Biology subjects

Kowalko, J. E.

Publications and source records attributed to Kowalko, J. E..

At least 19 recordsLinked to original sources

bioRxiv2026

Cave evolution on repeat: reuse of the same genomic regions across lineages but not across traits in Astyanax mexicanus

Similar traits repeatedly evolve across independent populations in response to similar environmental conditions. For many repeatedly evolved traits it is unknown if populations evolve similar traits through the same or different genetic mechanisms. To address this question, we leveraged the Mexican tetra fish, Astyanax mexicanus, which has evolved repeatedly through altering many traits including reduced sleep duration, eye degeneration, and metabolic shifts to accommodate limited nutrient availability. We defined whether shared or independent genetic architecture govern the repeated evolution of sleep loss, increased food consumption, early onset adipose deposition, and eye loss in different evolutionary origins of the cavefish phenotype by using Quantitative Trait Locus (QTL) mapping across three cave x surface F2 mapping populations. We found that, among the traits evaluated, eye loss exhibits the most genetic repeatability, with [~]43% of QTL shared across lineages. Sleep loss and metabolic traits (i.e., feeding, adiposity) were genetically less repeatable, with only [~]25-33% of QTL shared across lineages. Next, we explored whether QTL for metabolism, eye loss, and sleep traits in cavefish co-localize in the cavefish genome and could be inherited together to facilitate potential cavefish adaptation. Although these traits have repeatedly co-evolved in cave populations, we did not find evidence for extensive genetic linkage among them. Overall, we found that genetic repeatability is a common feature in the repeated evolution of cave traits, the extent of genetic repeatability varies across cave traits, and that there is little evidence for widespread co-localization of sleep, eye loss, and metabolic traits within the genome. SummaryIndependent populations that evolve similar traits in response to similar environmental conditions provide us with natural replicates for studying what constrains evolutionary change. Iconic examples of repeated trait evolution often involve repeated mutations in the same genes, suggesting there are limits on the type of genes and mutations that can contribute to phenotypic evolution. Here we conduct a multi-trait, multi-population QTL analysis for similar eye loss, sleep loss and metabolic shifts across two lineages of Astyanax mexicanus. Genetic repeatability is present for most traits, but its extent is highly trait dependent and occurs at the level of genomic regions rather than specific genes, highlighting the mosaic of constraint and flexibility involved in genetic repeatability.

evolutionary biology↗

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

Hybrid Solid-Liquid Optics Enable Scalable, High-Resolution, Multi-Immersion Light-Sheet Microscopy

Modern biology increasingly depends on data-driven discovery, requiring scalable and affordable high-content 3D imaging across molecular to organ scales. Although tissue clearing, expansion microscopy, and light-sheet microscopy (LSM) enable subcellular-resolution imaging of intact specimens, their scalability remains fundamentally limited by detection optics: immersion objectives deliver high-resolution, aberration-free imaging but with short working distances, high cost, and multi-immersion incompatibility, while air objectives offer long working distances and portability at lower cost but suffer from severe aberrations and reduced photon collection when imaging immersed samples. We introduce the Hybrid Solid-Liquid Immersion Lens (HySIL) framework, which pairs an off-the-shelf solid optical component with a refractive index-matched liquid to precompensate aberrations and enhance resolution. Building on HySIL, we developed SCOPE and Super-SCOPE, objective-agnostic imaging devices achieving submicron lateral resolution (<0.75 {micro}m) across centimeter-scale samples using inexpensive air objectives with >30 mm working distances. Integration with a low-cost LSM platform yielded a compact, scalable system demonstrated for multi-immersion, multi-color, subcellular-resolution mapping of cleared or expanded mouse, salamander, and cavefish brains, human iPSC-derived organoids, and 3D histopathology of breast tissue. HySIL and SCOPE establish an accessible foundation for scalable, high-resolution volumetric imaging, advancing data-driven biological discovery.

bioengineering↗

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

The rx3 gene contributes to the evolution of eye loss in the cavefish Astyanax mexicanus

