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Sprumont H, Allione F, Schwab F, Wang B, Mucignat C, Lunati I, Scheyer T, Ijspeert A, Jusufi A. Asymmetric fin shape changes swimming dynamics of ancient marine reptiles' soft robophysical models. BIOINSPIRATION & BIOMIMETICS 2024; 19:046005. [PMID: 38626775 DOI: 10.1088/1748-3190/ad3f5e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Accepted: 04/16/2024] [Indexed: 05/09/2024]
Abstract
Animals have evolved highly effective locomotion capabilities in terrestrial, aerial, and aquatic environments. Over life's history, mass extinctions have wiped out unique animal species with specialized adaptations, leaving paleontologists to reconstruct their locomotion through fossil analysis. Despite advancements, little is known about how extinct megafauna, such as the Ichthyosauria one of the most successful lineages of marine reptiles, utilized their varied morphologies for swimming. Traditional robotics struggle to mimic extinct locomotion effectively, but the emerging soft robotics field offers a promising alternative to overcome this challenge. This paper aims to bridge this gap by studyingMixosauruslocomotion with soft robotics, combining material modeling and biomechanics in physical experimental validation. Combining a soft body with soft pneumatic actuators, the soft robotic platform described in this study investigates the correlation between asymmetrical fins and buoyancy by recreating the pitch torque generated by extinct swimming animals. We performed a comparative analysis of thrust and torque generated byCarthorhyncus,Utatsusaurus,Mixosaurus,Guizhouichthyosaurus, andOphthalmosaurustail fins in a flow tank. Experimental results suggest that the pitch torque on the torso generated by hypocercal fin shapes such as found in model systems ofGuizhouichthyosaurus,MixosaurusandUtatsusaurusproduce distinct ventral body pitch effects able to mitigate the animal's non-neutral buoyancy. This body pitch control effect is particularly pronounced inGuizhouichthyosaurus, which results suggest would have been able to generate high ventral pitch torque on the torso to compensate for its positive buoyancy. By contrast, homocercal fin shapes may not have been conducive for such buoyancy compensation, leaving torso pitch control to pectoral fins, for example. Across the range of the actuation frequencies of the caudal fins tested, resulted in oscillatory modes arising, which in turn can affect the for-aft thrust generated.
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Affiliation(s)
- Hadrien Sprumont
- Soft Kinetic Group, Engineering Sciences Department, Empa, 8600 Zuerich, Switzerland
- Biorobotics Laboratory, School of Engineering, EPFL, 1015 Lausanne, Switzerland
| | - Federico Allione
- Soft Kinetic Group, Engineering Sciences Department, Empa, 8600 Zuerich, Switzerland
| | - Fabian Schwab
- Soft Kinetic Group, Engineering Sciences Department, Empa, 8600 Zuerich, Switzerland
| | - Bingcheng Wang
- Soft Kinetic Group, Engineering Sciences Department, Empa, 8600 Zuerich, Switzerland
- Institute of Neuroinformatics, University of Zuerich and ETH Zuerich, 8057 Zuerich, Switzerland
| | - Claudio Mucignat
- Laboratory for Computational Engineering, Empa, 8600 Zuerich, Switzerland
| | - Ivan Lunati
- Laboratory for Computational Engineering, Empa, 8600 Zuerich, Switzerland
| | - Torsten Scheyer
- Paläontologisches Institut und Museum, Universität Zürich, 8006 Zuerich, Switzerland
| | - Auke Ijspeert
- Biorobotics Laboratory, School of Engineering, EPFL, 1015 Lausanne, Switzerland
| | - Ardian Jusufi
- Soft Kinetic Group, Engineering Sciences Department, Empa, 8600 Zuerich, Switzerland
- Institute of Neuroinformatics, University of Zuerich and ETH Zuerich, 8057 Zuerich, Switzerland
- Paläontologisches Institut und Museum, Universität Zürich, 8006 Zuerich, Switzerland
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Chen HI, Turakhia Y, Bejerano G, Kingsley DM. Whole-genome Comparisons Identify Repeated Regulatory Changes Underlying Convergent Appendage Evolution in Diverse Fish Lineages. Mol Biol Evol 2023; 40:msad188. [PMID: 37739926 PMCID: PMC10516590 DOI: 10.1093/molbev/msad188] [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] [Indexed: 09/24/2023] Open
Abstract
Fins are major functional appendages of fish that have been repeatedly modified in different lineages. To search for genomic changes underlying natural fin diversity, we compared the genomes of 36 percomorph fish species that span over 100 million years of evolution and either have complete or reduced pelvic and caudal fins. We identify 1,614 genomic regions that are well-conserved in fin-complete species but missing from multiple fin-reduced lineages. Recurrent deletions of conserved sequences in wild fin-reduced species are enriched for functions related to appendage development, suggesting that convergent fin reduction at the organismal level is associated with repeated genomic deletions near fin-appendage development genes. We used sequencing and functional enhancer assays to confirm that PelA, a Pitx1 enhancer previously linked to recurrent pelvic loss in sticklebacks, has also been independently deleted and may have contributed to the fin morphology in distantly related pelvic-reduced species. We also identify a novel enhancer that is conserved in the majority of percomorphs, drives caudal fin expression in transgenic stickleback, is missing in tetraodontiform, syngnathid, and synbranchid species with caudal fin reduction, and alters caudal fin development when targeted by genome editing. Our study illustrates a broadly applicable strategy for mapping phenotypes to genotypes across a tree of vertebrate species and highlights notable new examples of regulatory genomic hotspots that have been used to evolve recurrent phenotypes across 100 million years of fish evolution.
