22 Works

Data from: An examination of the accuracy of a sequential PCR and sequencing test used to detect the incursion of an invasive species: the case of the red fox in Tasmania

David S. L. Ramsey, Anna J. MacDonald, Sumaiya Quasim, Candida Barclay & Stephen D. Sarre
1. Polymerase Chain Reaction (PCR) diagnostic tests are increasingly applied to the identification of wildlife. Yet rigorous verification is rare and the estimation of test accuracy (the probability that true positive and true negative samples are correctly identified – test sensitivity and specificity, respectively), particularly in combination with sequencing, is uncommon. This is important because PCR-based tests are prone to contamination in sampling and the laboratory. 2. Here, we use an experimental case–control approach to...

Data from: Multilocus phylogeography reveals nested endemism in a gecko across the monsoonal tropics of Australia

Craig Moritz, Matthew Fujita, Dan F. Rosauer, Rosa Agudo, Gayleen Bourke, Russell Palmer, Mitzy Pepper, Sally Potter, Renae Pratt, Mitchell Scott, Maria Tonione, Stephen Donnellan, Paul Doughty, D. Rosauer & M. K. Fujita
Multilocus phylogeography can uncover taxonomically unrecognized lineage diversity across complex biomes. The Australian monsoonal tropics includes vast, ecologically intact savanna-woodland plains interspersed with ancient sandstone uplands. Though recognized in general for its high species richness and endemism, the biodiversity of the region remains underexplored due to its remoteness. This is despite a high rate of ongoing species discovery, especially in wetter regions and for rock-restricted taxa. To provide a baseline for ongoing comparative analyses, we...

Data from: Not so colourful after all: eggshell pigments constrain avian eggshell colour space

Daniel Hanley, Tomáš Grim, Phillip Cassey & Mark E. Hauber
Birds' eggshells are renowned for their striking colours and varied patterns. Although often considered exceptionally diverse, we report that avian eggshell coloration, sampled here across the full phylogenetic diversity of birds, occupies only 0.08–0.10% of the avian perceivable colour space. The concentrations of the two known tetrapyrrole eggshell pigments (protoporphyrin and biliverdin) are generally poor predictors of colour, both intra- and interspecifically. Here, we show that the constrained diversity of eggshell coloration can be accurately...

Data from: Restoring Study 329: efficacy and harms of paroxetine and imipramine in treatment of major depression in adolescence

Joanna C. Le Noury, John M. Nardo, David Healy, Jon Jureidini, Melissa Raven, Catalin Tufanaru & Elia Abi-Jaoude
Objectives: To reanalyse SmithKline Beecham’s Study 329 (published by Keller and colleagues in 2001), the primary objective of which was to compare the efficacy and safety of paroxetine and imipramine with placebo in the treatment of adolescents with unipolar major depression. The reanalysis under the restoring invisible and abandoned trials (RIAT) initiative was done to see whether access to and reanalysis of a full dataset from a randomised controlled trial would have clinically relevant implications...

Data from: Temporal modelling of ballast water discharge and ship-mediated invasion risk to Australia

Robert C. Cope, Thomas A. A. Prowse, Joshua V. Ross, Talia A. Wittmann & Phillip Cassey
Biological invasions have the potential to cause extensive ecological and economic damage. Maritime trade facilitates biological invasions by transferring species in ballast water, and on ships' hulls. With volumes of maritime trade increasing globally, efforts to prevent these biological invasions are of significant importance. Both the International Maritime Organization and the Australian government have developed policy seeking to reduce the risk of these invasions. In this study, we constructed models for the transfer of ballast...

Data from: Direct and indirect effects of nursery habitats on coral-reef fish assemblages, grazing pressure, and benthic dynamics

Alastair R. Harborne, Ivan Nagelkerken, Nicholas H. Wolff, Yves-Marie Bozec, Martijn Dorenbosch, Monique G. G. Grol & Peter J. Mumby
Migrating species are common within seascapes, but the potential for these movements to alter the populations and functional roles of non-migrating species (e.g. by increasing predation) is rarely investigated. This study considers whether the presence of nursery habitats (mangroves and seagrass) simply enhances the abundance of nursery-using parrotfishes and piscivores on nearby coral reefs, or also affects other parrotfishes. Data from 131 reef sites and multiple seascape configurations across 13 degrees of latitude were used...

