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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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2
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Sadier A, Sears KE, Womack M. Unraveling the heritage of lost traits. JOURNAL OF EXPERIMENTAL ZOOLOGY. PART B, MOLECULAR AND DEVELOPMENTAL EVOLUTION 2022; 338:107-118. [PMID: 33528870 DOI: 10.1002/jez.b.23030] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 12/22/2020] [Accepted: 01/03/2021] [Indexed: 12/22/2022]
Abstract
We synthesize ontogenetic work spanning the past century that show evolutionarily lost structures are rarely entirely absent from earlier developmental stages. We discuss morphological and genetic insights from developmental studies reveal about the evolution of trait loss and regain.
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Affiliation(s)
- Alexa Sadier
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, California, USA
| | - Karen E Sears
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, California, USA
| | - Molly Womack
- Department of Biology, Utah State University, Logan, Utah, USA
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Devos L, Agnès F, Edouard J, Simon V, Legendre L, El Khallouki N, Barbachou S, Sohm F, Rétaux S. Eye morphogenesis in the blind Mexican cavefish. Biol Open 2021; 10:bio059031. [PMID: 34590124 PMCID: PMC8565469 DOI: 10.1242/bio.059031] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 09/24/2021] [Indexed: 01/13/2023] Open
Abstract
The morphogenesis of the vertebrate eye consists of a complex choreography of cell movements, tightly coupled to axial regionalization and cell type specification processes. Disturbances in these events can lead to developmental defects and blindness. Here, we have deciphered the sequence of defective events leading to coloboma in the embryonic eye of the blind cavefish of the species Astyanax mexicanus. Using comparative live imaging on targeted enhancer-trap Zic1:hsp70:GFP reporter lines of both the normal, river-dwelling morph and the cave morph of the species, we identified defects in migratory cell behaviours during evagination that participate in the reduced optic vesicle size in cavefish, without proliferation defect. Further, impaired optic cup invagination shifts the relative position of the lens and contributes to coloboma in cavefish. Based on these results, we propose a developmental scenario to explain the cavefish phenotype and discuss developmental constraints to morphological evolution. The cavefish eye appears as an outstanding natural mutant model to study molecular and cellular processes involved in optic region morphogenesis.
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Affiliation(s)
- Lucie Devos
- Paris-Saclay Institute of Neuroscience, CNRS, Université Paris-Saclay, 91198 Gif sur Yvette, France
| | - François Agnès
- Paris-Saclay Institute of Neuroscience, CNRS, Université Paris-Saclay, 91198 Gif sur Yvette, France
| | - Joanne Edouard
- AMAGEN, CNRS, INRA, Université Paris-Saclay, 91198, Gif sur Yvette, France
| | - Victor Simon
- Paris-Saclay Institute of Neuroscience, CNRS, Université Paris-Saclay, 91198 Gif sur Yvette, France
- AMAGEN, CNRS, INRA, Université Paris-Saclay, 91198, Gif sur Yvette, France
| | - Laurent Legendre
- AMAGEN, CNRS, INRA, Université Paris-Saclay, 91198, Gif sur Yvette, France
| | - Naima El Khallouki
- AMAGEN, CNRS, INRA, Université Paris-Saclay, 91198, Gif sur Yvette, France
| | - Sosthène Barbachou
- AMAGEN, CNRS, INRA, Université Paris-Saclay, 91198, Gif sur Yvette, France
| | - Frédéric Sohm
- AMAGEN, CNRS, INRA, Université Paris-Saclay, 91198, Gif sur Yvette, France
| | - Sylvie Rétaux
- Paris-Saclay Institute of Neuroscience, CNRS, Université Paris-Saclay, 91198 Gif sur Yvette, France
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Tovar RU, Cantu V, Fremaux B, Gonzalez Jr P, Spikes A, García DM. Comparative development and ocular histology between epigean and subterranean salamanders ( Eurycea) from central Texas. PeerJ 2021; 9:e11840. [PMID: 34395082 PMCID: PMC8325428 DOI: 10.7717/peerj.11840] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2018] [Accepted: 07/01/2021] [Indexed: 11/24/2022] Open
Abstract
The salamander clade Eurycea from the karst regions of central Texas provides an ideal platform for comparing divergent nervous and sensory systems since some species exhibit extreme phenotypes thought to be associated with inhabiting a subterranean environment, including highly reduced eyes, while others retain an ancestral ocular phenotype appropriate for life above ground. We describe ocular morphology, comparing three salamander species representing two phenotypes-the surface-dwelling Barton Springs salamander (E. sosorum) and San Marcos salamander (E. nana) and the obligate subterranean Texas blind salamander (E. rathbuni) - in terms of structure and size of their eyes. Eyes were examined using confocal microscopy and measurements were made using ImageJ. Statistical analysis of data was carried out using R. We also provide a developmental series and track eye development and immunolocalization of Pax6 in E. sosorum and E. rathbuni. Adult histology of the surface-dwelling San Marcos salamander (E. nana) shows similarities to E. sosorum. The eyes of adults of the epigean species E. nana and E. sosorum appear fully developed with all the histological features of a fully functional eye. In contrast, the eyes of E. rathbuni adults have fewer layers, lack lenses and other features associated with vision as has been reported previously. However, in early developmental stages eye morphology did not differ significantly between E. rathbuni and E. sosorum. Parallel development is observed between the two phenotypes in terms of morphology; however, Pax6 labeling seems to decrease in the latter stages of development in E.rathbuni. We test for immunolabeling of the visual pigment proteins opsin and rhodopsin and observe immunolocalization around photoreceptor disks in E. nana and E. sosorum, but not in the subterranean E. rathbuni. Our results from examining developing salamanders suggest a combination of underdevelopment and degeneration contribute to the reduced eyes of adult E. rathbuni.
