366 Works

Data from: Catchment zoning for freshwater conservation: refining plans to enhance action on the ground

Virgilio Hermoso, Lorenzo Cattarino, Mark J. Kennard, Matthew Watts, Simon Linke & Mathew Watts
1. Recent advances in freshwater conservation planning allow addressing some of the specific needs of these systems. These include spatial connectivity or propagation of threats along stream networks, essential to ensure the maintenance of ecosystem processes and the biodiversity they sustain. However, these peculiarities make conservation recommendations difficult to implement as they often require considering large areas that cannot be managed under conventional conservation schemes (e.g. strict protection). 2. To facilitate the implementation of conservation...

Data from: Not the time or the place: the missing spatio-temporal link in publicly available genetic data

Lisa C. Pope, Libby Liggins, Jude Keyse, Silvia B. Carvalho & Cynthia Riginos
Genetic data are being generated at unprecedented rates. Policies of many journals, institutions and funding bodies aim to ensure that these data are publicly archived so that published results are reproducible. Additionally, publicly archived data can be ‘repurposed’ to address new questions in the future. In 2011, along with other leading journals in ecology and evolution, Molecular Ecology implemented mandatory public data archiving (the Joint Data Archiving Policy). To evaluate the effect of this policy,...

Data from: Re-visiting the phylogeography and demography of European badgers (Meles meles) based on broad sampling, multiple markers and simulations

Alain C. Frantz, Allan D. McDevitt, Lisa C. Pope, Joanna Kochan, John Davison, Chris F. Clements, Morten Elmeros, Guillem Molina-Vacas, Aritz Ruiz-Gonzalez, Alessandro Balestrieri, Koen Van Den Berge, Peter Breyne, Emmanuel Do Linh San, Erik O. Ågren, Franz Suchentrunk, Laurent Schley, Rafał Kowalczyk, Berit I. Kostka, Dusko Ćirović, Nikica Šprem, Marc Colyn, Marco Ghirardi, Venislava Racheva, Christophe Braun, Rita Oliveira … & Terry Burke
Although the phylogeography of European mammals has been extensively investigated since the 1990s, many studies were limited in terms of sampling distribution, the number of molecular markers used and the analytical techniques employed, frequently leading to incomplete postglacial recolonisation scenarios. The broad-scale genetic structure of the European badger (Meles meles) is of interest as it may result from historic restriction to glacial refugia and/or recent anthropogenic impact. However, previous studies were based mostly on samples...

Data from: Trait compensation and sex-specific aging of performance in male and female professional basketball players

Simon P. Lailvaux, Robbie Wilson & Michael M. Kasumovic
Phenotypic traits are often influenced by dynamic resource allocation trade-offs which, when occurring over the course of individual lifespans, may manifest as trait aging. Although aging is studied for a variety of traits that are closely tied to reproduction or reproductive effort, the aging of multiple traits related to fitness in other ways are less well understood. We took advantage of almost 30 years of data on human whole-organism performance in the National Basketball Association...

Data from: Genomic evidence that sexual selection impedes adaptation to a novel environment

Stephen F. Chenoweth, Nicolas C. Appleton, Scott L. Allen & Howard D. Rundle
Sexual selection is widely appreciated for generating remarkable phenotypic diversity, but its contribution to adaptation and the purging of deleterious mutations is unresolved. To provide insight into the impact of sexual selection on naturally segregating polymorphisms across the genome, we previously evolved 12 populations of Drosophila serrata in a novel environment employing a factorial manipulation of the opportunities for natural and sexual selection. Here, we genotype more than 1,400 SNPs in the evolved populations and...

Data from: Clock model makes a large difference to age estimates of long-stemmed clades with no internal calibration: a test using Australian grasstrees

Michael D. Crisp, Nate B. Hardy & Lyn G. Cook
Background: Estimating divergence times in phylogenies using a molecular clock depends on accurate modeling of nucleotide substitution rates in DNA sequences. Rate heterogeneity among lineages is likely to affect estimates, especially in lineages with long stems and short crowns (“broom” clades) and no internal calibration. We evaluate the performance of the random local clocks model (RLC) and the more routinely employed uncorrelated lognormal relaxed clock model (UCLN) in situations in which a significant rate shift...

