Linneaus and the Ackronyme project (satire)

The following fragment was pieced together from notes written by Jakob Rindler and only recently discovered in a shed at the Liverpool Botanic Garden. It is thought the notes were acquired, together with many other documents and specimens from the Linneaus estate, by Sir James Smith in 1783.

Although not an "apostle" student of Linneaus, Rindler was a summertime house-guest at the Linneaus farm at Hammarby, now a suburb of Uppsala. In the early 1760s a botanic garden was planted at Hammarby, and in several letters from Linneaus, Rindler is mentioned as a young and enthusiastic botanist who was of great help in tending the Hammarby plantings.

Judging from internal evidence, the meeting reported by Rindler probably took place in 1764 or 1765. It is curious that Linneaus never mentioned the interview with Sir Edward Ackronyme in later correspondence.

I have taken the liberty of translating Rindler's notes into reasonably modern English.

***

The master was visited today by an English gentleman, Sir Edward Ackronyme, who carried letters of introduction from Earl Macclesfield [Royal Society of London] and Philip Miller [Chelsea Physic Garden].

The gentleman appeared to be very intelligent and spoke both Swedish and Latin. He praised the master's many contributions to knowledge. He said the master was a scientific colossus of the age and respected by all who knew the master's work. He said famam extendere factis [through our deeds we extend our fame] on the master's coat-of-arms was an inspiration to all natural philosophers.

The gentleman said he had read the second edition of the master's Species Plantarum, and had observed that it was supplemented with corrections to the text and with additional notes. The gentleman had a proposal to make in connection with this.

He proceeded to describe correctly and in interesting detail how Species Plantarum had been written and published, which greatly surprised the master. The gentleman said that his proposal did not, however, concern the production of scholarly books, but instead the use and diffusion of the knowledge in the books.

The gentleman explained that he and others had invented a method for reproducing the master's descriptions, using a large number of scribes and a new means of printing which was very swift and not expensive. The words of the master concerning individual species would be copied out by the scribes and printed in large numbers as separata.

The separata might then be sold more widely than the Species Plantarum. The gentleman gave an example, in which a philosopher in Virginia could acquire the descriptions of plants and animals native to Virginia. The two volumes of Species Plantarum contained many descriptions of plants and animals which were not found in Virginia and might not be of interest to philosophers there. The separata pertaining to Virginia, or to any other place, could be gathered up and placed in a pouch.

The gentleman said that if a purchaser was only interested in Pisces in the master's Systema Naturae, then the separata for Pisces could be gathered together for the purchaser.

The master observed that this was very clever. At this point the gentleman asked the master if the master could see value in this method of diffusion of knowledge. The master replied that it indeed had value.

The gentleman was pleased to hear this, and said that he had also received encouraging replies to this question from other philosophers. The gentleman had spoken directly to Dr Scopoli in Idrija and to other philosophers who had published works of natural history. Each had agreed that there was much merit in the idea of spreading more widely their descriptions and classifications.

The gentleman said that if the master wished to make a correction or addition to any one of his species, that information could be sent to the scribes, who would make the correction or addition in a new separatum. The new separatum would be sent to all those who had purchased an uncorrected version. The gentleman said this was possible because the cost of printing separata by the new method was hardly of consequence, and the number printed could be one or a thousand.

The gentleman produced a small sheet of paper and gave it to the master. On the paper had been printed a description from Species Plantarum of a species, and beneath the description was the name of the master. Beneath the name was an addition the master had made to the description, and this too was subscribed with the name of the master. At the bottom of the paper was a date, which the gentleman said was the date on which the separatum had been printed.

The master again praised the cleverness of the idea of separata. He begged leave to ask questions, and the gentleman agreed.

The master asked first whether there would be a cost to himself in the production of separata. The gentleman said there would be no cost to the master or to other philosophers. The work of the scribes and the printing of separata would have royal patronage. He was not presently permitted to name the royal courts from which the patronage would come.

The master expressed surprise to hear that more than one kingdom was offering to assist. The gentleman explained that the idea of diffusion of knowledge through separata was not his alone. He was one of a group of interested gentlemen distributed throughout Europe. Each member of the group made a particular contribution. His own contribution related to printing, regarding which he could modestly admit to having acquired a degree of expertise.

The group of gentlemen met on occasions in various European cities. Their next meeting would take place in Paris. They would consider the question of whether separata should be printed only in Latin, or also in various modern languages, and if the latter, whether one separatum should be printed in more than one language. The gentleman said there were arguments for and arguments against, and the question might have to be resolved at a later meeting in another city.

Now the master asked, whether the patronage enjoyed by the gentlemen could be extended to natural philosophers and their students. The gentleman apologised because he did not think it possible. The production and distribution of separata was a matter of diffusion of knowledge, not of the generation of knowledge. The gentleman said that he and the other gentlemen greatly appreciated the work done by the master and other natural philosophers. It was the humble role of the gentleman and his associates to spread that knowledge and to make it more useful.

