164 Works

Data from: An examination of the accuracy of a sequential PCR and sequencing test used to detect the incursion of an invasive species: the case of the red fox in Tasmania

David S. L. Ramsey, Anna J. MacDonald, Sumaiya Quasim, Candida Barclay & Stephen D. Sarre
1. Polymerase Chain Reaction (PCR) diagnostic tests are increasingly applied to the identification of wildlife. Yet rigorous verification is rare and the estimation of test accuracy (the probability that true positive and true negative samples are correctly identified – test sensitivity and specificity, respectively), particularly in combination with sequencing, is uncommon. This is important because PCR-based tests are prone to contamination in sampling and the laboratory. 2. Here, we use an experimental case–control approach to...

Data from: A data-driven model for influenza transmission incorporating media effects

Lewis Mitchell & Joshua V. Ross
Numerous studies have attempted to model the effect of mass media on the transmission of diseases such as influenza, however quantitative data on media engagement has until recently been difficult to obtain. With the recent explosion of “big data” coming from online social media and the like, large volumes of data on a population’s engagement with mass media during an epidemic are becoming available to researchers. In this study we combine an online data set...

Data from: Previous exposure to myxomatosis reduces survival of European rabbits during outbreaks of rabbit haemorrhagic disease

Louise K. Barnett, Thomas A. A. Prowse, David E Peacock, Gregory J Mutze, Ron G. Sinclair, John Kovaliski, Brian D. Cooke & Corey J. A. Bradshaw
1. Exploiting disease and parasite synergies could increase the efficacy of biological control of invasive species. In Australia, two viruses were introduced to control European rabbits Oryctolagus cuniculus — myxoma virus in 1950, and rabbit haemorrhagic disease virus in 1995. While these biological controls caused initial declines of > 95% in affected populations, today rabbits remain a problem in many areas, despite recurring outbreaks of both diseases. 2. We used eighteen years of capture-mark-recapture, dead...

Data from: Heat tolerance is more variable than cold tolerance across species of Iberian lizards after controlling for intraspecific variation

Salvador Herrando-Pérez, Camila Monasterio, Wouter Beukema, Verónica Gomes, Francisco Gomes Ferri-Yáñez, Josabel Belliure, Steven L. Chown, Lauren B Buckley, David R. Vieites & Miguel B. Araújo
The widespread observation that heat tolerance is less variable than cold tolerance (‘cold-tolerance asymmetry’) leads to the prediction that species exposed to temperatures near their thermal maxima should have reduced evolutionary potential for adapting to climate warming. However, the prediction is largely supported by species-level global studies based on single estimates of both physiological metrics per taxon. We ask if cold-tolerance asymmetry holds for Iberian lizards after accounting for intraspecific variation in critical thermal maxima...

Data from: Range‐wide population genetic structure of the Caribbean marine angiosperm Thalassia testudinum

Kor-Jent Van Dijk, Eric Bricker, Brigitta Ine Van Tussenbroek & Michelle Waycott
Many marine species have widespread geographic ranges derived from their evolutionary and ecological history particularly their modes of dispersal. Seagrass (marine angiosperm) species have ranges that are unusually widespread, which is not unexpected following recent reviews of reproductive strategies demonstrating the potential for long distance dispersal combined with longevity through clonality. An exemplar of these dual biological features is turtlegrass (Thalassia testudinum) which is an ecologically important species throughout the tropical Atlantic region. Turtlegrass has...

Data from: Testing the impact of calibration on molecular divergence times using a fossil-rich group: the case of Nothofagus (Fagales)

Hervé Sauquet, Simon Y. W. Ho, Maria A. Gandolfo, Gregory J. Jordan, Peter Wilf, David J. Cantrill, Michael J. Bayly, Lindell Bromham, Gillian K. Brown, Raymond J. Carpenter, Daphne M. Lee, Daniel J. Murphy, J. M. Kale Sniderman & Frank Udovicic
Although temporal calibration is widely recognized as critical for obtaining accurate divergence-time estimates using molecular dating methods, few studies have evaluated the variation resulting from different calibration strategies. Depending on the information available, researchers have often used primary calibrations from the fossil record or secondary calibrations from previous molecular dating studies. In analyses of flowering plants, primary calibration data can be obtained from macro- and mesofossils (e.g., leaves, flowers, and fruits) or microfossils (e.g., pollen)....

