"The affinities of all the beings of the same class have sometimes been represented as a great tree. I believe this simile largely speaks the truth. .... As buds give rise by growth to fresh buds, and these, if vigorous, branch out and overtop on all sides many a feebler branch, so by generation I believe it has been with the great Tree of Life, which fills with its dead and broken branches the crust of the earth, and covers the surface with its ever-branching and beautiful ramifications." - Charles Darwin, The Origin of Species, 1859
Darwin was not the first to envision a great tree of life, but his suggestion of the mechanism that leads to the tree, descent with modification, was paradigmatic. Together with the birth of modern genetics, his work revolutionized biology. Today, phylogenetic trees help us to understand the evolution of species, genomes, developmental systems, communities, and biomes. Further, phylogenetic approaches help us identify and fight disease, enhance agricultural production, predict responses to climate change, and conserve biodiversity.
Our work in phylogenetics relies on data from protein-coding nuclear genes (phytochromes) and from the plastid genome (from single genes to whole plastomes). Studies of phytochrome evolution are a particular interest, and they are a unifying theme in the lab, being the source of phylogenetic data and the basis for our functional synthesis work.
Phytochromes and Phylogeny
Data from phytochromes have proven remarkably informative for phylogenetic problems at a number of 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.
In various collaborations, we have used phytochrome data to infer relationships within several angiosperm families (including the grasses, legumes, broomrapes), among major clades of angiopserms, and of seed plants. Recently, they have been used to identify the relatives of the genetic model system, Arabidopsis thaliana, by former Mercer Postdoctoral Fellow Mark Beilstein, and to reveal the timing and pattern of evolution within cycads by postdoctoral fellows Nathalie Nagalingum and Hardeep Rai. 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).
Functional synthesis project on Phytochrome Photoreceptors
Comparative sequence analyses expand the array of mutant alleles for genetic experiments by revealing historic mutations that occurred during gene lineage splitting and divergence. In this way, evolutionary studies provide unique and complementary insights into molecular genetic studies seeking to characterize the structural basis of protein function. Reciprocally, functional experiments can test the role of these historic mutations in the evolution of novel function or in the subdivision of existing functions among duplicates. Moreover, when the historic mutations occurred at sites that were subject to positive selection, functional experiments provide a way to test the contribution of adaptive change to protein divergence and the origin of novel function.
In the phytochrome gene family, we postulate that parallel events of duplication and functional
divergence may have coincided with the evolution of canopy shade and the increasing complexity of the
light environment, leading to a greater precision of response by plants to their environment (Mathews 2006).
Furthermore, we provided evidence of episodic positive selection during a putative neofunctionalization event
(Mathews et al. 2003), suggesting that functional changes provided an adaptive advantage to flowering plants
as they faced the challenge of colonizing the dimly lit understory of ferns and gymnosperms. We are using the
genetic model, Arabidopsis thaliana, to test the link between neofunctionalization and selection at specific
amino acid sites.
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