Criteria for prioritisation of invertebrate taxonomy

From A/Prof. Michael Braby, Visiting Scientist, Australian National Insect Collection, based on recommendations from the paper Biosystematics and conservation biology: critical scientific disciplines for the management of insect biological diversity. Austral Entomology 55:1-17 (see

Given finite resources for biosystematics, we argue that at least two criteria be considered for selection of invertebrate groups for prioritisation for taxonomic focus and their application in conservation biology: (1) the taxon is reasonably well known taxonomically (i.e. total inventory is estimated to be 90% complete, and/or morphospecies have been circumscribed through the availability of parataxonomists and well-curated reference collections); and (2) the taxon is known to be informative as bioindicators. 

Here are our main visions for taxonomy from a stakeholders perspective (biodiversity conservation):

  1.  Increased investment in taxonomic research capacity (of prioritised taxa) to systematically catalogue known species and describe new species, including university training and resources for museum collections, curation, digitisation of material (including type specimens), DNA sequencing and development of taxonomic databases on the Internet.
  2. Greater attention towards molecular genetic methods, such as DNA barcode technology and application of genomic data through next-generation sequencing together with population genetic studies of species will assist with rapid identification of field samples, especially where morphospecies approach is used for some prioritised taxa, as well as recognition of conservation units within species. This technology should not be used at the expense of traditional taxonomy, but rather complement it.
  3. Complete reconstruction of the evolutionary history or tree of life, which will form the framework for the development of reliable guidelines and conceptual basis as to how phylogenetic diversity can be incorporated into biodiversity conservation planning compared with traditional measures, such as species richness, endemism and threatened species.
  4. Development of national databases to document the spatial distribution of species, and predictive spatial modelling of biodiversity. The ALA and related activities, such as the Australian Natural Heritage Assessment Tool, are excellent government-funded initiatives in the field of bioinformatics and are currently the best platforms on which to build at the national level.
  5. Increased capacity-building through greater participation of citizen science programmes in collecting spatial and temporal data and indices of relative abundance of species. These data can then be used in conjunction with databased vouchered specimens for evaluation of geographical range, phenology and conservation status of threatened species. Networks consisting of government agencies, NGOs, scientists, community groups, natural history societies and volunteers are likely to be the future for the conservation management and monitoring of insect biodiversity in Australia.

Ensuring adequate communication between environmental consultants and taxonomists

From Stephen Ambrose, Director, Ambrose Ecological Services Pty Ltd

In general, there are two types of ecological consultant:

  1. Specialists who focus their activities on one group of taxa (e.g. birds, bats, reptiles, marine animals) or in one industry sector (e.g. mining, urban development).
  2. General Practitioners who don’t have a particular focus and work across a broader range of ecological consultancy issues at a more superficial level than specialist consultants.

Specialist consultants tend to keep abreast with the taxonomic and biosystematic changes in the taxa that are the focus of their interest.  They usually do this by following the scientific literature, attending conferences, and occasionally being the drivers of the taxonomic and biosystematic studies.

However, generalist consultants cover too broad an area to easily keep up with revisions of all taxa that they deal with during the course of their work.  It is this group of consultants who would benefit the most from better communication about these revisions.

While the onus is on individual consultants to keep up with these revisions, taxonomists could assist with facilitating communication with them.  One possible way of doing this in NSW would be for taxonomists and evolutionary biologists to send hyperlinks to the Ecological Consultants Association of NSW (the ECA) to relevant online publications or websites.  The ECA’s Administration Officer would then forward this information to ECA members, either as a regular ECA Information Emails or as collated information in the ECA’s regular journal, Consulting Ecology.

There is probably an opportunity for taxonomists to receive information from ecological consultants, too, based on field work associated with development assessments, but I’m not sure how best to facilitate that interaction, especially as there is usually a commercial-in-confidence agreement between consultant and client.  There is also the likelihood that there will be less opportunity for this to happen with ecological consultants (in NSW, at least) spending less time in the field, and more time in front of the computer, under the new environmental legislation.

Counting species - questions and meta-questions

Yet another paper has come out (Larsen et al. "Inordinate fondness multiplied and redistributed: The number of species on earth and a new pie of life" The Quarterly Review of Biology 92(3): 229-265, 2017) asking the perennial "how many species are there on earth" question.

This is potentially an important question, and potentially a non-question. The question (whether it's important or not a question) is in turn important for the decadal plan, but also more broadly for biology as a whole. I'll return to the decadal plan later.