Uncovering mechanisms by which sensory systems evolve is critical for understanding how organisms adapt to a novel environment. Astyanax mexicanus is a species of fish with populations of surface fish that inhabit rivers and streams and cavefish that have adapted to life within caves. Cavefish have evolved sensory system changes relative to their surface fish counterparts, providing an opportunity to investigate mechanisms underlying sensory system evolution. Here, we report the role of the gene retinal homeobox 3 (rx3) in cavefish eye evolution. We generated surface fish with putative loss-of-function mutations in the rx3 gene using CRISPR-Cas9 to determine the role of this gene in eye development in this species. These rx3 mutant surface fish fail to develop eyes, demonstrating that rx3 is required for surface fish eye development. Further, rx3 mutant surface fish exhibit altered behaviors relative to wild-type surface fish, suggesting that the loss of eyes impacts sensory-dependent behaviors. Finally, eye development is altered in cave-surface hybrid fish that inherit the mutant allele of rx3 from surface fish relative to siblings that inherit a wild-type surface fish rx3 allele, suggesting that cis-regulatory variation at the rx3 locus contributes to eye size evolution in cavefish. Together, these findings demonstrate that, as in other species, rx3 is required for eye development in A. mexicanus. Moreover, they suggest that variation at the rx3 locus plays a role in the evolved reduction of eye size in cavefish, shedding light on the genetic mechanisms underlying sensory system evolution in response to extreme environmental changes.

evolutionary biology↗

bioRxiv2024

Phylogenetic mapping of sleep loss in wild-caught cavefish

Sleep is an evolutionarily ancient and nearly universal behavior throughout the animal kingdom. Multiple cave-dwelling populations of the Mexican tetra, Astyanax mexicanus, have converged on sleep loss compared to river-dwelling surface fish. However, sleep has not been assessed in the vast majority of the 34 known A. mexicanus cave populations. Moreover, whether cavefish sleep less than surface individuals in their natural habitats is currently unknown. Analyzing the distribution of sleep loss and its relationship with other regressive traits in a phylogenetic framework is critical to inform the selective pressures across the different lineages. We measured sleep and locomotor activity in 15 distinct populations of A. mexicanus, including lineages that are broadly representative of the 34 cavefish populations identified to date. Sleep was drastically reduced in all cave and hybrid populations that were tested. A subset of caves contain hybrid populations of A. mexicanus, which show a broad range of eye and pigmentation phenotypes, yet have evolved near-complete loss of sleep. Mapping behavioral changes onto the phylogeny of A. mexicanus populations revealed that loss of sleep and elevated locomotor activity have evolved at least three times. Analysis of sleep in the wild confirms that the sleep loss phenotype observed in lab-reared fish is also present in the natural environment. Together, these findings reveal deep evolutionary convergence on sleep loss in cavefish and provide evidence for sleep loss as a primary trait contributing to cave adaptation.

evolutionary biology↗

bioRxiv2024

Evolution of a central dopamine circuit underlies adaptation of light-evoked sensorimotor response in the blind cavefish, Astyanax mexicanus.

Adaptive behaviors emerge in novel environments through functional changes in neural circuits. While relationships between circuit function and behavior have been well studied, how evolution shapes those circuits and leads to behavioral adpation is poorly understood. The Mexican cavefish, Astyanax mexicanus, provides a unique genetically amendable model system, equipped with above ground eyed surface fish and multiple evolutionarily divergent populations of blind cavefish that have evolved in complete darkness. These differences in environment and vision provide an opprotunity to examine how a neural circuit is functionally influenced by the presence of light. Here, we examine differences in the detection, and behavioral response induced by non visual light reception. Both populations exhibit photokinetic behavior, with surface fish becoming hyperactive following sudden darkness and cavefish becoming hyperactive following sudden illumination. To define these photokinetic neural circuits, we integrated whole brain functional imaging with our Astyanax brain atlas for surface and cavefish responding to light changes. We identified the caudal posterior tuberculum as the central modulator for both light or dark stimulated photokinesis. To unconver how spatiotemporal neuronal activity differed between surface fish and cavefish, we used stable pan-neuronal GCaMP Astyanax transgenics to show that a subpopulation of darkness sensitve neurons in surface fish are now light senstive in cavefish. Further functional analysis revealed that this integrative switch is dependent on dopmane signaling, suggesting a key role for dopamine and a highly conserved dopamine circuit in modulating the evolution of a circuit driving an essential behavior. Together, these data shed light into how neural circuits evolved to adapte to novel settings, and reveal the power of Astyanax as a model to elucidate mechanistic ingiths underlying sensory adaptation. O_FIG O_LINKSMALLFIG WIDTH=173 HEIGHT=200 SRC="FIGDIR/small/605141v1_ufig1.gif" ALT="Figure 1"> View larger version (34K): org.highwire.dtl.DTLVardef@145efeforg.highwire.dtl.DTLVardef@8b41e6org.highwire.dtl.DTLVardef@936979org.highwire.dtl.DTLVardef@1f18c5b_HPS_FORMAT_FIGEXP M_FIG C_FIG

