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Mayeur H, Leyhr J, Mulley J, Leurs N, Michel L, Sharma K, Lagadec R, Aury JM, Osborne OG, Mulhair P, Poulain J, Mangenot S, Mead D, Smith M, Corton C, Oliver K, Skelton J, Betteridge E, Dolucan J, Dudchenko O, Omer AD, Weisz D, Aiden EL, McCarthy S, Sims Y, Torrance J, Tracey A, Howe K, Baril T, Hayward A, Martinand-Mari C, Sanchez S, Haitina T, Martin K, Korsching SI, Mazan S, Debiais-Thibaud M. The sensory shark: high-quality morphological, genomic and transcriptomic data for the small-spotted catshark Scyliorhinus canicula reveal the molecular bases of sensory organ evolution in jawed vertebrates. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.23.595469. [PMID: 39005470 PMCID: PMC11244906 DOI: 10.1101/2024.05.23.595469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
Cartilaginous fishes (chimaeras and elasmobranchs -sharks, skates and rays) hold a key phylogenetic position to explore the origin and diversifications of jawed vertebrates. Here, we report and integrate reference genomic, transcriptomic and morphological data in the small-spotted catshark Scyliorhinus canicula to shed light on the evolution of sensory organs. We first characterise general aspects of the catshark genome, confirming the high conservation of genome organisation across cartilaginous fishes, and investigate population genomic signatures. Taking advantage of a dense sampling of transcriptomic data, we also identify gene signatures for all major organs, including chondrichthyan specializations, and evaluate expression diversifications between paralogs within major gene families involved in sensory functions. Finally, we combine these data with 3D synchrotron imaging and in situ gene expression analyses to explore chondrichthyan-specific traits and more general evolutionary trends of sensory systems. This approach brings to light, among others, novel markers of the ampullae of Lorenzini electro-sensory cells, a duplication hotspot for crystallin genes conserved in jawed vertebrates, and a new metazoan clade of the Transient-receptor potential (TRP) family. These resources and results, obtained in an experimentally tractable chondrichthyan model, open new avenues to integrate multiomics analyses for the study of elasmobranchs and jawed vertebrates.
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Yuan Z, Song Y, Zhang S, Chen Y, Xu M, Fan G, Liu X. The Chromosome-Scale Genome of Chitala ornata Illuminates the Evolution of Early Teleosts. BIOLOGY 2024; 13:478. [PMID: 39056673 PMCID: PMC11274187 DOI: 10.3390/biology13070478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2024] [Revised: 06/20/2024] [Accepted: 06/25/2024] [Indexed: 07/28/2024]
Abstract
Teleosts are the most prolific vertebrates, occupying the vast majority of aquatic environments, and their pectoral fins have undergone remarkable physiological transformations throughout their evolution. Studying early teleost fishes, such as those belonging to the Osteoglossiformes order, could offer crucial insights into the adaptive evolution of pectoral fins within this group. In this study, we have assembled a chromosomal-level genome for the Clown featherback (Chitala ornata), achieving the highest quality genome assembly for Osteoglossiformes to date, with a contig N50 of 32.78 Mb and a scaffold N50 of 40.73 Mb. By combining phylogenetic analysis, we determined that the Clown featherback diverged approximately 202 to 203 million years ago (Ma), aligning with continental separation events. Our analysis revealed the intriguing discovery that a unique deletion of regulatory elements is adjacent to the Gli3 gene, specifically in teleosts. This deletion might be tied to the specialized adaptation of their pectoral fins. Furthermore, our findings indicate that specific contractions and expansions of transposable elements (TEs) in teleosts, including the Clown featherback, could be connected to their adaptive evolution. In essence, this study not only provides a high-quality genomic resource for Osteoglossiformes but also sheds light on the evolutionary trajectory of early teleosts.
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Affiliation(s)
- Zengbao Yuan
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; (Z.Y.)
- BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China; (Y.S.); (Y.C.)
- BGI-Shenzhen, Shenzhen 518083, China
| | - Yue Song
- BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China; (Y.S.); (Y.C.)
- BGI-Shenzhen, Shenzhen 518083, China
| | - Suyu Zhang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; (Z.Y.)
- BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China; (Y.S.); (Y.C.)
- BGI-Shenzhen, Shenzhen 518083, China
| | - Yadong Chen
- BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China; (Y.S.); (Y.C.)
| | - Mengyang Xu
- BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China; (Y.S.); (Y.C.)
| | - Guangyi Fan
- BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China; (Y.S.); (Y.C.)
- BGI-Shenzhen, Shenzhen 518083, China
| | - Xin Liu
- BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China; (Y.S.); (Y.C.)
- BGI-Shenzhen, Shenzhen 518083, China
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3
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Bayramov AV, Yastrebov SA, Mednikov DN, Araslanova KR, Ermakova GV, Zaraisky AG. Paired fins in vertebrate evolution and ontogeny. Evol Dev 2024; 26:e12478. [PMID: 38650470 DOI: 10.1111/ede.12478] [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: 10/28/2023] [Revised: 02/28/2024] [Accepted: 04/08/2024] [Indexed: 04/25/2024]
Abstract
The origin of paired appendages became one of the most important adaptations of vertebrates, allowing them to lead active lifestyles and explore a wide range of ecological niches. The basic form of paired appendages in evolution is the fins of fishes. The problem of paired appendages has attracted the attention of researchers for more than 150 years. During this time, a number of theories have been proposed, mainly based on morphological data, two of which, the Balfour-Thacher-Mivart lateral fold theory and Gegenbaur's gill arch theory, have not lost their relevance. So far, however, none of the proposed ideas has been supported by decisive evidence. The study of the evolutionary history of the appearance and development of paired appendages lies at the intersection of several disciplines and involves the synthesis of paleontological, morphological, embryological, and genetic data. In this review, we attempt to summarize and discuss the results accumulated in these fields and to analyze the theories put forward regarding the prerequisites and mechanisms that gave rise to paired fins and limbs in vertebrates.
