321 Works

Data from: Local endemism and within-island diversification of shrews illustrate the importance of speciation in building Sundaland mammal diversity

Terrence C. Demos, Anang S. Achmadi, Thomas C. Giarla, Heru Handika, , Kevin C. Rowe & Jacob A. Esselstyn
Island systems are important models for evolutionary biology because they provide convenient, discrete biogeographic units of study. Continental islands with a history of intermittent dry land connections confound the discrete definitions of islands and have led zoologists to predict (1) little differentiation of terrestrial organisms among continental shelf islands and (2) extinction, rather than speciation, to be the main cause of differences in community composition among islands. However, few continental island systems have been subjected...

Mammal detection data for the SAFE project site, Sabah, Malaysian Borneo, 2015 [HMTF]

N.J. Deere, G. Guillera-Arroita, E.L. Baking, H. Bernard, M. Pfeifer, G. Reynolds, O.R. Wearn, Z.G. Davies & M.J. Struebig
This data set contains stacked detection matrices for 28 recorded mammal species across 115 sampling locations at the Stability of Altered Forest Ecosystems (SAFE) project site located in Sabah, Malaysian Borneo. Information for each camera trap sampling location, including spatial information and sampling effort is included. Data were collected in order to determine the contribution of carbon-based policies to biodiversity conservation in agricultural land-use mosaics. These data are essential to the development of the occupancy...

Randomised trials in maternal and perinatal health in low- and middle-income countries from 2010 to 2019: A systematic scoping review

Alexander Eggleston, Annabel Richards, Elise Farrington, Wai Chung Tse, Jack Williams, Ayeshini Sella Hewage, Steve McDonald, Tari Turner & Joshua Vogel
Objectives: To identify and map all trials in maternal health conducted in low- and middle-income countries (LMIC) over the 10-year period 2010-2019, to identify geographical and thematic trends, as well as compare to global causes of maternal death and pre-identified priority areas. Design: Systematic scoping review. Primary and secondary outcome measures: Extracted data included location, study characteristics and whether trials corresponded to causes of mortality and identified research priority topics. Results: Our search identified 7,269...

Population structure and demographic analyses of Acanthocybium solandri from the Indo-Pacific and Atlantic oceans

Joshua Thia
This repository contains scripts, data and results for a populaton genomics study of genetic structure and demography of wahoo, Acanthocybium solandri, published in Journal of Biogeography: Haro-Bilbao et al. (2021) Global connections with some genomic differentiation occur between Indo-Pacific and Atlantic Ocean wahoo, a large circumtropical pelagic fish. In this work, we generated population allele frequencies for wahoo sampled at 11 locations around the globe using a pooled ezRAD approach. Using thousands of genome-wide SNPs,...

Research Data Management in Health and Biomedical Citizen Science: Practices and Prospects

Ann Borda
Background: Public engagement in health and biomedical research is being influenced by the paradigm of citizen science. However, conventional health and biomedical research relies on sophisticated research data management tools and methods. Considering these, what contribution can citizen science make in this field of research? How can it follow research protocols and produce reliable results? Objective: The aim of this paper is to analyse research data management practices in existing biomedical citizen science studies, so...

Spatial and temporal variation in prey colour patterns for background-matching across a continuous heterogeneous environment

Marleen Baling, Devi Stuart-Fox, Dianne H. Brunton & James Dale
In heterogeneous habitats, camouflage via background-matching can be challenging because visual characteristics can vary dramatically across small spatial scales. Additionally, temporal variation in signalling functions of colouration can affect crypsis, especially when animals use colouration seasonally for intraspecific signalling (e.g. mate selection). We currently have a poor understanding of how wild prey optimise background-matching within continuously heterogeneous habitats, and whether this is affected by requirements of intraspecific signalling across biological seasons. Here, we quantified colour...

Anthropogenic and natural barriers affect genetic connectivity in an Alpine butterfly

Daronja Trense, Tom Schmidt, Qiong Yang, Jessica Chung, Ary Hoffmann & Klaus Fischer
Dispersal is a key biological process serving several functions including connectivity among populations. Habitat fragmentation caused by natural or anthropogenic structures may hamper dispersal, thereby disrupting genetic connectivity. Investigating factors affecting dispersal and gene flow is important in the current era of anthropogenic global change, as dispersal comprises a vital part of a species’ resilience to environmental change. Using fine-scale landscape genomics, we investigate gene flow and genetic structure of the Sooty Copper butterfly (Lycaena...

The roles of acclimation and behavior in buffering climate change impacts along elevational gradients

Urtzi Enriquez-Urzelai, Reid Tingley, Michael Kearney, Martina Sacco, Antonio Palacio, Miguel Tejedo & Alfredo Nicieza
1. The vulnerability of species to climate change is jointly influenced by geographic phenotypic variation, acclimation, and behavioral thermoregulation. The importance of interactions between these factors, however, remains poorly understood. 2. We demonstrate how advances in mechanistic niche modelling can be used to integrate and assess the influence of these sources of uncertainty in forecasts of climate change impacts. 3. We explored geographic variation in thermal tolerance (i.e. maximum and minimum thermal limits) and its...

