# Application of Microsatellites in Genetic Diversity Analysis and Population Discrimination of Coilia nasus from the Yangtze River

## TL;DR

This study uses microsatellites to analyze the genetic diversity and population structure of tapertail anchovy in the Yangtze River and a cultured population, revealing high genetic variation and evolutionary relationships.

## Contribution

A method for accurate population assignment of Coilia nasus using microsatellite data is developed.

## Key findings

- High genetic diversity was observed with most variation occurring within individuals.
- The Shanghai population clustered closely with Anqing, followed by Taizhou, Hukou, and Yangzhong.
- A discriminant function enabled accurate identification of fish populations.

## Abstract

Understanding the genetic connections and population characteristics of tapertail anchovy (Coilia nasus) is crucial for protecting this species and its living resources. This study examined five Coilia nasus populations—four wild populations living in the Yangtze River and one cultured population—by analyzing special genetic markers with high variability. The results showed high genetic diversity among these groups, with different degrees of genetic differences between them. Most genetic variation existed within individual fish, while variation between groups was small. Genetic analysis also revealed the evolutionary relationships between the groups: the Shanghai population clustered first with Anqing, followed by Taizhou, Hukou, and finally Yangzhong. We also developed a method to accurately identify which population each fish belongs to. These findings clarify the genetic links of Coilia nasus populations and provide important guidance for protecting and properly managing this species’ resources.

The genetic diversity and population structure of five tapertail anchovy (Coilia nasus) populations—four wild populations from the Yangtze River (Taizhou, Anqing, Shanghai, Hukou) and one cultured population from Yangzhong—were analyzed using 18 highly polymorphic microsatellite loci. All loci exhibited high polymorphism, with genetic parameters as follows: mean number of alleles = 20.567, expected heterozygosity = 13.506, Shannon information index = 2.743, and polymorphic information content = 0.9624. F-statistics ranged from 0.02898 to 0.05714, indicating varying degrees of genetic differentiation between all populations. Analysis of molecular variance revealed that 4% of the total genetic variation was attributable to differences among populations, 23% to variation among individuals within populations, and 73% to within-individual genetic variation. A UPGMA phylogenetic tree based on Nei’s genetic distance showed that the Shanghai population clustered first with Anqing, followed by Taizhou, Hukou, and finally Yangzhong. Additionally, discriminant functions developed from microsatellite data enabled accurate population assignment for all individuals. These findings provide critical insights into the genetic relationships and structure of C. nasus populations, offering valuable implications for their conservation and management.