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Affiliation(s)
- Andrey V Bayramov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Sergey A Yastrebov
- Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Moscow, Russia
| | - Dmitry N Mednikov
- Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Moscow, Russia
| | - Karina R Araslanova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Galina V Ermakova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Andrey G Zaraisky
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
- Department of Regenerative Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
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4
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Hintermann A, Bolt CC, Hawkins MB, Valentin G, Lopez-Delisle L, Gitto S, Gómez PB, Mascrez B, Mansour TA, Nakamura T, Harris MP, Shubin NH, Duboule D. EVOLUTIONARY CO-OPTION OF AN ANCESTRAL CLOACAL REGULATORY LANDSCAPE DURING THE EMERGENCE OF DIGITS AND GENITALS. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.24.586442. [PMID: 38585989 PMCID: PMC10996561 DOI: 10.1101/2024.03.24.586442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
The transition from fins to limbs has been a rich source of discussion for more than a century. One open and important issue is understanding how the mechanisms that pattern digits arose during vertebrate evolution. In this context, the analysis of Hox gene expression and functions to infer evolutionary scenarios has been a productive approach to explain the changes in organ formation, particularly in limbs. In tetrapods, the transcription of Hoxd genes in developing digits depends on a well-characterized set of enhancers forming a large regulatory landscape1,2. This control system has a syntenic counterpart in zebrafish, even though they lack bona fide digits, suggestive of deep homology3 between distal fin and limb developmental mechanisms. We tested the global function of this landscape to assess ancestry and source of limb and fin variation. In contrast to results in mice, we show here that the deletion of the homologous control region in zebrafish has a limited effect on the transcription of hoxd genes during fin development. However, it fully abrogates hoxd expression within the developing cloaca, an ancestral structure related to the mammalian urogenital sinus. We show that similar to the limb, Hoxd gene function in the urogenital sinus of the mouse also depends on enhancers located in this same genomic domain. Thus, we conclude that the current regulation underlying Hoxd gene expression in distal limbs was co-opted in tetrapods from a preexisting cloacal program. The orthologous chromatin domain in fishes may illustrate a rudimentary or partial step in this evolutionary co-option.
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Affiliation(s)
- Aurélie Hintermann
- Department of Genetics and Evolution, University of Geneva, 30 quai Ernest Ansermet, 1211, Geneva, Switzerland
| | - Christopher Chase Bolt
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne EPFL, 1015 Lausanne, Switzerland
| | - M. Brent Hawkins
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA, Department of Orthopedic Research, Boston Children’s Hospital, Boston, Massachusetts, USA
| | - Guillaume Valentin
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne EPFL, 1015 Lausanne, Switzerland
| | - Lucille Lopez-Delisle
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne EPFL, 1015 Lausanne, Switzerland
| | - Sandra Gitto
- Department of Genetics and Evolution, University of Geneva, 30 quai Ernest Ansermet, 1211, Geneva, Switzerland
| | - Paula Barrera Gómez
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne EPFL, 1015 Lausanne, Switzerland
| | - Bénédicte Mascrez
- Department of Genetics and Evolution, University of Geneva, 30 quai Ernest Ansermet, 1211, Geneva, Switzerland
| | | | - Tetsuya Nakamura
- Department of Genetics, Rutgers University, New Brunswick, NJ, USA
| | - Matthew P. Harris
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA, Department of Orthopedic Research, Boston Children’s Hospital, Boston, Massachusetts, USA
| | - Neil H. Shubin
- Department of Organismal Biology and Anatomy, The University of Chicago, Chicago, IL, USA
| | - Denis Duboule
- Department of Genetics and Evolution, University of Geneva, 30 quai Ernest Ansermet, 1211, Geneva, Switzerland
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne EPFL, 1015 Lausanne, Switzerland
- Center for Interdisciplinary Research in Biology CIRB, Collège de France, CNRS, INSERM, Université PSL, Paris, France
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5
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da Silva JPCB, Vaz DFB. Morphology and phylogenetic significance of the pelvic articular region in elasmobranchs (Chondrichthyes). Cladistics 2023; 39:155-197. [PMID: 36856203 DOI: 10.1111/cla.12528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Revised: 01/20/2023] [Accepted: 01/21/2023] [Indexed: 03/02/2023] Open
Abstract
The morphology of paired fins is commonly overlooked in morphological studies, particularly the pelvic girdle and fins. Consequently, previous phylogenetic studies incorporating morphological data used few skeletal characters from this complex. In this paper, the phylogenetic significance of pelvic articular characters for elasmobranchs is discussed in light of the morphological variation observed in 130 species, the most comprehensive study exploring the morphology of the pelvic girdle done so far. The 10 morphological characters proposed herein for the pelvic articulation were incorporated into a molecular matrix of NADH2 sequences and submitted to an analysis of maximum parsimony employing extended implied weighting. The most stable tree was selected based on the distortion coefficients, SPR distances (subtree pruning and regrafting) and fit values. Some of the striking synapomorphies recovered within elasmobranchs include the presence of an articular surface for the first enlarged pelvic radial supporting Elasmobranchii and the pelvic articular region for the basipterygium extending from the posterolatral margin of the pelvic girdle over its lateral surface in Echinorhinus + Hexanchiformes. Additionally, the proposed characters and their distributions are discussed considering the relationships recovered and also compared with previous morphological and molecular phylogenetic hypotheses.
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Affiliation(s)
- João Paulo C B da Silva
- Departamento de Sistemática e Ecologia, Centro de Ciências Exatas e da Natureza, Universidade Federal da Paraíba, Castelo Branco, João Pessoa, 58051-900, Brazil
| | - Diego F B Vaz
- Museum of Comparative Zoology, Harvard University, 26 Oxford Street, Cambridge, MA, 02143, USA.,Biorepository Collaboratorium Guam EPSCoR, Marine Laboratory, University of Guam, 303 University Dr, UOG Station, Mangilao, GU, 96923, USA
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6
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The Development of the Chimaeroid Pelvic Skeleton and the Evolution of Chondrichthyan Pelvic Fins. J Dev Biol 2022; 10:jdb10040053. [PMID: 36547475 PMCID: PMC9782884 DOI: 10.3390/jdb10040053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 10/11/2022] [Accepted: 11/01/2022] [Indexed: 12/14/2022] Open
Abstract
Pelvic girdles, fins and claspers are evolutionary novelties first recorded in jawed vertebrates. Over the course of the evolution of chondrichthyans (cartilaginous fish) two trends in the morphology of the pelvic skeleton have been suggested to have occurred. These evolutionary shifts involved both an enlargement of the metapterygium (basipterygium) and a transition of fin radial articulation from the pelvic girdle to the metapterygium. To determine how these changes in morphology have occurred it is essential to understand the development of extant taxa as this can indicate potential developmental mechanisms that may have been responsible for these changes. The study of the morphology of the appendicular skeleton across development in chondrichthyans is almost entirely restricted to the historical literature with little contemporary research. Here, we have examined the morphology and development of the pelvic skeleton of a holocephalan chondrichthyan, the elephant shark (Callorhinchus milii), through a combination of dissections, histology, and nanoCT imaging and redescribed the pelvic skeleton of Cladoselache kepleri (NHMUK PV P 9269), a stem holocephalan. To put our findings in their evolutionary context we compare them with the fossil record of chondrichthyans and the literature on pelvic development in elasmobranchs from the late 19th century. Our findings demonstrate that the pelvic skeleton of C. milii initially forms as a single mesenchymal condensation, consisting of the pelvic girdle and a series of fin rays, which fuse to form the basipterygium. The girdle and fin skeleton subsequently segment into distinct components whilst chondrifying. This confirms descriptions of the early pelvic development in Scyliorhinid sharks from the historical literature and suggests that chimaeras and elasmobranchs share common developmental patterns in their pelvic anatomy. Alterations in the location and degree of radial fusion during early development may be the mechanism responsible for changes in pelvic fin morphology over the course of the evolution of both elasmobranchs and holocephalans, which appears to be an example of parallel evolution.
