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Xu H, Huang L, Chen T, Wang C, Wu Z, Cheng Y, Su Q, Kang B, Yan Y, Zhang X. Phylogeography and population structure of Lagocephalus spadiceus (Richardson, 1845) (Tetraodontiformes, Tetraodontidae) in the South China Sea. Ecol Evol 2024; 14:e11320. [PMID: 38681184 PMCID: PMC11045559 DOI: 10.1002/ece3.11320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2023] [Revised: 03/25/2024] [Accepted: 04/03/2024] [Indexed: 05/01/2024] Open
Abstract
The climate fluctuations during the Late Pleistocene significantly influenced the phylogeographic structure and historical dynamics of marine fishes in the marginal seas of the western Pacific Ocean. The puffer fish, Lagocephalus spadiceus, holds substantial nutritional and economic value in the South China Sea. To investigate the demographic history and population structure of the L. spadiceus, the mitochondrial DNA COI and Cyt b gene datasets from 300 individuals across eight populations in the South China Sea were sequenced. Our findings revealed high haplotype diversity (0.874 ± 0.013) and low nucleotide diversity (0.00075 ± 0.00058). The phylogenetic tree and haplotype networks revealed no significant genetic differentiation along the northern coast of South China Sea. Neutrality tests, mismatch distribution analyses, and Bayesian skyline plots suggested that L. spadiceus underwent population expansion during the Late Pleistocene. Both ocean currents and climate change significantly influenced the geographical distribution and genetic population structure of L. spadiceus.
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Affiliation(s)
- Hao Xu
- College of Environmental Science and EngineeringGuilin University of TechnologyGuilinChina
- Guangxi Key Laboratory of Theory and Technology for Environmental Pollution ControlGuilinChina
| | - Liangliang Huang
- College of Environmental Science and EngineeringGuilin University of TechnologyGuilinChina
- Collaborative Innovation Center for Water Pollution Control and Water Safety in Karst AreasGuilinChina
| | - Tao Chen
- College of Basic MedicineGuilin Medical UniversityGuilinChina
| | - Caiguang Wang
- College of Environmental Science and EngineeringGuilin University of TechnologyGuilinChina
- Guangxi Key Laboratory of Theory and Technology for Environmental Pollution ControlGuilinChina
| | - Zhiqiang Wu
- College of Environmental Science and EngineeringGuilin University of TechnologyGuilinChina
- Collaborative Innovation Center for Water Pollution Control and Water Safety in Karst AreasGuilinChina
| | - Yanan Cheng
- College of Environmental Science and EngineeringGuilin University of TechnologyGuilinChina
- Guangxi Key Laboratory of Theory and Technology for Environmental Pollution ControlGuilinChina
| | - Qiongyuan Su
- College of Environmental Science and EngineeringGuilin University of TechnologyGuilinChina
- Guangxi Key Laboratory of Theory and Technology for Environmental Pollution ControlGuilinChina
| | - Bin Kang
- Fisheries CollegeOcean University of ChinaQingdaoChina
| | - Yunrong Yan
- Fisheries CollegeGuangdong Ocean UniversityZhanjiangChina
| | - Xiuguo Zhang
- Guangxi Jinggong Marine Science and Technology LtdBeihaiChina
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Gu S, Yan YR, Yi MR, Luo ZS, Wen H, Jiang CP, Lin HD, He XB. Genetic pattern and demographic history of cutlassfish (Trichiurus nanhaiensis) in South China Sea by the influence of Pleistocene climatic oscillations. Sci Rep 2022; 12:14716. [PMID: 36042258 PMCID: PMC9427976 DOI: 10.1038/s41598-022-18861-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Accepted: 08/22/2022] [Indexed: 11/09/2022] Open
Abstract
Trichiurus nanhaiensis is one of the most important commercial fish species in the South China Sea. This study aimed to investigate the level of genetic variation and population genetic structure of T. nanhaiensis in the South China Sea for the first time, using 281 individuals collected from seven locations along the coast of mainland China, Taiwan, and Hainan Island. A high level of haplotype diversity and low nucleotide diversity were detected in the mitochondrial DNA cyt b gene and nuDNA RYR 3 gene. The overall expected heterozygosity (He = 0.693) among the seven populations ranged from 0.681 to 0.706 in microsatellite DNA data, which revealed high levels of genetic diversity. Significant genetic differentiation was found in Taidong populations in Taiwan, revealing the prevention of gene flow caused by the Kuroshio Current. Two major lineages based on the cyt b gene suggested that the Taiwan Strait acted as a geographic barrier for T. nanhaiensis during the glacier periods in the late Pleistocene. The Bayesian skyline plot also revealed that population demographic expansion of T. nanhaiensis was estimated to have occurred in 0.1 Mya. Our results indicated that all populations of T. nanhaiensis had experienced a recent genetic bottleneck following recent expansion based on ABC analysis.
