79 Works

Data from: Genomic analysis of a migratory divide reveals candidate genes for migration and implicates selective sweeps in generating islands of differentiation

Kira E. Delmore, Sariel Hübner, Nolan C. Kane, Richard Schuster, Rose L. Andrew, Francisco Câmara, Roderic Guigo & Darren E. Irwin
Differential gene flow, reductions in diversity following linked selection and/or features of the genome can structure patterns of genomic differentiation during the process of speciation. Possible sources of reproductive isolation are well studied between coastal and inland subspecies groups of Swainson's thrushes, with differences in seasonal migratory behaviour likely playing a key role in reducing hybrid fitness. We assembled and annotated a draft reference genome for this species and generated whole-genome shotgun sequence data for...

Data from: Strong and stable geographic differentiation of swamp buffalo maternal and paternal lineages indicates domestication in the China/Indochina border region

Yi Zhang, Yongfang Lu, Marnoch Yindee, Kuan-Yi Li, Hsiao-Yun Kuo, Yu-Ten Ju, Shaohui Ye, , Qiang Li, Yachun Wang, Vu Chi Cuong, Lan Doan Pham, Bounthong Bouahom, Bingzhuang Yang, Xianwei Liang, Zhihua Cai, Dianne Vankan, Wallaya Manatchaiworakul, Nonglid Kowlim, Somphot Duangchantrasiri, Worawidh Wajjwalku, Ben Colenbrander, Yuan Zhang, Peter Beerli, Johannes A. Lenstra … & J. Stuart F. Barker
The swamp type of the Asian water buffalo is assumed to have been domesticated by about 4000 years BP, following the introduction of rice cultivation. Previous localizations of the domestication site were based on mitochondrial DNA (mtDNA) variation within China, accounting only for the maternal lineage. We carried out a comprehensive sampling of China, Taiwan, Vietnam, Laos, Thailand, Nepal and Bangladesh and sequenced the mtDNA Cytochrome b gene and control region and the Y-chromosomal ZFY,...

Data from: Increasing belief but issue fatigue: changes in Australian Household Climate Change Segments between 2011 and 2016

Mark Morrison, Kevin Parton, Don W. Hine & Donald W. Hine
We applied the segmentation methodology developed by Leiserowitz, Maibach, and Roser-Renouf (2009) to national Australian samples collected in 2011 (n=1927) and 2016 (n=2503). In both samples we identified six Australian household segments which we labelled alarmed, concerned, cautious, disengaged, doubtful and dismissive. Between the two periods, we found the proportion of households in the alarmed and concerned segments was stable; however there was a decrease (28% to 20%) in the proportion of households in the...

Data from: Your infections are what you eat: how host ecology shapes the helminth parasite communities of lizards

Tommy L.F. Leung, Janet Koprivnikar & Tommy L. F. Leung
1. Understanding how parasite communities are assembled, and the factors that influence their richness, can improve our knowledge of parasite-host interactions and help to predict the spread of infectious diseases. Previous comparative analyses have found significant influences of host ecology and life history, but focused on a few select host taxa. 2. Host diet and habitat use play key roles in the acquisition of parasitic helminths as many are trophically-transmitted, making these attributes potentially key...

Data from: Short-term response of a declining woodland bird assemblage to the removal of a despotic competitor

Galen Davitt, Kimberly Maute, Richard E. Major, Paul G. McDonald & Martine Maron
Interspecific aggression by the noisy miner (Manorina melanocephala), a highly despotic species, is homogenizing woodland avifaunas across eastern Australia. Although a native species, the noisy miner's aggressive exclusion of small birds is a Key Threatening Process under national law. Large‐scale removal of noisy miners has been proposed as a management response to this threat following increases in miner presence due to anthropogenic land use practices. We tested this proposal by experimentally removing noisy miners from...

Data from: Livestock activity increases exotic plant richness, but wildlife increases native richness, with stronger effects under low productivity

David J. Eldridge, Manuel Delgado-Baquerizo, Samantha K. Travers, James Val, Ian Oliver, Josh W. Dorrough & Santiago Soliveres
1.Grazing by domestic livestock is one of the most widespread land uses worldwide, particularly in rangelands, where it co-occurs with grazing by wild herbivores. Grazing effects on plant diversity are likely to depend on intensity of grazing, herbivore type, coevolution with plants and prevailing environmental conditions. 2.We collected data on climate, plant productivity, soil properties, grazing intensity and herbivore type; and measured their effects on plant species richness from 451 sites across 0.4 M km2...