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7
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Spatial regulation by multiple Gremlin1 enhancers provides digit development with cis-regulatory robustness and evolutionary plasticity. Nat Commun 2021; 12:5557. [PMID: 34548488 PMCID: PMC8455560 DOI: 10.1038/s41467-021-25810-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 09/02/2021] [Indexed: 11/17/2022] Open
Abstract
Precise cis-regulatory control of gene expression is essential for normal embryogenesis and tissue development. The BMP antagonist Gremlin1 (Grem1) is a key node in the signalling system that coordinately controls limb bud development. Here, we use mouse reverse genetics to identify the enhancers in the Grem1 genomic landscape and the underlying cis-regulatory logics that orchestrate the spatio-temporal Grem1 expression dynamics during limb bud development. We establish that transcript levels are controlled in an additive manner while spatial regulation requires synergistic interactions among multiple enhancers. Disrupting these interactions shows that altered spatial regulation rather than reduced Grem1 transcript levels prefigures digit fusions and loss. Two of the enhancers are evolutionary ancient and highly conserved from basal fishes to mammals. Analysing these enhancers from different species reveal the substantial spatial plasticity in Grem1 regulation in tetrapods and basal fishes, which provides insights into the fin-to-limb transition and evolutionary diversification of pentadactyl limbs. The BMP antagonist Gremlin1 balances BMP and SHH signalling, endowing limb bud development with robustness. Here, the authors identify enhancers controlling Grem1 levels in an additive, and spatial regulation in a synergistic manner, providing digit patterning with cis-regulatory robustness and evolutionary plasticity.
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8
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Schwaner MJ, Hsieh ST, Braasch I, Bradley S, Campos CB, Collins CE, Donatelli CM, Fish FE, Fitch OE, Flammang BE, Jackson BE, Jusufi A, Mekdara PJ, Patel A, Swalla BJ, Vickaryous M, McGowan CP. Future Tail Tales: A Forward-Looking, Integrative Perspective on Tail Research. Integr Comp Biol 2021; 61:521-537. [PMID: 33999184 PMCID: PMC8680820 DOI: 10.1093/icb/icab082] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Synopsis Tails are a defining characteristic of chordates and show enormous diversity in function and shape. Although chordate tails share a common evolutionary and genetic-developmental origin, tails are extremely versatile in morphology and function. For example, tails can be short or long, thin or thick, and feathered or spiked, and they can be used for propulsion, communication, or balancing, and they mediate in predator-prey outcomes. Depending on the species of animal the tail is attached to, it can have extraordinarily multi-functional purposes. Despite its morphological diversity and broad functional roles, tails have not received similar scientific attention as, for example, the paired appendages such as legs or fins. This forward-looking review article is a first step toward interdisciplinary scientific synthesis in tail research. We discuss the importance of tail research in relation to five topics: (1) evolution and development, (2) regeneration, (3) functional morphology, (4) sensorimotor control, and (5) computational and physical models. Within each of these areas, we highlight areas of research and combinations of long-standing and new experimental approaches to move the field of tail research forward. To best advance a holistic understanding of tail evolution and function, it is imperative to embrace an interdisciplinary approach, re-integrating traditionally siloed fields around discussions on tail-related research.
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Affiliation(s)
- M J Schwaner
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA 92697, USA
| | - S T Hsieh
- Department of Biology, Temple University, Philadelphia, PA 19122, USA
| | - I Braasch
- Department of Integrative Biology and Program in Ecology, Evolution, and Behavior (EEB), Michigan State University, East Lansing, MI 48824, USA
| | - S Bradley
- Department of Biomedical Science, University of Guelph, Guelph N1G 2W1, Canada
| | - C B Campos
- Department of Biological Sciences, Sacramento State University, Sacramento, CA 95819, USA
| | - C E Collins
- Department of Biological Sciences, Sacramento State University, Sacramento, CA 95819, USA
| | - C M Donatelli
- Department of Biology, University of Ottawa, Ontario K1N 6N5, Canada
| | - F E Fish
- Department of Biology, West Chester University, West Chester, PA 19383, USA
| | - O E Fitch
- Department of Integrative Biology and Program in Ecology, Evolution, and Behavior (EEB), Michigan State University, East Lansing, MI 48824, USA
| | - B E Flammang
- Department of Biological Sciences, New Jersey Institute of Technology, Newark, NJ 07102, USA
| | - B E Jackson
- Department of Biological and Environmental Sciences, Longwood University, Farmville, VA 23909, USA
| | - A Jusufi
- Max Planck Institute for Intelligent Systems, Stuttgart 70569, Germany
| | - P J Mekdara
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
| | - A Patel
- Department of Electrical Engineering, University of Cape Town, Cape Town 7701, South Africa
| | - B J Swalla
- Department of Biology, University of Washington, Seattle, WA 98195, USA
| | - M Vickaryous
- Department of Biomedical Science, University of Guelph, Guelph N1G 2W1, Canada
| | - C P McGowan
- Department of Integrative Anatomical Sciences, University of Southern California, Los Angeles, CA 90033, USA
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9
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Thompson AW, Hawkins MB, Parey E, Wcisel DJ, Ota T, Kawasaki K, Funk E, Losilla M, Fitch OE, Pan Q, Feron R, Louis A, Montfort J, Milhes M, Racicot BL, Childs KL, Fontenot Q, Ferrara A, David SR, McCune AR, Dornburg A, Yoder JA, Guiguen Y, Roest Crollius H, Berthelot C, Harris MP, Braasch I. The bowfin genome illuminates the developmental evolution of ray-finned fishes. Nat Genet 2021; 53:1373-1384. [PMID: 34462605 PMCID: PMC8423624 DOI: 10.1038/s41588-021-00914-y] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 07/13/2021] [Indexed: 02/07/2023]
Abstract
The bowfin (Amia calva) is a ray-finned fish that possesses a unique suite of ancestral and derived phenotypes, which are key to understanding vertebrate evolution. The phylogenetic position of bowfin as a representative of neopterygian fishes, its archetypical body plan and its unduplicated and slowly evolving genome make bowfin a central species for the genomic exploration of ray-finned fishes. Here we present a chromosome-level genome assembly for bowfin that enables gene-order analyses, settling long-debated neopterygian phylogenetic relationships. We examine chromatin accessibility and gene expression through bowfin development to investigate the evolution of immune, scale, respiratory and fin skeletal systems and identify hundreds of gene-regulatory loci conserved across vertebrates. These resources connect developmental evolution among bony fishes, further highlighting the bowfin's importance for illuminating vertebrate biology and diversity in the genomic era.
