Bushwalk, lunch, sequence genome.

Today, if I wanted, I could go on a bushwalk and sequence a genome.

That might not sound very remarkable as my joints freely bend, I can see, and I don’t mind getting wet, muddy, sweaty and molested by insects, or my skin breached by armed plants and burned by the sun. In fact I sort of enjoy all of those things; well, not individually and in isolation (no, I do not have a dungeon...), but as part of the rich experiential symphony of life in the great outdoors. And being a taxonomist, field work is actually part of my job. I describe life, not in epic poetry, or stunning photography, but in scientific papers that are by some measures, a bit dour. I describe new species – taking the raw, unvarnished thrill that the discovery of an organism unknown to science elicits, and turning it into a scientific manuscript reporting in methodical, formal terms the characteristics of that new organism and giving it a scientific name such that that species becomes available for science and society.

And the life that I describe is found in the bush, and not uncommonly in a country like Australia where about 200 new plant species are described by taxonomists like me every year. THat's an extraordinary figure - 200 new plants a year - and even more startling when you realise it is ten percent of the world’s total. For a taxonomist, Australia really is the lucky country – so many species, and so much bush in which to walk and discover. And with so many new species of plants turning up, discovering a new one is often rather unremarkable.

It is also rather unremarkable that today, I can sequence a genome. I mean unremarkable not in the sense that it is unworthy of awe (because sequencing genomes is awesome), but unremarkable in the sense that everybody, at least in biology and medicine, is doing it. But this socialisation of genomics is very recent. The technology for reading genomes - the sequence of nucleotide bases (A, C, G, T), or ‘letters’ that inscribe the language of life, DNA – has advanced in such a mad headlong rush that by the time the sun set on 2015 it became possible to do in a weekend for less than $2000 something that in the 1990’s took more than a decade and at least half a billion dollars. This extraordinary efficiency gain has outstripped even that most celebrated example of technological advance, the decline in cost of computing power represented by Moore’s Law. This law describes the observation that the number of semiconductors that can be packed onto a silicon chip roughly doubles each year, which roughly translates to a halving of the cost of computing power each 18 months because of the additional savings made through chip manufacturing advances. Because of Moore’s Law my new mobile phone is more powerful in computing terms than my ten year old desktop machine, now unloved and gathering dust under the desk and accidentally assaulted by the toe of my leather winklepickers whenever I yawn and stretch. But the rate of advance in DNA sequencing technology blows Moore’s Law away. It wasn’t always the case. Prior to 2007 the cost of sequencing genomes was falling in line with that of computing power, meaning it could be roughly described by Moore’s Law. Thereafter however, things got really interesting. The cost fell catastrophically because new, more efficient sequencing technologies came online and in the years following drove cost reductions so spectacular that in the time it took computing power to become about 15 times cheaper, sequencing genomes became about 10,000 times cheaper. It’s hard to underestimate the impact this has had on biology and medicine, which are being revolutionised by access to genome data. Even taxonomists like me, working in small labs on small budgets, can now sequence genomes. It is fast becoming a routine, unremarkable, part of the work that we do.

But what is truly remarkable – transformative, disruptive, revolutionary ... whatever – is that it is now technically possible to go for a bushwalk and sequence a genome at the same time and in the same place. I’ll let that sink in.... as a scientist, I am now able to carry all the equipment necessary to sequence a genome into the field with me and sequence the genome of an organism I collect on the spot. Recently, Oxford Nanopore, a biotechnology company based in Oxford, UK, started selling a new DNA sequencing device, the minION. This device is smaller than a mobile phone, plugs into the USB port of a laptop computer, costs about $1000, and can sequence a bacterial genome between lunch and tea. The company is not the only one producing genome sequencing machines, but it is pretty much the only one whose signature device does not require a large, sturdy benchtop to hold it up, a specialist technician to run it, and hundreds of thousands of dollars of cold hard cash to purchase it. This is truly disruptive technology, which is really saying something in the context of a field that has been in constant disruption for nearly ten years. Its a game changer. While some technical details of the device need improvement (its accuracy is still unacceptable for many applications) this early generation product brings us within sight of the day when genome sequencers will be as much part of the field biologist’s toolkit as a GPS unit is now. 

