西江中下游鳤的遗传多样性与种群动态历史

doi:10.17520/biods.2018121

生物多样性 ›› 2018, Vol. 26 ›› Issue (12): 1289-1295. DOI: 10.17520/biods.2018121

• 研究报告: 动物多样性 • 上一篇下一篇

西江中下游鳤的遗传多样性与种群动态历史

杨计平¹, 李策^1,², 陈蔚涛¹, 李跃飞¹, 李新辉^1,^*()

1 中国水产科学研究院珠江水产研究所, 广州 510380
2 上海海洋大学海洋科学学院, 上海 201306

收稿日期:2018-04-16 接受日期:2018-04-16 出版日期:2018-12-20 发布日期:2019-02-11
通讯作者: 李新辉
作者简介:# 共同第一作者
基金资助:
中国水产科学研究院基本科研业务费(2016HY-ZC0503)

Genetic diversity and population demographic history of Ochetobius elongatus in the middle and lower reaches of the Xijiang River

Jiping Yang¹, Ce Li^1,², Weitao Chen¹, Yuefei Li¹, Xinhui Li^1,^*()

1 Pearl River Fisheries Research Institute, Chinese Academy of Fishery Science, Guangzhou 510380
2 College of Marine Sciences, Shanghai Ocean University, Shanghai 201306

Received:2018-04-16 Accepted:2018-04-16 Online:2018-12-20 Published:2019-02-11
Contact: Li Xinhui
About author:# 同等贡献作者 Contributed equally to this work

摘要/Abstract

摘要：

鳤(Ochetobius elongatus)曾经是我国许多河流的重要经济鱼类, 然而由于环境污染和人为干扰等原因, 鳤的资源量萎缩严重, 种群处于极度濒危的境地。目前, 常规采样方法获得鳤样本的难度较大, 致使相关研究难以开展。本研究通过仔鱼采集和成鱼采集的手段, 测定两个线粒体基因和两个核基因, 对西江中下游鳤的遗传多样性和种群动态历史进行研究。结果显示, 西江中下游鳤的遗传多样性处于较低水平并且出现了衰退的迹象, 可能经历了遗传瓶颈效应。此外, 种群动态历史分析发现, 西江中下游鳤在后更新世期间(0.06和0.13百万年前)经历了种群扩张, 刚好处于中更新世(0.78-0.126百万年前)冰期褪去之后, 表明更新世气候的波动影响了西江中下游鳤的种群动态。作为鳤可能的重要产卵场, 西江中下游部分江段可以考虑建立鳤的自然保护区, 用于保育和修复鳤的种质资源。

关键词: 鳤, 仔鱼采集, 线粒体基因和核基因, 种群扩张, 保护

Abstract

Ochetobius elongatus used to be an economically important fish species in many rivers of China. However, due to environmental destruction and human disturbance the resources of this fish species have reduced rapidly, and its populations are in a critically endangered condition. At present, it is very difficult to obtain specimens of O. elongatus, which limits research on this species. We obtained specimens of O. elongatus via larva and adult fish collection. Two mitochondrial genes and two nuclear genes were used to explore the genetic diversity and population demography of O. elongatus in middle and lower Xijiang River. Results showed that the genetic diversity of O. elongatus was low and is in recession, suggesting that O. elongatus might have undergone a genetic bottleneck event. Additionally, population demographic analyses revealed that O. elongatus population expanded during the Late Pleistocene (0.06 and 0.13 Million years ago), following the glacial retreat of the Middle Pleistocene glaciations (0.78-0.126 Million years ago). The results also revealed that Pleistocene climatic fluctuations have influenced the population demography of O. elongatus. Due to its potential as an important spawning ground for O. elongatus, sections of middle and lower Xijiang River should be considered as candidates for creating nature reserves to conserve and restore its genetic resources.

Key words: Ochetobius elongatus, larva fish collection, mitochondrial and nuclear genes, population expansion, conservation

杨计平, 李策, 陈蔚涛, 李跃飞, 李新辉 (2018) 西江中下游鳤的遗传多样性与种群动态历史. 生物多样性, 26, 1289-1295. DOI: 10.17520/biods.2018121.

Jiping Yang, Ce Li, Weitao Chen, Yuefei Li, Xinhui Li (2018) Genetic diversity and population demographic history of Ochetobius elongatus in the middle and lower reaches of the Xijiang River. Biodiversity Science, 26, 1289-1295. DOI: 10.17520/biods.2018121.

