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Xue M, Huang N, Luo Y, Yang X, Wang Y, Fang M. Combined Transcriptomics and Metabolomics Identify Regulatory Mechanisms of Porcine Vertebral Chondrocyte Development In Vitro. Int J Mol Sci 2024; 25:1189. [PMID: 38256262 PMCID: PMC10816887 DOI: 10.3390/ijms25021189] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 01/09/2024] [Accepted: 01/12/2024] [Indexed: 01/24/2024] Open
Abstract
Porcine body length is closely related to meat production, growth, and reproductive performance, thus playing a key role in the profitability of the pork industry. Cartilage development is critical to longitudinal elongation of individual vertebrae. This study isolated primary porcine vertebral chondrocytes (PVCs) to clarify the complex mechanisms of elongation. We used transcriptome and target energy metabolome technologies to confirm crucial genes and metabolites in primary PVCs at different differentiation stages (0, 4, 8, and 12 days). Pairwise comparisons of the four stages identified 4566 differentially expressed genes (DEGs). Time-series gene cluster and functional analyses of these DEGs revealed four clusters related to metabolic processes, cartilage development, vascular development, and cell cycle regulation. We constructed a transcriptional regulatory network determining chondrocyte maturation. The network indicated that significantly enriched transcription factor (TF) families, including zf-C2H2, homeobox, TF_bZIP, and RHD, are important in cell cycle and differentiation processes. Further, dynamic network biomarker (DNB) analysis revealed that day 4 was the tipping point for chondrocyte development, consistent with morphological and metabolic changes. We found 24 DNB DEGs, including the TFs NFATC2 and SP7. Targeted energy metabolome analysis showed that most metabolites were elevated throughout chondrocyte development; notably, 16 differentially regulated metabolites (DRMs) were increased at three time points after cell differentiation. In conclusion, integrated metabolome and transcriptome analyses highlighted the importance of amino acid biosynthesis in chondrocyte development, with coordinated regulation of DEGs and DRMs promoting PVC differentiation via glucose oxidation. These findings reveal the regulatory mechanisms underlying PVC development and provide an important theoretical reference for improving pork production.
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Affiliation(s)
- Mingming Xue
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, MOA Key Laboratory of Animal Genetics and Breeding, Beijing Key Laboratory for Animal Genetic Improvement, State Key Laboratory of Animal Biotech Breeding, Frontiers Science Center for Molecular Design Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (M.X.); (Y.L.); (X.Y.)
| | - Ning Huang
- Sanya Research Institute, China Agricultural University, Sanya 572025, China; (N.H.); (Y.W.)
| | - Yabiao Luo
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, MOA Key Laboratory of Animal Genetics and Breeding, Beijing Key Laboratory for Animal Genetic Improvement, State Key Laboratory of Animal Biotech Breeding, Frontiers Science Center for Molecular Design Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (M.X.); (Y.L.); (X.Y.)
| | - Xiaoyang Yang
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, MOA Key Laboratory of Animal Genetics and Breeding, Beijing Key Laboratory for Animal Genetic Improvement, State Key Laboratory of Animal Biotech Breeding, Frontiers Science Center for Molecular Design Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (M.X.); (Y.L.); (X.Y.)
| | - Yubei Wang
- Sanya Research Institute, China Agricultural University, Sanya 572025, China; (N.H.); (Y.W.)
| | - Meiying Fang
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, MOA Key Laboratory of Animal Genetics and Breeding, Beijing Key Laboratory for Animal Genetic Improvement, State Key Laboratory of Animal Biotech Breeding, Frontiers Science Center for Molecular Design Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (M.X.); (Y.L.); (X.Y.)
- Sanya Research Institute, China Agricultural University, Sanya 572025, China; (N.H.); (Y.W.)
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2
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Zhang K, Huang Y, Zhang Y, Liang R, Li Q, Li R, Zhao X, Bian C, Chen Y, Wu J, Shi Q, Lin L. A chromosome-level reference genome assembly of the Reeve's moray eel (Gymnothorax reevesii). Sci Data 2023; 10:501. [PMID: 37516767 PMCID: PMC10387071 DOI: 10.1038/s41597-023-02394-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 07/17/2023] [Indexed: 07/31/2023] Open
Abstract
Due to potentially hostile behaviors and elusive habitats, moray eels (Muraenidae) as one group of apex predators in coral reefs all across the globe have not been well investigated. Here, we constructed a chromosome-level genome assembly for the representative Reeve's moray eel (Gymnothorax reevesii). This haplotype genome assembly is 2.17 Gb in length, and 97.87% of the sequences are anchored into 21 chromosomes. It contains 56.34% repetitive sequences and 23,812 protein-coding genes, of which 96.77% are functionally annotated. This sequenced marine species in Anguilliformes makes a good complement to the genetic resource of eel genomes. It not only provides a genetic resource for in-depth studies of the Reeve's moray eel, but also enables deep-going genomic comparisons among various eels.
