Compositional shifts associated with major evolutionary transitions in plants

Conflict across genes trees and between morphological characters has been associated with several evolutionary innovations across the tree of life. Here, we examine heterogeneity in composition across a large transcriptomic dataset of plants in order to better understand whether locations of shifts in composition are shared across gene regions and whether directions of shifts within clades are shared across gene regions. We estimate mixed models of composition for both DNA and amino acids across a recent large scale transcriptomic dataset for plants. We find shifts in composition across both DNA and amino acid datasets with more shifts detected in DNA. We find that Chlorophytes and lineages within experience the most shifts. However, many shifts occur at the origins of land, vascular, and seed plants. While shifts in these clades across genes do not typically share the same composition, they tend to shift in the same direction, reflecting potential mutation bias exacerbated by life history changes and population size. Compositional heterogeneity has been highlighted as a potential problem for phylogenetic analysis, but the variation presented here highlights the need to further investigate these patterns for the signal of biological processes. Plain language summary We demonstrate that many nucleotide and amino acid compositional shifts in plants occur at the origins of major clades and while individual genes do not share the same composition, even at shifts, they often shift in the same direction. We suggest that these patterns warrant further exploration as to the biological processes that may be the cause.