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.

Biosecurity research positions available

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.

New Review: Parasites as biological tags to assess host population structure: Guidelines, recent genetic advances and comments on a holistic approach

A new review involving Environment Institute member Bronwyn Gillanders, as well as Sarah Catalano, Ian Whittington and Stephen Donnellan of the Australian Centre for Evolutionary Biology and Biodiversity has recently been published in the International Journal for Parasitology: Parasites and Wildlife.

This review, titled Parasites as biological tags to assess host population structure: Guidelines, recent genetic advances and comments on a holistic approach includes a summary of the population studies that have used parasites as biological tags for marine fish and cephalopods. The new ways that parasite genetic data can be incorporated into population structure studies is discussed.

Hundreds of dicyemid parasites (white, fuzzy strands) attached to the renal appendage (in red) of a cuttlefish individual.

Hundreds of dicyemid parasites (white, fuzzy strands) attached to the renal appendage (in red) of a cuttlefish individual.

Download the review to find out more.

Podcast for Kathy Belov seminar now available.

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

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.

Podcast download [50 MB]

Can we save the Tasmanian devil from extinction?

SEMINAR

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

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.

ACEBB/EELS/EI Seminar Series podcasts available

The Environment Institute, the Australian Centre for Evolutionary Biology and Biodiversity and the Ecology, Evolution and Landscape Science academic group in the School of Earth & Environmental Sciences hold a regular seminar series during semester.

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.

In the series so far:

3 May: A New World Down Under: biodiversity and evolution of subterranean animals from the Australian arid zone (m4a download)
Speaker: Professor Steven Cooper

30 May: Next generation amplicon sequencing to characterise fossil, faecal, food and forensic samples (m4a download)
Speaker: Dr Mike Bunce

14 June: Origins of the southwest Australian biodiversity hotspot: ecological and macroevolutionary perspectives  (m4a download)
Speaker: Dr Marcel Cardillo

Seminars are held regularly and presentations will be added to the ACEBB/EELS/EI Seminar Series webpage.

Dr Marcel Cardillo – Australian Biodiversity Seminar Today

Marcel CardilloEcology, Evolution and Landscape Sciences, The Environment Institute and the Australian Centre for Evolutionary Biology and Biodiversity present Dr Marcel Cardillo, ARC QEII Fellow and Associate Professor of Evolution and Biodiversity, Australian National University, on Friday 14 June 2013.

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

All welcome!

Research Interests

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.

DNA Sequencing: Dr Mike Bunce podcast now available

The podcast for the presentation by Dr Mike Bunce is now available for download.mikebunce

The Environment Institute, the Ecology, Evolution and Landscape Science group and the Australian Centre for Evolutionary Biology and Biodiversity presented Dr Mike Bunce, ARC future Fellow from the School of Biological Sciences and Biotechnology at Murdoch University, on Thursday 30 May 2013.

The presentation Next generation amplicon sequencing to characterise fossil, faecal, food and forensic samples discussed next-generation DNA sequencing.

Mike’s research interests revolve around using ancient DNA to study evolutionary processes and using ancient DNA profiles to investigate past biodiversity. He has worked on a diverse variety of projects with the common theme of extracting and amplifying degraded DNA; these include studies of New Zealand’s extinct birds and obtaining DNA profiles from ice/sediment cores. The lab research is focused around using ancient DNA as a tool to profile past biodiversity and extinction events. Mike says ‘Conservation and restoration of biodiversity is best achieved if we understand the past composition and function of the ecosystems we are trying to restore’.

Listen to the presentation

Animal Evolution in Arid Australia Seminar Friday 3 May

Environment Institute member Professor Steven Cooper will present a seminar on his research ‘A New World Down Under: biodiversity and evolution of subterranean animals from the Australian arid zone’.Steven Cooper

About the speaker

Professor Steven Cooper is a Principal Researcher at the South Australian Museum and an affiliate at the University of Adelaide, where he is a member of the Australian Centre for Evolutionary Biology and Biodiversity, associated with the School of Earth and Environmental Sciences. His research investigates the diversity, evolution and molecular ecology of Australian fauna, with a strong focus on subterranean and groundwater invertebrate fauna from the arid zone of Australia.

Where: G25 Benham Laboratories, The University of Adelaide
When: Friday 3 May 2013
Time: 12pm-1pm
Cost: free

All welcome!

New Paper – Leaf morphology shift: new data and analysis support climate link

A new paper involving Environment Institute members Greg Guerin and Andrew Lowe has recently been published in the Journal Biology Letters.

Samples from the Narrow-leaf Hopbush from the State Herbarium (Photo by Greg Guerin)

The paper titled ‘Leaf morphology shift: new data and analysis support climate link’ is following on from a previous paper written by Dr Guerin, Haixia Wen and Professor Lowe (‘Leaf morphology shift in response to climate change’) where the researchers concluded that climate change is changing the width of leaves.

This new research uses alternative data splits and statistical methods to re-test their original findings, including an extra 10 years’ worth of new data on leaf width from extra specimens collected up to 2011.

Read the paper to find out more

Professor Andrew Lowe has written an in depth Blog post about this research on Biodiversity Revolution called ‘First signs that climate change is causing adaptive shifts in plants’

Read an article relating to this research on ABC News

Read the Environment Institute’s previous blog post about this research and see past media coverage