Phylogeny and Evolution of the Genus Brachypodium

Abstract

We present an updated review of the phylogenetic and evolutionary studies conducted on the model genus Brachypodium. The genus, which contains approximately 20 globally distributed taxa (17 species, 1 variety, and 2 undescribed cytotypes) shows an intermediate evolutionary placement within the grass temperate pooid clade, being closer to the basal than to the recent Pooideae lineages. Our comprehensive molecular phylogenetic survey of all the currently known Brachypodium lineages illustrates a complex reticulate scenario of recently evolved diploid and allopolyploid lineages. Haplotypic statistical parsimony networks, multilabelled (multigenic) Minimum Evolution gene tree discordances, and Bayesian dating analysis have provided a testable hypothesis for the reconstruction of the Brachypodium species tree and for the estimation of its nodal divergence times. Our results support the early splits of the annual and short-rhizomatose lineages (B. stacei, B. mexicanum, B. distachyon) in the Holarctic region during the early-Middle Miocene (and B. hybridum in the Pleistocene), and a profusion of rapid splits for the perennial lineages since the late Miocene to the Pleistocene in the Mediterranean and Eurasian regions, with sporadic colonizations of more remote areas. Several perennial allopolyploid species (B. boissieri, B. retusum, B. phoenicoides, B. rupestre 4x, B. pinnatum 4x) showed homeologous copies from both ancestral and recent genome donors. More in-depth studies of the species of the B. distachyon complex have demonstrated the polyphyletic origin of the allotetraploid B. hybridum from bidirectional crosses of its diploid B. stacei and B. distachyon parents. Our niche modeling analysis has also detected distinct adaptations to different ecological tolerances in the diploids and evidence of niche conservatism for B. hybridum and each of its parents in their native Mediterranean region. Future perspectives include ongoing comparative genomics, phylogenomic and genotype-based phylogeographic studies of Brachypodium.