Biology subjects

Kowalko, J. E.

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

27 records · Page 2Linked to original sources

bioRxiv2021

"How do we do this at a distance?!" A descriptive study of remote undergraduate research programs during COVID-19

The COVID-19 pandemic shut down undergraduate research programs across the U.S. Twenty-three sites offered remote undergraduate research programs in the life sciences during summer 2020. Given the unprecedented offering of remote research experiences, we carried out a study to describe and evaluate these programs. Using structured templates, we documented how programs were designed and implemented, including who participated. Through focus groups and surveys, we identified programmatic strengths and shortcomings as well as recommendations for improvements from the perspectives of participating students. Strengths included the quality of mentorship, opportunities for learning and professional development, and development of a sense of community. Weaknesses included limited cohort building, challenges with insufficient structure, and issues with technology. Although all programs had one or more activities related to diversity, equity, inclusion, and justice, these topics were largely absent from student reports even though programs coincided with a peak in national consciousness about racial inequities and structural racism. Our results provide evidence for designing remote REUs that are experienced favorably by students. Our results also indicate that remote REUs are sufficiently positive to further investigate their affordances and constraints, including the potential to scale up offerings, with minimal concern about disenfranchising students.

scientific communication and education↗

bioRxiv2021

Hybridization underlies localized trait evolution in cavefish

Compared to selection on new mutations and standing genetic variation, the role of gene flow in generating adaptive genetic variation has been subject to much debate. Theory predicts that gene flow constrains adaptive evolution via natural selection by homogenizing allele frequencies among populations and introducing migrant alleles that may be locally maladaptive1. However, recent work has revealed that populations can diverge even when high levels of gene flow are present2-4 and that gene flow may play an underappreciated role in facilitating local adaptation by increasing the amount of genetic variation present for selection to act upon5-8. Here, we investigate how genetic variation introduced by gene flow contributes to adaptive evolution of complex traits using an emerging eco-evolutionary model system, the Mexican tetra (Astyanax mexicanus). The ancestral surface form of the Mexican tetra has repeatedly invaded and adapted to cave environments. The Chica cave is unique in that it contains several pool microenvironments inhabited by putative hybrids between surface and cave populations9, providing an opportunity to investigate the dynamics of complex trait evolution and gene flow on a local scale. Here we conduct high-resolution genomic mapping and analysis of eye morphology and pigmentation in fish from multiple pools within Chica cave. We demonstrate that hybridization between cave and surface populations contributes to highly localized variation in behavioral and morphological traits. Analysis of sleep and locomotor behaviors between individual pools within this cave revealed reduced sleep associated with an increase in ancestry derived from cave populations, suggesting pool-specific ecological differences may drive the highly-localized evolution of sleep and locomotor behaviors. Lastly, our analyses uncovered a compelling example of convergent evolution in a core circadian clock gene in multiple independent cavefish lineages and burrowing mammals, indicating a shared genetic mechanism underlying circadian disruption in subterranean vertebrates. Together, our results provide insight into the evolutionary mechanisms that promote adaptive genetic variation and the genetic basis of complex behavioral phenotypes involved in local adaptation.

evolutionary biology↗

bioRxiv2020

Pleiotropic function of the oca2 gene underlies the evolution of sleep loss and albinism in cavefish

Adaptation to novel environments often involves the evolution of multiple morphological, physiological and behavioral traits. One striking example of multi-trait evolution is the suite of traits that has evolved repeatedly in cave animals, including regression of eyes, loss of pigmentation, and enhancement of non-visual sensory systems [1,3]. The Mexican tetra, Astyanax mexicanus, consists of fish that inhabit at least 30 caves in Northeast Mexico and ancestral-like surface fish which inhabit the rivers of Mexico and Southern Texas [6]. Cave A. mexicanus are interfertile with surface fish and have evolved a number of traits that are common to cave animals throughout the world, including albinism, eye loss, and alterations to behavior [8-10]. To define relationships between different cave-evolved traits, we phenotyped 208 surface-cave F2 hybrid fish for numerous morphological and behavioral traits. We found significant differences in sleep between pigmented and albino hybrid fish, raising the possibility that these traits share a genetic basis. In cavefish and many other species, mutations in oculocutaneous albinism 2 (oca2) cause albinism [11-15]. Surface fish with CRISPR-induced mutations in oca2 displayed both albinism and reduced sleep. Further, this mutation in oca2 fails to complement sleep loss when surface fish harboring this engineered mutation are crossed to different, independently evolved populations of albino cavefish with naturally occurring mutations in oca2, confirming that oca2 contributes to sleep loss. Finally, analysis of the oca2 locus in wild caught cave and surface fish suggests that oca2 is under positive selection in at least three cave populations. Taken together, these findings identify oca2 as a novel regulator of sleep and suggest that a pleiotropic function of oca2 underlies the adaptive evolution of both of albinism and sleep loss.

evolutionary biology↗

bioRxiv2020

A chromosome level genome of Astyanax mexicanus surface fish for comparing population-specific genetic differences contributing to trait evolution.

