Phylogenomics

The phylogenomics working group have been set up and are currently working through the next steps required for a pilot study. Please see below for the background on the project’s Phylogenomics aims.


The GAP Phylogenomics project has the ambitious long-term goal of producing a published phylogenetic tree containing 95% of Australian angiosperm species (and their sisters). This is to be achieved by supporting collaborators to achieve their research goals where they contribute to GAP Phylogenomics goals, and coordinating efforts across the community. Work will proceed in three stages as follows. GAP will prioritise completion of the first two stages. The third stage is beyond current resources.

  1. In collaboration with Plant and Fungal Tree of Life project (PAFTOL)[1], generate a dataset containing one exemplar species of 95% of accepted (APC[2]) Australian angiosperm genera.
  2. Generate a dataset containing at least three exemplar species of 95% of accepted (APC) Australian angiosperm genera (for those genera with three or more species). At most one species per genus should be a non-Australian species.
  3. Generate a dataset that is 95% complete at species level.

The GAP phylogenomics project will initially adopt a target capture approach using a common set of 350-400 nuclear markers, with skimming for the plastid genes. This will maximise the chance of resolving the backbone of the phylogeny (i.e. to genus level) to provide a phylogenetic framework for continental scale systematic, ecological and evolutionary studies. Future work (i.e. stage 3 above) will focus on detailed studies of specific clades, which will likely require the development of bespoke markers sets on a clade by clade basis.

The GAP project will collaborate closely with the Plant and Fungal Tree of Life project (PAFTOL) to achieve the first of the three stages. PAFTOL aims to estimate a genus-complete phylogeny of the world’s angiosperms (c. 14,000 genera) using the Angiosperms353[3] target capture nuclear bait set. PAFTOL is in the final two years of its program and at current rates will fall substantially short of its target. Unless GAP collaborates with PAFTOL, it is unlikely that PAFTOL will complete more than 50-60% of Australian genera.

A species-complete phylogeny would transform research on and knowledge of the Australian flora, by providing a step change in data resources for systematics, ecology, evolutionary biology and conservation.

Importantly, it would help deliver many of the Strategic Actions under the Decadal Plan for Taxonomy and Systematics[4], particularly:

1.1 We will significantly increase the rate at which new species in Australia and New Zealand are discovered, resolved, named and documented,

1.3 We will build a comprehensive framework to understand the evolution of the Australian and New Zealand biota,

2.1 We will create a comprehensive, integrated, accessible service for the identification of Australian and New Zealand organisms, based on DNA sequences, morphology and images, and

4.3 We will build a curated, vouchered reference library of DNA sequences covering the breadth of the tree of life in our region.


[1] https://www.kew.org/science/our-science/projects/plant-and-fungal-trees-of-life

[2] Australian Plant Census – https://biodiversity.org.au/nsl/services/APC

[3] Johnson et al. (2018) – https://doi.org/10.1093/sysbio/syy086

[4] https://www.science.org.au/support/analysis/decadal-plans-science/discovering-biodiversity-decadal-plan-taxonomy