From Birdsong Metrics to Ancient Arctic DNA: Selected Publications from the 1st Quarter, 2014

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.

Ancient Teeth on TV

Late Iron Age/Roman woman showing large dental calculus deposit, from Cambridge area, UK. Photo: Alan Cooper

Late Iron Age/Roman woman showing large dental calculus deposit, from Cambridge area, UK. Photo: Alan Cooper

Professor Alan Cooper and Dr Laura Weyrich appeared on the August 1 episode of the ABC’s Catalyst talking about what ancient DNA and teeth can tell us sugar, bacteria, agriculture and disease.

“90% of the cells that you’re walking around with right now aren’t yours – they’re actually bacteria. You’re only about 10%. So, it’s probably a better way of describing it as you being their human rather than them being your bacteria.”

– Professor Cooper

“People have related these communities to anything from autism to obesity to depression. I mean, so, really, we have to think of these organisms as impacting everything from our mental health to our, you know, regular immune health.

“These communities change based on what we’re putting in our body. And so a lot of the bacteria that we’re finding in our bodies now are really associated with this high-sugar diet.”

– Dr Weyrich

Watch the segment here.

TEDx Adelaide Forum 4 May 2013

Environment Institute member Alan Cooper will be speaking at this year’s TEDx Adelaide forum on Saturday 4 May 2013.TEDx 2013

TEDx is a ideas forum and this year’s theme is Explore. Some of the brightest minds in the state will be discussing what it means to explore, what we explore and why.

Where: Bonython Hall, 231-232 North Terrace, Adelaide
When: Saturday 4 May 2013
Time: 12pm-6pm
Cost: $65 + booking fee


Session 1

Will Tamblyn & Gavin Smith: Open Volumetric: 3D holographic visualisation. Building a robot with a holographic head, before holographic projectors existed.

Kiera Lindsey: Lecturer in Australian History & Australian Studies, University of South Australia: Exploration tropes. How tropes of expectation and approach, discovery and disappointment, mystery and knowing are inherent to the concept of exploration.

Lucas Lovell: Exploring the Gobi Desert. Being forced to explore personal capacity and connect with the natural world in one of the world’s most stimulating environments.

Alan Cooper: Australian Centre for Ancient DNA: Using ancient DNA to track the impacts of human evolution on our bacteria and our health.

Kirsty Stark: Wastelander Panda: Exploring Opportunities Online.

Moira Deslandes: Resignation. Lessons from the inside, exploring the frontier of resignation.

Session 2

Larissa McGowan: Choreographer

Mike Lee: SA Museum: Technological change and alien encounters: Lessons from the fossil record. What will our world be like 100 years from now? What will aliens look like? The history of life on earth, as preserved in the fossil record, provides some disconcerting answers.

Peter Burdon: University of Adelaide, Wild Law. Law perpetuates the ecological crisis and needs to be radically reconfigured to facilitate a viable human presence on the Earth.

Travis TJ Ransom: Parkour

Sarah Agnew: On grace and humanity. The gift of story is an invitation into grace and healing, as we explore the human experience together.

Session 3

Drinks in Mezzanine at Hub Central


More information on the speakers can be found on the TEDx Adelaide homepage.

To find out more about the event see the TEDx event page.

To buy tickets visit the TEDx order page.

New paper analysing DNA of prehistoric remains in North East Europe

A new paper involving Environment Institute members Clio Der Sarkissian, Alan Cooper and Wolfgang Haak as well as Oleg Balanovsky(Russian Academy of Medical Sciences & Russian Academy of Sciences), Valery Zaporozhchenko (Russian Academy of Medical Sciences), Elena Balanovska (Russian Academy of Medical Sciences),Guido Brandt (Johannes Gutenberg University of Mainz), Kurt W. Alt (Johannes Gutenberg University of Mainz),Valery Khartanovich(Kunstkamera Museum), Vyacheslav Moiseyev (Kunstkamera Museum),Alexandra Buzhilova (Russian Academy of Sciences), Sergey Koshel (Moscow State University),Römisch-Germanisches (Zentralmuseum), Eugen Kolpakov(Russian Academy of Science), Vladimir Shumkin(Russian Academy of Science) has recently been published in the journal PLoS Genetics.

