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van der Weele CM, Hospes KC, Rowe KE, Jeffery WR. Hypoxia-sonic hedgehog axis as a driver of primitive hematopoiesis development and evolution in cavefish. Dev Biol 2024; 516:138-147. [PMID: 39173434 PMCID: PMC11402556 DOI: 10.1016/j.ydbio.2024.08.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2024] [Revised: 08/09/2024] [Accepted: 08/15/2024] [Indexed: 08/24/2024]
Abstract
The teleost Astyanax mexicanus consists of surface dwelling (surface fish) and cave dwelling (cavefish) forms. Cavefish have evolved in subterranean habitats characterized by reduced oxygen levels (hypoxia) and exhibit a subset of phenotypic traits controlled by increased Sonic hedgehog (Shh) signaling along the embryonic midline. The enhancement of primitive hematopoietic domains, which are formed bilaterally in the anterior and posterior lateral plate mesoderm, are responsible for the development of more larval erythrocytes in cavefish relative to surface fish. In this study, we determine the role of hypoxia and Shh signaling in the development and evolution of primitive hematopoiesis in cavefish. We show that hypoxia treatment during embryogenesis increases primitive hematopoiesis and erythrocyte development in surface fish. We also demonstrate that upregulation of Shh midline signaling by the Smoothened agonist SAG increases primitive hematopoiesis and erythrocyte development in surface fish, whereas Shh downregulation via treatment with the Smoothened inhibitor cyclopamine decreases these traits in cavefish. Together these results suggest that hematopoietic enhancement is regulated by hypoxia and Shh signaling. Lastly, we demonstrate that hypoxia enhances expression of Shh signaling along the midline of surface fish embryos. We conclude that hypoxia-mediated Shh plasticity may be a driving force for the adaptive evolution of primitive hematopoiesis and erythrocyte development in cavefish.
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Affiliation(s)
| | - Katrina C Hospes
- Department of Biology, University of Maryland, College Park, MD, 20742, USA
| | - Katherine E Rowe
- Department of Biology, University of Maryland, College Park, MD, 20742, USA
| | - William R Jeffery
- Department of Biology, University of Maryland, College Park, MD, 20742, USA.
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2
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Ng M, Ma L, Shi J, Jeffery WR. Natural reversal of cavefish heart asymmetry is controlled by Sonic Hedgehog effects on the left-right organizer. Development 2024; 151:dev202611. [PMID: 38940473 PMCID: PMC11273321 DOI: 10.1242/dev.202611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 06/19/2024] [Indexed: 06/29/2024]
Abstract
The direction of left-right visceral asymmetry is conserved in vertebrates. Deviations of the standard asymmetric pattern are rare, and the underlying mechanisms are not understood. Here, we use the teleost Astyanax mexicanus, consisting of surface fish with normal left-oriented heart asymmetry and cavefish with high levels of reversed right-oriented heart asymmetry, to explore natural changes in asymmetry determination. We show that Sonic Hedgehog (Shh) signaling is increased at the posterior midline, Kupffer's vesicle (the teleost left-right organizer) is enlarged and contains longer cilia, and the number of dorsal forerunner cells is increased in cavefish. Furthermore, Shh increase in surface fish embryos induces asymmetric changes resembling the cavefish phenotype. Asymmetric expression of the Nodal antagonist Dand5 is equalized or reversed in cavefish, and Shh increase in surface fish mimics changes in cavefish dand5 asymmetry. Shh decrease reduces the level of right-oriented heart asymmetry in cavefish. Thus, naturally occurring modifications in cavefish heart asymmetry are controlled by the effects of Shh signaling on left-right organizer function.
