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Wiese J, Richards E, Kowalko JE, McGaugh SE. Loci associated with cave-derived traits concentrate in specific regions of the Mexican cavefish genome. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.29.587360. [PMID: 38585759 PMCID: PMC10996652 DOI: 10.1101/2024.03.29.587360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
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.
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Affiliation(s)
- Jonathan Wiese
- Department of Ecology, Evolution, and Behavior, University of Minnesota, St. Paul, MN
| | - Emilie Richards
- Department of Ecology, Evolution, and Behavior, University of Minnesota, St. Paul, MN
| | | | - Suzanne E McGaugh
- Department of Ecology, Evolution, and Behavior, University of Minnesota, St. Paul, MN
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Paz A, Holt KJ, Clarke A, Aviles A, Abraham B, Keene AC, Duboué ER, Fily Y, Kowalko JE. Changes in local interaction rules during ontogeny underlie the evolution of collective behavior. iScience 2023; 26:107431. [PMID: 37636065 PMCID: PMC10448030 DOI: 10.1016/j.isci.2023.107431] [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: 04/03/2023] [Revised: 06/17/2023] [Accepted: 07/17/2023] [Indexed: 08/29/2023] Open
Abstract
Collective motion emerges from individual interactions which produce group-wide 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, Astyanax 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 mediated by changes in the way fish modulate speed and turning relative to neighbors. This transition begins with the tendency to align to neighbors emerging by 28 days post-fertilization and ends with the emergence of robust attraction by 70 days post-fertilization. Cavefish exhibit neither alignment nor attraction at any stage of development. These results reveal how evolution alters local interactions to produce striking differences in collective behavior.
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Affiliation(s)
- Alexandra Paz
- Wilkes Honors College, Florida Atlantic University, Jupiter, FL 33458, USA
| | - Karla J. Holt
- Wilkes Honors College, Florida Atlantic University, Jupiter, FL 33458, USA
| | - Anik Clarke
- Wilkes Honors College, Florida Atlantic University, Jupiter, FL 33458, USA
| | - Ari Aviles
- Wilkes Honors College, Florida Atlantic University, Jupiter, FL 33458, USA
| | - Briana Abraham
- Wilkes Honors College, Florida Atlantic University, Jupiter, FL 33458, USA
| | - Alex C. Keene
- Department of Biology, Texas A&M, College Station, TX 77840, USA
| | - Erik R. Duboué
- Wilkes Honors College, Florida Atlantic University, Jupiter, FL 33458, USA
| | - Yaouen Fily
- Wilkes Honors College, Florida Atlantic University, Jupiter, FL 33458, USA
| | - Johanna E. Kowalko
- Department of Biological Sciences, Lehigh University, Bethlehem, PA 18015, USA
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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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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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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] [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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Tanvir Z, Rivera D, Severi KE, Haspel G, Soares D. Evolutionary and homeostatic changes in morphology of visual dendrites of Mauthner cells in Astyanax blind cavefish. J Comp Neurol 2020; 529:1779-1786. [PMID: 33070322 DOI: 10.1002/cne.25056] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 10/13/2020] [Accepted: 10/14/2020] [Indexed: 01/12/2023]
Abstract
Mauthner cells are the largest neurons in the hindbrain of teleost fish and most amphibians. Each cell has two major dendrites thought to receive segregated streams of sensory input: the lateral dendrite receives mechanosensory input while the ventral dendrite receives visual input. These inputs, which mediate escape responses to sudden stimuli, may be modulated by the availability of sensory information to the animal. To understand the impact of the absence of visual information on the morphologies of Mauthner cells during developmental and evolutionary time scales, we examined the teleost Astyanax mexicanus. This species of tetra is found in two morphs: a seeing surface fish and a blind cavefish. We compared the structure of Mauthner cells in surface fish raised under daily light conditions, in surface fish raised in constant darkness, and in two independent lineages of cave populations. The length of ventral dendrites of Mauthner cells in dark-raised surface fish larvae were longer and more branched, while in both cave morphs the ventral dendrites were smaller or absent. The absence of visual input in surface fish with normal eye development leads to a homeostatic increase in dendrite size, whereas over evolution, the absence of light led to the loss of eyes and a reduction in dendrite size.
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Affiliation(s)
- Zainab Tanvir
- Federated Department of Biological Sciences, New Jersey Institute of Technology, Newark, New Jersey, USA
| | - Daihana Rivera
- Federated Department of Biological Sciences, New Jersey Institute of Technology, Newark, New Jersey, USA
| | - Kristen E Severi
- Federated Department of Biological Sciences, New Jersey Institute of Technology, Newark, New Jersey, USA
| | - Gal Haspel
- Federated Department of Biological Sciences, New Jersey Institute of Technology, Newark, New Jersey, USA
| | - Daphne Soares
- Federated Department of Biological Sciences, New Jersey Institute of Technology, Newark, New Jersey, USA
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