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: alistair.mctaggart@gmail.com

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)

Background

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 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.

Taxonomy 2028 Challenge: No net loss of FTE dedicated taxonomists

Posted on behalf of Dr Glenn Moore, Curator of Fishes, Department of Aquatic Zoology, Western Australian Museum


  1. By 2028 we will have no net loss of FTE dedicated taxonomists Australia-wide
  2. This will result in  security of taxonomic capacity and prevent the ‘brain drain’.
  3. This matters because there has been a well-documented global decline in dedicated taxonomists over the past few decades (eg Boero 2010; Disney 1998; Drew 2011).  This is despite the increasing need to understand the basic units of environmental, ecological, climate change and related research.  While much of the Decadal Plan is focussed on raising awareness of the role of taxonomy and its obvious importance to all fields of biological research, we also need to draw a line in the sand and stop any further reductions in taxonomic capacity in Australia.  We argue, with good reason, for increased staffing, training and students in the field, but this relies on increased funding.  The first step is to stop the decline, which already operates within funded models (at least to some degree).  Capacity needs to increase by 2028, but at the very least we must ensure it doesn’t decrease!
  4. Resources to achieve this will be recognition of the role of taxonomy, support from administrators, funding

Boero, F. (2010). The Study of Species in the Era of Biodiversity: A Tale of Stupidity. Diversity 2: 115.
Disney, H. (1998). Rescue plan needed for taxonomy. Nature394(6689), 120.
Drew, L. W. (2011). Are We Losing the Science of Taxonomy? As need grows, numbers and training are failing to keep up. BioScience61(12), 942-946.

Taxonomy 2028 Challenge: Greater engagement with the public and end users of taxonomy

Taxonomy is a field that celebrates the immense diversity of life and allows for effective communication across not only scientific disciplines related to biology, but also for a whole range of other fields and industries that are crucial to our society (e.g. medicine, biosecurity, horticulture etc.). Its central role across these disciplines often goes unnoticed and in many cases underappreciated (e.g. Garnett & Christidis 2017). 

The level of success that we hope to achieve from our decadal plan (and indeed also with all subsequent plans after it) will invariably depend on the support of not only the systematic and scientific community, but also the larger community as a whole. Therefore, I propose that:

By 2028 we will achieve greater awareness, appreciation, and engagement from the wider public about the role and importance of taxonomy and systematics.

This will only result in outcomes that will inevitably benefit taxonomy and systematics which in turn contributes to the wider society. E.g. Greater funding (hopefully!) for taxonomic research and infrastructure development due to an increased appreciation and demand for taxonomic knowledge from the public.

Resources to achieve this will include:

First, broad surveys conducted during the start of the decadal plan followed by subsequent surveys at regular intervals (e.g. annually), allowing us to quantify and track our progress. Consultation and collaboration across the systematic society and social sciences would be particularly important in this case.

Similar initiatives have been noted, for example a survey was conducted during last year’s ASBS conference at Alice Springs targeted to our systematics community, and for botanical collections (e.g. the State Botanical Collection Significance Assessment, Royal Botanic Gardens Victoria 2016), though none has been conducted to the wider public at present.

With awareness comes appreciation, and with appreciation comes engagement – a crucial component for any endeavour. Questionaires can be constructed following this order:

1)   Awareness:

Example Q: Are you familiar with the fields of taxonomy and systematics? Y/N

Example Q: Are you aware of what a herbarium is? (*most people I’ve asked don’t!) Y/N

Example Q: Do you think herbaria and museums play a role in the fields of taxonomy and systematics? Y/N

Example Q: What do you think are the roles of a taxonomist or systematist?

2)   Appreciation:

Example Q: How important do you think the fields of taxonomy and systematics are to our society?

rank from 1–5 (for economic importance, scientific importance, cultural importance etc.)

Example Q: How important do you think the fields of taxonomy and systematics are in understanding and classifying the diversity of life?

rank from 1–5

3)   Engagement:

Example Q: Is the level of engagement of the taxonomic community with the broader public and end users sufficient?

rank from 1–5

Example Q: How can we improve our level of engagement?

The brief example above is targeted for the broader general public. Similar surveys can be created for specific groups of end users such as consultants, horticulturalists, or even other scientists who are not in the fields of taxonomy or systematics. Questions can be crafted following discussions and consultations with members of our community.

