Population genetic structure of brushtooth lizardfish (Saurida undosquamis) based on mitochondrial cytochrome b gene sequences
-
摘要:
文章利用线粒体细胞色素b (cytochrome b, cytb)基因全序列作为分子标记，分析了中国近海和陆架的花斑蛇鲻(Saurida undosquamis)的遗传结构特征。从8个采样点266尾样本中共检测到142种单倍型，各采样点均表现出很高的单倍型多样性(0.925 1~0.992 9)和较低的核苷酸多样性(0.003 145~0.003 852)。单倍型的中间连接网络图呈现以4个优势共享单倍型为中心的星状发散结构，未发现与地理群体对应的谱系结构。分子方差分析表明花斑蛇鲻的遗传变异绝大部分(99.79%)来自种群内的个体之间，而群体之间几乎没有贡献遗传变异。成对遗传分化系数(FST)显示花斑蛇鲻群体间基因交流频繁，不存在明显的遗传差异，是一个随机交配群。中性检验表明种群历史动态显著偏离稳定种群模型，核苷酸错配分布表明花斑蛇鲻历史上曾经历过种群的快速扩张，扩张时间推算约在距今4万~10万年之前。研究结果表明，中国近海和陆架的花斑蛇鲻遗传分化不显著，在渔业上可以作为一个单元来管理。
Abstract:We examined the population genetic structure of brushtooth lizardfish (Saurida undosquamis) from the coastal waters and continental shelf of China based on the complete cytochrome b gene sequences. A total of 142 haplotypes have been derived from 266 individuals at eight sampling sites. Genetic diversity analysis shows that the S. undosquamis samples were characterized by rather high haplotype diversity (0.925 1−0.992 9) and relatively low nucleotide diversity (0.003 145−0.003 852). Median joining network shows that the haplotypes were connected in a star-like manner with four dominant haplotypes without clades of samples corresponding to sampling localities. Analyses of molecular variance suggest that nearly all the genetic variation (99.79%) was from individuals within population rather than from the populations. The pairwise FST reveals no genetic differentiation among different populations. A high rate of gene flow between populations implies a panmixia for S. undosquamis among the sampling sites. Neutrality tests show significant deviation of population historical dynamics from stable population model, and mismatch distribution analysis indicates a late Pleistocene expansion in S. undosquamis. The expansion time was estimated to be 40−100 thousands years ago. The results reveal that S. undosquamis from the coastal waters and continental shelf of China belong to the same population and can be managed as a unit in fisheries.
-
-
![]()
![]()
图 2 花斑蛇鲻cytb基因序列单倍型的中间连接网络图
圆的大小代表单倍型频率，颜色代表所属群体，空心圆代表未检测到的单倍型，省略了单倍型之间的突变数
Figure 2. Median-joining network for cytb gene sequence haplotypes of S. undosquamis
The size of the circles is proportional to haplotype frequency and the colors represent the corresponding population. Small hollow circles represent missing haplotypes. The mutation steps between two connected haplotypes are omitted.
![]()
图 3 花斑蛇鲻cytb序列单倍型核苷酸错配分布曲线
柱状图表示观测值, 虚线为突然扩张模型下的期望值，实线为空间扩散模型下的期望值
Figure 3. Mismatch distribution of cytb haplotypes for S. undosquamis
The observed pairwise differences are shown in bars and the expected values under the sudden expansion model and spatial expansion model are in dash line and solid line, respectively.
