Population Genetics of Manila Clam (Ruditapes philippinarum) in China Inferred from Microsatellite Markers

Simple Summary The Manila clam (Ruditapes philippinarum) is one of the most commercially important bivalves along the coast of China. The increasing expanding of clam culture may result in some serious problems. In this paper, we investigated the genetic diversity and differentiation of R. philippinarum populations and tested the hypothesis that clam population differentiation is influenced by the southern breeding and northern culture. The present findings will provide useful information for natural resource conservation and genetic breeding of the Manila clam in China. The Manila clam (Ruditapes philippinarum) is one of the most commercially important bivalves along the coast of China. With the continuous expansion of clam farming scale, it may lead to some serious problems, including loss of genetic variation, inbreeding depression, and reduced effective population size (N-e). In the present study, eleven microsatellite markers were used to investigate the genetic diversity and differentiation among 13 clam populations along the coast of China. As a result, 150 alleles were detected according to the genotyping results of eleven microsatellite loci. The observed heterozygosity (H-o) was estimated to be ranging from 0.437 to 0.678, while the expected heterozygosity (H-e) was calculated to be varying from 0.587 to 0.700. F-st values between populations ranged from 0.0046-0.1983. In particular, the Laizhou population had the highest genetic variability, which was significantly different from the others (all F-st values > 0.1). For all the clam populations, there was no significant linear regression between genetic and geographic distance, indicating that these populations do not follow a pattern of isolation by distance (IBD). Genetic structure was estimated according to NJ, principal coordinates (PCoA), and structure-based clustering. Estimates of effective population size range from dozens to thousands among different populations, based on linkage-disequilibrium and molecular coancestry methods. The results reveal the genetic diversity of clams and verify the hypothesis that clam population differentiation may be influenced by the mode of southern breeding and northern culture, providing guiding information for natural resource conservation and genetic breeding of clams.