Identifying the genetic factors that underlie complex traits is central to understanding the mechanistic underpinnings of evolution. In nature, adaptation to severe environmental change, such as encountered following colonization of caves, has dramatically altered genomes of species over varied time spans. Genomic sequencing approaches have identified mutations associated with troglomorphic trait evolution, but the functional impacts of these mutations remain poorly understood. The Mexican Tetra, Astyanax mexicanus, is abundant in the surface waters of northeastern Mexico, and also inhabits at least 30 different caves in the region. Cave-dwelling A. mexicanus morphs are well adapted to subterranean life and many populations appear to have evolved troglomorphic traits independently, while the surface-dwelling populations can be used as a proxy for the ancestral form. Here we present a high-resolution, chromosome-level surface fish genome, enabling the first genome-wide comparison between surface fish and cavefish populations. Using this resource, we performed quantitative trait locus (QTL) mapping analyses for pigmentation and eye size and found new candidate genes for eye loss such as dusp26. We used CRISPR gene editing in A. mexicanus to confirm the essential role of a gene within an eye size QTL, rx3, in eye formation. We also generated the first genome-wide evaluation of deletion variability that includes an analysis of the impact on protein-coding genes across cavefish populations to gain insight into this potential source of cave adaptation. The new surface fish genome reference now provides a more complete resource for comparative, functional, developmental and genetic studies of drastic trait differences within a species.Competing Interest StatementThe authors have declared no competing interest.View Full Text

genomics↗

bioRxiv2020

Analysis of stress responses in Astyanax larvae reveals heterogeneity among different populations

Stress responses are conserved physiological and behavioral outcomes as a result of facing potentially harmful stimuli, yet in pathological states, stress becomes debilitating. Stress responses vary considerably throughout the animal kingdom, but how these responses are shaped evolutionarily is unknown. The Mexican cavefish has emerged as a powerful system for examining genetic principles underlying behavioral evolution. Here, we demonstrate that cave Astyanax have reduced behavioral and physiological measures of stress when examined at larval stages. We also find increased expression of the glucocorticoid receptor, a repressible element of the neuroendocrine stress pathway. Additionally, we examine stress in three different cave populations, and find that some, but not all, show reduced stress measures. Together, these results reveal a mechanistic system by which cave-dwelling fish reduced stress, presumably to compensate for a predator poor environment. Research HighlightO_LICavefish populations of A. mexicanus have reduced stress relative to surface conspecific at larval stages C_LIO_LIWe show that a glucocorticoid receptor, a negative regulator of the neuroendocrine stress axis, is upregulated in stress-resistant cavefish C_LIO_LIThere exists much ontological heterogeneity between different cavefish populations. C_LI

neuroscience↗

bioRxiv2020

Analysis of social swimming dynamics in the Mexican cavefish

Fish display a remarkable diversity of social behaviors, from highly social to largely solitary. While social behaviors are likely critical for survival, surprisingly little is known about how they evolve in response to changing environmental pressures. With its highly social surface form and multiple populations of a largely asocial, blind, cave-dwelling form, the Mexican tetra, Astyanax mexicanus, provides a powerful model to study the evolution of social behavior. Given numerous morphological and behavioral differences between the surface and cave forms, a primary impediment to understanding how this behavior evolved is a lack of computational and statistical approaches that can precisely identify independent aspects of social behavior. Here, we use motion tracking and kinematic analysis to quantify social swimming patterns and argue that the absence of schooling in cavefish is not merely a consequence of their inability to see but rather a genuine behavioral adaptation that impacts the way they explore their cave environment. Surface fish school, maintaining both close proximity and alignment with each other. In the dark, surface fish no longer school, but we show that they still attempt to align and maintain proximity when they find themselves near another fish. Conversely, cavefish exhibit little preference for proximity or alignment, instead actively avoiding each other. Cavefish also slow down when more fish are present in the tank, which neither surface fish in the light or in the dark do. Using data-driven computer simulations, we show that those two traits - active avoidance and collective slowdown - are sufficient to shift the exploration strategy of cavefish from mostly-following-the-walls to exploring-the-entire-tank. Finally, we find that those differences in collective swimming patterns are largely consistent across independently-evolved cave populations, revealing an evolutionary convergence on this emergent social behavior. Author SummaryThe Mexican tetra fish offers a fascinating window into the evolution of schooling behavior. Its ancestral-like surface form is found in the rivers and lakes of Mexico and Texas and is highly social. Over the last million years, A. mexicanus repeatedly evolved a second, largely asocial cave form after colonizing a series of dark, underground caves. Here we use motion tracking technology to compare the collective displacement patterns of four populations and present evidence that the loss of schooling in cave populations (i) is a genuine example of parallel behavioral evolution rather than a mere consequence of not being able to see in the dark and (ii) could constitute a cave-specific exploration strategy.

