Evolutionary Histories of Gene Families in Angiosperm Trees
Genes can be grouped into families based on either the presence of conserved domains or by parameter-based clustering of pairwise alignments of the proteins they encode. The vast majority of gene families found in angiosperm trees have existed before the origin of seed plants, while the lineage-specific adaptations of trees have depended on highly dynamic but selective patterns of gene family gain and loss. The mechanisms governing the diversification of gene families, among them various types of gene duplication, horizontal gene transfer, protein domain re-arrangement and de novo evolution, each play distinct roles in expanding the functional repertoire of the core proteome of land plants. In this chapter we reconstructed a parsimonious evolutionary history of gene family gain and loss in angiosperm tree lineages relative to close herbaceous relatives, gymnosperms and nonvascular plants, revealing considerable variation in the frequency and functional enrichment of gain and loss events across lineages. Throughout the chapter, we highlight general and tree-specific examples of gene family adaptations that have contributed to the remarkable success of these organisms.