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Affiliation(s)
- Andrew W Thompson
- Department of Integrative Biology, Michigan State University, East Lansing, MI, USA
- Ecology, Evolution & Behavior Program, Michigan State University, East Lansing, MI, USA
| | - M Brent Hawkins
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Department of Orthopedic Research, Boston Children's Hospital, Boston, MA, USA
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA
| | - Elise Parey
- Institut de Biologie de l'ENS (IBENS), Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Dustin J Wcisel
- Department of Molecular Biomedical Sciences, NC State University, Raleigh, NC, USA
| | - Tatsuya Ota
- Department of Evolutionary Studies of Biosystems, SOKENDAI (the Graduate University for Advanced Studies), Hayama, Japan
| | - Kazuhiko Kawasaki
- Department of Anthropology, Pennsylvania State University, University Park, PA, USA
| | - Emily Funk
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
- Animal Science Department, University of California Davis, Davis, CA, USA
| | - Mauricio Losilla
- Department of Integrative Biology, Michigan State University, East Lansing, MI, USA
- Ecology, Evolution & Behavior Program, Michigan State University, East Lansing, MI, USA
| | - Olivia E Fitch
- Department of Integrative Biology, Michigan State University, East Lansing, MI, USA
- Ecology, Evolution & Behavior Program, Michigan State University, East Lansing, MI, USA
| | - Qiaowei Pan
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Romain Feron
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Alexandra Louis
- Institut de Biologie de l'ENS (IBENS), Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
| | | | - Marine Milhes
- GeT-PlaGe, INRAE, Genotoul, Castanet-Tolosan, France
| | - Brett L Racicot
- Department of Integrative Biology, Michigan State University, East Lansing, MI, USA
| | - Kevin L Childs
- Department of Plant Biology, Michigan State University, East Lansing, MI, USA
| | - Quenton Fontenot
- Department of Biological Sciences, Nicholls State University, Thibodaux, LA, USA
| | - Allyse Ferrara
- Department of Biological Sciences, Nicholls State University, Thibodaux, LA, USA
| | - Solomon R David
- Department of Biological Sciences, Nicholls State University, Thibodaux, LA, USA
| | - Amy R McCune
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
| | - Alex Dornburg
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC, USA
| | - Jeffrey A Yoder
- Department of Molecular Biomedical Sciences, NC State University, Raleigh, NC, USA
- Comparative Medicine Institute, NC State University, Raleigh, NC, USA
- Center for Human Health and the Environment, NC State University, Raleigh, NC, USA
| | | | - Hugues Roest Crollius
- Institut de Biologie de l'ENS (IBENS), Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Camille Berthelot
- Institut de Biologie de l'ENS (IBENS), Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Matthew P Harris
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Department of Orthopedic Research, Boston Children's Hospital, Boston, MA, USA
| | - Ingo Braasch
- Department of Integrative Biology, Michigan State University, East Lansing, MI, USA.
- Ecology, Evolution & Behavior Program, Michigan State University, East Lansing, MI, USA.
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10
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Conserved Mechanisms, Novel Anatomies: The Developmental Basis of Fin Evolution and the Origin of Limbs. DIVERSITY 2021. [DOI: 10.3390/d13080384] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The transformation of paired fins into tetrapod limbs is one of the most intensively scrutinized events in animal evolution. Early anatomical and embryological datasets identified distinctive morphological regions within the appendage and posed hypotheses about how the loss, gain, and transformation of these regions could explain the observed patterns of both extant and fossil appendage diversity. These hypotheses have been put to the test by our growing understanding of patterning mechanisms that regulate formation of the appendage axes, comparisons of gene expression data from an array of phylogenetically informative taxa, and increasingly sophisticated and elegant experiments leveraging the latest molecular approaches. Together, these data demonstrate the remarkable conservation of developmental mechanisms, even across phylogenetically and morphologically disparate taxa, as well as raising new questions about the way we view homology, evolutionary novelty, and the often non-linear connection between morphology and gene expression. In this review, we present historical hypotheses regarding paired fin evolution and limb origins, summarize key aspects of central appendage patterning mechanisms in model and non-model species, address how modern comparative developmental data interface with our understanding of appendage anatomy, and highlight new approaches that promise to provide new insight into these well-traveled questions.
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11
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Hawkins MB, Henke K, Harris MP. Latent developmental potential to form limb-like skeletal structures in zebrafish. Cell 2021; 184:899-911.e13. [PMID: 33545089 DOI: 10.1016/j.cell.2021.01.003] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 10/28/2020] [Accepted: 01/04/2021] [Indexed: 12/13/2022]
Abstract
Changes in appendage structure underlie key transitions in vertebrate evolution. Addition of skeletal elements along the proximal-distal axis facilitated critical transformations, including the fin-to-limb transition that permitted generation of diverse modes of locomotion. Here, we identify zebrafish mutants that form supernumerary long bones in their pectoral fins. These new bones integrate into musculature, form joints, and articulate with neighboring elements. This phenotype is caused by activating mutations in previously unrecognized regulators of appendage patterning, vav2 and waslb, that function in a common pathway. This pathway is required for appendage development across vertebrates, and loss of Wasl in mice causes defects similar to those seen in murine Hox mutants. Concordantly, formation of supernumerary bones requires Hox11 function, and mutations in the vav2/wasl pathway drive enhanced expression of hoxa11b, indicating developmental homology with the forearm. Our findings reveal a latent, limb-like pattern ability in fins that is activated by simple genetic perturbation.
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Affiliation(s)
- M Brent Hawkins
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Department of Orthopedic Research, Boston Children's Hospital, Boston, MA 02115, USA; Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA; Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138, USA
| | - Katrin Henke
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Department of Orthopedic Research, Boston Children's Hospital, Boston, MA 02115, USA
| | - Matthew P Harris
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Department of Orthopedic Research, Boston Children's Hospital, Boston, MA 02115, USA.
