# Genome-Wide Genetic Diversity and Population Structure of Sillago sinica (Perciformes, Sillaginidae) from the Coastal Waters of China: Implications for Phylogeographic Pattern and Fishery Management

## TL;DR

This study uses whole-genome resequencing to analyze the genetic diversity and population structure of Sillago sinica in China, revealing low genetic diversity and the need for region-specific fishery management.

## Contribution

The study provides the first genome-wide analysis of Sillago sinica's population structure and genetic diversity in China.

## Key findings

- Sillago sinica populations show low genetic diversity and significant genetic differentiation between northern and southern groups.
- Genetic divergence is likely influenced by environmental and geographical differences between regions.
- Region-specific fishery management is recommended to conserve and utilize S. sinica resources effectively.

## Abstract

Sillago sinica is a recently described Sillaginidae species along the coasts of China. Its population genetic characteristics remain largely unknown. In this study, we used whole-genome resequencing (WGR) to analyze the fine-scale genetic diversity and spatial population structure of S. sinica from four geographic locations: Dongying, Rushan, Wenzhou, and Zhoushan. Results revealed a relatively low level of genetic diversity and clear genetic differentiation among different populations. The findings highlight the need for region-specific fishery management to better conserve and utilize S. sinica resources.

The ability to detect population structure and determine the extent of genetic variation among populations is critical for understanding genetic background and effective fishery management. Fifty-eight individuals of S. sinica were resequenced with an average depth of 24× based on the Illumina sequencing platform. A total of 7,409,691 high-quality single nucleotide polymorphisms (SNPs) and 327,698 linkage disequilibrium-pruned SNPs were detected by comparing with the reference genome, and the average nucleotide diversity (π) and polymorphism information content (PIC) for all SNPs were 0.0036 ± 0.0023 and 0.2358 ± 0.1013, respectively, indicating the relatively low level of genetic diversity caused by limited gene flow and small effective population size (Ne). Integrated analyses of principal component analysis (PCA), ADMIXTURE, fixation index (Fst), and cladogram showed a significant genetic divergence between the north group (Dongying and Rushan populations) and the south group (Wenzhou and Zhoushan populations), which might be related to the differences in natural and geographical environments. The comprehensive results confirmed the genetic heterogeneity of S. sinica populations from the northern and southern sea areas of China, and suggested that regionalization fishery management should be adopted for further resource protection and utilization of S. sinica.