184 Works

Data from: Phylogenomics reveals the evolutionary timing and pattern of butterflies and moths

Akito Y. Kawahara, David Plotkin, Marianne Espeland, Karen Meusemann, Emmanuel F. A. Toussaint, Alexander Donath, France Gimnich, Paul B. Frandsen, Andreas Zwick, Mario Dos Reis, Jesse R. Barber, Ralph S. Peters, Shanlin Liu, Xin Zhou, Christoph Mayer, Lars Podsiadlowski, Caroline Storer, Jayne E. Yack, Bernhard Misof & Jesse W. Breinholt
Butterflies and moths (Lepidoptera) are one of the major super-radiations of insects, comprising nearly 160,000 described extant species. As herbivores, pollinators, and prey, Lepidoptera play a fundamental role in almost every terrestrial ecosystem. Lepidoptera are also indicators of environmental change and serve as model organisms for research on mimicry and genetics. They have been central to the development of co-evolutionary hypotheses, such as butterflies with flowering plants, and moths' evolutionary arms race with echolocating bats....

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: 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: 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: Geochemical analyses reveal the importance of environmental history for blue carbon sequestration

Jeffrey J. Kelleway, Neil Saintilan, Peter I. Macreadie, Jeff A. Baldock, Hendrik Heijnis, A. Zawadzkis, Patricia Gadd, Geraldine Jacobsen & Peter J. Ralph
Coastal habitats including saltmarshes and mangrove forests can accumulate and store significant blue carbon stocks, which may persist for millennia. Despite this implied stability, the distribution and structure of intertidal-supratidal wetlands is known to respond to changes imposed by geomorphic evolution, climatic, sea level and anthropogenic influences. In this study, we reconstruct environmental histories and biogeochemical conditions in four wetlands of similar contemporary vegetation in SE Australia. The objective is to assess the importance of...

Data from: Ants as ecological indicators of rainforest restoration: community convergence and the development of an Ant Forest Indicator Index in the Australian wet tropics

Michael J. Lawes, Anthony M. Moore, Alan N. Andersen, Noel D. Preece & Donald C. Franklin
Ecosystem restoration can help reverse biodiversity loss, but whether faunal communities of forests undergoing restoration converge with those of primary forest over time remains contentious. There is a need to develop faunal indicators of restoration success that more comprehensively reflect changes in biodiversity and ecosystem function. Ants are an ecologically dominant faunal group and are widely advocated as ecological indicators. We examine ant species and functional group responses on a chronosequence of rainforest restoration in...

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: Primers for Castilleja and their utility across Orobanchaceae: II. Single-copy nuclear loci

Maribeth Latvis, Sarah J. Jacobs, Sebastian M. E. Mortimer, Melissa Richards, Paul D. Blischak, Sarah Mathews & David C. Tank
Premise of the study: We developed primers targeting nuclear loci in Castilleja with the goal of reconstructing the evolutionary history of this challenging clade. These primers were tested across other major clades in Orobanchaceae to assess their broader utility. Methods and Results: We assembled low-coverage genomes for three taxa in Castilleja and developed primer combinations for the single-copy conserved ortholog set (COSII) and the pentatricopeptide repeat (PPR) gene family. These primer combinations were designed to...

Data from: Current and projected global distribution of Phytophthora cinnamomi, one of the world’s worst plant pathogens

Treena Burgess, John K. Scott, Keith L. McDougall, Michael J. C. Stukely, Colin Crane, William A. Dunstan, Frances Brigg, Vera Andjic, Diane White, Tim Rudman, Frans Arentz, Noboru Ota, Giles E. St.J. Hardy, Treena I. Burgess & Giles E. St. J. Hardy
Globally, Phytophthora cinnamomi is listed as one of the 100 worst invasive alien species and active management is required to reduce impact and prevent spread in both horticulture and natural ecosystems. Conversely, there are regions thought to be suitable for the pathogen where no disease is observed. We developed a CLIMEX model for the global distribution of P. cinnamomi based on the pathogen's response to temperature and moisture and by incorporating extensive empirical evidence on...

Data from: Loggerhead sea turtle embryos (Caretta caretta) regulate expression of stress-response and developmental genes when exposed to a biologically realistic heat stress

Blair P. Bentley, Brian J. Haas, Jamie N. Tedeschi & Oliver Berry
Oviparous reptile embryos are expected to breach their critical thermal maxima if temperatures reach those predicted under current climate change models due to the lack the maternal buffering processes and parental care. Heat shock proteins (HSPs) are integral in the molecular response to thermal stress, and their expression is heritable, but the roles of other candidate families such as the heat shock factors (HSFs) have not been determined in reptiles. Here we subject embryonic sea...

