基于线粒体控制区序列的黄海日本鳀(Engraulis japonicus)的群体遗传结构*

doi:10.11978/2020119

Abstract

Abstract:

Genetic diversity and population structure are important aspects in population dynamics study, and are the basis of fish resources evaluation and protection. Japanese anchovy (Engraulis japonicus) is an important fish species in the China East Coast, which has both ecological and economic values. In this study, the whole sequence of mitochondrial control region was used to analyze the genetic diversity, population genetic structure, and demographic history of its four geographical populations in the Yellow Sea, namely, north of the northern Yellow Sea (NYN), south of the northern Yellow Sea (NYS), north of the southern Yellow Sea (SYN), and central part of the southern Yellow Sea (SYC). A total of 126 haplotypes were detected in 131 samples of the four populations, and their haplotype diversity levels were high, among which the lowest was in the NYS (0.995±0.009) and the highest was in the SYC (1.000±0.014). In all populations, the nucleotide diversity was low (0.010±0.005 to 0.011±0.006). The results of Discriminant Analysis of Principal Components (DAPC) and F_st values indicated that there was no significant segregation among the four populations, and the level of genetic homogeneity among populations was high. There was no obvious population genetic structure, with the large molecular variation within the populations based on the Analysis of Molecular Variance (AMOVA). The Bayesian phylogenetic tree revealed two distinct lineages, which diverged at 0.701 million years ago, dating back to the Pleistocene period. Neutrality test and nucleotide mismatch distribution analyses demonstrated that these two lineages experienced demographic expansions. The effective population of Japanese anchovy in the Yellow Sea decreased significantly at 0.150 million years ago by analyzing the Bayesian skyline.

Key words: Yellow Sea, Engraulis japonicus, genetic diversity, population genetic structure, Pleistocene

CLC Number:

P735.54

ZOU Congcong, WANG Lijuan, WU Zhihao, YOU Feng. Population genetic structure of Japanese anchovy (Engraulis japonicus) in the Yellow Sea based on mitochondrial control region sequences^*[J].Journal of Tropical Oceanography, 2021, 40(5): 25-35.

Figures/Tables 11

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变异来源	平方和	变异百分比	F 统计	p
一个基因池
群体间	16.901	0.190
群体内	673.710	99.810	F_st = 0.00192	0.341
两个基因池(NYN、NYS)(SYN、SYC)
组群间	3.759	-0.84	F_ct = -0.00841	1.000
组群内群体间	13.141	0.74	F_sc = 0.00734	0.131
群体内	673.710	100.10	F_st = -0.00101	0.286
两个基因池(NYN、NYS、SYN)(SYC)
组群间	6.157	0.41	F_ct= 0.00414	0.483
组群内群体间	10.743	0.03	F_sc= 0.00035	0.392
群体内	673.710	99.55	F_st = 0.00448	0.329

群体	Tajima’s D		Fu’s F_s		Ramos-Onnsis and Roza’s R₂
群体	D	p	F_s	p	R₂	p
NYN	-1.307	0.073	-24.603	0.000	0.107	0.000
NYS	-1.013	0.162	-24.077	0.000	0.113	0.000
SYN	-1.348	0.070	-24.249	0.000	0.118	0.000
SYC	-0.702	0.284	-13.580	0.000	0.127	0.000
谱系 1	-1.532	0.034	-24.790	0.000	0.103	0.000
谱系 2	-1.435	0.041	-24.619	0.000	0.099	0.000

群体		群体扩张模型					空间扩张模型
群体	τ	t	θ₀	θ₁	SSD	HRI	τ	θ	M	SSD	HRI
NYN	10.578	0.172	0.000	1527.500	0.001	0.007	10.585	0.010	1574.756	0.001	0.007
NYS	9.396	0.153	1.331	386.250	0.002	0.009	9.232	1.480	206.480	0.002	0.009
SYN	9.855	0.160	0.000	280.625	0.003	0.011	8.745	1.201	99999.000	0.003	0.011
SYC	11.881	0.193	0.002	279.688	0.004	0.010	11.802	0.026	99999.000	0.004	0.010
谱系1	8.326	0.135	0.228	99999.000	0.001	0.010	8.543	0.103	99999.000	0.001	0.010
谱系2	10.109	0.164	0.025	118.896	0.001	0.005	9.189	0.860	287.179	0.001	0.005

Population genetic structure of Japanese anchovy (Engraulis japonicus) in the Yellow Sea based on mitochondrial control region sequences^*

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群体	样品数/个	单倍型数/个	单倍型多样性 (h±SD)	核苷酸多样性 (π±SD)	多态位点数/个	碱基转换数/个	碱基颠换数/个	碱基插入数/个
NYN	43	42	0.999±0.005	0.011±0.005	71	57	19	0
NYS	36	34	0.995±0.009	0.010±0.005	61	48	15	4
SYN	30	30	1.000±0.009	0.010±0.005	60	52	15	0
SYC	22	22	1.000±0.014	0.011±0.006	50	39	11	1
谱系1	61	60	1.000±0.003	0.008±0.004	72	59	23	1
谱系2	70	66	0.998±0.003	0.009±0.005	81	65	21	3
所有个体	131	126	0.999±0.001	0.010±0.005	108	85	38	4

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Population genetic structure of Japanese anchovy (Engraulis japonicus) in the Yellow Sea based on mitochondrial control region sequences*

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Population genetic structure of Japanese anchovy (Engraulis japonicus) in the Yellow Sea based on mitochondrial control region sequences^*