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Affiliation(s)
- Sui Gu
- College of Fisheries, Guangdong Ocean University, No.1 Haida Road, Mazhang District, Zhanjiang, 524088, China
| | - Yun-Rong Yan
- College of Fisheries, Guangdong Ocean University, No.1 Haida Road, Mazhang District, Zhanjiang, 524088, China.,Southern Marine Science and Engineering Guangdong Laboratory (Zhanjiang), Zhanjiang, 524000, China.,Guangdong Provincial Engineering and Technology Research Center of Far Sea Fisheries Management and Fishing of South China Sea, Guangdong Ocean University, Zhanjiang, 524088, China
| | - Mu-Rong Yi
- College of Fisheries, Guangdong Ocean University, No.1 Haida Road, Mazhang District, Zhanjiang, 524088, China.,Southern Marine Science and Engineering Guangdong Laboratory (Zhanjiang), Zhanjiang, 524000, China
| | - Zhi-Sen Luo
- College of Fisheries, Guangdong Ocean University, No.1 Haida Road, Mazhang District, Zhanjiang, 524088, China
| | - Hui Wen
- College of Fisheries, Guangdong Ocean University, No.1 Haida Road, Mazhang District, Zhanjiang, 524088, China
| | - Chang-Ping Jiang
- College of Fisheries, Guangdong Ocean University, No.1 Haida Road, Mazhang District, Zhanjiang, 524088, China
| | - Hung-Du Lin
- The Affiliated School of National Tainan First Senior High School, No. 1, Sec. 1, Mintzu Rd., Tainan, 701, Taiwan.
| | - Xiong-Bo He
- College of Fisheries, Guangdong Ocean University, No.1 Haida Road, Mazhang District, Zhanjiang, 524088, China. .,Guangdong Provincial Engineering and Technology Research Center of Far Sea Fisheries Management and Fishing of South China Sea, Guangdong Ocean University, Zhanjiang, 524088, China.
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Demographic history and population genetic structure of Anisakis pegreffii in the cutlassfish Trichiurus japonicus along the coast of mainland China and Taiwan. Parasitol Res 2022; 121:2803-2816. [PMID: 35918454 DOI: 10.1007/s00436-022-07611-7] [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: 10/06/2021] [Accepted: 07/25/2022] [Indexed: 10/16/2022]
Abstract
Studying the genetic diversity of nematode parasite populations is crucial to gaining insight into parasite infection dynamics and informing parasite phylogeography. Anisakiasis is a zoonotic disease caused by the consumption of infectious third-stage larvae (L3) of Anisakis spp. carried by marine fish. In the present study, a total of 206 mitochondrial DNA sequences (cytochrome c oxidase 2, cox2) were used to study the genetic diversity, genetic structure, and historical demography of twelve A. pegreffii populations from Trichiurus japonicas along the coast of mainland China and Taiwan. Two distinct evolutionary lineages of A. pegreffii and no significant genealogical structures corresponding to sampling localities suggested that isolation in the marginal seas shaped their patterns of phylogeographic distribution along the coast of mainland China and Taiwan during glaciation with lower sea levels. Furthermore, pairwise FST values and AMOVA did not indicate any significant genetic differentiation among groups with no relation to the geographic area, which might be attributed to fewer barriers to gene flow as well as large population sizes. The results of the neutrality test, mismatch distribution, and Bayesian skyline plot analyses showed that entire population underwent population expansion during the late Pleistocene. Analysis of the demographic history revealed that A. pegreffii underwent historical lineage diversification and admixture due to secondary contact based on ABC analysis. The present research represents the first definitive population structure and demographic history across sampling locations of A. pegreffii along the coast of mainland China and Taiwan.
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Genetic Structure and Diversity of the Yellowbelly Threadfin Bream Nemipterus bathybius in the Northern South China Sea. DIVERSITY 2021. [DOI: 10.3390/d13070324] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The genetic structure and demography of the yellowbelly threadfin bream, Nemipterus bathybius, in the northern South China Sea were examined using the mitochondrial DNA cytochrome b gene (1141 bp). High levels of haplotype and nucleotide diversities (0.98 and 5.26 × 10−3, respectively) showed that all populations exhibited a high level of genetic diversity. Analysis of molecular variance (AMOVA), FST statistics, and haplotype networks suggested the absence of significant genetic differentiation along the coast of the northern South China Sea. Although the results suggested that the lack of differentiation within the population structure of N. bathybius was shaped by ocean currents, our results also showed that the Qiongzhou Strait limited their migration between Beibu Gulf and the northern South China Sea. Neutrality tests and mismatch distributions indicated population expansion, but the Bayesian skyline plots and approximate Bayesian computation approaches suggested that the population sizes recently contracted. The diversification of multiple stocks, which were induced by two ocean current systems, contributed to these discordant results. Although these analyses of demographic history revealed no evidence for recent population bottlenecks, the population demography needs to be evaluated further.
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