141 Works

Data from: Nonrandom, diversifying processes are disproportionately strong in the smallest size classes of a tropical forest

Peter T. Green, Kyle E. Harms & Joseph H. Connell
A variety of ecological processes influence diversity and species composition in natural communities. Most of these processes, whether abiotic or biotic, differentially filter individuals from birth to death, thereby altering species’ relative abundances. Nonrandom outcomes could accrue throughout ontogeny, or the processes that generate them could be particularly influential at certain stages. One long-standing paradigm in tropical forest ecology holds that patterns of relative abundance among mature trees are largely set by processes operating at...

Data from: Genetic diversity and population structure of the threatened freshwater catfish, Tandanus tandanus, in Victoria, Australia

Erin Hill, Brett A. Ingram, Meaghan Rourke, John Mitchell & Jan M. Strugnell
In Australia, many species of freshwater fish have rapidly declined following European settlement in the late eighteenth century. The freshwater catfish (Tandanus tandanus) is listed as threatened in Victoria and accordingly, broodstock management and a captive breeding program to facilitate the reintroduction of hatchery bred fish into depleted populations have been suggested. Little work has been conducted on Victorian populations of T. tandanus, despite its threatened status. This study assessed the genetic diversity and genetic...

Data from: Stress induced gene expression drives transient DNA methylation changes at adjacent repetitive elements

David Secco, Chuang Wang, Huixia Shou, Matthew D. Schultz, Serge Chiarenza, Laurent Nussaume, Joseph R. Ecker, James Whelan & Ryan Lister
Cytosine DNA methylation (mC) is a genome modification that can regulate the expression of coding and non-coding genetic elements. However, little is known about the involvement of mC in response to environmental cues. Using whole genome bisulfite sequencing to assess the spatio-temporal dynamics of mC in rice grown under phosphate starvation and recovery conditions, we identified widespread phosphate starvation-induced changes in mC, preferentially localized in transposable elements (TEs) close to highly induced genes. These changes...

Data from: The evolutionary consequences of blood-stage vaccination on the rodent malaria Plasmodium chabaudi

Victoria C. Barclay, Derek Sim, Brian H. K. Chan, Lucas A. Nell, Maia A. Rabaa, Andrew S. Bell, Robin F. Anders & Andrew F. Read
Malaria vaccine developers are concerned that antigenic escape will erode vaccine efficacy. Evolutionary theorists have raised the possibility that some types of vaccine could also create conditions favoring the evolution of more virulent pathogens. Such evolution would put unvaccinated people at greater risk of severe disease. Here we test the impact of vaccination with a single highly purified antigen on the malaria parasite Plasmodium chabaudi evolving in laboratory mice. The antigen we used, AMA-1, is...

Data from: Habitat disturbance selects against both small and large species across varying climates

Heloise Gibb, Nathan J. Sanders, Robert R. Dunn, Xavier Arnan, Heraldo L. Vasconcellos, David A. Donoso, Alan N. Andersen, Rogerio R. Silva, Tom R. Bishop, Crisanto Gomez, Blair F. Grossman, Kalsum M. Yusah, Sarah H. Luke, Renata Pacheco, Jessica Pearce-Duvet, Javier Retana, Melanie Tista, Catherine L. Parr & H. L. Vasconcelos
Global extinction drivers, including habitat disturbance and climate change, are thought to affect larger species more than smaller species. However, it is unclear if such drivers interact to affect assemblage body size distributions. We asked how these two key global change drivers differentially affect the interspecific size distributions of ants, one of the most abundant and ubiquitous animal groups on earth. We also asked whether there is evidence of synergistic interactions and whether effects are...

Data from: Mating patterns and post-mating isolation in three cryptic species of the Engystomops petersi species complex

Paula A. Trillo, Andrea E. Narvaez, Santiago R. Ron & Kim L. Hoke
Determining the extent of reproductive isolation in cryptic species with dynamic geographic ranges can give us important insights into the processes that generate and maintain genetic divergence in the absence of severe geographic barriers. We studied mating patterns, propensity to crossbreed in nature and subsequent fertilization rates, as well as survival and development of hybrid F1 offspring for three species of the E. petersi species complex in Yasuní National Park, Ecuador. We found at least...

