MBE Advance Access published online on September 4, 2008
Molecular Biology and Evolution, doi:10.1093/molbev/msn194
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Research Article |
Patterns of divergence among conifer ESTs and polymorphism in Pinus sylvestris identify putative selective sweeps
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* Department of Evolutionary Functional Genomics, Uppsala University, S-752 36 Uppsala, Sweden
Department of Biology, FIN-90014 University of Oulu, Finland
Department of Biological Statistics and Computational Biology, 101 Biotechnology Building, Cornell University, Ithaca, NY 14853
1 Corresponding author. Current address: Department of Evolutionary Functional Genomics, Uppsala University, 752 36 Uppsala, Sweden. Telephone number: +46 (0)18 471 64 10, Fax number: +46 (0)18 471 64 24, e-mail: anna.palme{at}ebc.uu.se.
Received for publication April 16, 2008. Revision received August 26, 2008. Accepted for publication August 30, 2008.
Finding genes that are under positive selection is a difficult task, especially in non-model organisms. Here we have analyzed EST data from four species (Pinus pinaster, Pinus taeda, Picea glauca and Pseudotsuga menziesii) to investigate selection patterns during their evolution and to identify genes likely to be under positive selection. To confirm selection, population samples of these genes have been sequenced in Pinus sylvestris, a species that was not included in the EST data set. The estimates of branch specific Ka/Ks (non-synonymous/synonymous substitution rates) across all genes in the EST data set were similar or smaller than estimates from other higher plant species. There was no evidence for the traditional indication of positive selection, Ka/Ks above one. However, several lines of evidence based on polymorphism patterns suggest that genes with high Ka/Ks (0.20 – 0.52) in the EST data set are in fact more affected by positive selection in P. sylvestris than genes with low Ka/Ks (0.01 – 0.04). The high Ka/Ks genes have a higher level of polymorphism and more negative Tajima's D than the low Ka/Ks genes. Further, in the high Ka/Ks group the Hudson-Kreitman-Aguade test is significant. This suggests that the EST data set is a good starting point for finding genes under positive selection in conifers and that even moderate Ka/Ks values could be indicative of selection. A group of five genes with high Ka/Ks collectively show evidence for positive selection within P. sylvestris.
Key Words: selection • candidate genes • Ka/Ks • dn/ds • Pinus sylvestris • Scots pine
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