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Genome-Wide Resequencing Reveals High Connectivity and Localized Adaptive Signals in Manila Clam (Ruditapes philippinarum) Populations Along the Southeastern Coast of China
by
, ,
Yatong Yao
1,2,†,
Yaoran Fan
1,†,
Shuaijie Wang
1,
Yanming Sui
3
,
Baojun Tang
1,
Zhiguo Dong
4,5 and
Hanfeng Zheng
1,* 1
East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai 200090, China
2
College of Fisheries and Life Science, Dalian Ocean University, Dalian 116023, China
3
College of Marine and Biological Engineering, Yancheng Institute of Technology, Yancheng 224051, China
4
Co-Innovation Center of Jiangsu Marine Bio-Industry Technology, Jiangsu Ocean University, Lianyungang 222005, China
5
Jiangsu Key Laboratory of Marine Genetic Resources and Breeding, Jiangsu Ocean University, Lianyungang 222005, China
*
Author to whom correspondence should be addressed.
†
These authors contributed equally to this work.
Animals 2026, 16(12), 1897; https://doi.org/10.3390/ani16121897
Submission received: 11 May 2026
/
Revised: 9 June 2026
/
Accepted: 17 June 2026
/
Published: 18 June 2026
(This article belongs to the Special Issue Recent Research on Shellfish Aquaculture and Reproduction—2nd Edition)
Simple Summary
The Manila clam (Ruditapes philippinarum) is an important shellfish widely cultured along the Chinese coast, contributing both to aquaculture production and coastal ecosystem health. Understanding the genetic diversity and population structure of this species is essential for conserving its genetic resources and improving breeding strategies. In this study, we analyzed the genomes of Manila clam populations from five coastal regions of China. The results showed that these populations maintain high genetic diversity and are strongly connected through gene flow, resulting in only minor differences among locations. Despite the overall similarity, several specific genomic regions showed localized differentiation signals, suggesting that certain populations have evolved traits suited to their local environments. These findings provide a clearer understanding of the genetic makeup and connectivity of Manila clam populations, offering valuable guidance for sustainable breeding, germplasm conservation, and the long-term development of the aquaculture industry.
Abstract
The Manila clam (Ruditapes philippinarum) is an economically important bivalve widely cultured in coastal aquaculture systems of China. However, the genome-wide genetic background and germplasm differentiation of geographically distinct populations remain unclear, which constrains germplasm conservation and the development of selective breeding programs. In this study, 50 individuals from five representative coastal populations (QZ, ZZ, ZP, CL, and NH) in China were subjected to whole-genome resequencing, producing 126.67 Gb of clean data and 92,593,087 SNPs after stringent filtering. Genetic diversity analyses showed that nucleotide diversity (π) ranged from 0.2453 to 0.2588, observed heterozygosity (Ho) from 0.1316 to 0.1492, and expected heterozygosity (He) from 0.2303 to 0.2435, with the CL population exhibiting relatively lower diversity. Population differentiation was low to moderate, with pairwise FST values ranging from 0.0454 to 0.0557. Principal component analysis, neighbor-joining phylogenetic analysis, and Admixture clustering consistently indicated limited population structure and extensive genetic admixture. TreeMix analysis further revealed directional gene flow among populations. Rapid linkage disequilibrium decay and predominantly positive Tajima’s D values suggested relatively stable demographic histories. Despite low genome-wide differentiation, combined FST and nucleotide diversity ratio analyses identified localized selective sweep signals in specific genomic regions. These results provide preliminary genome-wide insights into genetic diversity, population connectivity, and candidate localized differentiation signals in R. philippinarum. Given the low sequencing depth, the findings should be interpreted as population-level observations that require further validation using higher-depth genomic datasets before being applied to germplasm conservation and selective breeding programs.
