title: Population genetics in nonmodel organisms: II. natural selection in marginal habitats revealed by deep sequencing on dual platforms.
abstract: 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.
authors.affiliation: State Key Laboratory of Biocontrol and Key Laboratory of Gene Engineering of the Ministry of Education, Sun Yat-sen University, Guangzhou, China.
authors.forename: Renchao
authors.initials: R
authors.lastname: Zhou
authors.forename: Shaoping
authors.initials: S
authors.lastname: Ling
authors.forename: Wenming
authors.initials: W
authors.lastname: Zhao
authors.forename: Naoki
authors.initials: N
authors.lastname: Osada
authors.forename: Sufang
authors.initials: S
authors.lastname: Chen
authors.forename: Meng
authors.initials: M
authors.lastname: Zhang
authors.forename: Ziwen
authors.initials: Z
authors.lastname: He
authors.forename: Hua
authors.initials: H
authors.lastname: Bao
authors.forename: Cairong
authors.initials: C
authors.lastname: Zhong
authors.forename: Bing
authors.initials: B
authors.lastname: Zhang
authors.forename: Xuemei
authors.initials: X
authors.lastname: Lu
authors.forename: David
authors.initials: D
authors.lastname: Turissini
authors.forename: Norman C
authors.initials: NC
authors.lastname: Duke
authors.forename: Jian
authors.initials: J
authors.lastname: Lu
authors.forename: Suhua
authors.initials: S
authors.lastname: Shi
authors.forename: Chung-I
authors.initials: CI
authors.lastname: Wu
mesh_terms: D002681:China; D003198:Computer Simulation; D017753:Ecosystem; D019143:Evolution, Molecular; D005828:Genetics, Population / Q000379:methods; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D029561:Lythraceae / Q000235:genetics; D020641:Polymorphism, Single Nucleotide; D012641:Selection, Genetic