Data from: High-throughput genotyping for species identification and diversity assessment in germplasm collections

Annaliese S. Mason, Jing Zhang, Reece Tollenaere, Paula Vasquez Teuber, Jessica Dalton-Morgan, Liyong Hu, Guijun Yan, David Edwards, Robert Redden & Jacqueline Batley
Germplasm collections provide an extremely valuable resource for breeders and researchers. However, misclassification of accessions by species often hinders the effective use of these collections. We propose that use of high-throughput genotyping tools can provide a fast, efficient and cost-effective way of confirming species in germplasm collections, as well as providing valuable genetic diversity data. We genotyped 180 Brassicaceae samples sourced from the Australian Grains Genebank across the recently released Illumina Infinium Brassica 60K SNP...

Data from: The emergent geography of biophysical dispersal barriers across the Indo-West Pacific

Eric A. Treml, Jason Roberts, Patrick N. Halpin, Hugh P. Possingham & Cynthia Riginos
Aim: To discover and evaluate potential dispersal barriers across the Indo-West Pacific Ocean and to develop spatially explicit hypotheses regarding the location of barriers and their capacity to filter taxa. Additionally, to compare model predictions with previously described barriers and build a more thorough understanding of the region's biogeographic patterns. Location: The reefs of the Indo-West Pacific Ocean, from 100 to 170°E and from 30°N to 30°S. Methods: A biophysical larval dispersal model was used...

Data from: Less is more: extreme genome complexity reduction with ddRAD using Ion Torrent semiconductor technology

Lilian Pukk, Freed Ahmad, Shihab Hasan, Veljo Kisand, Riho Gross & Anti Vasemägi
Massively parallel sequencing a small proportion of the whole genome at high coverage enables answering a wide range of questions from molecular evolution and evolutionary biology to animal and plant breeding and forensics. In this study, we describe the development of restriction-site associated DNA (RAD) sequencing approach for Ion Torrent PGM platform. Our protocol results in extreme genome complexity reduction using two rare-cutting restriction enzymes and strict size selection of the library allowing sequencing of...

Data from: Biodiversity gains from efficient use of private sponsorship for flagship species conservation

Joseph R. Bennett, Richard Maloney & Hugh P. Possingham
To address the global extinction crisis, both efficient use of existing conservation funding and new sources of funding are vital. Private sponsorship of charismatic ‘flagship’ species conservation represents an important source of new funding, but has been criticized as being inefficient. However, the ancillary benefits of privately sponsored flagship species conservation via actions benefiting other species have not been quantified, nor have the benefits of incorporating such sponsorship into objective prioritization protocols. Here, we use...

Data from: Skin sloughing in susceptible and resistant amphibians regulates infection with a fungal pathogen

Michel E. B. Ohmer, Rebecca L. Cramp, Catherine J. M. Russo, Craig R. White & Craig E. Franklin
The fungal pathogen Batrachochytrium dendrobatidis (Bd) has been implicated in amphibian population declines globally. Given that Bd infection is limited to the skin in post-metamorphic amphibians, routine skin sloughing may regulate infection. Skin sloughing has been shown to reduce the number of cultivatable microbes on amphibian skin, and Bd infection increases skin sloughing rates at high loads. However, it is unclear whether species specific differences in skin sloughing patterns could regulate Bd population growth on...

Data from: Optimizing the spatial planning of prescribed burns to achieve multiple objectives in a fire-dependent ecosystem.

Brooke A. Williams, Luke P. Shoo, Kerrie A. Wilson & Hawthorne L. Beyer
1. There is potential for negative consequences for the ecological integrity of fire-dependent ecosystems as a result of inappropriate fire regimes. This can occur when asset (property) protection is prioritised over conservation objectives in burn programs. 2. Optimisation of fire management for multiple objectives is rarely undertaken. Here, we use integer linear programming to identify burn scheduling solutions that will cost-effectively achieve asset protection and conservation objectives. 3. An approach to burn scheduling that favours...

Data from: How does mutation affect the distribution of phenotypes?

Katrina McGuigan & Ernest Aw
The potential for mutational processes to influence patterns of neutral or adaptive phenotypic evolution is not well understood. If mutations are directionally biased, shifting trait means in a particular direction, or if mutation generates more variance in some directions of multivariate trait space than others, mutation itself might be a source of bias in phenotypic evolution. Here, we use mutagenesis to investigate the affect of mutation on trait mean and (co)variances in zebrafish, Danio rerio....