evolutionary biology↗

bioRxiv2024

Postprandial sleep in short-sleeping Mexican cavefish

Interaction between sleep and feeding behaviors are critical for adaptive fitness. Diverse species suppress sleep when food is scarce to increase the time spent foraging. Post-prandial sleep, an increase in sleep time following a feeding event, has been documented in vertebrate and invertebrate animals. While interactions between sleep and feeding appear to be highly conserved, the evolution of postprandial sleep in response to changes in food availability remains poorly understood. Multiple populations of the Mexican cavefish, Astyanax mexicanus, have independently evolved sleep loss and increased food consumption compared to surface-dwelling fish of the same species, providing the opportunity to investigate the evolution of interactions between sleep and feeding. Here, we investigate effects of feeding on sleep in larval and adult surface fish, and two parallelly evolved cave populations of A. mexicanus. Larval surface and cave populations of A. mexicanus increase sleep immediately following a meal, providing the first evidence of postprandial sleep in a fish model. The amount of sleep was not correlated to meal size and occurred independently of feeding time. In contrast to larvae, postprandial sleep was not detected in adult surface or cavefish, that can survive for months without food. Together, these findings reveal that postprandial sleep is present in multiple short-sleeping populations of cavefish, suggesting sleep-feeding interactions are retained despite the evolution of sleep loss. These findings raise the possibility that postprandial sleep is critical for energy conservation and survival in larvae that are highly sensitive to food deprivation.

neuroscience↗

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↗

bioRxiv2024

Loci associated with cave-derived traits concentrate in specific regions of the Mexican cavefish genome

A major goal of modern evolutionary biology is connecting phenotypic evolution with its underlying genetic basis. The Mexican cavefish (Astyanax mexicanus), a characin fish species comprised of a surface ecotype and a cave-derived ecotype, is well suited as a model to study the genetic mechanisms underlying adaptation to extreme environments. Here we map 206 previously published quantitative trait loci (QTL) for cave-derived traits in A. mexicanus to the newest version of the surface fish genome assembly, AstMex3. This analysis revealed that QTL cluster in the genome more than expected by chance, and this clustering is not explained by the distribution of genes in the genome. To investigate whether certain characteristics of the genome facilitate phenotypic evolution, we tested whether genomic characteristics, such as highly mutagenic CpG sites, are reliable predictors of the sites of trait evolution but did not find any significant trends. Finally, we combined the QTL map with previously collected expression and selection data to identify a list of 36 candidate genes that may underlie the repeated evolution of cave phenotypes, including rgrb which is predicted to be involved in phototransduction. We found this gene has disrupted exons in all non-hybrid cave populations but intact reading frames in surface fish. Overall, our results suggest specific "evolutionary hotspots" in the genome may play significant roles in driving adaptation to the cave environment in Astyanax mexicanus and demonstrate how this compiled dataset can facilitate our understanding of the genetic basis of repeated evolution in the Mexican cavefish.

evolutionary biology↗

bioRxiv2023

Changes in local interaction rules during ontogeny underlie the evolution of collective behavior