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Affiliation(s)
- Kai Zhang
- College of Animal Science and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China
- Guangdong Provincial Water Environment and Aquatic Products Security Engineering Technology Research Center, Guangzhou, 510225, China
| | - Yu Huang
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, Shenzhen, 518081, China
- Laboratory of Aquatic Genomics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China
| | - Yuxuan Zhang
- College of Animal Science and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China
- Guangdong Provincial Water Environment and Aquatic Products Security Engineering Technology Research Center, Guangzhou, 510225, China
| | - Rishen Liang
- College of Animal Science and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China
- Guangdong Provincial Water Environment and Aquatic Products Security Engineering Technology Research Center, Guangzhou, 510225, China
| | - Qingqing Li
- College of Animal Science and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China
- Guangdong Provincial Water Environment and Aquatic Products Security Engineering Technology Research Center, Guangzhou, 510225, China
| | - Ruihan Li
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, Shenzhen, 518081, China
| | - Xiaomeng Zhao
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, Shenzhen, 518081, China
| | - Chao Bian
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, Shenzhen, 518081, China
- Laboratory of Aquatic Genomics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China
| | - Yongnan Chen
- College of Animal Science and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China
- Guangdong Provincial Water Environment and Aquatic Products Security Engineering Technology Research Center, Guangzhou, 510225, China
| | - Jinhui Wu
- Agro-Tech Extension Center of Guangdong Province, Guangzhou, 510225, China
| | - Qiong Shi
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, Shenzhen, 518081, China.
- Laboratory of Aquatic Genomics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China.
| | - Li Lin
- College of Animal Science and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China.
- Guangdong Provincial Water Environment and Aquatic Products Security Engineering Technology Research Center, Guangzhou, 510225, China.
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3
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Xu Q, Luo Y, Chao Z, Zhang J, Liu X, Tang Q, Wang K, Tan S, Fang M. Integrated Analysis of Transcriptome Expression Profiles Reveals miRNA-326-NKX3.2-Regulated Porcine Chondrocyte Differentiation. Int J Mol Sci 2023; 24:ijms24087257. [PMID: 37108419 PMCID: PMC10138716 DOI: 10.3390/ijms24087257] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Revised: 03/20/2023] [Accepted: 03/22/2023] [Indexed: 04/29/2023] Open
Abstract
The porcine body length trait is an essential factor affecting meat production and reproductive performance. It is evident that the development/lengthening of individual vertebrae is one of the main reasons for increases in body length; however, the underlying molecular mechanism remains unclear. In this study, RNA-seq analysis was used to profile the transcriptome (lncRNA, mRNA, and miRNA) of the thoracic intervertebral cartilage (TIC) at two time points (1 and 4 months) during vertebral column development in Yorkshire (Y) and Wuzhishan pigs (W). There were four groups: 1- (Y1) and 4-month-old (Y4) Yorkshire pigs and 1- (W1) and 4-month-old (W4) Wuzhishan pigs. In total, 161, 275, 86, and 126 differentially expressed (DE) lncRNAs, 1478, 2643, 404, and 750 DE genes (DEGs), and 74,51, 34, and 23 DE miRNAs (DE miRNAs) were identified in the Y4 vs. Y1, W4 vs. W1, Y4 vs. W4, and Y1 vs. W1 comparisons, respectively. Functional analysis of these DE transcripts (DETs) demonstrated that they had participated in various biological processes, such as cellular component organization or biogenesis, the developmental process, the metabolic process, bone development, and cartilage development. The crucial bone development-related candidate genes NK3 Homeobox 2 (NKX3.2), Wnt ligand secretion mediator (WLS), gremlin 1 (GREM1), fibroblast growth factor receptor 3 (FGFR3), hematopoietically expressed homeobox (HHEX), (collagen type XI alpha 1 chain (COL11A1), and Wnt Family Member 16 (WNT16)) were further identified by functional analysis. Moreover, lncRNA, miRNA, and gene interaction networks were constructed; a total of 55 lncRNAs, 6 miRNAs, and 7 genes formed lncRNA-gene, miRNA-gene, and lncRNA-miRNA-gene pairs, respectively. The aim was to demonstrate that coding and non-coding genes may co-regulate porcine spine development through interaction networks. NKX3.2 was identified as being specifically expressed in cartilage tissues, and it delayed chondrocyte differentiation. miRNA-326 regulated chondrocyte differentiation by targeting NKX3.2. The present study provides the first non-coding RNA and gene expression profiles in the porcine TIC, constructs the lncRNA-miRNA-gene interaction networks, and confirms the function of NKX3.2 in vertebral column development. These findings contribute to the understanding of the potential molecular mechanisms regulating pig vertebral column development. They expand our knowledge about the differences in body length between different pig species and provide a foundation for future studies.