Data from: The role of continental shelf width in determining freshwater phylogeographic patterns in southeastern Australian pygmy perches (Teleostei: Percichthyidae)

Peter J. Unmack, Michael P. Hammer, Mark Adams, Jerald B. Johnson & Thomas E. Dowling
Biogeographic patterns displayed by obligate freshwater organisms are intimately related to the nature and extent of connectivity between suitable habitats. Two of the more significant barriers to freshwater connections are seawater and major drainage divides. South-eastern Australia provides a contrast between these barriers as it has discrete areas that are likely influenced to a greater or lesser extent by each barrier type. We use continental shelf width as a proxy for the potential degree of...

Data from: Mating patterns and pollinator mobility are critical traits in forest fragmentation genetics

Martin F. Breed, Kym M. Ottewell, Michael G. Gardner, Maria H. K. Marklund, Eleanor E. Dormontt & Andrew J. Lowe
Most woody plants are animal-pollinated, but the global problem of habitat fragmentation is changing the pollination dynamics. Consequently, the genetic diversity and fitness of the progeny of animal-pollinated woody plants sired in fragmented landscapes tend to decline due to shifts in plant-mating patterns (for example, reduced outcrossing rate, pollen diversity). However, the magnitude of this mating-pattern shift should theoretically be a function of pollinator mobility. We first test this hypothesis by exploring the mating patterns...

Data from: Historical stocking data and 19th century DNA reveal human-induced changes to native diversity and distribution of cutthroat trout

Jessica L. Metcalf, Sierra L. Love Stowell, Christopher M. Kennedy, Kevin B. Rogers, Daniel McDonald, Kyle Keepers, Janet Epp, Alan Cooper, Jeremy J. Austin & Andrew P. Martin
Many species are threatened with extinction and efforts are underway worldwide to restore imperiled species to their native ranges. Restoration requires knowledge of species’ historic diversity and distribution, which may not be available. For some species, many populations were extirpated and humans moved individuals beyond their native range before native diversity and distribution were documented. Moreover, traditional taxonomic assessments often failed to accurately capture phylogenetic diversity. We illustrate a general approach for estimating regional native...

Data from: Optimum design of family structure and allocation of resources in association mapping with lines from multiple crosses

Wenxin Liu, Hans Peter Maurer, Jochen C. Reif, Albrecht E. Melchinger, H. F. Utz, Nicolas Ranc, Giovanni Della Porta, Matthew R. Tucker & Tobias Würschum
Family mapping is based on multiple segregating families and is becoming increasingly popular due to advantages over population mapping. Though much progress has been made recently, the optimum design and allocation of resources for family mapping remains unclear. Here, we addressed these issues using a simulation study, resample model averaging and cross-validation approaches. Our results show that in family mapping, the predictive power and the accuracy of QTL detection depend greatly on the population size...

Data from: Multilocus phylogeography reveals nested endemism in a gecko across the monsoonal tropics of Australia

Craig Moritz, Matthew Fujita, Dan F. Rosauer, Rosa Agudo, Gayleen Bourke, Russell Palmer, Mitzy Pepper, Sally Potter, Renae Pratt, Mitchell Scott, Maria Tonione, Stephen Donnellan, Paul Doughty, D. Rosauer & M. K. Fujita
Multilocus phylogeography can uncover taxonomically unrecognized lineage diversity across complex biomes. The Australian monsoonal tropics includes vast, ecologically intact savanna-woodland plains interspersed with ancient sandstone uplands. Though recognized in general for its high species richness and endemism, the biodiversity of the region remains underexplored due to its remoteness. This is despite a high rate of ongoing species discovery, especially in wetter regions and for rock-restricted taxa. To provide a baseline for ongoing comparative analyses, we...

Data from: Species decline under nitrogen fertilization increases community-level competence of fungal diseases

Xiang Liu, Shengman Lyu, Dexin Sun, Corey J. A. Bradshaw & Shurong Zhou
The artificial fertilization of soils can alter the structure of natural plant communities and exacerbate pathogen emergence and transmission. Although the direct effects of fertilization on disease resistance in plants have received some research attention, its indirect effects of altered community structure on the severity of fungal disease infection remain largely uninvestigated. We designed manipulation experiments in natural assemblages of Tibetan alpine meadow vegetation along a nitrogen-fertilization gradient over 5 years to compare the relative...