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Affiliation(s)
- Ruben U. Tovar
- Department of Biology, Texas State University, San Marcos, TX, United States of America
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, United States of America
| | - Valentin Cantu
- San Marcos Aquatic Resources Center, U.S. Fish and Wildlife Service, San Marcos, TX, United States of America
- Uvalde National Fish Hatchery, U.S. Fish and Wildlife Service, Uvalde, TX, United States of America
| | - Brian Fremaux
- Department of Biology, Texas State University, San Marcos, TX, United States of America
| | - Pedro Gonzalez Jr
- Department of Biology, Texas State University, San Marcos, TX, United States of America
| | - Amanda Spikes
- Department of Biology, Texas State University, San Marcos, TX, United States of America
| | - Dana M. García
- Department of Biology, Texas State University, San Marcos, TX, United States of America
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5
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Buchberger E, Bilen A, Ayaz S, Salamanca D, Matas de las Heras C, Niksic A, Almudi I, Torres-Oliva M, Casares F, Posnien N. Variation in Pleiotropic Hub Gene Expression Is Associated with Interspecific Differences in Head Shape and Eye Size in Drosophila. Mol Biol Evol 2021; 38:1924-1942. [PMID: 33386848 PMCID: PMC8097299 DOI: 10.1093/molbev/msaa335] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Revealing the mechanisms underlying the breathtaking morphological diversity observed in nature is a major challenge in Biology. It has been established that recurrent mutations in hotspot genes cause the repeated evolution of morphological traits, such as body pigmentation or the gain and loss of structures. To date, however, it remains elusive whether hotspot genes contribute to natural variation in the size and shape of organs. As natural variation in head morphology is pervasive in Drosophila, we studied the molecular and developmental basis of differences in compound eye size and head shape in two closely related Drosophila species. We show differences in the progression of retinal differentiation between species and we applied comparative transcriptomics and chromatin accessibility data to identify the GATA transcription factor Pannier (Pnr) as central factor associated with these differences. Although the genetic manipulation of Pnr affected multiple aspects of dorsal head development, the effect of natural variation is restricted to a subset of the phenotypic space. We present data suggesting that this developmental constraint is caused by the coevolution of expression of pnr and its cofactor u-shaped (ush). We propose that natural variation in expression or function of highly connected developmental regulators with pleiotropic functions is a major driver for morphological evolution and we discuss implications on gene regulatory network evolution. In comparison to previous findings, our data strongly suggest that evolutionary hotspots are not the only contributors to the repeated evolution of eye size and head shape in Drosophila.
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Affiliation(s)
- Elisa Buchberger
- Department of Developmental Biology, University of Göttingen, Göttingen, Germany
| | - Anıl Bilen
- Department of Developmental Biology, University of Göttingen, Göttingen, Germany
| | - Sanem Ayaz
- Department of Developmental Biology, University of Göttingen, Göttingen, Germany
| | - David Salamanca
- Department of Developmental Biology, University of Göttingen, Göttingen, Germany
- Present address: Department of Integrative Zoology, University of Vienna, Vienna, Austria
| | | | - Armin Niksic
- Department of Developmental Biology, University of Göttingen, Göttingen, Germany
| | - Isabel Almudi
- CABD (CSIC/UPO/JA), DMC2 Unit, Pablo de Olavide University Campus, Seville, Spain
| | - Montserrat Torres-Oliva
- Department of Developmental Biology, University of Göttingen, Göttingen, Germany
- Present address: Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Fernando Casares
- CABD (CSIC/UPO/JA), DMC2 Unit, Pablo de Olavide University Campus, Seville, Spain
| | - Nico Posnien
- Department of Developmental Biology, University of Göttingen, Göttingen, Germany
- Corresponding author: E-mail:
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6
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Regulation of ddb2 expression in blind cavefish and zebrafish reveals plasticity in the control of sunlight-induced DNA damage repair. PLoS Genet 2021; 17:e1009356. [PMID: 33544716 PMCID: PMC7891740 DOI: 10.1371/journal.pgen.1009356] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 02/18/2021] [Accepted: 01/12/2021] [Indexed: 11/19/2022] Open
Abstract
We have gained considerable insight into the mechanisms which recognize and repair DNA damage, but how they adapt to extreme environmental challenges remains poorly understood. Cavefish have proven to be fascinating models for exploring the evolution of DNA repair in the complete absence of UV-induced DNA damage and light. We have previously revealed that the Somalian cavefish Phreatichthys andruzzii, lacks photoreactivation repair via the loss of light, UV and ROS-induced photolyase gene transcription mediated by D-box enhancer elements. Here, we explore whether other systems repairing UV-induced DNA damage have been similarly affected in this cavefish model. By performing a comparative study using P. andruzzii and the surface-dwelling zebrafish, we provide evidence for a conservation of sunlight-regulated Nucleotide Excision Repair (NER). Specifically, the expression of the ddb2 gene which encodes a key NER recognition factor is robustly induced following exposure to light, UV and oxidative stress in both species. As in the case of the photolyase genes, D-boxes in the ddb2 promoter are sufficient to induce transcription in zebrafish. Interestingly, despite the loss of D-box-regulated photolyase gene expression in P. andruzzii, the D-box is required for ddb2 induction by visible light and oxidative stress in cavefish. However, in the cavefish ddb2 gene this D-box-mediated induction requires cooperation with an adjacent, highly conserved E2F element. Furthermore, while in zebrafish UV-induced ddb2 expression results from transcriptional activation accompanied by stabilization of the ddb2 mRNA, in P. andruzzii UV induces ddb2 expression exclusively via an increase in mRNA stability. Thus, we reveal plasticity in the transcriptional and post transcriptional mechanisms regulating the repair of sunlight-induced DNA damage under long-term environmental challenges.
