Population structure and genetic diversity of hairfin anchovy (<i>Setipinna tenuifilis</i>) revealed by microsatellite markers

Bingjian Liu; Shan Tong; Jiasheng Li; Xun Jin; Sixu Zheng; Yunpeng Wang; Luxiu Gao; Taobo Feng; Mingzhe Han; Yifan Liu

doi:10.1007/s13131-024-2369-9

doi: 10.1007/s13131-024-2369-9

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出版历程
- 收稿日期: 2023-12-08
- 录用日期: 2024-05-06
- 网络出版日期: 2025-03-12

Population structure and genetic diversity of hairfin anchovy (Setipinna tenuifilis) revealed by microsatellite markers

Bingjian Liu^{1, 2},
Shan Tong^{1, 2},
Jiasheng Li^{1, 2},
Xun Jin^{1, 2},
Sixu Zheng^{2, 3},
Yunpeng Wang^{1, 2},
Luxiu Gao^{1, 2},
Taobo Feng^{1, 2},
Mingzhe Han^{1, 2},
Yifan Liu^{2, 3
, ,}

1.
College of Marine Science and Technology, Zhejiang Ocean University, Zhoushan 316022, China
2.
National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, Zhoushan 316022, China
3.
National Engineering Research Center for Facilitated Marine Aquaculture, Zhejiang Ocean University, Zhoushan 316022, China

Funds: The Zhejiang Provincial Natural Science Foundation of China under contract Nos LY22D060001 and LY20C190008; the National Natural Science Foundation of China (NSFC) under contract No. 41806156; the Key Research and Development Projects in Xizang under contract No. XZ202301ZY0012N.

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Corresponding author: E-mail: et999927@163.com

摘要

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Abstract: Microsatellite markers with polymorphic advantages are widely used in the exploration and utilization of marine fishery resources. In this study, 16 polymorphic microsatellite markers were used to evaluate the diversity and population structure of Setipinna tenuifilis, a nearshore fish of economic and ecological value in the western Pacific and Indian Oceans. The genetic diversity of S. tenuifilis showed a high level (mean N_a=23.25, mean H_o=0.639, mean R_a=11.625, and PIC=0.844) similar to other Clupeiformes fish species. The nine wild S. tenuifilis populations showed significant differentiation (F_ST ranging from 0.00384 to 0.19346) and were generally divided into southern and northern populations based on genetic structure, except for the Zhoushan population, which exhibited genetic mixture. Our results provide fundamental but significant genetic insights for the management and conservation of S. tenuifilis fishery resources.
- microsatellite /
- population structure /
- genetic diversity /
- Setipinna tenuifilis

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Figure 1. Schematic map of sampling locations along the coastal waters of China. A total of 180 individuals of S. tenuifilis from nine geographic locations (DL, QH, QD, LY, NT, ZZ, PX, GS, and ZJ) were collected for population analysis.

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Figure 2. Plots of results of outlier tests. a. The hierarchical island model test for selection completed using the program Arlequin. The genetic differentiation (F_ST) is plotted against expected heterozygosity (H_e). b. The Bayesian test for selection completed using the program BayeScan. The dots on the right side of the vertical line are above a 0.99 probability of being candidates of selection.

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Figure 3. Population structure obtained from the STRUCTURE analysis (K=2, 3, 4). Individuals are represented by vertical bars. Different colours in the same individual indicate the percentage of the genome shared with each cluster according to the admixture proportions. The Y-axis represents the probability of belonging to a certain cluster, while the X-axis represents each population delimited by a black solid vertical line.

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Figure 4. Clustering result of the principal component analysis (PAC).

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Figure 5. Mean sea surface temperature (a) and mean sea surface salinity (b) in the coastal region of China.

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Table 1. The genetic diversity of 16 polymorphic microsatellite markers for S. tenuifilis