Collective motion emerges from individual interactions which produce groupwide patterns in behavior. While adaptive changes to collective motion are observed across animal species, how local interactions change when these collective behaviors evolve is poorly understood. Here, we use the Mexican tetra, A. mexicanus, which exists as a schooling surface form and a non-schooling cave form, to study differences in how fish alter their swimming in response to neighbors across ontogeny and between evolutionarily diverged populations. We find that surface fish undergo a transition to schooling during development that occurs through increases in inter-individual alignment and attraction mediated by changes in the way fish modulate speed and turning relative to neighbors. Cavefish, which have evolved loss of schooling, exhibit neither of these schooling-promoting interactions at any stage of development. These results reveal how evolution alters local interaction rules to produce striking differences in collective behavior.

evolutionary biology↗

bioRxiv2022

Selection-driven trait loss in independently evolved cavefish populations

Predicting the outcome of evolution is a central goal of modern biology, yet, determining the relative contributions of deterministic events (i.e., selection) and stochastic events (i.e., drift and mutation) to the evolutionary process remains a major challenge. Systems where the same traits have evolved repeatedly provide natural replication that can be leveraged to study the predictability of molecular evolution and the genetic basis of adaptation. Although mutational screens in the laboratory have demonstrated that a diversity of genetic mutations can produce phenocopies of one another, in natural systems, similar genetic changes frequently underly the evolution of phenotypes across independent lineages. This suggests a substantial role for constraint and determinism in evolution and supports the notion that there may be characteristics which make certain mutations more likely to contribute to phenotypic evolution. Here we use large-scale whole genome resequencing in the Mexican tetra, Astyanax mexicanus, to demonstrate that selection has played a primary role in repeated evolution of both trait loss and trait enhancement across independent cave lineages. We identify candidate genes underlying repeated adaptation to caves and infer the mode of repeated evolution, revealing that selection on standing genetic variation and de novo mutations both contribute substantially to repeated adaptation. Finally, we show that genes with evidence of repeated evolution have significantly longer coding regions compared to the rest of the genome, and this effect is most pronounced in genes evolving convergently via independent mutations. Importantly, our findings provide the first empirical support for the hypothesis that genes with larger mutational targets are more likely to be the substrate of repeated evolution and indicate that features of the novel cave environment may impact the rate at which mutations occur.

evolutionary biology↗

bioRxiv2022

Novel husbandry practices result in rapid rates of growth and sexual maturation without impacting adult behavior in the blind Mexican cavefish.

The development of animal model systems is dependent on the standardization of husbandry protocols that increase fecundity and reduce generation time. The blind Mexican tetra, Astyanax mexicanus, is an emerging genetic vertebrate model for evolution and biomedical research. Surface and cave populations of A. mexicanus have independently evolved, providing a model system for studying the genetic basis of divergent biological traits. While a rapid increase in the use of A. mexicanus has led to the generation of genetic tools including gene-editing and transgenesis, a slow and inconsistent growth rate remains a major limitation to the expanded application of A. mexicanus. The optimization of husbandry protocols that maximizes high-nutrient feed, smaller tank densities and larger tank sizes across development, would facilitate faster growth and expand the use of this model. Here, we describe standardized husbandry practices that optimize growth through a high protein diet, increased feeding, growth sorting of larvae and juveniles, and tank size transitions based on standard length. These changes to husbandry had a significant effect on growth rates and decreased the age of sexual maturity in comparison to our previous protocols. To determine whether our nutritional change and increased feeding impacted behavior, we tested fish in exploration and schooling assays. We found that a change in diet had no effect on the behaviors we tested, suggesting that increased feeding and rapid growth will not impact the natural variation in behavioral traits. Taken together, this standardized husbandry protocol will accelerate the development of A. mexicanus as a genetic model.

evolutionary biology↗

bioRxiv2022

Convergence on reduced aggression through shared behavioral traits in multiple populations of Astyanax mexicanus

