The rarity problem in Australian taxonomy

"Anybody could do that," replied the young fellow contemptuously. "I want to distinguish myself."

"Then I'll tell you what you'll do, Moriarty. Take a narrow branch of some scientific study, and restrict yourself to that. Say you devote your life to some special division of the Formicae?"

"The what?"

"Formicae. The name is plural. It embraces all the different species of ants."

"Why, there's only about three species of ants altogether; and there's nothing to learn about them except that they make different kinds of hills, and give different kinds of bites. That sort of study would about suit you. Fat lot of distinction a person could get out of ants."

- Tom Collins, Such Is Life (1903)

Moriarty could be forgiven for thinking there were only three species of ants on Runnymede Station. Those were the common species, the ones he saw every day. Moriarty didn't know that most species in any taxon are naturally rare.

Ecologists know about rarity. They do an exhaustive survey of some group of organisms on a study site, and find that there are a few very abundant species and a "long tail" of much less abundant species. They build a rank-abundance diagram (https://en.wikipedia.org/wiki/Rank_abundance_curve) from their results.

For ecologists, those many rare forms are a statistical nuisance, and there are hundreds (thousands?) of published articles in which the rare forms have been deliberately ignored: "Species represented by 10 or fewer individuals were excluded from the analysis."

The rare forms can also discomfit the ecologist with a taxonomist on tap. The latter has no trouble naming the abundant species, because these were collected and described long ago. But when the taxonomist sends the ecologist a final species list, many of the rare forms that were collected only have code names like "Improbabilidae sp. 1", because they hadn't been seen before. By anyone.

The rank-abundance relationship applies to terrestrial, freshwater and marine taxa. It's one of the principal obstacles to naming and describing the entire Australian biota, but it's not often discussed.

Think of taxonomy as the discovery, documentation and classification of life. The latter two activities can increase more or less proportionately with resourcing. The more money you put into training and funding taxonomists and systematists, the more species get properly documented and classified.

Discovery is different, because the amount of money needed to collect specimens increases with the rarity of the species. On day 1 of a field trip you can find 50% of the species at a study site. As time goes on, the rarer species drop one by one into the collecting bucket, but even after a week the species accumulation curve (https://en.wikipedia.org/wiki/Species_discovery_curve) may not have levelled off.

I'm currently working up a set of Tasmania's rarest millipedes, some of which are only known from single specimens. Not only are these species naturally rare, they have jackpot distributions on a small spatial scale. If I'm lucky, I'll find a jackpot of several adults in a metre-square patch of forest litter. Most of the time I'm unlucky. I'll go to the only known locality (usually it's a revisit to one of my previous sites) and won't find the target species, just new locality records for more abundant ones. So I keep looking. Field trips cost time and money, and these rare forms are costing far more than their more abundant congeners and confamilials did.

Mine is nearly a "best possible collecting" scenario, because millipedes in Tasmania can be collected in the right life stage at any time of year. Think of all the rare Australian species which are only findable or recognisable when the the season or the weather is right!

Bob Mesibov

Storing and sharing data

One aspect of our research that I don’t remember seeing much comment on in relation to the Decadal Plan currently being prepared (https://www.science.org.au/support/analysis/decadal-plans-science/biosystematics-taxonomy) is the safe long-term storage and sharing of data.
I was reminded of this by a very recent editorial by Theresa Culley in Applications in Plant Sciences 5(10): ‘The frontier of data discoverability: why we need to share our data’ (see http://www.bioone.org/doi/abs/10.3732/apps.1700111).
 
She points out that not only SHOULD we make data widely accessible, it is now often required by granting bodies and journals.
To quote from her abstract, there are good reasons for depositing data in permanent repositories:
 
‘(1) it prevents data loss due to accidents, theft, or death of the researcher; (2) it enables published research to be reproduced by others; (3) publications associated with accessible data sets can have higher citation rates; (4) deposited data sets are increasingly recognized for scholarly recognition and professional advancement; and (5) stored and accessible data can be used in the future for projects that are unanticipated today’.
 
Her article is based on the American situation, but the main points are also very applicable for Australasia.
She raises various questions about procedure such as: Who should set up such data repositories? Who should be responsible for seeing that data are stored in a suitable format and with appropriate metadata to make them intelligible in future? Who should pay (always a big question) for these repositories and for ongoing curation of data to ensure continuing accessibility?
 