Data from: Taphonomy of Isisfordia duncani specimens from the Lower Cretaceous (upper Albian) portion of the Winton Formation, Isisford, central-west Queensland

Caitlin E. Syme & Steven W. Salisbury
Taphonomic analysis of fossil material can benefit from including the results of actualistic decay experiments. This is crucial in determining the autochthony or allochthony of fossils of juvenile and adult Isisfordia duncani, a basal eusuchian from the Lower Cretaceous (upper Albian) distal-fluvial-deltaic lower Winton Formation near Isisford. The taphonomic characteristics of the I. duncani fossils were documented using a combination of traditional taphonomic analysis alongside already published actualistic decay data from juvenile Crocodylus porosus carcasses....

Data from: Congruent patterns of connectivity can inform management for broadcast spawning corals on the Great Barrier Reef

Lukoschek Vimoksalehi, Cynthia Riginos, Madeleine J.H. Van Oppen, Madeleine J. H. Van Oppen & Vimoksalehi Lukoschek
Connectivity underpins the persistence and recovery of marine ecosystems. The Great Barrier Reef (GBR) is the world's largest coral reef ecosystem and managed by an extensive network of no-take zones; however, information about connectivity was not available to optimize the network's configuration. We use multivariate analyses, Bayesian clustering algorithms and assignment tests of the largest population genetic data set for any organism on the GBR to date (Acropora tenuis, >2500 colonies; >50 reefs, genotyped for...

Data from: Mitochondrial genomes of Australian chicken Eimeria support the presence of ten species with low genetic diversity among strains

Jess A. T. Morgan, Rosamond M. Godwin & Jess A.T. Morgan
Modern molecular approaches have vastly improved diagnostic capabilities for differentiating among species of chicken infecting Eimeria. Consolidating information from multiple genetic markers, adding additional poultry Eimeria species and increasing the size of available data-sets is improving the resolving power of the DNA, and consequently our understanding of the genus. This study adds information from 25 complete mitochondrial DNA genomes from Australian chicken Eimeria isolates representing all 10 species known to occur in Australia, including OTU-X,...

Data from: Diversification across a heterogeneous landscape

Gregory M. Walter, Melanie J. Wilkinson, Maddie E. James, Thomas J. Richards, J. David Aguirre, Daniel Ortiz-Barrientos & Greg M. Walter
Adaptation to contrasting environments across a heterogeneous landscape favors the formation of ecotypes by promoting ecological divergence. Patterns of fitness variation in the field can show whether natural selection drives local adaptation and ecotype formation. However, to demonstrate a link between ecological divergence and speciation, local adaptation must have consequences for reproductive isolation. Using contrasting ecotypes of an Australian wildflower, Senecio lautus in common garden experiments, hybridization experiments, and reciprocal transplants, we assessed how the...

Data from: Immigrant inviability produces a strong barrier to gene flow between parapatric ecotypes of Senecio lautus

Thomas John Richards & Daniel Ortiz-Barrientos
Speciation proceeds when gene exchange is prevented between populations. Determining the different barriers preventing gene flow can therefore give insights into the factors driving and maintaining species boundaries. These reproductive barriers may result from intrinsic genetic incompatibilities between populations, from extrinsic environmental differences between populations, or a combination of both mechanisms. We investigated the potential barriers to gene exchange between three adjacent ecotypes of an Australian wildflower to determine the strength of individual barriers and...

Data from: Perioperative medication management: expanding the role of the preadmission clinic pharmacist in a single centre, randomised controlled trial of collaborative prescribing

Andrew R. Hale, Ian D. Coombes, Julie Stokes, David McDougall, Karen Whitfield, Elizabeth Maycock & Lisa Nissen
Objectives: Current evidence to support non-medical prescribing is predominantly qualitative, with little evaluation of accuracy, safety and appropriateness. Our aim was to evaluate a new model of service for the Australia healthcare system, of inpatient medication prescribing by a pharmacist in an elective surgery pre admission clinic (PAC) against usual care, using an endorsed performance framework. Design: Single centre, randomised controlled, two arm trial Setting: Elective surgery pre admission clinic in Brisbane based tertiary hospital...

