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Faculty, Biological Sciences, Lehigh University

Johanna Kowalko, Ph.D.

Johanna Kowalko, Ph.D.
Assistant Professor

Research Interest:
Evolutionary Biology

Iacocca Hall, D224


email Dr. Kowalko


Johanna Kowalko, Ph.D. hspace=Animals display a remarkable amount of variation in their behavior, however, the genetic and neural underpinnings of behavioral diversity are poorly understood. My research program seeks to address this by examining two main questions: What are the genetic, developmental and neural mechanisms that underlie differences in behavior? Further, how do behaviors evolve? To do so, we use the blind cavefish, Astyanax mexicanus. A. mexicanus exists in a river-dwelling surface form, as well as in multiple populations that have been trapped in, and have adapted to life in subterranean caves. Cavefish have adapted to survive and thrive in the cave environment through the modification of morphological, physiological and behavioral traits. While surface fish and cavefish have strikingly divergent phenotypes, they are interfertile, and are therefore a powerful genetic model of behavioral evolution. Furthermore, many of these cave populations have evolved from independent colonization events, allowing for the examination of repeated evolution. Many of the strengths of model organisms, including genetic manipulation and brain imaging, are now feasible in A. mexicanus, allowing for examination of the genetic and neural mechanisms that underlie these differences in behavior. In addition, the small size, ability to live and breed in the laboratory, and short generation time of these fish make Astyanax an extraordinary system for genetic and behavioral studies.

My laboratory currently focuses on four research programs:

Examining how natural genetic variation alters developmental processes to produce phenotypic change

Johanna Kowalko, Ph.D. hspace=Genetic changes can alter developmental processes, leading to differences in sensory systems and brains and ultimately, behavior. My laboratory is interested in investigating the developmental changes that lead to changes in the central nervous system that underlie morphological and behavioral evolution. For example, cavefish initially develop small eyes that subsequently degenerate. Further, eye regression has evolved in multiple cave populations. My laboratory is currently examining the developmental and genetic basis of eye loss in cavefish from populations that have evolved following independent colonization events to identify the alterations to development that contribute to these evolved changes in eye morphology and to determine if there are multiple ways A. mexicanus cavefish can lose eyes.

Understanding the role of pleiotropy in the evolution of behavior

Johanna Kowalko, Ph.D. hspace=While trait loss is common in evolution, the mechanisms by which traits are lost remain relatively unknown. Cave animals present important opportunities for understanding the evolutionary processes that contribute to trait loss, as multiple species of cave animals have repeatedly evolved reductions in pigmentation and regression or loss of eyes. My lab has been examining albinism, the complete loss of melanin pigmentation, to understand how evolution of pigmentation is related to evolution of other traits, and ultimately, how and why regressive traits evolve. We are currently testing the hypothesis the gene oca2 underlies the adaptive evolution of both albinism and behavior in cavefish.

Examining how and why behavioral plasticity evolves

Identical genotypes can produce different phenotypes in the context of different environmental conditions. This ability to alter traits in response to environmental conditions, known as phenotypic plasticity, is crucial for survival in a variable environment. While it is widely accepted that plasticity itself has a genetic basis, the genetic underpinnings of plasticity and how plasticity evolves are poorly understood. One striking example of phenotypic plasticity is the change in sleep observed in individuals under different nutrient availability conditions. While many organisms reduce sleep in response to a food-poor environment, presumably to increase time available for foraging, other organisms increase the amount they sleep under these conditions. Sleeping more is thought to conserve energy when food is not available. We are currently evaluating how plasticity in sleep has evolved in A. mexicanus by examining the genetic underpinnings of sleep and sleep plasticity in the lab. Further, we are examining sleep, feeding, and food availability in the field to define these behaviors in natural populations of fish and to identify the environmental conditions under which these behaviors have evolved.

