190 Works

Data from: Inferring contemporary and historical genetic connectivity from juveniles

Pierre Feutry, Oliver Berry, Peter M. Kyne, Richard D. Pillans, Rich Hillary, Peter M. Grewe, James R. Marthick, Grant Johnson, Rasanthi M. Gunasekera, Nicholas J. Bax, Mark Bravington & Richard M. Hillary
Measuring population connectivity is a critical task in conservation biology. While genetic markers can provide reliable long-term historical estimates of population connectivity, scientists are still limited in their ability to determine contemporary patterns of gene flow, the most practical time frame for management. Here, we tackled this issue by developing a new approach that only requires juvenile sampling at a single time period. To demonstrate the usefulness of our method, we used the Speartooth shark...

Data from: Diversity and linkage disequilibrium in farmed Tasmanian Atlantic salmon

James W. Kijas, Nick Elliot, Peter Kube, Bradley Evans, Natasha Botwright, Harry King, Craig R. Primmer, Klara Verbyla & J. Kijas
Farmed Atlantic salmon (Salmo salar) is a globally important production species, including in Australia where breeding and selection has been in progress since the 1960s. The recent development of SNP genotyping platforms means genome-wide association and genomic prediction can now be implemented to speed genetic gain. As a precursor, this study collected genotypes at 218 132 SNPs in 777 fish from a Tasmanian breeding population to assess levels of genetic diversity, the strength of linkage...

Data from: Molecular analysis of H7 avian influenza viruses from Australia and New Zealand: genetic diversity and relationships from 1976 to 2007

Dieter M. Bulach, David B. Boyle, Rebecca A. Halpin, David J. Spiro, Laura W. Pomeroy & Daniel A. Janies
Full genome sequencing of 11 Australian and one New Zealand subtype H7 avian influenza A isolates has enabled the comparison of sequences from each of the genome segments to other sequenced subtype H7 avian influenza A. The inference of phylogenetic relationships for each segment has been used to develop a model of the natural history of these viruses in Australia. The Australian H7 hemagglutinins form a monophyletic clade, consistent with the long-term, independent evolution due...

Data from: Selection signature analysis reveals genes associated with tail type in Chinese indigenous sheep

Zehu Yuan, Enming Liu, Z. Liu, J. W. Kijas, Caiye Zhu, Shijin Hu, Xiaomeng Ma, Li Zhang, Lixin Du, Huihua Wang & Caihong Wei
Fat-tailed sheep have commercial value because consumers prefer high-protein and low-fat food and producers care about feed conversion rate. However, fat-tailed sheep still have some scientific significance, as the fat tail is commonly regarded as a characteristic of environmental adaptability. Finding the candidate genes associated with fat tail formation is essential for breeding and conservation. To identify these candidate genes, we applied FST and hapFLK approaches in fat- and thin-tailed sheep with available 50K SNP...

Data from: Dynamic species co-occurrence networks require dynamic biodiversity surrogates

Ayesha I. T. Tulloch, Iadine Chadès, Yann Dujardin, Martin J. Westgate, Peter W. Lane & David Lindenmayer
In conservation it is inevitable that surrogates be selected to represent the occurrence of hard–to–find species and find priority locations for management. However, species co–occurrence can vary over time. Here we demonstrate how temporal dynamics in species co–occurrence influence the ability of managers to choose the best surrogate species. We develop an efficient optimisation formulation that selects the optimal set of complementary surrogate species from any co–occurrence network. We apply it to two Australian datasets...

Data from: Incorporating existing thermal tolerance into projections of compositional turnover under climate change

Alex Bush, Renee Catullo, Karel Mokany, Tom Harwood, Andrew Hoskins & Simon Ferrier
Aim: Observed, realized niche space often underestimates species’ physiological tolerances due to interactions with other species, dispersal constraints, and because some combinations of influential environmental factors do not currently exist in the real world. Conversely, correlative ecological niche models rely on the assumption that the range of environmental conditions encompassed by a species’ geographic distribution accurately reflects their environmental tolerances, including community-level approaches like Generalised Dissimilarity Modelling (GDM). We extend GDM to better understand what...

