Anthony Whalen

I'm the General Manager of the Australian Biological Resources Study; based in Canberra. I have a broad interest in Australian taxonomy, systematics, bioinformatics and conservation biology. I am strongly motivated by work that helps raise the awareness, understanding and appreciation of the Australian plants, animals and natural systems. Previous to this I worked in the a number of positions in the Australian Government's Department of the Environment (and its many taxonomic and nomenclatural synonyms). These roles included Species Information, Natural Heritage, Heritage Policy, the National Landcare Programme and Wildlife Trade.

My team and I are currently working on the Flora of Australia as one of our key priorities. With the help of the Atlas of Living Australia, Kevin Thiele and others, the Flora is rapidly evolving via a new dynamic e-flora platform. I am hopeful that resources such as the Flora of Australia can be highlighted within a Decadal Plan for Taxonomy and Biosystematics - in part for the role they can play to inform research and policy - but also to underline the importance of appropriately resourcing and developing such tools into the future.

I look forward to seeing the Decadal Plan go forward.

The Botany Bill

The American Society of Plant Taxonomists (ASPT) has been instrumental in negotiations towards a Botany Bill (formally, The Botanical Sciences and Native Plant Materials Research, Restoration and Promotion Act) recently introduced to the US House of Representatives by a Democrat-Republican co-sponsor pair. The aim of the Bill is to "support the botanical science capacity of the federal government". A press release on the Bill is here.

An interesting idea (and of course, an interesting time to introduce such a Bill in the US. To my knowledge, Trump has yet to tweet his opinion on the Bill.)

Ryonen Butcher

Hello – I’m Ryonen Butcher, and I’m a member of the world’s oldest profession – taxonomy. [Hi Ryonen!] My descent into this publicly-shunned and socially-misunderstood world began when I embarked on a BSc Honours project to resolve the Sphaerolobium macranthum Meisn. complex in south-western Australia. Little did I know that this was just a gateway project and that soon I’d need more… First I re-circumscribed one species and reinstated two others, but it wasn’t enough. Soon after, I recognised my first new species in the genus, and I was hooked. Before I knew it, there were publications… Oh. My. God - the high! THE HIGH!! Species followed species and genus followed genus as I spiralled into the all-encompassing vortex of plant taxonomy in a biodiversity hotspot. I’ve dragged others into this life, infecting the susceptible and excitable minds of university students with my obsessions and passions... It’s been years since I’ve seen my mother. I send her reprints to let her know I’m okay, but still she cries over the phone – Why? Why couldn’t you be a lawyer?? I’m sorry mum. I’m sorry…

(Ryonen counts SphaerolobiumMirbelia and Tephrosia (Fabaceae), Synaphea (Proteaceae), and Tetratheca and Platytheca (Elaeocarpaceae) among her addictions. She needs help. For obvious reasons.)

What are the big questions in plant systematics? - a report of a symposium on the future of global plant systematics

An interesting article in the last issue of American Journal of Botany. See especially the section discussing the big questions in plant systematics, and how we can address them. Thanks to David Cantrill for bringing this paper to our attention.

From the introduction to the paper:

"Forty botanists from 13 countries met this March in Amsterdam at a special colloquium at the Royal Netherlands Academy of Arts and Sciences to discuss the future of plant systematics (“Beyond the Tree of Life: the Future of Plant Systematics”; Fig. 1). The meeting was funded by the Netherlands Royal Academy and organized by Erik Smets (Naturalis Biodiversity Center, Leiden, Netherlands) and colleagues*; it addressed several paradoxes in our field. First, with an ongoing planetary-scale biodiversity crisis, the need for plant systematists has never been greater, and yet taxonomic expertise appears to be in steady decline, as noted by repeated calls for action (e.g., de Carvalho et al., 2007Drew, 2011). Despite this, new plant species are continuously being discovered, and plant systematics as a field has survived and even thrived, thanks to the common overarching goal of building and understanding the Tree of Life, spurred by the availability of new technology and powerful analytical frameworks. Yet, members of the public and colleagues outside biology often express surprise when new plant species are discovered or appear unaware that the Tree of Life is far from being fully resolved. In this context, how do we justify the importance of continued research on plant biodiversity and explain its importance to the general public, university administrators, funding agencies, and policy makers?"

Among other things, the colloquium asked the question "What are the cool, achievable questions in plants sytsematics, and how can we answer them?". Here's their answer:

"The third discussion session aimed at formulating questions and solutions that plant systematists as a community may realistically target in the near future. Four tentative key questions emerged: (1) How is plant life related, and how is diversity distributed in time and space? (2) What are the processes generating biodiversity? (3) How many species are there, and what do we know about them? (4) How do we break the barriers for training and employing systematists in the developing world? To address these questions, we thought that a flagship international project aimed at collecting/synthesizing in public databases, the phenotype, interactome, and genome from 100 specimens each of 1000 species over their distribution range and ecological gradients could attract excitement and major sources of funding and provide significant, novel answers and new questions."

This paper is useful and interesting food for thought for our own Decadal Plan process. The fill paper is at http://www.amjbot.org/content/103/12/2022.full 

Rob Davis

I'm an identification botanist and taxonomist. I have been with the WA Herbaium for the past 25 years. My initial role with the Herbarium was as a technical assistant, mostly working on WA's bioprospecting project and Regional Forest Assessments, among other survey projects. The past 15 years I have been primarily employed as an identification botanist. In this position, I'm identifying plants from a variety of organisations, either internal identification within the Department of Parks and Wildlife or from environmental consultants, the Department of Agriculture and the general public. I'm also involved in confirming rare and priority taxa for Western Australia. In addition, I'm involved in taxonomy, describing new species from a variety of plant families, but primarily from the genus Ptilotus.

 



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