Volume 42 Issue 6
Jun.  2023
Turn off MathJax
Article Contents
Jian Zheng, Yan Tang, Ran Xu, Xiaoying Zhang, Xiaodong Zheng. Molecular phylogenetics and population demographic history of Amphioctopus fangsiao, inferred from mitochondrial and microsatellite DNA markers[J]. Acta Oceanologica Sinica, 2023, 42(6): 39-48. doi: 10.1007/s13131-022-2105-2
Citation: Jian Zheng, Yan Tang, Ran Xu, Xiaoying Zhang, Xiaodong Zheng. Molecular phylogenetics and population demographic history of Amphioctopus fangsiao, inferred from mitochondrial and microsatellite DNA markers[J]. Acta Oceanologica Sinica, 2023, 42(6): 39-48. doi: 10.1007/s13131-022-2105-2

Molecular phylogenetics and population demographic history of Amphioctopus fangsiao, inferred from mitochondrial and microsatellite DNA markers

doi: 10.1007/s13131-022-2105-2
Funds:  The National Natural Science Foundation of China under contract Nos 32170536 and 31672257.
More Information
  • Corresponding author: xdzheng@ouc.edu.cn*
  • Received Date: 2022-06-20
  • Accepted Date: 2022-09-23
  • Publish Date: 2023-06-25
  • Amphioctopus fangsiao (Cephalopoda: Octopodidae) is an important commercial species in the coastal waters of China. In recent years, however, the resource of A. fangsiao have declined because of habitat destruction and overfishing. To analyze the genetic variations of A. fangsiao caused by the fluctuation of resources, the population genetic structure of nine sampling locations collected from the Bohai Sea to the South China Sea were investigated, using mtDNA COI fragments and microsatellite DNA. The results of F-statistics, AMOVA, STRUCTURE and PCA analyses showed three phylogeographic clades (Clades A, B and C), revealing limited genetic exchange between north and south populations. These clades diverged in 2.23 (Clades A and B) and 3.67 (Clades A, B and C) million years ago, during the dramatic environmental fluctuations, such as sea level and temperature changes, have exerted great influence on the survival distribution pattern of global organisms. Our results for low genetic connectivity among A. fangsiao populations provide insights into the development of management strategies, that is, to manage this species as separate management unit.
  • loading
  • Amor M D, Norman M D, Cameron H E, et al. 2014. Allopatric speciation within a cryptic species complex of Australasian octopuses. PLoS ONE, 9(6): e98982. doi: 10.1371/journal.pone.0098982
    Belkhir K, Borsa P, Chikhi L, et al. 2004. Genetix 4.05, logiciel sous windows TM pour la génétique des populations. Laboratoire Genome, Populations, Interactions. Montpellier, France: Universite de Montpellier II
    Bohonak A J. 2002. IBD (isolation by distance): a program for analyses of isolation by distance. Journal of Heredity, 93(2): 153–154. doi: 10.1093/jhered/93.2.153
    Botsford L W, Brumbaugh D R, Grimes C, et al. 2009. Connectivity, sustainability, and yield: bridging the gap between conventional fisheries management and marine protected areas. Reviews in Fish Biology and Fisheries, 19(1): 69–95. doi: 10.1007/s11160-008-9092-z
    Bouckaert R, Heled J, Kühnert D, et al. 2014. BEAST 2: a software platform for bayesian evolutionary analysis. PLoS Computational Biology, 10(4): e1003537. doi: 10.1371/journal.pcbi.1003537
    Chang Chia-hao, Shao Kwang-tsao, Lin Han-yang, et al. 2017. DNA barcodes of the native ray-finned fishes in Taiwan. Molecular Ecology Resources, 17(4): 796–805. doi: 10.1111/1755-0998.12601
    Charrier G, Coombs S H, McQuinn I H, et al. 2007. Genetic structure of whiting Merlangius merlangus in the northeast Atlantic and adjacent waters. Marine Ecology Progress Series, 330: 201–211. doi: 10.3354/meps330201
