Volume 40 Issue 5
Sep.  2019
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Dong-Dong Zhai, Wen-Jing Li, Huan-Zhang Liu, Wen-Xuan Cao, Xin Gao. Genetic diversity and temporal changes of an endemic cyprinid fish species, Ancherythroculter nigrocauda, from the upper reaches of Yangtze River. Zoological Research, 2019, 40(5): 427-438. doi: 10.24272/j.issn.2095-8137.2019.027
Citation: Dong-Dong Zhai, Wen-Jing Li, Huan-Zhang Liu, Wen-Xuan Cao, Xin Gao. Genetic diversity and temporal changes of an endemic cyprinid fish species, Ancherythroculter nigrocauda, from the upper reaches of Yangtze River. Zoological Research, 2019, 40(5): 427-438. doi: 10.24272/j.issn.2095-8137.2019.027

Genetic diversity and temporal changes of an endemic cyprinid fish species, Ancherythroculter nigrocauda, from the upper reaches of Yangtze River

doi: 10.24272/j.issn.2095-8137.2019.027
Funds:  the Special Program for Basic Science and Technology Research(2014FY120200);Research Project of China Three Gorges Corporation(0799570);Research Project of Hubei Key Laboratory of Three Gorges Project for Conservation of Fishes(SXSN/4381)
More Information
  • Corresponding author: Xin Gao
  • Received Date: 2018-12-01
  • Publish Date: 2019-09-18
  • Small populations with low genetic diversity are prone to extinction. Knowledge on the genetic diversity and structure of small populations and their genetic response to anthropogenic effects are of critical importance for conservation management. In this study, samples of Ancherythroculter nigrocauda, an endemic cyprinid fish from the upper reaches of Yangtze River, were collected from five sites to analyze their genetic diversity and population structure using mitochondrial cytochrome b gene and 14 microsatellite loci. Haplotype diversity, nucleotide diversity, and expected heterozygosity indicated that the A. nigrocauda populations had low genetic diversity, and decreased heavily from 2001 to 2016. Significant genetic differentiation was found among different populations in the cyt b gene and SSR markers based on the genetic differentiation index (F ST), whereas no differentiation was found in 2001. Haplotype genealogy showed that eight out of 15 haplotypes were private to one population. The SSR STRUCTURE analysis showed that there were four genetic clusters in the A. nigrocauda samples, with each population forming a single cluster, except for the Chishui River (CSR) and Mudong River (MDR) populations, which formed a common cluster. Therefore, loss of genetic diversity and increased genetic differentiation were found in the A. nigrocauda populations, which could be attributed to dam construction, overfishing, and water pollution in the upper Yangtze River. It is therefore recommended that the government should ban fishing, control water pollution, increase river connectivity, and establish artificial breeding and stocking.
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  • [1]
    null Altizer S , Harvell D , Friedle E . 2003. Rapid evolutionary dynamics and disease threats to biodiversity. Trends in Ecology and Evolution, 18(11): 589–596.
    null Bandelt HJ , Forster P , R?hl A . 1999. Median-joining networks for inferring intraspecific phylogenies. Molecular Biology and Evolution, 16(1): 37–48.
    null Cao W . 2011. The current situation and conservation measure of fish resource in the Yangtze River. Jiangxi Fishery Sciences and Technology , (2): 1–4. (in Chinese)
    null Cao W , Chang J , Qiao Y , Duan Z . 2007. Fish Resources of Early Life History Stages in Yangtze River. Beijing, China: China Water Power Press. (in Chinese)
    null Cornuet JM , Luikart G . 1996. Description and power analysis of two tests for detecting recent population bottlenecks from allele frequency data. Genetics, 144(4): 2001–2014.
    null Ding R . 1994. The Fishes of Sichuan, China. Chengdu, Sichuan, China: Sichuan Publishing House of Science and Technology. (in Chinese)
    null Dong YW , Wang HS , Han GD , Ke CH , Zhan X , Nakano T , Williams GA . 2012. The impact of Yangtze River discharge, ocean currents and historical events on the biogeographic pattern of Cellana toreuma along the China Coast. PLoS One , 7(4): e36178.
    null Dudgeon D . 2011. Asian river fishes in the Anthropocene: threats and conservation challenges in an era of rapid environmental change. Journal of Fish Biology, 79(6): 1487–1524.
    null Earl DA , Vonholdt BM . 2012. STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method. Conservation Genetics Resources, 4(2): 359–361.