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7
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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. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2020; 334:423-437. [PMID: 32614138 DOI: 10.1002/jez.b.22977] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2019] [Revised: 05/05/2020] [Accepted: 06/03/2020] [Indexed: 12/21/2022]
Abstract
Evolution in similar environments often leads to convergence of behavioral and anatomical traits. A classic example of convergent trait evolution is the reduced traits that characterize many cave animals: reduction or loss of pigmentation and eyes. While these traits have evolved many times, relatively little is known about whether these traits repeatedly evolve through the same or different molecular and developmental mechanisms. The small freshwater fish, Astyanax mexicanus, provides an opportunity to investigate the repeated evolution of cave traits. A. mexicanus exists as two forms, a sighted, surface-dwelling form and at least 29 populations of a blind, cave-dwelling form that initially develops eyes that subsequently degenerate. We compared eye morphology and the expression of eye regulatory genes in developing surface fish and two independently evolved cavefish populations, Pachón and Molino. We found that many of the previously described molecular and morphological alterations that occur during eye development in Pachón cavefish are also found in Molino cavefish. However, for many of these traits, the Molino cavefish have a less severe phenotype than Pachón cavefish. Further, cave-cave hybrid fish have larger eyes and lenses during early development compared with fish from either parental population, suggesting that some different changes underlie eye loss in these two populations. Together, these data support the hypothesis that these two cavefish populations evolved eye loss independently, yet through some of the same developmental and molecular mechanisms.
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Affiliation(s)
| | - Estephany Ferrufino
- Harriet L. Wilkes Honors College, Florida Atlantic University, Jupiter, Florida
| | - Sunishka Thakur
- Harriet L. Wilkes Honors College, Florida Atlantic University, Jupiter, Florida
| | | | - Michael Solomon
- Harriet L. Wilkes Honors College, Florida Atlantic University, Jupiter, Florida
| | - Courtney L Smith
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa
| | - Alex C Keene
- Department of Biological Sciences, Florida Atlantic University, Jupiter, Florida
| | - Jeffrey M Trimarchi
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa
| | - Johanna E Kowalko
- Harriet L. Wilkes Honors College, Florida Atlantic University, Jupiter, Florida
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8
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Development and regeneration dynamics of the Medaka notochord. Dev Biol 2020; 463:11-25. [PMID: 32173318 DOI: 10.1016/j.ydbio.2020.03.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 02/14/2020] [Accepted: 03/02/2020] [Indexed: 02/07/2023]
Abstract
The notochord is an embryonic tissue that acts as a hydrostatic skeleton until ossification begins in vertebrates. It is composed of outer sheath cells and inner vacuolated cells, which are generated from a common pool of disc-shaped precursors. Notochord extension during early embryogenesis is driven by the growth of vacuolated cells, reflecting in turn the expansion of their inner vacuole. Here we use desmogon, a novel desmosomal cadherin, to follow notochord development and regeneration in medaka (Oryzias latipes). We trace desmogon + disc-shaped precursors at the single cell level to demonstrate that they operate as unipotent progenitors, giving rise to either sheath or vacuolated cells. We reveal that once specified, vacuolated cells grow asynchronously and drive notochord expansion bi-directionally. Additionally, we uncover distinct regenerative responses in the notochord, which depend on the nature of the injury sustained. By generating a desmogon CRISPR mutant we demonstrate that this cadherin is essential for proper vacuolated cell shape and therefore correct notochord and spine morphology. Our work expands the repertoire of model systems to study dynamic aspects of the notochord in vivo, and provides new insights in its development and regeneration properties.
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9
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Huang Z, Titus T, Postlethwait JH, Meng F. Eye Degeneration and Loss of otx5b Expression in the Cavefish Sinocyclocheilus tileihornes. J Mol Evol 2019; 87:199-208. [PMID: 31332479 PMCID: PMC6711879 DOI: 10.1007/s00239-019-09901-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 07/13/2019] [Indexed: 12/17/2022]
Abstract
Cave animals possess remarkable phenotypes associated with existence in their dark environments. The Chinese cavefish Sinocyclocheilus tileihornes shows substantial eye degeneration, a trait shared by most cave species. The extent to which independent evolution of troglomorphic traits uses convergent molecular genetic mechanisms is as yet unknown. We performed transcriptome-wide gene expression profiling in S. tileihornes eyes and compared results with those from the closely related surface species S. angustiporus and an independently derived congeneric cavefish, S. anophthalmus. In total, 52.85 million 100 bp long paired-end clean reads were generated for S. tileihornes, and we identified differentially expressed genes between the three possible pairs of species. Functional analysis of genes differentially expressed between S. tileihornes and S. angustiporus revealed that phototransduction (KEGG id: dre04744) was the most significantly enriched pathway, indicating the obvious differences in response to captured photons between the cavefish S. tileihornes and the surface species S. angustiporus. Analysis of key genes regulating eye development showed complete absence of otx5b (orthodenticle homolog 5) expression in S. tileihornes eyes, probably related to degradation of rods, but normal expression of crx (cone-rod homeobox). The enriched pathways and Otx5 are involved in phototransduction, photoreceptor formation, and regulation of photoreceptor-related gene expression. Unlike the S. tileihornes reported here, S. anophthalmus has reduced crx and otx5 expression. These results show that different species of cavefish within the same genus that independently evolved troglodyte characteristics can have different genetic mechanisms of eye degeneration.
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Affiliation(s)
- Zushi Huang
- Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Tom Titus
- Institute of Neuroscience, University of Oregon, Eugene, OR, 97403, USA
| | | | - Fanwei Meng
- Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
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10
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Soares D, Niemiller ML. Extreme Adaptation in Caves. Anat Rec (Hoboken) 2018; 303:15-23. [PMID: 30537183 DOI: 10.1002/ar.24044] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2017] [Revised: 04/17/2018] [Accepted: 05/03/2018] [Indexed: 12/31/2022]
Abstract
Cave adaptation leads to unique anatomical specializations in many taxonomic groups. As the role of vision is reduced or disappears in a subterranean environment, other specializations arise to allow the organism to successfully detect and interact with their environment. A suite of unique, convergent phenotypes associated with subterranean adaptation has emerged (termed troglomorphy), with reduction or loss of pigmentation and eyes being the most conspicuous. Two vertebrate groups that have successfully colonized and adapted to subterranean environments are cavefishes and cave salamanders. There are many shared troglomorphic anatomical characters shared between these two groups, and we describe herein the morphological traits that are unique to fishes and salamanders that are adapted to caves and other subterranean habitats. Troglobionts, animals strictly bound and adapted to underground habitats, are outcomes of not just regressive evolution, but also constructive adaptation. There are skeletal changes, such as broadening and flattening of the head, as well as hypertrophy of non-visual modalities. Cavefishes and salamanders have lost eyes and pigmentation, but also enhanced mechanosenzation, chemosenzation and, in some cases, electroreception. Both cavefishes and cave salamanders have become important models in the study of the ecology, behavior, and evolution of subterranean colonization and adaptation. However, our knowledge is primarily limited to a few taxa and many questions remain to be studied. Anat Rec, 2018. © 2018 American Association for Anatomy.
