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Gene Regulation during Carapacial Ridge Development of Mauremys reevesii: The Development of Carapacial Ridge, Ribs and Scutes. Genes (Basel) 2022; 13:genes13091676. [PMID: 36140843 PMCID: PMC9498798 DOI: 10.3390/genes13091676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 08/26/2022] [Accepted: 09/14/2022] [Indexed: 11/17/2022] Open
Abstract
The unique topological structure of a turtle shell, including the special ribs-scapula relationship, is an evolutionarily novelty of amniotes. The carapacial ridge is a key embryonic tissue for inducing turtle carapace morphologenesis. However, the gene expression profiles and molecular regulatory mechanisms that occur during carapacial ridge development, including the regulation mechanism of rib axis arrest, the development mechanism of the carapacial ridge, and the differentiation between soft-shell turtles and hard-shell turtles, are not fully understood. In this study, we obtained genome-wide gene expression profiles during the carapacial ridge development of Mauremys reevesii using RNA-sequencing by using carapacial ridge tissues from stage 14, 15 and 16 turtle embryos. In addition, a differentially expressed genes (DEGs) analysis and a gene set enrichment analysis (GSEA) of three comparison groups were performed. Furthermore, a Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis was used to analyze the pathway enrichment of the differentially expressed genes of the three comparative groups. The result displayed that the Wnt signaling pathway was substantially enriched in the CrTK14 vs. the CrTK15 comparison group, while the Hedgehog signaling pathway was significantly enriched in the CrTK15 vs. the CrTK16 group. Moreover, the regulatory network of the Wnt signaling pathway showed that Wnt signaling pathways might interact with Fgfs, Bmps, and Shh to form a regulatory network to regulate the carapacial ridge development. Next, WGCNA was used to cluster and analyze the expression genes during the carapacial ridge development of M. reevesii and P. sinensis. Further, a KEGG functional enrichment analysis of the carapacial ridge correlation gene modules was performed. Interesting, these results indicated that the Wnt signaling pathway and the MAPK signaling pathway were significantly enriched in the gene modules that were highly correlated with the stage 14 and stage 15 carapacial ridge samples of the two species. The Hedgehog signaling pathway was significantly enriched in the modules that were strongly correlated with the stage 16 carapacial ridge samples of M. reevesii, however, the PI3K-Akt signaling and the TGF-β signaling pathways were significantly enriched in the modules that were strongly correlated with the stage 16 carapacial ridge samples of P. sinensis. Furthermore, we found that those modules that were strongly correlated with the stage 14 carapacial ridge samples of M. reevesii and P. sinensis contained Wnts and Lef1. While the navajo white 3 module which was strongly correlated with the stage 16 carapacial ridge samples of M. reevesii contained Shh and Ptchs. The dark green module strongly correlated with the stage 16 carapacial ridge samples of P. sinensis which contained Col1a1, Col1a2, and Itga8. Consequently, this study systematically revealed the signaling pathways and genes that regulate the carapacial ridge development of M. reevesii and P. sinensis, which provides new insights for revealing the molecular mechanism that is underlying the turtle's body structure.
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Klembara J, Ruta M, Hain M, Berman DS. Braincase and Inner Ear Anatomy of the Late Carboniferous Tetrapod Limnoscelis dynatis (Diadectomorpha) Revealed by High-Resolution X-ray Microcomputed Tomography. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.709766] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
The braincase anatomy of the Pennsylvanian diadectomorph Limnoscelis dynatis is described in detail, based upon high-resolution X-ray microcomputed tomography. Both supraoccipitals and most of the prootics and opisthotics are preserved. The known portions of the left prootic, opisthotic, and supraoccipital enclose complete sections of the endosseous labyrinth, including the anterior, posterior, and lateral semicircular canals, the vestibule, the cochlear recess, and the canal for the endolymphatic duct. The fossa subarcuata is visible anteromedial to the anterior semicircular canal. The presumed endolymphatic fossae occur in the dorsal wall of the posteromedial portion of the supraoccipital. Both the fossa subarcuata and the fossa endolymphatica lie in the cerebellar portion of the cranial cavity. In order to investigate the phylogenetic position of L. dynatis we used a recently published data matrix, including characters of the braincase, and subjected it to maximum parsimony analyses under a variety of character weighting schemes and to a Bayesian analysis. Limnoscelis dynatis emerges as sister taxon to L. paludis, and both species form the sister group to remaining diadectomorphs. Synapsids and diadectomorphs are resolved as sister clades in ∼90% of all the most parsimonious trees from the unweighted analysis, in the single trees from both the reweighted and the implied weights analyses, as well in the Bayesian tree.
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Lyson TR, Bever GS. Origin and Evolution of the Turtle Body Plan. ANNUAL REVIEW OF ECOLOGY, EVOLUTION, AND SYSTEMATICS 2020. [DOI: 10.1146/annurev-ecolsys-110218-024746] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The origin of turtles and their uniquely shelled body plan is one of the longest standing problems in vertebrate biology. The unfulfilled need for a hypothesis that both explains the derived nature of turtle anatomy and resolves their unclear phylogenetic position among reptiles largely reflects the absence of a transitional fossil record. Recent discoveries have dramatically improved this situation, providing an integrated, time-calibrated model of the morphological, developmental, and ecological transformations responsible for the modern turtle body plan. This evolutionary trajectory was initiated in the Permian (>260 million years ago) when a turtle ancestor with a diapsid skull evolved a novel mechanism for lung ventilation. This key innovation permitted the torso to become apomorphically stiff, most likely as an adaption for digging and a fossorial ecology. The construction of the modern turtle body plan then proceeded over the next 100 million years following a largely stepwise model of osteological innovation.
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Affiliation(s)
- Tyler R. Lyson
- Department of Earth Sciences, Denver Museum of Nature & Science, Denver, Colorado 80205, USA
| | - Gabriel S. Bever
- Department of Earth Sciences, Denver Museum of Nature & Science, Denver, Colorado 80205, USA
- Center for Functional Anatomy and Evolution, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
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Kadota M, Nishimura O, Miura H, Tanaka K, Hiratani I, Kuraku S. Multifaceted Hi-C benchmarking: what makes a difference in chromosome-scale genome scaffolding? Gigascience 2020; 9:5695848. [PMID: 31919520 PMCID: PMC6952475 DOI: 10.1093/gigascience/giz158] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Revised: 10/23/2019] [Accepted: 12/02/2019] [Indexed: 12/28/2022] Open
Abstract
Background Hi-C is derived from chromosome conformation capture (3C) and targets chromatin contacts on a genomic scale. This method has also been used frequently in scaffolding nucleotide sequences obtained by de novo genome sequencing and assembly, in which the number of resultant sequences rarely converges to the chromosome number. Despite its prevalent use, the sample preparation methods for Hi-C have not been intensively discussed, especially from the standpoint of genome scaffolding. Results To gain insight into the best practice of Hi-C scaffolding, we performed a multifaceted methodological comparison using vertebrate samples and optimized various factors during sample preparation, sequencing, and computation. As a result, we identified several key factors that helped improve Hi-C scaffolding, including the choice and preparation of tissues, library preparation conditions, the choice of restriction enzyme(s), and the choice of scaffolding program and its usage. Conclusions This study provides the first comparison of multiple sample preparation kits/protocols and computational programs for Hi-C scaffolding by an academic third party. We introduce a customized protocol designated “inexpensive and controllable Hi-C (iconHi-C) protocol,” which incorporates the optimal conditions identified in this study, and demonstrate this technique on chromosome-scale genome sequences of the Chinese softshell turtle Pelodiscus sinensis.