表 1 花斑蛇鲻样本信息及cytb基因序列遗传多样性参数
Table 1 Specimen information of S. undosquamis and genetic diversity parameters based on cytb gene sequences
采样点
sampling
site经度/纬度
longitude/
latitude样本量 (N)
number of
samples单倍型数量 (H)
number of
haplotypes多态性位点数 (S)
number of polym-
orphic sites单倍型多样性 (h±SD)
haplotype
diversity核苷酸多样性 (π±SD)
nucleotide
diversity防城港 FCG 108°30'E/21°00'N 32 21 25 0.943 5±0.028 7 0.003 145±0.001 823 北部湾 BBW 107°15'E/19°15'N 34 22 26 0.953 7±0.021 9 0.003 205±0.001 850 西沙 XS 109°24'E/16°40'N 34 31 37 0.992 9±0.009 9 0.003 852±0.002 168 三亚 SY 109°46'E/17°58'N 35 27 41 0.968 1±0.020 3 0.003 724±0.002 103 海口 HK 111°18'E/20°18'N 34 21 32 0.925 1±0.035 8 0.003 154±0.001 824 珠江口 ZJK 114°05'E/21°41'N 34 27 38 0.985 7±0.010 8 0.003 692±0.002 089 汕头 ST 116°55'E/23°00'N 32 23 34 0.949 6±0.029 0 0.003 497±0.001 997 泉州 QZ 119°02'E/24°36'N 31 22 29 0.961 3±0.021 6 0.003 393±0.001 948 总计 total − 266 142 144 0.965 0±0.006 1 0.003 455±0.001 921 
下载: 导出CSV
表 2 花斑蛇鲻8个地理群体cytb基因序列遗传变异的分子方差分析
Table 2 Analysis of molecular variance for eight populations of S. undosquamis based on cytb gene sequences
变异来源
source of variation自由度
degree of freedom变异百分比
percentage of variation分化系数
F statisticsP 群体间 among populations 7 0.21 0.002 1 0.572 6 群体内 within populations 258 99.79 所有样本 total samples 265
下载: 导出CSV
表 3 花斑蛇鲻两两地理群体间cytb基因序列的遗传分化系数 (对角线下方) 及显著性水平 (对角线上方)
Table 3 Pairwise FST (below diagonal) and P values (above diagonal) among geographic populations of S. undosquamis based on cytb gene sequences
群体 population FCG BBW XS SY HK ZJK ST QZ 防城港 FCG 0.773 8 0.372 0 0.342 6 0.288 2 0.540 9 0.779 1 0.807 2 北部湾 BBW −0.013 1 0.394 1 0.460 9 0.304 5 0.650 3 0.846 7 0.659 4 西沙 XS −0.000 9 −0.001 2 0.077 4 0.041 5 0.225 2 0.419 6 0.622 3 三亚 SY −0.000 2 −0.003 9 0.021 1 0.896 7 0.729 2 0.762 6 0.178 8 海口 HK 0.002 4 0.001 9 0.031 8 −0.012 9 0.747 6 0.588 1 0.118 5 珠江口 ZJK −0.006 7 −0.008 1 0.005 7 −0.008 9 −0.009 9 0.896 3 0.247 1 汕头 ST −0.012 5 −0.013 1 −0.002 4 −0.010 5 −0.007 9 −0.012 9 0.695 9 泉州 QZ −0.014 1 −0.009 9 −0.007 4 0.010 5 0.018 9 0.004 5 −0.010 3
下载: 导出CSV
表 4 花斑蛇鲻两两地理群体间随机交配假设检验的显著性水平
Table 4 P values of exact test of sample differentiation of S. undosquamis based on cytb gene haplotype frequencies
群体 population FCG BBW XS SY HK ZJK ST 北部湾 BBW 0.014 6 西沙 XS 0.067 7 0.109 4 三亚 SY 0.019 9 0.362 7 0.187 7 海口 HK 0.035 1 0.197 3 0.027 3 0.736 8 珠江口 ZJK 0.285 5 0.254 7 0.692 4 0.292 1 0.181 8 汕头 ST 0.390 6 0.236 1 0.269 5 0.704 2 0.873 0 0.674 6 泉州 QZ 0.527 0 0.310 6 0.128 8 0.303 3 0.486 4 0.392 6 0.945 3
下载: 导出CSV
表 5 花斑蛇鲻cytb基因序列核苷酸错配分布分析的参数估计值和中性检验统计值
Table 5 Mismatch distribution parameter estimates and neutrality tests statistics for S. undosquamis based on cytb gene sequences
群体
population错配分布 mismatch distribution 中性检验 neutrality test 突然扩张模型
sudden expansion model空间扩散模型
spatial expansion modelTajima' D Fu's FS 粗糙指数
HRIP 粗糙指数
