Genome-wide SNP-based diversity analysis and phylogeographic inference in the ark shell (Anadara broughtonii)

Abstract

The ark shell (Anadara broughtonii) is a marine bivalve inhabiting the West Pacific coasts. Its natural resources have declined considerably in recent years due to overexploitation. Understanding of the genetic diversity and population structure of A. broughtonii is important for conservation and species-specific management. The Specific-Locus Amplified Fragment Sequencing (SLAF-seq) method was used to screen the SNPs for exploring the genetic diversity and phylogeographic characterization in 40 Anadara broughtonii individuals, 10 each from 4 sample locations: China, Japan, Korea, and Russia. We generated 394,768 SLAFs and developed 452,144 polymorphic SNPs. The observed and expected heterozygosity (Ho and He) ranged from 0.1805 to 0.3216 and from 0.1504 to 0.2156, respectively. Relatively strong differentiation was detected between populations from China/Russia and those from Japan/Korea, possibly related to the barrier effects from the Shandong Peninsula and the Korean Peninsula. Phylogenetic and Discriminant analysis of principal components (DAPC) supported the 40 individuals were mainly classified into four genetically distinct groups according to their sampling locations. Overall, Japanese and Korean populations owned higher genetic diversity. However, the two native populations may probably be affected by human activities such as artificial culture and commercial transportation. In order to avoid the further admixture of the native population of A. broughtonii, more attention should be paid to the germplasm resources protection of this species. Our results demonstrated the capability and high resolution of SNPs derived from SLAF-seq to measure the population genetic diversity and phylogeographic structure of A. broughtonii.