Compositional shifts associated with major evolutionary transitions in plants

Abstract

SummaryHeterogeneity in gene trees, morphological characters, and composition has been associated with several major clades across the plant 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 genes in these clades do not typically share the same composition, they tend to shift in the same direction. We discuss potential causes of these patterns.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 summaryWe 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 they often shift in the same direction. We suggest that these patterns warrant further exploration as the signal of important biological processes during the evolution of plants.