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Affiliation(s)
- Qiao Xu
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, MOA Laboratory of Animal Genetics and Breeding, Beijing Key Laboratory for Animal Genetic Improvement, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Yabiao Luo
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, MOA Laboratory of Animal Genetics and Breeding, Beijing Key Laboratory for Animal Genetic Improvement, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Zhe Chao
- Institute of Animal Sciences and Veterinary, Hainan Academy of Agricultural Sciences, Haikou 571100, China
| | - Jibin Zhang
- Department of Molecular and Cellular Biology, Beckman Research Institute, City of Hope, Duarte, CA 91006, USA
| | - Ximing Liu
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, MOA Laboratory of Animal Genetics and Breeding, Beijing Key Laboratory for Animal Genetic Improvement, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Qiguo Tang
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, MOA Laboratory of Animal Genetics and Breeding, Beijing Key Laboratory for Animal Genetic Improvement, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Kejun Wang
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, MOA Laboratory of Animal Genetics and Breeding, Beijing Key Laboratory for Animal Genetic Improvement, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Shuyi Tan
- Institute of Animal Sciences and Veterinary, Hainan Academy of Agricultural Sciences, Haikou 571100, China
| | - Meiying Fang
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, MOA Laboratory of Animal Genetics and Breeding, Beijing Key Laboratory for Animal Genetic Improvement, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
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4
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Collar DC, DiPaolo ECC, Mai SL, Mehta RS. Body shape transformations by alternate anatomical adaptive peak shifts in blenniiform fishes. Evolution 2021; 75:1552-1566. [PMID: 33890296 DOI: 10.1111/evo.14238] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Revised: 02/24/2021] [Accepted: 04/05/2021] [Indexed: 12/18/2022]
Abstract
Extreme body elongation has occurred repeatedly in the evolutionary history of ray-finned fishes. Lengthening of the anterior-posterior body axis relative to depth and width can involve changes in the cranial skeleton and vertebral column, but to what extent is anatomical evolution determined by selective factors and intrinsic constraints that are shared broadly among closely related lineages? In this study, we fit adaptive (Ornstein-Uhlenbeck) evolutionary models to body shape and its anatomical determinants and identified two instances of extreme elongation by divergent anatomical peak shifts in the Blenniiformes, a radiation of small-bodied substrate-associated marine teleost fishes. Species in the genus Xiphasia (hairtail blennies) evolved toward a peak defined by a highly elongated caudal vertebral region but ancestral cranial and precaudal vertebral morphology. In contrast, a clade that includes the genera Chaenopsis and Lucayablennius (pike and arrow blennies) evolved toward a peak with a long slender skull but ancestral axial skeletal anatomy. Neither set of anatomical peak shifts aligns closely with the major axis of anatomical diversification in other blenniiform fishes. These results provide little evidence that ancestral constraints have affected body shape transformation, and instead suggest that extreme elongation arose with distinct shifts in selective factors and development.
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Affiliation(s)
- David C Collar
- Department of Organismal and Environmental Biology, Christopher Newport University, Newport News, VA, 23606
| | - Emma C C DiPaolo
- Department of Organismal and Environmental Biology, Christopher Newport University, Newport News, VA, 23606
| | - Sienna L Mai
- Department of Organismal and Environmental Biology, Christopher Newport University, Newport News, VA, 23606
| | - Rita S Mehta
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, 95060
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5
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Bonett RM, Ledbetter NM, Hess AJ, Herrboldt MA, Denoël M. Repeated ecological and life cycle transitions make salamanders an ideal model for evolution and development. Dev Dyn 2021; 251:957-972. [PMID: 33991029 DOI: 10.1002/dvdy.373] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 04/16/2021] [Accepted: 05/10/2021] [Indexed: 11/11/2022] Open
Abstract
Observations on the ontogeny and diversity of salamanders provided some of the earliest evidence that shifts in developmental trajectories have made a substantial contribution to the evolution of animal forms. Since the dawn of evo-devo there have been major advances in understanding developmental mechanisms, phylogenetic relationships, evolutionary models, and an appreciation for the impact of ecology on patterns of development (eco-evo-devo). Molecular phylogenetic analyses have converged on strong support for the majority of branches in the Salamander Tree of Life, which includes 764 described species. Ancestral reconstructions reveal repeated transitions between life cycle modes and ecologies. The salamander fossil record is scant, but key Mesozoic species support the antiquity of life cycle transitions in some families. Colonization of diverse habitats has promoted phenotypic diversification and sometimes convergence when similar environments have been independently invaded. However, unrelated lineages may follow different developmental pathways to arrive at convergent phenotypes. This article summarizes ecological and endocrine-based causes of life cycle transitions in salamanders, as well as consequences to body size, genome size, and skeletal structure. Salamanders offer a rich source of comparisons for understanding how the evolution of developmental patterns has led to phenotypic diversification following shifts to new adaptive zones.
