Lowe will lead a 2.5 million dollar project that uses “DNA barcoding” to rapidly and accurately identify key animal and plant species. He predicts that it would take at least another 2000 years to identify Earth’s remaining species using traditional taxonomy.
“With DNA barcoding, we can vastly accelerate this rate and generate significant scientific and economic benefits.”
The national collaborative project is a partnership with scientists from Kings Park Botanic Garden, CSIRO, James Cook University and the South Australian Museum. Research infrastructure organisation Bioplatforms Australia is project managing the project and will provide access to DNA sequencing infrastructure and genomics and bioinformatics expertise. The project has support also from Fortescue Metals Group and BHP through its Bush Blitz program.
authenticating labelling and geographical origin of fish in the retail marketplace;
mapping plant biodiversity in the Pilbara to help with mine site environmental impact assessment and restoration management;
biodiversity discovery and impact assessment of invertebrates that inhabit underground aquifers utilised by mining and farming; and
generating barcodes for Australia’s orchids to enhance conservation.
“DNA barcoding has significant potential to enhance our understanding of Australian biodiversity and become an essential tool in the environmental assessment process and conservation planning,” says Professor Lowe. “By utilising a genetic rather than morphological marker system, barcoding can help combat illegal trade in endangered and valuable species through more accurate identification and tracking.”
In the first quarter of 2014, researchers at The Environment Institute have published on a vast array of topics, from Ancient DNA in the Arctic, to birdsongs to recommendations for improvements to guidelines such as the Ecological Footprint in order to better inform policy makers.
A selection of these publications is listed below.
1. Fifty thousand years of Arctic vegetation and megafaunal diet.Nature Research into the type of vegetation present during the last 50 thousand years in the Arctic is presented. Rather than using fossilised pollen as the main source of data as has been the case for previous studies, this study used plant and nematode DNA from sites across the Arctic. This data brings into question the diet of megafauna such as the woolly mammoth.
2. Distribution and Diversity of Soil Microfauna from East Antarctica: Assessing the Link between Biotic and Abiotic Factors.PLOS ONE An investigation into soil microfauna composition, abundance, and distribution in East Antarctica. The study found that where a population exists is likely to be determined by soil geochemistry.
3. Higher Levels of Multiple Paternities Increase Seedling Survival in the Long-Lived Tree Eucalyptus gracilis.PLOS ONE Data from populations of Eucalyptus gracilis (white mallee or yorrell) across the Murray-Darling Basin in southern Australia was collected in order to gain an understanding of how local environments affect seed quality.
4. Rapid deforestation threatens mid‐elevational endemic birds but climate change is most important at higher elevations. Biodiversity Research The effect of deforestation and climate change on bird communities in Lore Lindu National Park, Sulawesi, Indonesia was investigated. The National Park is a globally important hotspot of avian endemism, and has lost almost 12% of its forest in the decade of 2000-2010.
5. Does the Shoe Fit? Real versus Imagined Ecological Footprints. PLOS BIOLOGY
This article seeks to demonstrate that “Ecological Footprint” measurements as currently constructed and presented misleading and cannot be used effectively in any serious science or policy context. Outlined are a set of principles that any ecological indicator should be based on in order to be scientifically sound and relevant for use in decision making.
6. Historical changes in mean trophic level of southern Australian fisheries. Marine and Freshwater Research
It is suggested that care in interpretation of mean trophic level (MTL) of catches should be taken because reductions do not necessarily reflect change in species high on the food chain by fishing pressure. They found that the change in MTL is mainly attributable to large catches of sardines.
7. Ecology Needs a Convention of Nomenclature. BioScience
A convention of ecological nomenclature as well as a transnational institution to manage it is proposed, in order to overcome the synonymy and polysemy across disciplines, which currently handicaps the progress of ecology.
8.Emerging Challenges for the Drinking Water Industry Environmental Science & Technology Three principles that underpin alternative water source choices are introduced: Reliability, thresholds and future projections of water quality and quantity.
9. The evolution of lncRNA repertoires and expression patterns in tetrapods. Nature
The first large-scale evolutionary study of long noncoding RNA (lncRNA) repertoires and expression patterns in eleven tetrapod species is presented. About 400 highly conserved lncRNA’s (of more than 10 000 identified) probably originated an astonishing 300 million years ago at least.