    null Estoup A , Rousset F , Michalakis Y , Cornuet J , Adriamanga M , Guyomard R . 1998. Comparative analysis of microsatellite and allozyme markers: a case study investigating microgeographic differentiation in brown trout (Salmo trutta). Molecular Ecology, 7(3): 339–353.
    null 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.
    null Excoffier L , Laval G , Schneider S . 2005. Arlequin (version 3. 0)an integrated software package for population genetics data analysis. Evolutionary Bioinformatics, 1(4A): 47–50.
    null Excoffier L , Smouse PE , Quattro JM . 1992. Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data. Genetics, 131(2): 479–491.
    null Falush D , Stephens M , Pritchard JK . 2003. Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies. Genetics, 164(4): 1567–1587.
    null Frankham R , Ballou JD , Briscoe DA . 2002. Introduction to Conservation Genetics. Cambridge: Cambridge University Press.
    null Fu C , Wu J , Chen J , Wu Q , Lei G . 2003. Freshwater fish biodiversity in the Yangtze River basin of China: patterns, threats and conservation. Biodiversity and Conservation, 12(8): 1649–1685.
    null Fu YX . 1997. Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection. Genetics, 147(2): 915–925.
    null Gao X . 2008. Conservation Biology of Rare and Endemic Fishes of the Yangtze River. Ph.D. dissertation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 155. (in Chinese)
    null Gibson JP , Rice SA , Stucke CM . 2008. Comparison of population genetic diversity between a rare narrowly distributed species and a common widespread species of Alnus (Betulaceae). American Journal of Botany, 95(5): 588–596.
    null Goudet J . 2001. FSTAT, a program to estimate and test gene diversities and fixation indices. http: // .
    null Guo SW , Thompson EA . 1992. Performing the exact test of Hardy-Weinberg proportion for multiple alleles. Biometrics, 48(2): 361–372.
    null Hamrick JL , Godt MJW . 1996. Conservation genetics of endemic plant species. In: Avise JC, Hamrick JL. Conservation Genetics. New York, USA: Chapman and Hall, 281–304.
    null Han ZQ , Zhu WB , Zheng W , Li PF , Shui BN . 2015. Significant genetic differentiation between the Yellow Sea and East China Sea populations of cocktail shrimp Trachypenaeus curvirostris revealed by the mitochondrial DNA COI gene. Biochemical Systematics and Ecology, 59: 78–84.
    null H?nfling B , Weetman D . 2006. Concordant genetic estimators of migration reveal anthropogenically-enhanced source-sink population structure in the river sculpin, Cottus gobio . Genetics, 173(3): 1487–1501.
    null Harrison S , Hastings A . 1996. Genetic and evolutionary consequences of metapopulation structure. Trends in Ecology and Evolution, 11(4): 180–183.
    null He Q , Peng S , Zhai J , Xiao H . 2011. Development and application of a water pollution emergency response system for the Three Gorges Reservoir in the Yangtze River, China. Journal of Environmental Sciences, 23(4): 595–600.
    null Hedrick PW , Kalinowski ST . 2000. Inbreeding depression in conservation biology. Annual Review of Ecology and Systematics, 31: 139–162.
    null Jager HI , Chandler JA , Lepla KB , Winkle WV . 2001. A theoretical study of river fragmentation by dams and its effects on white sturgeon populations. Environmental Biology of Fishes, 60(4): 347–361.
    null Jakobsson M , Rosenberg NA . 2007. CLUMPP: a cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure. Bioinformatics, 23(14): 1801–1806.
    null Kalinowski ST , Taper ML , Marshall TC . 2007. Revising how the computer program CERVUS accommodates genotyping error increases success in paternity assignment. Molecular Ecology, 16(5): 1099–1106.
    null Keyghobadi N . 2007. The genetic implications of habitat fragmentation for animals. Canadian Journal of Zoology, 85(10): 1049–1064.
    null Kocher TD , Thomas WK , Meyer A , Edwards SV , P??bo S , Villablanca FX , Wilson AC . 1989. Dynamics of mitochondrial DNA evolution in animals: amplification and sequencing with conserved primers. Proceedings of the National Academy of Sciences of the United States of America, 86(16): 6196–6200.
    null Kumar S , Stecher G , Tamura K . 2016. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Molecular Biology and Evolution, 33(7): 1870–1874.