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Affiliation(s)
- Ronald M Bonett
- Department of Biological Science, The University of Tulsa, Tulsa, Oklahoma, USA
| | | | - Alexander J Hess
- Department of Biological Science, The University of Tulsa, Tulsa, Oklahoma, USA
| | - Madison A Herrboldt
- Department of Biological Science, The University of Tulsa, Tulsa, Oklahoma, USA
| | - Mathieu Denoël
- Laboratory of Ecology and Conservation of Amphibians (LECA), Freshwater and Oceanic science Unit of reSearch (FOCUS), University of Liège, Liège, Belgium
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6
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Gartner SM, Mehta RS. Effects of Diet and Intraspecific Scaling on the Viscera of Muraenid Fishes. ZOOLOGY 2020; 139:125752. [DOI: 10.1016/j.zool.2020.125752] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 01/21/2020] [Accepted: 01/27/2020] [Indexed: 12/15/2022]
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7
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Macaluso L, Carnevale G, Casu R, Pietrocola D, Villa A, Delfino M. Structural and environmental constraints on reduction of paired appendages among vertebrates. Biol J Linn Soc Lond 2019. [DOI: 10.1093/biolinnean/blz097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
AbstractBurrowing habits or complex environments have generally been considered as potential drivers acting on reduction and loss of the appendicular skeleton among vertebrates. Herein, we suggest that this might be the case for lissamphibians and squamates, but that fin loss in fishes is usually prevented by important structural constraints, because pectoral fins are commonly used to control rolling and pitching. We provide an overview of the distribution of paired appendage reduction across vertebrates while examining the ecological affinities of finless and limbless clades. We analysed the correlation between lifestyle and fin or limb loss using the discrete comparative analysis. The resulting Bayesian factors indicate strong evidence of correlation between: (1) pectoral-fin loss and coexistence of anguilliform elongation and burrowing habits or complex habitat in teleost fishes; and (2) limb loss and a burrowing or grass-swimming lifestyle in squamate reptiles and lissamphibians. These correlations suggest that a complex environment or a fossorial habit is a driving force leading to appendage loss. The only style of locomotion that is functional even in the absence of paired appendages is the undulatory one, which is typical of all elongated reptiles and lissamphibians, but certainly less common in teleost fishes.
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Affiliation(s)
- Loredana Macaluso
- Dipartimento di Scienze della Terra, Università degli Studi di Torino, Via Valperga Caluso, Torino, Italy
| | - Giorgio Carnevale
- Dipartimento di Scienze della Terra, Università degli Studi di Torino, Via Valperga Caluso, Torino, Italy
| | - Raffaello Casu
- Dipartimento di Fisica, Università degli Studi di Torino, Via Pietro Giuria, Torino, Italy
| | - Daniel Pietrocola
- Dipartimento di Scienze della Terra, Università degli Studi di Torino, Via Valperga Caluso, Torino, Italy
| | - Andrea Villa
- Dipartimento di Scienze della Terra, Università degli Studi di Torino, Via Valperga Caluso, Torino, Italy
- Bayerische Staatssammlung für Paläontologie und Geologie, Richard-Wagner-Straße, München, Germany
| | - Massimo Delfino
- Dipartimento di Scienze della Terra, Università degli Studi di Torino, Via Valperga Caluso, Torino, Italy
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Edifici Z (ICTA-ICP), Carrer de les Columnes s/n, Campus de la UAB, Cerdanyola del Valles, Barcelona, Spain
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8
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Ito F, Matsumoto T, Hirata T. Frequent nonrandom shifts in the temporal sequence of developmental landmark events during teleost evolutionary diversification. Evol Dev 2019; 21:120-134. [PMID: 30999390 DOI: 10.1111/ede.12288] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Revised: 03/03/2019] [Accepted: 03/06/2019] [Indexed: 01/08/2023]
Abstract
Morphological transformations can be generated by evolutionary changes in the sequence of developmental events. In this study, we examined the evolutionary dynamics of the developmental sequence on a macroevolutionary scale in teleosts. Using the information from previous reports describing the development of 31 species, we extracted the developmental sequences of 19 landmark events involving the formation of phylogenetically conserved body parts; we then inferred ancestral developmental sequences by two different parsimony-based methods-event-pairing and continuous analysis. The phylogenetic comparisons of these sequences revealed event-dependent heterogeneity in the frequency of sequence changes. Most of the sequence changes occurred as exchanges of temporally neighboring events. These heterochronic changes in developmental sequences accumulated along evolutionary time, but the precise distribution of the changes over the teleostean phylogeny remains unclear due to technical limitations.
