189 Works

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: 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: 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: 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: 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: 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: 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],...

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: 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: 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...

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,...

Data from: Distorted views of biodiversity: spatial and temporal bias in species occurrence data

Elizabeth H. Boakes, Philip J. K. McGowan, Richard A. Fuller, Ding Chang-Qing, Natalie E. Clark, Kim O'Connor & Georgina M. Mace
Historical as well as current data on species distributions are needed to track changes in biodiversity. Species distribution data are found in a variety of sources but is likely that they include different biases towards certain time periods or places. By collating a large historical database of ~170,000 records of species in the avian order Galliformes dating back over two centuries and covering Europe and Asia, we investigate patterns of spatial and temporal bias in...

Data from: Environmental and historical imprints on beta diversity: insights from variation in rates of species turnover along gradients

Matthew C. Fitzpatrick, Nathan J. Sanders, Signe Normand, Jens-Christian Svenning, Simon Ferrier, Aaron D. Gove, Robert R. Dunn, N. J. Sanders, S. Normand, R. R. Dunn, J.-C. Svenning, A. D. Gove & S. Ferrier
A common approach for analysing geographical variation in biodiversity involves using linear models to determine the rate at which species similarity declines with geographical or environmental distance and comparing this rate among regions, taxa or communities. Implicit in this approach are weakly justified assumptions that the rate of species turnover remains constant along gradients and that this rate can therefore serve as a means to compare ecological systems. We use generalized dissimilarity modelling, a novel...

Data from: Amphibian chytridiomycosis in Japan: distribution, haplotypes, and possible entry into Japan

Koichi Goka, Jun Yokoyama, Yumi Une, Toshiro Kuroki, Kazutaka Suzuki, Miri Nakahara, Arei Kobayashi, Shigeki Inaba, Tomoo Mizutani & Alex Hyatt
A serious disease of amphibians caused by the chytrid fungus Batrachochytrium dendrobatidis was first found in Japan in December 2006 in imported pet frogs. This was the first report of chytridiomycosis in Asia. To assess the risk of pandemic chytridiomycosis to Japanese frogs, we surveyed the distribution of the fungus among captive and wild frog populations. We established a nested PCR assay that uses two pairs of PCR primers to amplify the internal transcribed spacer...

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: Genome-wide analyses of the Bemisia tabaci species complex reveal contrasting patterns of admixture and complex demographic histories

Samia Elfekih, Paul Etter, Weetek T. Tay, Matteo Fumagalli, Karl Gordon, Eric Johnson & Paul De Barro
Once considered a single species, the whitefly, Bemisia tabaci, is a complex of numerous morphologically indistinguishable species. Within the last three decades, two of its members (MED and MEAM1) have become some of the world's most damaging agricultural pests invading countries across Europe, Africa, Asia and the Americas and affecting a vast range of agriculturally important food and fiber crops through both feeding-related damage and the transmission of numerous plant viruses. For some time now,...

Data from: Primary productivity is related to niche width in the Australian Wet Tropics

Hugh M. Burley, Karel Mokany, Shawn W. Laffan, Kristen J. Williams, Dan Metcalfe, Helen T. Murphy, Andrew Ford, Tom D. Harwood & Simon Ferrier
Aim: A key ecological debate is whether ecosystem functions are distinctly influenced by biological diversity across broad scales. Although recent work has emphasized the importance of links between ecosystem functions and measures of ecological specialization as proxies of biodiversity, few studies have analysed macroecological relationships empirically in diverse environments. We tested whether gross primary productivity (GPP) in the Australian Wet Tropics (WT) was distinctly related to community‐level measures of the ecological specialization of component tree...

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...

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...

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...

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...

Data from: Contrasting processes drive ophiuroid phylodiversity across shallow and deep seafloors

Timothy J. O'Hara, Andrew F. Hugall, Skipton N.C. Woolley, Guadalupe Bribiesca-Contreras & Nocholas J. Bax
Our knowledge of the distribution and evolution of deep-sea life is limited, impeding our ability to identify priority areas for conservation. Here we analyse, for the first time, large integrated phylogenomic and distributional datasets of seafloor fauna from sea surface to abyss and equator to pole of the Southern Hemisphere for an entire class of invertebrates (Ophiuroidea). We find that latitudinal diversity gradients are assembled through contrasting evolutionary processes for shallow (0-200 m) and deep...

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: 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: Latitudinal variation in seagrass herbivory: global patterns and explanatory mechanisms

Adriana Vergés, Christopher Doropoulos, Rob Czarnik, Kathryn McMahon, Nil Llonch & Alistair G. B. Poore
Aim: The aim was to quantify latitudinal patterns in seagrass–herbivore interactions in the context of a warming climate. Location: We carried out a global meta‐analysis combined with a field experiment across 1,700 km and 12° of latitude in Western Australia. Time period: 1984–2014. Major taxa studied: Seagrasses. Methods: We first synthesized the global literature on herbivore exclusion experiments in seagrasses to test whether differences in herbivore impacts are related to latitude and sea surface temperature....

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