    De Luca D, Catanese G, Procaccini G, et al. 2014. An integration of historical records and genetic data to the assessment of global distribution and population structure in Octopus vulgaris. Frontiers in Ecology and Evolution, 2: 55
    Du Xun. 2018. Study on the phylogeography and adaptive differentiation of Octopus minor along the coast of China (in Chinese)[dissertation]. Zhoushan: Zhejiang Ocean University
    Evanno G, Regnaut S, Goudet J. 2005. Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Molecular Ecology, 14(8): 2611–2620. doi: 10.1111/j.1365-294X.2005.02553.x
    Excoffier L, Laval G, Schneider S. 2007. Arlequin (version 3.0): an integrated software package for population genetics data analysis. Evolutionary Bioinformatics Online, 1: 47–50
    Excoffier L, Smouse P, Quattro J M. 1992. Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data. Genetics, 131(2): 479–491. doi: 10.1093/genetics/131.2.479
    Fadhlaoui-Zid K, Knittweis L, Aurelle D, et al. 2012. Genetic structure of Octopus vulgaris (Cephalopoda, Octopodidae) in the central Mediterranean Sea inferred from the mitochondrial COIII gene. Comptes Rendus Biologies, 335(10–11): 625–636
    Faiz M, Chen Wei, Liu Liqin, et al. 2019. Genetic structure of Amphioctopus fangsiao (Mollusca, Cephalopoda) in Chinese waters inferred from variation in three mtDNA genes (Atpase 6, ND2, and ND5). Hydrobiologia, 838(1): 111–119. doi: 10.1007/s10750-019-03981-9
    FAO. 1984. Cephalopods of the World. An Annotated and Illustrated Catalogue of Species of Interest to Fisheries. Octopods and Vampire Squids. Rome: FAO, e215
    Feng Yanwei, Liu Wenfen, Xu Xin, et al. 2017. Construction of a normalized full-length cDNA library of cephalopod Amphioctopus fangsiao and development of microsatellite markers. Journal of Ocean University of China, 16(5): 897–904. doi: 10.1007/s11802-017-3291-y
    Gao Qiang, Wang Zhaoping, Wang Rucai, et al. 2002. Allozyme variation in five populations of Octopus ocellatus. Transactions of Oceanology and Limnology, (4): 46–51
    Goudet J. 1995. FSTAT (version 1.2): a computer program to calculate F-statistics. Journal of Heredity, 86(6): 485–486. doi: 10.1093/oxfordjournals.jhered.a111627
    Grande C, Templado J, Cervera J L, et al. 2004. Phylogenetic relationships among Opisthobranchia (Mollusca: Gastropoda) based on mitochondrial cox 1, trnV, and rrnL genes. Molecular Phylogenetics and Evolution, 33(2): 378–388. doi: 10.1016/j.ympev.2004.06.008
    Gupta P K, Varshney R K, Sharma P C. 1999. Molecular markers and their applications in wheat breeding. Plant Breeding, 118(5): 369–390. doi: 10.1046/j.1439-0523.1999.00401.x
    Harte M, Kaczynski V, Schreck C. 2007. Native fish conservation plan for the spring Chinook salmon. Rogue Species Management Unit, 16(4): 258–296
    Herbert T D, Schuffert J D, Andreasen D, et al. 2001. Collapse of the California current during glacial maxima linked to climate change on land. Science, 293(5527): 71–76. doi: 10.1126/science.1059209
    Hu Chengjian. 1998. Discussion on the introduction of small yellow croaker from the fishing in the Yellow Sea and East China Sea. Marine Fisheries (in Chinese), (1): 29–3
    Hulce D, Li X, Snyder-Leiby T, et al. 2011. GeneMarker® genotyping software: tools to increase the statistical power of DNA fragment analysis. Journal of Biomolecular Techniques: JBT, 22(S): S35–S36
    Jensen J L, Bohonak A J, Kelley S T. 2005. Isolation by distance, web service. BMC Genetics, 6: 13
    Jiang Dianhang, Zheng Xiaodong, Qian Yaosen, et al. 2020a. Development of Amphioctopus fangsiao (Mollusca: Cephalopoda) from eggs to hatchlings: indications for the embryonic developmental management. Marine Life Science & Technology, 2(1): 24–30
