27 Works

Data from: SNP discovery in non-model organisms: strand-bias and base-substitution errors reduce conversion rates

Anders Gonçalves Da Silva, William Barendse, James W. Kijas, Wes C. Barris, Sean McWilliam, Rowan J. Bunch, Russell McCulloch, Blair Harrison, A. Rus Hoelzel, Phillip R. England & Russell McCullough
Single nucleotide polymorphisms (SNPs) have become the marker of choice for genetic studies in organisms of conservation, commercial or biological interest. Most SNP discovery projects in nonmodel organisms apply a strategy for identifying putative SNPs based on filtering rules that account for random sequencing errors. Here, we analyse data used to develop 4723 novel SNPs for the commercially important deep-sea fish, orange roughy (Hoplostethus atlanticus), to assess the impact of not accounting for systematic sequencing...

Data from: Genome-wide association reveals the locus responsible for four-horned ruminant

James W. Kijas, Tracy Hadfield, Marina Naval Sanchez & Noelle Cockett
Phenotypic variability in horn characteristics, such as their size, number and shape, offers the opportunity to elucidate the molecular basis of horn development. The objective of this study was to map the genetic determinant controlling the production of four horns in two breeds, Jacob sheep and Navajo-Churro, and examine whether an eyelid abnormality occurring in the same populations is related. Genome-wide association mapping was performed using 125 animals from the two breeds that contain two-...

Data from: A high-resolution panorama camera system for monitoring colony-wide seabird nesting behaviour

Tim P. Lynch, Racheal Alderman, Alistair J. Hobday & Rachael Alderman
1. Obtaining accurate and representative demographic metrics for animal populations is critical to many aspects of wildlife monitoring and management. However, at remote animal colonies, metrics derived from sequential counts or other continuous monitoring are often subject to logistical, weather and disturbance challenges.The development of remote camera technologies has assisted monitoring, but limitations in spatial and temporal resolution and sample sizes remain. 2. Here we describe the application of a robotic camera system (Gigapan) which...

Data from: An integrated assessment model of seabird population dynamics: can individual heterogeneity in susceptibility to fishing explain abundance trends in Crozet wandering albatross?

Geoffrey N. Tuck, Robin B. Thomson, Christophe Barbraud, Karine Delord, Maite Louzao, Miguel Herrera & Henri Weimerskirch
1. Seabirds have been incidentally caught in distant-water longline fleets operating in the Southern Ocean since at least the 1970s, and breeding numbers for some populations have shown marked trends of decline and recovery concomitant with longline fishing effort within their distributions. However, lacking is an understanding of how forms of among-individual heterogeneity may interact with fisheries bycatch and influence population dynamics. 2. We develop a model that uses comprehensive data on the spatial and...

Data from: Heritable variation in heat shock gene expression: a potential mechanism for adaptation to thermal stress in embryos of sea turtles

Jamie N. Tedeschi, W. Jason Kennington, Joseph L. Tomkins, Oliver Berry, Scott Whiting, Mark G. Meekan & Nicola J. Mitchell
The capacity of species to respond adaptively to warming temperatures will be key to their survival in the Anthropocene. The embryos of egg-laying species such as sea turtles have limited behavioural means for avoiding high nest temperatures, and responses at the physiological level may be critical to coping with predicted global temperature increases. Using the loggerhead sea turtle (Caretta caretta) as a model, we used quantitative PCR to characterise variation in the expression response of...

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...

Data from: Population-level consequences of herbivory, changing climate and source-sink dynamics on a long-lived invasive shrub

R. D. Van Klinken, & J.-B. Pichancourt
Long-lived plant species are highly valued environmentally, economically, and socially, but can also cause substantial harm as invaders. Realistic demographic predictions can guide management decisions, and are particularly valuable for long-lived species where population response times can be long. Long-lived species are also challenging, given population dynamics can be affected by factors as diverse as herbivory, climate, and dispersal. We developed a matrix model to evaluate the effects of herbivory by a leaf-feeding biological control...

