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.

Ecological Armageddon in forest fragments

Malaysian rainforest. Image - jswakins/Flickr

Malaysian rainforest. Image – jswakins/Flickr

An international team of scientists including the University of Adelaide’s Professor Corey Bradshaw has found that species living in rainforest fragments could be far more likely to disappear than was previously assumed.

Published today in the leading journal Science, the researchers outlined a study spanning two decades in which they witnessed the near-complete extinction of native small mammals on forest islands created by a large hydroelectric reservoir in Thailand.

“Tropical forests remain one of the last great bastions of biodiversity, but they continue to be felled and fragmented into small ‘islands’ around the world,” says co-author Professor Corey Bradshaw, Director Ecological Modelling at the University of Adelaide’s Environment Institute.

“This study shows we need to be even more concerned than we thought – the speed at which there was near-total loss of native small mammals was alarming and shows that leaving fragments of forest behind is not nearly enough to protect these species.”

“It was like ecological Armageddon,” says Luke Gibson from the National University of Singapore, who led the study. “Nobody imagined we’d see such catastrophic local extinctions.”

The study was motivated by a desire to understand how long species can live in forest fragments. If they persist for many decades, then this gives conservationists a window of time to create wildlife corridors or restore surrounding forests to reduce the harmful effects of forest isolation.

However, the researchers saw native small mammals almost vanish at great speed, with just a handful remaining – on average, less than one individual per island – after 25 years.

As well as suffering the effects of population isolation, the small mammals also had to deal with a devastating invader – the Malayan field rat. In just a few years, the invading rat virtually displaced all native small mammals. The field rat normally favours villages and agricultural lands, but will also invade disturbed forests.

“This tells us that the double whammy of habitat fragmentation and invading species can be fatal for native wildlife,” says Dr Antony Lynam, from the US-based Wildlife Conservation Society. “And that’s frightening because invaders are increasing in disturbed and fragmented habitats around the world.”

“The bottom line is that we must conserve large, intact habitats for nature,” says Luke Gibson. “That’s the only way we can ensure biodiversity will survive.”

Near-complete extinction of native small mammal fauna 25 years after forest fragmentation is published in Science and is available at

Predicting publishing success in scientists.

Men with printing press circa 1930s Image - Flickr/ Seattle Municipal Archives.

Men with printing press circa 1930s
Image – Flickr/ Seattle Municipal Archives.

A provocative new study suggests it is straightforward to predict which academics will succeed as publishing scientists.

Those who publish earlier and more often while young are typically the long-term winners.

“We were really surprised,” said Professor William Laurance of James Cook University in Cairns, Australia, who led the study.

“It doesn’t matter if you go to Harvard or a low-ranked university. If you begin publishing scientific articles when you’re still a graduate student, you are far more likely to succeed in the long run.”

Laurance’s team scrutinized more than 1400 biologists on four continents, and then selected 182 to study intensively.

They found the researchers varied greatly – by almost a hundred-fold – in the number of scientific articles they published during their careers.

“For reasons that are not totally clear, some people just ‘get’ the publishing game early in their careers, and it’s these scientists who are most likely to keep on publishing strong research,” said Professor Corey Bradshaw of the University of Adelaide’s Environment Institute in South Australia.

Another finding was that women faced some disadvantages in publishing research, even those who overcame the well-documented attrition of senior female academics.

“Women have to jump a lot of hurdles in science,” said Carolina Useche of the Humboldt Institute in Colombia. “Family responsibilities weigh heavily on them, and they don’t seem to promote themselves as aggressively as some men do.”

Language also plays a role, according to Ms Useche. “Those who grow up speaking and writing English have an advantage, because most scientific journals are in English,” she said.

The research team reached two key conclusions.

First, far too few women make it to the top in science, in large part because they do not, on average, publish as often as men.

“For women scientists, it’s just not a level playing field, and we need to find ways to help them advance professionally,” Professor Bradshaw said.

Second, those who publish early and often are most likely to become scientific superstars, regardless of the international standing of the universities where they obtained their PhD.

“We need to pay a lot of attention to the early training of scientists,” Professor Laurance said. “If we do a good job, we can give them a head start that will last their whole lives. This research gives us a good evidence base for our efforts.”


Predicting publication success for biologists by William F. Laurance, D. Carolina Useche, Susan G. Laurance, and Corey J. A. Bradshaw was just published online in BioScience:


Dingo wrongly blamed for extinctions

Dingo , Fraser Island. Image - ogwens/Flickr

Dingo , Fraser Island. Image – ogwens/Flickr

Dingoes have been unjustly blamed for the extinctions on the Australian mainland of the Tasmanian tiger (or thylacine) and the Tasmanian devil, a University of Adelaide study has found.

In a paper published in the journal Ecology, the researchers say that despite popular belief that the Australian dingo was to blame for the demise of thylacines and devils on the mainland about 3000 years ago, in fact Aboriginal populations and a shift in climate were more likely responsible.