Age of first infection across a range of parasite taxa in a wild mammalian population

Caroline Glidden, Leigh Combrink, Brianna Beechler, Bryan Charleston, Anson Koehler, Danielle Sisson, Gasser Robin, Abdul Jabbar & Anna Jolles
Newborn mammals have an immature immune system that cannot sufficiently protect them against infectious diseases. However, variation in the effectiveness of maternal immunity against different parasites may couple with temporal trends in parasite exposure to influence disparities in timing of infection risk. Determining the relationship between age and infection risk is critical in identifying the portion of a host population that contributes to parasite dynamics, as well as the parasites that regulate host recruitment. While...

Data from: Iridescence untwined - Honey bees can separate hue variations in space and time

Leslie Ng, Laura Ospina-Rozo, Jair Garcia, Adrian Dyer & Devi Stuart-Fox
Iridescence is a phenomenon whereby the hue of a surface changes with viewing or illumination angle. Many animals display iridescence but it currently remains unclear whether relevant observers process iridescent color signals as a complex collection of colors (spatial variation), or as moving patterns of colors and shapes (temporal variation). This is important as animals may use only the spatial or temporal component of the signal, although this possibility has rarely been considered or tested....

Data from: Testing the niche breadth-range size hypothesis: habitat specialization versus performance in Australian alpine daisies

Megan J. Hirst, Philippa C. Griffin, Jason P. Sexton & Ary A. Hoffmann
Relatively common species within a clade are expected to perform well across a wider range of conditions than their rarer relatives, yet experimental tests of this “niche breadth—range size” hypothesis remain surprisingly scarce. Rarity may arise due to trade-offs between specialization and performance across a wide range of environments. Here we use common garden and reciprocal transplant experiments to test the niche breadth—range size hypothesis, focusing on four common and three rare endemic alpine daisies...

Data from: The effect of virus-blocking Wolbachia on male competitiveness of the dengue vector mosquito, Aedes aegypti

Michal Segoli, Ary A. Hoffmann, Jane Lloyd, Gavin J. Omodei & Scott A. Ritchie
Background: The bacterial endosymbiont Wolbachia blocks the transmission of dengue virus by its vector mosquito Aedes aegypti, and is currently being evaluated for control of dengue outbreaks. Wolbachia induces cytoplasmic incompatibility (CI) that results in the developmental failure of offspring in the cross between Wolbachia-infected males and uninfected females. This increases the relative success of infected females in the population, thereby enhancing the spread of the beneficial bacterium. However, Wolbachia spread via CI will only...

Data from: Female song is widespread and ancestral in songbirds

Karan J. Odom, Michelle L. Hall, Katharina Riebel, Kevin E. Omland & Naomi E. Langmore
Bird song has historically been considered an almost exclusively male trait, an observation fundamental to the formulation of Darwin’s theory of sexual selection. Like other male ornaments, song is used by male songbirds to attract females and compete with rivals. Thus, bird song has become a textbook example of the power of sexual selection to lead to extreme neurological and behavioural sex differences. Here we present an extensive survey and ancestral state reconstruction of female...

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: High nucleotide diversity and limited linkage disequilibrium in Helicoverpa armigera facilitates the detection of a selective sweep

Sue V. Song, Sharon Downes, Tracey Parker, John G. Oakeshott & Charles Robin
Insecticides impose extreme selective pressures on populations of target pests and so insecticide resistance loci of these species may provide the footprints of ‘selective sweeps’. To lay the foundation for future genome-wide scans for selective sweeps and inform genome-wide association study designs, we set out to characterize some of the baseline population genomic parameters of one of the most damaging insect pests in agriculture worldwide, Helicoverpa armigera. To this end, we surveyed nine Z-linked loci...

Data from: From ornament to armament or loss of function? Breeding plumage acquisition in a genetically monogamous bird

Marie Fan, Niki Teunissen, Michelle L. Hall, Nataly Hidalgo Aranzamendi, Sjouke A. Kingma, Michael Roast, Kaspar Delhey & Anne Peters
1. The evolution of conspicuous male traits is thought to be driven by female mate choice or male-male competition. These two mechanisms are often viewed as distinct processes, with most studies focusing on female choice. 2. However, both mechanisms of sexual selection can act simultaneously on the same trait (i.e. dual function) and/or interact in a synergistic or conflicting way. Dual function-traits are commonly assumed to originate through male-male competition before being used in female...

Data from: Low evolutionary potential for egg-to-adult viability in Drosophila melanogaster at high temperatures

Torsten Nygaard Kristensen, Johannes Overgaard, Jan Lassen, Ary A. Hoffmann & Carla M. Sgro
To cope with the increasing and less predictable temperature forecasts under climate change, many terrestrial ectotherms will have to migrate or rely on adaptation through plastic or evolutionary means. Studies suggest that some ectotherms have a limited potential to change their upper thermal limits via evolutionary shifts, but research has mostly focused on adult life stages under laboratory conditions. Here we use replicate populations of Drosophila melanogaster and a nested half sib/full sib quantitative genetic...

