212 Works

Data from: Point process models for presence-only analysis

Ian W. Renner, Jane Elith, Adrian Baddeley, William Fithian, Trevor Hastie, Steven Phillips, Gordana Popovic & David I. Warton
1. Presence-only data are widely used for species distribution modelling, and point process regression models are a exible tool that has considerable potential for this problem, when data arise as point events. 2. In this paper we review point process models, some of their advantages, and some common methods of fitting them to presence-only data. 3. Advantages include (and are not limited to): clarification of what the response variable is that is modelled; a framework...

Data from: A questionnaire study of injections prescribed and dispensed for patients diagnosed with mild/moderate community-acquired pneumonia in Mongolia

Gereltuya Dorj, Bruce Sunderland, Delia Hendrie & Richard W. Parsons
Purpose. The study aimed to determine the extent of and factors influencing the prescribing of injections for the treatment of mild/moderate community acquired pneumonia (CAP) in Mongolia. Methods. Questionnaires were developed and administered to medication providers (34 Pharmacists, 27 pharmacy technicians) and prescribers (22 general doctors and 49 medical specialists) working in Mongolia. Results. Cefalosporins were prescribed for patients with mild pneumonia and doctors tended to prescribe injectable cefalosporins (cefazolin) rather than oral dosage forms....

Data from: Evolutionary factors affecting the cross-species utility of newly developed microsatellite markers in seabirds

Yoshan Moodley, Juan F. Masello, Gopi K. Munimanda, Theresa L. Cole, Marco R. Thali, Rachael Alderman, Richard J. Cuthbert, Manuel Marin, Melanie Massaro, Joan Navarro, Richard A. Phillips, Peter G. Ryan, Cristián G. Suazo, Yves Cherel, Henri Weimerskirch, Petra Quillfeldt & Luciano Calderon
Microsatellite loci are ideal for testing hypotheses relating to genetic segregation at fine spatio-temporal scales. They are also conserved among closely related species, making them potentially useful for clarifying interspecific relationships between recently diverged taxa. However, mutations at primer binding sites may lead to increased nonamplification, or disruptions that may result in decreased polymorphism in nontarget species. Furthermore, high mutation rates and constraints on allele size may also with evolutionary time, promote an increase in...

Data from: Demonstrating multiple benefits from periodically harvested fisheries closures

Jordan S. Goetze, Joachim Claudet, Fraser Januchowski-Hartley, Timothy J. Langlois, Shaun K. Wilson, Crow White, Rebecca Weeks & Stacy D. Jupiter
1.Periodically harvested closures (PHCs) are one of the most common forms of fisheries management in Melanesia, demonstrating multiple objectives, including sustaining fish stocks and increasing catch efficiency to support small-scale fisheries. No studies have comprehensively assessed their ability to provide short-term fisheries benefits across the entire harvest regime. 2.We present a novel analytical framework to guide a meta-analysis and assist future research in conceptualizing and assessing the potential of PHCs to deliver benefits for multiple...

Data from: Integrated evidence reveals a new species in the ancient blue coral genus Heliopora (Octocorallia)

Zoe T. Richards, Nina Yasuda, Taisei Kikuchi, Taryn Foster, Chika Mitsuyuki, Michael Stat, Yoshihisa Suyama & Nerida G. Wilson
Maintaining the accretion potential and three dimensional structure of coral reefs is a priority but reef-building scleractinian corals are highly threatened and retreating. Hence future reefs are predicted to be dominated by non-constructional taxa. Since the Late Triassic however, other non-scleractinian anthozoans such as Heliopora have contributed to tropical and subtropical reef-building. Heliopora is an ancient and highly conserved reef building octocoral genus within the monospecific Family Helioporidae, represented by a single extant species –...

Data from: Debugging diversity – a pan‐continental exploration of the potential of terrestrial blood‐feeding leeches as a vertebrate monitoring tool

Ida Bærholm Schnell, Kristine Bohmann, Sebastian E. Schultze, Stine R. Richter, Dáithí C. Murray, Mikkel-Holger S. Sinding, David Bass, John E. Cadle, Mason J. Campbell, Rainer Dulch, David P. Edwards, Thomas N. E. Gray, Teis Hansen, Anh N. Q. Hoa, Christina Lehmkuhl Noer, Sigrid Heise-Pavlov, Adam F. Sander Pedersen, Juliot C. Ramamonjisoa, Mark E. Siddall, Andrew Tilker, Carl Traeholt, Nicholas Wilkinson, Paul Woodcock, Douglas W. Yu, Mads Frost Bertelsen … & Ida Baerholm Schnell
The use of environmental DNA (eDNA) has become an applicable non-invasive tool with which to obtain information about biodiversity. A sub-discipline of eDNA is iDNA (invertebrate-derived DNA), where genetic material ingested by invertebrates is used to characterise the biodiversity of the species that served as hosts. While promising, these techniques are still in their infancy, as they have only been explored on limited numbers of samples from only a single or a few different locations....

