Hybridisation and chloroplast capture between distinct Themeda triandra lineages in Australia

Ecotypes are distinct populations within a species that are adapted to
specific environmental conditions. Understanding how these ecotypes become
established, and how they interact when reunited, is fundamental to
elucidating how ecological adaptations are maintained. This study focuses
on Themeda triandra, a dominant grassland species across Asia, Africa and
Australia. It is the most widespread plant in Australia, where it has
distinct ecotypes that are usually restricted to either wetter and cooler
coastal regions or the drier and hotter interior. We generate a de novo
reference genome for T. triandra and use whole genome sequencing for over
80 Themeda accessions to reconstruct the evolutionary history of T.
triandra and related taxa. Organelle phylogenies confirm that Australia
was colonised by T. triandra twice, with the division between ecotypes
predating their arrival in Australia. The nuclear genome provides evidence
of differences in the dominant ploidal level and gene-flow among the
ecotypes. In northern Queensland there appears to be a hybrid zone between
ecotypes with admixed nuclear genomes and shared chloroplast haplotypes.
Conversely, in the cracking claypans of Western Australia, there is
cytonuclear discordance with individuals possessing the coastal
chloroplast and interior clade nuclear genome. This chloroplast capture is
potentially a result of adaptive introgression, with selection detected in
the rpoC2 gene which is associated with water use efficiency. The reason
why T. triandra is the most widespread plant in Australia appears to be a
result of distinct ecotypic genetic variation and genome duplication, with
the importance of each depending on the geographic scale considered.