At this the master became upset and spoke severely. He said he worked day and night on the investigation of a science that a thousand men will not be able to complete, to say nothing of the time he squandered every day on scientific correspondence, while the gentleman and his colleagues can constantly enjoy the amenities of life. The master said that separata may indeed be of value, but they add nothing at all to knowledge, and that the gaining of knowledge was his constant goal.

The gentleman said that he hoped nothing he had said had angered the master, and that he had one more question to ask. While the scribes were skilled and diligent, it occasionally happened that a copying error was made when producing the separata. The gentleman asked whether the master would be willing to examine drafts of separata before they were printed. He explained that he and his associates were not natural philosophers, and that natural philosophers would be the persons best able to locate and correct any errors.

This concluded the meeting with the gentleman. The master did not reply to the last question, but wished the gentleman a good day, and turned to me and said that there was work to be done in the garden.

- Bob Mesibov


A Dream of Invertebrate Utopia

I am continually impressed by the diversity of views and proposals for the Decadal Plan coming from different parts of the taxonomic community in Australia.  The project has brought some quite disparate communities together to discuss common goals as they have never done before.  

More and more I see the broader taxonomic community divided into two camps, those that are working on less diverse and relatively well-resourced taxonomic groups, and those that are working on very diverse but relatively poorly resourced groups.  Taxonomic groups don't switch between these camps, it is destiny, so resourcing differences become magnified and accentuated over generations and centuries.  

There has now be come such a huge divide between the "haves" and the "have-nots" that it has become a challenge in and of itself.  Much as rising income disparity is now seen as a major challenge for western democracies.  The differences between the "haves" and "have nots" are now so profound that priorities and solutions are often different depending on the camp the particular idea originated in.  I think it is also important to acknowledge the illogical, emotionally-driven and innately human process by which taxonomic groups end up in the "have" or "have not" category.  You could logically conclude that resources available to western science for taxonomy have only ever really scaled to the small groups of obvious macroscopic organisms, such as vertebrates and others, together representing just 5% or so of species.

The large and random differences in our taxonomic knowledge of different groups has a negative impact on biology generally.  It hampers any study that attempts to examine communities or ecosystems from a process or systems perspective.  We know some macroscopic species well, but are ignorant of species to which they are intimately connected and critically dependent, simply because those connected species happen to belong to one or more "have not" taxonomic groups.  

I wrote this little satirical piece of whimsy that imagined one of the "have not" groups, the weevils (Curculionoidea: Coleoptera), historically had been included as one of the "have" groups.  Hopefully it will cast some light on the different resource levels available to the "haves" and "have nots". I think we need to fully appreciate the challenges these institutional and resourcing differences have stamped on our communities before we can move forward together.

 

A Dream of Invertebrate Utopia

With satirical apologies to George Orwell’s Animal Farm

 

I don’t know how it all started, perhaps back in the 1700’s naturalists imagined that there were as many weevils as all other animals and plants, but that is not really my concern.  Quibble with the numbers, we now estimate that there are around 20,000-25,000 weevil species here, and they make up about 5% of Australia’s biota, in other words we have about as many weevil species as butterflies and moths, or plants. As we intensify our focus, we are discovering more and more new Australian weevil species.

Our scientific community studies weevils (Curculionoidea) because they are extremely diverse and occur all over Australia.  They are ecologically important, some species are pests, others are biosecurity threats and yet more are biological control agents.  You can walk into any Australian environment from the wet rainforests to the arid inland, and find a unique community of weevils.  Weevils first appear in the fossil record 160 million years ago, and Australia is home to some of the early branching lineages.  Our weevil fauna includes giant Eurhamphus that feed exclusively on southern hemisphere pines. Weevils are some of the most damaging pest of timber and stored grain, so understanding weevils is vitally important for our economy. Besides that, they are cool! 

Right back at the beginnings of the development of each state, and in the commonwealth, we set up large institutions devoted to the study of weevils, called Weevilariums.  These institutions are going strong today each with 20-30 paid staff beavering away studying the taxonomy, biogeography and phylogeny of Australia’s weevils.  And the good news is we are getting ever so close to finishing the job!

Each state Weevilarium has worked hard over more than a century on the taxonomy of the weevils from their state.  You really can gather some momentum with that sort of workforce over that many generations.  First we produced hard copy book series called Weevils of NSW, etc.  Turns out that we worked so hard in each state we had described many species more than once - especially those that cross state boundaries.  But that doesn’t matter-why just deliver when you can overdeliver, I say!  Now we are putting all the weevil treatments together electronically with commonwealth funding, and we really are going to have to sort out those overlaps once and for all.  Kind of a victory lap. Thank goodness for forward planning!

