123 Works

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: Assessing the trophic ecology of top predators across a recolonisation frontier using DNA metabarcoding of diets

Natasha Hardy, Tina Berry, Brendan P. Kelaher, Simon D. Goldsworthy, Michael Bunce, Melinda A. Coleman, Bronwyn M. Gillanders, Sean D. Connell, Michelle Blewitt, Will Figueira, BM Gillanders, SD Connell, BP Kelaher & SD Goldsworthy
Top predator populations, once intensively hunted, are rebounding in size and geographic distribution. The cessation of sealing along coastal Australia and subsequent recovery of Australian Arctocephalus pusillus doriferus and long-nosed A. forsteri fur seals represents a unique opportunity to investigate trophic linkages at a frontier of predator recolonisation. We characterised the diets of both species across 2 locations of recolonisation, one site an established breeding colony, and the other, a new but permanent haul-out site....

Data from: Management of behavioural change in patients presenting with a diagnosis of dementia: a video vignette study with Australian general practitioners

Moyez Jiwa, Pam Nichols, Parker Magin, Georgina Pagey, Xingqiong Meng, Richard Parsons & Vinita Pillai
Objective: To test the impact of feedback on the proposed management of standardised patients presenting with behavioural change with a diagnosis of dementia in Australian primary care. Materials and methods: A video vignette study was performed with Australian general practitioners (GPs) in 2013. Participants viewed six pairs of matched videos depicting people presenting changed behaviour in the context of a dementia diagnosis in two phases. In both phases GPs indicated their diagnosis and management. After...

Data from: Evaluation of the first pharmacist-administered vaccinations in Western Australia: a mixed-methods study

H. Laetitia Hattingh, T. Fei Sim, R. Parsons, P. Czarniak, A. Vickery & S. Ayadurai
Objectives This study evaluated the uptake of Western Australian (WA) pharmacist vaccination services, the profiles of consumers being vaccinated and the facilitators and challenges experienced by pharmacy staff in the preparation, implementation and delivery of services. Design Mixed-methods methodology with both quantitative and qualitative data through surveys, pharmacy computer records and immuniser pharmacist interviews. Setting Community pharmacies in WA that provided pharmacist vaccination services between March and October 2015. Participants Immuniser pharmacists from 86 pharmacies...

Data from: Silent fish surveys: bubble-free diving highlights inaccuracies associated with SCUBA-based surveys in heavily fished areas

Steven J. Lindfield, Jennifer L. McIlwain, Euan S. Harvey & Andrew R. Halford
1. Underwater visual census (UVC) using SCUBA is a commonly used method for assessing reef fish communities. Evidence suggests, however, that fish avoid divers due to the sound of bubbles produced by open-circuit SCUBA, and avoidance behaviour is more pronounced as fishing pressure increases. Despite the potential for producing biased counts and conclusions, these behavioural effects have rarely been quantified, especially when assessing the effectiveness of marine protected areas (MPAs). 2. To test the magnitude...

Data from: Environmental DNA metabarcoding studies are critically affected by substrate selection

Adam Koziol, Michael Stat, Tiffany Simpson, Simon Jarman, Joseph D. DiBattista, Euan S. Harvey, Michael Marnane, Justin McDonald & Michael Bunce
Effective biomonitoring is critical for driving management outcomes that ensure long-term sustainability of the marine environment. In recent years environmental DNA (eDNA), coupled with metabarcoding methodologies, has emerged as a promising tool for generating biotic surveys of marine ecosystems, including those under anthropogenic pressure. However, more empirical data is needed on how to best implement eDNA field sampling approaches to maximise their utility for each specific application. The effect of the substrate chosen for eDNA...

Data from: The molecular biogeography of the Indo-Pacific: testing hypotheses with multispecies genetic patterns

Eric D. Crandall, Cynthia Riginos, Chris E. Bird, Libby Liggins, Eric Treml, Maria Beger, Paul H. Barber, Sean R. Connolly, Peter F. Cowman, Joseph D. Dibattista, Jeff A. Eble, Sharon F. Magnuson, John B. Horne, Marc Kochzius, Harilaos A. Lessios, Shang Yin Vanson Liu, William B. Ludt, Hawis Madduppa, John M. Pandolfi, Robert R. Toonen, Contributing Members Of Diversity Of The Indo-Pacific Network & Michelle R. Gaither
Aim: To test hypothesized biogeographic partitions of the tropical Indo-Pacific Ocean with phylogeographic data from 56 taxa, and to evaluate the strength and nature of barriers emerging from this test. Location: The Indo-Pacific Ocean. Time Period: Pliocene through the Holocene. Major Taxa Studied: 56 marine species. Methods: We tested eight biogeographic hypotheses for partitioning of the Indo-Pacific using a novel modification to analysis of molecular variance. Putative barriers to gene flow emerging from this analysis...

