Biology subjects

Choy, S.

Publications and source records attributed to Choy, S..

5 recordsLinked to original sources

bioRxiv2025

CRISPR screening reveals genetic regulators associated with the evolution of eye degeneration

Determining the genetic factors contributing to trait evolution is critical for understanding how and why traits evolve; however, establishing which genes underlie the evolution of complex traits remains challenging. The freshwater fish Astyanax mexicanus, a species that includes blind, cave-dwelling and eyed, surface-dwelling fish, is a powerful model for evolutionary genetics. While genetic mapping studies in this species previously identified genomic regions associated with cave-derived traits, few causative genes and genetic changes have been identified. Here, we develop methods to identify and rapidly functionally assess candidate genes in A. mexicanus, focusing on a defining trait of cave animals, eye loss. Candidate genes were identified based on whether they fell within an eye-related quantitative trait locus, were differentially expressed between surface and cave eyes, and showed evidence of positive selection in cavefish. Single-nucleus RNA-sequencing revealed that these candidate genes were expressed in multiple cell types during development, including those in different tissues of the eye. CRISPR-Cas9-based mutagenesis demonstrated that disruption of nine of these candidate genes in surface fish resulted in altered eye size. Perturbation of one of these genes, fibulin-7 (fbln7), revealed changes in eye size across multiple stages of eye development. Together, this work identified multiple genes associated with the evolution of eye degeneration in A. mexicanus. Further, this study represents a roadmap for rapid identification and functional assessment of candidate genes implicated in the evolution of traits in cavefish that can be applied to other evolutionary genetic models.

genetics↗

bioRxiv2025

Analysis of multi-trait evolution across independently evolved cavefish populations reveals shared and independent evolution of suites of cave-associated traits

Environmental perturbations often lead to the evolution of multiple traits. Determining whether shared genetic factors underlie multi-trait evolution is a central question in evolutionary biology. In the Mexican tetra, Astyanax mexicanus, cave-dwelling populations have repeatedly evolved multiple traits. The repeated evolution of these traits, paired the robust environmental differences between the surface and cave habitats, provide an opportunity to investigate the genetic basis of multi-trait evolution. Here, we investigate the extent to which shared genetic mechanisms underlie the repeated evolution of multiple traits in cavefish. Across cave populations, we find evidence for shared and distinct genetic mechanisms contributing to the evolution of individual traits. Further, multiple traits covary in cave-surface F2 hybrids and many of the same trait correlations are found across independently evolved cave populations. Finally, we assessed traits that differ between pigmented and albino F2 fish in surface fish with mutations in the albinism gene oculocutaneous albinism 2 (oca2). This revealed that mutations in oca2 reduce bottom-dwelling behavior in A. mexicanus. Together, these findings suggest that multi-trait evolution occurs repeatedly through shared genetic factors across A. mexicanus cave populations. These results are consistent with pleiotropy or linkage playing a large role in multi-trait evolution in this species.

evolutionary biology↗

bioRxiv2025

Automated profiling of social behaviors to assess the genetic basis of evolution of aggressive behaviors in A. mexicanus

Across the animal kingdom, social behaviors such as aggression are critical for survival and reproductive success. While there is significant variation in social behaviors within and between species, the genetic mechanisms underlying natural variation in social behaviors are poorly understood. A central challenge to investigating the mechanisms contributing to the evolution of social behaviors is that these behaviors are typically complex, making them a challenge to quantify. The Mexican tetra, Astyanax mexicanus, is a powerful model for investigating the evolution of traits, as it is a single species that exists as populations of eyed, river-dwelling surface fish and blind cave-dwelling fish. The blind cavefish have evolved morphological and behavioral differences compared to surface fish, including reduced aggression. Here, we developed and validated an automated machine learning pipeline that integrates pose-estimation and supervised behavioral classification to track and quantify aggression-associated behaviors--striking, following, and circling. Using this pipeline, we established that these behaviors are quantitatively different between surface and cave fish during juvenile stages in A. mexicanus, similar to what was observed previously in adults. Moreover, assessment of these aggressive behaviors in surface-cave F2 hybrid fish revealed that striking and following are strongly positively correlated, while striking and circling are negatively correlated, suggesting that these behaviors evolved through some shared genetic mechanisms. These findings demonstrate the power of automated tracking and behavioral phenotyping in multiple fish in A. mexicanus and establish a foundation for future studies investigating the genetic basis of evolution of social behaviors.

evolutionary biology↗

bioRxiv2025

Automated behavioral profiling using neural networks reveals differences in stress-like behavior between cave and surface-dwelling Astyanax mexicanus

Behavioral stress responses allow animals to quickly adapt to local environments and are critical for survival. Stress responses provide an ideal model for investigating the evolution of complex behaviors due to their conservation across species, critical role in survival, and integration of behavioral and physiological components. The Mexican cavefish (Astyanax mexicanus) has evolved dramatically different stress responses compared to river-dwelling surface fish morphs, providing a model to investigate the neural and evolutionary basis of stress-like responses. Surface morphs inhabit predator-rich environments whereas cave-dwelling morphs occupy predator-free habitats. While these key ecological variables may underlie differences in stress responses, the complexity of the behavioral differences has not been thoroughly examined. By leveraging automated pose-tracking and machine learning tools, we quantified a range of behaviors associated with stress, including freezing, bottom-dwelling, and hyperactivity, during a novel tank assay. Surface fish exhibited heightened stress responses characterized by prolonged bottom-dwelling and frequent freezing, while cavefish demonstrated reduced stress behaviors, marked by greater exploration and minimal freezing. Analysis of F2 hybrids revealed that a subset of behaviors, freezing and bottom-dwelling, co-segregated, suggesting shared genetic or physiological underpinnings. Our findings illustrate the power of computational tools for high-throughput behavioral phenotyping, enabling precise quantification of complex traits and revealing the genetic and ecological factors driving their evolution. This study provides a framework for understanding how integrated behavioral and physiological traits evolve, offering broader insights into the mechanisms underlying the diversification of animal behavior in natural systems.

evolutionary biology↗

bioRxiv2024

Mutations in the albinism gene oca2 alter vision-dependent prey capture behavior in the Mexican tetra

Understanding the phenotypic consequences of naturally occurring genetic changes, as well as their impact on fitness, is fundamental to understanding how organisms adapt to an environment. This is critical when genetic variants have pleiotropic effects, as determining how each phenotype impacted by a gene contributes to fitness is essential to understand how and why traits have evolved. A striking example of a pleiotropic gene contributing to trait evolution is the oca2 gene, coding mutations in which underlie albinism and reductions of sleep in the blind Mexican cavefish, Astyanax mexicanus. Here, we characterize the effects of mutations in the oca2 gene on larval prey capture. We find that when conspecific surface fish with engineered mutations in the oca2 allele are hunting, they use cave-like, wide angle strikes to capture prey. However, unlike cavefish or surface fish in the dark, which rely on lateral line mediated hunting, oca2 mutant surface fish use vision when striking at prey from wide angles. Finally, we find that while oca2 mutant surface fish do not outcompete pigmented surface siblings in the dark, pigmented fish outcompete albino fish in the light. This raises the possibility that albinism is detrimental to larval feeding in a surface-like lighted environment, but does not have negative consequences for fish in cave-like, dark environments. Together, these results demonstrate that oca2 plays a role in larval feeding behavior in A. mexicanus. Further, they expand our understanding of the pleiotropic phenotypic consequences of oca2 in cavefish evolution.

animal behavior and cognition↗