Data from: Genetic diversity, population structure and ancestral origin of Australian wheat

Reem Joukhadar, Hans D. Daetwyler, Urmil K. Bansal, Anthony R. Gendall & Matthew J. Hayden
Since the introduction of wheat into Australia by the First Fleet settlers, germplasm from different geographical origins has been used to adapt wheat to the Australian climate through selection and breeding. In this paper, we used 482 cultivars, representing the breeding history of bread wheat in Australia since 1840, to characterize their diversity and population structure and to define the geographical ancestral background of Australian wheat germplasm. This was achieved by comparing them to a...

Data from: Plumage color manipulation has no effect on social dominance or fitness in zebra finches

Sofia Jerónimo, Mehdi Khadraoui, Daiping Wang, Katrin Martin, John A. Lesku, Kylie A. Robert, Emmi Schlicht, Wolfgang Forstmeier & Bart Kempenaers
Colourful plumage ornaments may evolve because they play a role in mate choice or in intrasexual competition, acting as signals of species identity or of individual quality. The zebra finch (Taeniopygia guttata) is a model organism for the study of mate choice and its colourful plumage ornaments are thought to be used in both of these contexts. Numerous genetic colour variants have been described for this species, but they are rare in the wild. This...

Data from: Leaf nutrients, not specific leaf area, are consistent indicators of elevated nutrient inputs

Jennifer Firn, James M. McGree, Eric Harvey, Habacuc Flores-Moreno, Martin Schütz, Yvonne M. Buckley, Elizabeth T. Borer, Eric W. Seabloom, Kimberly J. La Pierre, Andrew M. MacDougall, Suzanne M. Prober, Carly J. Stevens, Lauren L. Sullivan, Erica Porter, Emma Ladouceur, Charlotte Allen, Karine H. Moromizato, John W. Morgan, W. Stanley Harpole, Yann Hautier, Nico Eisenhauer, Justin P. Wright, Peter B. Adler, Carlos Alberto Arnillas, Jonathan D. Bakker … & Anita C. Risch
Leaf traits are frequently measured in ecology to provide a ‘common currency’ for predicting how anthropogenic pressures impact ecosystem function. Here, we test whether leaf traits consistently respond to experimental treatments across 27 globally distributed grassland sites across 4 continents. We find that specific leaf area (leaf area per unit mass)—a commonly measured morphological trait inferring shifts between plant growth strategies—did not respond to up to four years of soil nutrient additions. Leaf nitrogen, phosphorus...

Prey-switching does not protect a generalist turtle from bioenergetic consequences when its preferred food is scarce

James Van Dyke, Kristen Petrov, Ricky-John Spencer, Natasha Malkiewicz, Jessica Lewis & Claudia Keitel
Background: Optimal foraging theory explains how animals make foraging decisions based on the availability, nutritional content, and handling times of different food types. Generalists solve this problem by consuming a variety of food types, and switch between them with relative ease. Specialists eat few food types, and may starve if those food types are not available. We integrated stable isotope analyses with previously-published stomach contents and environmental data to investigate how the foraging ecologies of...

Fire and functional traits: using functional groups of birds and plants to guide management in fire-prone, heathy woodland ecosystem

Frederick Rainsford
Aim: Many dry forests and woodlands worldwide are fire-prone and support bird and plant communities shaped by fire. Changes in fire regimes, including the time between fires, have important implications for population trajectories. We studied the responses of bird and plant communities of heathy woodlands to time since the last fire, a key measure underpinning fire management, to evaluate whether current management strategies will enhance conservation of multiple taxa. Location: Otway Ranges, south-eastern Australia. Methods:...

Diverse parentage relationships in paternal mouth-brooders

Janine Abecia, Alison King, Osmar Luiz, David Crook, Dion Wedd & Sam Banks
While mouthbrooding is not an uncommon parental care strategy in fishes, paternal mouthbrooding only occurs in eight fish families and little studied. The high cost of paternal mouthbrooding to the male implies a low risk of investment in another male’s offspring but genetic parentage patterns are poorly known for paternal mouthbrooders. Here we used single nucleotide polymorphism (SNP) genetic data to investigate parentage relationships of broods of two mouthbrooders of northern Australian rivers, mouth almighty...

