What’s in a genome? Capturing nuclear genomic variation for phylogenetic and phylogeographic study of Australian Asparagales lineages

A project undertaken at The University of Melbourne supervised by Joanne Birch.

Co-investigators: Daniel Murphy, Bee Gunn, John Conran, and Chris Pires
Asparagales contains one third of all monocots including Orchidaceae and economically important taxa (e.g. onion, orchids, and irises). Australasia is the centre of diversity of non-Orchidaceae Asparagales and contains significant native diversity (48 genera, c. 327 species). Despite this species richness, the relationships of many genera and species are unknown. Multiple Asparagales taxa are ecologically significant and are keystone species of native vegetation (e.g., Lomandra species in Iron-grass Natural Temperate Grasslands, Xanthorrhoea species in grassy woodlands and Astelia alpina in alpine herbfields). Lack of understanding of associations among genetic, morphological, and ecological diversity of these taxa undermines their management to ensure resilience of native vegetation. This study applies a total evidence approach to infer the evolutionary history of Australian Asparagales and toidentify potential evolutionary drivers of Asparagales morphological and ecological diversity.
The project aims to:
  1. Apply bait-capture techniques to generate sequence data for nuclear exon targets that can be applied to study the divergence of Australian Asparagales taxa at deep and shallow time-scales.
  2. Assess congruence among phylogenies generated from chloroplast, mitochondrial, and nuclear data to determine the role of hybridisation in generating Australian Asparagales diversity. 
  3. Trace evolution of Asparagales ecological and morphological traits to assess their importance as evolutionary drivers of Asparagales diversity.

This study will provide tools (low-copy nuclear markers) to recover relationships within species complexes that are recalcitrant to resolution using traditional tools. The optimised protocols and pipelines that will be developed will overcome the technological limitations of working with DNA extracted from herbarium specimens, which is often fragmented, to make these specimens available for use in studies applying high-throughput methods to generate genome-scale datasets.




Figure 1. Astelia alpina var. alpina hummocks in Mt Field National Park, Tasmania, Australia.

Figure 2. Xanthorrhoea johnsonii in Noosa National Park, Queensland, Australia.