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Affiliation(s)
- Mandy Ng
- Department of Biology, University of Maryland, College Park, MD 20742, USA
| | - Li Ma
- Department of Biology, University of Maryland, College Park, MD 20742, USA
| | - Janet Shi
- Department of Biology, University of Maryland, College Park, MD 20742, USA
| | - William R. Jeffery
- Department of Biology, University of Maryland, College Park, MD 20742, USA
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3
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Policarpo M, Legendre L, Germon I, Lafargeas P, Espinasa L, Rétaux S, Casane D. The nature and distribution of putative non-functional alleles suggest only two independent events at the origins of Astyanax mexicanus cavefish populations. BMC Ecol Evol 2024; 24:41. [PMID: 38556874 PMCID: PMC10983663 DOI: 10.1186/s12862-024-02226-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 03/14/2024] [Indexed: 04/02/2024] Open
Abstract
BACKGROUND Several studies suggested that cavefish populations of Astyanax mexicanus settled during the Late Pleistocene. This implies that the cavefish's most conspicuous phenotypic changes, blindness and depigmentation, and more cryptic characters important for cave life, evolved rapidly. RESULTS Using the published genomes of 47 Astyanax cavefish from la Cueva de El Pachón, El Sótano de la Tinaja, La Cueva Chica and El Sótano de Molino, we searched for putative loss-of-function mutations in previously defined sets of genes, i.e., vision, circadian clock and pigmentation genes. Putative non-functional alleles for four vision genes were identified. Then, we searched genome-wide for putative non-functional alleles in these four cave populations. Among 512 genes with segregating putative non-functional alleles in cavefish that are absent in surface fish, we found an enrichment in visual perception genes. Among cavefish populations, different levels of shared putative non-functional alleles were found. Using a subset of 12 genes for which putative loss-of-function mutations were found, we extend the analysis of shared pseudogenes to 11 cave populations. Using a subset of six genes for which putative loss-of-function mutations were found in the El Sótano del Toro population, where extensive hybridization with surface fish occurs, we found a correlation between the level of eye regression and the amount of putative non-functional alleles. CONCLUSIONS We confirm that very few putative non-functional alleles are present in a large set of vision genes, in accordance with the recent origin of Astyanax mexicanus cavefish. Furthermore, the genome-wide analysis indicates an enrichment of putative loss-of-function alleles in genes with vision-related GO-terms, suggesting that visual perception may be the function chiefly impacted by gene losses related to the shift from a surface to a cave environment. The geographic distribution of putative loss-of-function alleles newly suggests that cave populations from Sierra de Guatemala and Sierra de El Abra share a common origin, albeit followed by independent evolution for a long period. It also supports that populations from the Micos area have an independent origin. In El Sótano del Toro, the troglomorphic phenotype is maintained despite massive introgression of the surface genome.
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Affiliation(s)
- Maxime Policarpo
- Université Paris-Saclay, CNRS, IRD, UMR Évolution, Génomes, Comportement Et Écologie, 91190, Gif-Sur-Yvette, France
- Present Address: Zoological Institute, Department of Environmental Sciences, University of Basel, Basel, Switzerland
| | - Laurent Legendre
- Université Paris-Saclay, CNRS, IRD, UMR Évolution, Génomes, Comportement Et Écologie, 91190, Gif-Sur-Yvette, France
| | - Isabelle Germon
- Université Paris-Saclay, CNRS, IRD, UMR Évolution, Génomes, Comportement Et Écologie, 91190, Gif-Sur-Yvette, France
| | - Philippe Lafargeas
- Université Paris-Saclay, CNRS, IRD, UMR Évolution, Génomes, Comportement Et Écologie, 91190, Gif-Sur-Yvette, France
| | - Luis Espinasa
- School of Science, Marist College, Poughkeepsie, NY, USA
| | - Sylvie Rétaux
- Institut de Neuroscience Paris-Saclay, Université Paris-Saclay and CNRS, 91400, Saclay, France.
| | - Didier Casane
- Université Paris-Saclay, CNRS, IRD, UMR Évolution, Génomes, Comportement Et Écologie, 91190, Gif-Sur-Yvette, France.
- Université Paris Cité, UFR Sciences du Vivant, 75013, Paris, France.
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4
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Sifuentes-Romero I, Aviles AM, Carter JL, Chan-Pong A, Clarke A, Crotty P, Engstrom D, Meka P, Perez A, Perez R, Phelan C, Sharrard T, Smirnova MI, Wade AJ, Kowalko JE. Trait Loss in Evolution: What Cavefish Have Taught Us about Mechanisms Underlying Eye Regression. Integr Comp Biol 2023; 63:393-406. [PMID: 37218721 PMCID: PMC10445413 DOI: 10.1093/icb/icad032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 04/18/2023] [Accepted: 04/24/2023] [Indexed: 05/24/2023] Open
Abstract
Reduction or complete loss of traits is a common occurrence throughout evolutionary history. In spite of this, numerous questions remain about why and how trait loss has occurred. Cave animals are an excellent system in which these questions can be answered, as multiple traits, including eyes and pigmentation, have been repeatedly reduced or lost across populations of cave species. This review focuses on how the blind Mexican cavefish, Astyanax mexicanus, has been used as a model system for examining the developmental, genetic, and evolutionary mechanisms that underlie eye regression in cave animals. We focus on multiple aspects of how eye regression evolved in A. mexicanus, including the developmental and genetic pathways that contribute to eye regression, the effects of the evolution of eye regression on other traits that have also evolved in A. mexicanus, and the evolutionary forces contributing to eye regression. We also discuss what is known about the repeated evolution of eye regression, both across populations of A. mexicanus cavefish and across cave animals more generally. Finally, we offer perspectives on how cavefish can be used in the future to further elucidate mechanisms underlying trait loss using tools and resources that have recently become available.
