MBE Advance Access published online on December 7, 2007
Molecular Biology and Evolution, doi:10.1093/molbev/msm272
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Research Article |
"Contrasting patterns of selection at Pinus pinaster Ait. drought stress candidate genes as revealed by genetic differentiation analyses"
1 INRA, UMR1202 Biodiversity Genes & Communities, 33612 CESTAS Cedex, FRANCE
2 Department of Forest Systems and Resources, Forest Research Institute, CIFOR-INIA, 28040 Madrid, Spain
* corresponding author: Pauline H. Garnier-Géré, INRA, UMR1202 Biodiversity Genes & Communities, 69 route d'Arcachon, 33612 CESTAS Cedex, FRANCE tél: +33 5 57 12 28 19 fax: +33 5 57 12 28 81 email: pauline{at}pierroton.inra.fr
Received for publication July 25, 2007. Revision received November 19, 2007. Accepted for publication December 4, 2007.
The importance of natural selection for shaping adaptive trait differentiation among natural populations of allogamous tree species has long been recognised. Determining the molecular basis of local adaptation remains largely unresolved, and the respective roles of selection and demography in shaping population structure are actively debated. Using a multilocus scan that aims to detect outliers from simulated neutral expectations, we analysed patterns of nucleotide diversity and genetic differentiation at 11 polymorphic candidate genes for drought stress tolerance in phenotypically contrasted Pinus pinaster Ait. populations across its geographical range. We compared three coalescent-based methods: two frequentist-like, including one approach specifically developed for bi-allelic SNPs here, and one Bayesian. Five genes showed outlier patterns which were robust across methods at the haplotype level for two of them. Two genes presented higher FST values than expected (PR-AGP4 and erd3), suggesting that they could have been affected by the action of diversifying selection among populations. In contrast, three genes presented lower FST values than expected (dhn-1, dhn2 and lp3-1), which could represent signatures of homogenising selection among populations. A smaller proportion of outliers were detected at the SNP level suggesting the potential functional significance of particular combinations of sites in drought-response candidate genes. The Bayesian method appeared robust to low sample sizes, flexible to assumptions regarding migration rates, and powerful for detecting selection at the haplotype level, but the frequentist-like method adapted to SNPs was more efficient for the identification of outlier SNPs showing low differentiation. Population-specific effects estimated in the Bayesian method also revealed populations with lower immigration rates, which could have led to favourable situations for local adaptation. Outlier patterns are discussed in regards to the different genes’ putative involvement in drought tolerance responses, from published results in transcriptomics and association mapping in P. pinaster and other related species. These genes clearly constitute relevant candidates for future association studies in P. pinaster.
Key Words: drought stress • candidate genes • adaptive evolution • Pinus pinaster