16 Works

Data from: Evolutionary factors affecting the cross-species utility of newly developed microsatellite markers in seabirds

Yoshan Moodley, Juan F. Masello, Gopi K. Munimanda, Theresa L. Cole, Marco R. Thali, Rachael Alderman, Richard J. Cuthbert, Manuel Marin, Melanie Massaro, Joan Navarro, Richard A. Phillips, Peter G. Ryan, Cristián G. Suazo, Yves Cherel, Henri Weimerskirch, Petra Quillfeldt & Luciano Calderon
Microsatellite loci are ideal for testing hypotheses relating to genetic segregation at fine spatio-temporal scales. They are also conserved among closely related species, making them potentially useful for clarifying interspecific relationships between recently diverged taxa. However, mutations at primer binding sites may lead to increased nonamplification, or disruptions that may result in decreased polymorphism in nontarget species. Furthermore, high mutation rates and constraints on allele size may also with evolutionary time, promote an increase in...

Data from: Point process models for presence-only analysis

Ian W. Renner, Jane Elith, Adrian Baddeley, William Fithian, Trevor Hastie, Steven Phillips, Gordana Popovic & David I. Warton
1. Presence-only data are widely used for species distribution modelling, and point process regression models are a exible tool that has considerable potential for this problem, when data arise as point events. 2. In this paper we review point process models, some of their advantages, and some common methods of fitting them to presence-only data. 3. Advantages include (and are not limited to): clarification of what the response variable is that is modelled; a framework...

Data from: A questionnaire study of injections prescribed and dispensed for patients diagnosed with mild/moderate community-acquired pneumonia in Mongolia

Gereltuya Dorj, Bruce Sunderland, Delia Hendrie & Richard W. Parsons
Purpose. The study aimed to determine the extent of and factors influencing the prescribing of injections for the treatment of mild/moderate community acquired pneumonia (CAP) in Mongolia. Methods. Questionnaires were developed and administered to medication providers (34 Pharmacists, 27 pharmacy technicians) and prescribers (22 general doctors and 49 medical specialists) working in Mongolia. Results. Cefalosporins were prescribed for patients with mild pneumonia and doctors tended to prescribe injectable cefalosporins (cefazolin) rather than oral dosage forms....

Data from: Geographic and temporal dynamics of a global radiation and diversification in the killer whale

Phillip A. Morin, Kim M. Parsons, Frederick I. Archer, María C. Ávila-Arcos, Lance G. Barrett-Lennard, Luciano Dalla Rosa, Sebastián Duchêne, John W. Durban, Graeme M. Ellis, Steven H. Ferguson, John K. Ford, Michael J. Ford, Cristina Gabrilao, M. Thomas P. Gilbert, Kristin Kaschner, Craig O. Matkin, Stephen D. Petersen, Kelly M. Robertson, Ingrid N. Visser, Paul R. Wade, Simon Y. W. Ho & Andrew D. Foote
Global climate change during the Late Pleistocene periodically encroached and then released habitat during the glacial cycles, causing range expansions and contractions in some species. These dynamics have played a major role in geographic radiations, diversification and speciation. We investigate these dynamics in the most widely distributed of marine mammals, the killer whale (Orcinus orca), using a global data set of over 450 samples. This marine top predator inhabits coastal and pelagic ecosystems ranging from...

Data from: Seascape genetics along environmental gradients in the Arabian Peninsula: insights from ddRAD sequencing of anemonefishes

Pablo Saenz-Agudelo, Joseph D. DiBattista, Marek J. Piatek, Michelle R. Gaither, Hugo B. Harrison, Gerrit B. Nanninga & Michael L. Berumen
Understanding the processes that shape patterns of genetic structure across space is a central aim of landscape genetics. However, it remains unclear how geographic features and environmental variables shape gene flow, particularly for marine species in large complex seascapes. Here, we evaluated the genomic composition of the two-band anemonefish Amphiprion bicinctus across its entire geographic range in the Red Sea and Gulf of Aden, as well as its close relative, Amphiprion omanensis endemic to the...

Data from: Ancient DNA microsatellite analyses of the extinct New Zealand giant moa (Dinornis robustus) identify relatives within a single fossil site

Morten E. Allentoft, Rasmus Heller, Richard N. Holdaway & Michael Bunce
By analysing ancient DNA (aDNA) from 74 14C-dated individuals of the extinct South Island giant moa (Dinornis robustus) of New Zealand, we identified four dyads of closely related adult females. Although our total sample included bones from four fossil deposits located within a 10 km radius, these eight individuals had all been excavated from the same locality. Indications of kinship were based on high pairwise genetic relatedness (rXY) in six microsatellite markers genotyped from aDNA,...

Data from: The rise and fall of arbuscular mycorrhizal fungal diversity during ecosystem retrogression

Manuela Krüger, François P. Teste, Etienne Laliberté, Hans Lambers, Megan Coghlan, Graham Zemunik & Michael Bunce
Ecosystem retrogression following long-term pedogenesis is attributed to phosphorus (P) limitation of primary productivity. Arbuscular mycorrhizal fungi (AMF) enhance P acquisition for most terrestrial plants, but it has been suggested that this strategy becomes less effective in strongly weathered soils with extremely low P availability. Using next generation sequencing of the large subunit ribosomal RNA gene in roots and soil, we compared the composition and diversity of AMF communities in three contrasting stages of a...