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Affiliation(s)
- Itzel Sifuentes-Romero
- Harriet L. Wilkes Honors College, Florida Atlantic University, Jupiter FL 33458, USA
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
| | - Ari M Aviles
- Harriet L. Wilkes Honors College, Florida Atlantic University, Jupiter FL 33458, USA
- Department of Cell Biology and Genetics, Texas A&M University, College Station, TX 77843, USA
| | - Joseph L Carter
- Harriet L. Wilkes Honors College, Florida Atlantic University, Jupiter FL 33458, USA
| | - Allen Chan-Pong
- Harriet L. Wilkes Honors College, Florida Atlantic University, Jupiter FL 33458, USA
| | - Anik Clarke
- Harriet L. Wilkes Honors College, Florida Atlantic University, Jupiter FL 33458, USA
| | - Patrick Crotty
- Harriet L. Wilkes Honors College, Florida Atlantic University, Jupiter FL 33458, USA
| | - David Engstrom
- Harriet L. Wilkes Honors College, Florida Atlantic University, Jupiter FL 33458, USA
| | - Pranav Meka
- Harriet L. Wilkes Honors College, Florida Atlantic University, Jupiter FL 33458, USA
- Charles E. Schmidt College of Medicine, Florida Atlantic University, Boca Raton, FL 33431, USA
| | - Alexandra Perez
- Harriet L. Wilkes Honors College, Florida Atlantic University, Jupiter FL 33458, USA
| | - Riley Perez
- Harriet L. Wilkes Honors College, Florida Atlantic University, Jupiter FL 33458, USA
| | - Christine Phelan
- Harriet L. Wilkes Honors College, Florida Atlantic University, Jupiter FL 33458, USA
| | - Taylor Sharrard
- Harriet L. Wilkes Honors College, Florida Atlantic University, Jupiter FL 33458, USA
| | - Maria I Smirnova
- Harriet L. Wilkes Honors College, Florida Atlantic University, Jupiter FL 33458, USA
- Charles E. Schmidt College of Medicine, Florida Atlantic University, Boca Raton, FL 33431, USA
- Stiles–Nicholson Brain Institute, Florida Atlantic University, Jupiter, FL 33458, USA
- Charles E. Schmidt College of Science, Florida Atlantic University, Boca Raton, FL 33431, USA
| | - Amanda J Wade
- Harriet L. Wilkes Honors College, Florida Atlantic University, Jupiter FL 33458, USA
| | - Johanna E Kowalko
- Harriet L. Wilkes Honors College, Florida Atlantic University, Jupiter FL 33458, USA
- Department of Biological Sciences, Lehigh University, Bethlehem, PA 18015, USA
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5
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Batista da Silva I, Aciole Barbosa D, Kavalco KF, Nunes LR, Pasa R, Menegidio FB. Discovery of putative long non-coding RNAs expressed in the eyes of Astyanax mexicanus (Actinopterygii: Characidae). Sci Rep 2023; 13:12051. [PMID: 37491348 PMCID: PMC10368750 DOI: 10.1038/s41598-023-34198-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 04/25/2023] [Indexed: 07/27/2023] Open
Abstract
Astyanax mexicanus is a well-known model species, that has two morphotypes, cavefish, from subterranean rivers and surface fish, from surface rivers. They are morphologically distinct due to many troglomorphic traits in the cavefish, such as the absence of eyes. Most studies on A. mexicanus are focused on eye development and protein-coding genes involved in the process. However, lncRNAs did not get the same attention and very little is known about them. This study aimed to fill this knowledge gap, identifying, describing, classifying, and annotating lncRNAs expressed in the embryo's eye tissue of cavefish and surface fish. To do so, we constructed a concise workflow to assemble and evaluate transcriptomes, annotate protein-coding genes, ncRNAs families, predict the coding potential, identify putative lncRNAs, map them and predict interactions. This approach resulted in the identification of 33,069 and 19,493 putative lncRNAs respectively mapped in cavefish and surface fish. Thousands of these lncRNAs were annotated and identified as conserved in human and several species of fish. Hundreds of them were validated in silico, through ESTs. We identified lncRNAs associated with genes related to eye development. This is the case of a few lncRNAs associated with sox2, which we suggest being isomorphs of the SOX2-OT, a lncRNA that can regulate the expression of sox2. This work is one of the first studies to focus on the description of lncRNAs in A. mexicanus, highlighting several lncRNA targets and opening an important precedent for future studies focusing on lncRNAs expressed in A. mexicanus.