Establising a baseline survey will be critical in monitoring our progress. E.g. what percentage of the public is aware of the roles that taxonomists and systematists have?

In addition, these surveys will allow us to tailor our approach and invest in areas that we are currently lacking in terms of outreach (besides new species discoveries that attract the attention of the press and often quirky names that are associated with these new taxa [e.g. in Crisp et al. 2017], other roles of taxonomy often goes unnoticed – such as breakthroughs linked with evolutionary biology, phylogenetics, and biogeography).

Any potential differences noted across different levels of demography would be of particular interest  ­­–  especially on the responses of the younger generations (i.e. prospective and current students of biology).

Attracting and engaging younger generations in the fields of taxonomy and systematics is crucial to the survival of these disciplines. Engaging the younger demographic would require the use of media channels that they are regularly exposed to e.g. social media channels.

Noteworthy examples that utilises social media for taxonomic outreach include:

Novataxa: A blog dedicated to disseminating taxonomy and science, by featuring newly described species from across the planet in a way that is accessible to the wider public (by including pictures and summary diagnoses that can be understood by a layperson).

www.novataxa.blogspot.com.au

www.facebook.com/novataxa/

In other cases, personal blogs or social media sites (e.g. www.instagram.com/francisnge/) can also serve as an effective medium for taxonomic outreach.

Herbaria across Australia have their own dedicated social media sites on Facebook, and indeed one also exists for the Australian Systematic Botanical Society. Perhaps a site specifically dedicated to disseminating taxonomy and systematics should be created for the Australasian region, featuring the immense diversity that we have. A working model could include some of the features noted in Novataxa and In Defense of Plants ­­– a popular American botanical site aimed at engaging biology students (www.indefenseofplants.com; Fig. 1), it’s facebook site has garnered over 29000 likes www.facebook.com/InDefenseOfPlants/

Figure 1. Attracting a wider audience to what taxonomy and systematics entails – the study of the diversity of life.

A more active engagement from the public could aslo be achieved through these social media sites, for example the Kwongan foundation (www.facebook.com/kwonganfoundation/), a community site created for the conservation of Australia’s biodiversity with input from people across all regions, including those outside of Australia. Active participation from the community is maintained through engagement with other relevant groups that are present on social media e.g.

The Wildflower Society of Western Australia (currently with over 7000 online members; www.facebook.com/groups/129636970391772/)

and the Australian Native Plant Enthusiasts forum (currently with over 9000 online members; www.facebook.com/groups/675253642559682/)

Of course, engaging through the use of social media is only one way in getting our message across, and there are numerous ways of doing so, including increasingly novel ways that evolve with the development of increasingly sophisticated technologies (e.g. apps for plant identification). Nevertheless, it is a useful medium for which we can disseminate information through to a wider audience.

Finally, additional subsequent outreach strategies can be drafted, developed, and implemented following surveys conducted to the relevant stakeholders and consultation with the wider community.

Contributed to the Taxonomy 2028 Challenge by Francis Nge, University of Adelaide and State herbarium of South Australia

References:

Crisp, M.D., Cayzer, L., Chandler, G.T. & Cook, L.G. (2017). A monograph of Daviesia (Mirbelieae, Faboideae, Fabaceae). Phytotaxa 300(1): 1–308.

Garnett, S.T. & Christidis, L. (2017). Comment. Taxonomy anarchy hampers conservation. Nature 546 Issue 7656 (1st June 2017 ): 25–27.

 

Taxonomy 2028 Challenge: a taxonomic emergency for vanishing coral reef fauna

The world’s coral reefs are facing imminent degradation from a variety of pressures. Current research suggests we have lost half of the world’s coral reefs in the last 30 years, and that reefs will disappear completely in the next 20-30 years. Despite this, the biodiversity of coral reefs is globally estimated to be represented by around 950,000 (±40%) multicellular species and only 10% of them have been described (Fisher et al. 2015). 

By 2028 we could double the number of described coral reef taxa.

This vision will result in a more comprehensive inventory for a fauna that we do not have the luxury of working steadily on for the next few decades. This is of great importance for a myriad of reasons, not least among which, coral reef organisms have contributed many new drugs that might preserve or improve human well-being.