Data from: Predicting climate warming effects on green turtle hatchling viability and dispersal performance

Catherine Cavallo, David Booth, Tim Dempster, Michael R. Kearney, Ella Kelly & Tim S. Jessop
1. Ectotherms are taxa considered highly sensitive to rapid climate warming. This is because body temperature profoundly governs their performance, fitness and life history. Yet, while several modelling approaches currently predict thermal effects on some aspects of life history and demography, they do not consider how temperature simultaneously affects developmental success and offspring phenotypic performance, two additional key attributes that are needed to comprehensively understand species responses to climate warming. 2. Here, we developed a...

Data from: Crossing the line: increasing body size in a trans-Wallacean lizard radiation (Cyrtodactylus, Gekkota)

Paul M. Oliver, Phillip Skipwith & Michael S. Y. Lee
The region between the Asian and Australian continental plates (Wallacea) demarcates the transition between two differentiated regional biotas. Despite this striking pattern, some terrestrial lineages have successfully traversed the marine barriers of Wallacea and subsequently diversified in newly colonized regions. The hypothesis that these dispersals between biogeographic realms are correlated with detectable shifts in evolutionary trajectory has however rarely been tested. Here, we analyse the evolution of body size in a widespread and exceptionally diverse...

Data from: A collection of Australian Drosophila datasets on climate adaptation and species distributions

Ary A. Hoffmann, Ailie Smith, Philippa C. Griffin & Sandra B. Hangartner
The Australian Drosophila Ecology and Evolution Resource (ADEER) collates Australian datasets on drosophilid flies, which are aimed at investigating questions around climate adaptation, species distribution limits and population genetics. Australian drosophilid species are diverse in climatic tolerance, geographic distribution and behaviour. Many species are restricted to the tropics, a few are temperate specialists, and some have broad distributions across climatic regions. Whereas some species show adaptability to climate changes through genetic and plastic changes, other...

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: Night warming on hot days produces novel impacts on development, survival and reproduction in a small arthropod

Fei Zhao, Wei Zhang, Ary A. Hoffmann & Chun-Sen Ma
1. An asymmetric increase of nighttime temperatures on hot days is one of the main features of global climate change. But the biological effects of an increased nighttime temperature combined with high daytime temperature are unclear. 2. We used six thermal regimens to simulate nighttime temperatures on hot days and investigated the effects of night warming on life history traits of the English grain aphid Sitobion avenae. Experimental temperatures fluctuated in continuous diurnal cycles, increasing...

Single molecule tracking raw data: SOX18 and its dominant-negative mutant SOX18RaOp

Alex McCann, Jieqiong Lou, Mehdi Moustaqil, Matthew Graus, Ailisa Blum, Frank Fontaine, Hui Liu, Winnie Luu, Peter Koopman, Emma Sierecki, Yann Gambin, Frédéric Meunier, Zhe Liu, Elizabeth Hinde & Mathias Francois
Few genetically dominant mutations involved in human disease have been fully explained at the molecular level. In cases where the mutant gene encodes a transcription factor, the dominant-negative mode of action of the mutant protein is particularly poorly understood. Here, we studied the genome-wide mechanism underlying a dominant-negative form of the SOX18 transcription factor (SOX18RaOp) responsible for both the classical mouse mutant Ragged Opossum and the human genetic disorder Hypotrichosis-Lymphedema-Telangiectasia-Renal Syndrome. Combining three single-molecule imaging...

Double-tagging scores of seabirds reveals that light-level geolocator accuracy is limited by species idiosyncrasies and equatorial solar profiles

Luke Halpin, Jeremy Ross, Raül Ramos, Rowan Mott, Nicholas Carlile, Nick Golding, José Manuel Reyes-González, Teresa Militão, Fernanda De Felipe, Zuzana Zajková, Marta Cruz Flores, Sarah Saldanha, Virginia Morera-Pujol, Leia Navarro-Herrero, Laura Zango, Jacob Gonzalez-Solis & Rohan Clarke
Light-level geolocators are popular bio-logging tools, with advantageous sizes, longevity, and affordability. Biologists tracking seabirds often presume geolocator spatial accuracies between 186-202 km from previously-innovative, yet taxonomically, spatially, and computationally limited, studies. Using recently developed methods, we investigated whether assumed uncertainty norms held across a larger-scale, multispecies study. We field-tested geolocator spatial accuracy by synchronously deploying these with GPS loggers on scores of seabirds across five species and 11 Mediterranean Sea, East Atlantic and South...

Multi-species models reveal that eDNA metabarcoding is more sensitive than backpack electrofishing for conducting fish surveys in freshwater streams

Emily McColl-Gausden, Andrew Weeks, Rhys Coleman, Katie Robinson, Sue Song, Tarmo Raadik & Reid Tingley
Environmental DNA (eDNA) sampling can provide accurate, cost-effective, landscape-level data on species distributions. Previous studies have compared the sensitivity of eDNA sampling to traditional sampling methods for single species, but similar comparative studies on multi-species eDNA metabarcoding are rare. Using hierarchical species occupancy-detection models, we examined whether key choices associated with eDNA metabarcoding (primer selection, low-abundance read filtering, and the number of positive water samples used to classify a species as present at a site)...

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