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Affiliation(s)
- Daphne Soares
- Department of Biological Sciences, New Jersey Institute of Technology, Newark, New Jersey
| | - Matthew L Niemiller
- Department of Biological Sciences, The University of Alabama in Huntsville, Huntsville, Alabama
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11
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Sovrano VA, Potrich D, Foà A, Bertolucci C. Extra-Visual Systems in the Spatial Reorientation of Cavefish. Sci Rep 2018; 8:17698. [PMID: 30523284 PMCID: PMC6283829 DOI: 10.1038/s41598-018-36167-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2018] [Accepted: 11/11/2018] [Indexed: 01/23/2023] Open
Abstract
Disoriented humans and animals are able to reorient themselves using environmental geometry ("metric properties" and "sense") and local features, also relating geometric to non-geometric information. Here we investigated the presence of these reorientation spatial skills in two species of blind cavefish (Astyanax mexicanus and Phreatichthys andruzzii), in order to understand the possible role of extra-visual senses in similar spatial tasks. In a rectangular apparatus, with all homogeneous walls (geometric condition) or in presence of a tactilely different wall (feature condition), cavefish were required to reorient themselves after passive disorientation. We provided the first evidence that blind cavefish, using extra-visual systems, were able i) to use geometric cues, provided by the shape of the tank, in order to recognize two geometric equivalent corners on the diagonal, and ii) to integrate the geometric information with the salient cue (wall with a different surface structure), in order to recover a specific corner. These findings suggest the ecological salience of the environmental geometry for spatial orientation in animals and, despite the different niches of adaptation, a potential shared background for spatial navigation. The geometric spatial encoding seems to constitute a common cognitive tool needed when the environment poses similar requirements to living organisms.
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Affiliation(s)
- Valeria Anna Sovrano
- Center for Mind/Brain Sciences, University of Trento, Rovereto, Italy.
- Department of Psychology and Cognitive Science, University of Trento, Rovereto, Italy.
| | - Davide Potrich
- Center for Mind/Brain Sciences, University of Trento, Rovereto, Italy
| | - Augusto Foà
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Cristiano Bertolucci
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
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12
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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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13
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Zhao H, Di Mauro G, Lungu-Mitea S, Negrini P, Guarino AM, Frigato E, Braunbeck T, Ma H, Lamparter T, Vallone D, Bertolucci C, Foulkes NS. Modulation of DNA Repair Systems in Blind Cavefish during Evolution in Constant Darkness. Curr Biol 2018; 28:3229-3243.e4. [PMID: 30318355 DOI: 10.1016/j.cub.2018.08.039] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2018] [Revised: 07/19/2018] [Accepted: 08/16/2018] [Indexed: 11/18/2022]
Abstract
How the environment shapes the function and evolution of DNA repair systems is poorly understood. In a comparative study using zebrafish and the Somalian blind cavefish, Phreatichthys andruzzii, we reveal that during evolution for millions of years in continuous darkness, photoreactivation DNA repair function has been lost in P. andruzzii. We demonstrate that this loss results in part from loss-of-function mutations in pivotal DNA-repair genes. Specifically, C-terminal truncations in P. andruzzii DASH and 6-4 photolyase render these proteins predominantly cytoplasmic, with consequent loss in their functionality. In addition, we reveal a general absence of light-, UV-, and ROS-induced expression of P. andruzzii DNA-repair genes. This results from a loss of function of the D-box enhancer element, which coordinates and enhances DNA repair in response to sunlight. Our results point to P. andruzzii being the only species described, apart from placental mammals, that lacks the highly evolutionary conserved photoreactivation function. We predict that in the DNA repair systems of P. andruzzii, we may be witnessing the first stages in a process that previously occurred in the ancestors of placental mammals during the Mesozoic era.
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Affiliation(s)
- Haiyu Zhao
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, Hermann-von-Helmholtz Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Giuseppe Di Mauro
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, Hermann-von-Helmholtz Platz 1, 76344 Eggenstein-Leopoldshafen, Germany; Department of Life Science and Biotechnology, University of Ferrara, Via Luigi Borsari 46, 44121 Ferrara, Italy
| | - Sebastian Lungu-Mitea
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, Hermann-von-Helmholtz Platz 1, 76344 Eggenstein-Leopoldshafen, Germany; Aquatic Ecology and Toxicology, Centre for Organismal Studies, University of Heidelberg, Im Neuenheimer Feld, 69120 Heidelberg, Germany; Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences, 75007 Uppsala, Sweden
| | - Pietro Negrini
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, Hermann-von-Helmholtz Platz 1, 76344 Eggenstein-Leopoldshafen, Germany; Department of Life Science and Biotechnology, University of Ferrara, Via Luigi Borsari 46, 44121 Ferrara, Italy
| | - Andrea Maria Guarino
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, Hermann-von-Helmholtz Platz 1, 76344 Eggenstein-Leopoldshafen, Germany; Department of Biology, University of Naples "Federico II," 80126 Naples, Italy
| | - Elena Frigato
- Department of Life Science and Biotechnology, University of Ferrara, Via Luigi Borsari 46, 44121 Ferrara, Italy
| | - Thomas Braunbeck
- Aquatic Ecology and Toxicology, Centre for Organismal Studies, University of Heidelberg, Im Neuenheimer Feld, 69120 Heidelberg, Germany
| | - Hongju Ma
- Botanical Institute, Karlsruhe Institute of Technology, 76128 Karlsruhe, Germany
| | - Tilman Lamparter
- Botanical Institute, Karlsruhe Institute of Technology, 76128 Karlsruhe, Germany
| | - Daniela Vallone
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, Hermann-von-Helmholtz Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Cristiano Bertolucci
- Department of Life Science and Biotechnology, University of Ferrara, Via Luigi Borsari 46, 44121 Ferrara, Italy
| | - Nicholas S Foulkes
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, Hermann-von-Helmholtz Platz 1, 76344 Eggenstein-Leopoldshafen, Germany.