This type of taxonomic emergency is something that scientists should come together to co-operate and speed up outcomes, before its too late.


[To be honest, I have no idea if this is achievable or not. It would require the description of 95,000 species in 10 years. Seems big. But achievable if big investment also occurs. And morally speaking, I think we should try!].


Taxonomy 2028 Challenge: The Australian National Biodiversity Collection

Australia currently has around 100 public biodiversity collections (based on the ALA's Collectory pages), with a combined holding of >50 million specimens covering all organismic groups, and an estimated value of >$5 billion. In aggregate, the collection comprises a megascience infrastructure for biodiversity research in Australia, our region and the world, similar in scale and value to other megascience initiatives such as the Square Kilometre Array or the Large Hadron Collider.

However, the collection is jurisdictionally very scattered. In general, each state and territory has a large or relatively large herbarium and museum collection, under a variety of jurisdictional and reporting arrangements (e.g. from semi-autonomy under an independent Board to embedded in botanic gardens or various government departments). Some universities have collections, ranging from small teaching collections to substantial holdings. There is also a long tail of smaller, special-purpose collections in universities and various government departments. 

This jurisdictional scatter has arisen for obvious historical reasons: the establishment of the major herbaria and museums was mandated or facilitated under state and territory legislation; the CSIRO collections were established under its research mandate; and the smaller collections were established by universities and government departments for specific purposes not adequately covered by the major institutions.

Importantly, funding decisions that affect our collections are made by a very wide variety of budgeting agencies (from local to state or territory to national), with very little national coordination or strategy that can buffer a given collection from the exigencies of its local funding pressures.

Further, the wide scatter of collections means that few "owners" of collections see their collection as part of a megascience infrastructure, and nor does the community as a whole.

So, here's my vision:

By 2028, all our biodiversity collections will be integrated to form the Australian National Biodiversity Collection

The main goal of the ANBC will be to change the way governments, industry and the community view our individual collections - from seeing them in isolation to seeing them as part of something much greater. For obvious reasons, each individual institution will remain under local jurisdictional control and management. However, we will market our collections as e.g. "The xxxx collection, part of the Australian National Biodiversity Collection". 

We will establish an arrangement under the Council of Australian Governments (COAG) whereby the importance of each collection as part of the whole is acknowledged, including if possible negotiated agreements on minimal required baseline funding for each collection. 

We will also establish a strategic governance structure for the ANBC as a whole, to ensure strategic planning for the aggregate as well as individual collections, rather than for individual collections alone, and to increase recognition of the strategic value of each collection and of the ANBC in aggregate, in order to increase profile and funding.

Taxonomy 2028 Challenge: Providing certainty in taxonomic applications through next generation sequencing

Holotypes are the universal standards we use to build our taxonomic knowledge. Since the integration of genetic data into our methods, our knowledge of diversity is rapidly increasing, but rarely can be linked back to species names. This has led to a divergence of knowledge systems where sometimes we have a parallel set of understanding that cannot be accurately tied together. In order to progress taxonomy, we need to be able to link all this new information with the centuries of foundational work based largely on morphology. Most holotypes are old, or preserved in a way that doesn’t easily allow the extraction of genetic information. However, newer technologies have overcome many of these issues (e.g. formalin preservation, degraded samples) and it should be possible to retrieve a barcode that could link historical type material with molecular studies.

By 2028 we will barcode 50% of holotypes in Australasian collections. This will result in the ability to link genetic information with available names and provide context for interpreting all molecular studies. This will solve some seemingly intractable taxonomic questions, and provide an essential resource for the future. This matters because currently, at best, molecular studies can include material re-collected from type localities, but most don’t, or can’t, since these areas may be highly impacted by human development. The proposed project will provide absolute certainty for contemporary identifications.

While it is not possible to utilise a single gene across all life, the key is unlocking the relevant marker for the groups of interest. Shotgun sequencing can be used to produce barcodes for type material. Shotgun sequencing breaks up DNA into small pieces, which get sequenced in short, overlapping fragments. These are assembled into continuous pieces, which will usually contain the high copy genes that we often use for species-level studies.