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Affiliation(s)
- Mitsutaka Kadota
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research (BDR), Kobe 650-0047, Japan
| | - Osamu Nishimura
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research (BDR), Kobe 650-0047, Japan
| | - Hisashi Miura
- Laboratory for Developmental Epigenetics, RIKEN BDR, Kobe 650-0047, Japan
| | - Kaori Tanaka
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research (BDR), Kobe 650-0047, Japan
| | - Ichiro Hiratani
- Laboratory for Developmental Epigenetics, RIKEN BDR, Kobe 650-0047, Japan
| | - Shigehiro Kuraku
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research (BDR), Kobe 650-0047, Japan
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5
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Cordero GA. Transcriptomic similarities and differences between the limb bud AER and unique carapacial ridge of turtle embryos. Evol Dev 2020; 22:370-383. [PMID: 32862496 DOI: 10.1111/ede.12351] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Revised: 07/10/2020] [Accepted: 08/02/2020] [Indexed: 01/04/2023]
Abstract
Evolutionary innovation may arise via major departures from an ancestral condition. Turtle shell morphogenesis depends on a unique structure known as the carapacial ridge (CR). This lateral tissue protrusion in turtle embryos exhibits similar properties as the apical ectodermal ridge (AER)-a well-known molecular signaling center involved in limb development. Still, how the CR influences shell morphogenesis is not entirely clear. The present study aimed to describe the CR transcriptome shortly before ribs were halted within its mesenchyme, as required for shell development. Analyses exposed that the mesenchymal marker VIM was one of the most highly co-expressed genes and numerous appendage formation genes were situated within the core of CR and AER co-expression networks. However, there were tissue-specific differences in the activity of these genes. For instance, WNT5A was most frequently assigned to appendage-related annotations of the CR network core, but not in the AER. Several homeobox transcription factors known to regulate limb bud patterning exhibited their highest expression levels in the AER, but were underexpressed in the CR. The results of this study corroborate that novel body plans often originate via alterations of pre-existing genetic networks. Altogether, this exploratory study enhances the groundwork for future experiments on the molecular underpinnings of turtle shell development and evolution.
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Affiliation(s)
- Gerardo A Cordero
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, Iowa, USA
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Smith Paredes D, Lord A, Meyer D, Bhullar BS. A developmental staging system and musculoskeletal development sequence of the common musk turtle (
Sternotherus odoratus
). Dev Dyn 2020; 250:111-127. [DOI: 10.1002/dvdy.210] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 05/24/2020] [Indexed: 01/02/2023] Open
Affiliation(s)
- Daniel Smith Paredes
- Department of Earth and Planetary Science, Peabody Museum of Natural History Yale University New Haven Connecticut USA
| | - Arianna Lord
- Department of Earth and Planetary Science, Peabody Museum of Natural History Yale University New Haven Connecticut USA
| | - Dalton Meyer
- Department of Earth and Planetary Science, Peabody Museum of Natural History Yale University New Haven Connecticut USA
| | - Bhart‐Anjan S. Bhullar
- Department of Earth and Planetary Science, Peabody Museum of Natural History Yale University New Haven Connecticut USA
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Clark-Hachtel CM, Tomoyasu Y. Two sets of candidate crustacean wing homologues and their implication for the origin of insect wings. Nat Ecol Evol 2020; 4:1694-1702. [PMID: 32747770 DOI: 10.1038/s41559-020-1257-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2019] [Accepted: 06/24/2020] [Indexed: 12/24/2022]
Abstract
The origin of insect wings is a biological mystery that has fascinated scientists for centuries. Identification of tissues homologous to insect wings from lineages outside of Insecta will provide pivotal information to resolve this conundrum. Here, through expression and clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated protein 9 (Cas9) functional analyses in Parhyale, we show that a gene network similar to the insect wing gene network (preWGN) operates both in the crustacean terga and in the proximal leg segments, suggesting that the evolution of a preWGN precedes the emergence of insect wings, and that from an evo-devo perspective, both of these tissues qualify as potential crustacean wing homologues. Combining these results with recent wing origin studies in insects, we discuss the possibility that both tissues are crustacean wing homologues, which supports a dual evolutionary origin of insect wings (that is, novelty through a merger of two distinct tissues). These outcomes have a crucial impact on the course of the intellectual battle between the two historically competing wing origin hypotheses.
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Affiliation(s)
- Courtney M Clark-Hachtel
- Department of Biology, Miami University, Oxford, OH, USA.,Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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Buskell A. Synthesising arguments and the extended evolutionary synthesis. STUDIES IN HISTORY AND PHILOSOPHY OF BIOLOGICAL AND BIOMEDICAL SCIENCES 2020; 80:101244. [PMID: 31917083 DOI: 10.1016/j.shpsc.2019.101244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 12/18/2019] [Accepted: 12/27/2019] [Indexed: 06/10/2023]
Abstract
Synthesising arguments motivate changes to the conceptual tools, theoretical structure, and evaluatory framework employed in a given scientific domain. Recently, a broad coalition of researchers has put forward a synthesising argument in favour of an Extended Evolutionary Synthesis ('EES'). Often this synthesising argument is evaluated using a virtue-based approach, which construes the EES as a wholesale alternative to prevailing practice. Here I argue this virtue-based approach is not fit for purpose. Taking the central concept of niche construction as a case study, I show that an agenda-based approach better captures the pragmatic and epistemological goals of the EES synthesising argument and diagnoses areas of empirical disagreement with prevailing practice.
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Affiliation(s)
- Andrew Buskell
- Department of History and Philosophy of Science, Free School Lane, University of Cambridge, Cambridge, CB2 3RH, UK.
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Fu J, Chen S, Zhao X, Luo Z, Zou P, Liu Y. Identification and characterization of the interferon-γ-inducible lysosomal thiol reductase gene in Chinese soft-shelled turtle, Pelodiscus sinensis. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2019; 90:55-59. [PMID: 30172908 DOI: 10.1016/j.dci.2018.08.019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2018] [Revised: 08/29/2018] [Accepted: 08/29/2018] [Indexed: 06/08/2023]
Abstract
The reduction of disulfide bonds of exogenous antigens is crucial to the MHC-II class antigen processing and presenting pathway and is catalysed by interferon-γ-inducible lysosomal thiol reductase (GILT). In this study, a reptile GILT gene from Chinese soft-shelled turtle, Pelodiscus sinensis (PsGILT), was identified. The full-length cDNA of PsGILT is 1631 nucleotides (nt), including a 5'-untranslated region (UTR) of 3 nt, a 3'-UTR of 860 nt and an open reading frame (ORF) of 768 nt encoding 255 amino acids (aa). The conserved features in known GILTs, such as signal peptide, CXXC motif, GILT signature sequence, N-glycosylation site and conserved cysteines, were all found in the putative PsGILT protein. Genomic analysis revealed that PsGILT kept the "7 exons and 6 introns" structure of vertebrate GILT genes. PsGILT was expressed in all examined organs/tissues and was mainly expressed in spleen and blood. Increased mRNA expression levels of PsIFN-γ and PsGILT in PBLs were observed after induction with LPS, PolyI:C and recombinant IFN-γ (rIFN-γ). We also tested the reductase activity of rGILT in vitro and found that it could reduce intact human IgG into H chains and L chains. These above results implied that PsGILT may play an important role in resisting bacterial and viral infections, like other vertebrate GILTs.