Data from: Soil-mediated eco-evolutionary feedbacks in the invasive plant Alliaria petiolata

Jeffrey A. Evans, Richard A. Lankau, Adam S. Davis, S. Raghu & Douglas A. Landis
Ecological and evolutionary processes historically have been assumed to operate on significantly different time scales. We know now from theory and work in experimental and model systems that these processes can feed back on each other on mutually relevant time scales. Here, we present evidence of a soil-mediated eco-evolutionary feedback on the population dynamics of an invasive biennial plant, Alliaria petiolata. As populations age, natural selection drives down production of A. petiolata's important anti-mycorrhizal allelochemical,...

Data from: Population structure and gene flow in the global pest, Helicoverpa armigera

Craig J. Anderson, Wee T. Tay, Angela McGaughran, Karl Gordon & Tom K. Walsh
Helicoverpa armigera is a major agricultural pest that is distributed across Europe, Asia, Africa and Australasia. This species is hypothesized to have spread to the Americas 1.5 million years ago, founding a population that is at present, a distinct species, Helicoverpa zea. In 2013, H. armigera was confirmed to have re-entered South America via Brazil and subsequently spread. The source of the recent incursion is unknown and population structure in H. armigera is poorly resolved,...

Data from: Counting with DNA in metabarcoding studies: how should we convert sequence reads to dietary data?

Bruce E. Deagle, Austen C. Thomas, Julie C. McInnes, Laurence J. Clarke, Eero J. Vesterinen, Elizabeth L. Clare, Tyler R. Kartzinel & J. Paige Eveson
Advances in DNA sequencing technology have revolutionised the field of molecular analysis of trophic interactions and it is now possible to recover counts of food DNA sequences from a wide range of dietary samples. But what do these counts mean? To obtain an accurate estimate of a consumer’s diet should we work strictly with datasets summarising frequency of occurrence of different food taxa, or is it possible to use relative number of sequences? Both approaches...

Data from: A statistical framework to explore ontogenetic growth variation among individuals and populations: a marine fish example

John R. Morrongiello & Ronald Everett Thresher
Growth is a fundamental biological process, driven by a multitude of intrinsic (within-individual) and extrinsic (environmental) factors, that underpins individual fitness and population demographics. Focussing on the comprehensive information stored in aquatic and terrestrial organism hard parts, we develop a series of increasingly complex hierarchical models to explore spatial and temporal sources of growth variation, ranging in resolution from within individuals to across a species. We apply this modelling framework to an extensive data set...

Data from: Do evolutionary constraints on thermal performance manifest at different organizational scales?

Ben L. Phillips, John Llewelyn, Amberlee Hatcher, Stewart Macdonald & Craig Moritz
The two foremost hypotheses on the evolutionary constraints on an organism's thermal sensitivity – the hotter-is-better expectation, and the specialist–generalist trade-off – have received mixed support from empirical studies testing for their existence. Could these conflicting results reflect confusion regarding the organizational level (i.e. species > population > individual) at which these constraints should manifest? We propose that these evolutionary constraints should manifest at different organizational levels because of differences in their underlying causes and...

Data from: Assessing bottom-trawling impacts based on the longevity of benthic invertebrates

Jan Geert Hiddink, Simon Jennings, Marija Sciberras, Stefan Bolam, Giulia Cambie, Robert McConnaughey, Tessa Mazor, Ray Hilborn, Jeremy Collie, C. Roland Pitcher, Ana Parma, Petri Suuronen, Michel Kaiser, Adriaan Rijnsdorp, Jeremy S. Collie, Michel J. Kaiser, Adriaan D. Rijnsdorp & Robert A. McConnaughey
1. Bottom trawling is the most widespread human activity directly affecting seabed habitats. Assessment and effective management of the effects of bottom trawling at the scale of fisheries requires an understanding of differences in sensitivity of biota to trawling. Responses to disturbance are expected to depend on the intrinsic rate of increase of populations (r), which is expected to be linearly related to the reciprocal of longevity. 2. We examine the relationship between the longevity...

Data from: Robust estimates of a high Ne/N ratio in a top marine predator, southern bluefin tuna

Robin S. Waples, Peter M. Grewe, Mark W. Bravington, Richard Hillarty & Pierre Feutry
Genetic studies of several marine species with high fecundity have produced “tiny” estimates (≤10−3) of the ratio of effective population size (Ne) to adult census size (N), suggesting that even very large populations might be at genetic risk. A recent study using close-kin mark-recapture methods estimated adult abundance at N ≈ 2 × 106 for southern bluefin tuna (SBT), a highly fecund top predator that supports a lucrative (~$1 billion/year) fishery. We used the same...