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Affiliation(s)
- Iuri Batista da Silva
- Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, 31270-901, Brazil
- Laboratory of Ecological and Evolutionary Genetics, Institute of Biological and Health Sciences, Federal University of Viçosa Campus Rio Paranaíba, Rio Paranaíba, MG, 38810-000, Brazil
| | - David Aciole Barbosa
- Integrated Biotechnology Center, University of Mogi das Cruzes (UMC), Av. Dr. Cândido X. de Almeida and Souza, 200 - Centro Cívico, Mogi das Cruzes, SP, 08780-911, Brazil
| | - Karine Frehner Kavalco
- Laboratory of Ecological and Evolutionary Genetics, Institute of Biological and Health Sciences, Federal University of Viçosa Campus Rio Paranaíba, Rio Paranaíba, MG, 38810-000, Brazil
| | - Luiz R Nunes
- Center for Natural and Human Sciences, Federal University of ABC, São Bernardo do Campo, SP, 09606-045, Brazil
| | - Rubens Pasa
- Laboratory of Ecological and Evolutionary Genetics, Institute of Biological and Health Sciences, Federal University of Viçosa Campus Rio Paranaíba, Rio Paranaíba, MG, 38810-000, Brazil.
| | - Fabiano B Menegidio
- Integrated Biotechnology Center, University of Mogi das Cruzes (UMC), Av. Dr. Cândido X. de Almeida and Souza, 200 - Centro Cívico, Mogi das Cruzes, SP, 08780-911, Brazil.
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6
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Kozol RA, Yuiska A, Han JH, Tolentino B, Lopatto A, Lewis P, Paz A, Keene AC, Kowalko JE, Duboué ER. Novel Husbandry Practices Result in Rapid Rates of Growth and Sexual Maturation Without Impacting Adult Behavior in the Blind Mexican Cavefish. Zebrafish 2023; 20:86-94. [PMID: 37071855 PMCID: PMC10123811 DOI: 10.1089/zeb.2023.0001] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/20/2023] Open
Abstract
Animal model systems are dependent on the standardization of husbandry protocols that maximize growth and reduce generation time. The Mexican tetra, Astyanax mexicanus, exists as eyed surface and blind cave dwelling populations. The opportunity for comparative approaches between independently evolved populations has led to the rapid growth of A. mexicanus as a model for evolution and biomedical research. However, a slow and inconsistent growth rate remains a major limitation to the expanded application of A. mexicanus. Fortunately, this temporal limitation can be addressed through husbandry changes that accelerate growth rates while maintaining optimal health outcomes. Here, we describe a husbandry protocol that produces rapid growth rates through changes in diet, feeding frequency, growth sorting and progressive changes in tank size. This protocol produced robust growth rates and decreased the age of sexual maturity in comparison to our previous protocol. To determine whether changes in feeding impacted behavior, we tested fish in exploration and schooling assays. We found no difference in behavior between the two groups, 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.