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Affiliation(s)
- Jianping Fu
- College of Life Sciences, Jiangxi Normal University, 99 Ziyang Road, Nanchang, Jiangxi Province, 330022, China
| | - Shannan Chen
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei Province, 430072, China
| | - Xin Zhao
- College of Life Sciences, Jiangxi Normal University, 99 Ziyang Road, Nanchang, Jiangxi Province, 330022, China
| | - Zhang Luo
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei Province, 430072, China
| | - Pengfei Zou
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei Province, 430072, China
| | - Yi Liu
- College of Life Sciences, Jiangxi Normal University, 99 Ziyang Road, Nanchang, Jiangxi Province, 330022, China.
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Evolution, Diversity, and Development of the Craniocervical System in Turtles with Special Reference to Jaw Musculature. HEADS, JAWS, AND MUSCLES 2019. [DOI: 10.1007/978-3-319-93560-7_8] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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11
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Abstract
Evolutionary theory has been extended almost continually since the evolutionary synthesis (ES), but except for the much greater importance afforded genetic drift, the principal tenets of the ES have been strongly supported. Adaptations are attributable to the sorting of genetic variation by natural selection, which remains the only known cause of increase in fitness. Mutations are not adaptively directed, but as principal authors of the ES recognized, the material (structural) bases of biochemistry and development affect the variety of phenotypic variations that arise by mutation and recombination. Against this historical background, I analyse major propositions in the movement for an 'extended evolutionary synthesis'. 'Niche construction' is a new label for a wide variety of well-known phenomena, many of which have been extensively studied, but (as with every topic in evolutionary biology) some aspects may have been understudied. There is no reason to consider it a neglected 'process' of evolution. The proposition that phenotypic plasticity may engender new adaptive phenotypes that are later genetically assimilated or accommodated is theoretically plausible; it may be most likely when the new phenotype is not truly novel, but is instead a slight extension of a reaction norm already shaped by natural selection in similar environments. However, evolution in new environments often compensates for maladaptive plastic phenotypic responses. The union of population genetic theory with mechanistic understanding of developmental processes enables more complete understanding by joining ultimate and proximate causation; but the latter does not replace or invalidate the former. Newly discovered molecular phenomena have been easily accommodated in the past by elaborating orthodox evolutionary theory, and it appears that the same holds today for phenomena such as epigenetic inheritance. In several of these areas, empirical evidence is needed to evaluate enthusiastic speculation. Evolutionary theory will continue to be extended, but there is no sign that it requires emendation.
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Affiliation(s)
- Douglas J. Futuyma
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY, USA
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12
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Jost J. Relations and dependencies between morphological characters. Theory Biosci 2017; 136:69-83. [PMID: 28569346 PMCID: PMC5486545 DOI: 10.1007/s12064-017-0248-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 05/10/2017] [Indexed: 12/03/2022]
Abstract
In biological classification, a character is a property of a taxon that can distinguish it from other taxa. Characters are not independent, and the relations between characters can arise from structural constraints, developmental pathways or functional constraints. That has lead to famous controversies in the history of biology. In addition, a character as a tool of data analysis has some subjective aspects. In this contribution, I develop algebraic and geometric schemes to address these issues in a mathematical framework.
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Affiliation(s)
- Jürgen Jost
- Max Planck Institute for Mathematics in the Sciences, Leipzig, Germany. .,Santa Fe Institute for the Sciences of Complexity, Santa Fe, New Mexico, USA.
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13
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Schmidt M, Mehlhorn M, Fischer MS. Shoulder girdle rotation, forelimb movement and the influence of carapace shape on locomotion in Testudo hermanni (Testudinidae). ACTA ACUST UNITED AC 2016; 219:2693-703. [PMID: 27340203 DOI: 10.1242/jeb.137059] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2016] [Accepted: 06/20/2016] [Indexed: 11/20/2022]
Abstract
Studies into the function of structures are crucial for making connections between morphology and behaviour of organisms, but are still rare for the terrestrial Testudinidae. We investigated the kinematics of shoulder girdle and forelimb motion in Hermann's tortoise Testudo hermanni using biplanar X-ray fluoroscopy with a twofold aim: firstly, to understand how the derived shapes of shoulder girdle and carapace together influence rotation of the girdle; and, secondly, to understand how girdle rotation affects forelimb excursion. The total degree of shoulder rotation in the horizontal plane is similar to a species with a less domed shell, but because of the long and nearly vertically oriented scapular prong, shoulder girdle rotation contributes more than 30% to the horizontal arc of the humerus and nearly 40% to the rotational component of step length. The antebrachium and manus, which act as a functional unit, contribute roughly 50% to this component of the step length because of their large excursion almost parallel to the mid-sagittal plane. This large excursion is the result of the complex interplay between humerus long-axis rotation, counter-rotation of the antebrachium, and elbow flexion and extension. A significant proportion of forelimb step length results from body translation that is due to the propulsive effect of the other limbs during their stance phases. Traits that are similar to other tortoises and terrestrial or semi-aquatic turtles are the overall slow walk because of a low stride frequency, and the lateral-sequence, diagonally coupled footfall pattern with high duty factors. Intraspecific variation of carapace shape and shoulder girdle dimensions has a corresponding effect on forelimb kinematics.
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Affiliation(s)
- Manuela Schmidt
- Institute of Systematic Zoology and Evolutionary Biology, Friedrich-Schiller-University Jena, Erbertstraße 1, Jena 07743, Germany
| | - Martin Mehlhorn
- Institute of Systematic Zoology and Evolutionary Biology, Friedrich-Schiller-University Jena, Erbertstraße 1, Jena 07743, Germany
| | - Martin S Fischer
- Institute of Systematic Zoology and Evolutionary Biology, Friedrich-Schiller-University Jena, Erbertstraße 1, Jena 07743, Germany
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Szczygielski T, Sulej T. Revision of the Triassic European turtlesProterochersisandMurrhardtia(Reptilia, Testudinata, Proterochersidae), with the description of new taxa from Poland and Germany. Zool J Linn Soc 2016. [DOI: 10.1111/zoj.12374] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Tomasz Szczygielski
- Institute of Palaeobiology; Polish Academy of Sciences; Twarda 51/55 00-818 Warsaw Poland
| | - Tomasz Sulej
- Institute of Palaeobiology; Polish Academy of Sciences; Twarda 51/55 00-818 Warsaw Poland
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15
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Moczek AP, Sears KE, Stollewerk A, Wittkopp PJ, Diggle P, Dworkin I, Ledon-Rettig C, Matus DQ, Roth S, Abouheif E, Brown FD, Chiu CH, Cohen CS, Tomaso AWD, Gilbert SF, Hall B, Love AC, Lyons DC, Sanger TJ, Smith J, Specht C, Vallejo-Marin M, Extavour CG. The significance and scope of evolutionary developmental biology: a vision for the 21st century. Evol Dev 2015; 17:198-219. [PMID: 25963198 DOI: 10.1111/ede.12125] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Evolutionary developmental biology (evo-devo) has undergone dramatic transformations since its emergence as a distinct discipline. This paper aims to highlight the scope, power, and future promise of evo-devo to transform and unify diverse aspects of biology. We articulate key questions at the core of eleven biological disciplines-from Evolution, Development, Paleontology, and Neurobiology to Cellular and Molecular Biology, Quantitative Genetics, Human Diseases, Ecology, Agriculture and Science Education, and lastly, Evolutionary Developmental Biology itself-and discuss why evo-devo is uniquely situated to substantially improve our ability to find meaningful answers to these fundamental questions. We posit that the tools, concepts, and ways of thinking developed by evo-devo have profound potential to advance, integrate, and unify biological sciences as well as inform policy decisions and illuminate science education. We look to the next generation of evolutionary developmental biologists to help shape this process as we confront the scientific challenges of the 21st century.