Data from: Competition drives the response of soil microbial diversity to increased grazing by vertebrate herbivores

David J. Eldridge, Manuel Delgado-Baquerizo, Samantha K. Travers, James Val, Ian Oliver, Kelly Hamonts & Brajesh K. Singh
Scientists have largely neglected the effects of grazing on soil microbial communities despite their importance as drivers of ecosystem functions and services. We hypothesised that changes in soil properties resulting from grazing regulate the diversity of soil microbes by releasing/suppressing subordinate microbial taxa via competition. To test this, we examined intensity of vertebrate herbivores influences the diversity and composition of soil bacteria and fungi at 216 soil samples from 54 sites and four microsites. Increasing...

Data from: Temporal variation in plant-pollinator networks from seasonal tropical environments: higher specialization when resources are scarce

Camila S. Souza, Pietro K. Maruyama, Camila Aoki, Maria Rosangela Sigrist, Josué Raizer, Caroline L. Gross & Andréa C. De Araujo
The temporal dynamics of plant phenology and pollinator abundance across seasons should influence the structure of plant-pollinator interaction networks. Nevertheless, such dynamics are seldom considered, especially for diverse tropical networks. Here, we evaluated the temporal variation of four plant-pollinator networks in two seasonal ecosystems in Central Brazil (Cerrado and Pantanal). Data were gathered on a monthly basis over one year for each network. We characterized seasonal and temporal shifts in plant-pollinator interactions, using temporally discrete...

Thinner bark increases sensitivity of wetter Amazonian tropical forests to fire

Ann Carla Staver, Paulo M. Brando, Jos Barlow, Douglas C. Morton, C.E. Timothy Paine, Yadvinder Malhi, Alejandro Araujo Murakami & Jhon Pasquel
Understory fires represent an accelerating threat to Amazonian tropical forests and can, during drought, affect larger areas than deforestation itself. These fires kill trees at rates varying from < 10 to c. 90% depending on fire intensity, forest disturbance history and tree functional traits. Here, we examine variation in bark thickness across the Amazon. Bark can protect trees from fires, but it is often assumed to be consistently thin across tropical forests. Here, we show...

Metabolic rates and growth data for: Do small precocial birds enter torpor to conserve energy during development?

Yaara Aharon-Rotman, Gerhard Körtner, Chris Wacker & Fritz Geiser
Precocial birds hatch feathered and mobile, but when they become fully endothermic soon after hatching, their heat loss is high and they may become energy-depleted. These chicks could benefit from using energy-conserving torpor, which is characterised by controlled reductions of metabolism and body temperature (Tb). We investigated at what age the precocial king quail Cortunix chinensis can defend a high Tb under a mild thermal challenge and whether they can express torpor soon after achieving...

Data from: Computational biomechanical analyses demonstrate similar shell-crushing abilities in modern and ancient arthropods

Russell D. C. Bicknell, Justin A. Ledogar, Stephen Wroe, Benjamin C. Gutzler, Winsor H. Watson, John R. Paterson & Winsor H. Watson
The biology of the extant American horseshoe crab, Limulus polyphemus, is well documented—including its dietary habits, particularly the ability to crush shell with its gnathobasic walking appendages—but virtually nothing is known about the feeding biomechanics of this iconic arthropod. This species is also considered the archetypal functional analogue for a range of extinct groups that have gnathobasic appendages, including eurypterids, trilobites, and some of the earliest arthropods, especially Sidneyia inexpectans from the middle Cambrian (508...

Supplemental data for: Three-dimensional kinematics of euchelicerate limbs uncover functional specialisation in eurypterid appendages

Russell D C Bicknell, Roland R Melzer & Michel Schmidt
Sea scorpions (Eurypterida; Euchelicerata) explored the extreme limits of the aquatic euchelicerate body plan. Indeed, the group contains the largest known marine euarthropods. Inferences on eurypterid life modes—in particular walking and eating—are commonly made by comparing the group to horseshoe crabs (Xiphosura; Euchelicerata). However, no models have been presented to test these hypotheses. Here, we reconstruct prosomal appendages of two exceptionally well-preserved eurypterids Eurypterus tetragonophthalmus and Pentecopterus decorahensis and kinematically model the flexure and extension...

