The proper processing of light signals is crucial for the success of all plants. Thus, photoreceptors play a critical role in plant development, serving as informational molecules that allow plants to determine where they are in space and time and to synchronize growth and development to a changing light regime. The control of plant form by ambient light conditions, a process known as photomorphogenesis, is mediated by phytochromes, which absorb red light and far-red light, along with distinct blue and ultra-violet absorbing photoreceptors. Phytochrome evolution in land plants is marked by a series of gene duplications that have led to independently evolving and functionally distinct lines. Flowering plants have the highest number of phytochromes and also are the most successful group of land plants. They total approximately 250,000 species, outnumbering all other plant groups combined, and dominate all but two of the earth's terrestrial vegetation zones. Their origin was followed by the decline of plant groups that had dominated since the Triassic, but their mode of origin and the factors that underlie their spectacular success remain unknown. This project integrates DNA sequence analyses with physiological characterization of seedlings from early-diverging flowering plants to test the hypothesis that evolution in light-sensing mechanisms was important for the early success of flowering plants. Specifically, it tests the hypothesis that the evolution of phytochrome A, a phytochrome unique to flowering plants, enhanced the ability of early angiosperms to survive in dense shade. Sequence analyses will determine whether functional divergence of phytochrome A occurred by positive selection or by relaxation of selective constraints, and will identify sites of functional divergence that distinguish it from its sister gene, which encodes phytochrome C. Physiological experiments will determine whether seedlings of early-diverging flowering plant species exhibit the responses to dense shade that have been characterized in more derived species such as Arabidopsis, and will determine whether any of these responses are found in seedlings of related seed plants. Together these analyses will test the hypothesis that phytochrome A function was an adaptive innovation that helped flowering plants gain a foothold under the forest canopy once dominated by ferns and gymnosperms. Comparative molecular analyses are an efficient mechanism for evaluating functional diversification in nonmodel species. Thus, the analyses undertaken in this project will further one goal of plant genomics, to move beyond model systems toward understanding the molecular basis of diversity. The sequence database that will be generated will be useful for determining whether other seed plants might have independently attained complex but parallel physiological responses to multiple facets of the light environment. This database also will be useful for identifying sites of functional specification in genes whose function has been difficult to characterize using traditional genetics approaches. The function of sites identified this way can be further tested in mutagenesis experiments. The physiological experiments in the field and greenhouse will characterize light optima for seedling regeneration of individual species. Thus, they will provide insight into how the composition of plant communities might change in response to ecosystem-wide disturbance or change.