Data from: Genetic status and timing of a weevil introduction to Santa Cruz Island, Galápagos

Hoi-Fei Mok, Courtney C. Stepien, Maryska Kaczmarek, Lázaro Roque Albelo & Andrea S. Sequeira
Successful invasive species can overcome or circumvent the potential genetic loss caused by an introduction bottleneck through a rapid population expansion and admixture from multiple introductions. We explore the genetic makeup and the timing of a species introduction to Santa Cruz Island in the Galápagos archipelago. We investigate the presence of processes that can maintain genetic diversity in populations of the broad-nosed weevil Galapaganus howdenae howdenae. Analyses of combined genotypes for 8 microsatellite loci showed...

Data from: Calibration of pelagic stereo-BRUVs and scientific longline surveys for sampling sharks

Julia Santana-Garcon, Matias Braccini, Tim J. Langlois, Stephen J. Newman, Rory B. McAuley & Euan S. Harvey
1. Our understanding of the ecology of sharks and other highly mobile marine species often relies on fishery-dependent data or extractive fishery-independent techniques that can result in catchability and size-selectivity biases. Pelagic Baited Remote Underwater stereo-Video Systems (pelagic stereo-BRUVs) provide a standardized, non-destructive and fishery-independent approach to estimate biodiversity measures of fish assemblages in the water column. However, the performance of this novel method has not yet been assessed relative to other standard sampling techniques....

Data from: A randomised trial deploying a simulation to investigate the impact of hospital discharge letters on patient care in general practice.

Moyez Jiwa, Xingqiong Meng, Carolyn O’Shea, Parker Magin, Ann Dadich & Vinita Pillai
Objective: To determine how the timing and length of hospital discharge letters impact on the number of ongoing patient problems identified by general practitioners (GPs). Trial design: GPs were randomised into four groups. Each viewed a video monologue of an actor-patient as he might present to his GP following a hospital admission with 10 problems. GPs were provided with a medical record as well as a long or short discharge letter, which was available when...

Data from: Scrutinizing key steps for reliable metabarcoding of environmental samples

Antton Alberdi, Ostaizka Aizpurua, M. Thomas P. Gilbert & Kristine Bohmann
1. Metabarcoding of environmental samples has many challenges and limitations that require carefully considered laboratory and analysis pipelines to ensure reliable results. We explore how decisions regarding study design, laboratory work and bioinformatic processing affect the final results, and provide guidelines for reliable study of environmental samples. 2. We evaluate the performance of four primer sets targeting COI and 16S regions characterising arthropod diversity in bat faecal samples, and investigate how metabarcoding results are affected...

Gene validation and remodelling using proteogenomics of Phytophthora cinnamomi, the causal agent of Dieback

Christina Andronis
This spectral data is in support for the manuscript 'Gene validation and remodelling using proteogenomics of Phytophthora cinnamomi, the causal agent of Dieback'. This data was used to detect errors in the draft genome and curate previously undescribed genes in the Phytophthora cinnamomi genome.

Data for: Spontaneous choices for insect-pollinated flower shapes by wild non-eusocial halictid bees

Scarlett Howard, Kit Prendergast, Matthew Symonds, Mani Shrestha & Adrian Dyer
The majority of angiosperms require animal pollination for reproduction and insects are the dominant group of animal pollinators. Bees are considered one of the most important and abundant insect pollinators. Research into bee behaviour and foraging decisions has typically centred on managed eusocial bee species, Apis mellifera and Bombus terrestris. Non-eusocial bees are understudied with respect to foraging strategies and decision-making, such as flower preferences. Understanding whether there are fundamental foraging strategies and preferences which...

Data from: A critical evaluation of how ancient DNA bulk bone metabarcoding complements traditional morphological analysis of fossil assemblages

Alicia C. Grealy, Matthew C. McDowell, Paul Scofield, Dáithí C. Murray, Diana A. Fusco, James Haile, Gavin J. Prideaux & Michael Bunce
When pooled for extraction as a bulk sample, the DNA within morphologically unidentifiable fossil bones can, using next-generation sequencing, yield valuable taxonomic data. This method has been proposed as a means to rapidly and cost-effectively assess general ancient DNA preservation at a site, and to investigate temporal and spatial changes in biodiversity; however, several caveats have yet to be considered. We critically evaluated the bulk bone metabarcoding (BBM) method in terms of its: (i) repeatability,...

Data from: Climate mediates the effects of disturbance on ant assemblage structure

Heloise Gibb, Nathan J. Sanders, Robert R. Dunn, Simon Watson, Manoli Photakis, Silvia Abril, Alan N. Andersen, Elena Angulo, Inge Armbrecht, Xavier Arnan, Fabricio B. Baccaro, Tom R. Bishop, Raphael Boulay, Cristina Castracani, Israel Del Toro, Thibaut Delsinne, Mireia Diaz, David A. Donoso, Martha L. Enríquez, Tom M. Fayle, Donald H. Feener, Matthew C. Fitzpatrick, Crisanto Gómez, Donato A. Grasso, Sarah Groc … & C. Gomez
Many studies have focused on the impacts of climate change on biological assemblages, yet little is known about how climate interacts with other major anthropogenic influences on biodiversity, such as habitat disturbance. Using a unique global database of 1128 local ant assemblages, we examined whether climate mediates the effects of habitat disturbance on assemblage structure at a global scale. Species richness and evenness were associated positively with temperature, and negatively with disturbance. However, the interaction...

