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Zhang C, Liu H, Huang X, Yuan Z, Zhang S, Xu S, Liu J, Wang Y, Wang D, Hu J. Comparative Analysis of the Systematics and Evolution of the Pampus Genus of Fish (Perciformes: Stromateidae) Based on Osteology, Population Genetics and Complete Mitogenomes. Animals (Basel) 2024; 14:814. [PMID: 38473197 DOI: 10.3390/ani14050814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 01/20/2024] [Accepted: 02/14/2024] [Indexed: 03/14/2024] Open
Abstract
Pampus is a widespread species of fish in the western Pacific and Indian Oceans that has significant commercial worth. Its evolutionary history and phylogenetics are still poorly understood, and details on its intraspecific taxonomy are debatable, despite some morphological and molecular research. Here, we analyzed this species using skeletal structure data as well as nuclear (S7 gene) and mitochondrial genetic information (COI, D-loop and mitogenomes). We found that the genetic distance between P. argenteus and P. echinogaster was much smaller than that between other Pampus species, and both maximum likelihood and Bayesian phylogenetic trees yielded almost identical tree topologies. An additional and adjacent M repeat was found in the downstream region of the IQM gene cluster of P. argenteus and P. echinogaster, and the trnL2 gene of P. minor was translocated. The genus Pampus experienced early rapid radiation during the Palaeocene with major lineages diversifying within a relatively narrow timescale. Additionally, three different methods were conducted to distinguish the genus Pampus species, proving that P. argenteus and P. echinogaster are the same species, and P. liuorum is speculated to be a valid species. Overall, our study provides new insights not only into the evolutionary history of Pampus but its intraspecific taxonomy as well.
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Affiliation(s)
- Cheng Zhang
- School of Marine Science, Ningbo University, Ningbo 315211, China
| | - Hanjing Liu
- School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Xiang Huang
- School of Marine Science, Ningbo University, Ningbo 315211, China
| | - Zi Yuan
- School of Marine Science, Ningbo University, Ningbo 315211, China
| | - Shun Zhang
- School of Marine Science, Ningbo University, Ningbo 315211, China
| | - Shanliang Xu
- School of Marine Science, Ningbo University, Ningbo 315211, China
| | - Jing Liu
- Laboratory of Marine Organism Taxonomy and Phylogeny, Qingdao Key Laboratory of Marine Biodiversity and Conservation, and The Key Laboratory of Experimental Marine Biology, Centre for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
| | - Yajun Wang
- School of Marine Science, Ningbo University, Ningbo 315211, China
- Key Laboratory of Applied Marine Biotechnology (Ningbo University), Ministry of Education, Ningbo 315211, China
- Key Laboratory of Marine Biotechnology of Zhejiang Province, Ningbo University, Ningbo 315211, China
| | - Danli Wang
- School of Marine Science, Ningbo University, Ningbo 315211, China
| | - Jiabao Hu
- School of Marine Science, Ningbo University, Ningbo 315211, China
- Key Laboratory of Applied Marine Biotechnology (Ningbo University), Ministry of Education, Ningbo 315211, China
- Key Laboratory of Marine Biotechnology of Zhejiang Province, Ningbo University, Ningbo 315211, China
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Espíndola VC, Johnson GD, De Pinna MCC. Facial and opercular muscles in the Anguilliformes (Elopomorpha: Teleostei): Comparative anatomy and phylogenetic implications for the basal position of Protanguilla. J Morphol 2023; 284:e21556. [PMID: 36630618 DOI: 10.1002/jmor.21556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 01/04/2023] [Accepted: 01/05/2023] [Indexed: 01/13/2023]
Abstract
The teleost order Anguilliformes, true eels, comprises more than 1000 described species in 20 families, commonly known as eels, congers, morays, and gulper eels. Comprehensive studies of Anguilliformes are limited, resulting in a lack of consensus for morphology-based phylogenetic hypotheses. A detailed morphological analysis of the cephalic and opercular myology offers a promising new source of characters to help elucidate the intrarelationships of Anguilliformes. Our study is the most extensive myological analysis for the group and includes 97 terminal taxa, with representatives from each of the 20 families of Anguilliformes plus outgroup clades. Results demonstrate that muscle characters inform phylogenetic relationships within Anguilliformes, and we propose two new synapomorphies for all extant members, including Protanguilla palau, the "living fossil"-adductor mandibulae originating on the parietal (vs. restricted to suspensorium) and segmentum mandibularis absent (vs. present). Exceptions for the first condition characterize highly modified saccopharyngoids, and for the second one, Notacanthidae. More importantly, we suggest three new synapomorphies for the remaining extant anguilliforms (except in highly modified saccopharyngoids)-adductor mandibulae originates on the frontals (vs. frontals naked), adductor mandibulae stegalis is separated from the rictalis (vs. ricto-stegalis fused into a single piece), and the levator operculi inserts on the lateral surface of the opercle (vs. medial surface of the opercle). Our phylogenetic optimization strongly corroborates the hypothesis that Protanguilla is the sister group of all other extant eels. A further goal of this paper is to clearly document the substantive conflicts between the available molecular data and the extensive and diverse morphological evidence.