    Jiang Dianhang, Zheng Xiaodong, Qian Yaosen, et al. 2020b. Embryonic development of Amphioctopus fangsiao under elevated temperatures: implications for resource management and conservation. Fisheries Research, 225: 105479. doi: 10.1016/j.fishres.2019.105479
    Kalyaanamoorthy S, Minh B Q, Wong T K F, et al. 2017. ModelFinder: fast model selection for accurate phylogenetic estimates. Nature Methods, 14(6): 587–589. doi: 10.1038/nmeth.4285
    Kimura M. 1980. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. Journal of Molecular Evolution, 16(2): 111–120. doi: 10.1007/BF01731581
    Lee S H, Kim Y, Shin M G. 2017. Spawning characteristics of Amphioctopus fangsiao in the southern coast of Korea. The Korean Journal of Malacology, 33(2): 131–136. doi: 10.9710/kjm.2017.33.2.131
    Lin Longshan, Li Zunlei, Jiang Yazhou. 2011. Current status of small yellow croaker resources in the southern Yellow Sea and the East China Sea. Chinese Journal of Oceanology and Limnology, 29(3): 547–555. doi: 10.1007/s00343-011-0182-8
    Liu Jinxian, Gao Tianxiang, Wu Shifang, et al. 2007. Pleistocene isolation in the northwestern Pacific marginal seas and limited dispersal in a marine fish, Chelon haematocheilus (temminck & schlegel, 1845). Periodical of Ocean University of China (in Chinese), 37(6): 931–938
    Liu Jinxian, Gao Tianxiang, Yokogawa K, et al. 2006. Differential population structuring and demographic history of two closely related fish species, Japanese sea bass (Lateolabrax japonicus) and spotted sea bass (Lateolabrax maculatus) in northwestern Pacific. Molecular Phylogenetics and Evolution, 39(3): 799–811. doi: 10.1016/j.ympev.2006.01.009
    Liu Liqin, Zhang Yao, Hu Xiaoyu, et al. 2019. Multiple paternity assessed in the cuttlefish Sepiella japonica (Mollusca, Cephalopoda) using microsatellite markers. ZooKeys, 880: 33–42. doi: 10.3897/zookeys.880.33569
    Lv Zhenming, Li Huan, Wu Changwen, et al. 2010. Genetic variation of Octopus ocellatus populations in China’s coastal waters based on the COI gene analysis. Haiyang Xuebao (in Chinese), 32(1): 130–138
    Marret F, de Vernal A, Pedersen T F, et al. 2001. Middle Pleistocene to Holocene palynostratigraphy of Ocean Drilling Program Site 887 in the Gulf of Alaska, northeastern north Pacific. Canadian Journal of Earth Sciences, 38(3): 373–386. doi: 10.1139/e00-092
    Meng Zining, Zhuang Zhimeng, Jin Xianshi, et al. 2003. Genetic diversity in small yellow croaker (Pseudosciaena polyactis) by RAPD analysis. Biodiversity Science (in Chinese), 11(3): 197–203. doi: 10.17520/biods.2003026
    Moritz C, Dowling T E, Brown W M. 1987. Evolution of animal mitochondrial DNA: relevance for population biology and systematics. Annual Review of Ecology and Systematics, 18: 269–292. doi: 10.1146/annurev.es.18.110187.001413
    Muhammad F, Dou Canfeng, Liu Liqin, et al. 2020. Genetic structure of Amphioctopus ovulum (Mollusca: Cephalopoda: Octopodidae) as revealed by mitochondrial and nuclear DNA. Thalassas: An International Journal of Marine Sciences, 36(2): 463–469. doi: 10.1007/s41208-020-00231-x
    Nei M. 1987. Molecular Evolutionary Genetics. New York: Columbia University Press
    Nguyen L T, Schmidt H A, von Haeseler A, et al. 2015. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Molecular Biology and Evolution, 32(1): 268–274. doi: 10.1093/molbev/msu300
    Ni Gang, Li Qi, Kong Lingfeng, et al. 2014. Comparative phylogeography in marginal seas of the northwestern Pacific. Molecular Ecology, 23(3): 534–548. doi: 10.1111/mec.12620
    Olivares-Paz A, Quinteiro J, Rey-Méndez M. 2006. Authentication of Fissurella species (Mollusca: Vetigastropoda), harvested in the Chilean coast, by PCR-RFLP. Investigaciones Marinas, 34(1): 113–118