The Australian Weevilariums are incredibly well connected globally, and we even have set up a bespoke international code of nomenclature just for weevils!  Nothing like a specialist tool for a specialized job.  Now the codes for weevils and the remaining biota have diverged quite a bit, like Spanish and Portugese.  Sometimes if you know one you can read bits of the other, but if people are talking nomenclature the two systems are incoherent!

Thanks to commonwealth weevil digitization funds, we now have almost all 10 million weevil specimens in the Weevilariums databased, we have developed great lists of all the weevil species in each state.  We are making great headway in imaging all weevil type specimens.  We can now map and model weevil distributions with great accuracy, and search for areas of endemism and high species diversity with great sophistication.  We have very detailed information on weevil abundance, and have listed many species as rare and threatened with the appropriate authorities.  Weevil conservation biology is now an expanding field, generating large amounts of external income for the community. We even had a Weevil Liason Officer position at the Natural History Museum in London for more than 50 years sorting out the curly issues to do with weevil type specimens in European museums.

We now have a great self-sustaining system with academics at universities studying weevil taxonomy, teaching courses in weevil taxonomy and biology, churning out PhD graduates that can take positions at the Weevilariums. Our Australian Systematic Weevil Society meetings are attended by more than one hundred engaged professionals and students each year. We even have our own special weevil subcommittee to assess and recommend commonwealth funds for weevil taxonomy.  Nothing like having real experts making the big decisions! Probably something like 40% of the resources available for taxonomy in Australia are now devoted to weevils. 

Weevil larvae eat plants, but we are so busy studying weevils that we rarely take samples of the plants they are feeding on.  Early on in my career I took a few samples to the grumpy old retired guy who passes for our Australian plant taxonomy expert.  I had to keep badgering him for the ID’s, and after a few months he said none of the plants were described anyway.  Bit of a waste of time, but I did at least give him a chance!

We even have a number of weevil egg banks dotted around the country.  Weevil eggs are in demand because they are used in biological control programs both here and overseas.  In Canberra we have an egg bank for small weevils, a separate egg bank for big weevils, and there is another one for weevil eggs of all sizes just outside of Sydney.  We are planning brand new facilities for the two Canberra egg banks.  You can’t have enough new weevil egg banks, I say!

Looking back over the field it is clear that the high level of investment in weevil taxonomy has given us a huge head start in comparison to the taxonomic knowledge of almost every other group.  I suppose we really could learn more about weevils place in ecosystems if we knew a little more about the plants they feed on, for example.  It would also help with their conservation as well.  I guess weevils are really a boutique slice (5%) of our biodiversity. But what a great example we have provided for the communities studying other taxonomic groups to follow!

Our real focus these days is the tiny (0.5-1.0 mm long) black and brown weevils.  I don’t know what we will do once we have finished the taxonomy of Australia’s weevils.  Maybe move on to the Cerambycidae (longicorn beetles), another hugely diverse, ecologically important, related group.  But there is a lot to be said for just sticking to weevils.  With grand institutions to fill, new technologies and theories to apply, we may never finish!

   

Then I woke up, and reality dawned on me.  There are no Weevilariums in Australia or the world.  There is one professional weevil taxonomist working here on our fauna of 20,000-25,000 species.  Our weevil taxonomist is entirely supported in the Australian National Insect Collection by a generous bequest of millions of dollars from a philanthropist.  Without this gift there would be precisely no weevil taxonomists in Australia. Our weevil taxonomist is expected to revise a large chunk of the Australian weevil fauna during his career, as well as provide continuing advice in biosecurity and pest management.

With this level of investment we will never know the weevil fauna of Australia in any coherent time frame, and we invest even less in the study of almost every other comparably-sized invertebrate group.  I have chosen weevils as the subject of this satirical piece for convenience, any number of other comparable invertebrate groups could substitute.

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.

Roger Shivas

I am a mycologist and plant pathologist. My research interests are the systematics of fungi, especially those that cause diseases of plants and insects.

Currently I have two jobs, one as curator of the Queensland Plant Pathology Herbarium, Department of Agriculture and Fisheries as well as a professor (mycology) at the University of Southern Queensland.

Further information about the work that my colleagues and I do can be found at http://collections.daff.qld.gov.au

Dr Roger Shivas

Principal Plant Pathologist
Biosecurity Queensland
Department of Agriculture and Fisheries
GPO Box 267, Brisbane, Qld 4001

Tel. 61 7 3708 8478
Email: roger.shivas@daf.qld.gov.au

 

What about the passionate?

You've probably noticed: taxonomists aren't quite like other scientists.

They have a powerful fascination, if not an embarrassingly strong affection, for "their" groups of organisms. As the TV professionals say, they're great talent, because they talk excitedly on camera about their favourite taxa.

They study particular taxa for decades, becoming the experts — the "names" — to whom the biosecurity and agriculture sectors turn for advice.