10. Direct evidence for organic carbon preservation as clay-organic nanocomposites in a Devonian black shale; from deposition to diagenesis Earth and Planetary Science Letters The temperature and oxygenation of the oceans are influenced by one of the most fundamental biogeochemical processes on Earth-the burial of organic carbon in marine sediments. This buried organic carbon also comprises the primary source of hydrocarbons. This paper presents research into the composition of Woodford Shale.
11. A guide to southern temperate seagrasses (Book, CSIRO Publishing)
A reference guide to the diverse seagrasses present in the ocean of the temperate parts of the southern hemisphere. Evolution, biology and ecology of the seagrasses is introduced. This book allows readers to rapidly identify a particular species, including those often confused with others.
12. A Potential Metric of the Attractiveness of Bird Song to Humans. Ethology
Bird species such as the common nightingale and European blackbird have songs that are known to have inspired classical music. Developing a metric for these songs might help identify birds that are present in international bird trade which could contribute to studies of invasion and conservation biology.
13. Genetics in conservation management: Revised recommendations for the 50/500 rules, Red List criteria and population viability analyses. Biological Conservation A review of recent theoretical and empirical evidence concludes that the population rules for minimising inbreeding and for maintaining evolutionary potential in perpetuity need to be at least doubled and sections of the IUCN Red List criteria require revision, to be more effective conservation tools.
We are currently seeking two individuals for a Research Assistant position and a Research Associate position. These positions are ARC funded positions in ‘Transport risk pathways for emerging invasive species’.
Research Assistant within the School of Earth & Environmental Sciences, University of Adelaide, Invasion Ecology Group (http://www.cassey-invasion-ecology.org/).
The successful applicant will be expected to engage with researchers in the School of Earth & Environmental Sciences as well as fostering ties with other research providers, industry risk creators, and State Government end-users. The successful applicant will work closely with researchers in the Invasion Ecology Group providing empirical support for projects relating to transport networks and incursion risk. Research will include the collation of empirical data from Australian (and international) biosecurity datasets, the visualisation of spatial data, and the curation of digital project meta‐data.
Research Associate within The School of Mathematical Sciences and the School of Earth and Environmental Sciences.
The successful candidate will work within the Operations Research Group of the School of Mathematical Sciences. The Operations Research Group consists of a number of leading mathematical modellers, with particular strengths in stochastic modelling and optimisation, and hosts a node of the ARC Centre of Excellence for ‘Mathematical and Statistical Frontiers of Big Data, Big Models, New Insights’, which shares strong links with this advertised position. Research will include the construction of complex pathway transport models supported by existing biosecurity datasets and the predictive mapping of ecologically-realistic environmental and climatic risk neighbourhoods. Computational and mathematical techniques will be used to forecast probabilities of future incursion risks into Australia.The successful applicant will also work closely with researchers in the Invasion Ecology Group, in the School of Earth and Environmental Sciences (http://www.cassey-invasion-ecology.org/), and will be expected to foster ties with other research providers, industry risk creators, and State Government end-users.
Closing date for these positions is Monday 17th March.
The podcast from the seminar by Kathy Belov Can we save the Tasmanian devil from extinction? is now available.
The iconic Tasmanian devil is under threat. Not only does it face traditional conservation pressures, a devastating facial tumor is wiping out populations across Tasmania. The species is the focus of numerous conservation efforts and research, but can the devil be saved from extinction? Professor Katherine Belov, ARC Future Fellow and Professor of Comparative Genetics at the University of Sydney, explores the fate of the Tasmanian devil.
Tasmanian Devil. Image – Flickr/Scott Nolan
Katherine Belov is Professor of Comparative Genomics at the Faculty of Veterinary Science of the University of Sydney and contributing author of the 2012 Annual Review of Genomics and Human Genetics. In this seminar, Prof. Belov discusses:
the origins of the Devil Facial Tumor Disease (DFTD), a transmissible cancer that has already caused the disappearance of 85 percent of the species and could lead to its extinction in the wild within 25 years.
what is known of the tumor based on its genomics
why it is transmitted between animals without causing immune recognition in the devils
conservation efforts to save the species from extinction.
