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.

ACAD member wins Next Generation Sequencer

Five members of the Environment Institute’s Australian Centre for Ancient DNA (ACAD) (Jeremy Austin, Jennifer Young, Jennifer Templeton, Denice Higgins and Janette Edson) attended and showcased their work at the International Symposium on Forensics, in Hobart 26-29th September.   Jennifer Templeton won 2nd prize for her poster, which illustrated ACAD’s recent work on enrichment strategies to retrieve whole mitochondrial genomes from forensic and ancient samples.

Jennifer subsequently attended the Asia-Pacific Sequencing Summit in Bali, run by LifeTech and took the ‘best poster’ award for her poster.  The prize was an Ion Torrent machine (Next Generation Sequencer).

Congratulations to Jennifer on this fantastic achievement and to all of the members of ACAD who were involved in the International Symposium.

Flightless parrots, burrowing bats helped parasitic Hades flower

Ancient dung from a cave in the South Island of New Zealand has revealed a previously unsuspected relationship between two of the country’s most unusual threatened species.

A New Zealand short-tailed bat pictured while eating dactylanthus.
Photo by Nga Manu Nature Reserve.

Fossilised dung (coprolites) of a now rare parrot, the nocturnal flightless kakapo, contained large amounts of pollen of a rare parasitic plant, dactylanthus (commonly known as “wood rose” or “Hades flower”), which lives underground and has no roots or leaves itself.

Researchers from the Environment Institute’s  Australian Centre for Ancient DNA (ACAD)  and Landcare Research and the Department of Conservation in New Zealand report the discovery in a new paper published in the journal Conservation Biology.

The paper is titled ‘A Lost Link between a Flightless Parrot and a Parasitic Plant and the Potential Role of Coprolites in Conservation Paleobiology‘ and was written by Jamie Wood (Landcare Research), Janet Wilmshurst (Landacare Research), Trevor Worthy (University of NSW), Avi Holzapfel (Department of Conservation, NZ) and Environment Institute member Alan Cooper (Director, ACAD).

Read the Media Release

Download the paper

New Paper: Historical stocking data and 19th century DNA reveal human-induced changes to native diversity and distribution of cutthroat trout

A new paper involving Environment Institute members Jessica Metcalf (now University of Colorado), Alan Cooper and Jeremy Austin, as well as Sierra Stowell (University of Colorado), Chris Kennedy (Colorado Fish and Wildlife Conservation Office), Kevin Rogers (Colorado Parks and Wildlife), Daniel McDonald (University of Colorado), Janet Epp (Pisces Molecular, LLC), Kyle Keepers (University of Colorado) and Andrew Martin (University of Colorado) has recently been published in the journal Molecular Ecology.

The paper, titled ‘Historical stocking data and 19th century DNA reveal human-induced changes to native diversity and distribution of cutthroat trout’. helps to clarify the native diversity and distribution of cutthroat trout in Colorado. The study is led by University of Colorado Boulder postdoctoral researcher Jessica Metcalf, a former postdoctoral researcher at the Environment Institute’s Australian Centre for Ancient DNA.

Download the Paper to find out more.

Read the Media Release produced by the University of Colorado.

ACAD Bioinformatics Early Career Researcher Workshop – Event

The Australian Centre for Ancient DNA is pleased to host the third Early Career Researcher workshop that builds on the successful workshops held in 2009 and 2010. This workshop is an intensive 5 day hands-on training course tutored by international experts in the field, utilising leading software packages for the analysis of Next Generation Sequencing (NGS) and SNP array data.

The course will focus on interpreting complex data sets, such as genomic and metagenomic samples, and review the most recent developments in the field. The tutors will provide detailed instructions on the analysis of model and empirical datasets, and focus on the latest techniques available.

When: Monday 5th November – Friday 9th November
The University of Adelaide, North Terrace Campus
Cost: Environment Institute members – $190 (Early Bird rate)
Non-Environment Institute members – $400 (Early Bird rate)

Early registration is strongly encouraged as seating is limited to 30 places, and there is strong demand.  Interested graduates are encouraged to apply for travel funds from their host institution.

Find out more and register
Download the registration form

Unsung Hero of South Australian Science Award 2012 – Dr Jeremy Austin

Dr Jeremy Austin

The Environment Institute would like to congratulate Dr Jeremy Austin on being presented with the ‘Unsung Hero of South Australian Science Award‘ for 2012 as part of National Science Week.

Dr Austin was presented with the award for his work with DNA and forensic indentification at the Australian Centre for Ancient DNA in South Australia (ACAD).

“Jeremy has made the quantum leap from using techniques for scientific research to using them for direct human benefit. He has pioneered the transfer of new methods and technology into practical applications suitable for industry, particularly the forensics community. Having this calibre of scientist in our state is of enormous importance to South Australia.” (National Science Week)

Congralutations to Dr Jeremy Austin

Find out more about the award
Discover more about Dr Austin’s work at ACAD

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