HRIP D P FS P 防城港 FCG 0.782 9 0.936 2 0.590 0 0.950 1 −1.493 5 0.048 6 −14.339 4 0 北部湾 BBW 0.066 7 0.067 2 0.028 5 0.061 4 −1.492 5 0.048 5 −15.139 0 0 西沙 XS 0.075 9 0.313 3 0.214 5 0.173 7 −1.854 0 0.013 3 −25.721 9 0 三亚 SY 0.049 8 0.188 5 0.151 9 0.513 6 −2.068 2 0.004 2 −23.293 0 0 海口 HK 0.749 0 0.897 7 0.629 0 0.911 5 −1.926 2 0.010 6 −13.437 8 0 珠江口 ZJK 0.050 7 0.047 7 0.045 6 0.077 7 −1.973 3 0.008 2 −24.127 8 0 汕头 ST 0.890 7 0.834 6 0.909 0 0.934 4 −1.909 1 0.011 5 −17.081 6 0 泉州 QZ 0.136 3 0.217 8 0.156 5 0.352 5 −1.680 7 0.026 9 −15.934 9 0 合计 total 0.177 0 0.439 0 0.076 1 0.601 0 −2.555 7 0 −25.510 6 0
下载: 导出CSV
-
[1] FROESE R, PAULY D. FishBase[DB/OL]. [2019-04-25]. https://www.fishbase.de/summary/Saurida-undosquamis.html.
[2] 江艳娥, 许友伟, 范江涛, 等. 南海北部陆架水域多齿蛇鲻与花斑蛇鲻的年龄与生长[J]. 中国水产科学, 2019, 26(1): 82-90. [3] 陈再超, 刘继兴. 南海经济鱼类[M]. 广州: 广东科学与技术出版社, 1982: 184-188. [4] 舒黎明, 邱永松. 南海北部花斑蛇鲻生长死亡参数估计及开捕规格[J]. 湛江海洋大学学报, 2004, 24(3): 29-35. doi: 10.3969/j.issn.1673-9159.2004.03.007 [5] 舒黎明, 邱永松. 南海北部多齿蛇鲻生物学分析[J]. 中国水产科学, 2004, 11(2): 154-158. doi: 10.3321/j.issn:1005-8737.2004.02.012 [6] 黄梓荣. 休渔对南海北部多齿蛇鲻资源的影响[J]. 湛江海洋大学学报, 2002, 22(6): 26-31. doi: 10.3969/j.issn.1673-9159.2002.06.006 [7] 卢伙胜, 颜云榕, 侯刚. 等. 2009年度南海渔业资源调查报告[R]. 湛江: 广东海洋大学, 2010. [8] 孙典荣, 林昭进. 北部湾主要经济鱼类资源变动分析及保护对策探讨[J]. 热带海洋学报, 2004, 2(2): 62-68. doi: 10.3969/j.issn.1009-5470.2004.02.008 [9] 陈作志, 邱永松, 徐姗楠, 等. 北部湾花斑蛇鲻生物学特征的演化[J]. 中国水产科学, 2012, 19(2): 321-328. [10] COATES D J, BYRNE M, MORITZ C. Genetic diversity and conservation units: dealing with the species-population continuum in the age of genomics[J/OL]. Front Ecol Evol, 2018, 60 [2019-04-26]. https://www.frontiersin.org/articles/10.3389/fevo.2018.00165/full. doi: 10.3389/fevo.2018.00165.
[11] REISS H, HOARAU G, DICKEY-COLLAS M, et al. Genetic population structure of marine fish: mismatch between biological and fisheries management units[J]. Fish Fish, 2009, 10(4): 361-395. doi: 10.1111/j.1467-2979.2008.00324.x
[12] GOETHEL D R, BERGER A M. Accounting for spatial complexities in the calculation of biological reference points: effects of misdiagnosing population structure for stock status indicators[J]. Can J Fish Aquat Sci, 2017, 74(11): 1878-1894. doi: 10.1139/cjfas-2016-0290
[13] PALSBØLL P J, BERUBE M, ALLENDORF F W. Identification of management units using population genetic data[J]. Trends Ecol Evol, 2007, 22(1): 11-16. doi: 10.1016/j.tree.2006.09.003
[14] MALI K S, KUMAR M V, FAREJIYA M K, et al. Reproductive biology of Saurida tumbil (Bloch 1795) and Saurida undosquamis (Richardson 1848) inhabiting Northwest coast of India[J]. Int J Pure App Biosci, 2017, 5(6): 957-964. doi: 10.18782/2320-7051.6080
[15] CHHANDAPRAJNADARSINI E M, ROUL S K, SWAIN S, et al. Biometric analysis of brushtooth lizard fish Saurida undosquamis (Richardson, 1848) from Mumbai waters[J]. J Entomol Zool Stud, 2018, 6(2): 1165-1171.
