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Ponnimbaduge Perera P, Perez Guerra D, Riddle MR. The Mexican Tetra, Astyanax mexicanus, as a Model System in Cell and Developmental Biology. Annu Rev Cell Dev Biol 2023; 39:23-44. [PMID: 37437210 DOI: 10.1146/annurev-cellbio-012023-014003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/14/2023]
Abstract
Our understanding of cell and developmental biology has been greatly aided by a focus on a small number of model organisms. However, we are now in an era where techniques to investigate gene function can be applied across phyla, allowing scientists to explore the diversity and flexibility of developmental mechanisms and gain a deeper understanding of life. Researchers comparing the eyeless cave-adapted Mexican tetra, Astyanax mexicanus, with its river-dwelling counterpart are revealing how the development of the eyes, pigment, brain, cranium, blood, and digestive system evolves as animals adapt to new environments. Breakthroughs in our understanding of the genetic and developmental basis of regressive and constructive trait evolution have come from A. mexicanus research. They include understanding the types of mutations that alter traits, which cellular and developmental processes they affect, and how they lead to pleiotropy. We review recent progress in the field and highlight areas for future investigations that include evolution of sex differentiation, neural crest development, and metabolic regulation of embryogenesis.
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Affiliation(s)
| | | | - Misty R Riddle
- Department of Biology, University of Nevada, Reno, Nevada, USA;
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2
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Fang Z, Atukorallaya D. Count Me in, Count Me out: Regulation of the Tooth Number via Three Directional Developmental Patterns. Int J Mol Sci 2023; 24:15061. [PMID: 37894742 PMCID: PMC10606784 DOI: 10.3390/ijms242015061] [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: 09/19/2023] [Revised: 10/05/2023] [Accepted: 10/08/2023] [Indexed: 10/29/2023] Open
Abstract
Tooth number anomalies, including hyperdontia and hypodontia, are common congenital dental problems in the dental clinic. The precise number of teeth in a dentition is essential for proper speech, mastication, and aesthetics. Teeth are ectodermal organs that develop from the interaction of a thickened epithelium (dental placode) with the neural-crest-derived ectomesenchyme. There is extensive histological, molecular, and genetic evidence regarding how the tooth number is regulated in this serial process, but there is currently no universal classification for tooth number abnormalities. In this review, we propose a novel regulatory network for the tooth number based on the inherent dentition formation process. This network includes three intuitive directions: the development of a single tooth, the formation of a single dentition with elongation of the continual lamina, and tooth replacement with the development of the successional lamina. This article summarizes recent reports on early tooth development and provides an analytical framework to classify future relevant experiments.
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Affiliation(s)
| | - Devi Atukorallaya
- Department of Oral Biology, Dr. Gerald Niznick College of Dentistry, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB R3E0W2, Canada;
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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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Atukorallaya D, Bhatia V, Gonzales J. Divergent tooth development mechanisms of Mexican tetra fish (Astyanax mexicanus) of Pachón cave origin. Cells Dev 2023; 173:203823. [PMID: 36496080 DOI: 10.1016/j.cdev.2022.203823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 11/11/2022] [Accepted: 11/29/2022] [Indexed: 12/13/2022]
Abstract
The Mexican tetra (Astyanax mexicanus) is one of the fresh water teleost fish models in evolutionary developmental biology. The existence of two morphs: eyed, pigmented surface fish and blind depigmented cavefish from multiple cave populations, provides a unique system to study adaptive radiation. Compared to the adult surface fish, cavefish have large oral jaws with an increased number of structurally-complex teeth. Early tooth development has not been studied in detail in cavefish populations. In this study, bone-stained growth series and vital dye staining was used to trace the development and replacement of dentitions in Pachón cavefish. Our results show that first tooth eruption was delayed in cavefish compared to the surface fish. In particular, the first tooth eruption cycle persisted until 35 days post fertilization (dpf). Unlike surface fish, there are multicuspid teeth in cavefish first generation dentition. In addition to the teeth in the marginal oral jaw bones, Pachón cavefish have teeth in the ectopterygoid bone of the palatine roof. Next, we characterised the expression of ectodysplasin signalling pathway genes in tooth-forming regions of surface and cavefish. Interestingly, higher expression of Eda and Edar was found in cavefish compared to the surface fish. The altered ectodysplasin expression needs further investigation to confirm the different molecular mechanisms for tooth development in the oral and pharyngeal regions of surface fish and cavefish.