Current examples of data repositories that have been widely accepted as useful are GenBank and EMBL for sequence data. Dryad (http://datadryad.org/) is another example. 
 
It would be useful if the Decadal Plan addressed at least the general question of data repositories in our field of research and what we might aspire to achieve in the next decade. Is data storage another role for the proposed coordinating body for biosystematics and taxonomy? Or is there enough activity in other parts of the world for us to just use what is being set up there?   
 
 
Karen L. Wilson AM
 
Honorary Research Associate, National Herbarium of New South Wales
Adjunct Associate Professor, University of New England, Armidale, NSW
Secretary, General Committee, International Code of Nomenclature for Algae, Fungi & Plants   
 
Botanic Gardens & Centennial Parklands
T +61 (02) 9231 8137 | E karen.wilson@rbgsyd.nsw.gov.au
Royal Botanic Gardens & Domain Trust, Mrs Macquaries Road, Sydney NSW 2000, Australia
 
 
 
 
 
 

Taxonomic Implications of Decadal Plan

Perceptions of a Sociopathic Taxonomist

Disclaimer: At the outset I will proffer my apologies to those who know me. If anyone asks, I completely understand if you choose to deny that you’ve ever had any association with me, implied or otherwise. The views upheld in this brief note are those of the author alone, not a single other person on the face of the Earth. God help us all if there’s others like this.

“The outcomes and recommendations in this report are aimed at informing the primary stakeholders of Australian astronomy of the current status of the field, the strengths and progress made by the Australian astronomy community, the big scientific questions that Australia is best equipped to answer, and the infrastructure and capability priorities for the future needed to realise this ambition.”

After reading the Decadal Plan for Australian Astronomy (DPAA), I couldn’t help but feel underwhelmed by its content as I walked away from it. Out of some 80 pages, half a dozen, at best, actually outlined any astronomical achievements, as it were, over the preceding 10 year period, and for the next 10 as proposed within the current plan. The underlying emphasis throughout the documentation, from my reading at least, was a focus on infrastructure; incessant reiteration; industry subservience; over-generalized, content-free catch-phrase statements; and collaboration on nationally decentralised projects (i.e. ownership no longer belongs specifically to Australia). One of their own stated objectives was “funding a skilled workforce is critical to exploit the next generation of scientific infrastructure”. That’s all well and good, but the sceptic in me couldn’t get past the feeling that the astronomy discipline has committed the very sin that our working groups have discussed as being one to avoid at all costs – reducing bureaucratic nonsense and other distractions and letting the taxonomists just do their research (not to mention the establishment of long-term research career paths within our industry as well). From what I see, they have devolved from being an astronomy-centric discipline to an institute comprising physics experts who are now acting as engineers for producing low-cost, high-end infrastructure for industry purposes/gains, astronomy hopefully getting some crumbs somewhere down the line:

“The scale of future astronomical facilities demands skills, expertise and technologies beyond the current capabilities of Australia’s academic community. Meaningful industry engagement is required to build partnerships that will design, develop and produce the next generation of astronomical instruments, and to harness the innovation flowing from fundamental research for commercial application.”

Whilst I am well aware that they don’t tell the whole story, and many jobs have been created within the industry, just what are those jobs? The examples they provided of career paths that astronomy PhD graduates can hope to realise all indicated that, after a short initial involvement in the field of astronomy, they invariably go off into other fields e.g. medical, renewable energies. Whilst those are commendable pursuits within themselves, it is hardly a ringing endorsement of Astronomy as a long-term career path, or indeed, the success of their decadal plan as it actually relates to Astronomy. The research focus, where it is broached, is centred on infrastructure and the acquisition of excessively large amounts of data. A glaring omission from the DPAA, Round 2, is any analysis of what existing members of the industry think of their positions, research, prospects and the success of the DPAA itself. Could make for interesting reading.

“The development and effective utilisation of the ASVO and other data-related initiatives will require the astronomy community to foster a new type of scientist, dedicated to data-intensive activities—managing, curating, manipulating, processing vast volumes of data, extracting information from it and making data and information available and accessible to other scientists. Currently these scientists are largely missing from the astronomy community and a challenge for the next decade will be to train such scientists and create career paths for them.”

