Mitochondrial DNA reveals genetically structured haplogroups of Bali sardinella (Sardinella lemuru) in Philippine waters

Abstract

Population genetic structure of Sardinella lemuru in Philippine waters was examined using mitochondrial DNA markers, control region (CR) and cytochrome oxidase I (COI). The sampling effort was focused along the northern coast of Mindanao where the species was previously reported to have regionally structured stocks. Sequences from online databases were included to expand geographic coverage of the analyses. Phylogeographic and population genetic inferences revealed the presence of genetically structured sympatric haplogroups across the archipelago (CR: n = 493, K = 3, between-group genetic distance = 0.038 – 0.054, global ΦST=0.41 p < 0.001; COI: n = 159, K = 2, between-group genetic distance = 0.012, global ΦST=0.77, p < 0.001). In contrast, little to no genetic differentiation was inferred when samples were assigned based on geographic location (CR global ΦST=0.01, p < 0.05; COI global ΦST=0.001, p > 0.05). These results suggest that (1) gene flow occurs across space, but is limited among sympatric haplogroups, (2) these sympatric haplogroups do not correspond to cryptic species, and (3) differences in mutation rates between the two markers may have led to a different number of haplogroups being recovered. High haplotype diversity (HCR=0.99; HCOI=0.798), low nucleotide diversity (πCR=0.041; πCOI=0.005), and significantly negative Fu’s FS values implied demographic expansion for all haplogroups. The mismatch distribution and Bayesian Skyline plot indicated that expansion occurred during the late Pleistocene. Based on our results, we hypothesize that the Philippines is a secondary contact zone for S. lemuru, and testing this requires that samples be obtained from the entire habitat range of the species along the Indo-West Pacific Region.