乔氏新银鱼基于细胞色素b序列的种群遗传结构和种群历史

doi:10.3724/SP.J.1003.2010.251

摘要/Abstract

摘要：

为促进乔氏新银鱼(Neosalanx jordani)种质资源的保护, 采集了长江流域和淮河流域5个乔氏新银鱼地理种群计129个样本, 利用线粒体细胞色素b基因(Cyt b)全序列作为分子标记, 初步分析了乔氏新银鱼种群的遗传多样性、遗传结构及种群历史动态。研究结果共检测到18个Cyt b单倍型, 发现和其他鱼类相比, 乔氏新银鱼具有较高的单倍型多样性(h, 0.590±0.047), 但核苷酸多样性较低(π, 0.00088±0.00011)。分子变异分析(AMOVA)表明, 乔氏新银鱼5个地理种群内个体间和流域内种群间均存在显著的遗传差异, 而长江流域与淮河流域之间遗传分化不明显, 显示乔氏新银鱼遗传分化与当前水系的分布格局不吻合。结果表明乔氏新银鱼目前的遗传格局主要是由于长距离独立的建群事件、基因流限制以及种群的持续扩张的共同作用而形成的。种群历史动态分析结果显示乔氏新银鱼种群为近期扩张种群, 其大部分变异发生在1.897万年之内, 与最后一次冰期全面消退、海平面上升、长江流域及淮河流域中下游大量湖泊(适宜生境)形成的时间相吻合。建议对现存的乔氏新银鱼种群, 特别是遗传多样性较高的那些种群(如鄱阳湖、太湖及洪泽湖种群)分别保护。

关键词: Neosalanx jordani, 细胞色素b, 遗传格局, 种群历史

Abstract

To assess the genetic diversity, population structure and demographic history of Neosalanx jordani, we sequenced complete mitochondrial DNA (1,141 bp) from the cytochrome b (cyt b) gene for 129 individuals from five populations in the Yangtze River and the Huaihe River basins. We identified18 haplotypes, and haplotype diversity was high (h=0.590±0.047). Nucleotide diversity was relatively low (π = 0.00088±0.00011) among all haplotypes. Phylogenetic analysis failed to detect significant geographic structure. Analysis of molecular variance (AMOVA) revealed significant genetic subdivision among individuals within populations and among populations within basins but not between basins, indicating distribution of genetic diversity was inconsistent with contemporary hydrological structure. We suggest that the present complex genetic pattern ofN. jordani resulted from multiple unrelated founding dispersal events (long-distance colonization), contiguous population expansion, and restricted gene flow. Demographic analysis revealed that this species may have experienced a relatively recent population expansion, and the majority of mutations occurred 18.97 kyr ago. This timing is consistent with the estimated time of sea level rise and the formation of large-scale appropriate habitats during the last glacial maximum (LGM). Thus, we suggest that all populations, especially those with high genetic diversity, should be separately managed and conserved.

Key words: Neosalanx jordani, cytochrome b, genetic structure, demographic history

赵亮, 张洁, 刘志瑾, 许木启, 李明 (2010) 乔氏新银鱼基于细胞色素b序列的种群遗传结构和种群历史. 生物多样性, 18, 251-261. DOI: 10.3724/SP.J.1003.2010.251.

Liang Zhao, Jie Zhang, Zhijin Liu, Muqi Xu, Ming Li (2010) Population genetic structure and demographic history of Neosalanx jordanibased on cytochrome b sequences. Biodiversity Science, 18, 251-261. DOI: 10.3724/SP.J.1003.2010.251.

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链接本文: https://www.biodiversity-science.net/CN/10.3724/SP.J.1003.2010.251

https://www.biodiversity-science.net/CN/Y2010/V18/I3/251

图/表 9

表1 线粒体细胞色素b单倍型在乔氏新银鱼各种群中的分布及数量

Table 1 Distribution and the number of mtDNA Cyt b haplotypes in each population ofNeosalanx jordani

单倍型 Haplotypes	长江流域 Yangtze River Basin			淮河流域 Huaihe River Basin		合计 Total
单倍型 Haplotypes	太湖 Taihu lake	南漪湖 Nanyihu lake	鄱阳湖 Poyanghu lake	洪泽湖 Hongzehu lake	瓦埠湖 Wabuhu lake	合计 Total
M01	1					1
M02	1					1
M03	3					3
M04	2					2
M05	1					1
M06	1					1
M07		1				1
M08		1				1
M09			4			4
M10			1			1
M11			1			1
M12	4		15	2		21
M13				3		3
M14				2		2
M15				1		1
M16				1	1	2
M17	17	23	3	16	21	80
M18					3	3
样本量 Sample number	30	25	24	25	25	129