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12
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Woltering JM, Irisarri I, Ericsson R, Joss JMP, Sordino P, Meyer A. Sarcopterygian fin ontogeny elucidates the origin of hands with digits. SCIENCE ADVANCES 2020; 6:eabc3510. [PMID: 32875118 PMCID: PMC7438105 DOI: 10.1126/sciadv.abc3510] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 07/09/2020] [Indexed: 05/03/2023]
Abstract
How the hand and digits originated from fish fins during the Devonian fin-to-limb transition remains unsolved. Controversy in this conundrum stems from the scarcity of ontogenetic data from extant lobe-finned fishes. We report the patterning of an autopod-like domain by hoxa13 during fin development of the Australian lungfish, the most closely related extant fish relative of tetrapods. Differences from tetrapod limbs include the absence of digit-specific expansion of hoxd13 and hand2 and distal limitation of alx4 and pax9, which potentially evolved through an enhanced response to shh signaling in limbs. These developmental patterns indicate that the digit program originated in postaxial fin radials and later expanded anteriorly inside of a preexisting autopod-like domain during the evolution of limbs. Our findings provide a genetic framework for the transition of fins into limbs that supports the significance of classical models proposing a bending of the tetrapod metapterygial axis.
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Affiliation(s)
- Joost M. Woltering
- Zoology and Evolutionary Biology, Department of Biology, Universität Konstanz, Universitätstrasse 10, 78464 Konstanz, Germany
| | - Iker Irisarri
- Zoology and Evolutionary Biology, Department of Biology, Universität Konstanz, Universitätstrasse 10, 78464 Konstanz, Germany
| | | | | | - Paolo Sordino
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy
| | - Axel Meyer
- Zoology and Evolutionary Biology, Department of Biology, Universität Konstanz, Universitätstrasse 10, 78464 Konstanz, Germany
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13
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Enny A, Flaherty K, Mori S, Turner N, Nakamura T. Developmental constraints on fin diversity. Dev Growth Differ 2020; 62:311-325. [PMID: 32396685 PMCID: PMC7383993 DOI: 10.1111/dgd.12670] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 03/17/2020] [Accepted: 04/06/2020] [Indexed: 12/31/2022]
Abstract
The fish fin is a breathtaking repository full of evolutionary diversity, novelty, and convergence. Over 500 million years, the adaptation to novel habitats has provided landscapes of fin diversity. Although comparative anatomy of evolutionarily divergent patterns over centuries has highlighted the fundamental architectures and evolutionary trends of fins, including convergent evolution, the developmental constraints on fin evolution, which bias the evolutionary trajectories of fin morphology, largely remain elusive. Here, we review the evolutionary history, developmental mechanisms, and evolutionary underpinnings of paired fins, illuminating possible developmental constraints on fin evolution. Our compilation of anatomical and genetic knowledge of fin development sheds light on the canalized and the unpredictable aspects of fin shape in evolution. Leveraged by an arsenal of genomic and genetic tools within the working arena of spectacular fin diversity, evolutionary developmental biology embarks on the establishment of conceptual framework for developmental constraints, previously enigmatic properties of evolution.
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Affiliation(s)
- Alyssa Enny
- Department of GeneticsRutgers the State University of New JerseyPiscatawayNJUSA
| | - Kathleen Flaherty
- Rutgers Animal CareRutgers the State University of New JerseyPiscatawayNJUSA
| | - Shunsuke Mori
- Department of GeneticsRutgers the State University of New JerseyPiscatawayNJUSA
| | - Natalie Turner
- Department of GeneticsRutgers the State University of New JerseyPiscatawayNJUSA
| | - Tetsuya Nakamura
- Department of GeneticsRutgers the State University of New JerseyPiscatawayNJUSA
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14
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Onimaru K. The evolutionary origin of developmental enhancers in vertebrates: Insights from non‐model species. Dev Growth Differ 2020; 62:326-333. [DOI: 10.1111/dgd.12662] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 03/10/2020] [Accepted: 03/11/2020] [Indexed: 11/28/2022]
Affiliation(s)
- Koh Onimaru
- Laboratory for Bioinformatics Research RIKEN Center for Biosystems Dynamics Research (BDR) Wako CitySaitama Japan
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15
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Scoones JC, Hiscock TW. A dot-stripe Turing model of joint patterning in the tetrapod limb. Development 2020; 147:dev183699. [PMID: 32127348 PMCID: PMC7174842 DOI: 10.1242/dev.183699] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 02/24/2020] [Indexed: 01/11/2023]
Abstract
Iterative joints are a hallmark of the tetrapod limb, and their positioning is a key step during limb development. Although the molecular regulation of joint formation is well studied, it remains unclear what controls the location, number and orientation (i.e. the pattern) of joints within each digit. Here, we propose the dot-stripe mechanism for joint patterning, comprising two coupled Turing systems inspired by published gene expression patterns. Our model can explain normal joint morphology in wild-type limbs, hyperphalangy in cetacean flippers, mutant phenotypes with misoriented joints and suggests a reinterpretation of the polydactylous Ichthyosaur fins as a polygonal joint lattice. By formulating a generic dot-stripe model, describing joint patterns rather than molecular joint markers, we demonstrate that the insights from the model should apply regardless of the biological specifics of the underlying mechanism, thus providing a unifying framework to interrogate joint patterning in the tetrapod limb.
