Abstract
Pampus minor is an important commercial fish. Due to the similarity of external morphological characteristics among the genus Pampus species, P. minor has often been identified as the juvenile group of both P. cinereus and P. argenteus. While little genetic background on this species is known, this study was based on control region sequences and provided the first evaluation of the genetic signature of 264 individuals of P. minor from 11 populations along the coasts of China and Malaysia. The results indicate high genetic haplotype diversity and low nucleotide diversity in this species. Additionally, two differentiated haplotype lineages were identified in the P. minor populations. However, phylogenetic structures corresponding to the geographical locations were unable to be established. Analysis of molecular variance identified a vast majority of the genetic variation occurring within populations. F-statistic test value (FST) of pairwise indicated that great differences existed between the Chinese and Malaysian P. minor populations. For the Chinese populations, the genetic differences were insignificant with the exception of the Xiamen population, which is a marginal population. During the late Pleistocene, a population expansion of P. minor occurred. These expanded populations originated from the glacial refugium in the South China Sea and then rapidly occupied and adapted to their new habitat. The results of this study provide genetic information for ensuring the protection and management of P. minor resources.
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References
Allendorf F W, England P R, Luikart G, et al. 2008. Genetic effects of harvest on wild animal populations. Trends in Ecology and Evolution, 23(6): 327–337, doi: https://doi.org/10.1016/j.tree.2008.02.008
Aris-Brosou S, Excoffier L. 1996. The impact of population expansion and mutation rate heterogeneity on DNA sequence polymorphism. Molecular Biology and Evolution, 13(3): 494–504, doi: https://doi.org/10.1093/oxfordjournals.molbev.a025610
Avise J C. 1998. The history and purview of phylogeography: a personal reflection. Molecular Ecology, 7(4): 371–379, doi: https://doi.org/10.1046/j.1365-294x.1998.00391.x
Avise J C, Neigel J E, Arnold J. 1984. Demographic influences on mitochondrial DNA lineage survivorship in animal populations. Journal of Molecular Evolution, 20(2): 99–105, doi: https://doi.org/10.1007/BF02257369
Bowen B W, Bass A L, Rocha L A, et al. 2007. Phylogeography of the trumpetfishes (Aulostomus): ring species complex on a global scale. Evolution, 55(5): 1029–1039, doi: https://doi.org/10.1111/j.0014-3820.2001.tb00619.x
Bridle J R, Vines T H. 2007. Limits to evolution at range margins: when and why does adaptation fail?. Trends in Ecology and Evolution, 22(3): 140–147, doi: https://doi.org/10.1016/j.tree.2006.11.002
Butchart S H M, Walpole M, Collen B, et al. 2010. Global biodiversity: indicators of recent declines. Science, 328(5982): 1164–1168, doi: https://doi.org/10.1126/science.1187512
Cui Zhaoxia, Liu Yuan, Liu Jing, et al. 2010. Molecular identification of Pampus fishes (Perciformes, Stromateidae). Ichthyological Research, 57(1): 32–39, doi: https://doi.org/10.1007/s10228-009-0119-9
Drummond A J, Suchard M A, Xie Dong, et al. 2012. Bayesian phylogenetics with BEAUti and the BEAST 1.7. Molecular Biology and Evolution, 29(8): 1969–1973, doi: https://doi.org/10.1093/molbev/mss075
Dynesius M, Jansson R. 2000. Evolutionary consequences of changes in species’ geographical distributions driven by Milankovitch climate oscillations. Proceedings of the National Academy of Sciences of the United States of America, 97(16): 9115–9120, doi: https://doi.org/10.1073/pnas.97.16.9115
Ellegren H. 2014. Genome sequencing and population genomics in non-model organisms. Trends in Ecology and Evolution, 29(1): 51–63, doi: https://doi.org/10.1016/j.tree.2013.09.008
Excoffier L, Laval G, Schneider S. 2005. Arlequin (version 3.0): an integrated software package for population genetics data analysis. Evolutionary Bioinformatics, 1: 47–50, doi: https://doi.org/10.1177/117693430500100003
Funk W C, McKay J K, Hohenlohe P A, et al. 2012. Harnessing genomics for delineating conservation units. Trends in Ecology and Evolution, 27(9): 489–496, doi: https://doi.org/10.1016/j.tree.2012.05.012