Data from: Low-cost automated flight intercept trap for the temporal sub-sampling of flying insects attracted to artificial light at night

Kylie Robert, Alicia Dimovski, Joel Robert & Stephen Griffiths
Sampling methods are selected depending on the targeted species or the spatial and temporal requirements of the study. However, most methods for passive sampling of flying insects have poor temporal resolution because it is time consuming, costly and/or logistically difficult. Effective sampling of flying insects attracted to artificial light at night (ALAN) requires sampling at user-defined time points (nighttime only) across well-replicated sites resulting in major time and labor-intensive survey effort or expensive automated technologies....

MO2, behaviour data and supplementary material for the first physiological evidence of sleep in sharks

Michael Kelly, Selwyn Collins, John Lesku, Jan Hemmi, Shaun Collin & Craig Radford
Sharks represent the earliest group of jawed vertebrates and as such, they may provide original insight for understanding the evolution of sleep in more derived animals. Unfortunately, beyond a single behavioural investigation, very little is known about sleep in these ancient predators. As such, recordings of physiological indicators of sleep in sharks have never been reported. Reduced energy expenditure arising from sustained restfulness and lowered metabolic rate during sleep have given rise to the hypothesis...

Birds and insects respond differently to combinations of semi-natural features in farm landscapes

Mark Hall, Dale Nimmo & Andrew F Bennett
Semi-natural features among farmland have a key role in maintaining wildlife in rural landscapes. Practical conservation requires knowledge of which combinations of features are of greatest value and whether this differs among faunal groups. We used a ‘landscape’ approach to investigate the relative importance to birds and insects (bees, flies, wasps) of combinations of three wooded features typical of farmland in south-eastern Australia: scattered trees, wooded roadsides and wooded streamside vegetation. We selected 44 landscapes...

Caecal dysfunction and neuro-immune alterations in a preclinical model of autism

Chalystha Yie Qin Lee, Gayathri K Balasuriya, Madushani Herath, Ashley Franks & Elisa Hill-Yardin
Autism Spectrum Disorder (ASD; autism) is commonly presented with gastrointestinal (GI) illness in addition to core diagnostic behavioural traits. Important for GI homeostasis is the appendix, or the caecum in mice, which functions as a key site for fermentation and a microbial reservoir. Even so, the role of the appendix and caecum in autism-associated GI symptoms remains uninvestigated. Here, we studied mice with an autism-associated missense mutation in the post-synaptic protein neuroligin-3 (NL3R451C), which impacts...

Additional file 1 of Clinical implications of circulating tumor DNA in predicting the outcome of diffuse large B cell lymphoma patients receiving first-line therapy

Miaomiao Li, Lan Mi, Chunyang Wang, Xiaojuan Wang, Jianhua Zhu, Fei Qi, Hui Yu, Yingying Ye, Dedao Wang, Jiaowu Cao, Dingyao Hu, Quanyu Yang, Dandan Zhao, Tonghui Ma, Yuqin Song & Jun Zhu
Additional file 1: Table S1. Gene list of Onco-LymScan panel. Table S2. Overview of patient characteristics. Table S3. Demographic of patient characteristics. Table S4. Sequencing quality data of tumor gDNA samples. Table S5. Sequencing quality data of cfDNA samples. Table S6. Univariate Cox proportional hazard regression survival analysis including pretreatment ctDNA levels and other clinical indices.

Whole-of-community invertebrate rewilding: Leaf litter transplants rapidly increase beetle diversity during restoration

Peter Contos, Nicholas Murphy & Heloise Gibb
Restoration of degraded areas is now a central tool in humanity’s response to continued species loss. However, restoration projects often report exceedingly slow or failed recolonization of fauna, especially dispersal-constrained groups such as invertebrates. Active interventions via reintroducing or “rewilding” invertebrates may assist recolonization and speed up the restoration of communities towards a desired target. However, invertebrate rewilding is rarely implemented during ecological restoration. Here, we studied the efficacy of invertebrate rewilding as a means...


Ruitao Jin
Models generated using 5XN5 and 1RQI as templates for wild-type GGPPS and its VA mutant in PDB format, water and ion are not included.

