基于线粒体控制区的序列变异分析中国东南部沿海凤鲚种群遗传结构

doi:10.3724/SP.J.1003.2009.08286

摘要/Abstract

摘要：

为了解中国东南部沿海凤鲚(Coilia mystus)的种群遗传多样性和遗传结构, 本文分析了长江口(CJ)、钱塘江口(QT)、闽江口(MJ)和九龙江口(JL)4个凤鲚地理群体的mtDNA控制区561 bp片段的序列变异。65尾样本共检测到28个单元型。4个群体总的单元型多样性和核苷酸多样性均较高(h = 0.9433 ± 0.0168, π = 0.0317 ± 0.0158), 但单个群体的核苷酸多样性水平却很低, 其中以CJ最高(π = 0.0080 ± 0.0046), MJ最低(π = 0.0015 ± 0.0013)。MJ与JL群体之间以及CJ与QT群体之间的平均K2P遗传距离很小, 分别为0.3%和0.8%; 而CJ、QT分别与MJ、JL群体之间的遗传距离均较大, 达到了6%。采用最大似然法(ML)、最大简约法(MP)和邻接法(NJ)分别构建的单元型间的系统发育树揭示, 4个凤鲚群体构成CJ-QT 和MJ-JL 2个支系, 且具有极高的支持率。单元型的网络分析也显示这两个支系间有高达28步的突变次数。AMOVA分析显示大部分的遗传变异来自这两支系群体间(90.77%), 表明凤鲚群体间存在着显著的地理分化。种群分化指数和基因流分析也表明, 支系间群体有着明显的遗传分化(F_ST > 0.9, N_m< 0.03)。所有分析结果支持所研究的凤鲚标本属于两个不同的地理种群, 且种群的分化至少已达到亚种水平。采用BEAST和TRACER软件得到凤鲚两个亚种的最近共同祖先约在0.34-0.46百万年前, 处于更新世晚期, 推测可能是第四纪晚期的气候旋回和海平面的升降导致了凤鲚的种群分化。

关键词: Coilia mystus, 东南沿海, 线粒体控制区, 遗传多样性, 单系群

Abstract

To analyze the genetic diversity and genetic structure of Coilia mystus, 65 individuals were sampled from four localities, including the Minjiang (MJ), Jiulongjiang (JL), Yangtze (CJ) and Qiantang rivers (QT). Mitochondrial DNA variation was analyzed using 561 bp segments of control region, among which 28 haplotypes were detected. The CJ population had the highest nucleotide diversity (0.0080 ± 0.0046) while the MJ population had the lowest (0.0015 ± 0.0013). Overall haplotype and nucleotide diversity were 0.9433 ± 0.0168 and 0.0317 ± 0.0158, respectively. Average pairwise Kimura 2-parameter distances between MJ and JL and between CJ and QT were 0.3% and 0.8%, respectively, while those between MJ and JL as well between CJ and QT were 6%. Phylogenetic trees constructed using maximum likelihood (ML), maximum parsimony (MP) and neighbor-joining (NJ) methods showed similar topology with two well-supported monophyletic groups. The haplotypes from MJ and JL formed a monophyletic group sister to that comprising the haplotypes of CJ and QT. This interrelationship was supported by network analysis with 28 mutation steps between the two monophyletic clades. Analysis of molecular variance (AMOVA) revealed that the variation between the MJ-JL and CJ-QT clades accounted for 90.77% of total variation, suggesting that significant geographical division was present. The low level of gene flow (N_m< 0.03) and high population differentiation values (F_ST > 0.9) of the two clades also showed considerable genetic isolation. Our results suggest that these four C. mystus populations are divided into two geographical units, and that these units might be considered at the subspecies level in terms of genetic data. The molecular clock estimated using BEAST and TRACER softwares indicated that the subdivision of C. mystus occurred in the late Pleistocene (about 0.34-0.46 million years BP). Climatic oscillations and recurrent marine regression during this period may have influenced the geographical isolation and genetic differentiation of C. mystus.

Key words: Coilia mystus, coastal waters of southeast China, mtDNA control region, genetic diversity, monophyletic group

阎雪岚, 唐文乔, 杨金权 (2009) 基于线粒体控制区的序列变异分析中国东南部沿海凤鲚种群遗传结构. 生物多样性, 17, 143-150. DOI: 10.3724/SP.J.1003.2009.08286.