[16] NAJMUDEEN T M, SEETHA P K, ZACHARIA P U. Stock dynamics of the brushtooth lizardfish Saurida undosquamis (Richardson, 1848) from a tropical multispecies fishery in the southeastern Arabian Sea[J/OL]. Aquat Living Resour, 2019, 32 [2019-04-26]. https://www.alr-journal.org/articles/alr/abs/2019/01/alr180110/alr180110.html. doi: 10.1051/alr/2019006.
[17] 张俊, 陈国宝, 陈作志, 等. 南沙南部陆架海域渔业资源声学评估[J]. 南方水产科学, 2015, 11(5): 1-10. doi: 10.3969/j.issn.2095-0780.2015.05.001 [18] 许友伟, 陈作志, 范江涛, 等. 南沙西南陆架海域底拖网渔获物组成及生物多样性[J]. 南方水产科学, 2015, 11(5): 76-81. doi: 10.3969/j.issn.2095-0780.2015.05.009 [19] HALL T, BIOSCIENCES I, CARLSBAD C. BioEdit: an important software for molecular biology[J]. GERF Bull Biosci, 2011, 2(1): 60-61.
[20] KUMAR S, STECHER G, TAMURA K. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets[J]. Mol Biol Evol, 2016, 33(7): 1870-1874. doi: 10.1093/molbev/msw054
[21] POSADA D. ModelTest Server: a web-based tool for the statistical selection of models of nucleotide substitution online[J]. Nucleic Acids Res, 2006, 34(sup 2): W700-W703.
[22] ROZAS J, FERRER-MATA A, SÁNCHEZ-DELBARRIO J C, et al. DnaSP 6: DNA sequence polymorphism analysis of large data sets[J]. Mol Biol Evol, 2017, 34(12): 3299-3302. doi: 10.1093/molbev/msx248
[23] POLZIN T, DANESCHMAND S V. On Steiner trees and minimum spanning trees in hypergraphs[J]. Oper Res Lett, 2003, 31(1): 12-20. doi: 10.1016/S0167-6377(02)00185-2
[24] BANDELT H J, FORSTER P, ROHL A. Median-joining networks for inferring intraspecific phylogenies[J]. Mol Biol Evol, 1999, 16(1): 37-48. doi: 10.1093/oxfordjournals.molbev.a026036
[25] EXCOFFIER L, LISCHER H E. Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows[J]. Mol Ecol Resour, 2010, 10(3): 564-567. doi: 10.1111/j.1755-0998.2010.02847.x
[26] TAJIMA F. Statistical-method for testing the neutral mutation hypothesis by DNA polymorphism[J]. Genetics, 1989, 123(3): 585-595.
[27] FU Y X. Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection[J]. Genetics, 1997, 147(2): 915-925.
[28] EXCOFFIER L. Patterns of DNA sequence diversity and genetic structure after a range expansion: lessons from the infinite-island model[J]. Mol Ecol, 2004, 13(4): 853-864. doi: 10.1046/j.1365-294X.2003.02004.x
[29] RAY N, CURRAT M, EXCOFFIER L. Intra-deme molecular diversity in spatially expanding populations[J]. Mol Biol Evol, 2003, 20(1): 76-86. doi: 10.1093/molbev/msg009
[30] HARPENDING H C. Signature of ancient population growth in a low-resolution mitochondrial DNA mismatch distribution[J]. Hum Biol, 1994, 66(4): 591-600.
[31] ROGERS A R, HARPENDING H. Population growth makes waves in the distribution of pairwise genetic differences[J]. Mol Biol Evol, 1992, 9(3): 552-569.