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Affiliation(s)
- Armin P Moczek
- Department of Biology, Indiana University, 915 East 3rd Street, Bloomington, IN 47405, USA
| | - Karen E Sears
- School of Integrative Biology and Institute for Genomic Biology, University of Illinois, 505 South Goodwin Avenue, Urbana, IL, 61801, USA
| | - Angelika Stollewerk
- School of Biological and Chemical Sciences, Queen Mary, University of London, Mile End Road, London, E1 4NS, UK
| | - Patricia J Wittkopp
- Department of Ecology and Evolutionary Biology, Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Pamela Diggle
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, 06269, USA
| | - Ian Dworkin
- Department of Biology, McMaster University, 1280 Main St. West Hamilton, Ontario, L8S 4K1, Canada
| | - Cristina Ledon-Rettig
- Department of Biology, Indiana University, 915 East 3rd Street, Bloomington, IN 47405, USA
| | - David Q Matus
- Department of Biochemistry and Cell Biology, Stony Brook University, 412 Life Sciences Building, Stony Brook, NY, 11794-5215, USA
| | - Siegfried Roth
- University of Cologne, Institute of Developmental Biology, Biocenter, Zülpicher Straße 47b, D-50674, Cologne, Germany
| | - Ehab Abouheif
- Department of Biology, McGill University, 1205 Avenue Docteur Penfield, Montréal Québec, H3A 1B1, Canada
| | - Federico D Brown
- Departamento de Zoologia, Instituto Biociências, Universidade de São Paulo, Rua do Matão, Travessa 14, no. 101, 05508-090, São Paulo, Brazil
| | - Chi-Hua Chiu
- Department of Biological Sciences, Kent State University, OH, USA
| | - C Sarah Cohen
- Biology Department, Romberg Tiburon Center for Environmental Studies, San Francisco State University, 3150 Paradise Drive, Tiburon, CA, 94920, USA
| | | | - Scott F Gilbert
- Department of Biology, Swarthmore College, Swarthmore, Pennsylvania 19081, USA and Biotechnology Institute, University of Helsinki, 00014, Helsinki, Finland
| | - Brian Hall
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, CA, B3H 4R2, USA
| | - Alan C Love
- Department of Philosophy, Minnesota Center for Philosophy of Science, University of Minnesota, USA
| | - Deirdre C Lyons
- Department of Biology, Duke University, Box 90338, Durham, NC, 27708, USA
| | - Thomas J Sanger
- Department of Molecular Genetics and Microbiology, University of Florida, P.O. Box 103610, Gainesville, FL, 32610, USA
| | - Joel Smith
- Marine Biological Laboratory, 7 MBL Street, Woods Hole, MA, 02543, USA
| | - Chelsea Specht
- Plant and Microbial Biology, Department of Integrative Biology, University and Jepson Herbaria, University of California, Berkeley, CA, USA
| | - Mario Vallejo-Marin
- Biological and Environmental Sciences, University of Stirling, FK9 4LA, Scotland, UK
| | - Cassandra G Extavour
- Department of Organismic and Evolutionary Biology, Department of Molecular and Cellular Biology, Harvard University, 16 Divinity Avenue, BioLabs 4103, Cambridge, MA, 02138, USA
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Nicholson DB, Holroyd PA, Benson RBJ, Barrett PM. Climate-mediated diversification of turtles in the Cretaceous. Nat Commun 2015; 6:7848. [PMID: 26234913 PMCID: PMC4532850 DOI: 10.1038/ncomms8848] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Accepted: 06/19/2015] [Indexed: 12/25/2022] Open
Abstract
Chelonians are ectothermic, with an extensive fossil record preserved in diverse palaeoenvironmental settings: consequently, they represent excellent models for investigating organismal response to long-term environmental change. We present the first Mesozoic chelonian taxic richness curve, subsampled to remove geological/collection biases, and demonstrate that their palaeolatitudinal distributions were climate mediated. At the Jurassic/Cretaceous transition, marine taxa exhibit minimal diversity change, whereas non-marine diversity increases. A Late Cretaceous peak in 'global' non-marine subsampled richness coincides with high palaeolatitude occurrences and the Cretaceous thermal maximum (CTM): however, this peak also records increased geographic sampling and is not recovered in continental-scale diversity patterns. Nevertheless, a model-detrended richness series (insensitive to geographic sampling) also recovers a Late Cretaceous peak, suggesting genuine geographic range expansion among non-marine turtles during the CTM. Increased Late Cretaceous diversity derives from intensive North American sampling, but subsampling indicates that Early Cretaceous European/Asian diversity may have exceeded that of Late Cretaceous North America.
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Affiliation(s)
- David B. Nicholson
- Department of Earth Sciences, The Natural History Museum, Cromwell Road, London, SW7 5BD, UK
| | - Patricia A. Holroyd
- Museum of Paleontology, University of California, 1101 Valley Life Sciences Building, Berkeley, California 94720, USA
| | - Roger B. J. Benson
- Department of Earth Sciences, University of Oxford, South Parks Road, Oxford OX1 3AN, UK
| | - Paul M. Barrett
- Department of Earth Sciences, The Natural History Museum, Cromwell Road, London, SW7 5BD, UK
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Joyce WG. The origin of turtles: a paleontological perspective. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2015; 324:181-93. [PMID: 25712176 DOI: 10.1002/jez.b.22609] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2014] [Accepted: 10/27/2014] [Indexed: 11/10/2022]
Abstract
The origin of turtles and their unusual body plan has fascinated scientists for the last two centuries. Over the course of the last decades, a broad sample of molecular analyses have favored a sister group relationship of turtles with archosaurs, but recent studies reveal that this signal may be the result of systematic biases affecting molecular approaches, in particular sampling, non-randomly distributed rate heterogeneity among taxa, and the use of concatenated data sets. Morphological studies, by contrast, disfavor archosaurian relationships for turtles, but the proposed alternative topologies are poorly supported as well. The recently revived paleontological hypothesis that the Middle Permian Eunotosaurus africanus is an intermediate stem turtle is now robustly supported by numerous characters that were previously thought to be unique to turtles and that are now shown to have originated over the course of tens of millions of years unrelated to the origin of the turtle shell. Although E. africanus does not solve the placement of turtles within Amniota, it successfully extends the stem lineage of turtles to the Permian and helps resolve some questions associated with the origin of turtles, in particular the non-composite origin of the shell, the slow origin of the shell, and the terrestrial setting for the origin of turtles.
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Affiliation(s)
- Walter G Joyce
- Department of Geoscience, University of Fribourg, Fribourg, Switzerland
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Rice R, Riccio P, Gilbert SF, Cebra-Thomas J. Emerging from the rib: resolving the turtle controversies. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2015; 324:208-20. [PMID: 25675951 DOI: 10.1002/jez.b.22600] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2014] [Accepted: 09/29/2014] [Indexed: 12/15/2022]
Abstract
Two of the major controversies in the present study of turtle shell development involve the mechanism by which the carapacial ridge initiates shell formation and the mechanism by which each rib forms the costal bones adjacent to it. This paper claims that both sides of each debate might be correct-but within the species examined. Mechanism is more properly "mechanisms," and there is more than one single way to initiate carapace formation and to form the costal bones. In the initiation of the shell, the rib precursors may be kept dorsal by either "axial displacement" (in the hard-shell turtles) or "axial arrest" (in the soft-shell turtle Pelodiscus), or by a combination of these. The former process would deflect the rib into the dorsal dermis and allow it to continue its growth there, while the latter process would truncate rib growth. In both instances, though, the result is to keep the ribs from extending into the ventral body wall. Our recent work has shown that the properties of the carapacial ridge, a key evolutionary innovation of turtles, differ greatly between these two groups. Similarly, the mechanism of costal bone formation may differ between soft-shell and hard-shell turtles, in that the hard-shell species may have both periosteal flattening as well as dermal bone induction, while the soft-shelled turtles may have only the first of these processes.