Data from: Diversification rates and phenotypic evolution in venomous snakes (Elapidae)

Michael S. Y. Lee, Kate L. Sanders, Benedict King & Alessandro Palci
The relationship between rates of diversification and of body size change (a common proxy for phenotypic evolution) was investigated across Elapidae, the largest radiation of highly venomous snakes. Time-calibrated phylogenetic trees for 175 species of elapids (more than 50% of known taxa) were constructed using seven mitochondrial and nuclear genes. Analyses using these trees revealed no evidence for a link between speciation rates and changes in body size. Two clades (Hydrophis, Micrurus) show anomalously high...

Data from: Evolutionary novelty in a butterfly wing pattern through enhancer shuffling

Richard W. R. Wallbank, Simon W. Baxter, Carolina Pardo-Diaz, Joseph J. Hanly, Simon H. Martin, James Mallet, Kanchon K. Dasmahapatra, Camilo Salazar, Mathieu Joron, Nicola Nadeau, W. Owen McMillan & Chris D. Jiggins
An important goal in evolutionary biology is to understand the genetic changes underlying novel morphological structures. We investigated the origins of a complex wing pattern found among Amazonian Heliconius butterflies. Genome sequence data from 142 individuals across 17 species identified narrow regions associated with two distinct red colour pattern elements, dennis and ray. We hypothesise that these modules in non-coding sequence represent distinct cis-regulatory loci that control expression of the transcription factor optix, which in...

Data from: Tick exposure and extreme climate events impact survival and threaten the persistence of a long-lived lizard

Alice R. Jones, C. Michael Bull, Barry W. Brook, Konstans Wells, Kenneth H. Pollock & Damien A. Fordham
1. Assessing the impacts of multiple, often synergistic, stressors on the population dynamics of long-lived species is becoming increasingly important due to recent and future global change. 2. Tiliqua rugosa (sleepy lizard) is a long-lived skink (>30 years) that is adapted to survive in semi-arid environments with varying levels of parasite exposure and highly seasonal food availability. We used an exhaustive database of 30-years of capture-mark-recapture records to quantify the impacts of both parasite exposure...

Data from: Ocean acidification boosts larval fish development but reduces the window of opportunity for successful settlement

Tullio Rossi, Ivan Nagelkerken, Stephen D. Simpson, Jennifer C.A. Pistevos, Sue-Ann Watson, Laurene Merillet, Peter Fraser, Philip L. Munday & Sean D. Connell
Locating appropriate settlement habitat is a crucial step in the life cycle of most benthic marine animals. In marine fish, this step involves the use of multiple senses, including audition, olfaction and vision. To date, most investigations of fish audition focus on the hearing thresholds to various frequencies of sounds without testing an ecological response to such sounds. Identifying responses to biologically relevant sounds at the development stage in which orientation is most relevant is...

Data from: Lean-season primary productivity and heat dissipation as key drivers of geographic body-size variation in a widespread marsupial

Rachel A. Correll, Thomas A. A. Prowse & Gavin J. Prideaux
Geographic body-size variation characterises many mammal species. Hypotheses centring around heat conservation, heat dissipation, primary productivity and seasonality have been advanced to explain geographic body-size patterns. However, identification of the primary body-size drivers has often been hampered by a paucity of data for broadly distributed species and the application of regression models that have not explicitly accounted for the spatial clustering inherent in such datasets. We used Australia's most widespread marsupial, the common brushtail possum...