They get better at what they do as time goes on. Taxonomists hit their stride in late career, peaking in their 50s and 60s and often publishing valuable papers in their 70s and 80s.

They can be relatively cheap to run. Unless they're focused on molecular systematics, the annual costs for their taxonomic work might amount to just a few thousand dollars.

They don't require a lot of formal training. Some of Australia's best taxonomists are self-taught in their specialty.

They can communicate with the public directly about ideas the public already understands: "species", "discovery", "natural habitats", "invasive organisms". Only rarely do taxonomists need a professional science writer to background and explain what they've done.

Granted all this, previous calls for more public support for taxonomy in Australia seem a bit misdirected.

There's the call for more training money in Australia's universities, which gave up teaching taxonomy long ago. Instead the universities turn out PhDs with only the dimmest understanding of the maths behind the sophisticated phylogeny-guessing software they've relied on, and a similarly limited understanding of their study taxon's biology. The door opens, the new PhDs leave and compete with all the other science PhDs for work, leaving behind an interest in the taxa that helped them get a degree.

There's the call for increased infrastructure spending on museums and herbaria, which is great, because taxonomists depend on collections. But if an increased collections spend isn't paralleled by increased taxonomic work in those collections, what's the point? Without more curators and supported visitors, museum managers are justified in asking "Why do you need more than one specimen of each species?" and "How is any of this bringing more people through our doors?"

There's the call for more IT spending to aggregate more collection and other species-tied data, and to put those data at the fingertips of... umm, somebody... with a browser. Who will then spend days cleaning the downloaded data because the IT funding included not one brass razoo for data cleaning at source (disclaimer: I'm a data auditor as well as a taxonomist).

What's missing from these calls? Any mention of the people we need more of, those passionate taxonomists.

Here are four ways those people could be encouraged and supported:

(1) Find them and train them: "We're looking for people who are absolutely fascinated with particular Australian life-forms, and we'll back your passion with taxonomic training. You may not get a career out of this, but we'll give you the tools for a lifetime of satisfying study and of contributions to knowledge of the Australian biota."

(2) Get the collections to reach out. Ensure that museums and herbaria have enough money to host taxonomist volunteers, and to sponsor short-term visits by specialists, including non-professionals.

(3) Reward productive taxonomic work. How about ABRS offering up to 50 $5000 annual grants per annum (up to $250 000 total) to currently publishing taxonomists, renewed every year? The money could be used for collection visits, field work, publishing fees, conference attendance and project-tied costs such as sequencing and SEM work. Unaffiliated and retired specialists would welcome even this small drip-feeding of taxonomic support. The risk per grant (the risk that the money is wasted) is trivial and easily minimised by cancelling payment if there's no evidence that productive taxonomic work was done in the preceding year.

(4) Pay for mentoring. There aren't any succession plans in Australian taxonomy, despite the fact that for every specialist there are dozens of non-specialists with an existing or potential interest in working with what could otherwise become an orphan group. We know those potential mentorees exist: the BowerBird project has brought hundreds of keen non-professionals out of the woodwork. Why not directly support the transfer of specialist knowledge, with travel grants for joint collection visits and field trips?

OK, it's obvious. I don't see taxonomy fitting entirely within an academic framework, which is how many taxonomy promoters want governments and other funding sources to see it. Instead I see taxonomy distributed widely within the Australian community, with weekend, holiday and retired collectors and enthusiasts being part of a broad collaborative effort. That's probably because I'm goal-focused. I want to see increased taxonomic effort in Australia, and that's not the same as an increased number of professional taxonomists.

- Bob Mesibov

Bob Mesibov

Bob Mesibov

I'm retired and I study millipedes.

Since 2002 (just before I retired) I've described or redescribed about 200 Australian millipede species. My Millipedes of Australia website is a resource for taxonomists and offers more than 14000 vetted locality records for named species as downloadable TSVs and KMLs.

In 43 years of collecting in Australia I've visited ca 3200 unique localities and deposited thousands of millipede specimens in museums in New South Wales, Queensland, Tasmania and Victoria.

I'm also a coder and data auditor, and spend a lot of my time happily working on the Linux command line.

For more about me and my Web resources, please visit polydesmida.info.


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 (andrew.taylor@dpird.wa.gov.au)


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:

https://www.nsf.gov/funding/pgm_summ.jsp?pims_id=5451

References

Doyle JJ (1992) Gene trees and species trees: Molecular systematics as one-character taxonomy. Syst. Bot. 17: 144-163.

Kiss L (2012) Limits of nuclear ribosomal DNA internal transcribed spacer (ITS) sequences as species barcodes for Fungi. Proc Natl Acad Sci USA 109: E1811.

Schoch CL, et al. (2012) Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi. Proc Natl Acad Sci USA 109: 6241-6246.