Geographic patterns and ecological adaptations of Manila clam (Ruditapes philippinarum) along the Chinese coast: Insights from migration dynamics and gene flow

The Manila Clam (Ruditapes Philippinarum) is one of the most economically significant marine bivalves along the China coast. In recent years, due to the escalating scale of aquaculture, the artificial activities of "cross-regional introduction" have to some extent exerted an influence on the genetic diversity and structure of clam larvae, leading to an ongoing occurrence of genetically mixed clam larvae populations and ambiguous genetic foundation of germplasm resources in China. Therefore, there is an imperative need to gain profound insights into the lineage, genetic structure, and assess the adaptability potential of clams originating from both northern and southern regions. We use Specific Locus Amplified Framents technology to simplify genome sequencing of wild clams along the coast of China. Through genetic diversity, genetic structure, gene flow, and selection elimination analysis, the results show that clams can be divided into distinct north-south lineages, with Wafangdian in Liaoning (RPLW), Zhangzi Island in Liaoning (RPLZ), and Laizhou in Shandong (RPSL) comprise the northern lineage, while Lianjiang in Fujian (RPFL) constitutes the southern lineage. The artificial relocation of clams in China has resulted in a blended population structure among local clams. The genetic functional differences between clams from the north and south are primarily manifest in energy metabolism, and the adaptive evolution of clams is mainly associated with temperature. This integrative research not only furnishes valuable insights into the genetic structure of clam populations, thereby contributing to the advancement of natural conservation and genetic breeding efforts for clams but also establishes the groundwork for a comprehensive exploration of clam adaptive evolution.