This sounds a lot more like tech jobs than research positions, as far as the nuts and bolts of astronomy are concerned that is. Forgive me for suggesting that the independence of the discipline has been compromised. Whilst there’s nothing wrong with tech jobs (and we certainly need more in our own science), before anyone gets indignant, we all recognise, I’m sure, that there is an ongoing need for the researchers as well.

On the other, more positive hand, however, the DPAA does purvey an ethos which I feel is almost completely lacking in the taxonomic sphere – they do present a strong sense of self-appreciation and self-value. They very strongly emphasise that they are important as an industry and that their skills are of a high standard, and those skills require a significant investment in education to acquire and apply. For my money, this is the taxonomic industry’s weakest link. I simply cannot get over what I have experienced as being the innate sense of unimportance most taxonomists appear to have. I was once told by a colleague that “this stuff could be done by a trained monkey.” Another said “what we do is nothing more than natural history.”

Well! I’m not sure I am in 100% agreeance with those statements. Maybe I’m even stupider than I originally thought, my perceptions of minimal intellectual competence being nothing more than misdirected self-indulgence. After writing this, there will no doubt be a lot more who agree with the latter. But honestly, why work in the industry if the previous statements are representative of your perspective? More on this later.

Back to the positives: there were three other salient points that were raised in the DPAA which I feel it would behove the ‘Australian Taxonomic Organisation’ (ATO) to adopt:

  • Australia’s astronomical research excellence rests on continued partnership between astronomical observatories and the universities.

  • The professional Australian astronomy community has undergone significant growth in the past decade with a rise in research capacity across the entire community, particularly in the training of higher-degree students and early-career researchers.

  • In the next decade, greater collaboration and partnership among astronomy research organisations and astronomy outreach providers is essential for expanding the public impact of astronomy.

It’s not really a lot out of 80 pages – just saying! Enough of dissing Astronomy though. Time to look in our own backyard.

Taxonomy 2028: Well! Where DO we go from here?

“By 2028, we will have a quality assurance and accreditation system for taxonomy and systematics across Australia and New Zealand.”

This statement (not mine by the way) was relayed in one of the brainstorming sessions Kevin held recently. If I were awarding prizes for the best idea presented, then I think this one would get it.

Quality control and an actual recognition of expertise. That would be nice. If we achieve nothing else, let’s at least aim for that.

It’s interesting to read all the blogs that have thus far been posted on this site. Some are egocentric (as is mine), some are left-field, many are subject-specific, some are measured, some are on the mark and others are unrealistic - at least according to my set of value judgements and set of experiences. Each of you will undoubtedly see it differently. How do we assemble all these differing suggestions and ideas to become an end product with which all stakeholders are at least reasonably satisfied? At the end of the day, what do we collectively want those end products to be and who will use them? More importantly though, I feel, is what to we want our industry to look like a decade from now? What do we want a position description for a taxonomist to look like a decade from now?

That’s the key, I think (pun noted). Collectively! Not as individual researchers. You know! “United we stand…..”. (Isn’t it ironic that it all seems to come back to the lumpers vs. splitters debate?)

The taxonomic/systematic ‘industry’ is a very diverse one – naturally. We study diversity. But just what IS that level of diversity? Scientists had enough problems in agreeing on how you define what a species or taxon is/was when they were only dealing with morphological characters. How do we define that which is arbitrary now? Therefore, on what basis do we enumerate it? Depending on the degree of genetic resolution that you use, each and every one of us is potentially a unique taxon. Only clones would be spared this ignominy, and I only know a few of those, albeit the evil ones. Why not just give us each a number and set us to work on the estate? I’m not entirely convinced (more than happy to be proven wrong) that we can engage the interest and concern of the general public by entreating them with statements like: ‘2,340 barcodes will become extinct if that development goes ahead’. Makes you feel all warm and fuzzy, doesn’t it? Makes the argument for the use of scientifically-generated names over common names a bit questionable for the everyday punter.

Taxonomy seems to have devolved into the art of ignoring multiple elephants in the room whilst simultaneously developing new and more complex technologies with which to confuse the science, and all the while spewing forth copious, more meaningless data for which storage issues constantly arise.