By maintaining project-level hubs at the involved institutions, existing databases will maintain the complete metadata record, while a purpose-built (very simple) database could list the species name and collection registration number. Using these two terms in a search of the public database GenBank, where data will be deposited, will retrieve all available data for that type. Other resources required would be salaries for project managers/scientists, a budget for sequencing, and the support of the involved institutions.

This project will increase the utility and integration of existing genetic information and provide absolute certainty of species-level identifications. It will also reduce the need for loaning or handling type material, which in many cases, becomes more fragile with age. This is future-proofing taxonomy!

By Nerida Wilson and Kym Abrams

Taxonomy 2028 Challenge: Life in the Late Anthropocene

Here's a wild idea for the Taxonomy 2028 Challenge - some thoughts that came from listening to Peter Raven's talk about the Shenzhen Declaration at the recent International Botanical Congress.

There are two possible scenarios for the future of humankind in the Anthropocene:

Scenario 1: we catastrophically over-reach the earth's carrying capacity, resulting in an uncontrolled crash back to a pre-industrial state (from which we will probably never fully recover given that all the easily accessible fossil fuels are now used up);

Scenario 2: we manage the coming demographic transition in a sustainable way, with population (and resource utilisation) peaking sometime mid-Century followed by a gradual decline in both population and resource use, and with continued increase in our technological capacity.

In either scenario, the Anthropocene will inevitably comprise a mass extinction event. In the first scenario, the living world will come through the mass extinction in much the same way as it has in the past, with diversity gradually rebuilding over the next several million years. 

In the second scenario, we have a more interesting (and optimistic) scenario. After the demographic transition, we will be able to gradually reduce our ecological footprint, and will be able to embark on a phase of "rewilding" the planet - we contract the amount of land we need for food production as we farm more intensively and technologically for a smaller population, which makes land available for restoring wild spaces and the ecological services these provide.

The problem is, we will have lost a significant amount of biodiversity by the time we can start the rewilding.

So here's the proposal:

By 2028 we will have collected and stored tissue samples from all Australasian biota in a genomic ark

Despite the inevitable mass extinction, we act now to store as much genetic diversity as possible in the form of DNA-stable tissue samples. Once the rewilding starts, we will almost undoubtedly have the technological capacity to recreate species from DNA samples, using CRISPR/Cas9 or other gene editing technologies. The limiting factor will be having the DNA material to do this.

So, by 2028 we will have an Australasian genomic ark, the main purpose of which (though not the only purpose) is to store stable genomic samples of as many organisms as possible from our region. This can be done in a variety of ways, e.g. dried leaf samples for plants and tissue samples for animals, environmental samples for fungi, microbes etc.

An interesting issue is that we need to try to sample as much biodiversity as possible including currently unknown taxa. The taxonomy can come later (perhaps even after the rewilding) - we don't need to have the taxonomy all worked out before we sample. We should aim to store as many tissue samples as possible, whether the know what the organism is or not. This has interesting implications for the sampling strategy we would employ for this.

Such an ark could become an absolutely invaluable resource in the future (if we can avoid scenario 1).

Taxonomy 2028 Challenge: Palaeobotany for future planning

Posted on behalf of Prof. Bob Hill (University of Adelaide), with help and contributions from a broad sector of the Australasian palaeontological community
By 2028 we will have a totally integrated record of fossil and living plants in Australia in a way that allows for the fossil pollen and spore record (microfossils) and the record of macrofossil remains to be linked as strongly as possible from the perspective of their taxonomic identity. This, along with the age and location of the fossils, can then be overlain on the current knowledge of living plants species and their distribution to demonstrate that the unique island laboratory that is Australia can be reconstructed vegetatively in a way that is unachievable elsewhere on Earth. 

Australia is unique in being a large, flat and mostly isolated land mass that has not undergone any major environmental upheavals for tens of millions of years except for climate change (and some coincidental changes in photoperiod and light availability). The plant fossil record is much larger than most people realize and it offers a stunning record of the change in vegetation that is about as extreme as it is possible to imagine for much of the continent (often from dense rainforest to arid desert). A full reconstruction of this would be an amazing achievement, and would highlight the precious nature of the Australian biota and its journey over millions of years. 