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Affiliation(s)
- Robert A. Kozol
- College of Arts and Sciences, Florida Atlantic University, Jupiter, Florida, USA
| | - Anders Yuiska
- College of Arts and Sciences, Florida Atlantic University, Jupiter, Florida, USA
| | - Ji Heon Han
- Department of Biological Sciences, Florida Atlantic University, Jupiter, Florida, USA
| | - Bernadeth Tolentino
- Department of Biology, University of Southern California, Los Angeles, California, USA
| | - Arthur Lopatto
- College of Arts and Sciences, Florida Atlantic University, Jupiter, Florida, USA
| | - Peter Lewis
- College of Arts and Sciences, Florida Atlantic University, Jupiter, Florida, USA
| | - Alexandra Paz
- College of Arts and Sciences, Florida Atlantic University, Jupiter, Florida, USA
| | - Alex C. Keene
- Department of Biology, Texas A&M, College Station, Texas, USA
| | - Johanna E. Kowalko
- Department of Biological Sciences, Lehigh University, Bethlehem, Pennsylvania, USA
| | - Erik R. Duboué
- College of Arts and Sciences, Florida Atlantic University, Jupiter, Florida, USA
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7
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Rodriguez-Morales R, Gonzalez-Lerma P, Yuiska A, Han JH, Guerra Y, Crisostomo L, Keene AC, Duboue ER, Kowalko JE. Convergence on reduced aggression through shared behavioral traits in multiple populations of Astyanax mexicanus. BMC Ecol Evol 2022; 22:116. [PMID: 36241984 PMCID: PMC9563175 DOI: 10.1186/s12862-022-02069-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 09/20/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Aggression is observed across the animal kingdom, and benefits animals in a number of ways to increase fitness and promote survival. While aggressive behaviors vary widely across populations and can evolve as an adaptation to a particular environment, the complexity of aggressive behaviors presents a challenge to studying the evolution of aggression. The Mexican tetra, Astyanax mexicanus exists as an aggressive river-dwelling surface form and multiple populations of a blind cave form, some of which exhibit reduced aggression, providing the opportunity to investigate how evolution shapes aggressive behaviors. RESULTS To define how aggressive behaviors evolve, we performed a high-resolution analysis of multiple social behaviors that occur during aggressive interactions in A. mexicanus. We found that many of the aggression-associated behaviors observed in surface-surface aggressive encounters were reduced or lost in Pachón cavefish. Interestingly, one behavior, circling, was observed more often in cavefish, suggesting evolution of a shift in the types of social behaviors exhibited by cavefish. Further, detailed analysis revealed substantive differences in aggression-related sub-behaviors in independently evolved cavefish populations, suggesting independent evolution of reduced aggression between cave populations. We found that many aggressive behaviors are still present when surface fish fight in the dark, suggesting that these reductions in aggression-associated and escape-associated behaviors in cavefish are likely independent of loss of vision in this species. Further, levels of aggression within populations were largely independent of type of opponent (cave vs. surface) or individual stress levels, measured through quantifying stress-like behaviors, suggesting these behaviors are hardwired and not reflective of population-specific changes in other cave-evolved traits. CONCLUSION These results reveal that loss of aggression in cavefish evolved through the loss of multiple aggression-associated behaviors and raise the possibility that independent genetic mechanisms underlie changes in each behavior within populations and across populations. Taken together, these findings reveal the complexity of evolution of social behaviors and establish A. mexicanus as a model for investigating the evolutionary and genetic basis of aggressive behavior.
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Affiliation(s)
| | - Paola Gonzalez-Lerma
- Department of Integrative Biology and Biomedical Sciences, Florida Atlantic University, 33431, Boca Raton, FL, USA
| | - Anders Yuiska
- Charles E. Schmidt College of Science, Florida Atlantic University, 33431, Boca Raton, FL, USA
| | - Ji Heon Han
- Charles E. Schmidt College of Science, Florida Atlantic University, 33431, Boca Raton, FL, USA
- Program in Integrative Biology and Neuroscience, Florida Atlantic University, 33458, Jupiter, FL, USA
| | - Yolanda Guerra
- Harriet L. Wilkes Honors College, Florida Atlantic University, 33458, Jupiter, FL, USA
| | - Lina Crisostomo
- Harriet L. Wilkes Honors College, Florida Atlantic University, 33458, Jupiter, FL, USA
| | - Alex C Keene
- Department of Biology, Texas A&M, College Station, TX, USA
| | - Erik R Duboue
- Charles E. Schmidt College of Science, Florida Atlantic University, 33431, Boca Raton, FL, USA
- Harriet L. Wilkes Honors College, Florida Atlantic University, 33458, Jupiter, FL, USA
| | - Johanna E Kowalko
- Department of Biological Sciences, Lehigh University, 18015, Bethlehem, PA, USA.