Data from: Applying the multistate capture-recapture robust design to characterize metapopulation structure

Delphine Chabanne, Kenneth H. Pollock, Hugh Finn, Lars Bejder & Delphine B. H. Chabanne
1. Population structure must be considered when developing mark-recapture (MR) study designs as the sampling of individuals from multiple populations (or subpopulations) may increase heterogeneity in individual capture probability. Conversely, the use of an appropriate MR study design which accommodates heterogeneity associated with capture-occasion varying covariates due to animals moving between ‘states’ (i.e. geographic sites) can provide insight into how animals are distributed in a particular environment and the status and connectivity of subpopulations. 2....

Data from: Using a butterflyfish genome as a general tool for RAD-Seq studies in specialized reef fish

Joseph D. DiBattista, Pablo Saenz-Agudelo, Marek J. Piatek, Xin Wang, Manuel Aranda & Michael L. Berumen
Data from a large-scale restriction site associated DNA (RAD-Seq) study of nine butterflyfish species in the Red Sea and Arabian Sea provided a means to test the utility of a recently published draft genome (Chaetodon austriacus) and assess apparent bias in this method of isolating nuclear loci. We here processed double-digest restriction-site (ddRAD) associated DNA sequencing data to identify single nucleotide polymorphism (SNP) markers and their associated function with and without our reference genome to...

Data from: Evaluating multilocus Bayesian species delimitation for discovery of cryptic mycorrhizal diversity

Michael R. Whitehead, Renee A. Catullo, Monica Ruibal, Kingsley W. Dixon, Rod Peakall & Celeste C. Linde
The increasing availability of DNA sequence data enables exciting new opportunities for fungal ecology. However, it amplifies the challenge of how to objectively classify the diversity of fungal sequences into meaningful units, often in the absence of morphological characters. Here, we test the utility of modern multilocus Bayesian coalescent-based methods for delimiting cryptic fungal diversity in the orchid mycorrhiza morphospecies Serendipita vermifera. We obtained 147 fungal isolates from Caladenia, a speciose clade of Australian orchids...

Data from: Precipitation drives global variation in natural selection

Adam Siepielski, Michael B. Morrissey, Mathieu Buoro, Stephanie M. Carlson, Christina M. Caruso, Sonya M. Clegg, Tim Coulson, Joseph DiBattista, Kiyoko M. Gotanda, Clinton D. Francis, Joe Hereford, Joel G. Kingsolver, Kate E. Augustine, Loeske E. B. Kruuk, Ryan A. Martin, Ben C. Sheldon, Nina Sletvold, Erik I. Svensson, Michael J. Wade & Andrew D. C. MacColl
Climate change has the potential to affect the ecology and evolution of every species on Earth. Although the ecological consequences of climate change are increasingly well documented, the effects of climate on the key evolutionary process driving adaptation—natural selection—are largely unknown. We report that aspects of precipitation and potential evapotranspiration, along with the North Atlantic Oscillation, predicted variation in selection across plant and animal populations throughout many terrestrial biomes, whereas temperature explained little variation. By...

The applicability of eDNA metabarcoding approaches for sessile benthic surveying in the Kimberley region, north-western Australia

Katrina West, Arne Adam, Nicole White, Will Robbins, Daniel Barrow, Adrian Lane & Zoe Richards
The application of environmental DNA technologies is a promising new approach to rapidly audit biodiversity across large-scale, remote regions. Here, we examine the efficacy of a dual-assay eDNA metabarcoding approach for sessile benthic bioassessments in the turbid waters of the Lalang-garram Marine Parks, in the inshore Kimberley region, north-western Australia. We ask three principal questions: 1. Is the eDNA released by sessile benthic taxa (i.e. hard and soft corals, sponges and tunicates) locally detectable? 2....

Data from: Subsistence practices, past biodiversity, and anthropogenic impacts revealed by New Zealand-wide ancient DNA survey

Frederik V. Seersholm, Theresa L. Cole, Alicia Grealy, Nicolas J. Rawlence, Karen Greig, Michael Knapp, Michael Stat, Anders J. Hansen, Luke J. Easton, Lara Shepherd, Alan J. D. Tennyson, R. Paul Scofield, Richard Walter & Michael Bunce
New Zealand’s geographic isolation, lack of native terrestrial mammals, and Gondwanan origins make it an ideal location to study evolutionary processes. However, since the archipelago was first settled by humans (c. 1280 AD), its unique biodiversity has been under pressure, and today an estimated 49% of the terrestrial avifauna is extinct. Current efforts to conserve the remaining fauna rely on a better understanding of the composition of past ecosystems, as well as the causes and...

Arctic shrub colonization lagged peak postglacial warmth: Molecular evidence in lake sediment from Arctic Canada

Sarah Crump, Gifford Miller, Matthew Power, Julio Sepúlveda, Nadia Dildar, Megan Coghlan & Michael Bunce
Arctic shrubification is an observable consequence of climate change, already resulting in ecological shifts and global-scale climate feedbacks including changes in land surface albedo and enhanced evapotranspiration. However, the rate at which shrubs can colonize previously glaciated terrain in a warming world is largely unknown. Reconstructions of past vegetation dynamics in conjunction with climate records can provide critical insights into shrubification rates and controls on plant migration, but paleoenvironmental reconstructions based on pollen may be...