Data from: Negative density dependence in the mortality and growth of tropical tree seedlings is strong, and primarily caused by fungal pathogens

Kirstie Hazelwood, Harald Beck & C. E. Timothy Paine
Natural enemies have been implicated as agents of negative density dependence (NDD) in tropical forests, but their relative contributions to NDD, and thus to the maintenance of diversity, are largely unknown. We monitored the rates of survival and relative growth rates on seedlings for ten years in tropical moist forest in Manu National Park, Peru. We then experimentally manipulated the plots to exclude fungal pathogens, insects, small mammals, and large mammals for an additional 31...

Self-organization and information transfer in Antarctic krill swarms

Ashley Ward, Alicia Burns, Timothy Schaerf, Joseph Lizier, So Kawaguchi, Martin Cox, Rob King & Jens Krause
Antarctic krill swarms are one of the largest known animal aggregations, and yet, despite being the keystone species of the Southern Ocean, little is known about how swarms are formed and maintained. Understanding the local interactions between individuals that provide the basis for these swarms is fundamental to knowing how swarms arise in nature, and what potential factors might lead to their breakdown. Here we analyzed the trajectories of captive, wild-caught krill in 3D to...

Data from: Infection dynamics, dispersal, and adaptation: understanding the lack of recovery in a remnant frog population following a disease outbreak

Donald McKnight, Leah Carr, Deborah Bower, Lin Schwarzkopf, Ross Alford & Kyall Zenger
Emerging infectious diseases can cause dramatic declines in wildlife populations. Sometimes these declines are followed by recovery, but many populations do not recover. Studying differential recovery patterns may yield important information for managing disease-afflicted populations and facilitating population recoveries. In the late1980s, a chytridiomycosis outbreak caused multiple frog species in Australia's Wet Tropics to decline. Populations of some species (e.g., Litoria nannotis) subsequently recovered, while others (e.g., Litoria dayi) did not. We examined the population...

Recipient and donor characteristics govern the hierarchical structure of heterospecific pollen competition networks

Jose B. Lanuza, Ignasi Bartomeus, Tia-Lynn Ashman & Romina Rader
Pollinator sharing can have negative consequences for plant fitness with the arrival of foreign (i.e. heterospecific) pollen, yet responses are often variable among species. Plant traits and relatedness of donor and recipient species have been suggested to drive the variations in plant fitness, but how they shape the structure of pollen competition networks has been overlooked at the community level. To understand the importance of reproductive traits and relatedness on the impacts of heterospecific pollen...

Modelling mycorrhizal fungi dispersal by the mycophagous swamp wallaby (Wallabia bicolor)

Melissa A. Danks, Natalie Simpson, Todd F. Elliott, C. E. Timothy Paine & Karl Vernes
Despite the importance of mammal-fungal interactions, tools to estimate the mammal-assisted dispersal distances of fungi are lacking. Many mammals actively consume fungal fruiting bodies, the spores of which remain viable after passage through their digestive tract. Many of these fungi form symbiotic relationships with trees and provide an array of other key ecosystem functions. We present a flexible, general model to predict the distance a mycophagous mammal would disperse fungal spores. We modelled the probability...

Environmental DNA reveals a multi-taxa biogeographic break across the Arabian Sea and Sea of Oman

Joseph DiBattista, Michael Berumen, Mark Priest, Maarten De Brauwer, Darren Coker, Tane Sinclair-Taylor, Amanda Hay, Gerd Bruss, Shawky Mansour, Michael Bunce, Christopher Goatley, Matthew Power & Alyssa Marshell
Environmental DNA (eDNA) is increasingly being used to assess community composition in marine ecosystems. Applying eDNA approaches across broad spatial scales now provide the potential to inform biogeographic analyses. However, to date, few studies have employed this technique to assess broad biogeographic patterns across multiple taxonomic groups. Here, we compare eDNA-derived communities of bony fishes and invertebrates, including corals and sponges, from 15 locations spanning the entire length of the Omani coast. This survey includes...

