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Selection on nuclear genes in a Pinus phylogeny
A E Palmé1, T Pyhäjärvi, W Wachowiak
1Department of Evolutionary Functional Genomics, Uppsala University, Uppsala, Sweden. anna.palme@ebc.uu.se
Molecular Biology and Evolution
|January 27, 2009
Summary
This study reveals efficient purifying selection in pine evolution, with low ratios of non-synonymous to synonymous substitutions (d(n)/d(s)) across most branches. Evidence for positive selection was found in specific genes, highlighting varied evolutionary pressures.
Area of Science:
- Evolutionary biology
- Genomics
- Phylogenetics
Background:
- Understanding natural selection is crucial for deciphering evolutionary processes in plant lineages.
- Pine (Pinus) species represent a diverse and ecologically significant group of conifers.
Purpose of the Study:
- To investigate patterns of natural selection acting on nuclear genes within a pine phylogeny.
- To construct a robust species tree for 10 pine species using DNA sequences from 18 nuclear genes.
Main Methods:
- Phylogenetic analysis using DNA sequences from 18 nuclear genes to build a species tree.
- Comparative analysis of evolutionary rates between Picea and Pinus.
- Application of various methods to study selection patterns, including calculation of branch-specific d(n)/d(s) ratios for 21 nuclear genes.
Main Results:
- A well-supported species tree for 10 pine species was constructed, largely consistent with previous studies but showing discrepancies with chloroplast phylogenies.
- Significant differences in evolutionary rates were observed between Picea and Pinus.
- Efficient purifying selection was the predominant pattern, with an average d(n)/d(s) ratio of 0.22, indicating strong constraint on protein-coding genes.
- Purifying selection was detected on at least 55% of branches.
- Evidence for positive selection was identified at specific sites in a phytocyanin homolog and in dehydrin 1.
Conclusions:
- Natural selection in pines is largely characterized by purifying selection, similar to other higher plants.
- Specific genes like phytocyanin homolog and dehydrin 1 show evidence of positive selection, suggesting adaptation in certain lineages or functional sites.
- The identified genes provide valuable markers for future phylogenetic studies across different divergence levels.
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