Locus	Na	Ho	He	PIC	HWE	Fnull
Sten01	20	0.794	0.869	0.899	NS	0.0664
Sten02	31	0.750	0.899	0.923	***	0.1080
Sten03	21	0.756	0.887	0.918	***	0.1013
Sten04	32	0.572	0.914	0.951	***	0.2498
Sten05	17	0.867	0.861	0.887	NS	0.0163
Sten06	18	0.394	0.680	0.677	***	0.2921
Sten07	27	0.611	0.770	0.792	***	0.1190
Sten08	22	0.544	0.877	0.906	***	0.2517
Sten09	45	0.467	0.914	0.956	***	0.3455
Sten10	28	0.450	0.889	0.936	***	0.3531
Sten11	17	0.700	0.808	0.818	***	0.0879
Sten12	21	0.817	0.880	0.904	NS	0.0551
Sten13	12	0.572	0.668	0.714	***	0.1288
Sten14	17	0.606	0.809	0.845	***	0.1739
Sten15	29	0.911	0.892	0.925	NS	0.0086
Sten16	15	0.411	0.418	0.445	NS	0.0645
Mean	23.25	0.639	0.815	0.844		0.1514
Notes: N_a represents number of alleles, H_o observed heterozygosity, H_e expected heterozygosity, PIC polymorphic information content, HWE deviation from the Hardy-Weinberg equilibrium (NS meaning non-significant and *** less than 0.0001), and F_null null allele frequency.

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Table 2. Genetic diversity of nine S. tenuifilis populations

Population	R_a	N_a	H_o	H_e
QH	12.125	12.125	0.616	0.805
DL	11.688	11.688	0.578	0.787
QD	12.188	12.188	0.638	0.798
LY	11.813	11.813	0.659	0.814
NT	11.688	11.688	0.625	0.805
ZZ	11.188	11.188	0.625	0.838
PX	11.188	11.188	0.663	0.816
GS	10.938	10.938	0.678	0.822
ZJ	11.813	11.813	0.669	0.847
Mean	11.625	11.625	0.639	0.815
Notes: R_a represents allelic richness, N_a number of alleles, H_o observed heterozygosity, and H_e expected heterozygosity.

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Table 3. Pairwise genetic differentiation (F_ST) for nine S. tenuifilis populations using microsatellites

	QH	DL	QD	LY	NT	ZZ	PX	GS	ZJ
QH
DL	0.0327
QD	0.0240	0.0229
LY	0.0190	0.0265	0.0174
NT	0.0120	0.0295	0.0147	0.0198
ZZ	0.0158	0.0345	0.0249	0.0249	0.0182
PX	0.0370	0.0504	0.0381	0.0312	0.0281	0.0220
GS	0.0373	0.0515	0.0443	0.0364	0.0329	0.0165	0.0076
ZJ	0.0368	0.0479	0.0466	0.0366	0.0423	0.0115	0.0227	0.0093
Notes: Extremely significant difference probability values (p<0.01) following correction for multiple tests are indicated in bold.

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Table 4. Analysis of molecular variance (AMOVA) of S. tenuifilis populations using microsatellites

Sources of variations	df	Sum of squares	Variance components	Percentage of variation	Fixation indices
Total (QH, DL, QD, LY, NT, PX, GS, ZJ)
Among all populations	7	105.728	0.21106 Va	3.07	F_ST = 0.03071*
Within populations	312	2078.400	6.66154 Vb	96.93
Two groups (QH, DL, QD, LY, NT) (PX, GS, ZJ)
Among groups	1	34.978	0.15458 Va	2.23	F_CT = 0.02226*
Among populations within group	6	70.750	0.12825 Vb	1.85	F_SC = 0.01889*
Within populations	312	2078.400	6.66154 Vc	95.93	F_ST = 0.04073*

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Table 5. Bottleneck analysis of S. tenuifilis populations under the two-phase mutation model (TPM) and stepwise mutation model (SMM)

Population	Wilcoxon test				Mode-shift test
	TPM		SMM
	One tail for H deficiency	One tail for H excess	One tail for H deficiency	One tail for H excess
QH	0.21660	0.79813	0.10571	0.90360	normal L-shaped
DL	0.01932	0.98323	0.00459	0.99619	normal L-shaped
QD	0.00912	0.99225	0.00775	0.99345	normal L-shaped
LY	0.37178	0.64714	0.23187	0.78340	normal L-shaped
NT	0.20187	0.81227	0.14893	0.86278	normal L-shaped
ZZ	0.62822	0.39098	0.44997	0.56987	normal L-shaped
PX	0.03696	0.96730	0.01677	0.98550	normal L-shaped
GS	0.21660	0.79813	0.09641	0.91232	normal L-shaped
ZJ	0.53006	0.48998	0.31609	0.70171	normal L-shaped

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doi: 10.1007/s13131-024-2369-9

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Population structure and genetic diversity of hairfin anchovy (Setipinna tenuifilis) revealed by microsatellite markers

Corresponding author: E-mail: et999927@163.com

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