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MBE Advance Access published online on January 23, 2009
Molecular Biology and Evolution, doi:10.1093/molbev/msp010
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© The Author 2009. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oxfordjournals.org

Research Article

Selection on nuclear genes in a Pinus phylogeny

AE Palmé*,{dagger}, T Pyhäjärvi{dagger}, W Wachowiak{dagger},§ and O Savolainen{dagger}

* Department of Evolutionary Functional Genomics, Uppsala University, 752 36 Uppsala, Sweden
{dagger} Department of Biology and Biocenter Oulu, University of Oulu, 90014, Oulu, Finland
§ Institute of Dendrology, Polish Academy of Sciences, Parkowa 5, 62-033 Kórnik, Poland

Corresponding author: Anna Palmé, 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 September 17, 2008. Revision received January 7, 2009. Accepted for publication January 15, 2009.

In this study we investigate natural selection in a pine phylogeny. DNA sequences from 18 nuclear genes were used to construct a very well supported species tree including 10 pine species. This tree is in complete agreement with a previously reported supertree constructed from morphological and molecular data but there are discrepancies with previous chloroplast phylogenies within the section Pinus. A significant difference in evolutionary rate between Picea and Pinus was found, which could potentially indicate a lower mutation rate in Picea, but other scenarios are also possible. Several approaches were used to study selection patterns in a set of 21 nuclear genes in pines and in some cases in Picea and Pseudotsuga. The overall pattern suggests efficient purifying selection resulting in low branch specific dn/ds ratios with an average of 0.22, which is similar to other higher plants. Evidence for purifying selection was common and found on at least 55% of the branches. Evidence of positive selection at several sites was found in a phytocyanin homolog and significant differences in dn/ds among the branches in the gene tree in dehydrin 1. Several genes suitable for further phylogenetic analysis at various levels of divergence were identified.

Key Words: selection • phylogeny • pine • nuclear genes • sequence polymorphisms • gene trees


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