Temporal dynamics of incomplete lineage sorting, introgression and divergence in eucalypts distributed across an expansive and ancient landscape
Harvey K Orel, Rachael M Fowler, Todd G B McLay, David J Cantrill, Donald C Franklin, Daniel J Murphy, Michael J BaylyAbstract
Background and Aims
The eucalypt clade composed of Angophora, Blakella and Corymbia (the ‘bloodwood eucalypts’) includes over 110 species and dominates the vast savannahs, open forests and woodlands of northern Australia. Relationships within this clade have been difficult to decipher despite significant previous investigation.
Methods
Using target-capture data from a eucalypt-specific bait set (568 nuclear genes) and whole plastome sequences, we conducted a phylogenomic study of Angophora, Blakella and Corymbia (sampling 97 species with 168 accessions) employing tree, network, divergence dating, and coalescent simulation analyses to investigate evolutionary relationships and patterns of phylogenomic discordance.
Key Results
Phylogenetic relationships in Angophora, Blakella and Corymbia are affected by extensive phylogenomic discordance, attributed to persistently high levels of incomplete lineage sorting through time, and frequent introgression concentrated at particular branches. Branches affected by introgression were consistently co-affected by incomplete lineage sorting, and nuclear genes with higher recombination rates more frequently supported discordant topologies affected by incomplete lineage sorting. Additionally, a mixture of incomplete lineage sorting, plastid capture and sex-biased dispersal are likely responsible for substantial cytonuclear discordance. Based on molecular divergence dating analyses, diversification of lineages within genera was estimated to have commenced during the late Oligocene.
Conclusions
We provide a robust framework phylogeny for Angophora, Blakella and Corymbia, and further support for the position of Blakella sister to Angophora and Corymbia .We attribute the difficulty in resolving this trichotomy to incomplete lineage sorting during divergence, with subsequent hybridisation between Blakella and Corymbia. Patterns of high discordance, incomplete lineage sorting and introgression across the phylogeny indicate that evolution at the genomic level does not follow a single, bifurcating species tree. Ultimately, our results demonstrate the intrinsic entwinement of diversification and discordance-inducing processes in the evolutionary history of eucalypts and highlight the group as an example of a phylogenomic mosaic.