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Affiliation(s)
| | - Tom W Hiscock
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, UK
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK
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16
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Woltering JM, Holzem M, Meyer A. Lissamphibian limbs and the origins of tetrapod hox domains. Dev Biol 2019; 456:138-144. [DOI: 10.1016/j.ydbio.2019.08.014] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 08/21/2019] [Accepted: 08/22/2019] [Indexed: 12/30/2022]
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17
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Hamada H, Uemoto T, Tanaka Y, Honda Y, Kitajima K, Umeda T, Kawakami A, Shinya M, Kawakami K, Tamura K, Abe G. Pattern of fin rays along the antero-posterior axis based on their connection to distal radials. ZOOLOGICAL LETTERS 2019; 5:30. [PMID: 31548912 PMCID: PMC6751676 DOI: 10.1186/s40851-019-0145-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 08/26/2019] [Indexed: 06/10/2023]
Abstract
BACKGROUND Teleost paired fins are composed of two endoskeletal domains, proximal and distal radials, and an exoskeletal domain, the fin ray. The zebrafish pectoral fin displays elaborately patterned radials along the anteroposterior (AP) axis. Radials are considered homologous to tetrapod limb skeletons, and their patterning mechanisms in embryonic development are similar to those of limb development. Nevertheless, the pattern along the AP axis in fin rays has not been well described in the zebrafish pectoral fin, although several recent reports have revealed that fin ray development shares some cellular and genetic properties with fin/limb endoskeleton development. Thus, fin ray morphogenesis may involve developmental mechanisms for AP patterning in the fin/limb endoskeleton, and may have a specific pattern along the AP axis. RESULTS We conducted detailed morphological observations on fin rays and their connection to distal radials by comparing intra- and inter-strain zebrafish specimens. Although the number of fin rays varied, pectoral fin rays could be categorized into three domains along the AP axis, according to the connection between the fin rays and distal radials; additionally, the number of fin rays varied in the posterior part of the three domains. This result was confirmed by observation of the morphogenesis process of fin rays and distal radials, which showed altered localization of distal radials in the middle domain. We also evaluated the expression pattern of lhx genes, which have AP patterning activity in limb development, in fin rays and during distal radial development and found these genes to be expressed during morphogenesis in both fin rays and distal radials. CONCLUSION The fin ray and its connection to the endoskeleton are patterned along the AP axis, and the pattern along the AP axis in the fin ray and the radial connection is constructed by the developmental mechanism related to AP patterning in the limb/fin bud. Our results indicate the possibility that the developmental mechanisms of fin rays and their connection are comparable to those of the distal element of the limb skeleton.
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Affiliation(s)
- Hiroki Hamada
- Laboratory of Organ Morphogenesis, Department of Ecological Developmental Adaptability Life Sciences, Graduate School of Life Sciences, Tohoku University, Sendai, 980-8578 Japan
| | - Toshiaki Uemoto
- Laboratory of Organ Morphogenesis, Department of Ecological Developmental Adaptability Life Sciences, Graduate School of Life Sciences, Tohoku University, Sendai, 980-8578 Japan
| | - Yoshitaka Tanaka
- Laboratory of Organ Morphogenesis, Department of Ecological Developmental Adaptability Life Sciences, Graduate School of Life Sciences, Tohoku University, Sendai, 980-8578 Japan
| | - Yuki Honda
- Laboratory of Organ Morphogenesis, Department of Ecological Developmental Adaptability Life Sciences, Graduate School of Life Sciences, Tohoku University, Sendai, 980-8578 Japan
| | - Keiichi Kitajima
- Laboratory of Organ Morphogenesis, Department of Ecological Developmental Adaptability Life Sciences, Graduate School of Life Sciences, Tohoku University, Sendai, 980-8578 Japan
| | - Tetsuya Umeda
- Laboratory of Organ Morphogenesis, Department of Ecological Developmental Adaptability Life Sciences, Graduate School of Life Sciences, Tohoku University, Sendai, 980-8578 Japan
| | - Atsushi Kawakami
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, 226-8501 Japan
| | - Minori Shinya
- Department of Biology, Keio University, Yokohama, 223-8521 Japan
| | - Koichi Kawakami
- Laboratory of Molecular and Developmental Biology, National Institute of Genetics, Mishima, Shizuoka, 411-8540 Japan
- Department of Genetics, SOKENDAI (The Graduate University for Advanced Studies), Mishima, Shizuoka, 411-8540 Japan
| | - Koji Tamura
- Laboratory of Organ Morphogenesis, Department of Ecological Developmental Adaptability Life Sciences, Graduate School of Life Sciences, Tohoku University, Sendai, 980-8578 Japan
| | - Gembu Abe
- Laboratory of Organ Morphogenesis, Department of Ecological Developmental Adaptability Life Sciences, Graduate School of Life Sciences, Tohoku University, Sendai, 980-8578 Japan
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18
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Wood TWP, Nakamura T. Problems in Fish-to-Tetrapod Transition: Genetic Expeditions Into Old Specimens. Front Cell Dev Biol 2018; 6:70. [PMID: 30062096 PMCID: PMC6054942 DOI: 10.3389/fcell.2018.00070] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Accepted: 06/15/2018] [Indexed: 12/30/2022] Open
Abstract
The fish-to-tetrapod transition is one of the fundamental problems in evolutionary biology. A significant amount of paleontological data has revealed the morphological trajectories of skeletons, such as those of the skull, vertebrae, and appendages in vertebrate history. Shifts in bone differentiation, from dermal to endochondral bones, are key to explaining skeletal transformations during the transition from water to land. However, the genetic underpinnings underlying the evolution of dermal and endochondral bones are largely missing. Recent genetic approaches utilizing model organisms—zebrafish, frogs, chickens, and mice—reveal the molecular mechanisms underlying vertebrate skeletal development and provide new insights for how the skeletal system has evolved. Currently, our experimental horizons to test evolutionary hypotheses are being expanded to non-model organisms with state-of-the-art techniques in molecular biology and imaging. An integration of functional genomics, developmental genetics, and high-resolution CT scanning into evolutionary inquiries allows us to reevaluate our understanding of old specimens. Here, we summarize the current perspectives in genetic programs underlying the development and evolution of the dermal skull roof, shoulder girdle, and appendages. The ratio shifts of dermal and endochondral bones, and its underlying mechanisms, during the fish-to-tetrapod transition are particularly emphasized. Recent studies have suggested the novel cell origins of dermal bones, and the interchangeability between dermal and endochondral bones, obscuring the ontogenetic distinction of these two types of bones. Assimilation of ontogenetic knowledge of dermal and endochondral bones from different structures demands revisions of the prevalent consensus in the evolutionary mechanisms of vertebrate skeletal shifts.
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Affiliation(s)
- Thomas W P Wood
- Department of Genetics, Rutgers, The State University of New Jersey, Piscataway, NJ, United States
| | - Tetsuya Nakamura
- Department of Genetics, Rutgers, The State University of New Jersey, Piscataway, NJ, United States
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19
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Expression of meis and hoxa11 in dipnoan and teleost fins provides new insights into the evolution of vertebrate appendages. EvoDevo 2018; 9:11. [PMID: 29719716 PMCID: PMC5924435 DOI: 10.1186/s13227-018-0099-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 04/20/2018] [Indexed: 11/22/2022] Open
Abstract
Background The concerted activity of Meis and Hoxa11 transcription factors is essential for the subdivision of tetrapod limbs into proximo-distal (PD) domains; however, little is know about the evolution of this patterning mechanism. Here, we aim to study the expression of meis and hoxa11 orthologues in the median and paired rayed fins of zebrafish and in the lobed fins of the Australian lungfish. Results First, a late phase of expression of meis1.1 and hoxa11b in zebrafish dorsal and anal fins relates with segmentation of endochondral elements in proximal and distal radials. Second, our zebrafish in situ hybridization results reveal spatial and temporal changes between pectoral and pelvic fins. Third, in situ analysis of meis1, meis3 and hoxa11 genes in Neoceratodus pectoral fins identifies decoupled domains of expression along the PD axis. Conclusions Our data raise the possibility that the origin of stylopod and zeugopod lies much deeper in gnathostome evolution and that variation in meis and hoxa11 expression has played a substantial role in the transformation of appendage anatomy. Moreover, these observations provide evidence that the Meis/Hoxa11 profile considered a hallmark of stylopod/zeugopod patterning is present in Neoceratodus. Electronic supplementary material The online version of this article (10.1186/s13227-018-0099-9) contains supplementary material, which is available to authorized users.