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Affiliation(s)
- Vinicius C Espíndola
- Division of Fishes, National Museum of Natural History, Smithsonian Institution, Washington, District of Columbia, USA
| | - G David Johnson
- Division of Fishes, National Museum of Natural History, Smithsonian Institution, Washington, District of Columbia, USA
| | - Mario C C De Pinna
- Museu de Zoologia, Setor de ictiologia, Universidade de São Paulo, São Paulo, SP, Brazil
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Chen J, Zeng H, Lv W, Sun N, Wang C, Xu W, Hu M, Gan X, He L, He S, Fang C. Pseudo-chromosome-length genome assembly for a deep-sea eel Ilyophis brunneus sheds light on the deep-sea adaptation. SCIENCE CHINA. LIFE SCIENCES 2023:10.1007/s11427-022-2251-8. [PMID: 36648612 DOI: 10.1007/s11427-022-2251-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 11/22/2022] [Indexed: 01/18/2023]
Abstract
High hydrostatic pressure, low temperature, and scarce food supply are the major factors that limit the survival of vertebrates in extreme deep-sea environments. Here, we constructed a high-quality genome of the deep-sea Muddy arrowtooth eel (MAE, Ilyophis brunneus, captured below a depth of 3,500 m) by using Illumina, PacBio, and Hi-C sequencing. We compare it against those of shallow-water eel and other outgroups to explore the genetic basis that underlies the adaptive evolution to deep-sea biomes. The MAE genome was estimated to be 1.47 Gb and assembled into 14 pseudo-chromosomes. Phylogenetic analyses indicated that MAE diverged from its closely related shallow-sea species, European eel, ∼111.9 Mya and experienced a rapid evolution. The genome evolutionary analyses primarily revealed the following: (i) under high hydrostatic pressure, the positively selected gene TUBGCP3 and the expanded family MLC1 may improve the cytoskeleton stability; ACOX1 may enhance the fluidity of cell membrane and maintain transport activity; the expansion of ABCC12 gene family may enhance the integrity of DNA; (ii) positively selected HARS likely maintain the transcription ability at low temperatures; and (iii) energy metabolism under a food-limited environment may be increased by expanded and positively selected genes in AMPK and mTOR signaling pathways.
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Affiliation(s)
- Jie Chen
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, 572000, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Honghui Zeng
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Wenqi Lv
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ning Sun
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Cheng Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wenjie Xu
- School for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi'an, 710072, China
| | - Mingliang Hu
- School for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi'an, 710072, China
| | - Xiaoni Gan
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Lisheng He
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, 572000, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Shunping He
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, 572000, China. .,State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.
| | - Chengchi Fang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China.
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Poulsen JY, Sado T, Miya M. Unique mitochondrial gene order in Xenodermichthys copei (Alepocephalidae: Otocephala) – a first observation of a large-scale rearranged 16S–WANCY region in vertebrates. Mitochondrial DNA B Resour 2019. [DOI: 10.1080/23802359.2018.1551082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Affiliation(s)
- Jan Yde Poulsen
- Department of Fish and Shellfish, Pinngortitaleriffik (Greenland Institute of Natural Resources), Nuuk, Greenland
- Department of Ecology and Environmental Sciences, Natural History Museum and Institute, Chiba, Japan
| | - Tetsuya Sado
- Department of Ecology and Environmental Sciences, Natural History Museum and Institute, Chiba, Japan
| | - Masaki Miya
- Department of Ecology and Environmental Sciences, Natural History Museum and Institute, Chiba, Japan
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