*Article* **Comparative Analysis of Genetic Structure and Diversity in Five Populations of Yellowtail Kingfish (***Seriola aureovittata***)**

**Aijun Cui 1,2, Yongjiang Xu 1,2,\*, Kiyoshi Kikuchi 3, Yan Jiang 1,2, Bin Wang 1,2, Takashi Koyama <sup>3</sup> and Xuezhou Liu 1,2**


**Abstract:** To clarify the population genetic structure, intrapopulation diversity, and interpopulation differentiation of yellowtail kingfish (*Seriola aureovittata*), we sampled 143 individuals from five collections of yellowtail kingfish: farmed (n = 30) and wild (n = 33) collections in China, a wild collection in Japan (n = 20), and farmed (n = 31) and wild (n = 29) collections in Australia. Using 2b-RAD simplified genome sequencing, we obtained an average of 287,594 unique tags per population, with an average sequencing depth of 27.13×. Our final genotype dataset included 48,710 SNPs (Single Nucleotide Polymorphisms). The five collections were all in Hardy–Weinberg equilibrium, and the interpopulation differentiation varied among the sample collections. The genetic differentiation coefficients (*Fst*) between the Chinese and Japanese yellowtail kingfish collections were low and the gene flow (*Nm*) values were high. These results suggest continuous gene flow occurs frequently between the collections, indicating that they belong to the same population. In contrast, genetic differentiation was high between the Australian collections and the Chinese and Japanese populations, suggesting different evolutionary origins and belonging to different populations. The farmed and wild Australian collections fell into distinct clades in a neighbor-joining phylogeny tree, suggesting farmed fish have begun to differentiate from the wild collection. A similar level of genetic diversity between the wild collections in China and Japan suggests that they originated from the same spawning ground. This, therefore, reminds us that in future aquaculture processes attention is needed regarding implementing targeted breeding strategies. In addition, our data will contribute to Chinese yellowtail kingfish genetic breeding and the sustainable use of Chinese yellowtail kingfish germplasms.

**Keywords:** *Seriola aureovittata*; population genetics; single nucleotide polymorphisms; 2b-RAD sequencing