“Perhaps because the public perception of dingoes as ‘sheep-killers’ is so firmly entrenched, it has been commonly assumed that dingoes killed off the thylacines and devils on mainland Australia,” says researcher Dr Thomas Prowse, Research Associate in the School of Earth and Environmental Sciences and the Environment Institute.

“There was anecdotal evidence too: both thylacines and devils lasted for over 40,000 years following the arrival of humans in Australia; their mainland extinction about 3000 years ago was just after dingoes were introduced to Australia; and the fact that thylacines and devils persisted on Tasmania, which was never colonised by dingoes.

“However, and unfortunately for the dingo, most people have overlooked that about the same time as dingoes came along, the climate changed rather abruptly and Aboriginal populations were going through a major period of intensification in terms of population growth and technological advances.”

The researchers built a complex series of mathematical models to recreate the dynamic interaction between the main potential drivers of extinction (dingoes, climate and humans), the long-term response of herbivore prey, and the viability of the thylacine and devil populations.

The models included interactions and competition between predators as well as the influence of climate on vegetation and prey populations.

The simulations showed that while dingoes had some impact, growth and development in human populations, possibly intensified by climate change, was the most likely extinction driver.

“Our multi-species models showed that dingoes could reduce thylacine and devil populations through both competition and direct predation, but there was low probability that they could have been the sole extinction driver,” Dr Prowse says.

“Our results support the notion that thylacines and devils persisted on Tasmania not because the dingo was absent, but because human density remained low there and Tasmania was less affected by abrupt climate changes.”

The study ‘An ecological regime shift resulting from disrupted predator-prey interactions in Holocene Australia’ also involved Professors Corey Bradshaw and Barry Brook from the University of Adelaide’s Environment Institute and Professor Chris Johnson from the University of Tasmania.

Making national parks truly national.

Kakadu National Park - Flickr/Marc Dalmulder

Kakadu National Park – Flickr/Marc Dalmulder

Environment Insitute member Corey Bradshaw co-authored this piece on The Conversation on June 14, 2013.

Australia boasts over 500 national parks covering 28 million hectares of land, or about 3.6% of Australia. You could be forgiven for thinking we’re doing well in the biodiversity-conservation game.

But did you know that of those more than 500 national parks, only six are managed by the Commonwealth Government? For marine parks, it’s a little more: 61 of the 130-plus are managed primarily by the Commonwealth. This means that the majority of our important biodiversity refuges are managed exclusively by state and territory governments. In other words, our national parks aren’t “national” at all.

In a world of perfect governance, this wouldn’t matter. But we’re seeing the rapid “relaxation” of laws designed to protect our “national” and marine parks by many state governments. Would making all of them truly national do more to conserve biodiversity?

One silly decision resulting in a major ecosystem disturbance in a national park can take decades if not hundreds of years to heal. Ecosystems are complex interactions of millions of species that take a long time to evolve – they cannot be easily repaired once the damage is done.

The full article can be accessed here.

New paper: Evaluating options for sustainable energy mixes in South Korea using scenario analysis

A new paper involving Environment Institute members Corey Bradshaw and Barry W. Brook has recently been published in the journal Energy.

The paper, titled Evaluating options for sustainable energy mixes in South Korea using scenario analysis, examines the possibilities for sustainable energy generation in South Korea.


To mitigate greenhouse gas emissions, coal-fired electricity infrastructure needs to be replaced by low-carbon electricity generation options. Here we examine a range of possible alternative scenarios for sustainable electricity generation in South Korea, considering both physical and economic limits of current technologies. The results show that South Korea cannot achieve a 100% renewable energy mix and requires at least 55 GW of backup capacity. Given that constraint, we modelled seven scenarios: (i) the present condition, (ii) the First National Electricity Plan configuration, (iii) renewable energy (including 5 GW photovoltaic) with fuel cells or (iv) natural gas backup, (v) maximum renewable energy (including 75 GW photovoltaic) with natural gas, (vi) maximum nuclear power, and (vii) nuclear power with natural gas. We then quantify levelised cost of electricity, energy security, greenhouse gas emissions, fresh water consumption, heated water discharge, land transformation, air pollutant emissions, radioactive waste disposal, solid waste disposal and safety issues for each modelled mix. Our analysis shows that the maximum nuclear power scenario yields the fewest overall negative impacts, and the maximum renewable energy scenario with fuel cells would have the highest negative impacts.

Visit ScienceDirect to find out more.

New paper investigating whale shark populations

A new paper involving Environment Institute members Ana Sequeira, Camille Mellin (also Australian Institute of Marine Science) and Corey Bradshaw (also SARDI) as well as Mark Meekan (Australian Institute of Marine Science) and David Sims (Marine Biological Association of the United Kingdom) has recently been published in the Journal of Fish Biology.