    null Li W , Wang H , Liu H , Cao W , Wang X , Yu J , Zhu X . 2018. Genetic diversity and population demographic history of Hemiculterella sauvagei in the Chishui River. Acta Hydrobiologica Sinica, 42(1): 106–113. (in Chinese)
    null Librado P , Rozas J . 2009. DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics, 25(11): 1451–1452.
    null Liu C . 2013. Studies on the Biology, Population Dynamics and Genetic Diversity of Ancherythroculter nigrocauda . Ph.D. dissertation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 139. (in Chinese)
    null Liu C , Gao X , Wang H , Liu H , Cao W , Danley PD . 2013. Reproductive characteristics of Ancherythroculter nigrocauda, an endemic fish in the upper Yangtze River, China. Fisheries Science, 79(5): 799–806.
    null Liu H , Zhu Y , Wang J , Tan D . 2005. Population genetic structure of an endemic cyprinid fish, Ancherythroculter nigrocauda, in the upper reaches of the Yangtze River and its implication for conservation. Korean Journal of Genetics, 27(4): 361–367.
    null Liu RM , Yang ZF , Shen ZY , Yu SL , Ding XW , Xing W , Fang L . 2009. Estimating nonpoint source pollution in the upper Yangtze River using the export coefficient model, remote sensing, and geographical information system. Journal of Hydraulic Engineering, 135(9): 698–704.
    null Matthews WJ . 1998. Patterns in Freshwater Fish Ecology. New York, USA: Chapman and Hall.
    null Meldgaard T , Nielsen EE , Loeschcke V . 2003. Fragmentation by weirs in a riverine system: A study of genetic variation in time and space among populations of European grayling (Thymallus thymallus) in a Danish river system. Conservation Genetics, 4(6): 735–747.
    null Moritz C . 1999. Conservation units and translocations: strategies for conserving evolutionary processes. Hereditas, 130(3): 217–228.
    null Mukesh, Fernandes M , Han J , Sathyakumar S . 2013. Genetics driven interventions for ex situ conservation of red junglefowl (Gallus gallus murghi) populations in India. Zoo Biology, 32(5): 476–483.
    null Neraas LP , Spruell P . 2001. Fragmentation of riverine systems: the genetic effects of dams on bull trout (Salvelinus confluentus) in the Clark Fork River system. Molecular Ecology, 10(5): 1153–1164.
    null Nilsson C , Reidy CA , Dynesius M , Revenga C . 2005. Fragmentation and flow regulation of the world’s large river systems. Science, 308(5720): 405–408.
    null Oliveira R , Godinho R , Randi E , Ferrand N , Alves PC . 2008. Molecular analysis of hybridisation between wild and domestic cats (Felis silvestris) in Portugal: implications for conservation. Conservation Genetics, 9(1): 1–11.
    null Park YS , Chang J , Sovan L , Cao W , Brosse S . 2003. Conservation strategies for endemic fish species threatened by the Three Gorges Dam. Conservation Biology, 17(6): 1748–1758.
    null Pinsky ML , Palumbi SR . 2014. Meta-analysis reveals lower genetic diversity in overfished populations. Molecular Ecology, 23(1): 29–39.
    null Piry S , Luikart G , Cornuet JM . 1999. Computer note. BOTTLENECK: a computer program for detecting recent reductions in the effective size using allele frequency data. Journal of Heredity, 90(4): 502–503.
    null Pritchard JK , Stephens M , Donnelly P . 2000. Inference of population structure using multilocus genotype data. Genetics, 155(2): 945–959.
    null Rice WR . 1989. Analyzing tables of statistical tests. Evolution, 43(1): 223–225.
    null Rogers AR , Harpending H . 1992. Population growth makes waves in the distribution of pairwise genetic differences. Molecular Biology and Evolution, 9(3): 552–569.
    null Rosenberg NA . 2003. DISTRUCT: a program for the graphical display of population structure. Molecular Ecology Notes, 4(1): 137–138.
    null Rousset F . 2008. GENEPOP'007: a complete re-implementation of the genepop software for Windows and Linux. Molecular Ecology Resources, 8(1): 103–106.
    null Slatkin M , Hudson RR . 1991. Pairwise comparisons of mitochondrial DNA sequences in stable and exponentially growing populations. Genetics, 129(2): 555–562.
    null Tajima F . 1989. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics, 123(3): 585–595.
