A phylogenomic perspective on interspecific competition

Evolutionary processes may have substantial impacts on community assembly, but evidence for phylogenetic relatedness as a determinant of interspecific interaction strength remains mixed. In this perspective, we consider a possible role for discordance between gene trees and species trees in the interpretation of phylogenetic signal in studies of community ecology. Modern genomic data show that the evolutionary histories of many taxa are better described by a patchwork of histories that vary along the genome rather than a single species tree. If a subset of genomic loci harbor trait-related genetic variation, then the phylogeny at these loci may be more informative of interspecific trait differences than the genome background. We develop a simple method to detect loci harboring phylogenetic signal and demonstrate its application through a proof of principle analysis of Penicillium genomes and pairwise interaction strength. Our results show that phylogenetic signal that may be masked genome-wide could be detectable using phylogenomic techniques and may provide a window into the genetic basis for interspecific interactions. Data & code accessibilityData and code for this project are freely available in the repository linked below and will be permanently archived upon publication. Statement of authorshipNL, BEW, and LHU designed the research; NL performed experiments; NL and LHU performed computational analyses; NL, BEW, and LHU wrote the manuscript. Code repositoryhttps://github.com/uricchio/ILSComp