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Affiliation(s)
- Ritva Rice
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
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Moustakas-Verho JE, Zimm R, Cebra-Thomas J, Lempiäinen NK, Kallonen A, Mitchell KL, Hämäläinen K, Salazar-Ciudad I, Jernvall J, Gilbert SF. The origin and loss of periodic patterning in the turtle shell. Development 2014; 141:3033-9. [DOI: 10.1242/dev.109041] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The origin of the turtle shell over 200 million years ago greatly modified the amniote body plan, and the morphological plasticity of the shell has promoted the adaptive radiation of turtles. The shell, comprising a dorsal carapace and a ventral plastron, is a layered structure formed by basal endochondral axial skeletal elements (ribs, vertebrae) and plates of bone, which are overlain by keratinous ectodermal scutes. Studies of turtle development have mostly focused on the bones of the shell; however, the genetic regulation of the epidermal scutes has not been investigated. Here, we show that scutes develop from an array of patterned placodes and that these placodes are absent from a soft-shelled turtle in which scutes were lost secondarily. Experimentally inhibiting Shh, Bmp or Fgf signaling results in the disruption of the placodal pattern. Finally, a computational model is used to show how two coupled reaction-diffusion systems reproduce both natural and abnormal variation in turtle scutes. Taken together, these placodal signaling centers are likely to represent developmental modules that are responsible for the evolution of scutes in turtles, and the regulation of these centers has allowed for the diversification of the turtle shell.
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Affiliation(s)
- Jacqueline E. Moustakas-Verho
- Developmental Biology Program, Institute of Biotechnology, University of Helsinki, P.O. Box 56, Helsinki FIN-00014, Finland
| | - Roland Zimm
- Developmental Biology Program, Institute of Biotechnology, University of Helsinki, P.O. Box 56, Helsinki FIN-00014, Finland
| | - Judith Cebra-Thomas
- Biology Department, Millersville University, P.O. Box 1002, Millersville, PA 17551, USA
| | - Netta K. Lempiäinen
- Developmental Biology Program, Institute of Biotechnology, University of Helsinki, P.O. Box 56, Helsinki FIN-00014, Finland
| | - Aki Kallonen
- Division of Materials Physics, Department of Physics, University of Helsinki, P.O. Box 64, Helsinki FIN-00014, Finland
| | - Katherine L. Mitchell
- Biology Department, Swarthmore College, 500 College Avenue, Swarthmore, PA 19081, USA
| | - Keijo Hämäläinen
- Division of Materials Physics, Department of Physics, University of Helsinki, P.O. Box 64, Helsinki FIN-00014, Finland
| | - Isaac Salazar-Ciudad
- Developmental Biology Program, Institute of Biotechnology, University of Helsinki, P.O. Box 56, Helsinki FIN-00014, Finland
- Departament de Genètica i Microbiologia, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Barcelona, Spain
| | - Jukka Jernvall
- Developmental Biology Program, Institute of Biotechnology, University of Helsinki, P.O. Box 56, Helsinki FIN-00014, Finland
| | - Scott F. Gilbert
- Developmental Biology Program, Institute of Biotechnology, University of Helsinki, P.O. Box 56, Helsinki FIN-00014, Finland
- Biology Department, Swarthmore College, 500 College Avenue, Swarthmore, PA 19081, USA
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Nagashima H, Sugahara F, Takechi M, Sato N, Kuratani S. On the homology of the shoulder girdle in turtles. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2014; 324:244-54. [PMID: 25052382 DOI: 10.1002/jez.b.22584] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2014] [Revised: 04/30/2014] [Accepted: 06/16/2014] [Indexed: 12/15/2022]
Abstract
The shoulder girdle in turtles is encapsulated in the shell and has a triradiate morphology. Due to its unique configuration among amniotes, many theories have been proposed about the skeletal identities of the projections for the past two centuries. Although the dorsal ramus represents the scapular blade, the ventral two rami remain uncertain. In particular, the ventrorostral process has been compared to a clavicle, an acromion, and a procoracoid based on its morphology, its connectivity to the rest of the skeleton and to muscles, as well as with its ossification center, cell lineage, and gene expression. In making these comparisons, the shoulder girdle skeleton of anurans has often been used as a reference. This review traces the history of the debate on the homology of the shoulder girdle in turtles. And based on the integrative aspects of developmental biology, comparative morphology, and paleontology, we suggest acromion and procoracoid identities for the two ventral processes.
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Affiliation(s)
- Hiroshi Nagashima
- Division of Gross Anatomy and Morphogenesis, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
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21
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Nagashima H, Shibata M, Taniguchi M, Ueno S, Kamezaki N, Sato N. Comparative study of the shell development of hard- and soft-shelled turtles. J Anat 2014; 225:60-70. [PMID: 24754673 PMCID: PMC4089346 DOI: 10.1111/joa.12189] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/18/2014] [Indexed: 12/23/2022] Open
Abstract
The turtle shell provides a fascinating model for the investigation of the evolutionary modifications of developmental mechanisms. Different conclusions have been put forth for its development, and it is suggested that one of the causes of the disagreement could be the differences in the species of the turtles used - the differences between hard-shelled turtles and soft-shelled turtles. To elucidate the cause of the difference, we compared the turtle shell development in the two groups of turtle. In the dorsal shell development, these two turtle groups shared the gene expression profile that is required for formation, and shared similar spatial organization of the anatomical elements during development. Thus, both turtles formed the dorsal shell through a folding of the lateral body wall, and the Wnt signaling pathway appears to have been involved in the development. The ventral portion of the shell, on the other hand, contains massive dermal bones. Although expression of HNK-1 epitope has suggested that the trunk neural crest contributed to the dermal bones in the hard-shelled turtles, it was not expressed in the initial anlage of the skeletons in either of the types of turtle. Hence, no evidence was found that would support a neural crest origin.
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Affiliation(s)
- Hiroshi Nagashima
- Division of Gross Anatomy and Morphogenesis, Niigata University Graduate School of Medical and Dental SciencesNiigata, Japan
| | - Masahiro Shibata
- Division of Gross Anatomy and Morphogenesis, Niigata University Graduate School of Medical and Dental SciencesNiigata, Japan
| | - Mari Taniguchi
- Suma Aqualife ParkKobe, Japan
- Sea Turtle Association of JapanHirakata, Japan
| | - Shintaro Ueno
- Suma Aqualife ParkKobe, Japan
- Sea Turtle Association of JapanHirakata, Japan
| | - Naoki Kamezaki
- Suma Aqualife ParkKobe, Japan
- Sea Turtle Association of JapanHirakata, Japan
| | - Noboru Sato
- Division of Gross Anatomy and Morphogenesis, Niigata University Graduate School of Medical and Dental SciencesNiigata, Japan
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22
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Hirasawa T, Pascual-Anaya J, Kamezaki N, Taniguchi M, Mine K, Kuratani S. The evolutionary origin of the turtle shell and its dependence on the axial arrest of the embryonic rib cage. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2014; 324:194-207. [PMID: 24898540 DOI: 10.1002/jez.b.22579] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Revised: 04/25/2014] [Accepted: 05/07/2014] [Indexed: 12/22/2022]
Abstract
Turtles are characterized by their possession of a shell with dorsal and ventral moieties: the carapace and the plastron, respectively. In this review, we try to provide answers to the question of the evolutionary origin of the carapace, by revising morphological, developmental, and paleontological comparative analyses. The turtle carapace is formed through modification of the thoracic ribs and vertebrae, which undergo extensive ossification to form a solid bony structure. Except for peripheral dermal elements, there are no signs of exoskeletal components ontogenetically added to the costal and neural bones, and thus the carapace is predominantly of endoskeletal nature. Due to the axial arrest of turtle rib growth, the axial part of the embryo expands laterally and the shoulder girdle becomes encapsulated in the rib cage, together with the inward folding of the lateral body wall in the late phase of embryogenesis. Along the line of this folding develops a ridge called the carapacial ridge (CR), a turtle-specific embryonic structure. The CR functions in the marginal growth of the carapacial primordium, in which Wnt signaling pathway might play a crucial role. Both paleontological and genomic evidence suggest that the axial arrest is the first step toward acquisition of the turtle body plan, which is estimated to have taken place after the divergence of a clade including turtles from archosaurs. The developmental relationship between the CR and the axial arrest remains a central issue to be solved in future.
