Selection and rapidly-evolving genes

Rapidly-evolving genes which exhibit an increased rate of amino acid substitution, resulting in greater amino acid sequence difference, often provide insight into the mechanisms of adaptation and speciation. In this dissertation research, the evolution of rapidly-evolving genes under selection was examined. Homologues to the Arabidopsis APETALA3 (ASAP3/ TM6) and APETALA1 (ASAP1) floral regulatory genes and the CHLOROPHYLL A/B BINDING PROTEIN9 (ASCAB9) photosynthetic structural gene were isolated from species in the Hawaiian silversword alliance, a premier example of plant adaptive radiation. The two floral homeotic genes are found in duplicate copies within members of the Hawaiian silversword alliance and appear to have arisen as a result of interspecific hybridization between two North American tarweed species. Molecular phylogenetic analyses suggest that the interspecific hybridization event involved members of lineages that include Carlquistia muirii (and perhaps Harmonia nutans) and Anisocarpus scabridus. Next, rates of regulatory and structural gene evolution in the Hawaiian species were compared to those in related species of North American tarweeds. Molecular evolutionary analyses indicate significant increases in nonsynonymous relative to synonymous nucleotide substitution rates in the ASAP3/TM6 and ASAP1 regulatory genes in the rapidly evolving Hawaiian species. By contrast, no general increase is evident in neutral mutation rates for these loci in the Hawaiian species. Finally, a group of potential rapidly-evolving genes were identified in Arabidopsis using a powerful evolutionary expressed sequence tag (EST) approach. One indicator of adaptive selection at the molecular level is an excess of amino acid replacement fixed differences per replacement site relative to the number of silent fixed differences per silent site (ω = Ka/Ks). The evolutionary EST approach was used to estimate the distribution of ω among 304 orthologous loci between Arabidopsis thaliana and Arabidopsis lyrata to identify genes potentially involved in the adaptive divergence between these two Brassicaceae species. Twenty-one of 304 genes (7%) were found to have an estimated ω > 1 and are candidates for genes associated with adaptive divergence. A hierarchical Bayesian analysis of protein coding region evolution within and between species also indicates that the selection intensities of these genes are elevated compared to typical A. thaliana nuclear loci.