This work will result in a data base that will allow for sophisticated reconstructions of the past impact of climate change, the arrival of humans, changing fire regimes and much more. In the best case this will play directly into matters of significant community importance like planning for future climate change and best managing fire into the future. On another level it will provide researchers with unparalleled access to fossil data when utilizing the living flora for detailed evolutionary studies. Taxonomically well-validated fossils are critical for such studies, and are increasingly showing that molecular-derived dates of lineage divergences are often much too young. There is also potential amongst more recent fossils for ancient DNA and chemical fingerprinting of both micro- and macrofossils to better separate out genera and species. Overall this contributes to a stronger integration of the fossil vegetation record with the extant vegetation. 

All this matters because Australia has undergone extreme change in the past 40 million years and is highly vulnerable to future change. By increasing our level of understanding of the past and how it has shaped the present, we stand a better chance to influence what the future might look like. 

Resources to achieve this include smart young researchers who are committed to their own, but also to the collective, good. None of the research required here is expensive, but it needs a new generation of people with research skills that are fast disappearing. It also requires a very sophisticated databasing approach and firm overall control so that data is compatible across all areas. The approach taken should match that used for databasing the living Australian vegetation, but will include the need for better access to modern microscopy (scanning and transmission electron microscopy), automontage microscopy and some of the newer techniques for analyzing specimens such as neutron tomography, which is available at ANSTO. 

Taxonomy 2028 Challenge: Every Australian species genomed (is that even a verb yet?)

Posted on behalf of Dr Peter Johnston, LandCare Research, New Zealand


By 2028, every species in Australasia has had its genome sequenced. 

This includes named species, as well as species known from specimens or living cultures in curated scientific collections, but not formally named.

The IT infrastructure needed to manage this data, analyse it, interpret it, and deliver it in a way that is useful to humans, is available. This interpreted data will be delivered to users in real time and updated as new taxa are discovered.

This will provide:

  • a truly robust phylogeny of Australasia’s biota, from population through to kingdom.
  • understanding of the Australasian species and lineages that make this part of world special, irrespective of kingdom [e.g. from koala to epacridaceous root endophytes]
  • recognition of the species and linaeges that are exotic, prediction of their putative biology, and understanding of their potential risk to Australasia’s economy and inidigenous biota.
  • ability to place taxa known only from environmental DNA sampling in the phylogeny, irrespective of the gene or genes used for that sampling.
  • important management tool for dealing with the high-risk and unique parts of Australasia’s biological diversity through accurate mapping across space and time, based on national landscape-scale eDNA surveys. 

Taxonomy 2028 Challenge: Microbial diversity

 Using the potential of microbial diversity in innovative ways:

By 2028 we will be in the age of microbiology, with micro-organisms contributing to the majority of industrial processes.  We urgently need to explore their diversity and potential. 

This will result in using microorganisms and their enzymes to improve human health, increase crop yield, recycle waste products and eventually replace much of the fossil(ised) economy.

This matters, because with an increasing population and increasing demand for animal protein, agriculture must become more efficient, as there are finite resources on earth there is an urgent need to reduce or recycle waste, and a moral requirement to reduce pollution from industry.

Resources to achieve this will be

·         Public support so that people are aware of, and in agreement with, using microorganisms and their enzymes to ensure a more sustainable future.

·         The political will to look forward, by investing in discovery programmes focussed on the microbial communities of Australia in ancient rocks, in highly leached soils, and from the unique flora and fauna that occurs in diverse climatic regions.  These programmes will include not just what is there, but how these organisms are able to survive in such unusual environments.  An outcome with be to determine how this ability can be exploited in novel ways in new industries.

·         Investment from the extractive industries in microbial discovery in low pH and highly saline environments in order to develop enhanced biomining and bioleaching of mineral ores.  This will enable these techniques to be applied to a wider range of materials, under a greater range of physical condition than is possible at present.

·         Investment from the agricultural industries for developing microbial products for the better use of waste products.  An example is the use of fungal enzymes for recycling keratin from animal waste into nitrogen-rich products such as plant fertiliser and animal feed.

·         Investment by manufacturing industries in the use of microbial enzymes to minimise waste and pollution, so that this becomes part of their licence to operate.  Examples are the use of fungal enzymes in the pulp and paper industry, and in tanning leather.

 

This list could go on….and on….


Elaine Davison