Genetic Structure and Historical Dynamics of the Economic Species Phascolosoma esculenta in Southeastern China

<i>Phascolosoma esculenta</i> is an economic species endemic in China and a highly prized delicacy along the country's southeastern coast. This study focused on five <i>P. esculenta</i> populations and investigated their genetic diversity, population structure, and historical population dynamics. These populations were sampled from five locations, namely Beihai (BH) and Fangchenggang (FCG), in Guangxi; Putian, in Fujian (FJ); Danzhou, in Hainan (HN); and Zhanjiang (ZJ), in Guangdong. Genomic data were obtained through restriction site-associated DNA sequencing (RAD-seq) of 100 individuals. After quality filtering, a panel of 158,264 high-quality single nucleotide polymorphism (SNP) markers was established for subsequent analysis. The results revealed that the observed heterozygosity (<i>Ho</i> = 0.1872-0.2065) was lower than the expected heterozygosity (<i>He</i> = 0.2304-0.2382), with inbreeding coefficients (<i>Fis</i>) ranging from 0.1114 to 0.1592, indicating heterozygote deficiency and moderate inbreeding. Genetic diversity was moderate across all populations, as reflected in the values I (0.5220-0.5530), π (0.2415-0.2478), and <i>PIC</i> (0.1914-0.1982). Low genetic differentiation was observed among populations (<i>F</i>st: 0.0339-0.0509) accompanied by high gene flow (Nm = 4.6658-7.1192), suggesting ongoing genetic exchange between populations. Analysis of Molecular Variance (AMOVA) indicated that most genetic variation occurred within populations. Genetic distance and genetic similarity ranged from 0.0345 to 0.0522 and 0.9491 to 0.9661, respectively, with no significant isolation by distance (Mantel test, R = 0.0793, <i>p</i> = 0.4307). Analysis of the species' historical population dynamics suggests that <i>P. esculenta</i> may have experienced a substantial population contraction beginning approximately 300 years ago. Overall, the five populations exhibit moderate genetic diversity, though signs of inbreeding and recent population decline may indicate early stages of germplasm degradation. These findings provide important insights for the conservation and sustainable aquaculture of this species.