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Affiliation(s)
- Fumihiro Ito
- Mammalian Genetics Laboratory, Genetic Strains Research Center, National Institute of Genetics, Mishima, Shizuoka, Japan.,Department of Genetics, SOKENDAI (The Graduate University for Advanced Studies), Mishima, Shizuoka, Japan
| | - Tomotaka Matsumoto
- Department of Genetics, SOKENDAI (The Graduate University for Advanced Studies), Mishima, Shizuoka, Japan.,Division of Evolutionary Genetics, Department of Population Genetics, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Tatsumi Hirata
- Department of Genetics, SOKENDAI (The Graduate University for Advanced Studies), Mishima, Shizuoka, Japan.,Division of Brain Function, National Institute of Genetics, Mishima, Shizuoka, Japan
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9
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Sherratt E, Coutts FJ, Rasmussen AR, Sanders KL. Vertebral evolution and ontogenetic allometry: The developmental basis of extreme body shape divergence in microcephalic sea snakes. Evol Dev 2019; 21:135-144. [DOI: 10.1111/ede.12284] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 02/04/2019] [Accepted: 02/05/2019] [Indexed: 12/25/2022]
Affiliation(s)
- Emma Sherratt
- Department of Ecology and Evolutionary Biology School of Biological Sciences, The University of Adelaide Adelaide South Australia Australia
| | - Felicity J. Coutts
- Department of Ecology and Evolutionary Biology School of Biological Sciences, The University of Adelaide Adelaide South Australia Australia
- Earth Sciences Section, South Australian Museum Adelaide South Australia Australia
| | - Arne R. Rasmussen
- The Royal Danish Academy of Fine Arts, Schools of Architecture, Design and Conservation Copenhagen Denmark
| | - Kate L. Sanders
- Department of Ecology and Evolutionary Biology School of Biological Sciences, The University of Adelaide Adelaide South Australia Australia
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10
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Aguirre WE, Young A, Navarrete-Amaya R, Valdiviezo-Rivera J, Jiménez-Prado P, Cucalón RV, Nugra-Salazar F, Calle-Delgado P, Borders T, Shervette VR. Vertebral number covaries with body form and elevation along the western slopes of the Ecuadorian Andes in the Neotropical fish genusRhoadsia(Teleostei: Characidae). Biol J Linn Soc Lond 2019. [DOI: 10.1093/biolinnean/blz002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Affiliation(s)
- Windsor E Aguirre
- Department of Biological Sciences, DePaul University, Chicago, IL, USA
| | - Ashley Young
- Department of Biological Sciences, DePaul University, Chicago, IL, USA
| | | | | | - Pedro Jiménez-Prado
- Escuela de Gestión Ambiental, Pontificia Universidad Católica del Ecuador Sede Esmeraldas, Esmeraldas, Ecuador
| | - Roberto V Cucalón
- Department of Biological Sciences, DePaul University, Chicago, IL, USA
| | - Fredy Nugra-Salazar
- Laboratorio de Zoología de Vertebrados de la Universidad del Azuay, Cuenca, Ecuador
| | - Paola Calle-Delgado
- Facultad de Ciencias de la Vida, Escuela Superior Politécnica del Litoral, Casilla, Guayaquil, Ecuador
| | - Thomas Borders
- Department of Biological Sciences, DePaul University, Chicago, IL, USA
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11
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Ribout C, Bech N, Briand MJ, Guyonnet D, Letourneur Y, Brischoux F, Bonnet X. A lack of spatial genetic structure of Gymnothorax chilospilus (moray eel) suggests peculiar population functioning. Biol J Linn Soc Lond 2018. [DOI: 10.1093/biolinnean/bly107] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- C Ribout
- CEBC, UMR 7372 CNRS-ULR, Villiers en Bois, France
| | - N Bech
- Laboratoire Ecologie et Biologie des Interactions, UMR CNRS 7267, Equipe ‘Ecologie, Evolution, Symbiose’, Université de Poitiers, Poitiers, France
| | - M J Briand
- Institut Méditerranéen d’Océanologie (MIO), UMR CNRS 7294, Aix-Marseille Université, Marseille Cedex, France
| | - D Guyonnet
- Signalisation et transports ioniques membranaires (STIM), ERL 7368/EA-7349, Université de Poitiers, Poitiers, France
| | - Y Letourneur
- Université de la Nouvelle-Calédonie, Institut ISEA - EA 7484 and LabEx « Corail », Nouméa cedex, New Caledonia
| | - F Brischoux
- CEBC, UMR 7372 CNRS-ULR, Villiers en Bois, France
| | - X Bonnet
- CEBC, UMR 7372 CNRS-ULR, Villiers en Bois, France
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12
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Evidence for complex life cycle constraints on salamander body form diversification. Proc Natl Acad Sci U S A 2017; 114:9936-9941. [PMID: 28851828 DOI: 10.1073/pnas.1703877114] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Metazoans display a tremendous diversity of developmental patterns, including complex life cycles composed of morphologically disparate stages. In this regard, the evolution of life cycle complexity promotes phenotypic diversity. However, correlations between life cycle stages can constrain the evolution of some structures and functions. Despite the potential macroevolutionary consequences, few studies have tested the impacts of life cycle evolution on broad-scale patterns of trait diversification. Here we show that larval and adult salamanders with a simple, aquatic-only (paedomorphic) life cycle had an increased rate of vertebral column and body form diversification compared to lineages with a complex, aquatic-terrestrial (biphasic) life cycle. These differences in life cycle complexity explain the variations in vertebral number and adult body form better than larval ecology. In addition, we found that lineages with a simple terrestrial-only (direct developing) life cycle also had a higher rate of adult body form evolution than biphasic lineages, but still 10-fold lower than aquatic-only lineages. Our analyses demonstrate that prominent shifts in phenotypic evolution can follow long-term transitions in life cycle complexity, which may reflect underlying stage-dependent constraints.