The paper titled ‘Inferred global connectivity of whale shark Rhincodon typus populations’ collates available data on sightings, tracked movements and distribution information of whale sharks (Rhincodon Typus).

Currently, information on population geographic connectivity, migration and demography of whale sharks is still limited and scattered. However, understanding whale sharks migratory behaviour is central to its conservation management. The study provides evidence for the hypothesis of broad-scale connectivity among populations, and generates a model describing how the world’s whale sharks are part of a single, global meta-population.

Image: Whale Shark, coutesy of KAZ2.0/Flickr

Image: Whale Shark, coutesy of KAZ2.0/Flickr

The model provides a worldwide perspective of possible whale shark migration routes, and suggests a modified focus for additional research to test its predictions. The authors suggest that the framework can be used to trim the hypotheses for whale shark movements and aggregation timings, thereby isolating possible mating and breeding areas that are currently unknown. They believe this will assist efforts to predict the longer-term response of the species to ocean warming and changing patterns of human-induced mortality.

Download the paper to find out more.

New Paper – No need for disease: testing extinction hypotheses for the thylacine using multi-species metamodels

A new paper involving Environment Institute members Thomas Prowse, Corey Bradshaw (also SARDI), Michael Watts and Barry Brook as well as Christopher Johnson (University of Tasmania), Robert Lacy (Chicago Zoological Society) and John Pollak (Cornell University) has recently been published in the Journal of Animal Ecology.

The paper titled ‘No need for disease: testing extinction hypotheses for the thylacine using multi-species metamodels’ designed a new population viability approach (PVA) that includes species interactions explicitly by networking species models within a single ‘metamodel’.

Thylacine Thylacinus cynocephalusImage: Kelly Garbato

Thylacine Thylacinus cynocephalus
Image: Kelly Garbato (Flikr)

Population viability analysis (PVA) is used to assess the extinction risk of threatened species and to evaluate different management strategies. However, conventional PVA neglects important biotic interactions and therefore can fail to identify important threatening processes.

This study demonstrates the utility of PVA metamodels by using them to reinterpret the extinction of the carnivorous, marsupial thylacine Thylacinus cynocephalus (Tasmanian Tiger) in Tasmania. In particular, they test the claim that well-documented impacts of European settlement cannot account for this extinction and that an unknown disease must have been an additional and necessary cause.

Read the paper to find out more.


New Paper: Population biology and vulnerability to fishing of deep-water Eteline snappers

A new paper involving Environment Institute members Kim Loeun (also ADECAL), Camille Mellin (also Australian Institute of Marine Science) and Corey Bradshaw (also SARDI), as well as A.J Williams (Oceanic Fisheries Programme), S.J Nicol (Oceanic Fisheries Programme), P. Chavance (ADECAL), M. Ducrocq (ADECAL), S.J Harley (Oceanic Fisheries Programme), G.M Pilling (Oceanic Fisheries Programme) and V. Allain (Oceanic Fisheries Programme) has recently been published in the Journal of Applied Ichthyology.

The paper titled ‘Population biology and vulnerability to fishing of deep-water Eteline snappers’ looks into the concern from fisheries about the sustainability of current fishing rates of deep-water fish in the tropical and sub-tropical Pacific Ocean.

Currently, significant assessments of deep-water stocks in the Pacific region have been limited by the lack of suitable biological and fisheries data. However, estimates are provided of age-based demographic parameters for two important deep-water snapper species in the Pacific, Etelis carbunculus and E. coruscans. The study applied a spawner biomass-per-recruit (SPR) model to determine fishing mortality rates for each species that would achieve specified biological targets and limit reference points, and examine the sensitivity of the model to variation in natural mortality and age at first capture. The SPR analysis demonstrated that lower rates of fishing mortality were required for the E. coruscans species than for the E. carbunculus species to maintain spawning biomass above estimated biological reference points. The results showed that estimates of SPR were more sensitive to variation in natural mortality than in the age at first capture, suggesting that regulating fishing mortality rather than gear selectivity would be a more effective management measure for both species.

Read the paper to find out more about this research.

New Paper: Exogenous and endogenous determinants of spatial aggregation patterns in Tibetan Plateau meadow vegetation

A new paper involving Environment Institute member Corey Bradshaw (also SARDI) as well as Jiajia Liu (Fudan University). Deyan Wu (Lanzhou University), Xiaoyu Peng (Lanzhou University) and Shurong Zhou (Fudan University) was recently published in the Journal of Plant Ecology.

The paper titled ‘Exogenous and endogenous determinants of spatial aggregation patterns in Tibetan Plateau meadow vegetation’ aimed to measure the relative importance of various endogenous and exogenous processes influencing the spatial distribution of the individuals of plant species at different temporal and spatial scales in a species-rich and high-cover meadow in the eastern Tibetan Plateau.The  results indicate that self-thinning and habitat heterogeneity all contribute to determine the spatial aggregation patterns of plant individuals in the area.

Download the paper to find out more.