Plastome phylogenomics of Poaceae: alternate topologies depend on alignment gaps

In Poaceae there is an evolutionary radiation of c. 5000 species called the ‘PACMAD’ grasses. Two hypotheses explain deep PACMAD relationships: the ‘aristidoid sister’ and the ‘panicoid sister’ hypotheses. In each case, the named subfamily is sister to all other taxa. These hypotheses were investigated with data partitions from plastid genomes (plastomes) of 169 grasses including five newly sequenced aristidoids. Plastomes were analysed 40 times with successive addition of more gapped positions introduced by sequence alignment, until all such positions were included. Alignment gaps include low complexity, AT-rich regions. Without gaps, the panicoid sister hypothesis (P(ACMAD)) was moderately supported, but as gaps were gradually added into the input matrix, the topology and support values fluctuated through a transition zone with stripping thresholds from 2–11% until a weakly supported aristidoid sister topology was retrieved. Support values for the aristidoid sister topology then rose and plateaued for remaining analyses until all gaps were allowed. The fact that the aristidoid sister hypothesis was retrieved largely when gapped positions were included suggests that this result might be artefactual. Knowledge of the deep PACMAD topology explicitly impacts our understanding of the radiation of PACMAD grasses into open habitats.