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13
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Schumacher EL, Owens BD, Uyeno TA, Clark AJ, Reece JS. No support for Heincke's law in hagfish (Myxinidae): lack of an association between body size and the depth of species occurrence. JOURNAL OF FISH BIOLOGY 2017; 91:545-557. [PMID: 28653326 DOI: 10.1111/jfb.13361] [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: 03/07/2016] [Accepted: 05/24/2017] [Indexed: 06/07/2023]
Abstract
This study tests for interspecific evidence of Heincke's law among hagfishes and advances the field of research on body size and depth of occurrence in fishes by including a phylogenetic correction and by examining depth in four ways: maximum depth, minimum depth, mean depth of recorded specimens and the average of maximum and minimum depths of occurrence. Results yield no evidence for Heincke's law in hagfishes, no phylogenetic signal for the depth at which species occur, but moderate to weak phylogenetic signal for body size, suggesting that phylogeny may play a role in determining body size in this group.
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Affiliation(s)
- E L Schumacher
- Valdosta State University, Department of Biology, 1500 N Patterson Street, Valdosta, GA 31698, U.S.A
| | - B D Owens
- Valdosta State University, Department of Biology, 1500 N Patterson Street, Valdosta, GA 31698, U.S.A
| | - T A Uyeno
- Valdosta State University, Department of Biology, 1500 N Patterson Street, Valdosta, GA 31698, U.S.A
| | - A J Clark
- College of Charleston, Department of Biology, 58 Coming Street, Rm 214, Charleston, SC 29401, U.S.A
| | - J S Reece
- California State University at Fresno, Department of Biology, 2555 East San Ramon Ave MS/73, Fresno, CA 93740, U.S.A
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Effects of prey characteristics on the feeding behaviors of an apex marine predator, the California moray ( Gymnothorax mordax). ZOOLOGY 2017; 122:80-89. [DOI: 10.1016/j.zool.2017.03.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Revised: 11/05/2016] [Accepted: 03/06/2017] [Indexed: 11/18/2022]
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15
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Kawakami T, Yamada Y, Tanaka S, Tsukamoto K. Prolongation of somitogenesis in two anguilliform species, the Japanese eel Anguilla japonica and pike eel Muraenesox cinereus, with refined descriptions of their early development. JOURNAL OF FISH BIOLOGY 2017; 90:1533-1547. [PMID: 28097653 DOI: 10.1111/jfb.13249] [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: 05/20/2015] [Revised: 11/13/2015] [Accepted: 11/22/2016] [Indexed: 06/06/2023]
Abstract
The embryonic development of the Japanese eel Anguilla japonica and pike eel Muraenesox cinereus was morphologically investigated with laboratory-reared specimens to clarify the characteristics of somitogenesis. In A. japonica, somites were first observed at 18 h post fertilization (hpf) when epiboly reached 90%. Somitogenesis progressed at a rate of 1·6 h-1 at mean ± s.d. 22·6 ± 0·7° C and completed at 107 hpf (3 days post hatching; dph) when total number of somites (ST) reached 114, which corresponds to the species' number of vertebrae (112-119). In M. cinereus, somites were first observed at 14 hpf when epiboly completed. Somitogenesis progressed at a rate of 1·9 h-1 at mean ± s.d. 24·4 ± 0·2° C and completed at 90 hpf (2 dph) with 149 ± 4 ST, which corresponds to the species' number of vertebrae (142-158). Both species hatched before somitogenesis was completed, at 37 hpf with 47 ST and 42 hpf with 82 ± 4 ST, respectively. The formation of other organs such as the heart, mouth and pectoral fin bud occurred during somitogenesis. Comparison with the development of zebrafish Danio rerio indicates a prolongation of somitogenesis in A. japonica and M. cinereus. Their somitogenesis rates, however, correspond well with that of D. rerio estimated at the same temperature and their developmental stages at hatching are almost equivalent to other fishes having similar yolk sizes. Therefore, the prolongation of somitogenesis in A. japonica and M. cinereus may be accounted for solely by the increased numbers of somites to be formed, not by a slow somitogenesis rate or an acceleration in organogenesis.