导出引用管理器 EndNote|Ris|BibTeX

链接本文: https://www.biodiversity-science.net/CN/10.17520/biods.2018121

https://www.biodiversity-science.net/CN/Y2018/V26/I12/1289

图/表 6

参考文献 35

1	Araujo-Lima CARM, Oliveira EC (1998) Transport of larval fish in the Amazon. Journal of Fish Biology, 53, 297-306.
2	Bandelt HJ, Forster P, Rohl A (1999) Median-joining networks for inferring intraspecific phylogenies. Molecular Biology and Evolution, 16, 37-48.
3	Chen WJ, Miya M, Saitoh K, Mayden RL (2008) Phylogenetic utility of two existing and four novel nuclear gene loci in reconstructing Tree of Life of ray-finned fishes: The order Cypriniformes (Ostariophysi) as a case study. Gene, 423, 125-134.
4	Chen YY, Cao WX, Zheng CY (1986) Ichthyofauna of the Zhujiang River with a discussion on zoogeographical divisions for freshwater fishes. Acta Hydrobiologica Sinica, 10, 228-234. (in Chinese with English abstract)
	[陈宜瑜, 曹文宣, 郑慈英 (1986) 珠江的鱼类区系及其动物地理区划的讨论. 水生生物学报, 10, 228-234.]
5	Drummond AJ, Rambaut A (2007) BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evolutionary Biology, 7, 214.
6	Drummond AJ, Rambaut A, Shapiro B, Pybus OG (2005) Bayesian coalescent inference of past population dynamics from molecular sequences. Molecular Biology and Evolution, 22, 1185-1192.
7	Durand JD, Tsigenopoulos CS, Unlu E, Berrebi P (2002) Phylogeny and biogeography of the family Cyprinidae in the Middle East inferred from cytochrome b DNA—Evolutionary significance of this region. Molecular Phylogenetics and Evolution, 25, 91-100.
8	Edgar RC (2004) MUSCLE: Multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research, 32, 1792-1797.
9	Excoffier L, Lischer HEL (2010) Arlequin suite ver 3.5: A new series of programs to perform population genetics analyses under Linux and Windows. Molecular Ecology Resources, 10, 564-567.
10	Fu YX (1997) Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection. Genetics, 147, 915-925.
11	Gascoyne M, Benjamin GJ, Schwarcz HP, Ford DC (1979) Sea-level lowering during the Illinoian glaciation: Evidence from a Bahama “blue hole”. Science, 205, 806-808.
12	Grant WS, Bowen BW (1998) Shallow population histories in deep evolutionary lineages of marine fishes: Insights from sardines and anchovies and lessons for conservation. Journal of Heredity, 89, 415-426.
13	Hewitt GM (2004) Genetic consequences of climatic oscillations in the Quaternary. Philosophical Transactions of the Royal Society B-Biological Sciences, 359, 183-195.
14	Jiang ZG, Jiang JP, Wang YZ, Zhang E, Zhang YY, Li LL, Xie F, Cai B, Cao L, Zheng GM, Dong L, Zhang ZW, Ding P, Luo ZH, Ding CQ, Ma ZJ, Tang SH, Cao WX, Li CW, Hu HJ, Ma Y, Wu Y, Wang YX, Zhou KY, Liu SY, Chen YY, Li JT, Feng ZJ, Wang Y, Wang B, Li C, Song XL, Cai L, Zang CX, Zeng Y, Meng ZB, Fang HX, Ping XG (2016) Red List of China’s Vertebrates. Biodiversidy Science, 24, 500-551.
	[蒋志刚, 江建平, 王跃招, 张鹗, 张雁云, 李立立, 谢锋, 蔡波, 曹亮, 郑光美, 董路, 张正旺, 丁平, 罗振华, 丁长青, 马志军, 汤宋华, 曹文宣, 李春旺, 胡慧建, 马勇, 吴毅, 王应祥, 周开亚, 刘少英, 陈跃英, 李家堂冯祚建, 王燕, 王斌, 李成, 宋雪琳, 蔡蕾, 臧春鑫, 曾岩, 孟智斌, 方红霞, 平晓鸽 (2016) 中国脊椎动物红色名录. 生物多样性, 24, 500-551.]
15	Ketmaier V, Bianco PG, Cobollia M, Krivokapic M, Caniglia R, De Matthaeis E (2004) Molecular phylogeny of two lineages of Leuciscinae cyprinids (Telestes and Scardinius) from the peri-Mediterranean area based on cytochrome b data. Molecular Phylogenetics and Evolution, 32, 1061-1071.
16	Li J, Li XH, Jia XP, Li YF, He MF, Tan XC, Wang C, Jiang WX (2010) Evolvement and diversity of fish community in Xijiang River. Journal of Fishery Sciences of China, 17, 298-311. (in Chinese with English abstract)
	[李捷, 李新辉, 贾晓平, 李跃飞, 何美峰, 谭细畅, 王超, 蒋万祥 (2010) 西江鱼类群落多样性及其演变. 中国水产科学, 17, 298-311.]
17	Li SF, Lü GQ, Bernatchez L (1998) Diversity of mitochondrial DNA in the populations of silver carp, bighead carp, grass carp and black carp in the middle- and lower reaches of the Yangtze River. Acta Zoologica Sinica, 44, 82-93. (in Chinese with English abstract)
	[李思发, 吕国庆, Bernatchez L (1998) 长江中下游鲢鳙草青四大家鱼线粒体DNA多样性分析. 动物学报, 44, 82-93.]
18	Li YF, Li XH, Tan XC, Li J, Wang C (2012) Occurrence of larval Elopichthys bambusa and its relationship with hydrological conditions in the middle and lower reaches of Pearl River. Journal of Fisheries of China, 36(4), 15-22. (in Chinese with English abstract)
	[李跃飞, 李新辉, 谭细畅, 李捷, 王超 (2012) 珠江中下游鳡鱼苗的发生及其与水文环境的关系. 水产学报, 36, 15-22.]
19	Liang ZS, Mo RL, Chen FC (1985) Species identification and spawning type of common fish species in Xijiang River during early phase. In: The Report of Fishery Research in Pearl River Basin. Compilation Committee of Fishery Resources Survey of Pearl River Basin, Guangzhou. (in Chinese)
	[梁秩燊, 莫瑞林, 陈福才 (1985) 西江常见鱼类早期发育的分类鉴定及其产卵类型. 见: 珠江水系渔业资源调查研究报告. 珠江水系渔业资源调查编委会, 广州.]
20	Librado P, Rozas J (2009) DnaSP v5: A software for comprehensive analysis of DNA polymorphism data. Bioinformatics, 25, 1451-1452.
21	Lovejoy NR, Collette BB (2001) Phylogenetic relationships of new world needlefishes (Teleostei: Belonidae) and the biogeography of transitions between marine and freshwater habitats. Copeia, 2001, 324-338.
22	Meyer A (1993) Evolution of Mitochondrial DNA in Fishes. Elsevier, The Hague.
23	Nesler TP, Muth RT, Wasowicz AF (1988) Evidence for baseline flow spikes as spawning cues for Colorado squawfish in the Yampa River, Colorado. In: American Fisheries Society Symposium, pp. 68-79. Bethesda, Maryland.
24	Nylander JAA (2004) MrModeltest v2. Evolutionary Biology Centre, Uppsala University, Uppsala.
25	Rambaut A, Drummond A (2007) Tracer v1.4.. (accessed on 2018-3-2).