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Affiliation(s)
- Heidi I Chen
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Yatish Turakhia
- Department of Electrical and Computer Engineering, University of California, San Diego, CA, USA
| | - Gill Bejerano
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA, USA
- Department of Computer Science, Stanford University School of Engineering, Stanford, CA, USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - David M Kingsley
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA
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Wang H, He J, Han X, Wu X, Ye X, Lv W, Zu Y. hoxa1a-Null Zebrafish as a Model for Studying HOXA1-Associated Heart Malformation in Bosley-Salih-Alorainy Syndrome. BIOLOGY 2023; 12:899. [PMID: 37508332 PMCID: PMC10376578 DOI: 10.3390/biology12070899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 05/23/2023] [Accepted: 05/30/2023] [Indexed: 07/30/2023]
Abstract
Mutations in HOXA1 can lead to diseases such as Bosley-Salih-Alorainy syndrome, involving severe cardiovascular malformations. However, the role of HOXA1 in cardiac morphogenesis remains unclear. hoxa1a is a homologous gene to human HOXA1 in zebrafish. We used CRISPR to make hoxa1a-null zebrafish that exhibited multiple heart malformations. In situ hybridization and sections revealed the morphological changes in mutants: enlarged ventricle with thickened myocardium and increased trabeculae, intensified OFT and inadequate heart looping, with electrocardiography supporting these pathological changes. High-speed photography captured cardiac pumping and revealed a significant decrease in cardiac output. Furthermore, lacking hoxa1a led to posterior body abnormality that affected movement ability, corresponding with the motor development delay in patients. Upregulation of hox paralogues in hoxa1a-null fish implied a compensatory mechanism between hox genes. Accordingly, we successfully constructed a hoxa1a-null model with a cardiac disease pattern which occurred in human HOXA1-associated heart malformation. The study of hoxa1a in zebrafish can further promote the understanding of hox genes and related diseases.
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Affiliation(s)
- Hongjie Wang
- International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai 201306, China
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai 201306, China
| | - Jingwei He
- International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai 201306, China
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai 201306, China
| | - Xuemei Han
- International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai 201306, China
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai 201306, China
| | - Xiuzhi Wu
- International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai 201306, China
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai 201306, China
| | - Xuebin Ye
- International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai 201306, China
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai 201306, China
- Marine Biomedical Science and Technology Innovation Platform of Lin-gang Special Area, Shanghai 201306, China
| | - Wenchao Lv
- International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai 201306, China
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai 201306, China
| | - Yao Zu
- International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai 201306, China
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai 201306, China
- Marine Biomedical Science and Technology Innovation Platform of Lin-gang Special Area, Shanghai 201306, China
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Wu RX, Miao BB, Han FY, Niu SF, Liang YS, Liang ZB, Wang QH. Chromosome-Level Genome Assembly Provides Insights into the Evolution of the Special Morphology and Behaviour of Lepturacanthus savala. Genes (Basel) 2023; 14:1268. [PMID: 37372448 DOI: 10.3390/genes14061268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 06/13/2023] [Accepted: 06/13/2023] [Indexed: 06/29/2023] Open
Abstract
Savalani hairtail Lepturacanthus savala is a widely distributed fish along the Indo-Western Pacific coast, and contributes substantially to trichiurid fishery resources worldwide. In this study, the first chromosome-level genome assembly of L. savala was obtained by PacBio SMRT-Seq, Illumina HiSeq, and Hi-C technologies. The final assembled L. savala genome was 790.02 Mb with contig N50 and scaffold N50 values of 19.01 Mb and 32.77 Mb, respectively. The assembled sequences were anchored to 24 chromosomes by using Hi-C data. Combined with RNA sequencing data, 23,625 protein-coding genes were predicted, of which 96.0% were successfully annotated. In total, 67 gene family expansions and 93 gene family contractions were detected in the L. savala genome. Additionally, 1825 positively selected genes were identified. Based on a comparative genomic analysis, we screened a number of candidate genes associated with the specific morphology, behaviour-related immune system, and DNA repair mechanisms in L. savala. Our results preliminarily revealed mechanisms underlying the special morphological and behavioural characteristics of L. savala from a genomic perspective. Furthermore, this study provides valuable reference data for subsequent molecular ecology studies of L. savala and whole-genome analyses of other trichiurid fishes.