‘We have ALL this data!’

And….?

Look at it this way - within the lifespan of this proposed Decadal Plan, somewhere in the order of 130 million hectares of land will be cleared globally (based on current rates and assuming no deviation from that rate). That is 1.3 million km squared. That’s about 70% of the state of Queensland, assuming it was completely covered in vegetation to start with. So just how are we assisting conservation goals again? That is one of our mantras after all. Likewise, how on earth do we define rarity under the genetic code regime? Surely that answer will be as diverse as the number of geneticists out there. All this data. No more answers. Fewer workers.

There seems to be a hole in the taxonomic bucket, Dear Liza, Dear Liza (my sincere apology to anyone who IS actually named Liza and who may end up reading this). A lot of posts here, and responses to the brainstorming sessions, highlight what projects the respective authors consider can be achieved by 2028. Many present a wish list. Good thing the draft document will be ready just before Christmas. In the infrequent event that my left brain cell interfaces with my right brain cell, I can’t help but thinking, fleetingly, that some of the important questions SHOULD be:

How is it funded? (I know – Duh?)

How is it staffed? (Ditto)

Who will train the staff?

What are we producing?

Why are we producing it?

Who really wants it?

Who really cares?

Will the products we are producing now, and the new technologies we are using, still have relevance in 2028?

Come 2028, will our industry be well poised to conduct a second Decadal Plan?

What will a position description look like in 2028? (This is particularly relevant if we refer to our stated objective of an increase in taxonomic positions.)

How do we expect to convince politicians, the general public, and even other scientists that our research is important if we can’t agree on anything (present a united front), and if we are perceived as being a discordant discipline applying arbitrary principles to an ever-shrinking diversity base? How do they gain TRUST in our science and its outputs, and the quality thereof?

On that note – quality assurance – just what is it about taxonomic science that impels us to cut our own throats? I am going to create a LOT of bad blood by suggesting this because it has seemingly become the driving force behind our vocation in recent years, and now a government initiative (why do you suppose that is?), but why are we pushing so many resources into citizen science at the expense of resuscitating/replenishing our own profession? This comes back to the whole self-value/self-appreciation factor that the DPAA got right. Citizen Science, from memory at least, wasn’t addressed in the DPAA. Don’t misrepresent me, however. I do believe they have roles to play, but I think we need to adopt those with more of a self-preserving outlook.

L: Why are there so few taxonomists now employed in Australia?

H: “Because there aren’t the jobs”

L: “But there won’t be either if there’s a workforce doing it all for free”.

H: “That’s OK! We just need someone to train the public”.

L: “But who trains the trainer, and who does the research if the only qualified people are training volunteers? No-one is being professionally trained in this discipline anymore!”

H: “Why not?”

L: “Because there aren’t any jobs”.

Pass the bucket, Liza.

Why are we so amenable to giving everything, especially our hard-fought knowledge, away for free, or next to it? Just because many of us are employed with public funds? If that’s the logic, then no goods or services coming from government departments should incur a charge. Yeah, Right! Why do we blithely accept our lot and hand over our intellectual productivity for public manipulation and misrepresentation just because we’re paid from the public purse? Don’t we have a responsibility to also act as custodians of that information/data? After all, isn’t it allegedly generated in the national interest, much of it feeding into our longer term heritage and prosperity? Just saying!

What good does it do for us to push for university placements if the jobs aren’t there at the conclusion? Are we to become more like the astronomists, producing high-quality graduates for other industries? (What an absolute waste of time for the few experts that we do have). What incentives exist for students to study in this profession, apart from passion? Is there a career path? Is it one where you can still be conducting research at the upper limits of progression? Do students  want to spend the best part of a decade undertaking hard work, often under trying circumstances, to end up just handing that expertise over to the public on a plate (that plate being some form of bright, shiny, multi-functional technological marvel which will then have to be replaced almost immediately with whatever technology has been freshly developed at that point), only to have to spend the rest of their career trying to convince the latter that they don’t actually know more than the former (in most cases)?