This issue is a problem, because current estimates for the number of species on earth vary from ~2 million (see refs in paper above) to ~1 trillion (I don't even really know how big a trillion is, but it's much bigger than 2 million). The paper above takes a stab in the dark (the authors would dispute this) and puts the figure at 1–6 billion. 

Take your pick. That's our problem. The number can be almost anything you want it to be.

But I think there's a bigger problem, which is that none of the studies that make these estimates ask what I think is the most important question, which is: does the how-many-species question make any sense? (Or more precisely, is the question answerable? The studies assume that it is, without justifying this assumption.) 

This is a meta-question, a question about a question. Until we can answer the meta-question, trying to answer the question is almost certainly futile. Let me explain; but first, let me digress to the late 18th Century.

At that time, some of the most influential French scientists (Jussieu, Adanson, De Candolle) had an important argument about the "shape" of nature. Jussieu (one of the leading scientists in the post-Linnaean world) argued from first principles that nature was continuous. He believed that somewhere out there (and increasingly being discovered during the great age of exploration) existed an intermediate form between every recognised taxon. There would be found organisms that would bridge the apparent gap between all species, between all genera, all families, all orders etc. Nature, in Jussieu's view, would prove to be a complete continuum, and taxonomy would eventually become an utterly arbitrary division of that continuum, just as colour terms arbitrarily divide the spectrum of visible light. Jussieu, by the way, was perfectly comfortable with this.

Adanson and De Candolle, by contrast, believed that the gaps observed between clusters of closely similar organisms were real, and that a relatively non-arbitrary ("natural") taxonomy could be based on the identification of these gaps. What's more, they believed that the cluster-and-gaps pattern could be discerned at all taxonomic levels, allowing us to create a natural classification of species, genera, families etc.

Adanson and De Candolle won. Nature was found to be inherently gappy; they had invented a (non-algorithmic) form of the phenetic method; and a century-and-a-half of a "taxonomy of the gaps" ensued.

Phylogenetics has slightly changed our views on all this, but only slightly. We're now interested in clades and all that, of course, but (at least at species level) we're still very keen on gaps. We now use terms like coalescence; the issue may take the form of working out what percentage difference between two barcodes is required to infer two species; it's still about gaps.

But - what if Jussieu was right? Not exactly right in the sense that there is a continuum of forms, but right in the sense that there's a continuum of gaps. What if there are big gaps (between e.g. a tuatara and its nearest relatives) down to small gaps (between two closely realted species) to smaller gaps (perhaps between "cryptic species") to very small gaps (the ones that the next generation of taxonomic splitters may use to ensure that taxonomy is a never-ending science, and that some orchid taxonomists use today - sorry, couldn't resist the dig). 

What does this mean to our question "how many species are there"? It may mean that the answer is whatever number you want it to be. Curiously, that seems to be about where we're at.

The problem can be rephrased in modern terms: is the pattern of variation in nature (call it its shape) fractal? A fractal pattern would be one where the pattern of "gappiness" is about the same all the way down. The gaps become finer and finer, but we can discern gaps all the way. If nature is fractal in this sense, then asking the question "how many species are there" is as meaningless as the classic fractal example "how long is the coastline of Australia?" There's no answer to that question. If you measure Australia's coastline on a 1:1,000,000 map you'll come up with one estimate; if you trace around every headland and minor prominence you'll get a much larger answer; if you trace around every grain of sand on every beach you'll get a larger answer still. In a fractal system, some questions are silly.

If, however, the shape of nature is non-fractal and there's a minimum observable gap, which we could use to objectively delimit species, then the question isn't silly at all (it's merely difficult).

So - I think we need to answer the meta-question ("Is the pattern of variation in nature such that the question of how many species exist is answerable?") before we try to answer the question ("how many species exist?"). An important question is - how could we go about answering the meta-question?

A thought experiment may help. Imagine that we had a full genome sequence of every individual organism on earth (no, I'm not suggesting this as a goal for the decadal plan). We could then use a super-super-computer to calculate the pairwise distances of every individual from every other individual, and plot these on a graph (increasing distance on the x-axis, frequency of that distance value on the y-axis). There would be a wide spread of pairwide distances on our plot, from close to zero to some arbitrarily large number. 

If the shape of nature is fractal, we'd see a complete spread of distance values with only random troughs and peaks; if, however, there's a real "species-gap", we'd see a distinct, non-random dip in the frequency distribution at some distance value somewhere closeish to the x-origin.

