Population Genetic Study of Triplophysa yarkandensis in Tarim River Basin in Xinjiang
ZHAO Wenhao1, YI Shaokui2, ZHOU Qiong1, SHEN Jianzhong1, LI Dapeng1, ZHOU Xiaoyun1
1. Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture and Rural Affaires, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China; 2. College of Life Sciences, Huzhou University, Huzhou 313000, China
Abstract：To understand the population genetic characteristics of Triplophysa yarkandensis in Tarim River Basin in Xinjiang, eight populations of T. yarkandensis were collected from two tributaries of the Tarim River Basin (Qarqan River and Weigan River), and the genetic diversity and population structure were analyzed using mitochondrial COⅠ gene, as well as the newly developed SSR markers. Based on COⅠ sequences, 22 haplotypes were detected, with average haplotype diversity index of 0.8829 and nucleotide diversity index of 0.0032. Based on SSR markers, there was polymorphism information content of 0.629—0.696, observed heterozygosity of 0.607—0.736 and expected heterozygosity range of 0.655—0.755. The results above suggested a high level of genetic diversity in each population. Both COⅠ and SSR results exhibited lower genetic differentiation between populations; the AMOVA results showed that the genetic variations were primarily derived from intra-population (COⅠ, 95.12%; SSR, 97.23%); the genetic distance exhibited a lower level; and the gene flow in the studied populations were higher than 1, suggesting a weak degree of genetic differentiation and an obviously gene flow between populations. The UPGMA phylogenetic tree constructed based on SSR markers showed that the populations from Qarqan River and Weigan River were clustered into separate genetic branch; there was obviously different genetic composition between populations from the two tributaries based on the population structure analysis; and potential genetic barriers were observed based on Barrier analysis. These results indicated that some genetic variation occurred between populations from the two tributaries. To sum up, the genetic diversity of T. yarkandensis populations was found to be relative higher in Tarim River, and obvious gene flow between populations can be detected. However, because of the habitat fragmentation in Tarim River system, potential gene flow barriers occurred between populations from Qarqan River and Weigan River, which resulted in obvious genetic differentiation between populations from the two tributaries. Thus, it is necessary to take effective measure to protect the habitat environment of T. yarkandensis to avoid the potential loss of genetic diversity.
赵文浩, 易少奎, 周琼, 沈建忠, 李大鹏, 周小云. 新疆塔里木河叶尔羌高原鳅群体遗传学研究[J]. 水产科学, 2023, 42(4): 664-673.
ZHAO Wenhao, YI Shaokui, ZHOU Qiong, SHEN Jianzhong, LI Dapeng, ZHOU Xiaoyun. Population Genetic Study of Triplophysa yarkandensis in Tarim River Basin in Xinjiang. Fisheries Science, 2023, 42(4): 664-673.
[1]马燕武,郭焱,张人铭,等.新疆塔里木河水系土著鱼类区系组成与分布[J].水产学报,2009,33(6):949-956. [2]陈国柱,仇玉萍,李丽萍.塔里木盆地鱼类入侵及区系演变趋势[J].生态学报,2017,37(2):700-714. [3]肖武汉,张亚平.鱼类线粒体DNA的遗传与进化[J].水生生物学报,2000,24(4):384-391. [4]高焕,于飞,栾生,等.中国明对虾基因组微卫星重复单元类型与其多态性关系[J].水生生物学报,2009,33(1):94-102. [5]TSOI K H, CHAN T Y, CHU K H. Molecular population structure of the kuruma shrimp Penaeus japonicus species complex in western Pacific[J].Marine Biology,2007,150(6):1345-1364. [6]袁希平,严莉,徐树英,等.长江流域铜鱼和圆口铜鱼的遗传多样性[J].中国水产科学,2008,15(3):377-385. [7]李宏俊,张晶晶,袁秀堂,等.利用线粒体COⅠ和微卫星标记分析文蛤7个地理群体的遗传变异[J].生态学报,2016,36(2):499-507. [8]王锦秀,任道全,王新月,等.塔里木河流域5个地理种群的叶尔羌高原鳅遗传多样性分析[J].渔业科学进展,2021,42(4):46-54. [9]郭焱.新疆鱼类志[M].