Gao Jingsong. 2013. The research on the eddy in the northern South China Sea and circulation in the Beibu Gulf [dissertation] (in Chinese). Qingdao: Ocean University of China
Ge Qian. 2010. Paleoenvironmental and paleoclimatic records from the South China Sea since the late last Glaical Period [dissertation] (in Chinese). Wuhan: China University of Geosciences
Gong Gwoching, Liu Konkee, Chiang Kuoping, et al. 2011. Yangtze River floods enhance coastal ocean phytoplankton biomass and potential fish production. Geophysical Research Letters, 38(13): L13603, doi: https://doi.org/10.1029/2011GL047519
Grant W S, Bowen B W. 1998. Shallow population histories in deep evolutionary lineages of marine fishes: Insights from sardines and anchovies and lessons for conservation. Journal of Heredity, 89(5): 415–426, doi: https://doi.org/10.1093/jhered/89.5.415
Guo Enmian, Liu Yuan, Liu Jing, et al. 2010. DNA barcoding discriminates Pampus minor (Liu et al., 1998) from Pampus species. Chinese Journal of Oceanology and Limnology, 28(6): 1266–1274, doi: https://doi.org/10.1007/s00343-010-9917-1
Guo Qinfeng, Kelt D A, Sun Zhongyu, et al. 2013. Global variation in elevational diversity patterns. Scientific Reports, 3: 3007, doi: https://doi.org/10.1038/srep03007
Han Zhiqiang, Yanagimoto T, Zhang Yaping, et al. 2012. Phylogeography study of Ammodytes personatus in northwestern Pacific: Pleistocene isolation, temperature and current conducted secondary contact. PLoS One, 7: e37425, doi: https://doi.org/10.1371/journal.pone.0037425
He Lijun, Mukai T, Chu Kahou, et al. 2015. Biogeographical role of the Kuroshio Current in the amphibious mudskipper Periophthalmus modestus indicated by mitochondrial DNA data. Scientific Reports, 5: 15645, doi: https://doi.org/10.1038/srep15645
He Lijun, Zhang Aibing, Weese D, et al. 2014. Demographic response of cutlassfish (Trichiurus japonicus and T. nanhaiensis) to fluctuating palaeo-climate and regional oceanographic conditions in the China seas. Scientific Reports, 4: 6380, doi: https://doi.org/10.1038/srep06380
Hewitt G. 2000. The genetic legacy of the Quaternary ice ages. Nature, 405(6789): 907–913, doi: https://doi.org/10.1038/35016000
Jian Zhimin, Wang Lüjiang, Kienast M. 1999. Late Quaternary surface paleoproductivity and variations of the East Asian Monsoon in the South China Sea. Quaternary Sciences (in Chinese), 19(1): 32–40
Jin Xianshi, Zhao Xianyong, Meng Tianxiang, et al. 2005. Biology Resource and Environment in the Bohai Sea and Yellow Sea (in Chinese). Beijing: Scientific Press, 287–299
Jing Chunsheng, Zhu Xueming, Bao Xianwen, et al. 2011. Three dimensional tidal current numerical simulation based on FV-COM in and around Xiamen Bay. Journal of Oceanography in Taiwan Strait (in Chinese), 30(1): 103–113
Lambeck K, Esat T M, Potter E K. 2002. Links between climate and sea levels for the past three million years. Nature, 419(6903): 199–206, doi: https://doi.org/10.1038/nature01089
Lecomte F, Grant W S, Dodson J J, et al. 2004. Living with uncertainty: genetic imprints of climate shifts in East Pacific anchovy (Engraulis mordax) and sardine (Sardinops sagax). Molecular Ecology, 13(8): 2169–2182, doi: https://doi.org/10.1111/j.1365-294X.2004.02229.x
Li Yuan, Gao Tianxiang, Zhou Yongdong, et al. 2019a. Spatial genetic subdivision among populations of Pampus chinensis between China and Pakistan: testing the barrier effect of the Malay Peninsula. Aquatic Living Resources, 32(8): 1–10, doi: https://doi.org/10.1051/alr/2019004
Li Yuan, Lin Longshan, Song Na, et al. 2018. Population genetics of Pampus echinogaster along the Pacific coastline of China: Insights from the mitochondrial DNA control region and microsatellite molecular markers. Marine and Freshwater Research, 69(6): 971–981, doi: https://doi.org/10.1071/MF17218
Li Yuan, Zhang Yan, Lin Longshan, et al. 2017. New genetic perspectives of the ambiguous pomfret as revealed by CR sequences. ZooKeys, 719: 59–73, doi: https://doi.org/10.3897/zookeys.719.19914
Li Yuan, Zhang Liyan, Loh K, et al. 2019b. Genetic diversity comparison of Pampus minor between Chinese and Malaysian populations inferred from mtDNA Cytb. Pakistan Journal of Zoology, 51(1): 149–157, doi: https://doi.org/10.17582/journal.pjz/2019.51.1.149.157
