Evolution of the rbcS gene family in Solanaceae: concerted evolution and gain and loss of introns, with a description of new statistical guidelines for determining the number of unique gene copies.

Thesis (Ph.D.)--University of Washington, 2014

Concerted evolution is a pattern of gene evolution resulting from mechanisms that homogenize gene copies within a lineage. Two mechanisms have been identified that may homogenize <italic>rbcS</italic> copies within Solanaceae. Selection was examined as a mechanism of homogenization through separation of synonymous and nonsynonymous substitutions, through the branch site test of positive selection, and codon usage. Strong negative selection and selection for codon usage were identified, but positive selection also was found to be contributing to homogenization of paralogs in one lineage within <italic>Solanum</italic>. No evidence was found for gene conversion. The results support a role for positive selection as a mechanism in concerted evolution and highlight the danger of inferring a species tree from any set of genes undergoing homogenization. Chapter 1, Supplementary Table 4 (attached as separate file) lists ENc and 3rd codon position composition. Among land plants <italic>rbcS</italic> copies contain two introns at homologous locations. In addition to 2-intron rbcS copies, Solanaceae lineages have rbcS copies with three introns. rbcS copies with 3-introns at homologous positions to other 3-intron Solanaceae copies was identified from <italic>Cestrum</italic>. Phylogenetic analyses indicate this novel, third intron may have originated from a locus of tandemly repeated <italic>rbcS</italic> copies with 2-introns. Numerous sequence motifs similar to transposable elements and containing direct repeats and inverted repeats were identified. These sequence features may contribute to a high divergence in intron sequence between these 3-intron <italic>rbcS</italic> copies. Gene duplication has long been thought to play an important evolutionary role and many genes are now known to differ in copy number between closely related lineages. PCR, cloning, and sequencing is a commonly employed method to examine gene copies from a group of taxa but a standard statistical method to determine whether the actual number of gene copies has been sequenced is lacking from most studies. Simulations indicate the lower bounds for the number of clones necessary to find a given number of unique gene copies and a parametric bootstrap test provides researchers with a method to gauge whether more copies remain unidentified.