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Affiliation(s)
- Tatsuya Hirasawa
- Laboratory for Evolutionary Morphology, RIKEN Center for Developmental Biology, Kobe, Japan
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23
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Fu JP, Chen SN, Zou PF, Huang B, Guo Z, Zeng LB, Qin QW, Nie P. IFN-γ in turtle: conservation in sequence and signalling and role in inhibiting iridovirus replication in Chinese soft-shelled turtle Pelodiscus sinensis. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2014; 43:87-95. [PMID: 24239708 DOI: 10.1016/j.dci.2013.11.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2013] [Revised: 11/03/2013] [Accepted: 11/03/2013] [Indexed: 06/02/2023]
Abstract
The IFN-γ gene was identified in a turtle, the Chinese soft-shelled turtle, Pelodiscus sinensis, with its genome consisting of 4 exons and 3 introns. The deduced amino acid sequence of this gene contains a signal peptide, an IFN-γ family signature motif (130)IQRKAVNELFPT, an NLS motif (155)KRKR and three potential N-glycosylation sites. As revealed by real-time quantitative PCR, the gene was constitutively expressed in all tested organs/tissues, with higher level observed in blood, intestine and thymus. An induced expression of IFN-γ at mRNA level was observed in peripheral blood leucocytes (PBLs) in response to in vitro stimulation of LPS and PolyI:C. The overexpression of IFN-γ in the Chinese soft-shelled turtle artery (STA) cell line resulted in the increase in the expression of transcriptional regulators, such as IRF1, IRF7 and STAT1, and antiviral genes, such as Mx, PKR, implying possibly the existence of a conserved signalling network and role for IFN-γ in the turtle. Furthermore, the infection of soft-shelled turtle iridovirus (STIV) in the cell line transfected with IFN-γ may cause the cell death as demonstrated with the elevated lactate dehydrogenase (LDH) level and cell mortality. However, the mechanism involved in the antiviral activity may require further investigation.
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Affiliation(s)
- Jian Ping Fu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei Province 430072, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shan Nan Chen
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei Province 430072, China
| | - Peng Fei Zou
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei Province 430072, China
| | - Bei Huang
- College of Fisheries, Jimei University, 43 Yindou Road, Xiamen, Fujian Province 361021, China
| | - Zheng Guo
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei Province 430072, China
| | - Ling Bing Zeng
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, Hubei Province 430223, China
| | - Qi Wei Qin
- Key Laboratory of Tropical Marine Bioresources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou, Guangdong Province 510301, China
| | - Pin Nie
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei Province 430072, China; College of Fisheries, Jimei University, 43 Yindou Road, Xiamen, Fujian Province 361021, China.
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Joyce WG, Schoch RR, Lyson TR. The girdles of the oldest fossil turtle, Proterochersis robusta, and the age of the turtle crown. BMC Evol Biol 2013; 13:266. [PMID: 24314094 PMCID: PMC4077068 DOI: 10.1186/1471-2148-13-266] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2013] [Accepted: 11/26/2013] [Indexed: 12/02/2022] Open
Abstract
Background Proterochersis robusta from the Late Triassic (Middle Norian) of Germany is the oldest known fossil turtle (i.e. amniote with a fully formed turtle shell), but little is known about its anatomy. A newly prepared, historic specimen provides novel insights into the morphology of the girdles and vertebral column of this taxon and the opportunity to reassess its phylogenetic position. Results The anatomy of the pectoral girdle of P. robusta is similar to that of other primitive turtles, including the Late Triassic (Carnian) Proganochelys quenstedti, in having a vertically oriented scapula, a large coracoid foramen, a short acromion process, and bony ridges that connect the acromion process with the dorsal process, glenoid, and coracoid, and by being able to rotate along a vertical axis. The pelvic elements are expanded distally and suturally attached to the shell, but in contrast to modern pleurodiran turtles the pelvis is associated with the sacral ribs. Conclusions The primary homology of the character “sutured pelvis” is unproblematic between P. robusta and extant pleurodires. However, integration of all new observations into the most complete phylogenetic analysis that support the pleurodiran nature of P. robusta reveals that this taxon is more parsimoniously placed along the phylogenetic stem of crown Testudines. All current phylogenetic hypotheses therefore support the basal placement of this taxon, imply that the sutured pelvis of this taxon developed independently from that of pleurodires, and conclude that the age of the turtle crown is Middle Jurassic.
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Affiliation(s)
- Walter G Joyce
- Department of Geosciences, University of Tübingen, Hölderlinstr, 12, 72074 Tübingen, Germany.
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25
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Cebra-Thomas JA, Terrell A, Branyan K, Shah S, Rice R, Gyi L, Yin M, Hu Y, Mangat G, Simonet J, Betters E, Gilbert SF. Late-emigrating trunk neural crest cells in turtle embryos generate an osteogenic ectomesenchyme in the plastron. Dev Dyn 2013; 242:1223-35. [PMID: 23904174 DOI: 10.1002/dvdy.24018] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2013] [Revised: 06/13/2013] [Accepted: 07/03/2013] [Indexed: 02/03/2023] Open
Abstract
BACKGROUND The turtle plastron is composed of a keratinized epidermis overlying nine dermal bones. Its developmental origin has been controversial; recent evidence suggests that the plastral bones derive from trunk neural crest cells (NCCs). RESULTS This study extends the observations that there is a turtle-specific, second wave of trunk NCC delamination and migration, after the original NCCs have reached their destination and differentiated. This second wave was confirmed by immunohistochemistry in whole-mounts and serial sections, by injecting DiI (1,1', di-octadecyl-3,3,3',3',-tetramethylindo-carbocyanine perchlorate) into the lumen of the neural tube and tracing labeled cells into the plastron, and by isolating neural tubes from older turtle embryos and observing delaminating NCCs. This later migration gives rise to a plastral ectomesenchyme that expresses NCC markers and can be induced to initiate bone formation. CONCLUSIONS The NCCs of this second migration have properties similar to those of the earlier NCCs, but also express markers characteristic of cranial NCCs. The majority of the cells of the plastron mesenchyme express neural crest markers, and have osteogenic differentiation capabilities that are similar or identical to craniofacial ectomesenchyme. Our evidence supports the contention that turtle plastron bones are derived from a late emigrating population of cells derived from the trunk neural crest.
