Genetic patchiness of the endangered giant clam Tridacna maxima from Peninsular Malaysia

In the marine realm, the interpretation of gene flows is often not as linear as terrestrial but requires an understanding of organisms’ life history traits, especially for marine invertebrates with bipartite life stages, as well as the local prevailing seascape features. Giant clams have suffered population decline across the Asia–Pacific region, leading to local extinction. Among giant clam species, Tridacna maxima is considered the most widespread. In this study, we investigated the genetic diversity and connectivity of T. maxima populations along the east coast of Peninsular Malaysia, using both sequence and microsatellite markers. Overall, high haplotype diversity was observed (H_d = 0.67–1.00) in the partial mitochondrial cytochrome oxidase I gene, but microsatellite markers showed heterozygote deficiency (H_o = 0.40–0.53) and high inbreeding coefficient (F_IS = 0.19–0.53) among the populations. The possibility of subpopulations was hinted at moderate genetic differentiation among the population. Based on nuclear microsatellite analysis, no obvious genetic structure was detected in AMOVA between northern and southern zone based on geographic distance, yet subpopulations were revealed in Discriminant Analysis of Principal Component (DAPC) and Bayesian inference with optimal K = 2. Pairwise genetic distance and migration networks further highlighted fine-scale genetic differentiation despite the close proximity among sites. Results revealed typical genetic patchiness in T. maxima populations, a feature often associated with marine bivalves. This study underscores the importance of using genetic tools to assess the genetic connectivity of endangered marine species such as giant clams, which is crucial for the genetic conservation of their populations.