The paper titled Ancient DNA Reveals Prehistoric Gene-Flow from Siberia in the Complex Human Population History of North East Europeanalysed the mitochondrial DNA of prehistoric remains from archaeological sites in North East Europe dated to 7,500 and 3,500 years Before Present.

Wolfgang Haak, one of the contributing authors on the paper

Wolfgang Haak, one of the contributing authors on the paper

This region in Europe displays a significant cultural and linguistic diversity today, however no ancient human DNA was available before. The resutls show that prehistoric hunter-gatherers of North East Europe were genetically similar to other European foragers. The authors also detected a prehistoric genetic input from Siberia, followed by migrations from Western Europe into North East Europe.

This research contributes to the understanding of the origins and past dynamics of human population in Europe.

Download the paper to find out more.

Ancient genes may explain modern threat to Tasmanian devils

Researchers at the University of Sydney and the University of Adelaide have discovered that Tasmanian devils had low immune gene diversity for hundreds, and possibly thousands, of years before the emergence of Devil Facial Tumour Disease.

The study, published today in the journal Biology letters, involves Environment Institute member Jeremy Austin from the Australian Centre for Ancient DNA. The study was led by Associate Professor Kathy Belov from the University of Sydney’s Faculty of Veterinary Science and also involved senior author Katrina Morris, a PhD candidate at the University of Sydney.

“It is well known that low genetic diversity is a major extinction risk factor, but when and how devils lost their immune diversity has remained a mystery until now,” said senior author Katrina Morris, a PhD candidate at the University of Sydney.

Dr Jeremy Austin from the Australian Centre for Ancient DNA

Dr Jeremy Austin from the Australian Centre for Ancient DNA

“Devils once lived across much of mainland Australia, but became extinct sometime in the last few thousand years,” said Dr Jeremy Austin, from the Australian Centre for Ancient DNA.

“We looked at subfossil bones of these extinct mainland devils, as well as museum specimens of Tasmanian devils collected over the last 200 years. They capture the genetic diversity of the past allowing us to see how the immune gene diversity has changed over thousands of years.”

The research was supported by funding from the Australian Research Council, the Save the Tasmanian Devil Foundation and Zoos SA.

Read the full Media Release on the University of Sydney’s website to find out more.

New Paper: The extinction of the Giant Moa was not caused by climate change

Professor Alan Cooper

A new paper titled ‘The effect of climate and environmental change on the megafaunal moa of New Zealand in the absence of humans‘ investigates using ancient DNA to assess the effect of climate and environmental changes on the now extinct Giant Moa. The researchers discovered that climate and environmental changes did not have a signifcant impact on the population of the extinct New Zealand bird.

The paper involves Environment Institute members Nicolas Rawlence (also of the University of Waikato), Jeremy Austin (also of Museum Victoria) and Alan Cooper as well as Jessica Metcalf (University of Colorado), Jamie Wood (Landcare Research), Trevor Worthy (Australian Centre for Ancient DNA) and has been published in Quaternary Science Reviews.

Download the paper to read about their findings
Read the University of Adelaide’s media release

New Paper: Ancient DNA identifies post-glacial recolonisation, not recent bottlenecks, as the primary driver of contemporary mtDNA phylogeography and diversity in Scandinavian brown bears

A new paper involving Environment Institute members Sarah Bray, Jeremy Austin (also Museum Victoria), Jessica Metcalf (also University of Colorado), Christina Adler (also University of Sydney) and Alan Cooper as well as Kjartan Østbye (University of Oslo & Hedmark University College, Norway), Elvind Østbye (University of Oslo), Stein-Erik Lauritzen (University of Bergen, Norway), Kim Aaris-Sørensen (University of Copenhagen) and Cristina Valdiosera (Universidad Complutense de Madrid–Instituto de Salud Carlos III de Evolucion y Comportamiento Humanos, Madrid) has recently been published in the journal Diversity and Distributions.