Data from: Does genetic distance between parental species influence outcomes of hybridisation among coral reef butterflyfishes?

Stefano R. Montanari, Jean-Paul A. Hobbs, Morgan S. Pratchett, Line K. Bay & Lynne Van Herwerden
Christmas Island is located at the overlap of the Indian and Pacific Ocean marine provinces and is a hot spot for marine hybridization. Here, we evaluate the ecological framework and genetic consequences of hybridization between butterflyfishes Chaetodon guttatissimus and Chaetodon punctatofasciatus. Further, we compare our current findings to those from a previous study of hybridization between Chaetodon trifasciatus and Chaetodon lunulatus. For both species groups, habitat and dietary overlap between parental species facilitate frequent heterospecific...

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: Metabarcoding under Brine: Microbial ecology of five hyper-saline lakes at Rottnest Island (WA, Australia)

Mattia Saccò, Nicole E. White, Matthew Campbell, Sebastian Allard, William F. Humphreys, Paul Pringle, Farid Sepanta, Alex Laini & Morten E. Allentoft
Hypersaline ecosystems - aquatic environments where concentration of salt exceeds 35 g/L - host microbial communities which are highly specialized to cope with these extreme conditions. However, our knowledge on the taxonomic diversity and functional metabolisms characterising microbial communities in the water columns of hypersaline ecosystems is still limited, and this lack of knowledge may compromise the future preservation of these unique environments. DNA metabarcoding provides a reliable and affordable tool to investigate environmental dynamics...

Data from: Population genetics of a broadcast-spawning coral across a tropical-temperate transition zone reveals regional differentiation and isolation of high-latitude reefs

Richard Evans, Luke Thomas, W. Jason Kennington, Nicole Ryan, Nerida Wilson, Zoe Richards, Ryan Lowe & Chenae Tuckett
Aim: Genetic connectivity is a key component of species resilience to climate change in terms of recovery capacity following disturbance and capacity to disperse to novel locations as the climate warms and isotherms shift poleward. We aimed to strengthen our understanding of resilience in this context by characterizing patterns of connectivity and genetic diversity in a broadcast spawning coral across a tropical-temperate transition zone. We hypothesize genetic differentiation between tropical and temperate populations and decreasing...

High resolution distribution modelling of a threatened short-range endemic plant informed by edaphic factors.

Sean Tomlinson, Wolfgang Lewandrowski, Carole Elliott, Ben Miller & Shane Turner
Short-range endemic plants often have edaphic specialisations that, with their restricted distributions, expose them to increased risk of anthropogenic extinction. Here, we present a modelling approach to understand habitat suitability for Ricinocarpos brevis R.J.F.Hend. & Mollemans (Euphorbiaceae), a threatened shrub confined to three isolated populations in the semi-arid south-west of Western Australia. The model is a maximum entropy species distribution projection constructed on the basis of physical soil characteristics and geomorphology data at approximately 25...

Predicting hydrologic responses to climate changes in highly glacierized and mountainous region Upper Indus Basin

Muhammad Izhar Shah, Asif Khan, Tahir Ali Akbar, Quazi K Hassan, Asim Jahangir Khan & Ashraf Dewan
The Upper Indus Basin (UIB) is a major source of supplying water to different areas because of snow and glaciers melt and is also enduring the regional impacts of global climate change. The expected changes in temperature, precipitation, and snowmelt could be reasons for further escalation of the problem. Therefore, estimation of hydrological processes is critical for UIB. The objectives of this paper were to estimate the impacts of climate change on water resources and...

Spatial reconstruction parameters for the atom probe analysis of common minerals

Denis Fougerouse, David Saxey, William Rickard, Steven Reddy & Rick Verberne

Population genomic response to geographic gradients by widespread and endemic fishes of the Arabian Peninsula

Joseph DiBattista, Pablo Saenz-Agudelo, Marek Piatek, Fernando Cagua, Brian Bowen, John Choat, Luiz Rocha, Michelle Gaither, Jean-Paul Hobbs, Tane Sinclair-Taylor, Jennifer McIlwain, Mark Priest, Camrin Braun, Nigel Hussey, Steven Kessel & Michael Berumen
Genetic structure within marine species may be driven by local adaptation to their environment, or alternatively by historical processes, such as geographic isolation. The gulfs and seas bordering the Arabian Peninsula offer an ideal setting to examine connectivity patterns in coral reef fishes with respect to environmental gradients and vicariance. The Red Sea is characterized by a unique marine fauna, historical periods of desiccation and isolation, as well as environmental gradients in salinity, temperature, and...

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