Data from: Lost at sea: ocean acidification undermines larval fish orientation via altered hearing and marine soundscape modification

Tullio Rossi, Ivan Nagelkerken, Jennifer C. A. Pistevos & Sean D. Connell
The dispersal of larvae and their settlement to suitable habitat is fundamental to the replenishment of marine populations and the communities in which they live. Sound plays an important role in this process because for larvae of various species, it acts as an orientational cue towards suitable settlement habitat. Because marine sounds are largely of biological origin, they not only carry information about the location of potential habitat, but also information about the quality of...

Data from: Partial migration: growth varies between resident and migratory fish

Bronwyn M. Gillanders, Christopher Izzo, Zoë A. Doubleday & Qifeng Ye
Partial migration occurs in many taxa and ecosystems and may confer survival benefits. Here, we use otolith chemistry data to determine whether fish from a large estuarine system were resident or migratory, and then examine whether contingents display differences in modelled growth based on changes in width of otolith growth increments. Sixty-three per cent of fish were resident based on Ba : Ca of otoliths, with the remainder categorized as migratory, with both contingents distributed...

Data from: Sinonasal microbiome sampling: a comparison of techniques

Ahmed Bassiouni, Edward John Cleland, Alkis James Psaltis, Sarah Vreugde & Peter-John Wormald
Background: The role of the sino-nasal microbiome in CRS remains unclear. We hypothesized that the bacteria within mucosal-associated biofilms may be different from the more superficial-lying, free-floating bacteria in the sinuses and that this may impact on the microbiome results obtained. This study investigates whether there is a significant difference in the microbiota of a sinonasal mucosal tissue sample versus a swab sample. Methods: Cross-sectional study with paired design. Mucosal biopsy and swab samples were...

Data from: Conservatism and novelty in the genetic architecture of adaptation in Heliconius butterflies

Bárbara Huber, Annabel Whibley, Yann Le Poul, Nicolas Navarro, Arnaud Martin, Simon Baxter, Abhijeet Shah, Benoît Gilles, Thierry Wirth, W. Owen McMillan & Mathieu Joron
Understanding the genetic architecture of adaptive traits has been at the centre of modern evolutionary biology since Fisher; however, evaluating how the genetic architecture of ecologically important traits influences their diversification has been hampered by the scarcity of empirical data. Now, high-throughput genomics facilitates the detailed exploration of variation in the genome-to-phenotype map among closely related taxa. Here, we investigate the evolution of wing pattern diversity in Heliconius, a clade of neotropical butterflies that have...

Data from: Combined DNA, toxicological and heavy metal analyses provides an auditing toolkit to improve pharmacovigilance of traditional Chinese medicine (TCM).

Megan L. Coghlan, Garth Maker, Elly Crighton, James Haile, Dáithí C. Murray, Nicole E. White, Roger W. Byard, Matthew I. Bellgard, Ian Mullaney, Robert Trengove, Richard J. N. Allcock, Christine Nash, Claire Hoban, Kevin Jarrett, Ross Edwards, Ian F. Musgrave & Michael Bunce
Globally, there has been an increase in the use of herbal remedies including traditional Chinese medicine (TCM). There is a perception that products are natural, safe and effectively regulated, however, regulatory agencies are hampered by a lack of a toolkit to audit ingredient lists, adulterants and constituent active compounds. Here, for the first time, a multidisciplinary approach to assessing the molecular content of 26 TCMs is described. Next generation DNA sequencing is combined with toxicological...

Data from: Where did all the trees come from? A novel multispecies approach reveals the impacts of biogeographical history and functional diversity on rain forest assembly

Maurizio Rossetto, Hannah McPherson, Juelian Siow, Robert Kooyman, Marlien Van Der Merwe & Peter D. Wilson
Aim: We take advantage of next generation sequencing-based technology to assess how landscape-level dynamics, biogeographical history and functional factors shape the distribution of genetic diversity in rain forest trees. To achieve this, we explore chloroplast genomic diversity and divergence patterns across multiple, co-distributed species from three major centres of rain forest diversity. Location: Subtropical rain forests in south-eastern Australia: Nightcap–Border Ranges, Dorrigo and Washpool. Methods: We assembled chloroplast genomic data from whole-genome shotgun libraries for...

