Posted on behalf of Professor Levente Kiss, Centre for Crop Health, Institute for Agriculture and the Environment, University of Southern Queensland
Prof. Kiss writes: As a newcomer in the Australian scientific community (I started to work here this year), I am deeply impressed by, and highly value, the Decadal initiative. During the past >25 years, I have been mainly interested in the biology, and taxonomy, of obligate biotrophic fungi, so I’ll focus on this group below.
We’d like you to scan the horizon, and share what you see.
It is an ‘easy’ assumption that during the next years more and more DNA loci will be used for taxonomic purposes. In fungal taxonomy, these new, or already exploited loci may not be useful for the whole Kingdom, and could be lineage-specific, as already shown in some cases by Schoch et al. (2012). (If interested, see my commentary about this paper: Kiss 2012). By the way, the identification of phylogenetically / taxonomically relevant lineage-specific DNA markers could be a general trend in future taxonomic works, within each Kingdom. Also, it is likely that whole genome analyses will be more widely used in taxonomic works, although this approach will always be limited by availability of funds, no matter how inexpensive will sequencing become, and methodology constrains, as well.
One aspect, which, in my opinion, has sometimes been forgotten, or at least neglected, especially in fungal (and, more generally, in microbial) ‘phylogeny only’ taxonomic works, is that, after all, different taxa have to be recognized as entities held together through gene flow. In obligate biotrophic fungi, where neither growth nor asexual and sexual reproduction are possible without being structurally and nutritionally linked to the living host tissues, gene flow cannot be envisaged if the respective fungi do not share the same hosts. However, in some groups of such strictly host-associated fungi, current practice is to apply the same taxon name for organisms that are unable to meet, and recombine, in/on the same hosts due to their narrow host specializations, but share identical, or highly similar, DNA barcode sequences. It has long been highlighted that gene phylogenies should not regarded as species phylogenies (Doyle 1992); however, the DNA barcode approach, as a quick-and-dirty method, has often been used in describing, for example, strictly host-associated taxa without taking in consideration obvious constraints in gene flow.
Where would you like taxonomy and systematics to be in a decade?
In obligate biotrophic fungi, when it comes to the future of taxonomy, my prediction is that their experimentally revealed host range, and, thus, the detection of whether gene flow is at all possible within a newly recognized taxon, will be much more considered during species descriptions, and will become a basic requirement in this process, in addition to developing better phylogenies for different taxa. Personally, I don’t think this approach can be skipped by whole genome analyses, as host specificity may be determined by a very small fraction of the genome, which may remain unrevealed when performing analyses of huge datasets.
What
achievements or programs would you like to see in place? What milestones would
you like us to pass?
I assume sequencing coupled with new DNA barcode developments, with direct taxonomic implications, will continue, and will always be fueled by the biotech sector. Specific taxonomic and/or biodiversity programmes (such as many more ABRS projects) focusing on those groups of organisms (in our case: fungi), which are challenging from a methodological point of view, and require specific approaches, in addition to the sequencing work, would lead to real breakthroughs in this field.
What
innovations in technology, infrastructure, funding or organisation will make a
big difference to your work and to our taxonomy and systematics?
I’d focus on the taxonomy of those groups of organisms (fungi) which are difficult to handle, due to their specific way of life (e.g., obligate biotrophs vs. free-living fungi). In taxonomy, personal expertise, special skills, are usually much more important than special infrastructure, therefore funding schemes should focus on key scientists and their students (i.e., salaries, fellowships), and should provide long-term support. In the USA, the NSF PEET scheme seems to be a great initiative to support taxonomic research, and especially training a new generation of taxonomists:
https://www.nsf.gov/funding/pgm_summ.jsp?pims_id=5451
References
Doyle JJ (1992) Gene trees and species trees: Molecular systematics as one-character taxonomy. Syst. Bot. 17: 144-163.
Kiss L (2012) Limits of nuclear ribosomal DNA internal
transcribed spacer (ITS) sequences as species barcodes for Fungi. Proc Natl
Acad Sci USA 109: E1811.
Schoch CL, et al. (2012) Nuclear ribosomal internal
transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi.
Proc Natl Acad Sci USA 109: 6241-6246.