Phytochrome photoreceptors regulate almost all aspects of plant development, including agronomically important processes such as flowering time, fruit maturation, and shade avoidance. Gene duplication and divergence have produced a seed plant phytochrome family with two key players, phyA and phyB, which function complementarily and antagonistically in open and shaded habitats to promote plant development in all terrestrial ecosystems. Many steps in light-mediated signaling are now understood, but the coding-sequence basis for the distinctive activities of phyA and phyB is poorly understood.

Marsilea and Nymphaea leaves

Our studies of phytochrome molecular evolution bear directly on this problem. We found that phyA and phyB have been diverging from one another since the origin of living seed plants, and that episodes of selection helped shape their distinctive activities. This is not surprising given the critical role of photoreceptors in the adaptation of plants to their environments. Additionally, evolutionary studies revealed bursts of mutation that do not give a signal of selection, but that represent radical amino acid changes that distinguish phyA from phyB. We are using null mutants of the genetic model, Arabidopsis thaliana, to test the role of these historical amino acid mutations by reconstructing proteins with ancestral amino acid states at these sites. This will identify the structural determinants of protein specificity and the genetic mechanisms underlying plant adaptation.

Plant phylogenetics

Until recently, the field of plant phylogenetics has relied almost exclusively on data from organellar genomes, which are uniparentally inherited, or on high-copy number nuclear genes, which have limited information content. We pioneered the use of nuclear data from the phytochrome gene family. These data have proven remarkably informative for phylogenetic problems at many levels. Notably, they have enabled the inference of well-supported trees from a small number of characters relative to the larger multilocus data sets obtained to address the same problems, and they provide an important complement to data gathered from uniparentally inherited organellar genomes.

Phyllocladus alpinus

In various collaborations, we have used phytochrome data to infer relationships within several angiosperm families (including the grasses, legumes, parasitic broomrapes), and among major clades of angiosperms. Recently, they were used by former Mercer Postdoctoral Fellow Mark Beilstein to date the origin and identify the relatives of the genetic model system, Arabidopsis thaliana, and by former postdoc Nathalie Nagalingum to show that species diversity in an ancient seed-plant lineage, the cycads, result from bursts of speciation that took place in the Miocene, only 10-12 million years ago. The success of these studies highlights the utility of data from protein-coding nuclear data and anticipates the results from analyses of the greater amount of this class of data that is becoming available through transcriptome sequencing projects.

Gymnosperms are the focus of a major phylogenetic effort in the lab. They are critical to understanding seed plant relationships, the clade of plants that provides the majority of our food, fiber, and shelter. Our work in this area is funded by the National Science Foundation’s Assembling the Tree of Life program (link to our project page).

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