Posted on behalf of Alistair McTaggart, Postdoctoral Fellow, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria. Email: firstname.lastname@example.org
Web Pages: FABI profile (current employment), Google Scholar profile, Rust Fungi of Australia (taxonomy of rust fungi from prior post doc), Smut Fungi of Australia (taxonomy of smut fungi), Rust Fungi of Southern Africa (taxonomy of rust fungi in South Africa from current post doc)
I am an early career researcher interested in the systematics of rust and smut fungi, which are both groups of plant pathogenic fungi. I dabble in the taxonomy of all other microfungi. I am currently based in South Africa and am being trained in genomics. I believe genomics is the best field to resolve the taxonomy and long-standing biological questions for my taxa of interest.
My answers largely reflect the field for taxonomy of fungi.
Where would you like taxonomy and systematics to be in a decade?
For pure taxonomy, I would like to see incorporation of new taxa into comprehensive, dynamic, public platforms, and an end to esoteric monographs. Taxonomy and application of a name should be accessible to everyone. This is possible through the development of public Lucid and Silverlight keys (here is an example of my friend Tim’s key to Carex in the United States: http://tinyurl.com/zjodnbb) that are open for collaboration within the community and are easy for non-experts to use. Single species descriptions are fine, but without incorporation into a bigger taxonomic picture, they pass by unnoticed. The community needs to embrace bigger picture treatments for their organisms. In the world of rust and smut fungi (and others), it’s already happening!
For systematics, I would like (and think it will
happen) a total shift to phylogenomics, even if this means including a few loci
of a taxon into a phylogenomic dataset. Cryptic species are rife in the
mycological world and morphology only gets a taxonomist so far. Experts of a
group rely on molecular barcodes and might not be able to make a confident
identification of species (or genera) without molecular data. Mycologists have
gradually progressed from single loci, to concordant and concatenated phylogenetic
species hypotheses. Last year, we saw the first phylogenomic study of
Zygomycota, which was casually published in a low-impact (but excellent
quality) mycology journal. This will be the standard in the future. The sooner
we get there, the sooner people will stop changing the taxonomy with every new
gene they sequence. People working on genomic data will determine markers that may
resolve a particular group, or markers that need to be included to determine
populations, species, genera, families… The mycological community (at least) is
going to have to embrace phylogenomics because this will happen within a decade
(1K Fungal Genomes almost complete). This month I sequenced my first genome on
a MinION (NanoPore™) with a desktop computer. In 10 years such a procedure will
be less exciting for those taking part, and huge amounts of data will be at our
What achievements or programs would you like to see in place?
Opportunities similar to the 1K Fungal Genomes project (or 10K Plant Genomes) for Australian taxa, particularly microorganisms.
High Performance Computing facilities made publicly
available to researchers that need to work with large datasets (compare to the
CHPC in South Africa).
Secure, electronic repositories to store genomic sequencing
data before (and after) genomes are uploaded to public databases.
What innovations in technology, infrastructure, funding or organisation
will make a big difference to your work and to our taxonomy and systematics?
- Technology to sequence genomes from small amounts of starting material (such as Chromium 10X).
- Desktop sequencing platforms (such as MinION).
- Reduced cost of genome sequencing.
- Access to electronic storage and high performance computing.