Evolutionary approaches to identify genetic architecture regulating social behavior

Effectively engaging with other individuals of the same species is important for survival, and extreme social behaviors can have negative consequences for both individuals and social groups. While a significant body of research has contributed to our understanding of the genetic and neural bases of social behaviors like aggression and parental care, much less is known about how natural genetic variation alters neural circuits to produce differences in social behaviors between individuals, or how social behaviors evolve. A. mexicanus surface fish are highly social, whereas cavefish from multiple populations have evolved reductions in multiple social behaviors, including aggression and schooling. We are exploring the genetic and neural mechanisms that contribute to these differences in social behaviors.



O’Gorman M, Thakur S, Imrie G, Moran RL, Choy S, Sifuentes-Romero I, Bilandžija H, Renner KJ, Duboue E, Rohner N, McGaugh SE, Keene AC, Kowalko JE. Pleiotropic function of the oca2 gene underlies the evolution of sleep loss and albinism in cavefish. Current Biology. 2021 Aug 23.

Mack KL, Jaggard JB, Persons JL, Passow CN, Stahl BA, Ferrufino E, Tsuchiya D, Smith SE, Slaughter B, Kono TJY, Kowalko JE, Rohner N, Keene AC, McGaugh SE. Repeated evolution of circadian clock dysfunction in cavefish populations. PLoS Genet. 2021 Jul 12.

Warren WC, Boggs TE, Borowsky R, Carlson B, Ferrufino E, Gross JB, Hillier L, Hu Z, Keene AC, Kenzior A, Kowalko JE, Tomlison C, Kremitzki M, Lemieux ME, Graves-Lindsay T, McGaugh SE, Miller JT, Mommersteeg MTM, Moran RL, Peuß R, Rice ES, Riddle MR, Sifuentes-Romero I, Stanhope BA, Tabin CJ, Thakur S, Yamamoto Y, Ro-021-21733-zhner N. A chromosome-level genome of Astyanax mexicanus surface fish for comparing population-specific genetic differences contributing to trait evolution. Nat Commun. 2021 Mar 4.

Kowalko JE, Franz-Odendall T, Rohner N. Introduction to the Special Issue: Cavefish – Adaptation in the dark. J Exp Zool B Mol Dev Evol. 2020 Dec 1.

Jaggard J, Lloyd E, Yuiska A, Patch A, Fily Y, Kowalko JE, Appelbaum L, Duboue ER, Keene AC. Cavefish brain atlases reveal functional and anatomical convergence across independently evolved populations. Science Advances. 2020 Sep 16.

Mammola S, Amorim IR, Bichuette ME, Borges PA, Cheeptham N, Cooper SJB, Culver DC, Deharveng L, Eme D, Ferreira RL, Fiser C, Fiser Z, Fong DW, Griebler C, Jeffery WR, Jugovic J, Kowalko JE, Lilley TM, Malard F, Manenti R, Martinez A, Meierhofer MB, Niemiller ML, Northup DE, Pellegrini TG, Pipan T, Protas M, Reboleira ASPS, Venarsky MP, Wynne JJ, Zamajster M, Cardoso P. Fundamental research questions in subterranean biology. Biol Rev Camb Philos Soc. 2020 Aug 25.

Kowalko JE. In the Spotlight – Early Career Researcher. J Exp Zool B Mol Dev Evol. 2020 Aug 10.

Paz A, McDole B, Kowalko JE, Duboue ER, Keene AC. Evolution of the acoustic startle response of Mexican cavefish. J Exp Zool B Mol Dev Evol. 2020 Aug 10.

Chin JSR, Loomis CL, Albert LT, Medina-Trenche S, Kowalko J, Keene AC, Duboue ER. Analysis of stress responses in Astyanax larvae reveals heterogeneity among different populations. J Exp Zool B Mol Dev Evol. 2020 Aug 6.

McGaugh SE, Kowalko JE, Duboue E, Lewis P, Franz-Odendall T, Rohner N, Gross JB, Keene A. Dark world rises: The emergence of cavefish as a model of the study of evolution, behavior and disease. J Exp Zool B Mol Dev Evol. 2020 July 7.