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20
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Tulenko FJ, Massey JL, Holmquist E, Kigundu G, Thomas S, Smith SME, Mazan S, Davis MC. Fin-fold development in paddlefish and catshark and implications for the evolution of the autopod. Proc Biol Sci 2018; 284:rspb.2016.2780. [PMID: 28539509 DOI: 10.1098/rspb.2016.2780] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 04/24/2017] [Indexed: 01/04/2023] Open
Abstract
The evolutionary origin of the autopod involved a loss of the fin-fold and associated dermal skeleton with a concomitant elaboration of the distal endoskeleton to form a wrist and digits. Developmental studies, primarily from teleosts and amniotes, suggest a model for appendage evolution in which a delay in the AER-to-fin-fold conversion fuelled endoskeletal expansion by prolonging the function of AER-mediated regulatory networks. Here, we characterize aspects of paired fin development in the paddlefish Polyodon spathula (a non-teleost actinopterygian) and catshark Scyliorhinus canicula (chondrichthyan) to explore aspects of this model in a broader phylogenetic context. Our data demonstrate that in basal gnathostomes, the autopod marker HoxA13 co-localizes with the dermoskeleton component And1 to mark the position of the fin-fold, supporting recent work demonstrating a role for HoxA13 in zebrafish fin ray development. Additionally, we show that in paddlefish, the proximal fin and fin-fold mesenchyme share a common mesodermal origin, and that components of the Shh/LIM/Gremlin/Fgf transcriptional network critical to limb bud outgrowth and patterning are expressed in the fin-fold with a profile similar to that of tetrapods. Together these data draw contrast with hypotheses of AER heterochrony and suggest that limb-specific morphologies arose through evolutionary changes in the differentiation outcome of conserved early distal patterning compartments.
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Affiliation(s)
- Frank J Tulenko
- Department of Molecular and Cellular Biology, Kennesaw State University, GA 30144, USA.,Australian Regenerative Medicine Institute, Monash University, Victoria, 3800, Australia
| | - James L Massey
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, CO 80309, USA
| | - Elishka Holmquist
- Department of Molecular and Cellular Biology, Kennesaw State University, GA 30144, USA
| | - Gabriel Kigundu
- Department of Molecular and Cellular Biology, Kennesaw State University, GA 30144, USA
| | - Sarah Thomas
- Department of Molecular and Cellular Biology, Kennesaw State University, GA 30144, USA
| | - Susan M E Smith
- Department of Molecular and Cellular Biology, Kennesaw State University, GA 30144, USA
| | - Sylvie Mazan
- CNRS, Sorbonne Universités, UPMC Univ Paris 06, UMR7232, Observatoire Océanologique, F-66650 Banyuls-sur-Mer, France
| | - Marcus C Davis
- Department of Molecular and Cellular Biology, Kennesaw State University, GA 30144, USA
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21
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Paço A, Freitas R. Hox D genes and the fin-to-limb
transition: Insights from fish studies. Genesis 2017; 56. [DOI: 10.1002/dvg.23069] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Revised: 08/14/2017] [Accepted: 09/08/2017] [Indexed: 11/07/2022]
Affiliation(s)
- Ana Paço
- IBMC - Instituto de Biologia Celular e Molecular; Porto Portugal
- I3S - Instituto de Investigação e Inovação em Saúde; Porto Portugal
- Universidade do Porto; Porto Portugal
| | - Renata Freitas
- IBMC - Instituto de Biologia Celular e Molecular; Porto Portugal
- I3S - Instituto de Investigação e Inovação em Saúde; Porto Portugal
- Universidade do Porto; Porto Portugal
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22
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Amaral DB, Schneider I. Fins into limbs: Recent insights from sarcopterygian fish. Genesis 2017; 56. [PMID: 28834157 DOI: 10.1002/dvg.23052] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2017] [Revised: 08/10/2017] [Accepted: 08/15/2017] [Indexed: 02/03/2023]
Abstract
Limbs with digits evolved as sarcopterygian fish transitioned to a terrestrial life, giving rise to modern tetrapods. Since the Devonian, most of the sarcopterygian fish diversity became extinct, with the only surviving representatives being two coelacanth and six lungfish species. As the sister group of tetrapods, sarcopterygian fish constitute the ideal models to address questions regarding the transition of vertebrates from water to land. However, distantly related yet experimentally amenable teleost fish species have instead become the organisms of choice for geneticists and developmental biologists. Comparative studies using teleosts, such as zebrafish, have greatly enriched our knowledge on the genetic and regulatory mechanisms underlying fin development. However, their highly derived fin anatomy provides limited insights on the origin of limbs and the teleost-specific whole-genome duplication represents a further complication to comparisons of gene function and regulation. In recent years, refined morphological and behavioral studies and access to lungfish embryos and availability of genetic resources have underscored the value of nontetrapod sarcopterygians as model organisms. Here we review recent studies using lungfishes and coelacanths that shed light on various aspects of the evolution of the tetrapod limb, including the origin of the tetrapod pelvis, limb musculature, digits, locomotion, and regenerative capacity.
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Affiliation(s)
- Danielson B Amaral
- Instituto de Ciências Biológicas, Universidade Federal do Pará, Rua Augusto Corrêa, 01, Belém, 66075-900, Brazil
| | - Igor Schneider
- Instituto de Ciências Biológicas, Universidade Federal do Pará, Rua Augusto Corrêa, 01, Belém, 66075-900, Brazil
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23
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Tanaka M. Alterations in anterior-posterior patterning and its accompanying changes along the proximal-distal axis during the fin-to-limb transition. Genesis 2017; 56. [PMID: 28834131 DOI: 10.1002/dvg.23053] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2017] [Revised: 08/11/2017] [Accepted: 08/15/2017] [Indexed: 11/07/2022]
Abstract
The evolution from fins to limbs was one of the most successful innovations for vertebrates, allowing them to vastly expand their behaviors and habitats. Fossil records suggest that morphological changes occurred not only along the proximal-distal axis included appearance of the autopod, but also occurred along the anterior-posterior axis included reductions in the size and number of basal bones and digits. This review focuses on recent progress in developmental and genetic studies aimed at elucidating the mechanisms underlying alteration of anterior-posterior patterning and its accompanying changes along the proximal-distal axis during the fin-to-limb transition.