Residual CO2 trapping in oil-wet sandstone

Adriana Paluszny, Stefan Iglauer & Maxim Lebedev
MicroCT images of residual CO2 trapping in oil wet sandstone.

The construction of small-scale, quasi-mechanistic spatial models of insect energetics in habitat restoration: a case study of beetles in Western Australia

Sean Tomlinson
Aim: The management and restoration of ecological processes mediated by biotic interactions is now broadly advocated, and may be achieved by the targeting restoration towards key agents. Although theoretically examined, a practical approach to incorporating the physiology and energetics of insects into restoration planning is poorly articulated. I aimed to provide a case study using the thermal biology and energetics of beetles to identify the distribution of habitat suitability in a large restoration landscape. Location:...

The evolution of autotomy in leaf-footed bugs

Zachary Emberts, Colette M St. Mary, Cody Coyotee Howard, Michael Forthman, Philip W. Bateman, Ummat Somjee, Wei Song Hwang, Daiqin Li, Rebecca T Kimball & Christine W Miller
Sacrificing body parts is one of many behaviors that animals use to escape predation. This trait, termed autotomy, is classically associated with lizards. However, several other taxa also autotomize, and this trait has independently evolved multiple times throughout Animalia. Despite having multiple origins and being an iconic anti-predatory trait, much remains unknown about the evolution of autotomy. Here, we combine morphological, behavioral, and genomic data to investigate the evolution of autotomy within leaf-footed bugs and...

Data from: Association of putatively adaptive genetic variation with climatic variables differs between a parasite and its host

Sheree Walters, Todd Robinson, Margaret Byrne, Grant Wardell-Johnson & Paul Nevill
Parasitism is a pervasive phenomenon in nature with the relationship between species driving evolution in both the parasite and host. Due to their host-dependent lifestyle, parasites may adapt to the abiotic environment in ways that differ from their hosts or from free living relatives; yet rarely has this been assessed. Here, we test two competing hypotheses related to whether putatively adaptive genetic variation in a specialist mistletoe associates with the same, or different, climatic variables...

A large scale temporal and spatial environmental DNA biodiversity survey of offshore marine vertebrates in Brazil following the upriver Fundão tailings dam failure

Rose Lines, Manjeeti Juggernauth, Georgia Peverley, James Keating, Tiffany Simpson, Mahsa Mousavi-Derazmahalleh, Michael Bunce, Tina Berry, Alice Taysom, Angelo F. Bernardino & Phillip Whittle
Seawater contains a wealth of genetic information, representing the biodiversity of numerous species residing within a particular marine habitat. Environmental DNA (eDNA) metabarcoding offers a cost effective, non-destructive method for large scale monitoring of environments, as diverse taxonomic groups are detected using metabarcoding assays. A large-scale eDNA monitoring program of marine vertebrates was conducted across three sampling seasons (Spring 2018, Autumn 2019 and Spring 2019) in coastal waters of Brazil. The program was designed to...

Drakaea glyptodon nuclear microsatellite and chloroplast haplotype data

Dorset Trapnell, Patrick Smallwood, Kingsley Dixon & Ryan Phillips
Many orchids are characterized by small, patchily distributed populations. Resolving how they persist is important for understanding the ecology of this hyper-diverse family, many members of which are of conservation concern. Ten populations of the common terrestrial orchid Drakaea glyptodon from Southwest Australia were genotyped with ten nuclear and five chloroplast SSR markers. Levels and partitioning of genetic variation, and effective population sizes (Ne), were estimated. Spatial genetic structure of nuclear diversity, together with chloroplast...

Data from: Getting to the root of organic inputs in groundwaters: stygofaunal plant consumption in a calcrete aquifer

Mattia Saccò
Groundwater environments interact with and support subterranean biota as well as superficial aquatic and terrestrial ecosystems. However, knowledge of subterranean energy flows remains incomplete. Cross-boundary investigations are needed to better understand the trophic structures of groundwater ecosystems and their reliance on carbon inputs from aboveground. In this study we used carbon and nitrogen stable isotope analyses combined with radiocarbon fingerprints to characterise organic flows in groundwater ecosystems. We coupled these data with DNA metabarcoding of...

Voucher specimen image of Krueger 26 (Utricularia gibba; Lentibulariaceae).

Thilo Krueger

Mapping Boodjar Walyalup Fremantle

Neville Collard, Herbert Bropho, Farley Garlett, Freda Ogilvie, Gladys Yarran, Connie Collard, Barbara Bynder, Holly Farley, Joe Bean, Tod Jones, Kim Mahood, Alison Nannup, Denise Smith-Ali, Jason Thomas, Greg Grabasch, George Hayden & Jane Fyfe

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  • Curtin University
  • University of Western Australia
  • Baylor College of Medicine
  • University of Cape Town
  • Jilin University
  • Temple University
  • Fudan University Shanghai Cancer Center
  • Wenzhou Medical University
  • Sichuan University
  • Fudan University