70 Works

Data for: Density dependence and spatial heterogeneity limit the population growth rate of invasive pines at the landscape scale

Rowan Sprague, Philip Hulme, Elena Moltchanova & William Godsoe
Determining population growth across large scales is difficult because it is often impractical to collect data at large scales and over long timespans. Instead, the growth of a population is often only measured at a small, plot-level scale and then extrapolated to derive a mean field estimate. However, this approach is prone to error since it simplifies spatial processes such as the neighbourhood effects of density and dispersal. We present a novel approach that estimates...

Data from: Spending limited resources on de-extinction could lead to net biodiversity loss

Joseph R. Bennett, Richard F. Maloney, Tammy E. Steeves, James Brazill-Boast, Hugh P. Possingham & Phillip J. Seddon
There is contentious debate surrounding the merits of de-extinction as a biodiversity conservation tool. Here, we use extant analogues to predict conservation actions for potential de-extinction candidate species from New Zealand and the Australian state of New South Wales, and use a prioritization protocol to predict the impacts of reintroducing and maintaining populations of these species on conservation of extant threatened species. Even using the optimistic assumptions that resurrection of species is externally sponsored, and...

Data from: Organic farming promotes biotic resistance to food-borne human pathogens

Matthew S. Jones, Zhen Fu, John P. Reganold, Daniel S. Karp, Thomas E. Besser, Jason M. Tylianakis & William E. Snyder
Farmland biodiversity benefits pollination, biological control and other key ecosystem services. Food safety has been seen as an exception to this broader pattern, as diverse farmlands attract wildlife that vector foodborne human pathogens. Resulting mitigation efforts thus often seek to deter wildlife by removing natural habitats, while also excluding vertebrate livestock. However, surprising recent evidence suggests that farm simplification actually increases the likelihood that produce will be contaminated with human pathogens. Here, we consider the...

Data from: Inferring predator-prey interactions in food webs

Justin Page Pomeranz, Ross M. Thompson, Timothée Poisot, Jon S. Harding & Justin P. F. Pomeranz
1. Food webs are a powerful way to represent the diversity, structure, and function of ecological systems. However, the accurate description of food webs requires significant effort in time and resources, limiting their widespread use in ecological studies. Newly published methods allow for the inference of feeding interactions using proxy variables. Here, we compare the accuracy of two recently described methods, as well as describe a composite model of the two, for the inference of...

Data from: Effects of gene flow on phenotype matching between two varieties of Joshua tree (Yucca brevifolia; Agavaceae) and their pollinators

Jeremy B. Yoder, Christopher I. Smith, Daniel J. Rowley, Ramona Flatz, William Godsoe, Christopher Drummond & Olle Pellmyr
In animal-pollinated plants, local adaptation to pollinator behaviour or morphology can restrict gene flow among plant populations; but gene flow may also prevent divergent adaptation. Here, we examine possible effects of gene flow on plant-pollinator trait matching in two varieties of Joshua tree (Agavaceae: Yucca brevifolia). The two varieties differ in strikingly in floral morphology, which matches differences in the morphology of their pollinators. However, this co-divergence is not present at a smaller scale: within...

Data from: Genotype matching in a parasitoid-host genotypic food web: an approach for measuring effects of environmental change

Blas Lavandero & Jason M. Tylianakis
Food webs typically quantify interactions between species, whereas evolution operates through the success of alleles within populations of a single species. To bridge this gap, we quantify genotypic interaction networks among individuals of a single specialized parasitoid species and its obligately to cyclically parthenogenetic aphid host along a climatic gradient. As a case study for the kinds of questions genotype food webs could be used to answer, we show that genetically-similar parasitoids became more likely...

Data from: Priority effects are interactively regulated by top-down and bottom-up forces: evidence from wood decomposer communities

Devin R. Leopold, J. Paula Wilkie, Ian A. Dickie, Robert B. Allen, Peter K. Buchanan & Tadashi Fukami
Both top-down (grazing) and bottom-up (resource availability) forces can determine the strength of priority effects, or the effects of species arrival history on the structure and function of ecological communities, but their combined influences remain unresolved. To test for such influences, we assembled experimental communities of wood-decomposing fungi using a factorial manipulation of fungivore (Folsomia candida) presence, nitrogen availability, and fungal assembly history. We found interactive effects of all three factors on fungal species composition...

Data from: Mechanisms of trophic niche compression: evidence from landscape disturbance

Francis J. Burdon, Angus R. McIntosh & Jon S. Harding
1. Natural and anthropogenic disturbances commonly alter patterns of biodiversity and ecosystem functioning. However, how networks of interacting species respond to these changes remains poorly understood. We described aquatic food webs using invertebrate and fish community composition, functional traits, and stable isotopes from twelve agricultural streams along a landscape disturbance gradient. 2. We predicted that excessive deposition of fine inorganic sediment (sedimentation) associated with agricultural activities would negatively influence aquatic trophic diversity (e.g., reduced vertical...