Data set for article: Fusing ToF-SIMS images for spatial-spectral resolution enhancement using a convolutional neural network

Wil Gardner
This data set is uploaded as supporting information for the publication entitled: Fusing ToF-SIMS images for spatial-spectral resolution enhancement using a convolutional neural network
Files are as follows: gold_mesh_data.mat - MATLAB workspace file containing peak-picked ToF-SIMS data (hyperspectral array) for the gold mesh sample. tumor_tissue_data.mat - MATLAB workspace file containing peak-picked ToF-SIMS data (hyperspectral array) for the tumor tissue sample. Additional details about the datasets can be found in the published article.

N alexis FAM validation data.xlsx

Kelly Williams, Kylie Robert, Rupert Palme & Kerry Fanson
Faecal androgen metabolites from male spinifix hopping mice (Notomys alexis), an Australian native rodent. Faeces collected non-invasively for validating two enzyme immunoassays.
Pre-print of article associated with the data is available in SSRN: https://ssrn.com/abstract=4072560 or http://dx.doi.org/10.2139/ssrn.4072560 Williams-Kelly, Kelly S. and Robert, Kylie A. and Palme, Rupert and Fanson, Kerry V., Validation of an Enzyme Immunoassay for the Non-Invasive Measurement of Faecal Androgen Metabolites in Spinifex Hopping Mice ( Notomys Alexis).

Reprdocutive biology of Grevillea bedggoodiana study. Microsatellite data and R-code.

Stanislaw Wawrzyczek, Susan Hoebee & Gareth Holmes
Microasatellite allele data and R-code used in the study: Wawrzyczek, S., Holmes, G.D. & Hoebee, S.E. Reproductive biology and population structure of the endangered shrub Grevillea bedggoodiana (Proteaceae). Conserv Genet (2022). https://doi.org/10.1007/s10592-022-01480-4

Landscape Zones of the Lake Eyre Basin

Gresley Wakelin-King
The dataset divides the Lake Eyre Basin into nine landscape zones, based on the elements that govern form and processes of the surface waters. They are: Uplands, Rocky Fringe, Western Rivers, Northern Plains, Central Plains, Channel Country-Vertic Downs, Channel Country-Stony Domes, Lakes & Dunes, Mega-lakes. This dataset is described in Gresley A. Wakelin-King (2022) Landscapes of the Lake Eyre Basin: the catchment-scale context that creates fluvial diversity, Transactions of the Royal Society of South Australia,...

Data from: Optimising the hatching success of artificially incubated eggs for use in a conservation program for the western saw-shelled turtle (Myuchelys bellii)

Louise Streeting, Deborah Bower, Martin Dillon, Phil Spark, Michael Gough, Adam Skidmore, Paul McDonald, Hannah Delaney, Adrienne Burns, Sandy Watson, Duminda Dissanayake, Arthur Georges & Donald McKnight
Artificial incubation of eggs and the release of hatchlings into the wild is a common conservation intervention designed to augment threatened turtle populations. We investigate a range of incubation temperatures to establish an optimal temperature for maximum hatching success of western saw-shelled turtle (Myuchelys bellii) eggs. We report on the influence of incubation temperature on incubation duration and hatching success and describe two experimental incubation methods which, for the same incubation temperature, resulted in 77%...

Additional file 3 of The Venturia inaequalis effector repertoire is dominated by expanded families with predicted structural similarity, but unrelated sequence, to avirulence proteins from other plant-pathogenic fungi

Mercedes Rocafort, Joanna K. Bowen, Berit Hassing, Murray P. Cox, Brogan McGreal, Silvia de la Rosa, Kim M. Plummer, Rosie E. Bradshaw & Carl H. Mesarich
Additional file 3: Differentially expressed genes of Venturia inaequalis during infection of susceptible apple cultivar ‘Royal Gala’, when compared to growth of the fungus in culture on the surface of cellophane membranes overlying potato dextrose agar.

Registration Year

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Resource Types

  • Dataset


  • La Trobe University
  • Monash University
  • University of Melbourne
  • University of Tasmania
  • Massey University
  • Huazhong University of Science and Technology
  • Plant & Food Research
  • James Cook University
  • University of Edinburgh
  • Sun Yat-sen University