Data from: Isolation by resistance across a complex coral reef seascape

Luke Thomas, W. Jason Kennington, Michael Stat, Shaun P. Wilkinson, Jonathan T. Kool & Gary A. Kendrick
A detailed understanding of the genetic structure of populations and an accurate interpretation of processes driving contemporary patterns of gene flow are fundamental to successful spatial conservation management. The field of seascape genetics seeks to incorporate environmental variables and processes into analyses of population genetic data to improve our understanding of forces driving genetic divergence in the marine environment. Information about barriers to gene flow (such as ocean currents) is used to define a resistance...

Data from: Vocalisations of killer whales (Orcinus orca) in the Bremer Canyon, Western Australia

Rebecca Wellard, Christine Erbe, Leila Fouda & Michelle Blewitt
To date, there has been no dedicated study in Australian waters on the acoustics of killer whales. Hence no information has been published on the sounds produced by killer whales from this region. Here we present the first acoustical analysis of recordings collected off the Western Australian coast. Underwater sounds produced by Australian killer whales were recorded during the months of February and March 2014 and 2015 in the Bremer Canyon in Western Australia. Vocalisations...

Data from: From benchtop to desktop: important considerations when designing amplicon sequencing workflows

Dáithí C. Murray, Megan L. Coghlan & Michael Bunce
Amplicon sequencing has been the method of choice in many high-throughput DNA sequencing (HTS) applications. To date there has been a heavy focus on the means by which to analyse the burgeoning amount of data afforded by HTS. In contrast, there has been a distinct lack of attention paid to considerations surrounding the importance of sample preparation and the fidelity of library generation. No amount of high-end bioinformatics can compensate for poorly prepared samples and...

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: 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: Directional selection for flowering time leads to adaptive evolution in Raphanus raphanistrum (Wild radish)

Michael B. Ashworth, Michael J. Walsh, Kenneth C. Flower, Martin M. Vila-Aiub, Stephen B. Powles & Ken C. Flower
Herbicides have been the primary tool for controlling large populations of yield depleting weeds from agro-ecosystems, resulting in the evolution of widespread herbicide resistance. In response, nonherbicidal techniques have been developed which intercept weed seeds at harvest before they enter the soil seed bank. However, the efficiency of these techniques allows an intense selection for any trait that enables weeds to evade collection, with early-flowering ecotypes considered likely to result in early seed shedding. Using...

Data from: Tag jumps illuminated – reducing sequence-to-sample misidentifications in metabarcoding studies

Ida Bærholm Schnell, Kristine Bohmann, M. Thomas P. Gilbert & Ida Baerholm Schnell
Metabarcoding of environmental samples on second-generation sequencing platforms has rapidly become a valuable tool for ecological studies. A fundamental assumption of this approach is the reliance on being able to track tagged amplicons back to the samples from which they originated. In this study, we address the problem of sequences in metabarcoding sequencing outputs with false combinations of used tags (tag jumps). Unless these sequences can be identified and excluded from downstream analyses, tag jumps...

Data from: A critical evaluation of how ancient DNA bulk bone metabarcoding complements traditional morphological analysis of fossil assemblages

Alicia C. Grealy, Matthew C. McDowell, Paul Scofield, Dáithí C. Murray, Diana A. Fusco, James Haile, Gavin J. Prideaux & Michael Bunce
When pooled for extraction as a bulk sample, the DNA within morphologically unidentifiable fossil bones can, using next-generation sequencing, yield valuable taxonomic data. This method has been proposed as a means to rapidly and cost-effectively assess general ancient DNA preservation at a site, and to investigate temporal and spatial changes in biodiversity; however, several caveats have yet to be considered. We critically evaluated the bulk bone metabarcoding (BBM) method in terms of its: (i) repeatability,...

Data from: Climate mediates the effects of disturbance on ant assemblage structure

Heloise Gibb, Nathan J. Sanders, Robert R. Dunn, Simon Watson, Manoli Photakis, Silvia Abril, Alan N. Andersen, Elena Angulo, Inge Armbrecht, Xavier Arnan, Fabricio B. Baccaro, Tom R. Bishop, Raphael Boulay, Cristina Castracani, Israel Del Toro, Thibaut Delsinne, Mireia Diaz, David A. Donoso, Martha L. Enríquez, Tom M. Fayle, Donald H. Feener, Matthew C. Fitzpatrick, Crisanto Gómez, Donato A. Grasso, Sarah Groc … & C. Gomez
Many studies have focused on the impacts of climate change on biological assemblages, yet little is known about how climate interacts with other major anthropogenic influences on biodiversity, such as habitat disturbance. Using a unique global database of 1128 local ant assemblages, we examined whether climate mediates the effects of habitat disturbance on assemblage structure at a global scale. Species richness and evenness were associated positively with temperature, and negatively with disturbance. However, the interaction...

Registration Year

  • 2015

Resource Types

  • Dataset


  • Curtin University
  • University of Copenhagen
  • University of Western Australia
  • Stanford University
  • University of Adelaide
  • Murdoch University
  • Flinders University
  • French National Centre for Scientific Research
  • University of Venda
  • University of Sydney