[32] KOCHER T D, STEPIEN C A. Molecular systematics of fishes[M]. New York: Academic Press, 1997: 113-128.
[33] FRANKHAM R, BALLOU J D, BRISCOE D A. Introduction to conservation genetics[M]. Cambridge: Cambridge University Press, 2002: 78-104.
[34] 边力, 王鹏飞, 陈四清, 等. 基于线粒体Cytb基因序列的绿鳍马面鲀6个野生群体的遗传结构分析[J]. 中国水产科学, 2018, 25(4): 827-836. [35] 熊丹, 李敏, 李永振, 等. 南海短尾大眼鲷线粒体Cyt b基因序列及种群判别分析[J]. 中国水产科学, 2016, 23(1): 188-197. [36] 夏月恒, 章群, 高志远, 等. 中国近海鮸鱼遗传多样性的细胞色素b全序列分析[J]. 广东农业科学, 2013, 40(3): 101-105. doi: 10.3969/j.issn.1004-874X.2013.03.034 [37] 彭博, 章群, 赵爽, 等. 中国近海小黄鱼遗传变异的细胞色素b序列分析[J]. 广东农业科学, 2010, 37(2): 131-135. doi: 10.3969/j.issn.1004-874X.2010.02.045 [38] 沈朕, 关洪斌, 郑风荣, 等. 基于cytb 和D-loop的4个大泷六线鱼群体遗传多样性分析[J]. 海洋科学进展, 2017, 35(4): 524-534. doi: 10.3969/j.issn.1671-6647.2017.04.009 [39] PINSKY M L, PALUMBI S R. Meta-analysis reveals lower genetic diversity in overfished populations[J]. Mol Ecol, 2014, 23(1): 29-39. doi: 10.1111/mec.12509
[40] GRANT W S, BOWEN B W. Shallow population histories in deep evolutionary lineages of marine fishes: insights from sardines and anchovies and lessons for conservation[J]. J Hered, 1998, 89(5): 415-426. doi: 10.1093/jhered/89.5.415
[41] WANG P. Response of western Pacific marginal seas to glacial cycles: paleoceanographic and sedimentological features[J]. Mar Geol, 1999, 156(1): 5-39.
[42] IMBRIE J, BOYLE E A, CLEMENS S C, et al. On the structure and origin of major glaciation cycles 1. Linear responses to Milankovitch forcing[J]. Paleoceanography, 1992, 7(6): 701-738. doi: 10.1029/92PA02253
[43] 黄小林, 李文俊, 林黑着, 等. 基于线粒体DNA D-loop序列的黄斑篮子鱼群体遗传多样性分析[J]. 热带海洋学报, 2018, 37(4): 45-51. [44] 李敏, 张鹏, 李玉芳, 等. 南海扁舵鲣种群遗传结构和遗传多样性评价[J]. 南方水产科学, 2015, 11(5): 82-89. doi: 10.3969/j.issn.2095-0780.2015.05.010 [45] 李敏, 李玉芳, 张鹏, 等. 基于线粒体控制区序列的南海圆舵鲣种群遗传结构分析[J]. 南方水产科学, 2016, 12(4): 88-95. doi: 10.3969/j.issn.2095-0780.2016.04.011 [46] HEWITT G M. The genetic legacy of the Quaternary ice ages[J]. Nature, 2000, 405(6789): 907-913. doi: 10.1038/35016000
[47] PALUMBI S R. Genetic divergence, reproductive isolation, and marine speciation[J]. Annu Rev Ecol Syst, 1994, 25: 547-572. doi: 10.1146/annurev.es.25.110194.002555
[48] 苏纪兰. 中国近海水文[M]. 北京: 海洋出版社, 2005: 1-367. [49] 孙冬芳, 董丽娜, 李永振, 等. 南海北部海域多齿蛇鲻的种群分析[J]. 水产学报, 2010, 34(9): 1387-1394. [50] LAIKRE L, PALM S, RYMAN N. Genetic population structure of fishes: Implications for coastal zone management[J]. Ambio, 2005, 34(2): 111-119. doi: 10.1579/0044-7447-34.2.111
计量
- 文章访问数: 5672
- HTML全文浏览量: 2856
- PDF下载量: 75
粤公网安备 44010502001741号