Will this day come? I think so. In fact it will come pretty soon for me. I am hoping to take one with me in March 2017 when I participate in a species discovery expedition on Cape York Peninsula in the remote northeast of Australia. As part of the multiyear BushBlitz species discovery partnership, I will be helping survey Quinkan country, a sandstone landscape renowned for its extensive Aboriginal rock art near the small town of Laura. I’m astounded that I will witness scientists bring samples in from the field that they think may represent species new to science, extract the DNA and offer a small drop to the sequencer who in a few hours will deliver its verdict, confirming or denying their hunches. Imagine the field efficiency gains this will drive: “Jenny, the DNA of that one doesn’t match anything known so very probably a new species. See if you can get more specimens tomorrow.”, or “Boring, just a malnourished and malformed individual of a well known species, don’t bother with any more of that one”. The efficiency gains are important, but rather prosaic. What is deeply inspiring is the utter collapse of the barriers to genome knowledge. A species discovered in the time of the so-called father of taxonomy, Carl von Linne (a.k.a Linnaeus, 1707-1778) would have to wait around 250 years to have its genome revealed. A species discovered today need only wait a few hours...

And what kind of world will this technology usher in for taxonomists and other biologists? What will we do when we are as blase about sequencing whole genomes in the field as we are about cooking our camp dinner? Its hard to fully imagine, but here are a couple of possibilities beyond the obvious “What species is it, what is its population genetic structure and who is it related to phylogenetically?”:

·      Real time species tracking: by discovering DNA discharged downstream by defoliation, defecation or death, field biologists could determine the presence of species of interest upstream and adjust survey plans accordingly.

·      Real time population diversity assessment: by comparing sequences of samples from across the local range of a species one day, researchers may be able to pinpoint the best areas for the following day’s sampling or survey.

This new world is one of great promise and to maximise its opportunities, I want some bright spark to build me a mobile genome lab. I’m thinking a capable 4WD with a raised roof and internally fitted out with a bench, a portable electricity generator and fridge, and the small lab items needed for extracting and purifying DNA to load into the sequencer. And if I pitch this vehicle as the ‘Genome-o-Rover’ then I might just attract the attention and sponsorship dollars of a certain vehicle manufacturer that shall remain nameless. I would volunteer my time to travel the nation, sequencing genomes in situ in the most remote and inhospitable locations, and dropping in to schools and communities along the way to talk about what I am doing. And if I do my job well, I just might find myself a couple of decades from now passing the baton (or sequencer) to some bright eyed graduate who asked me a probing question about plant DNA in the outback 20 years prior.

Who will join me?

The eFlora of Australia

The Flora of Australia is a standard reference work for Australian vascular plants, providing standard Flora treatments (descriptions, nomenclature, keys, distributions) etc for all covered families, genera and species. The first taxonomic volume of the series was published in 1982 (Volume 8, Lecythidales to Batales). Since then, 25 vascular plant volumes (of a planned 50 volumes) have been published, covering c. 12,000 taxa (including two volumes dealing with Australia’s island territories).

In 2014, a decision was made to discontinue hardcopy publication of the Flora of Australia, and to move instead to a web-based platform. This has obvious advantages: the hardcopy volumes are mostly out-of-print and many are out-of-date, and transitioning to a web platform will allow quicker publication, easier management and updates, and a wider reach to a more diverse audience.

The Atlas of Living Australia (ALA) is creating a new web-based platform for building, managing and maintaining eFloras, including the new eFlora of Australia. Work has commenced to move existing taxonomic treatments from the Flora of Australia to the new platform, including both published and unpublished treatments. Under the editorial management of the Australian Biological Resources Study (ABRS) and supported by an Editorial Committee including representatives from the Council of Heads of Australasian Herbaria (CHAH) and the Australian Systematic Botany Society, the new eFlora platform will allow the eFlora of Australia to be managed and edited using a new, decentralised, community-wide model.

The eFlora of Australia and ALA eFlora platform are not yet ready for public release, but work is progressing well and a release in 2017 is anticipated. Watch this space for more...

