Mining genomes to understand evolution of the iconic Australian eucalypts

A project undertaken at The Plant Systematics Research Group, The University of Melbourne, and supervised by Tanja Schuster and Josquin Tibbits

Background

The eucalypts (tribe Eucalypteae) include the sclerophyll genera Eucalyptus (>665 species), Corymbia (ca. 100 species), and Angophora (9–10 species) plus the rainforest genera Allosyncarpia (1 species), Arillastrum (1 species), Eucalyptopsis (2 species), and Stockwellia (1 species). The sclerophylls are ecologically important, because they dominate a large proportion of the Australian continent and several species also have great economic importance as timber, pulp, and ornamental trees. 

Classification of eucalypts is still not settled and their diversification patterns are not clear; in particular, relationships among and within Eucalyptus, Corymbia, and Angophora are under debate. The bloodwood eucalypts, currently classified in the genus Corymbia K.D.Hill & L.A.S.Johnson, were taxonomically segregated from Eucalyptus L'Her., because bloodwoods are morphologically distinct. Also based on morphological characters, bloodwoods include the following groups: the red bloodwoods (subg. Corymbia), yellow bloodwoods (subg. Blakella sect. Naviculares), ghost gums or paper-fruited bloodwoods (subg. Blakella sect. Abbreviatae), spotted gums (subg. Blakella sect. Maculatae), and cadaghi (monotypic subg. Blakella sect. Torellianae). However, the morphological classification conflicts with analyses of molecular data and between molecular phylogenies depending on number of taxa included and molecular markers used.

Aims

Our aim was to produce a resolved and well-supported phylogeny of eucalypts in order to support investigations of the biogeographic history of the Australian continent (e.g., divergence and diversification in monsoonal savannah, rainforest, and temperate biomes), inform conservation management (e.g., identifying regions of phylogenetic diversity and significance), and enable coevolutionary studies (e.g., repeated evolution of gall-forming scale insects restricted to certain sclerophyll species). Therefore, our main goal was to test the monophyly of Corymbia and to clarify relationships between it, Angophora, and Eucalyptus.

Next-generation DNA sequencing (NGS) methods provide new opportunities for addressing these persistent questions about diversification patterns in eucalypts. We generated a big chloroplast dataset (121,017 base pairs, 123 accessions) and analysed individual genes from the nuclear genome (e.g., ITS using 663 base pairs, 119 accessions) to construct phylogenies with Maximum Likelihood (ML) and Maximum Parsimony (MP) methods. Several species were represented by multiple accessions to test the monophyly of Angophora and Corymbia species.

Findings

Our results show that ML and MP analyses of chloroplast data resolve well supported phylogenetic trees, which strongly reject the monophyly of Corymbia, the subgenera Corymbia and Blakella, the taxonomic sections Septentrionales, Abbreviatae, Maculatae, Naviculares, and several species of Corymbia and Angophora. Nuclear ribosomal ITS trees also indicate Corymbia to be paraphyletic, though with weak support. However, ITS trees are highly incongruent with the chloroplast DNA analyses as they show both subgenera and some of the taxonomic sections of Corymbia asmonophyletic. Due to the strong incongruence of chloroplast vs. nuclear (ITS) phylogenies and classifications based on morphological data, as well as an underlying geographic signal, our findings suggest that there is chloroplast introgression between bloodwood taxa. Our study highlights the prevalence of hybridisation and introgression in the evolutionary history of most eucalypts. This may find application in breeding programmes of economically valuable bloodwoods.

 
Figure 1. Angophora leiocarpa (NSW Nov 2014)

Figure 2. Angophora euryphylla (NSW Nov 2014)

Figure 3. Angophora bakeri leaf oil glands (NSW Nov 2014)

Figure 4. Corymbia torelliana fallen calyptra and capsules (NSW Nov 2014)