Code and sequence data pertaining to: 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.