Our dataset would allow more sophisticated analyses. We could partition the data into different taxonomic groups (do we see a species-gap in, say, spiders as well as in bacteria, birds and plants - and importantly, if we do is it in the same place?). We could also partition into different ecological niches (do rainforest taxa have a gap in the same place as arid-zone taxa?; do r-strategists have a gap in the same place as K-strategists?), or breeding systems (do taxa that use sexual selection have a gap in the same place as taxa that don't?).

When you think about it, a graph like this would give us crucial insights, not only into the meta-question discussed here, but to help assess utility of e.g. barcodes for species delimitation. 

For what it's worth, my own guess is that we wouldn't see a magic value on a graph like this, but rather a random pattern of peaks and troughs all the way down. That is, my guess is that the question "how many species are there?" is a silly question.

Of course, like all good thought experiments, we could never do this. So this opens a new question - can we approximate the graph using real-world data sets? One possibility may be to use environmental genomic data - this has the advantage that it's presumably sampling sequences from every individual in the genomic soup, with no inherent taxonomic bias or pre-assumed taxonomy. I have no idea whether this idea has merit, and would be pleased to hear from someone who actually knows what they're talking about in this space.

One final question - do we try to deal with this issue in the decadal plan? We need to be careful about admitting that we have absolutely no idea how many species are in Australia and any estimate could be out by many orders of magnitude (this is not a great starting point for asking for funding to document our biodiversity). But we could argue for a project that addresses the meta-question, if indeed there's a way to address it. Now that would be a world scoop, I reckon.

As always, thoughts and comments very welcome.

Taxonomy 2028 Challenge: 75% of species of Australian arthropods described by 2028

Posted on behalf of Penelope Mills, PhD candidate at The University of Queensland, working on the systematics and evolution of two groups of gall-inducing scale insects of Apiomorpha (Hemiptera: Eriococcidae).

By 2028 we will have described ~75% of species of Australian arthropods.

Arguably, phylum Arthropoda contains some of the most important species on the planet. They are also the most numerous group, and include about 80% of all the described species. However, much of the biodiversity within arthropods remain undescribed. Even within this current age of genomics, much of the research concerning Arthropoda focusses on a narrow breadth of species (e.g. medically-important species, agricultural pests, species of quarantine concern).

Many biodiversity surveys and estimates use species as the unit of measure. This means that better-known groups (e.g. chordates, angiosperms) are commonly included in biodiversity estimates, whereas the most numerous groups (e.g. Arthropoda) tend to be ignored because most species are yet to be described or can not be identified to species level.

There are already systematic grants available from ABRS and BushBlitz to nurture the discovery and documentation of Australia’s biodiversity. However, additional funding from government agencies, including the ARC, should be sought for funding basic taxonomic research to increase the achievability of the proposed goal.

The difficulty will be in convincing the funding panels and the public that this research is necessary and has far-reaching implications. Putting a name to a species allows it to be considered for biodiversity and conservation purposes, and the additional data provided by the description can be used by multiple digital platforms currently in place (e.g. Atlas of Living Australia, BowerBird) to examine additional questions about Australia’s biodiversity.

Taxonomy 2028 Challenge: Using citizen surveillance applications to increase the number and frequency of culture collection samples for genomic analysis.

Posted on behalf of Andrew Taylor, PhD candidate Murdoch University and Research Officer DPIRD WA (

By 2028 genome sequencing will be common place amongst laboratories as technology improves and costs fall. This will result in more organisms having their genome sequenced and will lead to the taxonomic re-evaluation of a number of economically important plant pathogens. The oomycetes are one group of plant pathogens that are economically important to a diverse number of horticultural commodities and amongst natural ecosystems. In many instances they are also known to develop fungicide resistance rapidly, making control problematic. It appears from the number of oomycetes that have had their genome sequenced a taxonomic re-evaluation is likely.  

A characteristic of a number of oomycetes is that they are obligate biotrophs, meaning they can only be stored in culture collections on samples of the infected host. Often only a few of these representative samples exist and the collection dates are sporadic, in many cases multiple decades apart. This creates issues for researchers as it means samples lodged in collections are not allowed to be released as DNA extractions are considered destructive sampling. It also creates issues with biosecurity policy. With the likely taxonomic changes as a result of genome sequencing it will be difficult to gain access to old samples to be able to update prohibited organisms under re-evaluated classifications.