Data from: Accounting for kin sampling reveals genetic connectivity in Tasmanian and New Zealand school sharks, Galeorhinus galeus

Floriaan Devloo-Delva, Gregory E. Maes, Sebastián I. Hernández, Jaime D. Mcallister, Rasanthi M. Gunasekera, Peter M. Grewe, Robin B. Thomson & Pierre Feutry
Fishing represents a major problem for conservation of chondrichthyans, with a quarter of all species being overexploited. School sharks, Galeorhinus galeus, are targeted by commercial fisheries in Australia and New Zealand. The Australian stock has been depleted to below 20% of its virgin biomass, and the species is recorded as Conservation Dependent within Australia. Individuals are known to move between both countries, but it is disputed whether the stocks are reproductively linked. Accurate and unbiased...

Data from: Marine environmental DNA biomonitoring reveals seasonal patterns in biodiversity and identifies ecosystem responses to anomalous climatic events

Tina E. Berry, Benjamin J. Saunders, Megan L. Coghlan, Michael Stat, Simon Jarman, Anthony J. Richardson, Claire H. Davies, Oliver Berry, Euan S. Harvey & Michael Bunce
Marine ecosystems are changing rapidly as the oceans warm and become more acidic. The physical factors and the changes to ocean chemistry that they drive can all be measured with great precision. Changes in the biological composition of communities in different ocean regions are far more challenging to measure because most biological monitoring methods focus on a limited taxonomic or size range. Environmental DNA (eDNA) analysis has the potential to solve this problem in biological...

Data from: Source population characteristics affect heterosis following genetic rescue of fragmented plant populations

Melinda Pickup, David L. Field, David M. Rowell & Andrew G. Young
Understanding the relative importance of heterosis and outbreeding depression over multiple generations is a key question in evolutionary biology and is essential for identifying appropriate genetic sources for population and ecosystem restoration. Here we use 2455 experimental crosses between 12 population pairs of the rare perennial plant Rutidosis leptorrhynchoides (Asteraceae) to investigate the multi-generational (F1, F2, F3) fitness outcomes of inter-population hybridisation. We detected no evidence of outbreeding depression, with inter-population hybrids and backcrosses showing...

Modelled mid-trophic pelagic prey fields improve understanding of marine predator foraging behaviour

David Green, Sophie Bestley, Rowan Trebilco, Stuart Corney, Patrick Lehodey, Clive McMahon, C. Guinet & Mark A. Hindell
Biophysical interactions are influential in determining the scale of key ecological processes within marine ecosystems. For oceanic predators, this means foraging behaviour is influenced by processes shaping the distribution of prey. However, oceanic prey is difficult to observe and its abundance and distribution is regionally generalised. We use a spatiotemporally resolved simulation model to describe mid-trophic prey distribution within the Southern Ocean and demonstrate insights that this modelled prey field provides into the foraging behaviour...

Data from: Groundwater enhances aboveground growth in mangroves

Matthew A. Hayes, Amber Jesse, Nina Welti, Basam Tabet, David Lockington & Catherine E. Lovelock
1. Groundwater flow through coastal wetlands plays an important role in the maintenance of productivity of intertidal ecosystems. Groundwater can reduce salinity and increase nutrient availability which can enhance plant growth and alter plant biomass allocation patterns. 2. Here, we used stable isotopes of oxygen and hydrogen to assess how groundwater influences belowground and aboveground growth in the widespread mangrove species Avicennia marina. 3. We found source water within tree stems varied seasonally, with non-saline...

Data from: Mate-guarding by male mandrills (Mandrillus sphinx) is associated with female MHC genotype

Joanna M. Setchell, Shane A. Richards, Kristin M. Abbott & Leslie A. Knapp
Female choice for male major histocompatibility complex (MHC) genotype has been widely tested, but the relationship between male mating strategies and female MHC genotype has received far less attention. Moreover, few studies of MHC-associated mate choice test for the fitness effects underlying such choice. We examined mate-guarding by male mandrills, a species with intense male–male competition and female offspring care. We developed a statistical model based on 10 years of observations to describe how the...

Data from: Trade-offs and evolution of thermal adaptation in the Irish potato famine pathogen Phytophthora infestans

Li-Na Yang, Wen Zhu, E-Jiao Wu, Ce Yang, Peter H. Thrall, Jeremy J. Burdon, Li-Ping Jin, Li-Ping Shang & Jiasui Zhan
Temperature is one of the most important environmental parameters with crucial impacts on nearly all biological processes. Due to anthropogenic activity, average air temperatures are expected to increase by a few degrees in coming decades, accompanied by an increased occurrence of extreme temperature events. Such global trends are likely to have various major impacts on human society through their influence on natural ecosystems, food production and biotic interactions, including diseases. In this study, we used...

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,...

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