animal behavior and cognition↗

bioRxiv2020

Repeated evolution of circadian clock dysregulation in cavefish populations

Circadian rhythms are nearly ubiquitous throughout nature, suggesting they are critical for survival in diverse environments. Organisms inhabiting environments with arrhythmic days, such as caves, offer a unique opportunity to study the evolution of circadian rhythms in response to changing ecological pressures. Here we demonstrate that the cave environment has led to the repeated disruption of the biological clock across multiple populations of Mexican cavefish, with the circadian transcriptome showing widespread reductions in rhythmicity and changes to the timing of the activation/repression of genes in the core pacemaker. Then, we investigate the function of two genes with decreased rhythmic expression in cavefish. Mutants of these genes phenocopy reductions in sleep seen in multiple cave populations, suggesting a link between circadian dysregulation and sleep reduction. Altogether, our results reveal that evolution in an arrhythmic environment has resulted in dysregulation to the biological clock across multiple populations by diverse molecular mechanisms.

evolutionary biology↗

bioRxiv2019

Cavefish brain atlases reveal functional and anatomical convergence across independently evolved populations

Environmental perturbation can drive the evolution of behavior and associated changes in brain structure and function. The generation of computationally-derived whole-brain atlases have provided insight into neural connectivity associated with behavior in many model systems. However, these approaches have not been used to study the evolution of brain structure in vertebrates. The Mexican tetra, A. mexicanus, comprises river-dwelling surface fish and multiple independently evolved populations of blind cavefish, providing a unique opportunity to identify neuroanatomical and functional differences associated with behavioral evolution. We employed intact brain imaging and image registration on 684 larval fish to generate neuroanatomical atlases of surface fish and three different cave populations. Analyses of brain regions and neural circuits associated with behavioral regulation identified convergence on hypothalamic expansion, as well as changes in transmitter systems including elevated numbers of catecholamine and hypocretin neurons in cavefish populations. To define evolutionarily-derived changes in brain function, we performed whole brain activity mapping associated with feeding and sleep. Feeding evoked neural activity in different sensory processing centers in surface and cavefish. We also identified multiple brain regions with sleep-associated activity across all four populations, including the rostral zone of the hypothalamus and tegmentum. Together, these atlases represent the first comparative brain-wide study of intraspecies variation in a vertebrate model, and provide a resource for studying the neural basis underlying behavioral evolution.

neuroscience↗

bioRxiv2019

Evolution of the acoustic startle response of Mexican cavefish

The ability to detect threatening sensory stimuli and initiate an escape response is essential for survival and under stringent evolutionary pressure. In diverse fish species, acoustic stimuli activate Mauthner neurons, which initiate a stereotypical C-start escape response. This reflexive behavior is highly conserved across aquatic species and provides a model for investigating the neural mechanism underlying the evolution of escape behavior. Here, we define evolved differences in the C-start response between populations of the Mexican cavefish, Astyanax mexicanus. Cave populations of A. mexicanus inhabit in an environment devoid of light and macroscopic predation, resulting in evolved differences in diverse morphological and behavioral traits. We find that the C-start is present in multiple populations of cavefish and river-dwelling surface fish, but response kinematics and probability differ between populations. The Pachon population of cavefish have an increased response probability, a slower response and reduction of the maximum bend angle, revealing evolved differences between surface and cave populations. In two other independently evolved populations of cavefish, the response probability and the kinematics of the response differ from one another, as well as from surface fish, suggesting the independent evolution of differences in the C-start response. Investigation of surface-cave hybrids reveals a relationship between angular speed and peak angle, suggesting these two kinematic characteristics are related at the genetic or functional levels. Together, these findings provide support for the use of A. mexicanus as a model to investigate the evolution of escape behavior.

neuroscience↗