    Page R D M. 1996. Tree view: an application to display phylogenetic trees on personal computers. Computer Applications in the Biosciences, 12(4): 357–358. doi: 10.1093/bioinformatics/12.4.357
    Pang Yumeng, Tian Yongjun, Fu Caihong, et al. 2020. Growth and distribution of Amphioctopus fangsiao (d’Orbigny, 1839–1841) in Haizhou Bay, Yellow Sea. Journal of Ocean University of China, 19(5): 1125–1132. doi: 10.1007/s11802-020-4322-7
    Parida S K, Kalia S K, Kaul S, et al. 2009. Informative genomic microsatellite markers for efficient genotyping applications in sugarcane. Theoretical and Applied Genetics, 118(2): 327–338. doi: 10.1007/s00122-008-0902-4
    Park S D E. 2001. Trypanotolerace in West African Cattle and the population genetic effects of selection [dissertation]. Dublin: Trinity College
    Prentis P J, Sigg D P, Raghu S, et al. 2009. Understanding invasion history: genetic structure and diversity of two globally invasive plants and implications for their management. Diversity and Distributions, 15(5): 822–830. doi: 10.1111/j.1472-4642.2009.00592.x
    Pritchard J K, Stephens M, Donnelly P. 2000. Inference of population structure using multilocus genotype data. Genetics, 15(2): 945–959
    R. R Development Core Team. 2006. A language and environment for statistical computing. Computing, 1: 12–21
    Rambaut A, Drummond A J, Xie Dong, et al. 2018. Posterior summarization in Bayesian phylogenetics using tracer 1.7. Systematic Biology, 67(5): 901–904. doi: 10.1093/sysbio/syy032
    Raymond M, Rousset F. 1995. GENEPOP (Version 1.2): population genetics software for exact tests and ecumenicism. Journal of Heredity, 86(3): 248–249. doi: 10.1093/oxfordjournals.jhered.a111573
    Sambrook J, Fritsch E R, Maniatis T. 1989. Molecular Cloning: A Laboratory Manual. 2nd ed. Cold Spring Harbor: Cold Spring Harbor Laboratory Press
    Segawa S, Nomoto A. 2002. Laboratory growth, feeding, oxygen consumption and ammonia excretion of Octopus ocellatus. Bulletin of Marine Science, 71(2): 801–813
    Sekino M, Hara M. 2001. Microsatellite DNA loci in Pacific abalone Haliotis discus discus (mollusca, gastropoda, haliotidae). Molecular Ecology Notes, 1(1–2): 8–10
    Shabani A, Askari G, Moradi A. 2013. Genetic variation of Garra rufa fish in Kermanshah and Bushehr provinces, Iran, using ssr microsatellite markers. Molecular Biology Research Communications, 2(3): 81–88
    Shao K T. 2009. Marine biodiversity and fishery sustainability. Asia Pacific Journal of Clinical Nutrition, 18(4): 527–531
    Simbine L, Viana da Silva J, Hilsdorf A W S. 2014. The genetic diversity of wild Oreochromis mossambicus populations from the Mozambique southern watersheds as evaluated by microsatellites. Journal of Applied Ichthyology, 30(2): 272–280. doi: 10.1111/jai.12390
    Simons A M, Wood R M, Heath L S, et al. 2001. Phylogenetics of Scaphirhynchus based on mitochondrial DNA sequences. Transactions of the American Fisheries Society, 130(3): 359–366. doi: 10.1577/1548-8659(2001)130<0359:POSBOM>2.0.CO;2
    Song Na, Li Pengfei, Zhang Xiumei, et al. 2018. Changing phylogeographic pattern of Fenneropenaeus chinensis in the Yellow Sea and Bohai Sea inferred from microsatellite DNA: implications for genetic management. Fisheries Research, 200: 11–16. doi: 10.1016/j.fishres.2017.12.003
    Song Na, Ma Guoqiang, Zhang Xiumei, et al. 2014. Genetic structure and historical demography of Collichthys lucidus inferred from mtDNA sequence analysis. Environmental Biology of Fishes, 97(1): 69–77. doi: 10.1007/s10641-013-0124-8
    Strugnell J M, Watts P C, Smith P J, et al. 2012. Persistent genetic signatures of historic climatic events in an antarctic octopus. Molecular Ecology, 21(11): 2775–2787. doi: 10.1111/j.1365-294X.2012.05572.x