Li Naisheng, Zhao Songling, Wasiliev B. 2000. Geology of Marginal Seas in the Northwest Pacific (in Chinese). Harbin: Heilongjiang Education Press, 60–68, 485–486
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). Molecular Ecology, 16(2): 275–288, doi: https://doi.org/10.1111/j.1365-294X.2006.03140.x
Liu Jing, Li Chunsheng. 1998. A new pomfret species, Pampus minor sp. nov. (Stromateidae) from Chinese waters. Chinese Journal of Oceanology and Limnology, 16(3): 280–285, doi: https://doi.org/10.1007/BF02848735
Pauly D, Christensen V. 1995. Primary production required to sustain global fisheries. Nature, 374(6519): 255–257, doi: https://doi.org/10.1038/374255a0
Qiao Fangli. 2012. Regional Oceanography of China Seas: Physical Oceanography (in Chinese). Beijing: China Ocean Press, 310–350
Rogers A R, Harpending H. 1992. Population growth makes waves in the distribution of pairwise genetic differences. Molecular Biology and Evolution, 9(3): 552–569, doi: https://doi.org/10.1093/oxfordjournals.molbev.a040727
Rosel P E, Haygood M G, Perrin W F. 1995. Phylogenetic relationships among the true porpoises (Cetacea: Phocoenidae). Molecular Phylogenetics and Evolution, 4(4): 463–474, doi: https://doi.org/10.1006/mpev.1995.1043
Shen Kangning, Jamandre B W, Hsu C C, et al. 2011. Plio-Pleistocene sea level and temperature fluctuations in the northwestern Pacific promoted speciation in the globally-distributed flathead mullet Mugil cephalus. BMC Evolutionary Biology, 11(1): 83, doi: https://doi.org/10.1186/1471-2148-11-83
Stepien C A. 1999. Phylogeographical structure of the Dover sole Microstomus pacificus: the larval retention hypothesis and genetic divergence along the deep continental slope of the Northeastern Pacific Ocean. Molecular Ecology, 8(6): 923–939, doi: https://doi.org/10.1046/j.1365-294x.1999.00643.x
Stockwell C A, Hendry A P, Kinnison M T. 2003. Contemporary evolution meets conservation biology. Trends in Ecology & Evolution, 18(2): 94–101, doi: https://doi.org/10.1016/S0169-5347(02)00044-7
Sun Peng, Tang Baojun. 2018. Low mtDNA variation and shallow population structure of the Chinese pomfret Pampus chinensis along the China coast. Journal of Fish Biology, 92(1): 214–228, doi: https://doi.org/10.1111/jfb.13515
Tamura K, Peterson D, Peterson N, et al. 2011. MEGA 5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Molecular Biology and Evolution, 28(10): 2731–2739, doi: https://doi.org/10.1093/molbev/msr121
Wang Pinxian. 1999. Response of Western Pacific marginal seas to glacial cycles: paleoceanographic and sedimentological features. Marine Geology, 156(1–4): 5–39, doi: https://doi.org/10.1016/S0025-3227(98)00172-8
Wright S. 1965. The interpretation of population structure by F-statistics with special regard to systems of mating. Evolution, 19(3): 395–420, doi: https://doi.org/10.1111/j.1558-5646.1965.tb01731.x
Wu Renxie, Liang Xiuhe, Zhuang Zhimeng, et al. 2012. Mitochondrial CO I sequance variation of silver pomfret (Pampus argentus) from Chinese coastal waters. Acta Zootaxonomica Sinica (in Chinese), 37(3): 480–488
Acknowledgements
We thank assistance from Xiang Zhang, Binbin Shan, Yan Li and Karhoe Loh during the collection of P. minor specimens. We also thank the anonymous reviewers for their helpful comments.
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Foundation item: The National Key Research and Development Program of China under contract No. 2018YFC1406302; the National Programme on Global Change and Air-Sea Interaction under contract No. GASI-02-SCS-YDsum; the Fond of Fujian Provincial Research Institutes of Basic Research and Public Service Special Operations under contract No. 2017R1006-5; the Fond of Bilateral Cooperation of Maritime Affairs under contract No. 2200207.
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Li, Y., Zhang, L., Zhang, J. et al. Levels and patterns of genetic variation in Pampus minor: Assessment of a mitochondrial DNA control region sequence. Acta Oceanol. Sin. 40, 74–83 (2021). https://doi.org/10.1007/s13131-021-1784-4
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DOI: https://doi.org/10.1007/s13131-021-1784-4