190 Works

Does rapid utilisation of elevated nutrient availability allow eucalypts to dominate in the tropical savannas of Australia?

Harinandanan Paramjyothi, Brett Murphy, Michael Lawes, Natalie Rossitet-Rachor & Anna Richards
Northern Australia's savannas are amongst the most fire-prone biomes on Earth, and are dominated by eucalypts (Eucalyptus and Corymbia spp.). It is not clear what processes allows this group to dominate under such extreme fire frequencies and if a superior ability to compete for nutrients and water might play a role. There is evidence that eucalypts are adapted to frequent fires; juvenile eucalypts escape the fire trap by growing rapidly in height between fires. However,...

Supporting data for the paper 'Small-scale capillary heterogeneity linked to rapid plume migration during CO2 storage' by S.J. Jackson and S. Krevor 2020

Samuel Jackson & Samuel Krevor
Herein lies the supporting data for the paper 'Small-scale capillary heterogeneity linked to rapid plume migration during CO2 storage'. We supply experimental, analytical and numerical simulation data used in the paper. The supplied zipped folders follow the same order as the main paper, with codes to reproduce each figure (and those in the supporting information PDF). There are also video files (in the 5_Field_scale_simulation zipped folder) showing the final CO2 plume evolution from the static...

Data from: Local demographic and epidemiological patterns in the Linum marginale – Melampsora lini association – a multi-year study

Hanna Susi, Peter H. Thrall, Luke G. Barrett & Jeremy J. Burdon
1.Many theoretical and empirical studies operate from an assumption that pathogens have a significant influence on the fecundity and lifespan of their host species. However, there is surprisingly little data investigating the long-term fitness impacts and genetic consequences that arise from pathogen infection in natural populations. Here, we address this gap through the analysis of a dataset investigating the local population dynamics of a native host plant (Linum marginale) and an associated rust pathogen (Melampsora...

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: Predicting local adaptation in fragmented plant populations: implications for restoration genetics

Melinda Pickup, David L. Field, David M. Rowell & Andrew G. Young
Understanding patterns and correlates of local adaptation in heterogeneous landscapes can provide important information in the selection of appropriate seed sources for restoration. We assessed the extent of local adaptation of fitness components in 12 population pairs of the perennial herb Rutidosis leptorrhynchoides (Asteraceae) and examined if spatial scale (0.7 – 600km), environmental distance, quantitative Q_ST and neutral genetic differentiation F_ST, and size of the local and foreign populations could predict patterns of adaptive differentiation....

Data from: Marine plastic pollution in waters around Australia: characteristics, concentrations, and pathways

Julia Reisser, Jeremy Shaw, Chris Wilcox, Britta Denise Hardesty, Maira Proietti, Michele Thums & Charitha Pattiaratchi
Plastics represent the vast majority of human-made debris present in the oceans. However, their characteristics, accumulation zones, and transport pathways are still poorly assessed. We characterised and estimated the concentration of marine plastics in waters around Australia using surface net tows, and inferred their potential pathways using particle-tracking models and real drifter trajectories. The 839 marine plastics recorded were predominantly small fragments (“microplastics”, median length = 2.8 mm, mean length = 4.9 mm) resulting from...

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: Limits of use of social media for monitoring biosecurity events

Marijke Welvaert, Omar Al-Ghattas, Mark Cameron & Peter Caley
Compared to applications that trigger massive information streams, like earthquakes and human disease epidemics, the data input for agricultural and environmental biosecurity events (ie. the introduction of unwanted exotic pests and pathogens), is expected to be sparse and less frequent. To investigate if Twitter data can be useful for the detection and monitoring of biosecurity events, we adopted a three-step process. First, we confirmed that sightings of two migratory species, the Bogong moth (Agrotis infusa)...

Data from: Genome-wide scans detect adaptation to aridity in a widespread forest tree species.

Dorothy A. Steane, Brad M. Potts, Elizabeth McLean, Suzanne M. Prober, William D. Stock, René E. Vaillancourt & Margaret Byrne
Patterns of adaptive variation within plant species are best studied through common garden experiments, but these are costly and time-consuming, especially for trees that have long generation times. We explored whether genome-wide scanning technology combined with outlier marker detection could be used to detect adaptation to climate and provide an alternative to common garden experiments. As a case study, we sampled nine provenances of the widespread forest tree species, Eucalyptus tricarpa, across an aridity gradient...