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14
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Evolution shapes the responsiveness of the D-box enhancer element to light and reactive oxygen species in vertebrates. Sci Rep 2018; 8:13180. [PMID: 30181539 PMCID: PMC6123470 DOI: 10.1038/s41598-018-31570-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Accepted: 06/26/2018] [Indexed: 12/27/2022] Open
Abstract
The circadian clock is a highly conserved cell-autonomous mechanism that directs daily rhythms in most aspects of biology. Daily entrainment by environmental signals, notably light, is essential for its function. However, our understanding of the mechanisms and the evolution of photic entrainment remains incomplete. Fish represent attractive models for exploring how light regulates the circadian clock due to the direct light sensitivity of their peripheral clocks. Central to this property is the light induced expression of clock genes that is mediated by D-box enhancer elements. Here, using zebrafish cells, we reveal that the light responsive D-box enhancer serves as a nuclear target for reactive oxygen species (ROS). We demonstrate that exposure to short wavelengths of visible light triggers increases in ROS levels via NADPH oxidase activity. Elevated ROS activates the JNK and p38 MAP kinases and in turn, induces clock gene expression via the D-box. In blind cavefish and mammals, where peripheral clocks are no longer entrained by direct illumination, ROS levels are still increased upon light exposure. However, in these species ROS no longer induces D-box driven clock gene transcription. Thus, during evolution, alterations in ROS-responsive signal transduction pathways underlie fundamental changes in peripheral clock photoentrainment.
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15
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Mutations in blind cavefish target the light-regulated circadian clock gene, period 2. Sci Rep 2018; 8:8754. [PMID: 29884790 PMCID: PMC5993827 DOI: 10.1038/s41598-018-27080-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 05/21/2018] [Indexed: 01/09/2023] Open
Abstract
Light represents the principal signal driving circadian clock entrainment. However, how light influences the evolution of the clock remains poorly understood. The cavefish Phreatichthys andruzzii represents a fascinating model to explore how evolution under extreme aphotic conditions shapes the circadian clock, since in this species the clock is unresponsive to light. We have previously demonstrated that loss-of-function mutations targeting non-visual opsins contribute in part to this blind clock phenotype. Here, we have compared orthologs of two core clock genes that play a key role in photic entrainment, cry1a and per2, in both zebrafish and P. andruzzii. We encountered aberrantly spliced variants for the P. andruzzii per2 transcript. The most abundant transcript encodes a truncated protein lacking the C-terminal Cry binding domain and incorporating an intronic, transposon-derived coding sequence. We demonstrate that the transposon insertion leads to a predominantly cytoplasmic localization of the cavefish Per2 protein in contrast to the zebrafish ortholog which is distributed in both the nucleus and cytoplasm. Thus, it seems that during evolution in complete darkness, the photic entrainment pathway of the circadian clock has been subject to mutation at multiple levels, extending from opsin photoreceptors to nuclear effectors.
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16
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Seleit A, Krämer I, Riebesehl BF, Ambrosio EM, Stolper JS, Lischik CQ, Dross N, Centanin L. Neural stem cells induce the formation of their physical niche during organogenesis. eLife 2017; 6. [PMID: 28950935 PMCID: PMC5617629 DOI: 10.7554/elife.29173] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Accepted: 09/05/2017] [Indexed: 12/18/2022] Open
Abstract
Most organs rely on stem cells to maintain homeostasis during post-embryonic life. Typically, stem cells of independent lineages work coordinately within mature organs to ensure proper ratios of cell types. Little is known, however, on how these different stem cells locate to forming organs during development. Here we show that neuromasts of the posterior lateral line in medaka are composed of two independent life-long lineages with different embryonic origins. Clonal analysis and 4D imaging revealed a hierarchical organisation with instructing and responding roles: an inner, neural lineage induces the formation of an outer, border cell lineage (nBC) from the skin epithelium. Our results demonstrate that the neural lineage is necessary and sufficient to generate nBCs highlighting self-organisation principles at the level of the entire embryo. We hypothesise that induction of surrounding tissues plays a major role during the establishment of vertebrate stem cell niches.