Data from: A multigene molecular assessment of cryptic biodiversity in the iconic freshwater blackfishes (Teleostei: Percichthyidae: Gadopsis) of south-eastern Australia

Michael P. Hammer, Peter J. Unmack, Mark Adams, Tarmo A. Raadik & Jerald B. Johnson
Freshwater biodiversity is under ever increasing threat from human activities, and its conservation and management require a sound knowledge of species-level taxonomy. Cryptic biodiversity is a common feature for aquatic systems, particularly in Australia, where recent genetic assessments suggest that the actual number of freshwater fish species may be considerably higher than currently listed. The freshwater blackfishes (genus Gadopsis) are an iconic group in south-eastern Australia and, in combination with their broad, naturally divided distribution...

Data from: Ancient DNA reveals elephant birds and kiwi are sister taxa and clarifies ratite bird evolution

Kieren J. Mitchell, Bastien Llamas, Julien Soubrier, Nicolas J. Rawlence, Trevor H. Worthy, Jamie Wood, Michael S. Y. Lee & Alan Cooper
The evolution of the ratite birds has been widely attributed to vicariant speciation, driven by the Cretaceous breakup of the supercontinent Gondwana. The early isolation of Africa and Madagascar implies that the ostrich and extinct Madagascan elephant birds (Aepyornithidae) should be the oldest ratite lineages. We sequenced the mitochondrial genomes of two elephant birds and performed phylogenetic analyses, which revealed that these birds are the closest relatives of the New Zealand kiwi and are distant...

Data from: Detection of subclinical atherosclerosis in asymptomatic subjects using ultrasound radiofrequency-tracking technology

Lili Niu, Yanling Zhang, Long Meng, Yang Xiao, Kelvin K. L. Wong, Derek Abbott, Hairong Zheng, Rongqin Zheng & Ming Qian
Objective: Atherosclerosis is a chronic and systemic disease and its developmental process involves the synergism of multiple risk factors such as hypertension, dyslipidemia, diabetes, obesity and smoking. The diagnosis of subclinical atherosclerosis is essential for strategic guidance towards suitable treatments and efficient prevention against acute cardiovascular events. This study employed ultrasound radiofrequency (RF) tracking technology to characterize human carotid arteries in vivo in terms of intima-media thickness (IMT) and artery stiffness, and evaluated the statistical...

Data from: Understanding the biological invasion risk posed by the global wildlife trade: propagule pressure drives the introduction and establishment of Nearctic turtles

Pablo García-Díaz, Joshua V. Ross, César Ayres & Phillip Cassey
Biological invasions are a key component of human-induced global change. The continuing increase in global wildlife trade has raised concerns about the parallel increase in the number of new invasive species. However, the factors that link the wildlife trade to the biological invasion process are still poorly understood. Moreover, there are analytical challenges in researching the role of global wildlife trade in biological invasions, particularly issues related to the under-reporting of introduced and established populations...

Data from: Genetic diversity and drivers of dwarfism in extinct island emu populations

Vicki A. Thomson, Kieren J. Mitchell, Rolan Eberhard, Joe Dortch, Jeremy J. Austin & Alan Cooper
Australia’s iconic emu (Dromaius novaehollandiae novaehollandiae) is the only living representative of its genus, but fossil evidence and reports from early European explorers suggest that three island forms (at least two of which were dwarfs) became extinct during the 19th century. While one of these - the King Island emu - has been found to be conspecific with Australian mainland emus, little is known about how the other two forms - Kangaroo Island and Tasmanian...

Data from: Effects of sampling effort on biodiversity patterns estimated from environmental DNA metabarcoding surveys

Erin K. Grey, Louis Bernatchez, Phillip Cassey, Kristy Deiner, Marty Deveney, Kimberley L. Howland, Anaïs Lacoursière-Roussel, Sandric Chee Yew Leong, Yiyuan Li, Brett Olds, Michael E. Pfrender, Thomas A. A. Prowse, Mark A. Renshaw & David M. Lodge
Environmental DNA (eDNA) metabarcoding can greatly enhance our understanding of global biodiversity and our ability to detect rare or cryptic species. However, sampling effort must be considered when interpreting results from these surveys. We explored how sampling effort influenced biodiversity patterns and nonindigenous species (NIS) detection in an eDNA metabarcoding survey of four commercial ports. Overall, we captured sequences from 18 metazoan phyla with minimal differences in taxonomic coverage between 18 S and COI primer...

