Adaptive and purifying selection in island and mainland plant species

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The actual proportion of genes under adaptive selection and the proportion of amino acid replacements fixed by positive selection is unknown and hotly debated in the scientific literature (Smith and Eyre-Walker 2002; Fay et al 2002; Ohta 2002). The estimate of the number of genes under adaptive selection was recently obtained for Drosophila and humans (Smith and Eyre-Walker 2002; Fay et al 2001); but no estimates are available for plant genomes and our study will fill this gap. The action of natural selection during adaptive radiations is almost completely unstudied and Hawaiian endemic plant genera provide an opportunity to shed light on this question. To study the action of natural selection in island versus mainland plant species we will use both population genetic and phylogenetic approaches to compare the patterns of intraspecific DNA diversity and interspecific divergence in species from the endemic Hawaiian plant genus Schiedea and the mainland plant genus Silene. The two genera belong to the same family (Caryophyllaceae) and are relatively closely related (silent divergence approximately 30 per cent). During our previous work over 300 Silene latifolia genes have been sequenced. Using PCR primers for Silene latifolia genes we will isolate 25-30 protein-coding genes from Schiedea. The use of Silene primers in Schiedea has proved to work well: in our preliminary experiments eight out of twelve genes amplified successfully. For the molecular phylogenetic analysis the homologous Schiedea and Silene genes will be sequenced in ten morphologically and ecologically different Schiedea species and from five mainland and one Hawaiian endemic Silene species. These sequences will be used to estimate the silent non-silent substitution rates and infer the intensity of adaptive and purifying selection in the island Schiedea and mainland Silene species. To distinguish the effects of positive and negative selection, we will use codon-based maximum likelihood analysis, allowing for variable selective pressures across the codons (Yang et al 2000). For the population genetics analysis the same set of genes will be sequenced in 20 Schiedea globosa and 20 Silene latifolia individuals, which will allow us to study the action of natural selection at the population level.