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Tokita M, Chaeychomsri W, Siruntawineti J. Skeletal gene expression in the temporal region of the reptilian embryos: implications for the evolution of reptilian skull morphology. SPRINGERPLUS 2013; 2:336. [PMID: 24711977 PMCID: PMC3970585 DOI: 10.1186/2193-1801-2-336] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Accepted: 07/08/2013] [Indexed: 01/17/2023]
Abstract
Reptiles have achieved highly diverse morphological and physiological traits that allow them to exploit various ecological niches and resources. Morphology of the temporal region of the reptilian skull is highly diverse and historically it has been treated as an important character for classifying reptiles and has helped us understand the ecology and physiology of each species. However, the developmental mechanism that generates diversity of reptilian skull morphology is poorly understood. We reveal a potential developmental basis that generates morphological diversity in the temporal region of the reptilian skull by performing a comparative analysis of gene expression in the embryos of reptile species with different skull morphology. By investigating genes known to regulate early osteoblast development, we find dorsoventrally broadened unique expression of the early osteoblast marker, Runx2, in the temporal region of the head of turtle embryos that do not form temporal fenestrae. We also observe that Msx2 is also uniquely expressed in the mesenchymal cells distributed at the temporal region of the head of turtle embryos. Furthermore, through comparison of gene expression pattern in the embryos of turtle, crocodile, and snake species, we find a possible correlation between the spatial patterns of Runx2 and Msx2 expression in cranial mesenchymal cells and skull morphology of each reptilian lineage. Regulatory modifications of Runx2 and Msx2 expression in osteogenic mesenchymal precursor cells are likely involved in generating morphological diversity in the temporal region of the reptilian skull.
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Affiliation(s)
- Masayoshi Tokita
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tenno-dai 1-1-1, Tsukuba, Ibaraki, 305-8572 Japan ; Department of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138 USA
| | - Win Chaeychomsri
- Department of Zoology, Kasetsart University, 50 Ngam Wong Wan Road, Chatuchak, Bangkok, 10900 Thailand
| | - Jindawan Siruntawineti
- Department of Zoology, Kasetsart University, 50 Ngam Wong Wan Road, Chatuchak, Bangkok, 10900 Thailand
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27
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Evolutionary Origin of the Turtle Shell. Curr Biol 2013; 23:1113-9. [DOI: 10.1016/j.cub.2013.05.003] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2013] [Revised: 04/03/2013] [Accepted: 05/01/2013] [Indexed: 11/30/2022]
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The draft genomes of soft-shell turtle and green sea turtle yield insights into the development and evolution of the turtle-specific body plan. Nat Genet 2013; 45:701-706. [PMID: 23624526 PMCID: PMC4000948 DOI: 10.1038/ng.2615] [Citation(s) in RCA: 285] [Impact Index Per Article: 25.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2012] [Accepted: 03/27/2013] [Indexed: 12/23/2022]
Abstract
The unique anatomical features of turtles have raised unanswered questions about the origin of their unique body plan. We generated and analyzed draft genomes of the soft-shell turtle (Pelodiscus sinensis) and the green sea turtle (Chelonia mydas); our results indicated the close relationship of the turtles to the bird-crocodilian lineage, from which they split ∼267.9-248.3 million years ago (Upper Permian to Triassic). We also found extensive expansion of olfactory receptor genes in these turtles. Embryonic gene expression analysis identified an hourglass-like divergence of turtle and chicken embryogenesis, with maximal conservation around the vertebrate phylotypic period, rather than at later stages that show the amniote-common pattern. Wnt5a expression was found in the growth zone of the dorsal shell, supporting the possible co-option of limb-associated Wnt signaling in the acquisition of this turtle-specific novelty. Our results suggest that turtle evolution was accompanied by an unexpectedly conservative vertebrate phylotypic period, followed by turtle-specific repatterning of development to yield the novel structure of the shell.
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Origin of the Turtle Body Plan: The Folding Theory to Illustrate Turtle-Specific Developmental Repatterning. VERTEBRATE PALEOBIOLOGY AND PALEOANTHROPOLOGY 2013. [DOI: 10.1007/978-94-007-4309-0_4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/13/2023]
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31
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Three Ways to Tackle the Turtle: Integrating Fossils, Comparative Embryology, and Microanatomy. VERTEBRATE PALEOBIOLOGY AND PALEOANTHROPOLOGY 2013. [DOI: 10.1007/978-94-007-4309-0_6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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32
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Lyson TR, Joyce WG. Evolution of the turtle bauplan: the topological relationship of the scapula relative to the ribcage. Biol Lett 2012; 8:1028-31. [PMID: 22809725 PMCID: PMC3497105 DOI: 10.1098/rsbl.2012.0462] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2012] [Accepted: 06/21/2012] [Indexed: 11/12/2022] Open
Abstract
The turtle shell and the relationship of the shoulder girdle inside or 'deep' to the ribcage have puzzled neontologists and developmental biologists for more than a century. Recent developmental and fossil data indicate that the shoulder girdle indeed lies inside the shell, but anterior to the ribcage. Developmental biologists compare this orientation to that found in the model organisms mice and chickens, whose scapula lies laterally on top of the ribcage. We analyse the topological relationship of the shoulder girdle relative to the ribcage within a broader phylogenetic context and determine that the condition found in turtles is also found in amphibians, monotreme mammals and lepidosaurs. A vertical scapula anterior to the thoracic ribcage is therefore inferred to be the basal amniote condition and indicates that the condition found in therian mammals and archosaurs (which includes both developmental model organisms: chickens and mice) is derived and not appropriate for studying the developmental origin of the turtle shell. Instead, among amniotes, either monotreme mammals or lepidosaurs should be used.
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Affiliation(s)
- Tyler R Lyson
- Department of Geology and Geophysics, Yale University, New Haven, CT 06511, USA.
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Tokita M, Chaeychomsri W, Siruntawineti J. Developmental basis of toothlessness in turtles: insight into convergent evolution of vertebrate morphology. Evolution 2012; 67:260-73. [PMID: 23289576 DOI: 10.1111/j.1558-5646.2012.01752.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
The tooth is a major component of the vertebrate feeding apparatus and plays a crucial role in species survival, thus subjecting tooth developmental programs to strong selective constraints. However, irrespective of their functional importance, teeth have been lost in multiple lineages of tetrapod vertebrates independently. To understand both the generality and the diversity of developmental mechanisms that cause tooth agenesis in tetrapods, we investigated expression patterns of a series of tooth developmental genes in the lower jaw of toothless turtles and compared them to that of toothed crocodiles and the chicken as a representative of toothless modern birds. In turtle embryos, we found impairment of Shh signaling in the oral epithelium and early-stage arrest of odontoblast development caused by termination of Msx2 expression in the dental mesenchyme. Our data indicate that such changes underlie tooth agenesis in turtles and suggest that the mechanism that leads to early-stage odontogenic arrest differs between birds and turtles. Our results demonstrate that the cellular and molecular mechanisms that regulate early-stage arrest of tooth development are diverse in tetrapod lineages, and odontogenic developmental programs may respond to changes in upstream molecules similarly thereby evolving convergently with feeding morphology.
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Affiliation(s)
- Masayoshi Tokita
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tenno-dai 1-1-1, Tsukuba, Ibaraki 305-8572, Japan.