Data from: Reliable species distributions are obtainable with sparse, patchy and biased data by leveraging over species and data types

Samantha L. Peel, Nicole A. Hill, Scott D. Foster, Simon J. Wotherspoon, Claudio Ghiglione & Stefano Schiaparelli
1. New methods for species distribution models (SDMs) utilise presence‐absence (PA) data to correct the sampling bias of presence‐only (PO) data in a spatial point process setting. These have been shown to improve species estimates when both data sets are large and dense. However, is a PA data set that is smaller and patchier than hitherto examined able to do the same? Furthermore, when both data sets are relatively small, is there enough information contained...

Data from: Space use by 4 strains of laying hens to perch, wing flap, dust bathe, stand and lie down

Elizabeth R. Riddle, Ahmed B. A. Ali, Dana L. M. Campbell & Janice M. Siegford
The laying hen industry is implementing aviary systems intended to improve welfare by providing hens with more space and resources to perform species-specific behaviors. To date, limited research has examined spatial requirements of various strains of laying hens for performing key behaviors and none has been conducted within an alternative housing system. This study investigated the amount of space used by 4 strains of laying hens (Hy-Line Brown [HB], Bovans Brown [BB], DeKalb White [DW],...

Data from: A seascape genetic analysis of a stress-tolerant coral species along the Western Australian coast

Richard D. Evans, Nicole M. Ryan, Michael J. Travers, Ming Feng, Yvette Hitchen & W. Jason Kennington
Genetic diversity and connectivity are key factors in determining a population’s resilience to future disturbance. This is especially relevant to corals, which are in global decline due to increasing frequency and strength of thermal anomalies and severe tropical cyclones. While many studies have investigated genetic diversity and population structure in corals, they focused on species being removed at the greatest rate from coral reefs, Acroporids and Pocilloporids, and it is unclear whether the patterns observed...

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...

CPR dataset for: Testing Bergmann's Rule in Marine Copepods

Max D. Campbell, David S. Schoeman, William Venables, Rana Abu-Alhaija, Sonia D. Batten, Sanae Chiba, Frank Coman, Claire H. Davies, Martin Edwards, Ruth Eriksen, Jason D. Everett, Yutaka Fukai, Mitsuo Fukuchi, Octavio Esquivel Garrote, Graham Hosie, Jenny Huggett, David G. Johns, John A. Kitchener, Philippe Koubbi, Felicity R. McEnnulty, Erik Muxagata, Clare Ostle, Karen V. Robinson, Anita Slotwinski, Kerrie M. Swadling … & Anthony J. Richardson
This is the global dataset used for the Campbell et al. (2021) paper “Testing Bergmann’s Rule in marine copepods”. The dataset includes the mean length of copepods weighted by abundance found in 97,830 continuous plankton recorder (CPR) samples. Further, it contains satellite observations for sea surface temperature, chlorophyll-a, and dissolved oxygen (see paper for details). It was a massive collaborative effort to get this dataset assembled by the Global Alliance of CPR Surveys (GACS 2011,...

Complex histories of gene flow and a mitochondrial capture event in a non-sister pair of bird

Ethan Gyllenhaal, Michael Andersen, Jenna McCullough, Xena Mapel, Tri Haryoko, Knud Jønsson & Leo Joseph
Hybridization, introgression, and reciprocal gene flow during speciation, specifically the generation of mitonuclear discordance, are increasingly observed as parts of the speciation process. Genomic approaches provide insight into where, when, and how adaptation operates during and after speciation and can measure historical and modern introgression. Whether adaptive or neutral in origin, hybridization can cause mitonuclear discordance by placing the mitochondrial genome of one species (or population) in the nuclear background of another species. The latter,...

Data from: The loss of self-incompatibility in a range expansion

Francisco Encinas-Viso, Andrew Young & John Pannell
It is commonly observed that plant species’ range margins are enriched for increased selfing rates and, in otherwise self-incompatible species, for self-compatibility (SC). This has often been attributed to a response to selection under mate and/or pollinator limitation. However, range expansion can also cause reduced inbreeding depression, and this could facilitate the evolution of selfing in the absence of mate or pollinator limitation. Here, we explore this idea using spatially explicit individual-based simulations of a...