The iconic Tasmanian devil is under threat. Not only does it face traditional conservation pressures, a devastating facial tumor is wiping out populations across Tasmania. The species is the focus of numerous conservation efforts and research, but can the devil be saved from extinction?
Professor Katherine Belov, ARC Future Fellow and Professor of Comparative Genetics at the University of Sydney, will explore the fate of the Tasmanian devil in a lunchtime seminar.
When: 12 Noon, 22 November, 2013
Where: Horrace Lamb Lecture Theatre
Tasmanian Devil. Image – Flickr/Scott Nolan
Katherine Belov, Professor of Comparative Genomics at the Faculty of Veterinary Science of the University of Sydney and contributing author of the 2012 Annual Review of Genomics and Human Genetics, Prof. Belov will discuss the origins of the Devil Facial Tumor Disease (DFTD), a transmissible cancer that has already caused the disappearance of 85 percent of the species and could lead to its extinction in the wild within 25 years. She will talk about what is known of the tumor based on its genomics, why it is transmitted between animals without causing immune recognition in the devils, and what are the conservation efforts to save the species from extinction.
Environment Institute researchers Mike Lee and Julien Soubrier, with Greg Edgecombe have resolved a mystery that has puzzled scientists for centuries, Darwin’s Dilemma. They have published their findings in Current Biology, Mike explains below in an article he produced for The Conversation.
Evolution’s ‘big bang’ explained (and it’s slower than predicted)
Meet your flatmate. A living arthropod (centipede Cormocephalus) crawls over two 515-million-year-old relatives (Estaingia trilobites) which lived during the Cambrian explosion. All are found on what is now Kangaroo Island, southern Australia. Michael Lee
The sudden appearance of a range of modern animals about half a billion years ago, during evolution’s “big bang”, has intrigued and puzzled generations of biologists from Charles Darwin onwards.
A new study by Greg Edgecombe from London’s Natural History Museum, Julien Soubrier from the University of Adelaide, and I, and published today in Current Biology, suggests that the evolution of all these animals during the lower Cambrian can be explained by only a relatively minor increase in evolutionary rates – sustained over 20-30 million years.
Minor changes acting cumulatively over substantial periods generate huge differences: Albert Einstein termed compound interest “the most powerful force in the universe”, and his observation also applies to evolutionary change.
The near-simultaneous appearance of a plethora of advanced animals around 530 million years ago is known as the Cambrian explosion.
Within a geologically brief interval of perhaps 20 million years, virtually every modern animal phylum made its fossil debut, including arthropods (represented today by insects, crustaceans and arachnids), molluscs (clams, snails, octopus and squid) and chordates (sea-squirts and vertebrates).
Alongside these familiar forms were a range of much more bizarre creatures, such as Opabinia (with five eyes and a stalked jaw), Diania (which looked like a walking cactus), and Anomalocaris (which looked like the head of a lobster grafted onto the body of a squid).
Measuring evolution’s big bang
Evolution’s big bang has fascinated and perplexed scientists for hundreds of years. Some scientists have speculated (with little evidence) that animals evolved at light speed during this time, hundreds or thousands of times faster than they are evolving today.
It certainly made Charles Darwin feel uneasy: he thought incremental evolution through natural selection could not easily explain such an abrupt pattern.
Rather, he predicted that modern animal groups would appear in a staggered fashion, preceded by a range of precursors. Such reservations have predictably been exploited by opponents of evolution.
But it has been notoriously difficult to measure evolutionary rates during this pivotal interval of earth history, for good reason. = Such inferences require an exceptional fossil record.
To observe and date changes in ancestral and descendant species, we need complete animals preserved in rocks that span a substantial and continuous interval of time. Unfortunately, the Cambrian fossil record is far too patchy: good fossils are thinly scattered across time and space, making it impossible to directly “read” evolutionary rates from the rocks.
Branches on the evolutionary tree
Our team used a novel approach to measure evolutionary rates during this pivotal moment in earth history, using living animals. Just as astronomers can infer much about the origin of the universe from the nature and movements of the galaxies today, we can learn much about the Cambrian explosion (the origin of animals) from the anatomy, genes, and current evolutionary trajectory of living animals.
