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MBE Advance Access originally published online on January 23, 2009
Molecular Biology and Evolution 2009 26(4):893-905; 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 Articles

Selection on Nuclear Genes in a Pinus Phylogeny

A.E. Palmé*,{dagger},§, T. Pyhäjärvi{dagger},§, W. Wachowiak{dagger},{ddagger},§ and O. Savolainen{dagger},§

* Department of Evolutionary Functional Genomics, Uppsala University, Uppsala, Sweden
{dagger} Department of Biology, University of Oulu, Oulu, Finland
§ Biocenter Oulu, University of Oulu, Oulu, Finland
{ddagger} Institute of Dendrology, Polish Academy of Sciences, Kórnik, Poland

E-mail: anna.palme{at}ebc.uu.se.

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

Koichiro Tamura, Associate Editor


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