It has been another productive year of research for the Environment Institute in 2016. Showcased below are 10 of our most pivotal journal articles of the year*.

1. Cultural innovation and megafauna interaction in the early settlement of arid Australia. Nature

[caption id="attachment_11527" align="alignright" width="300"] Warratyi rock shelter - Photo by Giles Hamm[/caption]

This paper describes research proving that humans occupied Australia’s arid interior and began developing sophisticated tools 10,000 years earlier than previously documented – around 49,000 years ago. The Warratyi rock shelter is about 550km north of Adelaide, in the Flinders Ranges. The findings from the cave show it to contain the oldest evidence of Aboriginal occupation in South Australia. Humans arrived in Australia about 50,000 years ago but the timing of their settlement in arid regions and cultural innovation have been uncertain.

The project was led by arid zone research archaeologist Giles Hamm, an Honorary Fellow of the South Australian Museum and La Trobe University PhD candidate, working with geochronology specialists at the University of Adelaide Dr Lee Arnold and Professor Nigel Spooner, along with geomorphologist Dr Peter Mitchell, and other researchers from Flinders University and the University of Queensland. They have worked for the last nine years with the Adnyamathanha people in the Flinders Ranges.

Citation: Hamm, G., Mitchell, P., Arnold, L. J., Prideaux, G. J., Questiaux, D., Spooner, N. A., . . . Johnston, D. (2016). Cultural innovation and megafauna interaction in the early settlement of arid Australia. [10.1038/nature20125]. Nature, 539(7628), 280-+. doi: http://dx.doi.org/10.1038/nature20125

2. Predicting and mitigating future biodiversity loss using long-term ecological proxies. Nature Climate Change

[caption id="attachment_11706" align="alignright" width="300"] Spatial demographic models are built using 'best estimates' for demographic and environmental attributes, using information from congeneric species and allometry.[/caption]

Uses of long-term ecological proxies in strategies for mitigating future biodiversity loss are too limited in scope. Recent advances in geochronological dating, palaeoclimate reconstructions and molecular techniques for inferring population dynamics offer exciting new prospects for using retrospective knowledge to better forecast and manage ecological outcomes in the face of global change. Opportunities include using fossils, genes and computational models to identify ecological traits that caused species to be differentially prone to regional and range-wide extinction, test if threatened-species assessment approaches work and locate habitats that support stable ecosystems in the face of shifting climates. These long-term retrospective analyses will improve efforts to predict the likely effects of future climate and other environmental change on biodiversity, and target conservation management resources most effectively.

Citation: Fordham, D. A., Akçakaya, H. R., Alroy, J., Saltré, F., Wigley, T. M. L., & Brook, B. W. (2016). Predicting and mitigating future biodiversity loss using long-term ecological proxies. [10.1038/nclimate3086]. Nature Climate Change, 6(10), 909-916. doi: http://dx.doi.org/10.1038/nclimate3086

3. Ocean acidification alters fish populations indirectly through habitat modification. Nature Climate Change

[caption id="attachment_11131" align="alignright" width="300"] Sharks likely to experience behavioural changes amidst a changing climate[/caption]

As the Earth’s oceans warm, sea-dwelling creatures experience a raft of changes. While much attention has been directed towards small-bodied fishes, we know relatively little about the effects of ocean warming and acidification on large predators like sharks. This paper has uncovered the climate-sensitive metabolic and behavioural changes of large predators.

The research was brought to you by Jennifer Pistevos, Associate Professor Ivan Nagelkerken, Dr Tullio Rossi and Professor Sean Connell.

Citation: Nagelkerken, I., Russell, B. D., Gillanders, B. M., & Connell, S. D. (2016). Ocean acidification alters fish populations indirectly through habitat modification. [10.1038/nclimate2757]. Nature Climate Change, 6(1), 89-93. doi: http://dx.doi.org/10.1038/nclimate2757

4. Biological role in the transformation of platinum-group mineral grains. Nature Geoscience

[caption id="attachment_11742" align="alignright" width="291"] Biofilms can be used to find platinum-group minerals[/caption]

Platinum-group minerals are an important resource, yet finding them amongst the geological terrain can be a challenge. Research by Dr Frank Reith and an international team of experts has shown that microorganisms can help us to detect platinum-group metals. The team used scanning electron microscopy to analyse biofilms covering mineral grains in Australia, Columbia and Brazil. Biofilms are capable of forming or transforming platinum-group mineral grains, and may play an important role for platinum-group element dispersion and re-concentration in surface environments.

