Phylogenetic Methods to Study Light Signaling
Phylogenetic comparative methods (PCM) represent a rigorous approach for inferring functional evolution. To infer the origin and evolution of a function, PCM use a phylogenetic tree of the species in which the function has evolved and functional data from those species. These data enable reconstruction of ancestral states and inference of how the function evolved along the branches of the species tree. PCM can be applied to understand any aspect of light signaling, from early events in photoactivation, to interactions with signaling partners, to physiological responses. Integrating evolutionary histories of individual aspects of light signaling obtained through PCM with network modeling of protein–protein interactions for light signaling would enable a deep understanding of the evolution in light signaling pathways and their roles in helping plants adapt to changing environments. Here we describe the steps for using PCM to infer functional evolution using a species tree and trait data.
KeywordsFunctional evolution Light signaling Phytochromes Phylogenetic comparative methods
- 2.Pagel M (1999) The Maximum Likelihood approach to reconstructing ancestral character states of discrete characters on phylogenies. Syst Biol 48:612–622Google Scholar
- 20.Freyman WA (2015) SUMAC: constructing phylogenetic supermatrices and assessing partially decisive taxon coverage. Evol Bioinformatics Online 11:263–266Google Scholar
- 23.Page RDM, Holmes EC (1998) Molecular evolution: a phylogenetic approach. Blackwell Science, Oxford/Malden, MAGoogle Scholar