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Affiliation(s)
- Ren-Xie Wu
- College of Fisheries, Guangdong Ocean University, Zhanjiang 524088, China
| | - Ben-Ben Miao
- College of Fisheries, Guangdong Ocean University, Zhanjiang 524088, China
| | - Fang-Yuan Han
- College of Fisheries, Guangdong Ocean University, Zhanjiang 524088, China
| | - Su-Fang Niu
- College of Fisheries, Guangdong Ocean University, Zhanjiang 524088, China
| | - Yan-Shan Liang
- College of Fisheries, Guangdong Ocean University, Zhanjiang 524088, China
| | - Zhen-Bang Liang
- College of Fisheries, Guangdong Ocean University, Zhanjiang 524088, China
| | - Qing-Hua Wang
- College of Fisheries, Guangdong Ocean University, Zhanjiang 524088, China
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Chen HI, Turakhia Y, Bejerano G, Kingsley DM. Whole-genome comparisons identify repeated regulatory changes underlying convergent appendage evolution in diverse fish lineages. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.30.526059. [PMID: 36778215 PMCID: PMC9915506 DOI: 10.1101/2023.01.30.526059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Fins are major functional appendages of fish that have been repeatedly modified in different lineages. To search for genomic changes underlying natural fin diversity, we compared the genomes of 36 wild fish species that either have complete or reduced pelvic and caudal fins. We identify 1,614 genomic regions that are well-conserved in fin-complete species but missing from multiple fin-reduced lineages. Recurrent deletions of conserved sequences (CONDELs) in wild fin-reduced species are enriched for functions related to appendage development, suggesting that convergent fin reduction at the organismal level is associated with repeated genomic deletions near fin-appendage development genes. We used sequencing and functional enhancer assays to confirm that PelA , a Pitx1 enhancer previously linked to recurrent pelvic loss in sticklebacks, has also been independently deleted and may have contributed to the fin morphology in distantly related pelvic-reduced species. We also identify a novel enhancer that is conserved in the majority of percomorphs, drives caudal fin expression in transgenic stickleback, is missing in tetraodontiform, s yngnathid, and synbranchid species with caudal fin reduction, and which alters caudal fin development when targeted by genome editing. Our study illustrates a general strategy for mapping phenotypes to genotypes across a tree of vertebrate species, and highlights notable new examples of regulatory genomic hotspots that have been used to evolve recurrent phenotypes during 100 million years of fish evolution.
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Affiliation(s)
- Heidi I. Chen
- Department of Developmental Biology, Stanford University School of Medicine, CA
| | - Yatish Turakhia
- Department of Electrical and Computer Engineering, University of California, San Diego, San Diego, CA
| | - Gill Bejerano
- Department of Developmental Biology, Stanford University School of Medicine, CA
- Department of Biomedical Data Science, Stanford University School of Medicine, CA
- Department of Computer Science, Stanford University School of Engineering, CA
- Department of Pediatrics, Stanford University School of Medicine, CA
| | - David M. Kingsley
- Department of Developmental Biology, Stanford University School of Medicine, CA
- Howard Hughes Medical Institute, Stanford University, CA
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Evolutionary analysis of swimming speed in early vertebrates challenges the 'New Head Hypothesis'. Commun Biol 2022; 5:863. [PMID: 36002583 PMCID: PMC9402584 DOI: 10.1038/s42003-022-03730-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 07/15/2022] [Indexed: 12/05/2022] Open
Abstract
The ecological context of early vertebrate evolution is envisaged as a long-term trend towards increasingly active food acquisition and enhanced locomotory capabilities culminating in the emergence of jawed vertebrates. However, support for this hypothesis has been anecdotal and drawn almost exclusively from the ecology of living taxa, despite knowledge of extinct phylogenetic intermediates that can inform our understanding of this formative episode. Here we analyse the evolution of swimming speed in early vertebrates based on caudal fin morphology using ancestral state reconstruction and evolutionary model fitting. We predict the lowest and highest ancestral swimming speeds in jawed vertebrates and microsquamous jawless vertebrates, respectively, and find complex patterns of swimming speed evolution with no support for a trend towards more active lifestyles in the lineage leading to jawed groups. Our results challenge the hypothesis of an escalation of Palaeozoic marine ecosystems and shed light into the factors that determined the disparate palaeobiogeographic patterns of microsquamous versus macrosquamous armoured Palaeozoic jawless vertebrates. Ultimately, our results offer a new enriched perspective on the ecological context that underpinned the assembly of vertebrate and gnathostome body plans, supporting a more complex scenario characterized by diverse evolutionary locomotory capabilities reflecting their equally diverse ecologies.