Citation: Reith, F., Zammit, C. M., Shar, S. S., Etschmann, B., Bottrill, R., Southam, G., . . . Brugger, J. (2016). Biological role in the transformation of platinum-group mineral grains. [10.1038/ngeo2679]. Nature Geoscience, 9(4), 294-298. doi: http://dx.doi.org/10.1038/ngeo2679

5. Early cave art and ancient DNA record the origin of European bison. Nature Communications

[caption id="attachment_11447" align="alignright" width="300"] Black painting of bison (putative European bison, or wisent) at Grotte de Niaux (Niaux cave in Ariège, France), dated to the Magdalenian period (~17,000 years ago).
Under Creative Commons licence.[/caption]

Ancient DNA research revealed that Ice Age cave artists recorded a previously unknown, hybrid species of bison and cattle on cave walls more than 15,000 years ago. The mystery species, known affectionately by the researchers as the 'Higgs Bison' because of its elusive nature, originated over 120,000 years ago through the hybridisation of the extinct Aurochs (the ancestor of modern cattle) and the Ice Age Steppe Bison, which ranged across the cold grasslands from Europe to Mexico.

This research was led by the Australian Centre for DNA researchers Dr Julien Soubrier and Professor Alan Cooper, working with an international team including those from the University of California, Santa Cruz (UCSC), Polish bison conservation researchers, and palaeontologists across Europe and Russia.

Citation: Soubrier, J., Gower, G., Chen, K., Richards, S. M., Llamas, B., Mitchell, K. J., . . . Cooper, A. (2016). Early cave art and ancient DNA record the origin of European bison. [10.1038/ncomms13158]. Nature Communications, 7(ARTN 13158), 13158-13151-13158-13157. doi: http://dx.doi.org/10.1038/ncomms13158

6. Global proliferation of cephalopods. Current Biology

[caption id="attachment_10491" align="alignright" width="300"] Credit: Scott Portelli[/caption]

This research was a huge cause for celebration. Unlike the declining populations of many fish species, the number of cephalopods (octopus, cuttlefish and squid) has increased in the world’s oceans over the past 60 years.

Cephalopods have a unique set of biological traits, enabling them to adapt quickly to changing environmental conditions, more so than many marine creatures. As the marine environment has been transformed due to increased human use and climate change, cephalopods have responded with a surge in population numbers. But 'why?' remains the elusive question.

This paper was led by Dr Zoe Doubleday and Professor Bronwyn Gillanders, working with an international team of researchers.

Citation: Doubleday, Z. A., Prowse, T. A. A., Arkhipkin, A., Pierce, G. J., Semmens, J., Steer, M., . . . Gillanders, B. M. (2016). Global proliferation of cephalopods. [10.1016/j.cub.2016.04.002]. Current Biology, 26(10), R406-R407. doi: http://dx.doi.org/10.1016/j.cub.2016.04.002

7. Carbon isotope discrimination in leaves of the broad-leaved paperbark tree, Melaleuca quinquenervia, as a tool for quantifying past tropical and subtropical rainfall. Global Change Biology

[caption id="attachment_11747" align="alignright" width="221"] The broad-leaved paperbark tree[/caption]

Leaves of the Melaleuca quinquenervia (broad-leaved paperbark tree) were found to be an excellent predictor of rainfall patterns. This paper came about from an amazing stroke of good fortune, when researchers discovered that Professor Margaret Greenway had collected leaves of Melaleuca quinquenervia every month for 12 years

This extraordinary resource allowed researchers to link the carbon isotope ratio in leaves to historical rainfall records, a relationship which can be used to determine past rainfall levels in Australia by looking at leaves that have been preserved in sediment thousands of years ago.

The research will help Australia understand how the droughts and flooding rains we've experienced in recent history compare to the past. The project was led by Dr John Tibby.

