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

## TL;DR

This study examines the genetic diversity and population structure of the economically important Phascolosoma esculenta in China to guide conservation and aquaculture efforts.

## Contribution

The study provides new insights into the genetic structure and historical population decline of Phascolosoma esculenta using RAD-seq data from five locations.

## Key findings

- All populations show moderate genetic diversity but signs of inbreeding and heterozygote deficiency.
- Low genetic differentiation and high gene flow suggest ongoing genetic exchange among populations.
- Historical analysis indicates a population decline beginning around 300 years ago.

## Abstract

Phascolosoma esculenta is an economic species endemic in Southeastern China, with its wild populations thought to be under threat. This study investigated its genetic diversity and population structure across five locations to inform conservation and sustainable development efforts. Results suggest all examined populations have moderate genetic diversity, with possible ongoing genetic exchange among them. Historical demographic dynamics imply a potential rapid population decline starting around 300 years ago. These findings indicate P. esculenta may be undergoing genetic degradation, and this research provides valuable baseline information for the conservation of wild populations and the sustainable development of its aquaculture industry.

Phascolosoma esculenta is an economic species endemic in China and a highly prized delicacy along the country’s southeastern coast. This study focused on five P. esculenta 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 (Ho = 0.1872–0.2065) was lower than the expected heterozygosity (He = 0.2304–0.2382), with inbreeding coefficients (Fis) 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 PIC (0.1914–0.1982). Low genetic differentiation was observed among populations (Fst: 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, p = 0.4307). Analysis of the species’ historical population dynamics suggests that P. esculenta 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.