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Affiliation(s)
- Ali Seleit
- Animal Physiology and Development, Centre for Organismal Studies Heidelberg, Heidelberg, Germany.,The Hartmut Hoffmann-Berling International Graduate School of Molecular and Cellular Biology, University of Heidelberg, Heidelberg, Germany
| | - Isabel Krämer
- Animal Physiology and Development, Centre for Organismal Studies Heidelberg, Heidelberg, Germany.,The Hartmut Hoffmann-Berling International Graduate School of Molecular and Cellular Biology, University of Heidelberg, Heidelberg, Germany
| | - Bea F Riebesehl
- Animal Physiology and Development, Centre for Organismal Studies Heidelberg, Heidelberg, Germany
| | - Elizabeth M Ambrosio
- Animal Physiology and Development, Centre for Organismal Studies Heidelberg, Heidelberg, Germany
| | - Julian S Stolper
- Animal Physiology and Development, Centre for Organismal Studies Heidelberg, Heidelberg, Germany.,Murdoch Childrens Research Institute, University of Melbourne, Melbourne, Australia
| | - Colin Q Lischik
- Animal Physiology and Development, Centre for Organismal Studies Heidelberg, Heidelberg, Germany.,The Hartmut Hoffmann-Berling International Graduate School of Molecular and Cellular Biology, University of Heidelberg, Heidelberg, Germany
| | - Nicolas Dross
- Nikon Imaging Center at the University of Heidelberg, Heidelberg, Germany
| | - Lazaro Centanin
- Animal Physiology and Development, Centre for Organismal Studies Heidelberg, Heidelberg, Germany
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17
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Raible F, Takekata H, Tessmar-Raible K. An Overview of Monthly Rhythms and Clocks. Front Neurol 2017; 8:189. [PMID: 28553258 PMCID: PMC5428424 DOI: 10.3389/fneur.2017.00189] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Accepted: 04/20/2017] [Indexed: 12/18/2022] Open
Abstract
Organisms have evolved to cope with geophysical cycles of different period lengths. In this review, we focus on the adaptations of animals to the lunar cycle, specifically, on the occurrence of biological rhythms with monthly (circalunar) or semi-monthly (circasemilunar) period lengths. Systematic experimental investigation, starting in the early twentieth century, has allowed scientists to distinguish between mythological belief and scientific facts concerning the influence of the lunar cycle on animals. These studies revealed that marine animals of various taxa exhibit circalunar or circasemilunar reproductive rhythms. Some of these rely on endogenous oscillators (circalunar or circasemilunar clocks), whereas others are directly driven by external cues, such as the changes in nocturnal illuminance. We review current insight in the molecular and cellular mechanisms involved in circalunar rhythms, focusing on recent work in corals, annelid worms, midges, and fishes. In several of these model systems, the transcript levels of some core circadian clock genes are affected by both light and endogenous circalunar oscillations. How these and other molecular changes relate to the changes in physiology or behavior over the lunar cycle remains to be determined. We further review the possible relevance of circalunar rhythms for terrestrial species, with a particular focus on mammalian reproduction. Studies on circalunar rhythms of conception or birth rates extend to humans, where the lunar cycle was suggested to also affect sleep and mental health. While these reports remain controversial, factors like the increase in "light pollution" by artificial light might contribute to discrepancies between studies. We finally discuss the existence of circalunar oscillations in mammalian physiology. We speculate that these oscillations could be the remnant of ancient circalunar oscillators that were secondarily uncoupled from a natural entrainment mechanism, but still maintained relevance for structuring the timing of reproduction or physiology. The analysis and comparison of circalunar rhythms and clocks are currently challenging due to the heterogeneity of samples concerning species diversity, environmental conditions, and chronobiological conditions. We suggest that future research will benefit from the development of standardized experimental paradigms, and common principles for recording and reporting environmental conditions, especially light spectra and intensities.
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Affiliation(s)
- Florian Raible
- Max Perutz Laboratories, University of Vienna, Vienna Biocenter, Vienna, Austria
- Research Platform “Rhythms of Life”, University of Vienna, Vienna Biocenter, Vienna, Austria
| | - Hiroki Takekata
- Max Perutz Laboratories, University of Vienna, Vienna Biocenter, Vienna, Austria
- Research Platform “Rhythms of Life”, University of Vienna, Vienna Biocenter, Vienna, Austria
| | - Kristin Tessmar-Raible
- Max Perutz Laboratories, University of Vienna, Vienna Biocenter, Vienna, Austria
- Research Platform “Rhythms of Life”, University of Vienna, Vienna Biocenter, Vienna, Austria
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18
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Grandi G, Pezzi M, Marchetti MG, Chicca M. Immunocytochemical identification and ontogeny of adenohypophyseal cells in a cave fish, Phreatichthys andruzzii (Cypriniformes: Cyprinidae). JOURNAL OF FISH BIOLOGY 2017; 90:1797-1822. [PMID: 28144938 DOI: 10.1111/jfb.13267] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Accepted: 12/21/2016] [Indexed: 06/06/2023]
Abstract
The morphogenesis of the pituitary gland and the chronological appearance of adenohypophyseal cells were investigated for the first time in the Somalian cave fish Phreatichthys andruzzii by immunocytochemistry. The adult adenohypophysis contained: a rostral pars distalis, with prolactin (PRL) cells arranged in follicles and adrenocorticotropic (ACTH) cells, a proximal pars distalis with somatotropic (GH), β-thyrotropic (TSH), β-gonadotropic type I (FSH) and type II (LH) cells and a pars intermedia with α-somatolactin (SL), α-melanotropic (MSH) and β-endorphin (END) cells. All regions were deeply penetrated by neurohypophyseal branches. At hatching (24 h post-fertilization) the pituitary was an oval cell mass, close to the ventral margin of diencephalon. The first immunoreactive cells appeared as follows: PRL at 0·5 days after hatching (dah), GH and SL at 1·5 dah, END at 2 dah, TSH, ACTH and MSH at 2·5 dah, FSH at 28 dah and LH at 90 dah. The neurohypophysis appeared at 5 dah and branched extensively inside the adenohypophysis at 130 dah, but there was no boundary between rostral pars distalis and proximal pars distalis at this stage. The potential indices of prolactin and growth hormone production increased until 28 and 60 dah, respectively. The potential index of growth hormone production correlated positively with total length. Activity of PRL and GH cells, measured as ratio of cell area to nucleus area, was significantly higher in juveniles than in larvae.
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Affiliation(s)
- G Grandi
- Department of Life Sciences and Biotechnology, University of Ferrara, via L. Borsari 46, 44100, Ferrara, Italy
| | - M Pezzi
- Department of Life Sciences and Biotechnology, University of Ferrara, via L. Borsari 46, 44100, Ferrara, Italy
| | - M G Marchetti
- Department of Life Sciences and Biotechnology, University of Ferrara, via L. Borsari 46, 44100, Ferrara, Italy
| | - M Chicca
- Department of Life Sciences and Biotechnology, University of Ferrara, via L. Borsari 46, 44100, Ferrara, Italy
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19
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Krishnan J, Rohner N. Cavefish and the basis for eye loss. Philos Trans R Soc Lond B Biol Sci 2017; 372:20150487. [PMID: 27994128 PMCID: PMC5182419 DOI: 10.1098/rstb.2015.0487] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/08/2016] [Indexed: 11/12/2022] Open
Abstract
Animals have colonized the entire world from rather moderate to the harshest environments, some of these so extreme that only few animals are able to survive. Cave environments present such a challenge and obligate cave animals have adapted to perpetual darkness by evolving a multitude of traits. The most common and most studied cave characteristics are the regression of eyes and the overall reduction in pigmentation. Studying these traits can provide important insights into how evolutionary forces drive convergent and regressive adaptation. The blind Mexican cavefish (Astyanax mexicanus) has emerged as a useful model to study cave evolution owing to the availability of genetic and genomic resources, and the amenability of embryonic development as the different populations remain fertile with each other. In this review, we give an overview of our current knowledge underlying the process of regressive and convergent evolution using eye degeneration in cavefish as an example.This article is part of the themed issue 'Evo-devo in the genomics era, and the origins of morphological diversity'.