Data from: Echidna venom gland transcriptome provides insights into the evolution of monotreme venom

Emily S. W. Wong, Stewart Nichol, Wesley C. Warren, Katherine Belov & Stewart Nicol
Monotremes (echidna and platypus) are egg-laying mammals. One of their most unique characteristic is that males have venom/crural glands that are seasonally active. Male platypuses produce venom during the breeding season, delivered via spurs, to aid in competition against other males. Echidnas are not able to erect their spurs, but a milky secretion is produced by the gland during the breeding season. The function and molecular composition of echidna venom is as yet unknown. Hence,...

Data from: Pattern edges improve predator learning of aposematic signals

Naomi F. Green, Holly H. Urquhart, Cedric P. Van Den Berg, N. Justin Marshall & Karen L. Cheney
Edges are salient visual cues created by abrupt changes in luminance and color, and are crucial in perceptual tasks such as motion detection and object recognition. Disruptively colored animals exploit edge detection mechanisms to obscure their body outline and/or to conceal themselves against their background. Conversely, aposematic species may use contrasting patterns with well-defined edges to create highly salient, memorable warning signals. In this study, we investigated how the amount of internal pattern edge, colored...

Data from: Assessment of plasma proteomics biomarker’s ability to distinguish benign from malignant lung nodules

Gerard A. Silvestri, Nichole T. Tanner, Paul Kearney, Anil Vachani, Pierre P. Massion, Alexander Porter, Steven C. Springmeyer, Kenneth C. Fang, David Midthun, Peter J. Mazzone, D. Madtes, J. Landis, A. Levesque, K. Rothe, M. Balaan, B. Dimitt, B. Fortin, N. Ettinger, A. Pierre, L. Yarmus, K. Oakjones-Burgess, N. Desai, Z. Hammoud, A. Sorenson, R. Murali … & F. Allison
Background: Lung nodules are a diagnostic challenge, with an estimated yearly incidence of 1.6 million in the United States. This study evaluated the accuracy of an integrated proteomic classifier in identifying benign nodules in patients with a pretest probability of cancer (pCA) ≤ 50%. Methods: A prospective, multicenter observational trial of 685 patients with 8- to 30-mm lung nodules was conducted. Multiple reaction monitoring mass spectrometry was used to measure the relative abundance of two...

Data from: Accurate predictions of coexistence in natural systems require the inclusion of facilitative interactions and environmental dependency

Malyon D. Bimler, Daniel B. Stouffer, Hao Ran Lai & Margaret M. Mayfield
1. Coexistence between plant species is well known to depend on the outcomes of species interactions within an environmental context. The incorporation of environmental variation into empirical studies of coexistence are rare, however, due to the complex experiments needed to do so and the lack of feasible modelling approaches for determining how environmental factors alter specific coexistence mechanisms. 2. In this paper, we present a simple modelling framework for assessing how variation in species interactions...

Data from: Environmental influences and ontogenetic differences in vertical habitat use of black marlin (Istiompax indica) in the southwestern Pacific

Samuel M. Williams, Bonnie J. Holmes, Sean R. Tracey, Julian G. Pepperell, Michael L. Domeier & Michael B. Bennett
The black marlin (Istiompax indica) is a highly migratory billfish that occupies waters throughout the tropical and subtropical Indo-Pacific. To characterize the vertical habitat use of I. indica, we examined the temperature-depth profiles collected using 102 pop-up satellite archival tags deployed off the east coast of Australia. Modelling of environmental variables revealed location, sea-surface height deviation, mixed layer depth and dissolved oxygen to all be significant predictors of vertical habitat use. Distinct differences in diel...

Data from: Using virtual reality to estimate aesthetic values of coral reefs

Julie Vercelloni, Sam Clifford, M. Julian Caley, Alan R. Pearse, Ross Brown, Allan James, Bryce Christensen, Tomasz Bednarz, Ken Anthony, Manuel González-Rivero, Kerrie Mengersen & Erin E. Peterson
Aesthetic value, or beauty, is important to the relationship between humans and natural environments and is, therefore, a fundamental socioeconomic attribute of conservation alongside other ecosystem services. However, beauty is difficult to quantify and is not estimated well using traditional approaches to monitoring coral reef aesthetics. To improve the estimation of ecosystem aesthetic values, we developed and implemented a novel framework used to quantify features of coral reef aesthetics based on people’s perceptions of beauty....

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