Amino acids (AA) all genes for: Beyond Drosophila: resolving the rapid radiation of schizophoran flies with phylotranscriptomics

Keith Bayless, Michelle Trautwein, Karen Meusemann, David Yeates & Brian Wiegmann
Background: The largest radiation of animal life since the end Cretaceous extinction event 66 million years ago is that of schizophoran flies: a third of fly diversity including Drosophila lab fruit flies, house flies, and many other well and poorly known true flies. Rapid diversification has hindered previous attempts to elucidate the phylogenetic relationships among major schizophoran clades. A robust phylogenetic hypothesis for the major lineages containing these 55,000 described species would be critical to...

Climate more important than soils for predicting forest biomass at the continental scale

Alison Bennett, Trent Penman, Stefan Arndt, Stephen Roxburgh & Lauren Bennett
Above-ground biomass in forests is critical to the global carbon cycle as it stores and sequesters carbon from the atmosphere. Climate change will disrupt the carbon cycle hence understanding how climate and other abiotic variables determine forest biomass at broad spatial scales is important for validating and constraining Earth System models and predicting the impacts of climate change on forest carbon stores. We examined the importance of climate and soil variables to explaining above-ground biomass...

Identification of Y chromosome markers in the eastern three-lined skink (Bassiana duperreyi) using in silico whole genome subtraction

Duminda Dissanayake, Clare Holleley & Arthur Georges
Background: Homologous sex chromosomes can differentiate over time because recombination is suppressed in the region of the sex determining locus, leading to the accumulation of repeats, progressive loss of genes that lack differential influence on the sexes and sequence divergence on the hemizygous homolog. Divergence in the non-recombining regions leads to the accumulation of Y or W specific sequence useful for developing sex-linked markers. Here we use in silico whole-genome subtraction to identify putative sex-linked...

Data from: Comparative genomics of the mimicry switch in Papilio dardanus

Martijn J. T. N. Timmermans, Simon W. Baxter, Rebecca Clark, David G. Heckel, Heiko Vogel, Steve Collins, Alexie Papanicolaou, Iva Fukova, Mathieu Joron, Martin J. Thompson, Chris D. Jiggins, Richard H. Ffrench-Constant & Alfried P. Vogler
The African Mocker Swallowtail, Papilio dardanus, is a textbook example in evolutionary genetics. Classical breeding experiments have shown that wing pattern variation in this polymorphic Batesian mimic is determined by the polyallelic H locus that controls a set of distinct mimetic phenotypes. Using bacterial artificial chromosome (BAC) sequencing, recombination analyses and comparative genomics, we show that H co-segregates with an interval of less than 500 kb that is collinear with two other Lepidoptera genomes and...

Data from: Physiological plasticity and local adaptation to elevated pCO2 in calcareous algae: an ontogenetic and geographic approach

Jacqueline L. Padilla-Gamiño, Juan D. Gaitán-Espitia, Morgan W. Kelly & Gretchen E. Hofmann
To project how ocean acidification will impact biological communities in the future, it is critical to understand the potential for local adaptation and the physiological plasticity of marine organisms throughout their entire life cycle, as some stages may be more vulnerable than others. Coralline algae are ecosystem engineers that play significant functional roles in oceans worldwide, and are considered vulnerable to ocean acidification. Using different stages of coralline algae, we tested the hypothesis that populations...

Data from: Phylogenetic diversity is a better measure of biodiversity than taxon counting

Joseph T. Miller, Garry Jolley-Rogers, Brent D. Mishler & Andrew H. Thornhill
Biodiversity is most commonly measured in taxonomic richness. For example, it is common to describe how diverse a genus or a geographic area is by counting the number of species within them. Phylogenetic diversity (PD), a measurement of the branch lengths in a phylogenetic tree, is a better measure of biodiversity that provides a comparable, evolutionary measure of biodiversity not possible with species counts. Despite its advantages, PD is rarely used as the primary measure...