The proposal I put forward is to use the development of citizen surveillance applications that are being developed for a number of horticultural commodities across Australia to place call outs for samples of oomycete plant pathogens on a regular basis so that a greater number of culture collection samples can be submitted. A regular basis could be every 5 years or based on all diseases of a specific commodity using a similar timeline. Sample bags can be sent to responders with specific instructions to optimise collection and storage quality. Approaching the rural levy provider to fund the sampling and provide advertising would assist in costs associated with the sampling. 

The benefits of this proposal:

  • Provide enough samples in the collections to allow for DNA extractions without restrictions or as the technology improves.
  • Population data on a number of economically important plant diseases. This could be further used for:
    • Surveillance data for biosecurity purposes (includes nil results).
    • Genotypic information for fungicide resistance projects.
    • Information on the lineage of the disease over time, is it moving to more aggressive strains?
  • Allow citizens and industry to be included and feel invested in potential scientific research.
  • Cost effective way of collecting samples over a wide geographic area.
  • Cost effective for the levy providers as it would allow for long term collections rather than the boom and bust cycle of funding large scale projects. Often after large scale projects are completed the samples are destroyed meaning new projects spend money on recollecting samples.  
  • Provide information as to disease hot spots or location of prevalence over time.

This proposal could be broadened to a wider group of pathogens but I have written it from the basis of my PhD experience with oomycetes.

Taxonomy 2028 Challenge: We need to database all specimens in the national collection, focusing on museum collections

When the Australasian Virtual Herbarium (AVH) was initiated in 1999, herbaria had for many years been databasing specimens. The AVH was seen as a logical progression from isolated specimen databases in each institution to an aggregated, national database of all specimens. Funding, obtained on the basis that the AVH would stimulate research including taxonomy, was obtained and used to complete the databasing of Australian specimens in all major herbaria, to mount and database backlog specimens, and to develop the AVH infrastructure.

Museums and other zoology (e.g. entomology) collections have also been databasing specimens for many decades. However, no museum collection is fully databased. OZCAM, the museum equivalent of AVH, is also an aggregation service, but museum collections have not had the benefit of a large, national, coordinated, funded campaign to database all specimens. This is a severe constraint on biodiversity inventory, mapping, biogeographic and ecological analyses in Australia.

By 2028 we will have databased half of all specimens in museum and other zoology collections, with a sustainable program to database all specimens within the following decade

Databasing museum and other zoology collections is a substantially bigger task than databasing all herbarium collections. The AVH includes >8 million records, comprising c. 80% of the estimated number of plant, algae and fungi specimens in Australian and New Zealand herbaria. OZCAM includes <4 million Australian records, comprising c. 6% of the estimated total number of specimens in Australian zoological collections. The task is large.

However, the benefits are also very large. The fact that the vast majority of zoological specimens are un-databased precludes us from doing simple tasks like drawing accurate distribution maps for most taxa, assessing the conservation status of taxa, determining where rare taxa occur and whether they occur in sites targeted for development such as mining or agricultural clearing. The AVH is now used by researchers all around the world for novel biodiversity analyses in areas ranging from evolution, ecology, biogeography and conservation, and has amply proven its value. A completed OZCAM would be even more valuable.

We now need to work out a way to invest the necessary effort into our zoological collections.

Taxonomy 2028 Challenge: The view from an obligately biotrophic fungus

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:


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.

Taxonomy 2028 Challenge: Collection and characterisation of parasites and symbionts alongside their hosts

Posted on behalf of Dan Huston - PhD Candidate, School of Biological Sciences, The University of Queensland

Organisms do not exist in isolation. Rather they exist in a web of complex associations with other organisms across space and time. Parasites and other symbionts are intimately associated with their host organisms and represent a massive component of global biodiversity. This component is mostly unseen, and rarely considered during biodiversity and ecological surveys or in conservation planning. Threats to biodiversity are amplified in parasite and symbiont populations, and host-specific lineages are likely to face extinction before their hosts. If we seek to characterise all of Earth’s biodiversity then, we must consider symbionts. Obviously, study of these organisms requires examination of their hosts, and therefore presents excellent collaborative opportunities for systematic biologists working on various groups. However, most parasites and symbionts have specific collection protocols required for producing specimens of a quality useful for taxonomy. Therefore I propose that:

By 2028, we will have established and implemented a collaborative support network dedicated to the collection and characterisation of parasites and symbionts, alongside characterisation of their hosts.

