Resolving deep relationships of PACMAD grasses: a phylogenomic approach

Abstract

Background: Plastome sequences for 18 species of the PACMAD grasses (subfamilies Panicoideae, Aristidoideae, Chloridoideae, Micrairoideae, Arundinoideae, Danthonioideae) were analyzed phylogenomically. Next generation sequencing methods were used to provide complete plastome sequences for 12 species. Sanger sequencing was performed to determine the plastome of one species, Hakonechloa macra, to provide a reference for annotation. These analyses were conducted to resolve deep subfamilial relationships within the clade. Divergence estimates were assessed to determine potential factors that led to the rapid radiation of this lineage and its dominance of warmer open habitats.

Results: New plastomes were completely sequenced and characterized for 13 PACMAD species. An autapomorphic ~1140 bp deletion was found in Hakonechloa macra putatively pseudogenizing rpl14 and eliminating rpl16 from this plastome. Phylogenomic analyses support Panicoideae as the sister group to the ACMAD clade. Complete plastome sequences provide greater support at deep nodes within the PACMAD clade. The initial diversification of PACMAD subfamilies was estimated to occur at 32.4 mya.

Conclusions: Phylogenomic analyses of complete plastomes provides resolution for deep relationships of PACMAD grasses. The divergence estimate of 32.4 mya at the crown node of the PACMAD clade coincides with the Eocene-Oligocene Transition (EOT). The Eocene was a period of global cooling and drying, which led to forest fragmentation and the expansion of open habitats now dominated by these grasses. Understanding how these grasses are related and determining a cause for their rapid radiation allows for future predictions of grassland distribution in the face of a changing global climate.

Fig. 1

Maximum likelihood phylogram produced from a complete plastome analysis of 18 species of PACMAD grasses. Each node that was fully supported with a ML bs value = 100, MP bs value = 100 and a pp = 100 is labelled with *, except where noted (ML bs/MP bs value/pp). MP bootstrap values are marked NA in the one case where the topology differed

Fig. 2

Maximum likelihood phylogram produced from analysis of assembled and aligned mitochondrial matR and seven intron sequences from 15 species. Branch lengths are proportional to the substitution rate along the branch. Bambusa oldhamii was selected as the outgroup. Bs values >50 and <100 are noted. Nodes labelled with # denote bs values <50. Each node marked “I” was incongruent with our ML plastome analysis topology (Fig. 1)