26	Rogers AR, Harpending H (1992) Population growth makes waves in the distribution of pairwise genetic differences. Molecular Biology and Evolution, 9, 552-569.
27	Tajima F (1989) The effect of change in population size on DNA polymorphism. Genetics, 123, 597-601.
28	Tao W, Zou M, Wang X, Gan X, Mayden RL, He S (2010) Phylogenomic analysis resolves the formerly intractable adaptive diversification of the endemic clade of east Asian Cyprinidae (Cypriniformes). PLoS ONE, 5, e13508.
29	Tyus HM, Haines GB (1991) Distribution, habitat use, and growth of age-0 Colorado squawfish in the Green River basin, Colorado and Utah. Transactions of the American Fisheries Society, 120, 79-89.
30	Wang X, Li J, He S (2007) Molecular evidence for the monophyly of East Asian groups of Cyprinidae (Teleostei: Cypriniformes) derived from the nuclear recombination activating gene 2 sequences. Molecular Phylogenetics and Evolution, 42, 157-170.
31	Wu WJ, Peng M, Wang DP, Shi J, Li YS, Han YQ, Lei JJ, He AY (2015) Comparison of mitochondrial D-Loop and Cyt b sequences of Hypophthalmichthys molitrix. Open Journal of Fisheries Research, 2(4), 67-73. (in Chinese with English abstract)
	[吴伟军, 彭敏, 王大鹏, 施军, 李育森, 韩耀全, 雷建军, 何安尤 (2015) 红水河鲢线粒体D-Loop和Cyt b基因序列分析. 水产研究, 2(4), 67-73.]
32	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, 163-173.
33	Yue PQ (2000) Fauna Sinica, Osteichthyes, Cypriniformes II Science Press, Beijing. (in Chinese)
	[乐佩琦 (2000) 中国动物志. 硬骨鱼纲, 鲤形目, 中卷. 科学出版社, 北京.]
34	Zheng CY (1989) The Ichthyography of the Pearl River. Science Press, Beijing. (in Chinese)
	[郑慈英 (1989) 珠江鱼类志. 科学出版社. 北京.]
35	Zitek A, Schmutz S, Unfer G, Ploner A (2004) Fish drift in a Danube sidearm-system: I. Site-, inter- and intraspecific patterns. Journal of Fish Biology, 65, 1319-1338.