Data from: An assessment of ancient DNA preservation in Holocene-Pleistocene fossil bone excavated from the world heritage Naracoorte Caves, South Australia

Alicia Grealy, Amy Macken, Morten E. Allentoft, Nicolas J. Rawlence, Elizabeth Reed & Michael Bunce
Although there is a long history of research into the fossil deposits of the Naracoorte Caves (South Australia), ancient DNA (aDNA) has not been integrated into any palaeontological study from this World Heritage site. Here, we provide the first evidence of aDNA preservation in Holocene- and Pleistocene-aged fossil bone from a deposit inside Robertson Cave. Using a combination of metabarcoding and shotgun next-generation sequencing approaches, we demonstrate that aDNA from diverse taxa can be retrieved...

Data from: Genetic parentage analysis confirms a polygynandrous breeding system in the European grayling (Thymallus thymallus)

Peter Jørgen Haddeland, Claudia Junge, Dimitar Serbezov & Leif Asbjørn Vøllestad
Knowing the breeding system of a species is important in order to understand individual variation in reproductive success. Large variation in reproductive success and thus reproductive skew strongly impacts on the effective number of breeders and thus the long-term effective population size (Ne). Fishes, in particular species belonging to the salmonid family, exhibit a wide diversity of breeding systems. In general, however, breeding systems are rarely studied in detail in the wild. Here we examine...

Data from: Climate impacts on trans-ocean dispersal and habitat in gray whales from the Pleistocene to 2100

S. Elizabeth Alter, Matthias Meyer, Klaas Post, Paul Czechowski, Peter Gravlund, Cork Gaines, Howard C. Rosenbaum, Kristin Kaschner, Samuel T. Turvey, Johannes Van Der Plicht, Beth Shapiro & Michael Hofreiter
Arctic animals face dramatic habitat alteration due to ongoing climate change. Understanding how such species have responded to past glacial cycles can help us forecast their response to today's changing climate. Gray whales are among those marine species likely to be strongly affected by Arctic climate change, but a thorough analysis of past climate impacts on this species has been complicated by lack of information about an extinct population in the Atlantic. While little is...

Data from: The impact of anchored phylogenomics and taxon sampling on phylogenetic inference in narrow-mouthed frogs (Anura, Microhylidae)

Pedro L. V. Peloso, Darrel R. Frost, Stephen J. Richards, Miguel T. Rodrigues, Stephen Donnellan, Masafumi Matsui, Cristopher J. Raxworthy, S. D. Biju, Emily Moriarty Lemmon, Ward C. Wheeler, Alan R. Lemmon, Pedro L.V. Peloso & S.D. Biju
Despite considerable progress in unravelling the phylogenetic relationships of microhylid frogs, relationships among subfamilies remain largely unstable and many genera are not demonstrably monophyletic. Here, we used five alternative combinations of DNA sequence data (ranging from seven loci for 48 taxa to up to 73 loci for as many as 142 taxa) generated using the anchored phylogenomics sequencing method (66 loci, derived from conserved genome regions, for 48 taxa) and Sanger sequencing (seven loci for...

Data from: Reintroduction of locally extinct vertebrates impacts arid soil fungal communities

Laurence J. Clarke, Laura S. Weyrich & Alan Cooper
Introduced species have contributed to extinction of native vertebrates in many parts of the world. Changes to vertebrate assemblages are also likely to alter microbial communities through coextinction of some taxa and the introduction of others. Many attempts to restore degraded habitats involve removal of exotic vertebrates (livestock and feral animals) and reintroduction of locally extinct species, but the impact of such reintroductions on microbial communities is largely unknown. We used high-throughput DNA sequencing of...

Registration Year

  • 2015
    22

Resource Types

  • Dataset
    22

Affiliations

  • University of Adelaide
    22
  • Flinders University
    4
  • University of Tasmania
    2
  • Curtin University
    2
  • South Australian Museum
    2
  • University of Exeter
    2
  • City University of New York
    1
  • Bangor University
    1
  • Hunter College
    1
  • Murdoch University
    1