. DNA analysis was performed using predictive software that allowed them to analyze traits of the fish that could have been selected for. The results of this analysis led to the theory that due to the location and function of genes with a high frequency of PTCs, loss-of-function alleles could be attributed to genetic drift, as they were not experiencing strong selective pressure. The populations of cavefish are significantly smaller than the surface populations, illustrating that genetic drift is the driving force in these smaller populations.
To confirm this theory, the researchers used another analysis tool to compare surface and cave populations by observing the effects of PTCs. Pde6c is a gene that affects eye size and the ability of a fish to see. This gene has historically been associated with a high level of PTCs in cavefish that lead to total eye loss. Researchers artificially mutated this gene in surface fish by introducing a PTC that would be commonly found in cavefish. They then compared behaviors that rely on vision between normal surface fish and the mutated fish.
They found that fish with a mutated pde6c gene displayed an inability to react to visual cues and the normal surface fish demonstrated functional vision. Researchers assume that this PTC is common in cavefish because creating and maintaining eyes is energetically expensive. Fish that live in total darkness do not need eyes and thus gain an advantage over fish that do spend the extra energy required to have eyes. This is one of the most common examples of a loss-of-function PTC in cavefish. Small population sizes would allow genetic drift to act on this trait and make it common in the population.
Interview
Dr. McGaugh was kind enough to speak with us and offer some more insights into their research. She explained that PTCs were observed at much higher frequencies in the cave populations due to the smaller community sizes where the PTCs under selection are more rapidly fixed, meaning almost every individual will possess that mutation. McGaugh stated that their results showed loss of function was caused primarily by genetic drift with some purifying selection that maintains gene function. She shared with us that these cave populations exist due to flooding events that sweep species into cave systems. The cavefish have very high survival rates compared to other various species that are found in the caves, and she and her colleagues are seeking to understand what processes cause this. You can listen to the podcast to hear more from Dr. McGaugh!
Article: Roback, E.Y., E. Ferrufino, R.L. Moran, D. Shennard, C. Mulliniks, J. Gallop, J. Weagley, J. Miller, Y. Fily, C.P. Ornelas-García, N. Rohner, J.E. Kowalko, & S.E. McGaugh. 2025. Population genomics of premature termination codons in cavefish with substantial trait loss. Molecular Biology and Evolution 42: msaf012. https://doi.org/10.1093/molbev/msaf012
Find out more about the McGaugh lab at the University of Minnesota here: https://sites.google.com/view/mcgaughlab/.