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Desvignes T, Robbins AE, Carey AZ, Bailon-Zambrano R, Nichols JT, Postlethwait JH, Stankunas K. Coordinated patterning of zebrafish caudal fin symmetry by a central and two peripheral organizers. Dev Dyn 2022; 251:1306-1321. [PMID: 35403297 PMCID: PMC9357109 DOI: 10.1002/dvdy.475] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 03/17/2022] [Accepted: 04/03/2022] [Indexed: 11/07/2022] Open
Abstract
BACKGROUND Caudal fin symmetry characterizes teleosts and likely contributes to their evolutionary success. However, the coordinated development and patterning of skeletal elements establishing external symmetry remains incompletely understood. We explore the spatiotemporal emergence of caudal skeletal elements in zebrafish to consider evolutionary and developmental origins of caudal fin symmetry. RESULTS Transgenic reporters and skeletal staining reveal that the hypural diastema-defining gap between hypurals 2 and 3 forms early and separates progenitors of two plates of connective tissue. Two sets of central principal rays (CPRs) synchronously, sequentially, and symmetrically emerge around the diastema. The two dorsal- and ventral-most rays (peripheral principal rays, PPRs) arise independently and earlier than adjacent CPRs. Muscle and tendon markers reveal that different muscles attach to CPR and PPR sets. CONCLUSIONS We propose that caudal fin symmetry originates from a central organizer that establishes the hypural diastema and bidirectionally patterns surrounding tissue into two plates of connective tissue and two mirrored sets of CPRs. Further, two peripheral organizers unidirectionally specify PPRs, forming a symmetric "composite" fin derived from three fields. Distinct CPR and PPR ontogenies may represent developmental modules conferring ray identities, muscle connections, and biomechanical properties. Our model contextualizes mechanistic studies of teleost fin morphological variation.
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Affiliation(s)
- Thomas Desvignes
- Institute of Neuroscience, University of Oregon, Eugene OR 97403, USA
| | - Amy E. Robbins
- Institute of Molecular Biology, University of Oregon, Eugene OR 97403, USA
| | - Andrew Z. Carey
- Institute of Neuroscience, University of Oregon, Eugene OR 97403, USA
| | - Raisa Bailon-Zambrano
- Department of Craniofacial Biology, University of Colorado Anschutz Medical Campus, Aurora CO 80045, USA
| | - James T. Nichols
- Department of Craniofacial Biology, University of Colorado Anschutz Medical Campus, Aurora CO 80045, USA
| | | | - Kryn Stankunas
- Institute of Molecular Biology, University of Oregon, Eugene OR 97403, USA
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Schwaner MJ, Hsieh ST, Swalla BJ, McGowan CP. An introduction to an evolutionary tail: EvoDevo, structure and function of post-anal appendages. Integr Comp Biol 2021; 61:352-357. [PMID: 34124748 DOI: 10.1093/icb/icab134] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Although tails are common and versatile appendages that contribute to evolutionary success of animals in a broad range of ways, a scientific synthesis on the topic had yet to be initiated. For our Society for Integrative and Comparative Biology (SICB) symposium we brought together researchers from different areas of expertise (e.g., robotosists, biomechanists, functional morphologists, and evolutionary and developmental biologists), to highlight their research but also to emphasize the interdisciplinary nature of this topic. The four main themes that emerged based on the research presented in this symposium are: 1) How do we define a tail? 2) Development and regeneration inform evolutionary origins of tails, 3) Identifying key characteristics highlights functional morphology of tails, 4) Tail multi-functionality leads to the development of bioinspired technology. We discuss the research provided within this symposium, in light of these four themes. We showcase the broad diversity of current tail research and lay an important foundational framework for future interdisciplinary research on tails with this timely symposium.
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Affiliation(s)
- M J Schwaner
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA, USA
| | - S T Hsieh
- Department of Biology, Temple University, Philadelphia, PA, USA
| | - B J Swalla
- Department of Biology, University of Washington, Seattle, WA, USA
| | - C P McGowan
- Department of Integrative Anatomical Sciences, University of Southern California, Los Angeles, CA, USA
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