乌鲁木齐:新疆科学技术出版社,2012:49-50. [10]BURLAND T G. DNASTAR's Lasergene sequence analysis software[J].Methods in Molecular Biology (Clifton, N.J.),2000,132:71-91. [11]LIBRADO P, ROZAS J. DnaSP v5:a software for comprehensive analysis of DNA polymorphism data[J].Bioinformatics,2009,25(11):1451-1452. [12]EXCOFFIER L, LAVAL G, SCHNEIDER S. Arlequin (version 3.0):an integrated software package for population genetics data analysis[J].Evolutionary Bioinformatics Online,2007,1:47-50. [13]KUMAR S, STECHER G, TAMURA K. MEGA7:molecular evolutionary genetics analysis version 7.0 for bigger datasets[J].Molecular Biology and Evolution,2016,33(7):1870-1874. [14]MANNI F, GUÉRARD E, HEYER E. Geographic patterns of (genetic, morphologic, linguistic) variation:how barriers can be detected by using Monmonier's algorithm[J].Human Biology,2004,76(2):173-190. [15]LEIGH J W, BRYANT D. Popart:full-feature software for haplotype network construction[J].Methods in Ecology and Evolution,2015,6(9):1110-1116. [16]HOLLAND M M, PARSON W. GeneMarker® HID:a reliable software tool for the analysis of forensic STR data[J].Journal of Forensic Sciences,2011,56(1):29-35. [17]GLAUBITZ J C. Convert:a user-friendly program to reformat diploid genotypic data for commonly used population genetic software packages[J].Molecular Ecology Notes,2004,4(2):309-310. [18]KALINOWSKI S T, TAPER M L, MARSHALL T C. Revising how the computer program CERVUS accommodates genotyping error increases success in paternity assignment[J].Molecular Ecology,2007,16(5):1099-1106. [19]BEERLI P, FELSENSTEIN J. Maximum likelihood estimation of a migration matrix and effective population sizes in n subpopulations by using a coalescent approach[J].Proceedings of the National Academy of Sciences of the United States of America,2001,98(8):4563-4568. [20]PRITCHARD J K, STEPHENS M, DONNELLY P. Inference of population structure using multilocus genotype data[J].Genetics,2000,155(2):945-959. [21]EARL D A, VONHOLDT B M. STRUCTURE HARVESTER:a website and program for visualizing STRUCTURE output and implementing the Evanno method[J].Conservation Genetics Resources,2012,4(2):359-361. [22]JAKOBSSON M, ROSENBERG N A. CLUMPP:a cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure[J].Bioinformatics,2007,23(14):1801-1806. [23]ROSENBERG N A. Distruct:a program for the graphical display of population structure[J].Molecular Ecology Notes,2004,4(1):137-138. [24]BOTSTEIN D, WHITE R L, SKOLNICK M, et al. Construction of a genetic linkage map in man using restriction fragment length polymorphisms[J].American Journal of Human Genetics,1980,32(3):314-331. [25]THIEL T, MICHALEK W, VARSHNEY R, et al. Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare L.)[J].Theoretical and Applied Genetics,2003,106(3):411-422. [26]闫华超,高岚,付崇罗,等.鱼类遗传多样性研究的分子学方法及应用进展[J].水产科学,2004,23(12):44-48. [27]GRANT W, BOWEN B. Shallow population histories in deep evolutionary lineages of marine fishes:insights from sardines and anchovies and lessons for conservation[J].Journal of Heredity,1998,89(5):415-426. [28]武菲,王翠华,胡文革,等.基于细胞色素b基因河鲈养殖群体与野生群体遗传多样性分析[J].淡水渔业,2015,45(6):16-21. [29]李大命,孙文祥,许飞,等.高邮湖大银鱼、太湖新银鱼Cytb和COⅠ基因序列多态性分析[J].水产科学,2020,39(2):258-264. [30]DEWOODY J A, AVISE J C. Microsatellite variation in marine, freshwater and anadromous fishes compared with other animals[J].Journal of Fish Biology,2000,56(3):461-473. [31]WRIGHT S. Evolution in Mendelian populations[J].Bulletin of Mathematical Biology,1990,52(1/2):241-295. [32]SLATKINM. Estimating levels of gene flow in natural populations[J].Genetics,1981,99(2):323-335. [33]陈亚宁,李卫红,陈亚鹏,等.新疆塔里木河下游断流河道输水与生态恢复[J].生态学报,2007,27(2):538-545. [34]陈生熬,姚娜.塔里木河流域叶尔羌高原鳅的生物学调查[J].水生态学杂志,2008,29(5):100-102. [35]海萨·艾也力汗,郭焱,孟玮,等.基于线粒体控制区序列的塔里木裂腹鱼遗传多样性及种群分化分析[J].中国水产科学,2016,23(4):944-954. [36]孙建光,韩桂兰.塔里木河流域干旱区绿洲河道生境生态水权及其计量研究[J].灌溉排水学报,2015,34(3):81-85. [37]WALLACE D C. Structure and evolution of organelle genomes[J].Microbiological Reviews,1982,46(2):208-240.
2023, Vol. 42 