Data from: Quantitative DNA metabarcoding: improved estimates of species proportional biomass using correction factors derived from control material

Austen C. Thomas, Bruce E. Deagle, J. Paige Eveson, Corie H. Harsch & Andrew W. Trites
DNA metabarcoding is a powerful new tool allowing characterization of species assemblages using high-throughput amplicon sequencing. The utility of DNA metabarcoding for quantifying relative species abundances is currently limited by both biological and technical biases which influence sequence read counts. We tested the idea of sequencing 50/50 mixtures of target species and a control species in order to generate relative correction factors (RCFs) that account for multiple sources of bias and are applicable to field...

Data from: High nucleotide diversity and limited linkage disequilibrium in Helicoverpa armigera facilitates the detection of a selective sweep

Sue V. Song, Sharon Downes, Tracey Parker, John G. Oakeshott & Charles Robin
Insecticides impose extreme selective pressures on populations of target pests and so insecticide resistance loci of these species may provide the footprints of ‘selective sweeps’. To lay the foundation for future genome-wide scans for selective sweeps and inform genome-wide association study designs, we set out to characterize some of the baseline population genomic parameters of one of the most damaging insect pests in agriculture worldwide, Helicoverpa armigera. To this end, we surveyed nine Z-linked loci...

Data from: Host resistance and pathogen infectivity in host populations with varying connectivity

Ulla Carlsson-Graner & Peter H. Thrall
Theory predicts that hosts and pathogens will evolve higher resistance and aggressiveness in systems where populations are spatially connected than in situations where populations are isolated and dispersal is more local. In a large cross-inoculation experiment we surveyed patterns of host resistance and pathogen infectivity in anther-smut diseased Viscaria alpina populations from three contrasting areas where populations range from continuous, through patchy but spatially connected to highly isolated demes. In agreement with theory, isolated populations...

Data from: Genome-wide transcriptional signatures of migratory flight activity in a globally invasive insect pest

Christopher M. Jones, Alexie Papanicolaou, George K. Mironidis, John Vontas, Yihua Yang, Ka S. Lim, Kumar S. Singh, John G. Oakeshott, Christopher Bass, Jason W. Chapman & Chris Bass
Migration is a key life history strategy for many animals and requires a suite of behavioural, morphological and physiological adaptations which together form the ‘migratory syndrome’. Genetic variation has been demonstrated for many traits that make up this syndrome, but the underlying genes involved remain elusive. Recent studies investigating migration-associated genes have focussed on sampling migratory and nonmigratory populations from different geographic locations but have seldom explored phenotypic variation in a migratory trait. Here, we...

Data from: Impacts and recovery from Severe Tropical Cyclone Yasi on the Great Barrier Reef

Roger J. Beeden, Jeffrey Maynard, Marjetta Puotinen, Paul Marshall, Jen Dryden, Jeremy Goldberg, Gareth Williams & Roger Beeden
Full recovery of coral reefs from tropical cyclone (TC) damage can take decades, making cyclones a major driver of habitat condition where they occur regularly. Since 1985, 44 TCs generated gale force winds (≥17 metres/second) within the Great Barrier Reef Marine Park (GBRMP). Of the hurricane strength TCs (≥H1—Saffir Simpson scale; ≥ category 3 Australian scale), TC Yasi (February, 2011) was the largest. In the weeks after TC Yasi crossed the GBRMP, participating researchers, managers...

Data from: Genetic parameters in subtropical pine F1 hybrids: heritabilities, between-trait correlations and genotype-by-environment interactions

Washington J. Gapare, Pomerayi Mutete & Ruramai Murepa
Growth and stem straightness traits of 29 Pinus caribaea var. hondurensis × Pinus tecunumanii (PCH × PTEC) and 26 P. caribaea var. hondurensis × Pinus oocarpa (PCH × POOC) hybrid pair-crosses plus a total of 16 intraspecific families were assessed at ages 5, 8 and 15 years from planting at two sites. The PCH × PTEC hybrid was the most productive, yielding 37 % more than a Pinus elliottii local control and was 21 %...

