Genetic diversity and population structure of Chinese Gizzard Shad Clupanodon thrissa in South China based on morphological and molecular markers

Chinese Gizzard Shad Clupanodon thrissa is an important migratory fisheries species in estuaries, mainly distributed in the northwest Pacific Ocean. In order to understand the genetic diversity and resource status of C. thrissa, a total of 398 specimens of C. thrissa were collected from 12 geographical populations in South China. Based on morphometry, mitochondrial genes Cyt b and D-loop and nuclear gene RAG1, genetic diversity and population genetic structure of C. thrissa were studied. The results showed that there was no significant difference in the morphology of different populations of C. thrissa. Cluster analysis showed that BH, HP and QZ populations in Guangxi basin were more closely related to MM and CZ populations in Guangdong, while ND population in Fujian basin was more closely related to the six populations in the Pearl River Basin. Except for the MM population, all populations had high haplotype diversity and low nucleotide diversity. The haplotype network and phylogenetic tree based on mitochondrial genes revealed that QZ, BH and HP populations showed obvious lineage branches. AMOVA analysis showed that the genetic variation among groups and within populations of C. thrissa was the main source of total variation. Pairwise FST values showed significant or highly significant genetic differentiation between ND, CZ, MM, BH, HP, QZ populations and other populations, respectively. However, the haplotype network and phylogenetic tree of nuclear genes did not show lineage branches corresponding to geographical location, and the genetic variation within populations was the main source of total variation in the AMOVA analysis. The inconsistent results of mitochondrial and nuclear gene may be related to their different evolutionary rates. This study provides important reference for the resource management and conservation of C. thrissa in South China.