表2 乔氏新银鱼种群遗传多样性

Table 2 Genetic diversity indices of Neosalanx jordanipopulations

种群 Population	样本量 Number of samples (N)	单倍型数量 Number of haplotypes (H)	单倍型多样性 Haplotype diversity (h±SD)	多态性位点数 Number of polymorphic sites (S)	核苷酸多样性 Nucleotide diversity (π±SD)
长江流域 Yangtze River Basin
太湖 Taihu lake	30	8	0.664±0.089	7	0.00077±0.00015
南漪湖 Nanyihu lake	25	3	0.157±0.096	5	0.00035±0.00022
鄱阳湖 Poyanghu lake	24	5	0.587±0.102	5	0.00085±0.00019
小计 Subtotal	79	13	0.648±0.049	16	0.00093±0.00013
淮河流域 Huaihe River Basin
洪泽湖 Hongzehu lake	25	6	0.583±0.109	6	0.00067±0.00017
瓦埠湖 Wabuhu lake	25	3	0.290±0.109	5	0.00072±0.00028
小计 Subtotal	50	7	0.449±0.086	9	0.00071±0.00018
总体 All samples	129	18	0.590±0.047	24	0.00088±0.00011

图1 邻接法和最大似然法构建的以寡齿新银鱼为外群的乔氏新银鱼18种单倍型系统进化树。枝的根部为bootstrap值。

Fig. 1 Neighbor-joining and Maximum-likelihood tree for all 18 haplotypes of Neosalanx jordani and for one outgroup taxa, N. oligodontis. Values indicate bootstrap support for each node.

图2 使用TCS软件以最大简约法构建的最小跨度网络。图中每一个条线代表一个突变连接, 节点处的数字代表不同的单倍型, 节点大小对应单倍型出现频率。图中单倍型编号同表1, 白点代表未能在本研究中检测到的中间单倍型。围绕单倍型的方框确定了嵌套枝分析中的一步枝及两步枝。

Fig. 2 Minimum spanning network based on statistical parsimony using TCS software. Nodes indicate the haplotypes number and are proportional to the haplotype frequency. White nodes indicate undetected intermediate haplotype. Boxes indicate one-step to two-step nesting levels for the nested clade analysis.

表3 乔氏新银鱼线粒体细胞色素b基于Ф-统计量的AMOVA分析结果

Table 3 Results of AMOVA forNeosalanx jordani mtDNA Cyt b estimation using Ф-statistics

变异来源 Source of variation	自由度 d.f.	平方和 Sum of squares	变异组分 Variance components	变异百分比 % variation	Ф-统计量 Ф-statistics
流域间 Among basins	1	4.491	-0.0292	-4.40	Ф_CT =- 0.04396
流域内 Within basins	3	18.961	0.2269	34.17	Ф_SC= 0.3273^**
种群内 Within populations	124	57.817	0.4663	70.22	Ф_ST = 0.2978^**
总和 Total	128	81.270	0.6640

表4 乔氏新银鱼线粒体细胞色素b单倍型嵌套枝分析结果

Table 4 Results of the nested clade analysis of Neosalanx jordani mtDNACyt b haplotypes

嵌套枝 Nested clade	P 值 Pvalue	内部枝 Interior clades	枝距离 Clade distance (D_C)	嵌套枝距离 Nested clade distance (D_N)	推断 Inference
Clade 1-3	0.000	clade M02 (Tip)	181.97	195.76	1-2-11RE-12-13-14 LDC/PF
		clade M04 (Tip)	0.00S	249.12L
		clade M05 (Tip)	0.00	0.00
		clade M06 (Tip)	0.00S	178.79S
		clade M13 (Tip)	0.00S	261.54L
		clade M14 (Tip)	89.68 S	236.22 L
		clade M15 (Tip)	17.47S	130.44S
		clade M17 (Interior)	19.87S	194.75
		I-T	-3.78	0.00
Clade 2-1	0.000	clade 1-1 (Tip)	247.12L	281.70L	1-2-11RE-12CRE
		clade 1-2 (Interior)	54.98S	106.53S
		I-T	-192.14S	-175.16S
Clade 2-2	0.000	clade 1-3 (Interior)	129.83S	187.67	1-2-11RE-12CRE
		clade 1-4 (Tip)	44.50S	176.87
		clade 1-5 (Tip)	0.00S	312.79L
		clade 1-6 (Tip)	0.00S	196.43
		clade 1-7 (Tip)	41.62S	173.41
		clade 1-8 (Tip)	79.46	173.26
		I-T	98.96	0.96
Total cladogram	0.000	clade 2-1 (Tip)	239.66	227.23	1-2-11RE-12 CRE
		clade 2-2 (Interior)	0.00S	136.82S
		I-T	-241.43L	-1,100.14L

图3 有效种群大小随溯祖时间变化的Skyline图。虚线为Classic Skyline, 细实线为Generalized Skyline。

Fig. 3 Skyline plots of changes in effective population size on time. Classic Skyline was shown as dot line, and Generalized Skyline as slender line.

图4 歧点分布分析结果。虚线代表序列之间碱基两两差异的分布, 实线表示在扩张假设理论下歧点分布的期望曲线。

Fig. 4 Observed and expected mismatch distributions showing the frequencies of pair-wise differences. The observed pair-wise difference (dashed line), and the expected mismatch distributions under the sudden expansion model (solid line) ofCyt b.

图5 乔氏新银鱼线粒体细胞色素b基因树。该基因树通过1,000,000 次溯祖模拟构建。右侧坐标为距现在的溯祖时间(单位为千年), 基因树上的点表示突变发生的历史时间。

Fig. 5 Gene tree of the Neosalanx jordani mitochondrialCyt bgene. The tree is based on 1,000,000 coalescent simulations. The right coordinate is scaled by absolute coalescent time (kyr), and the dots in the tree shows the ancestral distribution of mutations in the population history.

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