Really! Why do we sell our science so short? Personally, I consider that to produce quality taxonomic output requires a specific set of skills, the combination of which is not as commonplace as some proclaim (and certainly beyond that of a trained monkey). What is our currency if it isn’t that particular set of skills? If any Joe Average can come off the street and do what we do, and just as well as those who have been trained for years, then why are we bothering with a Decadal Plan? Why WOULD the government bother to create FTE’s and invest funding? Pretty basic really. If you want the government or private industry to invest dollars, you have to have something to offer them that they can’t get elsewhere. So what are we doing/producing that stakeholders can’t get elsewhere?

Something I find to be a particularly noteworthy result emerging from the roadshow brainstorming sessions was the relatively minimal input of ideas on taxonomy itself. Of the 150 summary points recently circulated, only 11 (7·5%) pertained to the combination of the categories of Taxonomy, Nomenclature and Molecular Tools (all the stuff we actually DO), and even then some of those had considerable overlap. Even if you consider the individual contributions themselves, of the 418 put forward, only 36 (8·6%) gave consideration to those three factors. This can be viewed any number of ways, but maybe it’s a positive. Maybe, collectively, we consider taxonomic endeavour in and of itself to be in reasonable shape. Is it just the infrastructure, governance and resourcing of the industry that has fallen into a state of untenable disarray?

Given that no-one is likely to have persisted and read this far (I know I wouldn’t have), I’ll self-preservingly finish with an explanatory note.

Originally, I wasn’t going to bother having any input into this process. I know. Shame on me. It was remarkable, however, how many colleagues shared that viewpoint, considering it to be a waste of time, a pointless exercise producing a document that has little bearing on reality. I figure there’s plenty enough work to be done with the material I’ve got available to me – enough to see me to the end of my career and beyond. Of course, that is a self-centred outlook and one which only serves to achieve my objectives. A different perspective is required however. The task is bigger than me. It’s bigger than you. We all have our part to play, and whilst we may not always agree with each other, we need to be pulling in the same direction as a team. A good friend of mine has spent many years studying for a career in taxonomy. Not only that, the enthusiasm and infectious appetite they have for the science is exemplary and refreshing. If I abstain from involvement, if any of us do, then we rob people like that of their chance to realise a goal, a dream. That’s not fair and it’s not right! So this is my 10₵ worth; my 15 minutes.

This is about the future. There is extraordinary potential in this industry. There is still heaps of work to be done, particularly once you get past the flora and megafauna into studying the important organisms (that should get a reaction). I exhort the planning team to keep sight of what we are about and what we are producing. Let’s do our best to not resorting to prostituting our science as some form of quick fix to a seemingly insurmountable conundrum. We need our stakeholders to come up to our level, not allow them to drag us down to theirs. Above all, we need to keep the science real and avoid the trap of being caught up in the infinite quest to align our output with technology. We’ll never catch up and there’s still more than enough baseline taxonomy to be done to feed into all those wonderful databases and programs. At present, we’re creating products based on a fraction of the potential data which remains to be collected. Let’s focus on that at least as much as we focus on new ways of presenting existing data over and over again.

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 http://onlinelibrary.wiley.com/doi/10.1111/aen.12158/abstract)


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.


Direct action

A suburban mall, 2 pm. Mothers and grandmothers sit chatting in the shade. Toddlers squat together in a sandbox, their sun-hats almost touching. The lunchtime business crowd has gone back to their offices. A waiter wipes down the vacant outside tables and pushes chairs back into place. A white ibis (Threskiornis molucca) perches on the rim of a rubbish bin.

Inside the Café Vittoria, a young woman in sunglasses sits with a latte, idly flipping the pages of a magazine. She's been waiting half an hour and is running out of patience. The candle stub she's brought with her is burning low in an ashtray on the table. She wonders if she has another in her handbag.

Into the café sweeps an older woman, smiling and laden with shopping bags. Looking around the café, she spots the candle-lit table and bustles over, dumping her bags on and under the table's empty chairs.

"Whoosh!" she says, sitting down to face the younger woman. "Ontogeny recapitulates phylogeny."

"But morphospace is boundless," replies the other, coolly.

Passwords having been exchanged, the women shake hands and murmur "Luz" in unison. Thus begins another clandestine meeting of agents from the League of Unemployed Zoologists, LUZ, whose acronym means "light" in Spanish and whose emblem, the candle, symbolises the vulnerability of zoological knowledge.