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Chiari Y, Cahais V, Galtier N, Delsuc F. Phylogenomic analyses support the position of turtles as the sister group of birds and crocodiles (Archosauria). BMC Biol 2012; 10:65. [PMID: 22839781 PMCID: PMC3473239 DOI: 10.1186/1741-7007-10-65] [Citation(s) in RCA: 231] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2011] [Accepted: 07/27/2012] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND The morphological peculiarities of turtles have, for a long time, impeded their accurate placement in the phylogeny of amniotes. Molecular data used to address this major evolutionary question have so far been limited to a handful of markers and/or taxa. These studies have supported conflicting topologies, positioning turtles as either the sister group to all other reptiles, to lepidosaurs (tuatara, lizards and snakes), to archosaurs (birds and crocodiles), or to crocodilians. Genome-scale data have been shown to be useful in resolving other debated phylogenies, but no such adequate dataset is yet available for amniotes. RESULTS In this study, we used next-generation sequencing to obtain seven new transcriptomes from the blood, liver, or jaws of four turtles, a caiman, a lizard, and a lungfish. We used a phylogenomic dataset based on 248 nuclear genes (187,026 nucleotide sites) for 16 vertebrate taxa to resolve the origins of turtles. Maximum likelihood and Bayesian concatenation analyses and species tree approaches performed under the most realistic models of the nucleotide and amino acid substitution processes unambiguously support turtles as a sister group to birds and crocodiles. The use of more simplistic models of nucleotide substitution for both concatenation and species tree reconstruction methods leads to the artefactual grouping of turtles and crocodiles, most likely because of substitution saturation at third codon positions. Relaxed molecular clock methods estimate the divergence between turtles and archosaurs around 255 million years ago. The most recent common ancestor of living turtles, corresponding to the split between Pleurodira and Cryptodira, is estimated to have occurred around 157 million years ago, in the Upper Jurassic period. This is a more recent estimate than previously reported, and questions the interpretation of controversial Lower Jurassic fossils as being part of the extant turtles radiation. CONCLUSIONS These results provide a phylogenetic framework and timescale with which to interpret the evolution of the peculiar morphological, developmental, and molecular features of turtles within the amniotes.
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Affiliation(s)
- Ylenia Chiari
- Institut des Sciences de l'Evolution, UMR5554-CNRS-IRD, Université Montpellier 2, Montpellier, France
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, 4485-661 Vairão, Portugal
| | - Vincent Cahais
- Institut des Sciences de l'Evolution, UMR5554-CNRS-IRD, Université Montpellier 2, Montpellier, France
| | - Nicolas Galtier
- Institut des Sciences de l'Evolution, UMR5554-CNRS-IRD, Université Montpellier 2, Montpellier, France
| | - Frédéric Delsuc
- Institut des Sciences de l'Evolution, UMR5554-CNRS-IRD, Université Montpellier 2, Montpellier, France
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Chojnowski JL, Braun EL. An unbiased approach to identify genes involved in development in a turtle with temperature-dependent sex determination. BMC Genomics 2012; 13:308. [PMID: 22793670 PMCID: PMC3434017 DOI: 10.1186/1471-2164-13-308] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2011] [Accepted: 07/15/2012] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Many reptiles exhibit temperature-dependent sex determination (TSD). The initial cue in TSD is incubation temperature, unlike genotypic sex determination (GSD) where it is determined by the presence of specific alleles (or genetic loci). We used patterns of gene expression to identify candidates for genes with a role in TSD and other developmental processes without making a priori assumptions about the identity of these genes (ortholog-based approach). We identified genes with sexually dimorphic mRNA accumulation during the temperature sensitive period of development in the Red-eared slider turtle (Trachemys scripta), a turtle with TSD. Genes with differential mRNA accumulation in response to estrogen (estradiol-17β; E(2)) exposure and developmental stages were also identified. RESULTS Sequencing 767 clones from three suppression-subtractive hybridization libraries yielded a total of 581 unique sequences. Screening a macroarray with a subset of those sequences revealed a total of 26 genes that exhibited differential mRNA accumulation: 16 female biased and 10 male biased. Additional analyses revealed that C16ORF62 (an unknown gene) and MALAT1 (a long noncoding RNA) exhibited increased mRNA accumulation at the male producing temperature relative to the female producing temperature during embryonic sexual development. Finally, we identified four genes (C16ORF62, CCT3, MMP2, and NFIB) that exhibited a stage effect and five genes (C16ORF62, CCT3, MMP2, NFIB and NOTCH2) showed a response to E(2) exposure. CONCLUSIONS Here we report a survey of genes identified using patterns of mRNA accumulation during embryonic development in a turtle with TSD. Many previous studies have focused on examining the turtle orthologs of genes involved in mammalian development. Although valuable, the limitations of this approach are exemplified by our identification of two genes (MALAT1 and C16ORF62) that are sexually dimorphic during embryonic development. MALAT1 is a noncoding RNA that has not been implicated in sexual differentiation in other vertebrates and C16ORF62 has an unknown function. Our results revealed genes that are candidates for having roles in turtle embryonic development, including TSD, and highlight the need to expand our search parameters beyond protein-coding genes.
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Affiliation(s)
- Jena L Chojnowski
- Genetics Department, University of Georgia, 500 DW Brooks Dr., Coverdell Center Rm270, Athens, GA, 30602, USA
- Department of Biology, University of Florida, PO Box 118525, Gainesville, FL, 32607, USA
| | - Edward L Braun
- Department of Biology, University of Florida, PO Box 118525, Gainesville, FL, 32607, USA
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Nagashima H, Kuraku S, Uchida K, Kawashima-Ohya Y, Narita Y, Kuratani S. Body plan of turtles: an anatomical, developmental and evolutionary perspective. Anat Sci Int 2011; 87:1-13. [DOI: 10.1007/s12565-011-0121-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2011] [Accepted: 10/24/2011] [Indexed: 10/15/2022]
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Frazzetta TH. Flatfishes, Turtles, and Bolyerine Snakes: Evolution by Small Steps or Large, or Both? Evol Biol 2011. [DOI: 10.1007/s11692-011-9142-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Kawashima-Ohya Y, Narita Y, Nagashima H, Usuda R, Kuratani S. Hepatocyte growth factor is crucial for development of the carapace in turtles. Evol Dev 2011; 13:260-8. [PMID: 21535464 PMCID: PMC3121961 DOI: 10.1111/j.1525-142x.2011.00474.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Turtles are characterized by their shell, composed of a dorsal carapace and a ventral plastron. The carapace first appears as the turtle-specific carapacial ridge (CR) on the lateral aspect of the embryonic flank. Accompanying the acquisition of the shell, unlike in other amniotes, hypaxial muscles in turtle embryos appear as thin threads of fibrous tissue. To understand carapacial evolution from the perspective of muscle development, we compared the development of the muscle plate, the anlage of hypaxial muscles, between the Chinese soft-shelled turtle, Pelodiscus sinensis, and chicken embryos. We found that the ventrolateral lip (VLL) of the thoracic dermomyotome of P. sinensis delaminates early and produces sparse muscle plate in the lateral body wall. Expression patterns of the regulatory genes for myotome differentiation, such as Myf5, myogenin, Pax3, and Pax7 have been conserved among amniotes, including turtles. However, in P. sinensis embryos, the gene hepatocyte growth factor (HGF), encoding a regulatory factor for delamination of the dermomyotomal VLL, was uniquely expressed in sclerotome and the lateral body wall at the interlimb level. Implantation of COS-7 cells expressing a HGF antagonist into the turtle embryo inhibited CR formation. We conclude that the de novo expression of HGF in the turtle mesoderm would have played an innovative role resulting in the acquisition of the turtle-specific body plan.
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Affiliation(s)
- Yoshie Kawashima-Ohya
- Laboratory for Evolutionary Morphology, RIKEN Center for Developmental Biology (CDB), 2-2-3 Minatojima-minami, Kobe 650-0047, Japan
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