    Tamaki K, Honza E. 1991. Global tectionics and formation of marginal basins: role of the western Pacific. Episodes, 14(3): 224–230. doi: 10.18814/epiiugs/1991/v14i3/005
    Tamura K, Peterson D, Peterson N, et al. 2011. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Molecular Biology and Evolution, 28(10): 2731–2739. doi: 10.1093/molbev/msr121
    Tang Yan, Zheng Xiaodong, Liu Haijuan. 2020. Population genetics and comparative mitogenomic analyses reveal cryptic diversity of Amphioctopus neglectus (cephalopoda: octopodidae). Genomics, 112(6): 3893–3902. doi: 10.1016/j.ygeno.2020.06.036
    Tokuyama T, Shy J Y, Lin Huichen, et al. 2020. Genetic population structure of the fiddler crab Austruca lactea (De Haan, 1835) based on mitochondrial DNA control region sequences. Crustacean Research, 49: 141–153. doi: 10.18353/crustacea.49.0_141
    Tziouveli V, Yokoyama S. 2017. A comparison of the fatty acid profiles of newly hatched, fed, and starved juveniles of Amphioctopus fangsiao (d’orbigny 1839). Aquaculture International, 25(4): 1531–1542. doi: 10.1007/s10499-017-0130-5
    Waples R S. 1998. Separating the wheat from the chaff: patterns of genetic differentiation in high gene flow species. Journal of Heredity, 5: 438–450
    Weir B S, Cockerham C C. 1984. Estimating F-statistics for the analysis of population structure. Evolution, 38(6): 1358–1370
    Wirgin I, Waldman J R, Rosko J, et al. 2000. Genetic structure of Atlantic sturgeon populations based on mitochondrial DNA control region sequences. Transactions of the American Fisheries Society, 129(2): 476–486. doi: 10.1577/1548-8659(2000)129<0476:GSOASP>2.0.CO;2
    Ying Yiping, Chen Yong, Lin Longshan, et al. 2011. Risks of ignoring fish population spatial structure in fisheries management. Canadian Journal of Fisheries and Aquatic Sciences, 68(12): 2101–2120. doi: 10.1139/f2011-116
    Zane L, Bargelloni L, Patarnello T. 2002. Strategies for microsatellite isolation: a review. Molecular Ecology, 11(1): 1–16. doi: 10.1046/j.0962-1083.2001.01418.x
    Zhang Xiaoying. 2017. Studies on the cryptic species in Amphioctopus fangsiao based on morphology and complete mitochondrial genomes (in Chinese)[dissertation]. Qingdao: Ocean University of China
    Zhang Libing. 2020. Roles of land bridges in global biogeography and ecosystems. Cladistics, 36(2): 232–233. doi: 10.1111/cla.12398
    Zhang Longgang, Yang Jianmin, Liu Xiangquan, et al. 2009. The genetic diversity of Octopus ocellatus by AFLP markers. Oceanologia et limnologia Sinica, 40(6): 803–807
    Zheng Xiaodong, Ikeda M, Kong Lingfeng, et al. 2009. Genetic diversity and population structure of the golden cuttlefish, Sepia esculenta (Cephalopoda: sepiidae) indicated by microsatellite DNA variations. Marine Ecology, 30(4): 448–454. doi: 10.1111/j.1439-0485.2009.00294.x
    Zheng Jian, Li Congjun, Zheng Xiaodong. 2022. Toxic effects of polystyrene microplastics on the intestine of Amphioctopus fangsiao (Mollusca: Cephalopoda): from physiological responses to underlying molecular mechanisms. Chemosphere, 308: 136362
    Zheng Jian, Li Qi, Zheng Xiaodong. 2023. Ocean acidification increases copper accumulation and exacerbates copper toxicity in Amphioctopus fangsiao (Mollusca: Cephalopoda): A potential threat to seafood safety. The Science of the Total Environment, 891: 164473
  • 加载中

Catalog

    通讯作者: 陈斌, bchen63@163.com
    • 1. 

      沈阳化工大学材料科学与工程学院 沈阳 110142

    1. 本站搜索
    2. 百度学术搜索
    3. 万方数据库搜索
    4. CNKI搜索

    Figures(8)  / Tables(4)

    Article Metrics

    Article views (320) PDF downloads(12) Cited by()
    Proportional views
    Related

    /

    DownLoad:  Full-Size Img  PowerPoint
    Return
    Return