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8
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Lloyd E, McDole B, Privat M, Jaggard JB, Duboué ER, Sumbre G, Keene AC. Blind cavefish retain functional connectivity in the tectum despite loss of retinal input. Curr Biol 2022; 32:3720-3730.e3. [PMID: 35926509 DOI: 10.1016/j.cub.2022.07.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 04/07/2022] [Accepted: 07/07/2022] [Indexed: 11/26/2022]
Abstract
Sensory systems display remarkable plasticity and are under strong evolutionary selection. The Mexican cavefish, Astyanax mexicanus, consists of eyed river-dwelling surface populations and multiple independent cave populations that have converged on eye loss, providing the opportunity to examine the evolution of sensory circuits in response to environmental perturbation. Functional analysis across multiple transgenic populations expressing GCaMP6s showed that functional connectivity of the optic tectum largely did not differ between populations, except for the selective loss of negatively correlated activity within the cavefish tectum, suggesting positively correlated neural activity is resistant to an evolved loss of input from the retina. Furthermore, analysis of surface-cave hybrid fish reveals that changes in the tectum are genetically distinct from those encoding eye loss. Together, these findings uncover the independent evolution of multiple components of the visual system and establish the use of functional imaging in A. mexicanus to study neural circuit evolution.
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Affiliation(s)
- Evan Lloyd
- Department of Biological Science, Florida Atlantic University, Jupiter, FL 33458, USA; Department of Biology, Texas A&M University, College Station, TX 77843, USA; Harriet Wilkes Honors College, Florida Atlantic University, Jupiter, FL 33458, USA
| | - Brittnee McDole
- Department of Biological Science, Florida Atlantic University, Jupiter, FL 33458, USA
| | - Martin Privat
- Institut de Biologie de l'ENS (IBENS), Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France
| | - James B Jaggard
- Department of Biological Science, Florida Atlantic University, Jupiter, FL 33458, USA; Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Erik R Duboué
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - German Sumbre
- Institut de Biologie de l'ENS (IBENS), Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France.
| | - Alex C Keene
- Department of Biology, Texas A&M University, College Station, TX 77843, USA.
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9
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Oliva C, Hinz NK, Robinson W, Barrett Thompson AM, Booth J, Crisostomo LM, Zanineli S, Tanner M, Lloyd E, O'Gorman M, McDole B, Paz A, Kozol R, Brown EB, Kowalko JE, Fily Y, Duboue ER, Keene AC. Characterizing the genetic basis of trait evolution in the Mexican cavefish. Evol Dev 2022; 24:131-144. [PMID: 35924750 PMCID: PMC9786752 DOI: 10.1111/ede.12412] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 04/20/2022] [Accepted: 04/26/2022] [Indexed: 12/30/2022]
Abstract
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 inhabit 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 the measured behavioral and morphological traits. Taken together, this approach provides a novel system to identify genetic underpinnings of naturally occurring variation in morphological and behavioral traits.
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Affiliation(s)
- Camila Oliva
- NIH U‐RISE ProgramFlorida Atlantic UniversityJupiterFloridaUSA
| | | | - Wayne Robinson
- NIH U‐RISE ProgramFlorida Atlantic UniversityJupiterFloridaUSA
| | | | - Julianna Booth
- NIH U‐RISE ProgramFlorida Atlantic UniversityJupiterFloridaUSA
| | | | | | - Maureen Tanner
- NIH U‐RISE ProgramFlorida Atlantic UniversityJupiterFloridaUSA
| | - Evan Lloyd
- Jupiter Life Science InitiativeFlorida Atlantic UniversityJupiterFloridaUSA,Department of BiologyTexas A&M UniversityCollege StationTexasUSA
| | - Morgan O'Gorman
- Jupiter Life Science InitiativeFlorida Atlantic UniversityJupiterFloridaUSA,Department of BiologyTexas A&M UniversityCollege StationTexasUSA
| | - Brittnee McDole
- Jupiter Life Science InitiativeFlorida Atlantic UniversityJupiterFloridaUSA
| | - Alexandra Paz
- Jupiter Life Science InitiativeFlorida Atlantic UniversityJupiterFloridaUSA
| | - Rob Kozol
- Jupiter Life Science InitiativeFlorida Atlantic UniversityJupiterFloridaUSA
| | - Elizabeth B. Brown
- Jupiter Life Science InitiativeFlorida Atlantic UniversityJupiterFloridaUSA
| | - Johanna E. Kowalko
- Jupiter Life Science InitiativeFlorida Atlantic UniversityJupiterFloridaUSA,Department of Biological SciencesLehigh UniversityBethlehemPennsylvaniaUSA
| | - Yaouen Fily
- Jupiter Life Science InitiativeFlorida Atlantic UniversityJupiterFloridaUSA
| | - Erik R. Duboue
- Jupiter Life Science InitiativeFlorida Atlantic UniversityJupiterFloridaUSA
| | - Alex C. Keene