Data from: The biomechanics of foraging determines face length among kangaroos and their relatives

D. Rex Mitchell, Emma Sherratt, Justin A. Ledogar & Stephen Wroe
Increasing body size is accompanied by facial elongation across a number of mammalian taxa. This trend forms the basis of a proposed evolutionary rule, cranial evolutionary allometry (CREA). However, facial length has also been widely associated with the varying mechanical resistance of foods. Here, we combine geometric morphometric and computational biomechanical analyses to determine whether evolutionary allometry or feeding ecology have been dominant influences on facial elongation across sixteen species of kangaroos and relatives (Macropodiformes)....

Data from: Spontaneous forest regrowth in South-West Europe: consequences for nature’s contributions to people

Irene Martín-Forés, Sandra Magro, Andres Bravo-Oviedo, Raquel Alfaro-Sánchez, Josep M. Espelta, Theresa Frei, Elena Valdés-Correcher, Carmen Rodríguez Fernández-Blanco, Georg Winkel, Gabriel Gerzabek, Arndt Hampe & Fernando Valladares
Context European forests are expanding and becoming denser following the widespread abandonment of farmland and rural areas. Yet, little is known about the goods and services that spontaneous forest regrowth provide to people. Aims We assessed the changes in nature’s contributions to people (NCP) from spontaneous forest regrowth, i.e. forest expansion and densification, in South-West Europe. Methods We investigated 65 forest plots in four different landscapes with contrasting ecological and societal contexts. Two landscapes are...

Xylomelum occidentale (Proteaceae) accesses relatively mobile soil organic phosphorus without releasing carboxylates

Hongtao Zhong, Jun Zhou, Azrul Azmi, André Arruda, Ashlea Doolette, Ronald Smernik & Hans Lambers
1. Hundreds of Proteaceae species in Australia and South Africa typically grow on phosphorus (P)-impoverished soils, exhibiting a carboxylate-releasing P-mobilising strategy. In the Southwest Australian Biodiversity Hotspot, two Xylomelum (Proteaceae) species are widely distributed, but restricted within that distribution. 2. We grew X. occidentale in hydroponics at 1 μM P. Leaves, seeds, rhizosheath and bulk soil were collected in natural habitats. 3. Xylomelum occidentale did not produce functional cluster roots and occupied soils that are...

Data from: Multi-species restoration accelerates recovery of extinguished oyster reefs

Dominic McAfee, Catherine Larkin & Sean Connell
1. A multi-species approach to habitat restoration may boost the key processes (e.g. recruitment) that enable foundation species to overcome barriers to recovery. Natural systems tend to be formed by co-occurring foundation species whose synergy drives ecological productivity and resilience beyond that of single foundation species. Yet, restoration remains primarily a single-species focus enterprise where positive interactions are seldom incorporated into planning. A multi-species approach that prioritises species combinations to create emergent properties for their...

Signatures of selection in a recent invasion reveals adaptive divergence in a highly vagile invasive species

Katarina Stuart, Adam Cardilini, Phillip Cassey, Mark Richardson, William Sherwin, Lee Rollins & Craig Sherman
A detailed understanding of population genetics in invasive populations helps us to identify drivers of successful alien introductions. Here, we investigate putative signals of selection in Australian populations of invasive common starlings, Sturnus vulgaris, and seek to understand how these have been influenced by introduction history. We used reduced representation sequencing to determine population structure, and identify Single Nucleotide Polymorphisms (SNPs) that are putatively under selection. We found that since their introduction into Australia, starling...

Data from: High detectability with low impact: optimising large PIT tracking systems for cave-dwelling bats

Emmi Van Harten, Terry Reardon, Linda Lumsden, Noel Meyers, Thomas Prowse, John Weyland & Ruth Lawrence
Passive integrated transponder (PIT) tag technology permits the ‘resighting’ of animals tagged for ecological research without the need for physical re-trapping. While this is effective if animals pass within centimetres of tag readers, short-distance detection capabilities have prevented the use of this technology with many species. To address this problem, we optimised a large (15 m-long) flexible antenna system to provide a c. 8 m2 vertical detection plane for detecting animals in flight. We installed...

Data from: City life alters the gut microbiome and stable isotope profiling of the eastern water dragon (Intellagama lesueurii)

Bethan Littleford-Colquhoun, Laura Weyrich & Celine Frere
Urbanisation is one of the most significant threats to biodiversity, due to the rapid and large-scale environmental alterations it imposes on the natural landscape. It is, therefore, imperative that we understand the consequences of, and mechanisms by which, species can respond to it. In recent years, research has shown that plasticity of the gut microbiome may be an important mechanism by which animals can adapt to environmental change, yet empirical evidence of this in wild...

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