Regarding the F-word: the effects of data Filtering on inferred genotype-environment associations

Collin Ahrens, Rebecca Jordan, Jason Bragg, Peter Harrison, Tara Hopley, Helen Bothwell, Kevin Murray, Dorothy Steane, John Whale, Margaret Byrne, Rose Andrew & Paul Rymer
Genotype-environment association (GEA) methods have become part of the standard landscape genomics toolkit, yet, we know little about how to best filter genotype-by-sequencing data to provide robust inferences for environmental adaptation. In many cases, default filtering thresholds for minor allele frequency and missing data are applied regardless of sample size, having unknown impacts on the results. These effects could be amplified in downstream predictions, including management strategies. Here, we investigate the effects of filtering on...

Automated location invariant animal detection in camera trap images using publicly available data sources

Andrew Shepley, Greg Falzon, Paul D. Meek & Paul Kwan
1. A time-consuming challenge faced by ecologists is the extraction of meaningful data from camera trap images to inform ecological management. Automated object detection solutions are increasingly, however, most are not sufficiently robust to be deployed on a large scale due to lack of location invariance across sites. This prevents optimal use of ecological data and results in significant resource expenditure to annotate and retrain object detectors. 2. In this study, we aimed to (a)...

Data from: Biogeographic history and habitat specialisation shape floristic and phylogenetic composition across Amazonian forests

Christopher Baraloto, Jason Vleminckx, Julien Engel, Pascal Petronelli, Nállarett Dávila, Marcos Ríos, Elvis Harry Valderrama Sandoval, Italo Mesones, Juan Ernesto Guevara Andino, Claire Fortunel, Elodie Allie, C. E. Timothy Paine, Aurélie Dourdain, Jean-Yves Goret, Oscar J. Valverde-Barrantes, Freddie Draper & Paul V. A. Fine
A major challenge remains to understand the relative contributions of history, dispersal and environmental filtering to the assembly of hyperdiverse communities across spatial scales. Here, we examine the extent to which biogeographical history and habitat specialization have generated turnover among and within lineages of Amazonian trees across broad geographic and environmental gradients. We replicated standardised tree inventories in 102 0.1-ha plots located in two distant regions - the western Amazon and the eastern Guiana shield....

Agriculture is adapting to phenological shifts caused by climate change, but grassland songbirds are not

Noah Perlut, Allan Strong & Maeve McGowan
Migratory birds time their migration based on cues that signal resource availability for reproduction. However, with climate change, the timing of seasonal events may shift, potentially inhibiting the ability of some species to use them as accurate cues for migration. We studied the relationship between phenological shifts and reproduction by long- and short-distance migratory songbirds—Bobolinks (Dolichonyx oryzivorus) and Savannah Sparrows (Passerculus sandwichensis). Our study population breeds in hayfields and pastures in Vermont, USA, where farmers...

Data from: Selection at the Esterase-2 locus of Drosophila buzzatii? Perturbation-reperturbation experiments

J. Stuart F. Barker & Peter C. Thomson
Apparent selection affecting starch gel electrophoretic alleles at the Esterase-2 locus of Drosophila buzzatii has been detected in laboratory and natural populations. Perturbation-reperturbation of allele frequencies in replicated laboratory populations attempts to test direct selective effects at the locus versus effects of linked loci. Sequential gel electrophoresis has identified more alleles within starch classes, and three of these alleles (within the a, b and c starch alleles) were used in cage population experiments. Allele a/1.00/1.00/1.00...

Data from: Adaptive and neutral markers both show continent-wide population structure of mountain pine beetle (Dendroctonus ponderosae)

Philip D. Batista, Jasmine K. Janes, Celia K. Boone, Brent W. Murray & Felix A. H. Sperling
Assessments of population genetic structure and demographic history have traditionally been based on neutral markers while explicitly excluding adaptive markers. In this study, we compared the utility of putatively adaptive and neutral single-nucleotide polymorphisms (SNPs) for inferring mountain pine beetle population structure across its geographic range. Both adaptive and neutral SNPs, and their combination, allowed range-wide structure to be distinguished and delimited a population that has recently undergone range expansion across northern British Columbia and...

Data from: The importance of mammalian torpor for survival in a post-fire landscape

Clare Stawski, Gerhard Körtner, Julia Nowack & Fritz Geiser
Wildfires have increased in frequency and intensity worldwide with climate change as a main driving factor. While a number of studies have focused on population changes in regard to fires, there are essentially no quantitative data on behavioural and physiological adjustments that are vital for the persistence of individuals during and after fires. Here we show that brown antechinus, a small insectivorous marsupial mammal, (i) endured a prescribed fire in situ, (ii) remained in their...

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