The paper titled ‘Ancient DNA identifies post-glacial recolonisation, not recent bottlenecks, as the primary driver of contemporary mtDNA phylogeography and diversity in Scandinavian brown bears’ employed ancient DNA techniques to investigate the timing and origins of the mtDNA structure in brown bear populations in Scandinavia. Identifying the patterns of this mtDNA structure is important for conservation programs aimed at restoring populations to a natural state.

Download the paper to find out more about this interesting research.

ACAD Guest speaker: Johannes Krause – Podcast now available

Download a podcast of Associate Professor Johannes Krause presentation titled, ‘The Genome of the Black Death’ presented by the Australian Centre for Ancient DNA (ACAD).

Assoc. Professor Johannes Krause

Assoc. Professor Johannes Krause from the Institute for Archaeological Sciences University of Tübingen, Germany gave a special presentation on Thursday 17th May 2012.

The talk focused on Assoc. Professor Krause’s findings obtained by using high throughput DNA sequencing in combination with targeted DNA enrichment to reconstruct the ancient genome of Yersinia pestis from skeletons securely dated to the Black Death pandemic from the East Smithfield cemetery in London, England, 1348 – 1350.

Download a copy of the PowerPoint presentation.

Find out more and download the podcast.

The Neandertal in you: what have we learned from the Neandertal Genome Project

Listen to visiting Prof Carles Lalueza-Fox speak about findings from the Neandertal Genome Project.

The Australian Centre for Ancient DNA (ACAD) was pleased to host Professor Carles Lalueza-Fox who gave a free public talk on ‘The Neandertal in you: what have we learned from the Neandertal Genome Project?’ on 9 December at the University of Adelaide.

Prof. Carles Lalueza (Inst. of Evolutionary Biology, UPF, Barcelona) is an international expert on both ancient DNA and Neandertal genetics. He was a key member of the team that recently sequenced the entire Neandertal genome.  His work has included research on human evolution, including skin and hair colour, and other phenotypic traits, as well as evolutionary studies on a range of extinct species from around the world.

Prof. Lalueza spoke about the many findings that have come from the Neandertal genome project, such as the discovery that non-African populations around the world appear to possess a contribution of around 4% Neandertal DNA in their genomes.

For an insight into the migratory history of the human species on a global scale, you may be interested in the Genographic Project event recently held in Adelaide.

160 year old museum specimens identify rare parrot

An adult Western Ground Parrot photographed in Fitzgerald River National Park, Western Australia. Photo by Brent Barrett, WA Department of Environment and Conservation

A team of Australian researchers involving DNA experts from the University of Adelaide has identified a new, critically endangered species of ground parrot in Western Australia.

The team, led by Australian Wildlife Conservancy‘s Dr Stephen Murphy, used DNA from museum specimens up to 160 years old to reveal that populations of ground parrots in eastern and western Australia are highly distinct from each other and that the western populations should be recognised as a new species, Pezoporus flaviventris.

“The discovery has major conservation implications,” said Dr Murphy. “The Western Ground parrot has declined rapidly in the last 20 years, there are now only about 110 birds surviving in the wild and most of these are confined to a single national park. It is now one of the world’s rarest birds.”

WA Department of Environment and Conservation‘s Dr Allan Burbidge said: “A single wildfire through the national park or an influx of introduced predators, such as cats, could rapidly push the species to extinction. There is now an urgent need to prevent further population declines and to establish insurance populations into parts of the former range.”

“Our findings demonstrate that museum collections, some going back more than 150 years, continue to be relevant and can provide critical information for understanding and conserving the world’s biodiversity into the future,” said team member Dr Jeremy Austin, Deputy Director of the Australian Centre for Ancient DNA at the University of Adelaide.

Director of CSIRO’s Australian National Wildlife Collection, Dr Leo Joseph, said: “Even after 200 years of study, we are still recognising new species of birds in Australia. This finding highlights the need for further research on Australia’s unique, and sometimes cryptic, biodiversity.”

The team’s findings have been published this month in the international conservation research journal Conservation Genetics.