采样点 Sample site	采样日期 Sampling time	样本量 Sample size	经度 Longitude	纬度 Latitude
广西桂平 Guiping	2017.09	1	110°05°54.78°° E	23°24°08.25°° N
广西梧州 Wuzhou	2017.09	1	111°17°15.32°° E	23°28°07.94°° N
广东肇庆 Zhaoqing	2011.05	22	112°23°40.13°° E	23°05°06.24°° N
广东肇庆 Zhaoqing	2013.05	28	112°23°40.13°° E	23°05°06.24°° N

采样点 Sample site	采样日期 Sampling time	样本量 Sample size	经度 Longitude	纬度 Latitude
广西桂平 Guiping	2017.09	1	110°05°54.78°° E	23°24°08.25°° N
广西梧州 Wuzhou	2017.09	1	111°17°15.32°° E	23°28°07.94°° N
广东肇庆 Zhaoqing	2011.05	22	112°23°40.13°° E	23°05°06.24°° N
广东肇庆 Zhaoqing	2013.05	28	112°23°40.13°° E	23°05°06.24°° N

	引物名 Primer	引物序列 Primer sequence (5′-3′)	退火温度 Annealed temperature (℃)	参考文献 Reference
Cytb	L14724	GACTTGAAA AACCACCGTTG	58-64	Xiao et al, 2001
	H15915	CTCCGATCTCCGGATTACAAGAC		Xiao et al, 2001
ND2	AFND2L	AAGCTYTYGGGCCCATACC	58	黎瑞宝, 2013^①
	AFND2R	TCCYGCTTAGGGCTTTGAAGG
myh6	myh6_F459	CATMTTYTCCATCTCAGATAATGC	53	Chen et al, 2008
	myh6_R1325	ATTCTCACCACCATCCAGTTGAA
RAG2	RAG2-f2a	AARCGCTCMTGTCCMACTGG	55	Lovejoy & Collette, 2001
	RAG2-R6a	TGRTCCARGCAGAAGTACTTG		Lovejoy & Collette, 2001

	引物名 Primer	引物序列 Primer sequence (5′-3′)	退火温度 Annealed temperature (℃)	参考文献 Reference
Cytb	L14724	GACTTGAAA AACCACCGTTG	58-64	Xiao et al, 2001
	H15915	CTCCGATCTCCGGATTACAAGAC		Xiao et al, 2001
ND2	AFND2L	AAGCTYTYGGGCCCATACC	58	黎瑞宝, 2013^①
	AFND2R	TCCYGCTTAGGGCTTTGAAGG
myh6	myh6_F459	CATMTTYTCCATCTCAGATAATGC	53	Chen et al, 2008
	myh6_R1325	ATTCTCACCACCATCCAGTTGAA
RAG2	RAG2-f2a	AARCGCTCMTGTCCMACTGG	55	Lovejoy & Collette, 2001
	RAG2-R6a	TGRTCCARGCAGAAGTACTTG		Lovejoy & Collette, 2001