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: Fire, fragmentation, and windstorms: a recipe for tropical forest degradation

Divino V. Silvério, Paulo M. Brando, Mercedes M.C. Bustamante, Francis E. Putz, Daniel Magnabosco Marra, Shaun R. Levick & Susan E. Trumbore
1. Widespread degradation of tropical forests is caused by a variety of disturbances that interact in ways that are not well understood. 2. To explore potential synergies between edge effects, fire and windstorm damage as causes of Amazonian forest degradation, we quantified vegetation responses to a 30-minute high-intensity windstorm that in 2012, swept through a large-scale fire experiment that borders an agricultural field. Our pre- and post-windstorm measurements include tree mortality rates and modes of...

Data from: Anthropogenic debris ingestion by avifauna in eastern Australia

Lauren Roman, Qamar A. Schuyler, Britta Denise Hardesty & Kathy A. Townsend
Anthropogenic debris in the world’s oceans and coastal environments is a pervasive global issue that has both direct and indirect impacts on avifauna. The number of bird species affected, the feeding ecologies associated with an increased risk of debris ingestion, and selectivity of ingested debris have yet to be investigated in most of Australia’s coastal and marine birds. With this study we aim to address the paucity of data regarding marine debris ingestion in Australian...

Data from: Going with the flow: the role of ocean circulation in global marine ecosystems under a changing climate

Simon J. Van Gennip, Ekaterina E. Popova, Andrew Yool, Gretta T. Pecl, Alistair J. Hobday & Cascade J. B. Sorte
Ocean warming, acidification, deoxygenation and reduced productivity are widely considered to be the major stressors to ocean ecosystems induced by emissions of CO2. However, an overlooked stressor is the change in ocean circulation in response to climate change. Strong changes in the intensity and position of the western boundary currents have already been observed, and the consequences of such changes for ecosystems are beginning to emerge. In this study, we address climatically induced changes in...

Climate change, sex reversal, and lability of sex determining systems

Lisa Schwanz, Arthur Georges, Clare Holleley & Stephen Sarre
Sex reversal at high temperatures during embryonic development (e.g. ZZ females) provides the opportunity for new genotypic crosses (e.g. ZZ male x ZZ female). This raises the alarming possibility that climatic warming could lead to the loss of an entire chromosome – one member of the sex chromosome pair (the Y or W) – and the transition of populations to environmental sex determination (ESD). Here we examine the evolutionary dynamics of sex-determining systems exposed to...

Data from: Bacterial epibiont communities of panmictic Antarctic krill are spatially structured

Laurence Clarke, Leonie Suter, Rob King, Andrew Bissett, Sophie Bestley & Bruce Deagle
Antarctic krill (Euphausia superba) are amongst the most abundant animals on Earth, with a circumpolar distribution in the Southern Ocean. Genetic and genomic studies have failed to detect any population structure for the species, suggesting a single panmictic population. However, the hyper-abundance of krill slows the rate of genetic differentiation, masking potential underlying structure. Here we use high-throughput sequencing of bacterial 16S rRNA genes to show that krill bacterial epibiont communities exhibit spatial structuring, driven...

Data from: Phylogeny of gracillariid leaf-mining moths: evolution of larval behaviour inferred from phylogenomic and Sanger data

Xuankun Li, Ryan St Laurent, Chandra Earl, Camiel Doorenweerd, Erik Van Nieukerken, Don Davis, Atsushi Kawakita, Shigeki Kobayashi, Andreas Zwick, Carlos Lopez-Vaamonde, Issei Ohshima & Akito Kawahara
Gracillariidae is the most taxonomically diverse cosmopolitan leaf-mining moth family, consisting of nearly 2000 named species in 105 described genera, classified into eight extant subfamilies. The majority of gracillariid species are internal plant feeders as larvae, creating mines and galls in plant tissue. Despite their diversity and ecological adaptations, their phylogenetic relationships, especially at the subfamily level, remain largely uncertain. Genomic data (83 taxa and 589 loci) were integrated with Sanger data (130 taxa and...

Data from: Resolving a phylogenetic hypothesis for parrots: implications from systematics to conservation

Kaiya L. Provost, Leo Joseph & Brian Tilston Smith
Advances in sequencing technology and phylogenetics have revolutionised avian biology by providing an evolutionary framework for studying natural groupings. In the parrots (Psittaciformes), DNA-based studies have led to a reclassification of clades, yet substantial gaps remain in the data gleaned from genetic information. Here we provide an overview of published genetic data of parrots, characterise sampling depth across the phylogeny, and evaluate support for existing systematic treatments. We inferred a concatenated tree with 307 species...