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Affiliation(s)
- T Kawakami
- Atmosphere and Ocean Research Institute, University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8564, Japan
- Graduate School of Agricultural and Life Sciences, University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Y Yamada
- IRAGO Institute, 377 Ehima-Shinden, Tahara, Aichi, 441-3605, Japan
| | - S Tanaka
- IRAGO Institute, 377 Ehima-Shinden, Tahara, Aichi, 441-3605, Japan
| | - K Tsukamoto
- Atmosphere and Ocean Research Institute, University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8564, Japan
- College of Bioresource Sciences, Nihon University, 1866 Kameino, Fujisawa, Kanagawa, 252-0880, Japan
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16
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Urošević A, Slijepčević MD, Arntzen JW, Ivanović A. Vertebral shape and body elongation in Triturus newts. ZOOLOGY 2016; 119:439-446. [DOI: 10.1016/j.zool.2016.05.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Revised: 02/18/2016] [Accepted: 05/18/2016] [Indexed: 12/29/2022]
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17
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Pfaff C, Zorzin R, Kriwet J. Evolution of the locomotory system in eels (Teleostei: Elopomorpha). BMC Evol Biol 2016; 16:159. [PMID: 27514517 PMCID: PMC4981956 DOI: 10.1186/s12862-016-0728-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Accepted: 07/25/2016] [Indexed: 11/28/2022] Open
Abstract
Background Living anguilliform eels represent a distinct clade of elongated teleostean fishes inhabiting a wide range of habitats. Locomotion of these fishes is highly influenced by the elongated body shape, the anatomy of the vertebral column, and the corresponding soft tissues represented by the musculotendinous system. Up to now, the evolution of axial elongation in eels has been inferred from living taxa only, whereas the reconstruction of evolutionary patterns and functional ecology in extinct eels still is scarce. Rare but excellently preserved fossil eels from the Late Cretaceous and Cenozoic were investigated here to gain a better understanding of locomotory system evolution in anguilliforms and, consequently, their habitat occupations in deep time. Results The number of vertebrae in correlation with the body length separates extinct and extant anguilliforms. Even if the phylogenetic signal cannot entirely be excluded, the analyses performed here reveal a continuous shortening of the vertebral column with a simultaneous increase in vertebral numbers in conjunction with short lateral tendons throughout the order. These anatomical changes contradict previous hypotheses based on extant eels solely. Conclusions The body curvatures of extant anguilliforms are highly flexible and can be clearly distinguished from extinct species. Anatomical changes of the vertebral column and musculotendinous system through time and between extinct and extant anguilliforms correlate with changes of the body plan and swimming performance and reveal significant shifts in habitat adaptation and thus behaviour. Evolutionary changes in the skeletal system of eels established here also imply that environmental shifts were triggered by abiotic rather than biotic factors (e.g., K/P boundary mass extinction event). Electronic supplementary material The online version of this article (doi:10.1186/s12862-016-0728-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Cathrin Pfaff
- Department of Palaeontology, University of Vienna, Faculty of Earth Sciences, Geozentrum, UZA II, Althanstraße 14, 1090, Vienna, Austria.