    null Tan DQ , Wang JW , Yan TM , Dan SG . 2004. Studies on the artificial propagation of Ancherythroculter nigrocauda . Resources and Environment in the Yangtze Basin, 13(2): 193–196. (in Chinese)
    null Van Oosterhout C , Hutchinson WF , Wills DPM , Shipley P . 2004. Micro-checker: software for identifying and correcting genotyping errors in microsatellite data. Molecular Ecology Resources, 4(3): 535–538.
    null Wang J . 1994. The cascade hydroelectric dams of Longxi River. Sichuan Water Conservancy, 15(6): 52–54. (in Chinese)
    null Wang T , Gao X , Wang J , Jakovli? I , Dan SG , Liu HZ . 2015. Life history traits and implications for conservation of rock carp Procypris rabaudi Tchang, an endemic fish in the upper Yangtze River, China. Fisheries Science, 81(3): 515–523.
    null Xiao W , Zhang Y , Liu H . 2001. Molecular systematics of Xenocyprinae (Teleostei: Cyprinidae): taxonomy, biogeography, and coevolution of a special group restricted in East Asia. Molecular Phylogenetics and Evolution, 18(2): 163–173.
    null Xiong F , Liu H , Duan X , Liu S , Chen D . 2016. Estimating population abundance and utilization of Rhinogobio ventralis, an endemic fish species in the upper Yangtze River. Biodiversity Science, 24(3): 304–312.
    null Xu Y . 2010. Study of Organic Pollution and Migration of Typical Organic Pollutants in the Upstream of the Yangtze River in Chongqing. Master thesis, University of Xinan, Chongqing, 46. (in Chinese)
    null Xue Z , He X . 2001. Studies on the age and growth of Ancherithroculter nigrocauda Yih et Woo. Journal of Southwest China Normal University, 26(6): 712–717. (in Chinese)
    null Yang M , Li X . 2018. Population genetic structure of the mantis shrimp Oratosquilla oratoria (Crustacea: Squillidae) in the Yellow Sea and East China Sea. Journal of Oceanology and Limnology, 36(3): 905–912.
    null Yi YJ , Sun J , Tang CH , Zhang SH . 2016. Ecological risk assessment of heavy metals in sediment in the upper reach of the Yangtze River. Environmental Science and Pollution Research, 23(11): 11002–11013.
    null Yin H , Lv H . 2010. Studies on artificial propagation of Ancherythroculter nigrocauda . Journal of Aquaculture, 31(5): 30–31. (in Chinese)
    null Young A , Boyle T , Brown T . 1996. The population genetic consequences of habitat fragmentation for plants. Trends in Ecology and Evolution, 11(10): 413–418.
    null Young EF , Tysklind N , Meredith MP , de Bruyn M , Belchier M , Murphy EJ , Carvalho GR . 2018. Stepping stones to isolation: Impacts of a changing climate on the connectivity of fragmented fish populations. Evolutionary Applications, 11(6): 978–994.
    null Yu X , Luo T , Zhou H . 2005. Large-scale patterns in species diversity of fishes in the Yangtze River Basin. Biodiversity Science, 13(6): 473–495. (in Chinese)
    null Zhang B , Li M , Zhang Z , Goossens B , Zhu L , Zhang S , Hu J , Bruford MW , Wei F . 2007. Genetic viability and population history of the Giant Panda, putting an end to the “Evolutionary Dead End”?. Molecular Biology and Evolution, 24(8): 1801–1810.
    null Zhang F , Duan Y , Cao S , Wang J , Tan D . 2011. High genetic diversity in population of Lepturichthys fimbriata from the Yangtze River revealed by microsatellite DNA analysis. Chinese Science Bulletin, 57(5): 487–491.
    null Zhang F , Tan D . 2010. Genetic diversity in population of largemouth bronze gudgeon (Coreius guichenoti Sauvage et Dabry) from Yangtze River determined by microsatellite DNA analysis. Genes and Genetic Systems, 85(5): 351–357.
    null Zhao L , Chenoweth EL , Liu J , Liu Q . 2016. Effects of dam structures on genetic diversity of freshwater fish Sinibrama macrops in Min River, China. Biochemical Systematics and Ecology, 68: 216–222.
    null Zhong Y , Power G . 1996. Environmental impacts of hydroelectric projects on fish resources in China. River Research and Applications, 12(1): 81–98.
    null Zhu D , Chang J . 2008. Annual variations of biotic integrity in the upper Yangtze River using an adapted index of biotic integrity (IBI). Ecological Indicators, 8(5): 564–572.
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