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Affiliation(s)
- Devi Atukorallaya
- Department of Oral Biology, Dr. Gerald Niznick College of Dentistry, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba R3E0W2, Canada.
| | - Vikram Bhatia
- Department of Oral Biology, Dr. Gerald Niznick College of Dentistry, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba R3E0W2, Canada
| | - Jessica Gonzales
- Department of Oral Biology, Dr. Gerald Niznick College of Dentistry, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba R3E0W2, Canada
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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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6
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Abstract
The small teleost fish Astyanax mexicanus has emerged as an outstanding model for studying many biological topics in the context of evolution. A major attribute is conspecific surface dwelling (surface fish) and blind cave dwelling (cavefish) morphs that can be raised in the laboratory and spawn large numbers of transparent and synchronously developing embryos. More than 30 cavefish populations have been discovered, mostly in northeastern Mexico, and some are thought to have evolved independently from surface fish ancestors, providing excellent models of parallel and convergent evolution. Cavefish have evolved eye and pigmentation regression, as well as modifications in brain morphology, behaviors, heart regenerative capacity, metabolic processes, and craniofacial organization. Thus, the Astyanax model provides researchers with natural "mutants" to study life in the challenging cave environment. The application of powerful genetic approaches based on hybridization between the two morphs and between the different cavefish populations are key advantages for deciphering the developmental and genetic mechanisms regulating trait evolution. QTL analysis has revealed the genetic architectures of gained and lost traits. In addition, some cavefish traits resemble human diseases, offering novel models for biomedical research. Astyanax research is supported by genome assemblies, transcriptomes, tissue and organ transplantation, gene manipulation and editing, and stable transgenesis, and benefits from a welcoming and interactive research community that conducts integrated community projects and sponsors the International Astyanax Meeting (AIM).
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Affiliation(s)
- William R Jeffery
- Department of Biology, University of Maryland, College Park, MD 20742 USA
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McGaugh SE, Kowalko JE, Duboué E, Lewis P, Franz-Odendaal TA, Rohner N, Gross JB, Keene AC. Dark world rises: The emergence of cavefish as a model for the study of evolution, development, behavior, and disease. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2020; 334:397-404. [PMID: 32638529 DOI: 10.1002/jez.b.22978] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2019] [Revised: 06/15/2020] [Accepted: 06/16/2020] [Indexed: 12/24/2022]
Abstract
A central question in biology is how naturally occurring genetic variation accounts for morphological and behavioral diversity within a species. The Mexican tetra, Astyanax mexicanus, has been studied for nearly a century as a model for investigating trait evolution. In March of 2019, researchers representing laboratories from around the world met at the Sixth Astyanax International Meeting in Santiago de Querétaro, Mexico. The meeting highlighted the expanding applications of cavefish to investigations of diverse aspects of basic biology, including development, evolution, and disease-based applications. A broad range of integrative approaches are being applied in this system, including the application of state-of-the-art functional genetic assays, brain imaging, and genome sequencing. These advances position cavefish as a model organism for addressing fundamental questions about the genetics and evolution underlying the impressive trait diversity among individual populations within this species.
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Affiliation(s)
- Suzanne E McGaugh
- Ecology, Evolution, and Behavior, University of Minnesota, Saint Paul, Minnesota
| | - Johanna E Kowalko
- The Jupiter Life Science Initiative and Program in Neurogenetics, Florida Atlantic University, Jupiter, Florida.,Harriet L. Wilkes Honors College, Florida Atlantic University, Jupiter, Florida
| | - Erik Duboué
- The Jupiter Life Science Initiative and Program in Neurogenetics, Florida Atlantic University, Jupiter, Florida.,Harriet L. Wilkes Honors College, Florida Atlantic University, Jupiter, Florida
| | - Peter Lewis
- The Jupiter Life Science Initiative and Program in Neurogenetics, Florida Atlantic University, Jupiter, Florida
| | | | - Nicolas Rohner
- Stowers Institute for Medical Research, Kansas City, Missouri
| | - Joshua B Gross
- Department of Biological Sciences, University of Cincinnati, Cincinnati, Ohio
| | - Alex C Keene
- The Jupiter Life Science Initiative and Program in Neurogenetics, Florida Atlantic University, Jupiter, Florida
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8
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Riddle MR, Tabin CJ. Little Fish, Big Questions: A Collection of Modern Techniques for Mexican Tetra Research. J Vis Exp 2020. [PMID: 32092048 PMCID: PMC7373155 DOI: 10.3791/60592] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Articles Discussed: Stahl, B. A. et al. Manipulation of Gene Function in Mexican Cavefish. Journal of Visualized Experiments. (146) (2019). Peuß, R. et al. Gamete Collection and In Vitro Fertilization of Astyanax mexicanus. Journal of Visualized Experiments. (147) (2019). Worsham, M. et al. Behavioral Tracking and Neuromast Imaging of Mexican Cavefish.Journal of Visualized Experiments. (147) (2019). Jaggard, J.B., Lloyd, E., Lopatto, A., Duboue, E.R., Keene, A.C. Automated Measurements of Sleep and Locomotor Activity in Mexican Cavefish. Journal of Visualized Experiments. (145) (2019). Luc, H., Sears, C., Raczka, A., Gross, J.B. Wholemount In Situ Hybridization for Astyanax Embryos. Journal of Visualized Experiments. (145) (2019). Riddle, M., Martineau, B., Peavey, M., Tabin, C. Raising the Mexican Tetra Astyanax mexicanus for Analysis of Post-larval Phenotypes and Whole-mount Immunohistochemistry. Journal of Visualized Experiments. (142) (2018).