Data from: Passive restoration of sub-tropical grassland after abandonment of cultivation

Rod J. Fensham, Don W. Butler, Russell J. Fairfax, Amy R. Quintin & John M. Dwyer
Passive restoration of grasslands after the abandonment of cultivation may be a viable restoration option where seed sources from remnant grasslands are available, and if the risk of deflected succession is low. Passive restoration of subtropical grassland in Queensland, Australia was evaluated along a chronosequence of abandoned cultivation (fallow) paddocks. Plant communities in fallow paddocks were compared with nearby remnant grassland. On average, species richness recovers after 60 years of abandonment and floristic composition shows...

Data from: Recent speciation and elevated Z-chromosome differentiation between sexually monochromatic and dichromatic species of Australian teals

Kirandeep K. Dhami, Leo Joseph, David A. Roshier & Jeffrey L. Peters
Sex chromosomes potentially have an important role in speciation and often have elevated differentiation between closely related species. In birds, traits associated with male plumage, female mate preference, and hybrid fitness have been linked to the Z-chromosome (females are heterogametic, ZW). We tested for elevated Z-differentiation between two recently diverged species of Australian ducks, the sexually monochromatic grey teal Anas gracilis and the dichromatic chestnut teal A. castanea. Despite prominent morphological differences, these two species...

Data from: PolyPatEx: an R package for paternity exclusion in autopolyploids

Alexander B. Zwart, Carole Elliott, Tara Hopley, David Lovell & Andrew Young
Microsatellite markers have demonstrated their value for performing paternity exclusion and hence exploring mating patterns in plants and animals. Methodology is well established for diploid species and several software packages exist for elucidating paternity in diploids, however these issues are not so readily addressed in polyploids due to the increased complexity of the exclusion problem and a lack of available software. We introduce PolyPatEx, an R package for paternity exclusion analysis using microsatellite data in...

Data from: Adapting environmental management to uncertain but inevitable change

Sam C. Nicol, Richard A. Fuller, Takuya Iwamura, Iadine Chades & S. Nicol
Implementation of adaptation actions to protect biodiversity is limited by uncertainty about the future. One reason for this is the fear of making the wrong decisions caused by the myriad future scenarios presented to decision-makers. We propose an adaptive management (AM) method for optimally managing a population under uncertain and changing habitat conditions. Our approach incorporates multiple future scenarios and continually learns the best management strategy from observations, even as conditions change. We demonstrate the...

Data from: Population structure and history of the Welsh sheep breeds determined by whole genome genotyping

Sarah E. Beynon, Gancho T. Slavov, Marta Farré, Bolormaa Sunduimijid, Kate Waddams, Brian Davies, William Haresign, James Kijas, Iona M. MacLeod, C. Jamie Newbold, Lynfa Davies & Denis M. Larkin
Background: One of the most economically important areas within the Welsh agricultural sector is sheep farming, contributing around £230 million to the UK economy annually. Phenotypic selection over several centuries has generated a number of native sheep breeds, which are presumably adapted to the diverse and challenging landscape of Wales. Little is known about the history, genetic diversity and relationships of these breeds with other European breeds. We genotyped 353 individuals from 18 native Welsh...

Data from: Lineage range estimation method reveals fine-scale endemism linked to Pleistocene stability in Australian rainforest herpetofauna

Dan F. Rosauer, Renee A. Catullo, Jeremy VanDerWal, Adnan Moussalli & Craig Moritz
Areas of suitable habitat for species and communities have arisen, shifted, and disappeared with Pleistocene climate cycles, and through this shifting landscape, current biodiversity has found paths to the present. Evolutionary refugia, areas of relative habitat stability in this shifting landscape, support persistence of lineages through time, and are thus crucial to the accumulation and maintenance of biodiversity. Areas of endemism are indicative of refugial areas where diversity has persisted, and endemism of intraspecific lineages...