"Life in Sydney has been good to you, I see", remarks the younger woman with a hint of sarcasm, nodding towards the shopping bags.

"They're empty boxes in those bags, sweetie", replies the other. "Part of my disguise. What's your UID? I'm Patiriella, Marine Section."

"So I was told. Austrochorema, Freshwater. You're late."

"Not by much. What do you have from Melbourne?"

Austrochorema sips her latte. "A little. Our colleague at Museums Victoria slipped a plea for donations into a squid being loaned to the Smithsonian."

"Really? Which part of the squid?"

The younger woman frowns. "Can we please stick to business?"

A waiter heads their way. "I'll have a long black," calls Patiriella, and the waiter retreats. "Sorry. Anything out of La Trobe?"

"Nothing good,'" replies Austrochorema. "The School of Life Sciences got wound up. Long-contract staff are going into the new Department of Resources, Econometrics and Accountancy Development.'

"A fitting acronym," observes Patiriella. "I don't suppose they'll be offering anything on invertebrates."

"Hardly. Listen!" Austrochorema leans forward, suddenly animated, speaking in a fast whisper. "There's a plan out of Edith Cowan. Do you remember the Bogong Incident, when millions of moths invaded Parliament House in Canberra?"

The conversation is interrupted by the arrival of the coffee.

"Of course," replies Patiriella, when the waiter is out of earshot. "How could I forget? Insects in the newspapers for days, ANIC footage on the TV news."

"This is bigger. Breeding colonies have been established at secret locations near Albany and two more are planned for the Launceston area."

"What is it? Another moth?"

"We aren't to know. There are hints, though. Conventional poisons won't help. The only way to control these things will be with an attractant, a pheromone tailored to this one, genetically modified disrupter."

Patiriella sighs. "I don't know. Terrorism seems so...extreme."

"This isn't terrorism," enthuses Austrochorema. "It's direct action. The Commonwealth just needs to be reminded of the importance of zoological expertise. Pheromone traps will be activated when our demands are met: full restoration of zoology faculties and courses at universities across Australia, return of ABRS funding to CPI-indexed 2015 levels, guest spots for soil zoologists on the ABC-TV gardening program..."

"I know, I've read the manifesto. But can we trust the bastards?"

Austrochorema smirks. "They'll keep their promises this time. If they want the beaches to be safe."

Patiriella's eyes widen. "I've heard nothing about this! And I'm in Marine Section!"

The younger woman breathes gently on the candle between them. For a moment, the flame grows. "We have friends overseas, Patiriella."

(To be continued, unless the Decadal Plan reverses the trends. If not... luz.)

Bob Mesibov

Taxonomy 2028 Challenge: Let’s digitally image poorly known described species and undescribed species in an Australian Biodiversity Portal – the end-users perspective

by Volker W. Framenau (Perth)

I am an invertebrate scientist publishing taxonomic and systematic studies predominantly on spiders. I am also an environmental practitioner conducting invertebrate surveys in Western Australia trying to identify spiders from often poorly sampled, remote regions.

I am therefore as much a taxonomist as I am an end-user. I am familiar with the taxonomic literature of described species in my area of expertise (and some other invertebrate groups such as millipedes and ants) and have little problems to identify species that had a very recent taxonomic treatment and for which biodiversity and distribution data is readily available (i.e. through identifies specimens in collections published in the Atlas of Living Australia).

What I need, as expert end-user, is a system that helps me identify a species that is not properly illustrated (i.e. historically named, but with poor original description) and those that are undescribed.

As end-user trying to protect rare species, I don’t need a Linnaean name for this, but I need to know if a species is potentially rare or widespread, which determines if it is subject to an environmental assessment or not. In Western Australia, a species does not have to be named scientifically to be protected by the Wildlife Conservation Act.

Imagine, I could find images of all undescribed and poorly described species online, with diagnostic images, i.e. all pedipalps of male spiders in ventral view for a family or genus side-by-side? Apply the ‘retrolateral’ filter, and then I get them all in a different view for identification. Or images of heads of undescribed ants of a genus side by side? Impossible by 2028? Of course not!