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Affiliation(s)
- Misty R Riddle
- Genetics Department, Blavatnik Institute, Harvard Medical School
| | - Clifford J Tabin
- Genetics Department, Blavatnik Institute, Harvard Medical School;
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Ma L, Ng M, van der Weele CM, Yoshizawa M, Jeffery WR. Dual roles of the retinal pigment epithelium and lens in cavefish eye degeneration. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2020; 334:438-449. [PMID: 31930686 DOI: 10.1002/jez.b.22923] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 11/04/2019] [Accepted: 12/21/2019] [Indexed: 01/03/2023]
Abstract
Astyanax mexicanus consists of two forms, a sighted surface dwelling form (surface fish) and a blind cave-dwelling form (cavefish). Embryonic eyes are initially formed in cavefish but they are subsequently arrested in growth and degenerate during larval development. Previous lens transplantation studies have shown that the lens plays a central role in cavefish eye loss. However, several lines of evidence suggest that additional factors, such as the retinal pigment epithelium (RPE), which is morphologically altered in cavefish, could also be involved in the eye regression process. To explore the role of the RPE in cavefish eye degeneration, we generated an albino eyed (AE) strain by artificial selection for hybrid individuals with large eyes and a depigmented RPE. The AE strain exhibited an RPE lacking pigment granules and showed reduced expression of the RPE specific enzyme retinol isomerase, allowing eye development to be studied by lens ablation in an RPE background resembling cavefish. We found that lens ablation in the AE strain had stronger negative effects on eye growth than in surface fish, suggesting that an intact RPE is required for normal eye development. We also found that the AE strain develops a cartilaginous sclera lacking boney ossicles, a trait similar to cavefish. Extrapolation of the results to cavefish suggests that the RPE and lens have dual roles in eye degeneration, and that deficiencies in the RPE may be associated with evolutionary changes in scleral ossification.
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Affiliation(s)
- Li Ma
- Department of Biology, University of Maryland, College Park, Maryland
| | - Mandy Ng
- Department of Biology, University of Maryland, College Park, Maryland
| | | | - Masato Yoshizawa
- Department of Biology, University of Maryland, College Park, Maryland
| | - William R Jeffery
- Department of Biology, University of Maryland, College Park, Maryland
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Atukorala ADS, Bhatia V, Ratnayake R. Craniofacial skeleton of MEXICAN tetra (Astyanax mexicanus): As a bone disease model. Dev Dyn 2018; 248:153-161. [PMID: 30450697 DOI: 10.1002/dvdy.4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 11/12/2018] [Accepted: 11/12/2018] [Indexed: 12/16/2022] Open
Abstract
A small fresh water fish, the Mexican tetra (Astyanax mexicanus) is a novel animal model in evolutionary developmental biology. The existence of morphologically distinct surface and cave morphs of this species allows simultaneous comparative analysis of phenotypic changes at different life stages. The cavefish harbors many favorable constructive traits (i.e., large jaws with an increased number of teeth, neuromast cells, enlarged olfactory pits and excess storage of adipose tissues) and regressive traits (i.e., reduced eye structures and pigmentation) which are essential for cave adaptation. A wide spectrum of natural craniofacial morphologies can be observed among the different cave populations. Recently, the Mexican tetra has been identified as a human disease model. The fully sequenced genome along with modern genome editing tools has allowed researchers to generate transgenic and targeted gene knockouts with phenotypes that resemble human pathological conditions. This review will discuss the anatomy of the craniofacial skeleton of A. mexicanus with a focus on morphologically variable facial bones, jaws that house continuously replacing teeth and pharyngeal skeleton. Furthermore, the possible applications of this model animal in identifying human congenital and metabolic skeletal disorders is addressed. Developmental Dynamics 248:153-161, 2019. © 2018 Wiley Periodicals, Inc.
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Affiliation(s)
- Atukorallaya Devi Sewvandini Atukorala
- Department of Oral Biology, Dr. Gerald Niznick College of Dentistry, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Vikram Bhatia
- Department of Oral Biology, Dr. Gerald Niznick College of Dentistry, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Ravindra Ratnayake
- Department of Oral Biology, Dr. Gerald Niznick College of Dentistry, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
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