Data from: Having a lot of a good thing: multiple important group memberships as a source of self-esteem

Jolanda Jetten, Nyla R. Branscombe, S. Alexander Haslam, Catherine Haslam, Tegan Cruwys, Janelle M. Jones, Lijuan Cui, Genevieve Dingle, James Liu, Sean Murphy, Anh Thai, Zoe Walter & Airong Zhang
Membership in important social groups can promote a positive identity. We propose and test an identity resource model in which personal self-esteem is boosted by membership in additional important social groups. Belonging to multiple important group memberships predicts personal self-esteem in children (Study 1a), older adults (Study 1b), and former residents of a homeless shelter (Study 1c). Study 2 shows that the effects of multiple important group memberships on personal self-esteem are not reducible to...

Data from: Density-dependent effects of a widespread invasive herbivore on tree survival and biomass during reforestation

David M. Forsyth, Michael P. Scroggie, Anthony D. Arthur, Michael Lindeman, David S. L. Ramsey, Steven R. McPhee, Tim Bloomfield & Ivor G. Stuart
Reforestation has been widely adopted as a solution to multiple global change issues. However, the role of herbivory by invasive species in the restoration of grassland to forest has received little attention. We conducted a field experiment to investigate the impacts of a widespread invasive mammalian herbivore, the European rabbit (Oryctolagus cuniculus), on trees planted in a landscape-scale reforestation program in south-eastern Australia. Three native tree species were planted inside and outside rabbit-proof exclosures within...

Data from: Biological introduction threats from shipping in a warming Arctic

Chris Ware, Jørgen Berge, Anders Jelmert, Steffen M. Olsen, Loïc Pellissier, Mary Wisz, Darren Kriticos, Georgy Semenov, Slawomir Kwasniewski & Inger G. Alsos
Several decades of research on invasive marine species have yielded a broad understanding of the nature of species invasion mechanisms and associated threats globally. However, this is not true of the Arctic, a region where ongoing climatic changes may promote species invasion. Here, we evaluated risks associated with non-indigenous propagule loads discharged with ships' ballast water to the high-Arctic archipelago, Svalbard, as a case study for the wider Arctic. We sampled and identified transferred propagules...

Data from: Citizen science program shows urban areas have lower occurrence of frog species, but not accelerated declines

Martin J. Westgate, Ben C. Scheele, Karen Ikin, Anke Maria Hoefer, R. Matthew Beaty, Murray Evans, Will Osborne, David Hunter, Laura Rayner & Don A. Driscoll
Understanding the influence of landscape change on animal populations is critical to inform biodiversity conservation efforts. A particularly important goal is to understand how urban density affects the persistence of animal populations through time, and how these impacts can be mediated by habitat provision; but data on this question are limited for some taxa. Here, we use data from a citizen science monitoring program to investigate the effect of urbanization on patterns of frog species...

Data from: Multiple host-shifts by the emerging honeybee parasite, Varroa jacobsoni

John M. K. Roberts, Denis L. Anderson & Wee Tek Tay
Host shifts are a key mechanism of parasite evolution and responsible for the emergence of many economically important pathogens. Varroa destructor has been a major factor in global honeybee (Apis mellifera) declines since shifting hosts from the Asian honeybee (Apis cerana) > 50 years ago. Until recently, only two haplotypes of V. destructor (Korea and Japan) had successfully host shifted to A. mellifera. In 2008, the sister species V. jacobsoni was found for the first...

Data from: Local origin of global contact numbers in frictional ellipsoid packings

Fabian M. Schaller, Max Neudecker, Mohammad Saadatfar, Gary W. Delaney, Gerd E. Schröder-Turk & Matthias Schröter
In particulate soft matter systems the average number of contacts Z of a particle is an important predictor of the mechanical properties of the system. Using x-ray tomography, we analyze packings of frictional, oblate ellipsoids of various aspect ratios α, prepared at different global volume fractions ϕg. We find that Z is a monotonically increasing function of ϕg for all α. We demonstrate that this functional dependence can be explained by a local analysis where...

Registration Year

  • 2015

Resource Types

  • Dataset


  • Commonwealth Scientific and Industrial Research Organisation
  • University of Queensland
  • Australian National University
  • Stanford University
  • University of Melbourne
  • University of Tasmania
  • French National Centre for Scientific Research
  • Department of Parks and Wildlife
  • James Cook University
  • University of Kansas