Kevin Thiele

I'm a systematist and taxonomist, a past Director of the Western Australian Herbarium, past Chair of the Council of Heads of Australasian Herbaria, and currently an independent scientist trading under the name Eubio Consulting. After a PhD at Melbourne University, where I worked on an early cladistic analysis of Banksia, I took up a post-doctoral position under Judy West at the Australian National Herbarium, working on a Flora of Australia treatment of Rhamnaceae. My wife and I then eschewed gainful employ and took our small but growing family to a small, off-grid farmlet in a remote and utterly beautiful part of East Gippsland, where we lived and worked for 12 years growing vegetables, raising children, helping out at the local school, and continuing our research work into, amongst other things, the conservation of grassy box woodlands, the taxonomy of Viola, and development of the Lucid suite of software tools. Another major change of lifestyle, occasioned by the children reaching high school age, saw us move to Perth and, for me, the position leading the WA Herbarium for a decade. My current work includes teaching systematics and evolution at the University of Western Australia, the taxonomy of Hibbertia in Western Australia, building an identification key to all Australian flowering plants, and working towards the Decadal Plan for Biosystematics and Taxonomy in Australasia.

The Decadal Plan for Biosystematics and Taxonomy in Australasia

Biosystematics and taxonomy – the disciplines that name, classify and determine the evolutionary relationships of all living organisms – are foundational sciences. Many other disciplines and activities in biology, including ecology, conservation, genetics, biosecurity, and medicine to name just a few, depend on the framework knowledge, nomenclature, and understanding of organisms provided by biosystematics and taxonomy.

Despite this, funding and infrastructure investment in biosystematics and taxonomy are declining. Biosystematics and taxonomy often “fly under the radar” of high-impact science, and their foundational role is often unacknowledged.

The current low base of funding for biosystematics and taxonomy in Australasia means that, in effect, we are drawing on previous investment in this sector (the past two centuries of endeavour and effort to understand and document the flora and fauna of Australasia) but no longer adequately investing in the future (building capacity and knowledge of the many currently known or undiscovered species that have not yet been named, and keeping our knowledge scientifically updated and current). This lack of investment is of particular concern in Australasia, one of very few areas of mega-biodiversity in the world.

Inadequate investment in this sector leads to negative consequences, and often substantial economic costs, for conservation, biosecurity, and sustainable development and growth. Important species will become extinct before they are recognised and their conservation needs and potential ecological and economic roles understood. Emerging biosecurity threats will be recognised too late, compromising early responses and leading to inadequate control measures and increased mitigation costs. These impacts in turn will compromise sustainable development and reduce our ability to minimise the effects of the current global wave of extinctions.

This project seeks to turn this situation around. Led by a core group of leading taxonomists and biosystematists, it centres on developing a Decadal Plan for the scientific discipline of biosystematics and taxonomy in Australasia that will:

  • document current opportunities and risks in the sector;
  • provide a forward-looking vision and roadmap for the discipline, including its impacts on and benefits for biodiversity, society and the economy;
  • provide a detailed investment plan for the next decade; and
  • initiate steps toward implementing the plan through engagement with the sector and its stakeholders.

Decadal Plans have been developed for a number of sectors in Australian science by the Australian Academy of Science - a listing of these can be obtained here

The Decadal Plan for Biosystematics and Taxonomy in Australasia will be a starting point for effecting a real change in the status, visibility and funding of biosystematics and taxonomy in Australasia.

Read the brochure below for more detail

Why I reckon there's never been a better time to be an Australian ..... botanist

We've heard from our politicians recently that there's never been a more exciting time to be an Australian. That may or may not be the case. But, here's a story that shows why I reckon there's never been a better time to be an Australian botanist.

Hibbertia huegelii is one of the most common species of Hibbertia in Western Australia. Every botanist, wildflower enthusiast and naturalist knows it. It's common from around Morawa to south of Perth. At least - that's what we thought...

