Our Discovery Mission
Our mission, should we choose to accept it, is to discover and document all remaining Australian species of plants, animals, fungi and other organisms ... in a generation.
Part 3 - Whiteboards
The ideas below have been contributed to the whiteboard for discussion during the roundtable breakouts. You can add to them on the Whiteboard ideas page
Roundtable 4: How can we most effectively use phylogenetics for our species discovery mission?
Phylogenetics and species delimitation are becoming more and more closely integrated. Placing specimens of a potentially new species into a phylogeny is a great start in any taxonomic project. However, for this to be maximally effective for an all-species mission such as we envisage, we really need a phylogeny of all known species. This roundtable will consider issues around phylogenetics and species discovery, including:
Is a phylogeny that includes all Australian species achievable in the medium term?
How would we best go about constructing such a phylogeny?
What systems would we need to have in place to manage a comprehensive phylogeny and allow it to be used effectively for species discovery and delimitation?
A phylogeny that includes all Australian species IS achievable in the medium term if we choose to adopt a super tree approach (i.e. a tree built from many individual clade-specific trees). An approach aiming for a resolvable single phylogenetic tree across all taxa, from a concordant data matrix, is a significantly more complex, very long-term, and is a potentially high-cost project. It would require fairly sophisticated standardisation.
Although some Australian groups are highly endemic, an enormous number have sister species and sister lineages from outside of Australia. This is particularly the case for aquatic and marine organisms, non-seed plants, fungi, and mico-organisms. Inclusion of just the Australian species could produce an arbitrary 'all-species' phylogeny of little intrinsic worth.
A realistic aim to infer a whole-of-nation phylogeny would need to sample the non-Australian sister lineages (which in some cases outnumber the indigenous component) to Australian species. Therefore, it is essential this discussion about standardisation of the approach be a global community discussion.
Without improved sampling of marine habitats for small-bodied organisms, especially deep-sea habitats and coral reefs a phylogeny that includes all Australian species isn't going to be possible anytime soon.
Such a phylogeny would probably be best assembled using a subclade alignment approach where trees are reconstructed for individual clades and then 'anchor' taxa who are sequenced for transcritomes or genomes and mined of highly conserved genes are used to provide support for deeper branches.
To be robust such an ''all-species" phylogeny robust would need to tied to real-world museum specimens.
Currently, for the marine scleractinian taxanomic group there is no single marker that can delineate species or even delineate to a genus level. Currently, mitogenomes prove to be the way forward in this taxa. The use of mitogenomes helps obtain new markers that help in the building of coral phylogenies.
More (or better) ideas? Add them here.