Population genetics in nonmodel organisms: II. natural selection in marginal habitats revealed by deep sequencing on dual platforms

Population genetics of species living in marginal habitats could be particularly informative about the genetics of adaptation, but such analyses have not been readily feasible until recently. Sonneratia alba, a mangrove species widely distributed in the Indo-West Pacific, provides a very suitable system for the study of local adaptation. In this study, we analyzed DNA variation by pooling 71 genes from 85-100 individuals for DNA sequencing. For each of the two nearby S. alba populations, we obtained ~2,500 × coverage on the Illumina GA platform and for the Sanya population, an additional 5,400 × coverage on the AB SOLiD platform. For the Sanya sample, although each sequencing method called many putative single nucleotide polymorphisms, the two sets of calls did not overlap, suggesting platform-dependent errors. Conventional sequencing corroborated that each population is monomorphic. The two populations differ by 54 bp of 79,000 sites, but 90% of the variants are found in 10% of the genes. Strong local adaptation and high migration may help to explain the extensive monomorphism shared by the two populations in the presence of a small number of highly differentiated loci.