Data from: Phylogenomics resolves the timing and pattern of insect evolution

Bernhard Misof, Shanlin Liu, Karen Meusemann, Ralph S. Peters, Alexander Donath, Christoph Mayer, Paul B. Frandsen, Jessica Ware, Tomas Flouri, Rolf G. Beutel, Oliver Niehuis, Malte Petersen, Fernando Izquierdo-Carrasco, Torsten Wappler, Jes Rust, Andre J. Aberer, Ulrike Aspöck, Horst Aspöck, Daniela Bartel, Alexander Blanke, Simon Berger, Alexander Böhm, Thomas Buckley, Brett Calcott, Junqing Chen … & Xin Zhou
Insects are the most speciose group of animals, but the phylogenetic relationships of many major lineages remain unresolved. We inferred the phylogeny of insects from 1478 protein-coding genes. Phylogenomic analyses of nucleotide and amino acid sequences, with site-specific nucleotide or domain-specific amino acid substitution models, produced statistically robust and congruent results resolving previously controversial phylogenetic relations hips. We dated the origin of insects to the Early Ordovician [~479 million years ago (Ma)], of insect flight...

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: The ‘heritability’ of domestication and its functional partitioning in the pig

Miguel Perez-Enciso, Gustavo De Los Campos, Nick Hudson, James Kijas & Antonio Reverter
We propose to estimate the proportion of variance explained by regression on genome-wide markers (or genomic heritability) when wild/domestic status is considered the phenotype of interest. This approach differs from the standard Fst in that it can accommodate genetic similarity between individuals in a general form. We apply this strategy to complete genome data from 47 wild and domestic pigs from Asia and Europe. When we partitioned the total genomic variance into components associated to...

Data from: Multi-locus sequence data illuminate demographic drivers of Pleistocene speciation in semi-arid southern Australian birds (Cinclosoma spp.)

Gaynor Dolman & Leo Joseph
Background: During the Pleistocene, shifts of species distributions and their isolation in disjunct refugia led to varied outcomes in how taxa diversified. Some species diverged, others did not. Here, we begin to address another facet of the role of the Pleistocene in generating today’s diversity. We ask which processes contributed to divergence in semi-arid southern Australian birds. We isolated 11 autosomal nuclear loci and one mitochondrial locus from a total of 29 specimens of the...

Data from: Landscape genomics reveals altered genome wide diversity within revegetated stands of Eucalyptus microcarpa (Grey Box)

Rebecca Jordan, Shannon K. Dillon, Suzanne M. Prober & Ary A. Hoffmann
In order to contribute to evolutionary resilience and adaptive potential in highly modified landscapes, revegetated areas should ideally reflect levels of genetic diversity within and across natural stands. Landscape genomic analyses enable such diversity patterns to be characterized at genome and chromosomal levels. Landscape-wide patterns of genomic diversity were assessed in Eucalyptus microcarpa, a dominant tree species widely used in revegetation in Southeastern Australia. Trees from small and large patches within large remnants, small isolated...

Data from: Burning for biodiversity: highly resilient ant communities respond only to strongly contrasting fire regimes in Australia’s seasonal tropics

Alan N. Andersen, Relena R. Ribbons, Magen Pettit & Catherine L. Parr
1. According to the pyrodiversity paradigm, a wide range of fire regimes is required to maintain biodiversity in fire-prone landscapes. However, the requisite level of pyrodiversity has seldom been tested and may actually be very low. 2. Here, we examine the sensitivity of tropical savanna ants to variation in fire regimes using results from a long-term fire experiment near Darwin, Australia. Six experimental fire regimes, with varying fire frequency and seasonality, have been applied to...

Data from: Introgression and the fate of domesticated genes in a wild mammal population

Philine G. D. Feulner, Jacob Gratten, James W. Kijas, Peter M. Visscher, Josephine M. Pemberton, Jon Slate & Jon. Slate
When domesticated species are not reproductively isolated from their wild relatives, the opportunity arises for artificially selected variants to be re-introduced into the wild. However, the evolutionary consequences of introgression of domesticated genes back into the wild are poorly understood. By combining high-throughput genotyping with 25 years of long-term ecological field data, we describe the occurrence and consequences of admixture between a primitive sheep breed, the free-living Soay sheep of St Kilda, and more modern...

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...

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