Genome-wide repeat dynamics reflect phylogenetic distance in closely related allotetraploid (Solanaceae).

sect. is a group of four allotetraploid species originating from a single allopolyploidisation event approximately 5 million years ago. Previous phylogenetic analyses support the hypothesis of as sister to the other three species. This is concordant with changes in genome size, separating those with genome downsizing () from those with genome upsizing (, , ). However, a recent analysis reflecting genome dynamics of different transposable element families reconstructed greater similarity between and the Revillagigedo Island taxa ( and ), thereby placing as sister to the rest of the group. This could reflect a different phylogenetic hypothesis or the unique evolutionary history of these particular elements. Here we re-examine relationships in this group and investigate genome-wide patterns in repetitive DNA, utilising high-throughput sequencing and a genome skimming approach. Repetitive DNA clusters provide support for as sister to the rest of the section, with sister to the two Revillagigedo Island species. Clade-specific patterns in the occurrence and abundance of particular repeats confirm the original ( ( ( + ))) hypothesis. Furthermore, overall repeat dynamics in the island species and confirm their similarity to and the distinctive patterns between these three species and . Together these results suggest that broad-scale repeat dynamics do in fact reflect evolutionary history and could be predicted based on phylogenetic distance.