Aggression is a complex behavior that is observed across the animal kingdom, and plays roles in resource acquisition, defense, and reproductive success. While there are many individual differences in propensity to be aggressive within and between populations, the mechanisms underlying differences in aggression between individuals in natural populations are not well understood. We addressed this using the Mexican tetra, Astyanax mexicanus, a powerful model organism to understand behavioral evolution. A. mexicanus exists in two forms: a river-dwelling surface form and multiple populations of a blind cave form. We characterized aggression in surface fish and cavefish in a resident/intruder assay through quantifying multiple behaviors occurring during social interactions. Surface fish, which are aggressive, display multiple social behaviors in this context, which we characterized into two types of behaviors: aggression- associated and escape-associated behaviors. The majority of these behaviors were reduced or lost in Pachon cavefish. Further, both aggression-associated and escape-associated behaviors were not dependent on the presence of light, and both surface fish and cavefish remained aggressive or non-aggressive, respectively, when opposed to fish from a different population. Additionally, we found that within populations, levels of stress response were not correlated with aggression- or escape-associated behaviors. Finally, when we compared aggression- and escape- associated behaviors across four cavefish populations, we found that both types of behaviors are reduced in three cave populations, while still present in one. Together, these results reveal that multiple cavefish populations have repeatedly evolved reduced aggression through shared behavioral components, while other cavefish have retained aggression. Summary StatementComparison of aggression between surface fish and cavefish demonstrates that multiple complex behaviors compose aggression in surface fish and reveals heterogeneity in loss of aggression in cave populations.

evolutionary biology↗

bioRxiv2022

A brain-wide analysis maps structural evolution to distinct anatomical modules

Brain anatomy is highly variable and it is widely accepted that anatomical variation impacts brain function and ultimately behavior. The structural complexity of the brain, including differences in volume and shape, presents an enormous barrier to define how variability underlies differences in function. In this study, we sought to investigate the evolution of brain anatomy in relation to brain region volume and shape across the brain of a single species with variable genetic and anatomical morphs. We generated a high-resolution brain atlas for the blind Mexican cavefish and coupled the atlas with automated computational tools to directly assess brain region shape and volume variability across all populations. We measured the volume and shape of every neuroanatomical region of the brain and assess correlations between anatomical regions in surface, cavefish and surface to cave F2 hybrids, whose phenotypes span the range of surface to cave. We find that dorsal regions of the brain are contracted in cavefish, while ventral regions have expanded. Interestingly, in hybrid fish the volume and shape of dorsal regions are inversely proportional to ventral regions. This trend is true for both volume and shape, suggesting that these two parameters share developmental mechanisms necessary for remodeling the entire brain. Given the high conservation of brain anatomy and function among vertebrate species, we expect these data to studies reveal generalized principles of brain evolution and show that Astyanax provides a system for functionally determining basic principles of brain evolution by utilizing the independent genetic diversity of different morphs, to test how genes influence early patterning events to drive brain-wide anatomical evolution.

neuroscience↗

bioRxiv2021

Characterizing the genetic basis of trait evolution in the Mexican cavefish

Evolution in response to a change in ecology often coincides with various morphological, physiological, and behavioral traits. For most organisms little is known about the genetic and functional relationship between evolutionarily derived traits, representing a critical gap in our understanding of adaptation The Mexican tetra, Astyanax mexicanus, consists of largely independent populations of fish that inhabit at least 30 caves in Northeast Mexico, and a surface fish population, that inhabits the rivers of Mexico and Southern Texas. The recent application of molecular genetic approaches combined with behavioral phenotyping have established A. mexicanus as a model for studying the evolution of complex traits. Cave populations of A. mexicanus are interfertile with surface populations and have evolved numerous traits including eye degeneration, insomnia, albinism and enhanced mechanosensory function. The interfertility of different populations from the same species provides a unique opportunity to define the genetic relationship between evolved traits and assess the co-evolution of behavioral and morphological traits with one another. To define the relationships between morphological and behavioral traits, we developed a pipeline to test individual fish for multiple traits. This pipeline confirmed differences in locomotor activity, prey capture, and startle reflex between surface and cavefish populations. To measure the relationship between traits, individual F2 hybrid fish were characterized for locomotor behavior, prey-capture behavior, startle reflex and morphological attributes. Analysis revealed an association between body length and slower escape reflex, suggesting a trade-off between increased size and predator avoidance in cavefish. Overall, there were few associations between individual behavioral traits, or behavioral and morphological traits, suggesting independent genetic changes underlie the evolution of behavioral and morphological traits. Taken together, this approach provides a novel system to identify genes that underlie naturally occurring genetic variation in morphological and behavioral traits.

evolutionary biology↗