Sifuentes-Romero I, Ferrufino E, Thakur S, Laboissonniere LA, Solomon M, Smith CL, Keene AC, Trimarchi JM, Kowalko JE. Repeated evolution of eye loss in Mexican cavefish: Evidence of similar developmental mechanisms in independently evolved populations. J Exp Zool B Mol Dev Evol. 2020 July 2.

Krishnan J, Persons JL, Peuß R, Huzaifa H, Kenzior A, Xiong S, Olsen L, Maldonado E, Kowalko JE, Rohner N. Comparative transcriptome analysis of wild and lab populations of Astyanax mexicanus uncovers differential effects of environment and morphotype on gene expression. J Exp Zool B Mol Dev Evol. 2020 Feb 4.

Kowalko JE. Utilizing the blind cavefish Astyanax mexicanus to understand the genetic basis of behavioral evolution. J Exp Biol. 2020 Feb 7.

Stahl BA, Jaggard JB, Chin JSR, Kowalko JE, Keene AC, Duboue ER. Manipulation of gene function in Mexican cavefish. J Vis Exp. 2019 April 22.

Gunesch JT, Angelo LS, Mahaptra S, Deering RP, Kowalko JE, Sleiman P, Tobias JW, Monaco-Shawver L, Orange JS, Mace EM. Genome-wide analysis and functional profiling of human NK cell lines. Mol Immunol. 2018 Jul 24.

Tabin JA*, Aspiras A, Martineau B, Riddle M, Kowalko J, Borowsky R, Rohner N, Tabin CJ. Temperature preference of cave and surface populations of Astyanax mexicanus. Dev Biol 2018 April 25.

Klaassen H, Wang Y, Adamski K, Rohner N, Kowalko JE. CRISPR mutagenesis confirms the role of oca2 in melanin pigmentation in Astyanax mexicanus. Dev Biol 2018 Mar 16.

Kowalko JE, Ma L, Jeffery WR. Genome Editing in Astyanax mexicanus Using Transcription Activator-like Effector Nucleases. J Vis Exp 2016 June 20; (112).

Ma L, Jeffery WR, Essner JJ, Kowalko JE. Genome editing using TALENs in blind Mexican cavefish, Astyanax mexicanus. PLoS One 2015 Mar 16; 10(3): e0119370.

Kuo T, Kowalko JE, DiTommaso T, Nyambi M, Montoro DT, Essner JJ, Whited JL. TALEN-mediated gene editing of the thrombospondin-1 locus in axolotl. Regeneration 2015 Feb; 2(1): 37-43.

Rohner N, Jarosz DF, Kowalko JE, Yoshizawa M, Jeffery WR, Borowsky RL, Lindquist S, Tabin CJ. Cryptic variation in morphological evolution: HSP90 as a capacitor for the loss of eyes in cavefish. Science 2013 Dec 13; 342(6164): 1372-5.< br> Commentaries in: Cavefish study supports controversial evolutionary mechanism (Science 2013)< br> Evolution: An eye for cryptic variation (Nat Rev Genet. 2014)

Kowalko JE, Rohner N, Linden TA, Rompani SB, Warren WC, Borowsky R, Tabin CJ, Jeffery WR, Yoshizawa M. Convergence in feeding posture occurs through different genetic loci in independently evolved cave populations of Astyanax mexicanus. PNAS 2013 Oct 15; 110(42): 1633-8.

Kowalko JE, Rohner N, Rompani SB, Peterson BK, Linden TA, Yoshizawa M, Kay EH, Weber J, Hoekstra HE, Jeffery WR, Borowsky R, Tabin CJ. Loss of schooling behavior in cavefish through sight-dependent and sight-independent mechanisms. Curr Biol 2013 Oct 7; 23(19): 1874-83.< br> Commentary in:< br> Evolution: skipping school (Curr Biol 2013)

Kowalko JE, Sebert ME. The Streptococcus pneumoniae competence regulatory system influences respiratory tract colonization. Infect Immun 2008 Jul;76(7):3131-40.

Biological Sciences
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