A few weeks ago I realised that I needed to look into H. huegelii when I found that I couldn't figure out exactly how it differs from another, less well-known species in WA, H. pachyrrhiza

I assumed that a quick check through the specimens in the Western Australian Herbarium would sort this out. Pulling out a packet each of H. huegelii and H. pachyrrhiza (while I was at the Herbarium waiting for a student, to head out into the field to collect Banksia specimens for an Honours project), this at first seemed straightforward. The specimens of H. pachyrrhiza I looked at had obtuse leaves with a broad, shallow groove running down the midline, while the first few specimens of H. huegelii had very acute leaves with a distinct, narrow, deep groove along the leaf midline. This worked OK for a while - until I started coming across specimens in the H. huegelii packet that looked a lot like the ones in the H. pachyrrhiza packet. We all know how often something that starts out looking simple quickly becomes less so when you look at too many specimens. I left the Herbarium realising that I'd need to spend more time in the field during the coming spring trying to nut these species out.

An hour later, my student and I with some wonderful colleagues were in Wandoo National Park, at the first site where we were to collect our target Banksia. Getting out of the car, the first plant I saw was H. huegelii. Checking, I noted that it had obtuse leaves with no distinct groove. A metre or so away was another plant of H. huegelii ... that's interesting - this one had acute leaves with a distinct groove. A quick 50-metre walk through the area revealed dozens more plants - and all fell into one of two distinct groups based on these leaf characters. We happened to be in the middle of a mixed population of two distinctly different morphotypes.

That evening (after a successful Banksia field trip) I decided to quickly check to see which of these two morphotypes matched the type of H. huegelii. Global Plants answered that - I searched for the type (scanned from the Naturhistorisches Museum in Vienna) and zoomed into the specimen. It matched, without a doubt, the obtuse-leaved plants. Next step was to check for synonyms of H. huegelii on the Australian Plant Census and in old literature on the Biodiversity Heritage Library. These showed that another name, Candollea striata, had been synonymised with H. huegelii by Bentham in Flora Australiensis. Back to Global Plants, bring up the type of C. striata - this one in Paris - and there were the acute leaves and narrow groove of the other morphotype, as clear as day. It was looking very much like two species rather than one.

The acid test in situations like these is usually to go back into the herbarium. The Western Australian Herbarium holds over 270 specimens of H. huegelii. The next morning I worked through all of these, to see if the difference would hold up. It did - I was able to assign every specimen unambiguously to one or other of the two forms. Over 200 of the specimens matched Candollea striata while nearly 70 specimens matched H. huegelii sensu stricto.

But what of H. pachyrrhiza, one of the species where this story started? This had always seemed more geographically restricted than H. huegelii (as we used to understand it), to the Darling Range just east of Perth between Bindoon and Jarrahdale. Now that I had split H. huegelii into true H. huegelii and C. striata, the next step was to figure out their respective distributions. Scanning the specimen barcodes, I extracted specimen georeferences from the Herbarium database, and popped them into Google Earth to map the distributions. This immediately showed that true H. huegelii and H. pachyrrhiza were almost identically distributed. Having removed C. striata from H. huegelii, they were also morphologically suspiciously similar.

A quick check back at the Biodiversity Heritage Library showed that the original author of H. pachyrrhiza (the German botanist Ernst Steudel) noted that the plant was distinctive in having a thick taproot and numerous short, erect stems with hairy leaves; the specimens at the herbarium bore this out. But - this is exactly what would be expected in fire regrowth. A bit more fieldwork quickly solved the mystery - H. pachyrrhiza is merely post-fire regrowth of H. huegelii

The taxonomic outcome of all this will be a quick paper, to be published in the Western Australian Herbarium's journal Nuytsia, combining C. striata into Hibbertia (as H. striata) and sinking H. pachyrrhiza into a recircumscribed H. huegelii. A small mystery, and an understandable mistake made 150 years ago, solved.

So why is it so great being a botanist? First is the privilege of being able to discover such things. And second is having such great resources to work with - Global Plants, the Biodiversity Heritage Library, Google Earth, our specimen databases (and from those, other resources like the Australian Virtual Herbarium and Atlas of Living Australia). Using these, I was able to have this whole situation pretty much wrapped up and ready to write up in a little over a week, where only a few years ago it would have taken many months.

Only problem is - I didn't need to visit Paris and Vienna to view the type specimens!