New Zealand claims back the Kiwi after ancient DNA testing

Almost 20 years ago, Alan Cooper from the Australian Centre of Ancient DNA found that the Kiwi might actually originate from Australia.

Given that the emu and cassowary are the Kiwis closest living relatives and that New Zealand split off from Australia when Gondwana broke up, this was a logical suggestion.

Alan Cooper is from New Zealand himself and says: “This was a huge psychological blow in New Zealand and extremely unpopular”.

Photo: Kyle Davis and Paul Scofield

Photo: Kyle Davis and Paul Scofield

A new paper published today in Science sets the record straight. Alan Cooper and his team have been able to analyse the ancient DNA of two extinct birds from Madagascar and have found the Kiwis to be their closest relatives.

The emu, cassowary, ostrich, rhea and kiwi are known as “ratite birds” they can’t fly because they have lost the bone that wing muscles can attach to. The fact that the DNA of the kiwi closely matches the DNA of the extinct elephant bird from Madagascar means that birds of kiwi lineage must have flown at some point to get from Madagascar.

The connection between these birds undermines the idea that ratites evolved from ancestors that didn’t fly.

“Twenty years later it’s great to be able to show using ancient DNA that the kiwi is not an Australian bird. In fact its closest relative is the elephant bird from Madagascar,” he says.

“The New Zealanders will be much more comfortable with that. It’s their worst nightmare to be a derivative of Australia.”

Find out more about this story and flightless birds in Kieren Mitchell and Alan Cooper’s Conversation article and also in New Scientist, Science News and ABC Science Online articles.

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 DNA unravels Europe’s genetic diversity


Image – Flickr/leted

Ancient DNA recovered from a time series of skeletons in Germany spanning 4,000 years of prehistory has been used to reconstruct the first detailed genetic history of modern-day Europeans.

The study, published today in Science, reveals dramatic population changes with waves of prehistoric migration, not only from the accepted path via the Near East, but also from Western and Eastern Europe.

The research was a collaboration between the Australian Centre for Ancient DNA (ACAD), at the University of Adelaide, researchers from the University of Mainz, the State Heritage Museum in Halle (Germany), and National Geographic Society’s Genographic Project. The teams used mitochondrial DNA (maternally inherited DNA) extracted from bone and teeth samples from 364 prehistoric human skeletons – ten times more than previous ancient DNA studies.

“This is the largest and most detailed genetic time series of Europe yet created, allowing us to establish a complete genetic chronology,” says joint-lead author Dr Wolfgang Haak of ACAD. “Focussing on this small but highly important geographic region meant we could generate a gapless record, and directly observe genetic changes in ‘real-time’ from 7,500 to 3,500 years ago, from the earliest farmers to the early Bronze Age.”

“Our study shows that a simple mix of indigenous hunter-gatherers and the incoming Near Eastern farmers cannot explain the modern-day diversity alone,” says joint-lead author Guido Brandt, PhD candidate at the University of Mainz. “The genetic results are much more complex than that. Instead, we found that two particular cultures at the brink of the Bronze Age 4,200 years ago had a marked role in the formation of Central Europe’s genetic makeup.”

Professor Kurt Alt (University of Mainz) says: “What is intriguing is that the genetic signals can be directly compared with the changes in material culture seen in the archaeological record. It is fascinating to see genetic changes when certain cultures expanded vastly, clearly revealing interactions across very large distances.” These included migrations from both Western and Eastern Europe towards the end of the Stone Age, through expanding cultures such as the Bell Beaker and the Corded Ware (named after their pots).

“This transect through time has produced a wealth of information about the genetic history of modern Europeans,” says ACAD Director Professor Alan Cooper. “There was a period of stasis after farming became established and suitable areas were settled, and then sudden turnovers during less stable times or when economic factors changed, such as the increasing importance of metal ores and secondary farming products. While the genetic signal of the first farming populations becomes increasingly diluted over time, we see the original hunter-gatherers make a surprising comeback.”

Dr Haak says: “None of the dynamic changes we observed could have been inferred from modern-day genetic data alone, highlighting the potential power of combining ancient DNA studies with archaeology to reconstruct human evolutionary history.” The international team has been working closely on the genetic prehistory of Europeans for the past 7-8 years and is currently applying powerful new technologies to generate genomic data from the specimens.

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.