Check out www.antweb.org  and you can find thousands of images of ants (described and undescribed, the latter with morphocodes), can filter by bioregion, taxonomy and morphological view. Or closer to home, check out the Barrow Island QIM (http://www.padil.gov.au/barrow-island/search?queryType=all) funded by Chevron Australia as part of its biosecurity efforts for its Gorgon Project, that illustrates in access of 2,000 terrestrial invertebrate species, many with morphospecies codes. I have used this resource excessively for identifications of spiders and ants in the nearby Pilbara. Imagine a Barrow Island QIM for the whole of Australia, just better!

This of course will not work for all taxa, some cannot be easily identified by images alone, but for many it will work, as long as species-specific images are being presented (here the Barrow Island QIM falls short, at least for spiders).

There are three main elements that need to be developed for this:

  1. The database structure and gallery type web-design with appropriate filters for images that are meta-tagged for these filters.
  2. An Australia-wide pseudotaxonomic/morphospecies framework for undescribed species with unique species identifiers. This can be modelled on the Linnaean system, i.e. it will require ‘morphotypes’ to fix a morphospecies.
  3. Expert curators for specific groups, possibly at state-level, that oversea the addition of new species.

Addition of new species will likely be managed at the state level, so let’s think this through for WA and spiders. There are approximately 900 described species in the state, our best estimates of the total number of species is probably three times as much (round it up to 3,000). For arguments sake, let’s assume that about half of the described species have been recently revised and can be identified based on published revisions. That leaves us with ca. 2,500 to be illustrated online for identification (however, no reason to not also include described species by using the published images, copyrights permitting). Many of these will occur in the neighbouring states or even Australia-wide (Australia-wide, about 3,800 spider species are described of an estimated 10,000+ species).

This number for WA spiders is just about as much as the Barrow Island Quim has been done since 2004! Not only is it possible, it has actually been done.

Let’s now assume, like Antweb, an online image catalog is being contributed to by the whole scientific community, overseen by expert curators to guarantee taxonomic consistency of the system? For example, if I as environmental consultant with expertise identification skill find a species and cannot find it online, I submit standard images and the specimen to the ‘curator’ who simply has to upload the images, establish a morphotype and add distribution data to the database (maybe by IBRA region?). In a well-established online Contents Management System (CMS) this may take all put 15 min per species. It’s almost like the Encyclopedia of Life for undescribed species. Once it is set up with a core number of species for each taxon, I would hopefully again momentum. Imagine then, that museum curators use the system to identify new accessions, database these and the respective distribution data would be available on the ALA (which by then allows listing of the established morphotypes).

We would move from species description to species registration, which, of course, would ultimately enormously facilitate future taxonomic revisions.

Of course there will be errors in the system, but a species is only a hypothesis after all

We won’t be able to scientifically describe all invertebrate species by 2028, but we can document a large proportion of these within 10 years!

Sally Fryar

I am a fungal taxonomist, specialising in the marine and freshwater fungi of Australia. These are mostly ascomycetes and their asexual forms.

I completed my PhD at Flinders University in 1997 on the taxonomy and ecology of wood decay fungi (basidiomycetes), examining indirect effects of multi-species interactions. In 1998 I moved to Hong Kong as a postdoctoral fellow at the University of Hong Kong where I was introduced to the fascinating world of freshwater and marine fungi under the supervision of Professor Kevin Hyde. My research took me to various peat swamp forests, mangroves and streams in Borneo where I was a visiting fellow at the Universiti Brunei Darussalam. 

The challenge with studying marine and freshwater fungi is that species descriptions are scattered throughout the literature, often in obscure, inaccessible journals and with poor illustrations. While taking a career break to have children, I spent 10 years gathering as much literature as possible on marine and freshwater fungi, putting together a database on worldwide records of each species along with their descriptions.

My aim is to provide thorough, consistent, understandable descriptions of marine and freshwater fungi of Australia along with clear illustrations and images so that non-specialists are able to identify these species.

I often find new species and genera and I am in the process of describing and publishing a number of these along with phylogenetic analyses based on molecular data.

I am an adjunct senior lecturer at Flinders University where I do some teaching and molecular work.

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) admin@ecansw.org.au 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.