Citation: Tibby, J., Barr, C., McInerney, F. A., Henderson, A. C. G., Leng, M. J., Greenway, M., . . . McNeil, V. (2016). Carbon isotope discrimination in leaves of the broad-leaved paperbark tree, Melaleuca quinquenervia, as a tool for quantifying past tropical and subtropical rainfall. [10.1111/gcb.13277]. Global Change Biology, 22(10), 3474-3486. doi: http://dx.doi.org/10.1111/gcb.13277

8. The Illegal Wildlife Trade Is a Likely Source of Alien Species. Conservation Letters

[caption id="attachment_11741" align="alignright" width="300"] Illegally traded reptiles are a threat to Australia[/caption]

The illegal reptile trade in Australia, including venomous snakes, could put our wildlife, the environment and human lives at risk. This paper outlines a model developed that helps us to identify the likelihood of establishment an alien species (like snakes or other reptiles) establishing themselves that has been introduced to the wild, accidentally or on purpose. Of the 28 reptile species that were analysed, 5 were likely to be established in the wild, while a further 7 could be established without any recapture or control measures in place.

The thriving black market of illegal reptiles in Australia, which includes the distribution of venomous snakes, makes this research particularly important. This research was led by Pablo García-Díaz and Associate Professor Phill Cassey with support from the Invasive Animals CRC.

Citation: García-Díaz, P., Ross, J. V., Woolnough, A. P., & Cassey, P. (2016). The Illegal Wildlife Trade Is a Likely Source of Alien Species. [10.1111/conl.12301]. Conservation Letters. doi: http://dx.doi.org/10.1111/conl.12301

9. The role of phytoplankton as pre-cursors for disinfection by-product formation upon chlorination. Water Research

[caption id="attachment_11748" align="alignright" width="300"] Cleaning by-products threat to water quality[/caption]

Water quality remains one of the greatest concerns with regards to human health. Treating water with disinfectants is critical to eliminate pathogenic micro-organisms. However, disinfecting water sources leads to disinfection by-products, which have been related to birth-defects and cancers. This paper details the role of phytoplankton in the build-up of disinfection by-products. The research was led by Professor Justin Brookes and his team.

Citation: Tomlinson, A., Drikas, M., & Brookes, J. D. (2016). The role of phytoplankton as pre-cursors for disinfection by-product formation upon chlorination. [10.1016/j.watres.2016.06.024]. Water Research, 102(C), 229-240. doi: http://dx.doi.org/10.1016/j.watres.2016.06.024

10. Finding needles in a genomic haystack: targeted capture identifies clear signatures of selection in a non-model plant species. Molecular Ecology

[caption id="attachment_10966" align="alignright" width="300"] Australian native hopbush[/caption]

The Australian native hopbush can be described as a true Aussie battler, able to survive a vast spectrum of environmental conditions, whether it be cool and wet or hot and dry. Hopbush can adapt by non-permanently altering their structure and physiology or through long-term natural selection. Due to these amazing capabilities, hopbush is often studied as a means to identify how plants may adapt with a shifting climate.

This research used novel genomic techniques to investigate selection and adaptation at the level of the genome. The study focussed on populations of hopbush distributed along a 700 km aridity gradient along the Mount Lofty and Flinders Ranges. Genes shown to be under selection had a diversity of functions, including water use efficiency and adaptation to environmental stressors, such as temperature and salt. Findings in the current study provide potential links between the phenotypic variation observed in previous studies and the underlying genomic variation.

This research was done by PhD student Matthew Christmas under the supervision of Professor Andy Lowe.

Citation: Christmas, M. J., Biffin, E., Breed, M. F., & Lowe, A. J. (2016). Finding needles in a genomic haystack: targeted capture identifies clear signatures of selection in a non-model plant species. [10.1111/mec.13750]. Molecular Ecology, 25(17), 4216-4233. doi: http://dx.doi.org/10.1111/mec.13750

Want more research goodness? Dont miss also our Top 25 High Impact Peer-reviewed publications for 2016!

*NB: These papers were selected from a list of our top 25 peer-reviewed research papers to represent the quality and breadth of research published by Environment Institute researchers in 2016. The papers above are ranked by impact factor of the journal according to UofA Aurora data current at time of publication.