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Affiliation(s)
- Jaya Krishnan
- Stowers Institute for Medical Research, 1000 East 50th Street, Kansas City, MO 64110, USA
| | - Nicolas Rohner
- Stowers Institute for Medical Research, 1000 East 50th Street, Kansas City, MO 64110, USA
- Department of Molecular and Integrative Physiology, The University of Kansas Medical Center, Kansas City, KS 66160, USA
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20
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Seleit A, Krämer I, Ambrosio E, Dross N, Engel U, Centanin L. Sequential organogenesis sets two parallel sensory lines in medaka. Development 2017; 144:687-697. [PMID: 28087632 PMCID: PMC5312036 DOI: 10.1242/dev.142752] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Accepted: 12/29/2016] [Indexed: 01/10/2023]
Abstract
Animal organs are typically formed during embryogenesis by following one specific developmental programme. Here, we report that neuromast organs are generated by two distinct and sequential programmes that result in parallel sensory lines in medaka embryos. A ventral posterior lateral line (pLL) is composed of neuromasts deposited by collectively migrating cells whereas a midline pLL is formed by individually migrating cells. Despite the variable number of neuromasts among embryos, the sequential programmes that we describe here fix an invariable ratio between ventral and midline neuromasts. Mechanistically, we show that the formation of both types of neuromasts depends on the chemokine receptor genes cxcr4b and cxcr7b, illustrating how common molecules can mediate different morphogenetic processes. Altogether, we reveal a self-organising feature of the lateral line system that ensures a proper distribution of sensory organs along the body axis. Summary: Two parallel sensory lines in medaka share a common origin and are composed of identical organs that are, nevertheless, generated through different morphogenetic programmes.
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Affiliation(s)
- Ali Seleit
- Animal Physiology and Development, Centre for Organismal Studies (COS) Heidelberg, Im Neuenheimer Feld 230, Heidelberg 69120, Germany.,The Hartmut Hoffmann-Berling International Graduate School of Molecular and Cellular Biology (HBIGS), University of Heidelberg, Heidelberg, Germany
| | - Isabel Krämer
- Animal Physiology and Development, Centre for Organismal Studies (COS) Heidelberg, Im Neuenheimer Feld 230, Heidelberg 69120, Germany.,The Hartmut Hoffmann-Berling International Graduate School of Molecular and Cellular Biology (HBIGS), University of Heidelberg, Heidelberg, Germany
| | - Elizabeth Ambrosio
- Animal Physiology and Development, Centre for Organismal Studies (COS) Heidelberg, Im Neuenheimer Feld 230, Heidelberg 69120, Germany
| | - Nicolas Dross
- Animal Physiology and Development, Centre for Organismal Studies (COS) Heidelberg, Im Neuenheimer Feld 230, Heidelberg 69120, Germany.,Nikon Imaging Center at the University of Heidelberg, Heidelberg, Germany
| | - Ulrike Engel
- Animal Physiology and Development, Centre for Organismal Studies (COS) Heidelberg, Im Neuenheimer Feld 230, Heidelberg 69120, Germany.,Nikon Imaging Center at the University of Heidelberg, Heidelberg, Germany
| | - Lázaro Centanin
- Animal Physiology and Development, Centre for Organismal Studies (COS) Heidelberg, Im Neuenheimer Feld 230, Heidelberg 69120, Germany
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21
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López-Olmeda JF. Nonphotic entrainment in fish. Comp Biochem Physiol A Mol Integr Physiol 2016; 203:133-143. [PMID: 27642096 DOI: 10.1016/j.cbpa.2016.09.006] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Revised: 09/09/2016] [Accepted: 09/13/2016] [Indexed: 12/27/2022]
Abstract
Organisms that live on the Earth are subjected to environmental variables that display cyclic variations, such as light, temperature and tides. Since these cyclic changes in the environment are constant and predictable, they have affected biological evolution through selecting the occurrence of biological rhythms in the physiology of all living organisms, from prokaryotes to mammals. Biological clocks confer organisms an adaptive advantage as they can synchronize their behavioral and physiological processes to occur at a given moment of time when effectiveness and success would be greater and/or the cost and risk for organisms would be lower. Among environmental synchronizers, light has been mostly widely studied to date. However, other environmental signals play an important role in biological rhythms, especially in aquatic animals like fish. This review focuses on current knowledge about the role of nonphotic synchronizers (temperature, food and tidal cycles) on biological rhythms in fish, and on the entrainment of the fish circadian system to these synchronizers.
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Affiliation(s)
- Jose F López-Olmeda
- Department of Animal Physiology, Faculty of Biology, Regional Campus of International Excellence "Campus Mare Nostrum", University of Murcia, 30100 Murcia, Spain.
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22
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Relaxed selective constraints drove functional modifications in peripheral photoreception of the cavefish P. andruzzii and provide insight into the time of cave colonization. Heredity (Edinb) 2016; 117:383-392. [PMID: 27485669 DOI: 10.1038/hdy.2016.59] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Revised: 04/18/2016] [Accepted: 04/25/2016] [Indexed: 01/10/2023] Open
Abstract
The genetic basis of phenotypic changes in extreme environments is a key but rather unexplored topic in animal evolution. Here we provide an exemplar case of evolution by relaxed selection in the Somalian cavefish Phreatichthys andruzzii that has evolved in the complete absence of light for at least 2.8 million years. This has resulted in extreme degenerative phenotypes, including complete eye loss and partial degeneration of the circadian clock. We have investigated the molecular evolution of the nonvisual photoreceptor melanopsin opn4m2, whose mutation contributes to the inability of peripheral clocks to respond to light. Our intra- and inter-species analyses suggest that the 'blind' clock in P. andruzzii evolved because of the loss of selective constraints on a trait that was no longer adaptive. Based on this change in selective regime, we estimate that the functional constraint on cavefish opn4m2 was relaxed at ∼5.3 Myr. This implies a long subterranean history, about half in complete isolation from the surface. The visual photoreceptor rhodopsin, expressed in the brain and implicated in photophobic behavior, shows similar evolutionary patterns, suggesting that extreme isolation in darkness led to a general weakening of evolutionary constraints on light-responsive mechanisms. Conversely, the same genes are still conserved in Garra barreimiae, a cavefish from Oman, that independently and more recently colonized subterranean waters and evolved troglomorphic traits. Our results contribute substantially to the open debate on the genetic bases of regressive evolution.