It could be called something that would result in a hip acronym like ‘Systematics of Symbionts and Parasites Support Network’ (SSAPSN). The major goal of the network would be to facilitate parallel host and symbiont collection efforts through coordinated collecting expeditions and training about parasite and other symbiont collection techniques. This will result in more impact per unit of collecting effort and more complete biodiversity collections in museums and other institutions for current and future research. Collaborative efforts between those systematic biologists studying hosts, and those studying the symbionts of said hosts may be seen as a better value for money and could increase grant application success, and may lead to cross-field citations of research papers. Most importantly, such efforts will give us a better understanding of life and the complex interactions between organisms in general.

Examples of the importance of considering parasites and symbionts in the future of taxonomy and systematics can be gleaned from many of the challenges already posted here on Noto | Biotica. Elaine Davidson’s challenge to explore the diversity and potential of microorganisms highlights the value these organism have to humans in terms of medicine, agriculture and industry. The many endosymbiotic microorganisms present in plants and animals are sure to provide novel chemical processes and enzymes of value to us. Kevin Thiele’s posts ‘every Australasian species genomed’ and ‘life in the late Anthropocene’ challenge us to collect tissue samples for all Australasian biota and sequence their genomes. While many of the tissue samples required are already in museums, such an endeavour will still require a huge collecting effort. These collecting events should be coordinated between systematic biologists across disciplines so that both host tissue and symbiont tissues can be collected concurrently. Nerida Wilson challenged us to double the number of described coral reef taxa by 2028. This topic hits close to home as much of my PhD research has been on coral reef parasites. We have only just begun to scratch the surface in terms of understanding parasite and symbiont diversity on the Great Barrier Reef and increased effort in characterising these organisms will greatly aid in doubling the number of described species for the region. Juliet Wege’s post ‘Obtain high quality collections of all undescribed vascular plant taxa’ highlights the difficulties inherent in acquiring these specimens from remote areas, and the need to execute targeted field expeditions to take advantage of seasonal weather conditions. Expeditions for rare plants could benefit from a nematologist to collect and study plant-parasitic nematodes and an entomologist to collect and study associated insects. A simple alternative would be training in the collection of these organisms for the botanists tasked with undertaking such expeditions. I fully understand that having collectors plan on collecting symbiont organisms alongside the stuff they are really interested in is a big ask, so including extra personnel on such expeditions focused on symbionts would be ideal. In the end however, any collection would be better than none.

The obvious first step towards building such a network is a level of organisation and a platform for communication. The existence of the SASB and now Noto | Biotica already gets us most of the way there. Noto | Biotica could be used as a news platform to help connect parasite and symbiont systematic biologists with those studying other groups, coordinate collection events, ‘wanted organism’ ads, etc. Because many parasites and symbionts are hidden in not so obvious locations in their hosts, and many require specialised fixation and preservation, workshops designed to train other systematic biologists in how to find these organisms and how to preserve them would be beneficial. Perhaps some small grants could become available for biologists undertaking collecting expeditions to cover the cost of extra field days and equipment to collect symbionts, or perhaps travel grants could be used to bring a parasitologist (we make for interesting dinner conversation) along on the trip. At the very least, a better awareness of all those organisms that exist under cover of their host is sure to lead to significant progress in the task of characterising all of Earth’s biota.

Taxonomy 2028 Challenge: Let's digitally image all (or most) of our type specimens

 Posted on behalf of Kenny Travouillon, Curator of Mammalogy, Dept. of Terrestrial Zoology, Western Australian Museum

  1. By 2028 we will have digitalised the majority of type specimens in museum collections and made them available to researchers, industry and the general public.
  2. This will result in increased productivity of taxonomists, and make it easier to identify species in the field.  Several museums have already digitalised their type specimens and made them available on their website to the public, but achieving complete online access to all type data will help taxonomists recognise named species from new species more easily and also help create field guides, with keys to identify species in the field. This can not only be done for modern species, but also for fossil species, collected from more fragmented material.
  3. This matters because the taxonomic process is still a very slow process which requires years of research before making new species discovery. Yet, species are going extinct at an increasing rate, but many remain unnamed or have yet to be discovered. Digital access to type specimens will help speed up this process and get on with the job of conserving taxa earlier. Having a tool to make species identification in the field easier will also help researchers and industry with population monitoring. 
  4. Resources to achieve this will be funding to help institutions to hire additional staff to digitalise the collections, as well as IT staff to make this information available online for access by anyone. 

Taxonomy 2028 Challenge: A vision for fungal taxonomy and systematics

Posted on behalf of Alistair McTaggart, Postdoctoral Fellow, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria. Email:

Web Pages: FABI profile (current employment), Google Scholar profileRust 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: 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 fingertips.

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.