Taxonomy 2028 Challenge: Recording Indigenous nomenclature

Australia’s first nomenclaturists were those who first settled country, and in doing so began to utilise our plants and animals for food, tools, shelter, medicines and ceremony. During the more than 50,000 years of living on and with the land, Indigenous people have developed a rich nomenclature for taxa used in these ways. In each language group, specific words are used for around 10% of plants in the area, sometimes with multiple words for one Western-accepted species when there are multiple uses or different life stages are used. With many language groups and many species across Australia, this is a very large body of knowledge.

With the historical and ongoing disruptions to traditional knowledge, languages and cultural activities, many of these words, and their connections to knowledge, are endangered. This loss would be a tragedy, particularly as it would foreclose important connections to country for present and future generations.

I propose that by 2028, as part of the decadal plan, we will have implemented a national mechanism for recording these names for all language groups in Australia, in close and meaningful collaboration with their custodians and the communities for whom they are meaningful. This will be done in ways that are fully cognizant of the potential for cross-cultural miscommunication in any endeavour like this. Importantly, it will be done with due respect for the deep knowledge tradition that’s being recorded, and in a way that’s most appropriate for the needs of communities and of Indigenous people, rather than in ways that are most convenient for us. The prime goal is to record words for the language-speakers, with any advantages to our own community secondary.

 Specifically, this program will not:

  • Send out inexperienced people to record names as a shallow, one-off exercise – this would be disrespectful;
  • Record names in ways and on platforms that are convenient for us but of little use to communities – this would be useless;
  • Be rolled out with minimal consultation from communities themselves – this would not generate trust;
  • Be rolled out as a one-size-fits-all program – this would be ineffective.

 The program could work like this:

  1. A strategic assessment will be made, in collaboration with linguistic and cultural experts, of language groups throughout Australia that still have strong cultural knowledge of plant and animal names, but with the knowledge endangered by imminent loss of cultural custodians and first-language speakers;
  2. In each state or region, one or more skilled, retired botanists be identified and approached, to take part in the program;
  3. After training and with appropriate support, the botanists will build relationships with their counterparts in communities, and seek community views on the need to record names, and the most appropriate ways to do this
  4. During repeat visits, with support from linguists contracted as part of the program, names will be recorded in as simple and straightforward a way as possible
  5. Names will be provided back to communities in whatever format they consider most useful, as well as recorded in national databases to ensure they are safe in the medium to long term.

{Thanks very much to Glenn Whiteman, NT Herbarium, for useful discussions on this idea.}

Taxonomy 2028 Challenge: Knowing the origins of the Australian biota

By the year 2028 we will have compiled a database of information on the origin of Australia’s biota. This database will detail the area of origin for every genus within Australia, and the timing of its original arrival in Australia.

Initially, the database could be compiled from published phylogenetic data, eventually being replaced with phylogenetic information which has been analysed in a consistent methodology.  This goal could be achieved through the targeted sampling and molecular sequencing of lineages that have distributions spanning Australia and neighbouring landmasses (Southeast Asia, the Pacific, Antarctica, etc.) and then of lineages with more cosmopolitan distributions. This database will establish an understanding of the unique and varied evolutionary history of the Australian biota, determining which lineages are ancient Gondwanan relicts and more recent immigrants, as well as identifying spatio-temporal patterns of immigration, emigration and diversification in the history of the assembly of the Australian biota. It would also provide an invaluable resource for the advancement of research in Australian biogeography, biogeography theory, invasive species ecology, geology, palaeontology, evolutionary theory, trait evolution and ecology and for informing conservation priorities and strategies.

This phylogenetic information could be integrated into the ALA platform through the addition of interactive phylogenies on each taxon’s ALA page. Clicking on nodes of each phylogeny could show biogeographic, morphological trait and divergence age data for that taxon. Publication of phylogenetic information in such an interactive way would engage the public and raise understanding of the significance of the unique evolutionary histories of groups within the Australian biota. It would provide an alternative visual mechanism for exploring taxa by placing them in a phylogenetic context. It would also provide a platform through which evolutionary concepts are made accessible for lay people, encouraging the the exploration of integrative evolutionary questions and engaging them with concepts in systematics, evolution and taxonomy.

Lizzy Joyce
PhD Candidate - Australian Tropical Herbarium & James Cook University