We focused on arthropods, the dominant group of animals ever since the Cambrian, today making up more than 80% of animal life.
We reconstructed a detailed evolutionary tree of arthropods and inferred how much change had occurred on every branch of this tree, purely by looking at living animals. Then, using fossils, DNA and an accommodating supercomputer, we worked out how fast each branch was evolving.
It turns out that – on average – Cambrian animals were evolving about five times faster than modern animals. This is fast, but nowhere near the speediest estimates that had been previously thrown about.
More importantly, such rates are totally consistent with Darwinian evolution by natural selection: for instance, mammals that colonise novel island habitats evolve a few times faster than their mainland relatives.
What fuelled the explosion?
What could have driven prolonged rapid (but not impossibly fast) evolution during evolution’s big bang? Many game-changing adaptations first appeared during the Cambrian explosion, such as vision, predation, burrowing, and active swimming.
These innovations would also have opened up totally new niches that animals would have raced to exploit, and would have triggered rapid evolutionary “arms races” between predators and prey.
The magnitude of these innovations meant their evolutionary effects could have reverberated for substantial time. While the Cambrian explosion occurs over a time interval that is considered short on geological scales, it still occupied a considerable period.
The inferred five-fold increase in evolutionary rates, acting over perhaps 20 million years, would generate 100 million years “worth” of evolutionary change.
This helps resolves Darwin’s dilemma: moderately elevated evolutionary rates – sustained over 20 million years in the early Cambrian – could easily explain the relatively sudden appearance of a range of highly divergent modern animals.
The study discussed in this article was funded by Australian Research Council grants to Mike Lee.
“I wanted to help make restoration more efficient and more effective; I hoped to improve the ecology of SA. Previous work had already shown that restoration projects tended to have low success rates and researchers thought that genetic problems of the seeds used in restoration were likely the reasons for these low success rates.
My PhD research was the first to identify that two key genetic problems routinely impact plants used for restoration – high inbreeding and low pollen diversity. My PhD research showed how these genetic problems affect seed quality, when they are likely to be problems in restoration projects, and how some simple changes to seed collection policy could help overcome these problems, improving restoration outcomes. I argued in my thesis that improving the quality of seeds used in restoration projects is acutely important today due to the stress on restoration projects from climate change, habitat loss and invasive species. “
The Landscape Futures Analysis Tool (LFAT) won the Environment and Sustainability category at the South Australian Spatial Excellence Awards. The Environment and Sustainability Award recognises projects and products that help to resolve any issue in the environmental context. The LFAT is a GIS and modelling framework that brings together critical information about a region, enabling spatial projections of the viability of various land uses and provides options that will help adaptations.
Through collaborative work with NRM regions, four critical issues were identified for use in the model; mitigation of carbon emissions, biodiversity conservation, weed management and agricultural production. LFAT is highly interactive allowing users to explore future scenarios for up to 256 possible combinations of climate, agricultural commodity price, carbon price and input cost. The Tool can be found at www.lfat.org.au
In the individual categories (Undergraduate/Graduate Project Award) one of Bertram Ostendorf’s honours students, Tina Schroeder, won with her thesis on dingo predation effects in the Arid Recovery Project. Tanya’s project tested how cats and foxes interact with dingoes by applying static (spatial) and dynamic (temporal and spatial) interaction analyses based on GPS location data of feral cats, red foxes and dingoes obtained at 2 hour intervals during an experiment undertaken between 2008 – 2010 in arid northern South Australia.
The series includes seminars with invited high-profile speakers from across the Institute’s subject areas, including marine and climate science, energy, evolutionary biology, ecology and biodiversity, and ancient DNA.
The presentation is titled ‘Origins of the southwest Australian biodiversity hotspot: ecological and macroevolutionary perspectives’.
When: Friday 14 June Time: 12pm – 1pm Where: Benham G25, North Terrace Campus, The University of Adelaide (map) Cost: Free
Dr Cardillo works on a range of questions in community ecology, macroecology, macroevolution and conservation biology, mostly using a comparative or modelling approach. Most of his research has a phylogenetic perspective. Phylogenies can reveal more than just evolutionary relationships: they also carry information on ecological and evolutionary processes, and can be a powerful tool for analysing comparative data.