Xuelan Yan, Wenqiao Tang, Jinquan Yang* (2009) Population genetic structure of tapertail anchovy (Coilia mystus) in coastal waters of southeast China based on mtDNA control region sequences. Biodiversity Science, 17, 143-150. DOI: 10.3724/SP.J.1003.2009.08286.

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链接本文: https://www.biodiversity-science.net/CN/10.3724/SP.J.1003.2009.08286

https://www.biodiversity-science.net/CN/Y2009/V17/I2/143

图/表 6

表1 凤鲚的样本信息、28个单元型(H1-H28)的分布频率及群体mtDNA的遗传多样性

Table 1 Sample information, distribution frequency of 28 haplotypes (H1-H28), haplotype diversity (h) and nucleotide diversity (π) of Coilia mystus

采集地 Location	样本数Sample size	单元型数 Haplotype number	单元型 Haplotype	单元型多样性Haplotype diversity (h)	核苷酸多样性 Nucleotide diversity (π)
闽江 Minjiang River (MJ)	17	6	H1(1)、H2(1)、H4(2)、H5(1)、H7(1)、H8(11)	0.5882 ± 0.1348	0.0015 ± 0.0013
九龙江 Jiulong River (JL)	16	7	H1(1)、H3(1)、H6(1)、H8(10)、H9(1)、H10(1)、H11(1)	0.6250 ± 0.1390	0.0037 ± 0.0024
长江 Yangtze River (CJ)	18	11	H12(4)、H13(1)、H14(1)、H15(1)、H19(3)、H20(1)、H21(1)、H22(1)、H23(3)、H25(1)、 H27(1)	0.9216 ± 0.0417	0.0080 ± 0.0046
钱塘江 Qiantang River (QT)	14	10	H14(1)、H16(1)、H17(1)、H18(1)、H19(3)、H22(2)、H23(2)、H24(1)、H26(1)、H28(1)	0.9451 ± 0.0451	0.0077 ± 0.0046
总计 Total	65	28		0.9433 ± 0.0168	0.0317 ± 0.0158

表2 凤鲚样本群体内与群体间的K2P遗传距离

Table 2 The average K2P distance between and within Coilia mystus populations

种群 Population	闽江 MJ	九龙江 JL	长江 CJ	钱塘江 QT
闽江 MJ	0.002
九龙江 JL	0.003	0.004
长江 CJ	0.060	0.060	0.007
钱塘江 QT	0.060	0.059	0.008	0.008

图1 基于线粒体控制区序列构建的四个凤鲚群体的系统发育树。节点处的数值为bootstrap检验的支持率(仅显示支持率大于50%)、左为邻接树、中间为ML树、右为MP树(仅显示Ti/Tv为 2:1的加权树, 树长=137, CI = 0.8248, HI = 0.1752))。

Fig. 1 Phylogenetic trees of four Coilia mystus populations resulted from mtDNA control region sequence. Numbers at nodes are percent recovery in bootstrap analysis. Given for bootstrap values greater than 50% (Neighbor-joining left, maximum likelihood middle, maximum parsimony right (only shows Ti/Tv 2:1weighted; tree length = 137, CI = 0.8248 and HI = 0.1752)).

图2 4个凤鲚群体控制区序列单元型间的网络亲缘关系图。圆圈内字符为单元型编号, 连接两个圆圈线段上的斜线数表示变异步数。

Fig. 2 Minimum spanning networks showing genetic relationship among control region haplotypes for the four Coilia mystus populations. The characters within circles are haplotype codes. Slashes on the lines joining haplotypes denote number of observed mutations.

表3 凤鲚群体65个样本mtDNA 561 bp控制区序列片段的分子变异分析

Table 3 AMOVA of 561 bp mtDNA control region sequences for 65 individuals of Coilia mystus

变异来源 Source of variation	自由度 df	变异分量 Variance components	变异百分比 Percentage of variation
组间 Among groups	1	14.59231	90.77
组内种群间 Among populations within group	2	0.03239	0.20
种群内 Within population	61	1.45064	9.02
总计 Total	64	16.07535

表4 凤鲚群体间分化指数FST(对角线下)和基因流(Nm) (对角线上)

Table 4 Matrix of pairwise FST (below diagonal) and Nm (above diagonal) between four populations of Coilia mystus

种群 Population	闽江 MJ	九龙江 JL	长江 CJ	钱塘江 QT
闽江 MJ		82.96	0.02	0.02
九龙江 JL	0.0030		0.03	0.03
长江 CJ	0.9245	0.9060		19.91
钱塘江 QT	0.9183	0.8998	0.0120

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