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Affiliation(s)
- Mikiko Tanaka
- Department of Life Science and Technology, Tokyo Institute of Technology, B-17, 4259 Nagatsuta-cho, Midori-ku, Yokohama, 226-8501, Japan
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24
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Chen J, Liu X, Yao X, Gao F, Bao B. Dorsal fin development in flounder, Paralichthys olivaceus: Bud formation and its cellular origin. Gene Expr Patterns 2017; 25-26:22-28. [PMID: 28442438 DOI: 10.1016/j.gep.2017.04.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2016] [Revised: 04/15/2017] [Accepted: 04/19/2017] [Indexed: 01/25/2023]
Abstract
The development of the median fin has not been investigated extensively in teleosts, although in other fishes it has been proposed that it involves the same genetic programs operating in the paired appendages. Adult median fins develop from the larval bud; therefore an investigation of fin bud formation and its cellular origin is essential to understanding the maturation mechanisms. In Paralichthys olivaceus, skeletogenesis proceeds from an anterior to posterior direction providing a good opportunity to study the formation of dorsal fin bud. An apical ectodermal ridge appeared at the basal stratum of the presumptive dorsal fin was first observed at 3 days post hatching. Then the apical ectodermal fold formed as the bud outgrew in 6 days post-hatch larvae. The bud continued to grow, breaking through the dorsal fin fold in 9 days post-hatch larvae. At 13 days post-hatch, the bud grew beyond the edge of the fin fold and formed into the four future rays. Molecular markers of cell type showed the existence of neural crest cells, scleroblasts and sclerotomes in the dorsal fin bud. The earliest gene expression in the dorsal fin bud was Hoxd10 at 3 days post-hatch larvae, then Hoxd9, Hoxd11 and Hoxd12. This indicates Hoxd10 might be a candidate molecular marker of the bud formation site. Some key molecular markers for paired appendage development, such as FGF8, Wnt7, and Shh were expressed at the apical ectodermal ridge and later the apical ectodermal fold. Moreover, the form of the dorsal fin bud could be inhibited by Hh pathway inhibitor, further indicating that common basic molecular mechanisms might be utilized by median fins.
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Affiliation(s)
- Jie Chen
- The Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Education, Shanghai 201306, China; Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo 315211, China
| | - Xiaoyu Liu
- The Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Education, Shanghai 201306, China
| | - Xiaohua Yao
- The Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Education, Shanghai 201306, China
| | - Fei Gao
- The Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Education, Shanghai 201306, China
| | - Baolong Bao
- The Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Education, Shanghai 201306, China.
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25
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Fish ‘tails’ result from outgrowth and reduction of two separate ancestral tails. Curr Biol 2016; 26:R1224-R1225. [DOI: 10.1016/j.cub.2016.10.036] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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26
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Bhat R, Chakraborty M, Glimm T, Stewart TA, Newman SA. Deep phylogenomics of a tandem-repeat galectin regulating appendicular skeletal pattern formation. BMC Evol Biol 2016; 16:162. [PMID: 27538950 PMCID: PMC4989294 DOI: 10.1186/s12862-016-0729-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Accepted: 07/26/2016] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND A multiscale network of two galectins Galectin-1 (Gal-1) and Galectin-8 (Gal-8) patterns the avian limb skeleton. Among vertebrates with paired appendages, chondrichthyan fins typically have one or more cartilage plates and many repeating parallel endoskeletal elements, actinopterygian fins have more varied patterns of nodules, bars and plates, while tetrapod limbs exhibit tandem arrays of few, proximodistally increasing numbers of elements. We applied a comparative genomic and protein evolution approach to understand the origin of the galectin patterning network. Having previously observed a phylogenetic constraint on Gal-1 structure across vertebrates, we asked whether evolutionary changes of Gal-8 could have critically contributed to the origin of the tetrapod pattern. RESULTS Translocations, duplications, and losses of Gal-8 genes in Actinopterygii established them in different genomic locations from those that the Sarcopterygii (including the tetrapods) share with chondrichthyans. The sarcopterygian Gal-8 genes acquired a potentially regulatory non-coding motif and underwent purifying selection. The actinopterygian Gal-8 genes, in contrast, did not acquire the non-coding motif and underwent positive selection. CONCLUSION These observations interpreted through the lens of a reaction-diffusion-adhesion model based on avian experimental findings can account for the distinct endoskeletal patterns of cartilaginous, ray-finned, and lobe-finned fishes, and the stereotypical limb skeletons of tetrapods.
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Affiliation(s)
- Ramray Bhat
- Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
- Present Address: Department of Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bangalore, 560012 India
| | - Mahul Chakraborty
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA 92697 USA
| | - Tilmann Glimm
- Department of Mathematics, Western Washington University, Bellingham, WA 98229 USA
| | - Thomas A. Stewart
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520 USA
- Minnesota Center for Philosophy of Science, University of Minnesota, Minneapolis, MN 55455 USA
| | - Stuart A. Newman
- Department of Cell Biology and Anatomy, New York Medical College, Valhalla, NY 10595 USA
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Digits and fin rays share common developmental histories. Nature 2016; 537:225-228. [PMID: 27533041 PMCID: PMC5161576 DOI: 10.1038/nature19322] [Citation(s) in RCA: 99] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Accepted: 07/20/2016] [Indexed: 12/14/2022]
Abstract
Understanding the evolutionary transformation of fish fins into tetrapod limbs is a fundamental problem in biology. The search for antecedents of tetrapod digits in fish has remained controversial because the distal skeletons of limbs and fins differ structurally, developmentally, and histologically. Moreover, comparisons of fins with limbs have been limited by a relative paucity of data on the cellular and molecular processes underlying the development of the fin skeleton. Here, we provide a functional analysis, using CRISPR/Cas9 and fate mapping, of 5' hox genes and enhancers in zebrafish that are indispensable for the development of the wrists and digits of tetrapods. We show that cells marked by the activity of an autopodial hoxa13 enhancer exclusively form elements of the fin fold, including the osteoblasts of the dermal rays. In hox13 knockout fish, we find that a marked reduction and loss of fin rays is associated with an increased number of endochondral distal radials. These discoveries reveal a cellular and genetic connection between the fin rays of fish and the digits of tetrapods and suggest that digits originated via the transition of distal cellular fates.
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