Bioinformatics ’13

Bioinformatics 13: Advanced Bioinformatics Workshop for Early Career Researchers

11-15 November 2013, The Univeristy of Adelaide, North Terrace Campus

The Australian Centre for Ancient DNA (ACAD) is pleased to announce Bioinformatics 13: Advanced Bioinformatics Workshop for Early Career Researchers, which will be based on the very successful Bioinformatics 2012 workshop. This workshop is an intensive 5 day hands-on training course tutored by international experts Rob Knight (the University of Colorado), Ludovic Orlando (The University of Copenhagen), Joe Pickrell (Harvard Medical School), and Stephen Bent (The University of Adelaide), utilising the latest available software for the analysis of Next Generation Sequencing (NGS) Genomics and Metagenomics data. The course combines seminars and extensive hands-on practicals involving the analysis of a range of model and empirical datasets, focusing on current approaches in field-leading groups. There will also be a limited opportunity to work on your own dataset with the tutors.

Early registration is essential as seating is limited to 30 places with very strong demand.

Pre-requisites: Delegates must be familiar with UNIX environments and basic command lines, and will require a basic knowledge of the technology and analytical tools of NGS. Some background experience in this field is required.

Registration: now open. Early bird rate closes 31 August 2013.

Further information and registration: visit the Bioinformatics 13 website.

Environmental Linkage Grants

Congratulations to Environment Institute members Professor Alan Cooper and Professor Gus Nathan in securing funding in the following linkage projects:

Alan Cooper

Identifying the diversity and evolution of loci associated with adaptation to aridity/heat and salinity in ancient cereal crops

Project Summary

This project will use ancient grains of wheat, barley and rye to find ‘lost’ genetic diversity at key genes associated with resistance to aridity, salt and disease. This project will make the proteins of key genes, and study their interaction with the environment over time by measuring ions in the grains to reveal the ancient environmental conditions.

The role of epigenetic modifications in bovid adaptation to environmental change

Project Summary

This project will explore the role of epigenetic change, where gene expression is regulated without changing the deoxyribonucleic acid (DNA) sequence, in how animals adapt to rapid climate change. This project will trace epigenetic markers in ancient bison and cows through 30,000 years of climate change, and identify key adaptive genes for the cattle industry.

Gus Nathan

Oscillating water column efficiency improvement through impedance matching and active latching control techniques

Project Summary

The coastline of southern Australia is recognised as a world-class wave energy resource. This project will play a crucial role in seeing this resource exploited whilst simultaneously keeping Australia at the forefront of wave energy technology. Specifically, this project will develop a high-efficiency turbine technology for wave energy.

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 helps solve mystery of the history of the Falkland Islands Wolf

A new paper involving Environment Institute members Jeremy Austin (also Museum Victoria), Julien Soubrier and Alan Cooper as well as Francisco Prevosti (Museo Argentino de Ciencias Naturales ‘Bernardino Rivadavia’—CONICET), Luciano Prates (Museo de La Plata), Valentina Trejo (Las Condes) and Francisco Mena (Centro de Investigación en Ecosistemas de la Patagonia) has been published in the journal Nature Communications.

The paper titled ‘The origins of the enigmatic Falkland Islands wolf’ explains how the researchers used carefully extracted DNA from museum specimens of the Falkland Islands wolf (Warrah) and subfossil bones of an extinct South American wolf to discover that the ancestor of the warrah probably walked to the islands across a frozen, narrow marine strait during the last ice age, about 16,000 years ago.

Using DNA from these two extinct species the researchers were able to show they were very closely related. Determining how close was the key to identifying when the ancestor of the warrah reached the Falkland Islands.

Read the paper to find out more about this historical discovery.

EI scientists use preserved bacteria on ancient teeth to track the evolution of diseases

Researchers from the Environment Institute’s Australian Centre for Ancient DNA (ACAD) have led an International research team that have used DNA preserved in calcified bacteria on the teeth of ancient human skeletons to shed light on the health consequences of the evolving diet and behaviour from the Stone Age to the modern day.

The ancient genetic record reveals the negative changes in oral bacteria brought about by the dietary shifts as humans became farmers, and later with the introduction of food manufacturing in the Industrial Revolution.

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

The international team, led by ACAD, where the research was performed, has published the results in Nature Genetics today. Other team members include the Department of Archaeology at the University of Aberdeen and the Wellcome Trust Sanger Institute in Cambridge (UK).

“This is the first record of how our evolution over the last 7500 years has impacted the bacteria we carry with us, and the important health consequences,” says study leader Professor Alan Cooper, ACAD Director.

“Oral bacteria in modern man are markedly less diverse than historic populations and this is thought to contribute to chronic oral and other disease in post-industrial lifestyles.”

The researchers extracted DNA from tartar (calcified dental plaque) from 34 prehistoric northern European human skeletons, and traced changes in the nature of oral bacteria from the last hunter-gatherers, through the first farmers to the Bronze Age and Medieval times.

Read the full media release.