- Jupiter Life Science InitiativeFlorida Atlantic UniversityJupiterFloridaUSA,Department of BiologyTexas A&M UniversityCollege StationTexasUSA
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10
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Bradshaw SN, Allison WT. Hagfish to Illuminate the Developmental and Evolutionary Origins of the Vertebrate Retina. Front Cell Dev Biol 2022; 10:822358. [PMID: 35155434 PMCID: PMC8826474 DOI: 10.3389/fcell.2022.822358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 01/07/2022] [Indexed: 11/13/2022] Open
Abstract
The vertebrate eye is a vital sensory organ that has long fascinated scientists, but the details of how this organ evolved are still unclear. The vertebrate eye is distinct from the simple photoreceptive organs of other non-vertebrate chordates and there are no clear transitional forms of the eye in the fossil record. To investigate the evolution of the eye we can examine the eyes of the most ancient extant vertebrates, the hagfish and lamprey. These jawless vertebrates are in an ideal phylogenetic position to study the origin of the vertebrate eye but data on eye/retina development in these organisms is limited. New genomic and gene expression data from hagfish and lamprey suggest they have many of the same genes for eye development and retinal neurogenesis as jawed vertebrates, but functional work to determine if these genes operate in retinogenesis similarly to other vertebrates is missing. In addition, hagfish express a marker of proliferative retinal cells (Pax6) near the margin of the retina, and adult retinal growth is apparent in some species. This finding of eye growth late into hagfish ontogeny is unexpected given the degenerate eye phenotype. Further studies dissecting retinal neurogenesis in jawless vertebrates would allow for comparison of the mechanisms of retinal development between cyclostome and gnathostome eyes and provide insight into the evolutionary origins of the vertebrate eye.
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Affiliation(s)
| | - W. Ted Allison
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
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O'Gorman M, Thakur S, Imrie G, Moran RL, Choy S, Sifuentes-Romero I, Bilandžija H, Renner KJ, Duboué 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. Curr Biol 2021; 31:3694-3701.e4. [PMID: 34293332 DOI: 10.1016/j.cub.2021.06.077] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Revised: 03/22/2021] [Accepted: 06/25/2021] [Indexed: 12/29/2022]
Abstract
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.1,2 The Mexican tetra, Astyanax mexicanus, consists of fish that inhabit at least 30 caves in Mexico and ancestral-like surface fish that inhabit the rivers of Mexico and southern Texas.3 Cave A. mexicanus are interfertile with surface fish and have evolved a number of traits, including reduced pigmentation, eye loss, and alterations to behavior.4-6 To define relationships between different cave-evolved traits, we phenotyped 208 surface-cave F2 hybrid fish for numerous morphological and behavioral traits. We found differences in sleep between pigmented and albino hybrid fish, raising the possibility that these traits share a genetic basis. In cavefish and other species, mutations in oculocutaneous albinism 2 (oca2) cause albinism.7-12 Surface fish with 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 independently evolved populations of albino cavefish with naturally occurring mutations in oca2. Analysis of the oca2 locus in wild-caught cave and surface fish suggests that oca2 is under positive selection in 3 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 albinism and sleep loss.
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Affiliation(s)
- Morgan O'Gorman
- Jupiter Life Science Initiative, Florida Atlantic University, Jupiter, FL 33458, USA
| | - Sunishka Thakur
- Jupiter Life Science Initiative, Florida Atlantic University, Jupiter, FL 33458, USA
| | - Gillian Imrie
- Jupiter Life Science Initiative, Florida Atlantic University, Jupiter, FL 33458, USA
| | - Rachel L Moran
- Department of Ecology, Evolution, and Behavior. University of Minnesota, St. Paul, MN 55108, USA
| | - Stefan Choy
- Jupiter Life Science Initiative, Florida Atlantic University, Jupiter, FL 33458, USA
| | | | - Helena Bilandžija
- Department of Molecular Biology, Rudjer Boskovic Institute, 10000 Zagreb, Croatia
| | - Kenneth J Renner
- Department of Biology, University of South Dakota, Vermillion, SD 57069, USA
| | - Erik Duboué
- Jupiter Life Science Initiative, Florida Atlantic University, Jupiter, FL 33458, USA; Harriet L. Wilkes Honors College, Florida Atlantic University, Jupiter, FL 33458, USA
| | | | - Suzanne E McGaugh
- Department of Ecology, Evolution, and Behavior. University of Minnesota, St. Paul, MN 55108, USA
| | - Alex C Keene
- Jupiter Life Science Initiative, Florida Atlantic University, Jupiter, FL 33458, USA; Department of Biology Science, Florida Atlantic University, Jupiter, FL 33458, USA.