	单倍型数/个体数 Number of haplotype/ sample size	单倍型多态性 Haplotype diversity	近期核苷酸多态性 Current nucleotide diversity (θ_π, %)	历史核苷酸多态性 Historical nucleotide diversity (θ_w, %)	Tajima’s D 检验 Tajima’s D test	Fu’s Fs检验 Fu’s Fs test	最优模型 Optimal model
Cytb	13/52	0.784	0.197	0.470	-1.83^**	-5.43^**	HKY+I
ND2	17/52	0.869	0.239	0.272	-0.35	-8.16^***	F81+I+G
Cytb + ND2	26/52	0.940	0.219	0.366	-1.33	-14.54^***	-
myh6	2/52	0.462	0.060	0.029	-	-	HKY
RAG2	3/52	0.147	0.022	0.077	-	-	F81
myh6 + RAG2	5/52	0.546	0.040	0.055	-	-	-

西江中下游鳤的遗传多样性与种群动态历史

Genetic diversity and population demographic history of Ochetobius elongatus in the middle and lower reaches of the Xijiang River

RichHTML

PDF (PC)

可视化

被引次数

摘要/Abstract

引用本文

使用本文

图/表 6

参考文献 35

相关文章 15

编辑推荐

Metrics

本文评价

[1]	姜熠辉, 刘岳, 曾旭, 林喆滢, 王楠, 彭吉豪, 曹玲, 曾聪. 东海六个国家级海洋保护区鱼类多样性和连通性[J]. 生物多样性, 2024, 32(6): 24128-.
[2]	田瑜, 李俊生. 《昆明-蒙特利尔全球生物多样性框架》“3030”目标的内涵及实现路径分析[J]. 生物多样性, 2024, 32(6): 24086-.
[3]	蔡颖莉, 朱洪革, 李家欣. 中国生物多样性保护政策演进、主要措施与发展趋势[J]. 生物多样性, 2024, 32(5): 23386-.
[4]	鄢德奎. 中国生物多样性保护政策的共同要素、不足和优化建议[J]. 生物多样性, 2024, 32(5): 23293-.
[5]	杨锐, 侯姝彧, 张引, 赵智聪. 论建立中国自然保护兼用地的必要性和可行性[J]. 生物多样性, 2024, 32(4): 23454-.
[6]	刘荆州, 钱易鑫, 张燕雪丹, 崔凤. 基于潜在迪利克雷分布(LDA)模型的旗舰物种范式研究进展与启示[J]. 生物多样性, 2024, 32(4): 23439-.
[7]	李雪萌, 蒋际宝, 张曾鲁, 刘晓静, 王亚利, 吴宜钊, 李银生, 邱江平, 赵琦. 宝天曼国家级自然保护区蚯蚓物种多样性及其影响因素[J]. 生物多样性, 2024, 32(4): 23352-.
[8]	王启蕃, 刘小慧, 朱紫薇, 刘磊, 王鑫雪, 汲旭阳, 周绍春, 张子栋, 董红雨, 张明海. 黑龙江北极村国家级自然保护区鸟类与兽类多样性[J]. 生物多样性, 2024, 32(4): 24024-.
[9]	陶斯琦, 杨飞龄, 华朝朗, 武瑞东. 通过综合受威胁状态和保护价值评估云南省自然植被的保护优先性[J]. 生物多样性, 2024, 32(3): 23324-.
[10]	钟超, 廖亚琴, 刘伟杰, 隋昊志, 陈清华. 广东沿海海草床的现状、面临的威胁与保护建议[J]. 生物多样性, 2024, 32(2): 23201-.
[11]	所翟, 俞渃茜, 李媛辉, 徐基良. 基于实证分析中国自然保护区地方立法问题检视和优化路径[J]. 生物多样性, 2024, 32(2): 23287-.
[12]	刘啸林, 吴友贵, 张敏华, 陈小荣, 朱志成, 陈定云, 董舒, 李步杭, 丁炳扬, 刘宇. 浙江百山祖25 ha亚热带森林动态监测样地群落组成与结构特征[J]. 生物多样性, 2024, 32(2): 23294-.
[13]	黄小龙, 蒙秉顺, 李海波, 冉伟, 杨伟, 王丞, 谢波, 张旭, 冉景丞, 张明明. 基于红外相机的黔金丝猴及其同域分布物种种间关联[J]. 生物多样性, 2024, 32(2): 23402-.
[14]	陈进, 杨玺. 关于植物迁地保护若干问题的讨论[J]. 生物多样性, 2024, 32(2): 24064-.
[15]	刘夙, 杜诚, 胡永红. 迁地保护应当具有明确的灵活性[J]. 生物多样性, 2024, 32(2): 24037-.