Data from: Evolutionary history of the angiosperm flora of China

Li-Min Lu, Ling-Feng Mao, Tuo Yang, Jian-Fei Ye, Bing Liu, Hong-Lei Li, Miao Sun, Joseph T. Miller, Sarah Mathews, Hai-Hua Hu, Yan-Ting Niu, Dan-Xiao Peng, You-Hua Chen, Stephen A. Smith, Min Chen, Kun-Li Xiang, Chi-Toan Le, Viet-Cuong Dang, An-Ming Lu, Pamela S. Soltis, Douglas E. Soltis, Jian-Hua Li & Zhi-Duan Chen
High species diversity may result from recent rapid speciation in a ‘cradle’ and/or the gradual accumulation and preservation of species over time in a ‘museum’1,2. China harbours nearly 10% of angiosperm species worldwide and has long been considered as both a museum, owing to the presence of many species with hypothesized ancient origins3,4, and a cradle, as many lineages have originated as recent topographic changes and climatic shifts—such as the formation of the Qinghai–Tibetan Plateau...

Data from: Landscape context explains changes in the functional diversity of regenerating forests better than climate or species richness

Michael Sams, Hao Ran Lai, Stephen Bonser, Peter Vesk, Robert Kooyman, Daniel Metcalfe, John W. Morgan, Margaret Mayfield, M. A. Sams, D. J. Metcalfe, R. M. Kooyman & P. A. Vesk
Aim A rich literature on forest succession provides general expectations for the steps forests go through while reassembling after disturbance, yet we still have a surprisingly poor understanding of why the outcomes of forest recovery after logging (or other disturbances) vary so extensively. In this paper, we test the hypothesis that regional species pool, system productivity, climate and landscape structure are important drivers of forest reassembly outcomes. Location Transect 1,500 km in length along the...

Data from: Seascape genomics reveals fine-scale patterns of dispersal for a reef fish along the ecologically divergent coast of Northwestern Australia

Joseph D. DiBattista, Michael J. Travers, Glenn I. Moore, Richard D. Evans, Stephen J. Newman, Ming Feng, Samuel D. Moyle, Rebecca J. Gorton, Thor Saunders & Oliver Berry
Understanding the drivers of dispersal among populations is a central topic in marine ecology and fundamental for spatially explicit management of marine resources. The extensive coast of Northwestern Australia provides an emerging frontier for implementing new genomic tools to comparatively identify patterns of dispersal across diverse and extreme environmental conditions. Here, we focused on the stripey snapper (Lutjanus carponotatus), which is important to recreational, charter-based and customary fishers throughout the Indo-West Pacific. We collected 1,016...

Data from: Integrating complementary methods to improve diet analysis in fishery-targeted species

Jordan K. Matley, Gregory E. Maes, Floriaan Devloo-Delva, Roger Huerlimann, Gladys Chua, Andrew J. Tobin, Aaron T. Fisk, Colin A. Simpfendorfer & Michelle R. Heupel
Developing efficient, reliable, cost-effective ways to identify diet is required to understand trophic ecology in complex ecosystems and improve food web models. A combination of techniques, each varying in their ability to provide robust, spatially and temporally explicit information can be applied to clarify diet data for ecological research. This study applied an integrative analysis of a fishery-targeted species group - Plectropomus spp.in the central Great Barrier Reef, Australia by comparing three diet-identification approaches. Visual...

Data from: Direct measurement of ant predation of weed seeds in wheat cropping

Theodore A. Evans & Patrick V. Gleeson
The ecosystem service of predation of weed seeds by naturally occurring seed-eating animals, including ants, in agricultural fields has been suggested to be a potentially important biocontrol option. Laboratory and field tests have found high levels of seed removal from experimentally placed seed; however, the effect of predation on naturally dispersed weed seeds is unknown. We measured the effect of invertebrate seed predators on natural weed seed dispersal and germination in a field experiment under...

Data from: Mobulid rays feed on euphausiids in the Bohol Sea

Christoph A. Rohner, Katherine B. Burgess, Joshua M. Rambahiniarison, Joshua D. Stewart, Alessandro Ponzo & Anthony J. Richardson
Mobulid rays have a conservative life history and are caught in direct fisheries and as by-catch. Their subsequent vulnerability to overexploitation has recently been recognized, but fisheries management can be ineffective if it ignores habitat and prey preferences and other trophic interactions of the target species. Here, we assessed the feeding ecology of four mobulids (Manta birostris, Mobula tarapacana, M. japanica, M. thurstoni) in the Bohol Sea, Philippines, using stomach contents analysis of fisheries specimens...

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