| | - Roberto Zorzin
- Museo civico di Storia Naturale, Palazzo Pompei, Lungadige Porta Vittoria 9, 37129, Verona, Italy
| | - Jürgen Kriwet
- Department of Palaeontology, University of Vienna, Faculty of Earth Sciences, Geozentrum, UZA II, Althanstraße 14, 1090, Vienna, Austria
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Ficetola GF, Colleoni E, Renaud J, Scali S, Padoa-Schioppa E, Thuiller W. Morphological variation in salamanders and their potential response to climate change. GLOBAL CHANGE BIOLOGY 2016; 22:2013-2024. [PMID: 26910389 PMCID: PMC4972144 DOI: 10.1111/gcb.13255] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Revised: 01/09/2016] [Accepted: 02/04/2016] [Indexed: 05/30/2023]
Abstract
Despite the recognition that some species might quickly adapt to new conditions under climate change, demonstrating and predicting such a fundamental response is challenging. Morphological variations in response to climate may be caused by evolutionary changes or phenotypic plasticity, or both, but teasing apart these processes is difficult. Here, we built on the number of thoracic vertebrae (NTV) in ectothermic vertebrates, a known genetically based feature, to establish a link with body size and evaluate how climate change might affect the future morphological response of this group of species. First, we show that in old-world salamanders, NTV variation is strongly related to changes in body size. Secondly, using 22 salamander species as a case study, we found support for relationships between the spatial variation in selected bioclimatic variables and NTV for most of species. For 44% of species, precipitation and aridity were the predominant drivers of geographical variation of the NTV. Temperature features were dominant for 31% of species, while for 19% temperature and precipitation played a comparable role. This two-step analysis demonstrates that ectothermic vertebrates may evolve in response to climate change by modifying the number of thoracic vertebrae. These findings allow to develop scenarios for potential morphological evolution under future climate change and to identify areas and species in which the most marked evolutionary responses are expected. Resistance to climate change estimated from species distribution models was positively related to present-day species morphological response, suggesting that the ability of morphological evolution may play a role for species' persistence under climate change. The possibility that present-day capacity for local adaptation might help the resistance response to climate change can be integrated into analyses of the impact of global changes and should also be considered when planning management actions favouring species persistence.
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Affiliation(s)
- Gentile Francesco Ficetola
- Laboratoire d’Ecologie Alpine (LECA), Université Grenoble-Alpes. Grenoble 38000, France
- LECA, CNRS, Grenoble 38000, France
- Dipartimento di Scienze dell’Ambiente e del Territorio, e di Scienze della Terra, Università degli Studi di Milano-Bicocca. 20126 Milano, Italy
| | - Emiliano Colleoni
- Dipartimento di Scienze dell’Ambiente e del Territorio, e di Scienze della Terra, Università degli Studi di Milano-Bicocca. 20126 Milano, Italy
| | - Julien Renaud
- Laboratoire d’Ecologie Alpine (LECA), Université Grenoble-Alpes. Grenoble 38000, France
- LECA, CNRS, Grenoble 38000, France
| | - Stefano Scali
- Museo Civico di Storia Naturale di Milano, 20121 Milano, Italy
| | - Emilio Padoa-Schioppa
- Dipartimento di Scienze dell’Ambiente e del Territorio, e di Scienze della Terra, Università degli Studi di Milano-Bicocca. 20126 Milano, Italy
| | - Wilfried Thuiller
- Laboratoire d’Ecologie Alpine (LECA), Université Grenoble-Alpes. Grenoble 38000, France
- LECA, CNRS, Grenoble 38000, France
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Claverie T, Wainwright PC. A morphospace for reef fishes: elongation is the dominant axis of body shape evolution. PLoS One 2014; 9:e112732. [PMID: 25409027 PMCID: PMC4237352 DOI: 10.1371/journal.pone.0112732] [Citation(s) in RCA: 90] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2014] [Accepted: 10/14/2014] [Indexed: 11/18/2022] Open
Abstract
Tropical reef fishes are widely regarded as being perhaps the most morphologically diverse vertebrate assemblage on earth, yet much remains to be discovered about the scope and patterns of this diversity. We created a morphospace of 2,939 species spanning 56 families of tropical Indo-Pacific reef fishes and established the primary axes of body shape variation, the phylogenetic consistency of these patterns, and whether dominant patterns of shape change can be accomplished by diverse underlying changes. Principal component analysis showed a major axis of shape variation that contrasts deep-bodied species with slender, elongate forms. Furthermore, using custom methods to compare the elongation vector (axis that maximizes elongation deformation) and the main vector of shape variation (first principal component) for each family in the morphospace, we showed that two thirds of the families diversify along an axis of body elongation. Finally, a comparative analysis using a principal coordinate analysis based on the angles among first principal component vectors of each family shape showed that families accomplish changes in elongation with a wide range of underlying modifications. Some groups such as Pomacentridae and Lethrinidae undergo decreases in body depth with proportional increases in all body regions, while other families show disproportionate changes in the length of the head (e.g., Labridae), the trunk or caudal region in all combinations (e.g., Pempheridae and Pinguipedidae). In conclusion, we found that evolutionary changes in body shape along an axis of elongation dominates diversification in reef fishes. Changes in shape on this axis are thought to have immediate implications for swimming performance, defense from gape limited predators, suction feeding performance and access to some highly specialized habitats. The morphological modifications that underlie changes in elongation are highly diverse, suggesting a role for a range of developmental processes and functional consequences.
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Affiliation(s)
- Thomas Claverie
- CUFR de Mayotte, Route nationale 3, 97660 Dembeni, France
- * E-mail:
| | - Peter C. Wainwright
- Department of Evolution and Ecology, University of California Davis, Davis, California, United States of America
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