| | - Johanna E Kowalko
- Jupiter Life Science Initiative, Florida Atlantic University, Jupiter, FL 33458, USA; Harriet L. Wilkes Honors College, Florida Atlantic University, Jupiter, FL 33458, USA.
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12
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Warren WC, Boggs TE, Borowsky R, Carlson BM, Ferrufino E, Gross JB, Hillier L, Hu Z, Keene AC, Kenzior A, Kowalko JE, Tomlinson 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, Rohner N. A chromosome-level genome of Astyanax mexicanus surface fish for comparing population-specific genetic differences contributing to trait evolution. Nat Commun 2021; 12:1447. [PMID: 33664263 PMCID: PMC7933363 DOI: 10.1038/s41467-021-21733-z] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 02/02/2021] [Indexed: 01/31/2023] Open
Abstract
Identifying the genetic factors that underlie complex traits is central to understanding the mechanistic underpinnings of evolution. Cave-dwelling Astyanax mexicanus populations 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 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 across cavefish populations to gain insight into this potential source of cave adaptation. The surface fish genome reference now provides a more complete resource for comparative, functional and genetic studies of drastic trait differences within a species.
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Affiliation(s)
- Wesley C Warren
- Department of Animal Sciences, Institute for Data Science and Informatics, Bond Life Sciences Center, University of Missouri, Columbia, MO, USA.
- Department of Surgery, Institute for Data Science and Informatics, Bond Life Sciences Center, University of Missouri, Columbia, MO, USA.
| | - Tyler E Boggs
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, USA
| | | | - Brian M Carlson
- Department of Biological Sciences, Northern Kentucky University, Highland Heights, KY, USA
| | - Estephany Ferrufino
- Harriet L. Wilkes Honors College, Florida Atlantic University, Jupiter, FL, USA
| | - Joshua B Gross
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, USA
| | - LaDeana Hillier
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Zhilian Hu
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK
| | - Alex C Keene
- Department of Biological Sciences, Florida Atlantic University, Jupiter, FL, USA
| | | | - Johanna E Kowalko
- Harriet L. Wilkes Honors College, Florida Atlantic University, Jupiter, FL, USA
| | - Chad Tomlinson
- McDonnell Genome Institute, Washington University, St Louis, MO, USA
| | - Milinn Kremitzki
- McDonnell Genome Institute, Washington University, St Louis, MO, USA
| | | | | | - Suzanne E McGaugh
- Department of Ecology, Evolution, and Behavior, University of Minnesota, Saint Paul, MN, USA
| | - Jeffrey T Miller
- Department of Ecology, Evolution, and Behavior, University of Minnesota, Saint Paul, MN, USA
| | | | - Rachel L Moran
- Department of Ecology, Evolution, and Behavior, University of Minnesota, Saint Paul, MN, USA
| | - Robert Peuß
- Stowers Institute for Medical Research, Kansas City, MO, USA
- Institute for Evolution and Biodiversity, University of Münster, Münster, Germany
| | - Edward S Rice
- Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
| | - Misty R Riddle
- Genetics Department, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Department of Biology, University of Nevada, Reno, NV, USA
| | | | - Bethany A Stanhope
- Harriet L. Wilkes Honors College, Florida Atlantic University, Jupiter, FL, USA
- Department of Biological Sciences, Florida Atlantic University, Jupiter, FL, USA
| | - Clifford J Tabin
- Genetics Department, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Sunishka Thakur
- Harriet L. Wilkes Honors College, Florida Atlantic University, Jupiter, FL, USA
| | - Yoshiyuki Yamamoto
- Department of Cell and Developmental Biology, University College London, London, UK
| | - Nicolas Rohner
- Stowers Institute for Medical Research, Kansas City, MO, USA.
- Department of Molecular & Integrative Physiology, KU Medical Center, Kansas City, KS, USA.
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