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23
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Casane D, Rétaux S. Evolutionary Genetics of the Cavefish Astyanax mexicanus. ADVANCES IN GENETICS 2016; 95:117-59. [PMID: 27503356 DOI: 10.1016/bs.adgen.2016.03.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Blind and depigmented fish belonging to the species Astyanax mexicanus are outstanding models for evolutionary genetics. During their evolution in the darkness of caves, they have undergone a number of changes at the morphological, physiological, and behavioral levels, but they can still breed with their river-dwelling conspecifics. The fertile hybrids between these two morphotypes allow forward genetic approaches, from the search of quantitative trait loci to the identification of the mutations underlying the evolution of troglomorphism. We review here the past 30years of evolutionary genetics on Astyanax: from the first crosses and the discovery of convergent evolution of different Astyanax cavefish populations to the most recent evolutionary transcriptomics and genomics studies that have provided researchers with potential candidate genes to be tested using functional genetic approaches. Although significant progress has been made and some genes have been identified, cavefish have not yet fully revealed the secret of their adaptation to the absence of light. In particular, the genetic determinism of their loss of eyes seems complex and still puzzles researchers. We also discuss future research directions, including searches for the origin of cave alleles and searches for selection genome-wide, as well as the necessary but missing information on the timing of cave colonization by surface fish.
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Affiliation(s)
- D Casane
- Laboratory EGCE, CNRS and University of Paris-Sud, Gif-sur-Yvette, France; Paris Diderot University, Sorbonne Paris Cité, France
| | - S Rétaux
- Paris-Saclay Institute of Neuroscience, CNRS and University Paris-Sud, Gif-sur-Yvette, France
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24
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Abstract
The Genetics Society of America’s George W. Beadle Award honors individuals who have made outstanding contributions to the community of genetics researchers and who exemplify the qualities of its namesake as a respected academic, administrator, and public servant. The 2015 recipient is John Postlethwait. He has made groundbreaking contributions in developing the zebrafish as a molecular genetic model and in understanding the evolution of new gene functions in vertebrates. He built the first zebrafish genetic map and showed that its genome, along with that of distantly related teleost fish, had been duplicated. Postlethwait played an integral role in the zebrafish genome-sequencing project and elucidated the genomic organization of several fish species. Postlethwait is also honored for his active involvement with the zebrafish community, advocacy for zebrafish as a model system, and commitment to driving the field forward.
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25
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Wilkens H. Genetics and hybridization in surface and caveAstyanax(Teleostei): a comparison of regressive and constructive traits. Biol J Linn Soc Lond 2016. [DOI: 10.1111/bij.12773] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Horst Wilkens
- University of Hamburg; Centrum für Naturkunde - CeNak; Zoological Museum; Martin-Luther-King-Platz 3 20146 Hamburg Germany
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26
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Ellis NA, Glazer AM, Donde NN, Cleves PA, Agoglia RM, Miller CT. Distinct developmental genetic mechanisms underlie convergently evolved tooth gain in sticklebacks. Development 2015; 142:2442-51. [PMID: 26062935 DOI: 10.1242/dev.124248] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Accepted: 06/02/2015] [Indexed: 12/14/2022]
Abstract
Teeth are a classic model system of organogenesis, as repeated and reciprocal epithelial and mesenchymal interactions pattern placode formation and outgrowth. Less is known about the developmental and genetic bases of tooth formation and replacement in polyphyodonts, which are vertebrates with continual tooth replacement. Here, we leverage natural variation in the threespine stickleback fish Gasterosteus aculeatus to investigate the genetic basis of tooth development and replacement. We find that two derived freshwater stickleback populations have both convergently evolved more ventral pharyngeal teeth through heritable genetic changes. In both populations, evolved tooth gain manifests late in development. Using pulse-chase vital dye labeling to mark newly forming teeth in adult fish, we find that both high-toothed freshwater populations have accelerated tooth replacement rates relative to low-toothed ancestral marine fish. Despite the similar evolved phenotype of more teeth and an accelerated adult replacement rate, the timing of tooth number divergence and the spatial patterns of newly formed adult teeth are different in the two populations, suggesting distinct developmental mechanisms. Using genome-wide linkage mapping in marine-freshwater F2 genetic crosses, we find that the genetic basis of evolved tooth gain in the two freshwater populations is largely distinct. Together, our results support a model whereby increased tooth number and an accelerated tooth replacement rate have evolved convergently in two independently derived freshwater stickleback populations using largely distinct developmental and genetic mechanisms.
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Affiliation(s)
- Nicholas A Ellis
- Department of Molecular and Cell Biology, University of California-Berkeley, Berkeley, CA 94720, USA
| | - Andrew M Glazer
- Department of Molecular and Cell Biology, University of California-Berkeley, Berkeley, CA 94720, USA
| | - Nikunj N Donde
- Department of Molecular and Cell Biology, University of California-Berkeley, Berkeley, CA 94720, USA
| | - Phillip A Cleves
- Department of Molecular and Cell Biology, University of California-Berkeley, Berkeley, CA 94720, USA
| | - Rachel M Agoglia
- Department of Molecular and Cell Biology, University of California-Berkeley, Berkeley, CA 94720, USA
| | - Craig T Miller
- Department of Molecular and Cell Biology, University of California-Berkeley, Berkeley, CA 94720, USA
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