Data from: Effects of beneficial mutations in pykF gene vary over time and across replicate populations in a long-term experiment with bacteria

Fen Peng, Scott Widmann, Andrea Wunsche, Kristina Duan, Katherine A Donovan, Renwick C. J. Dobson, Richard E. Lenski & Tim F. Cooper
The fitness effects of mutations can depend on the genetic backgrounds in which they occur and thereby influence future opportunities for evolving populations. In particular, mutations that fix in a population might change the selective benefit of subsequent mutations, giving rise to historical contingency. We examine these effects by focusing on mutations in a key metabolic gene, pykF, that arose independently early in the history of 12 Escherichia coli populations during a long-term evolution experiment....

The population genomics of repeated freshwater colonizations by Gulf Pipefish

Sarah Flanagan, Emily Rose & Adam Jones
How organisms adapt to the novel challenges imposed by the colonization of a new habitat has long been a central question in evolutionary biology. When multiple populations of the same species independently adapt to similar environmental challenges, the question becomes whether the populations have arrived at their adaptations through the same genetic mechanisms. In recent years, genetic techniques have been used to tackle these questions by investigating the genome‐level changes underlying local adaptation. Here, we...

Plant Respiration Modelling with JULES for a changing climate (1860-2100)

C. Huntingford, O.K. Atkin, A. Martinez-De La Torre, L.M. Mercado, M.A. Heskel, A.B. Harper, K.J. Bloomfield, O.S. O'Sullivan, P.B. Reich, K.R. Wythers, E.E. Butler, M. Chen, K.L. Griffin, P. Meir, M.G. Tjoelker, M.H. Turnbull, S. Sitch, A. Wiltshire & Y. Malhi
The dataset contains annual global plant respiration (and related diagnostics, such as Net Primary Productivity, Gross Primary Productivity and soil respiration), applicable for pre-industrial times (taken as year 1860) through to the end of the 21st Century (year 2100). The spatial resolution of the data is 2.5 degrees latitude x 3.75 degrees longitude. These diagnostics are outputs from the Joint UK Land Environment Simulator (JULES land surface model) under four different approaches to calcluate leaf...

Cascading impacts of earthquakes and extreme heatwaves have destroyed populations of an iconic marine foundation species

Mads Thomsen
Aim: Ecologists traditionally study how contemporary local processes, such as biological interactions and physical stressors, affect the distribution and abundance of organisms. By comparison, biogeographers study the distribution of the same organisms, but focus on historic, larger-scale processes that can cause mass mortalities, such as earthquakes. Here we document cascading effects of rare biogeographical (seismic) and more common ecological (temperature-related) processes on the distribution and abundances of coastal foundation species. Location: Intertidal wave-exposed rocky reefs...

Data from: Landscape structure mediates zoochorous-dispersed seed rain under isolated pasture trees across distinct tropical regions

Lachlan S. Charles, John D. Dwyer, Hazel M. Chapman, Biplang G. Yadok & Margaret M. Mayfield
Context: Isolated pasture trees play an important role in forest recovery within fragmented tropical landscapes by attracting seed dispersers and facilitating seedling growth. However, studies with conflicting results have led to confusion about what drives variation in zoochorous-dispersed seed rain patterns under isolated tree canopies. Objectives: To assess the role of landscape and biological factors impacting zoochorous-dispersed seed rain under isolated pasture trees across three tropical regions of the world. Methods: We measured seed dispersal...

Data from: Identifying 'useful' fitness models: balancing the benefits of added complexity with realistic data requirements in models of individual plant fitness

Trace Martyn, Daniel Stouffer, Oscar Godoy, Ignasi Bartomeus, Abigail Pastore & Margaret Mayfield
Direct species interactions are commonly included in individual fitness models used for coexistence and local-diversity modeling. Though widely considered important for such models, direct interactions alone are often insufficient for accurately predicting fitness, coexistence or diversity outcomes. Incorporating higher-order interactions (HOIs) can lead to more accurate individual fitness models, but also adds many model terms, which can quickly result in model over-fitting. We explore approaches for balancing the trade-off between tractability and model accuracy that...

Cross-ecosystem bottlenecks alter reciprocal subsidies within meta-ecosystems

Amanda Klemmer, Mark Galatowitsch & Angus McIntosh
Reciprocal subsidies link ecosystems into meta-ecosystems, but energy transfer to organisms that do not cross boundaries may create sinks, reducing reciprocal subsidy transfer. We investigated how the type of subsidy and top predator presence influenced reciprocal flows of energy, by manipulating the addition of terrestrial leaf and terrestrial insect subsidies to experimental freshwater pond mesocosms with and without predatory fish. Over 18 months, fortnightly addition of subsidies (terrestrial beetle larvae) to top-predators was crossed with...

Data from: The role of species traits in mediating functional recovery during matrix restoration

Andrew D. Barnes, Rowan M. Emberson, Frank-Thorsten Krell & Raphael K. Didham
Reversing anthropogenic impacts on habitat structure is frequently successful through restoration, but the mechanisms linking habitat change, community reassembly and recovery of ecosystem functioning remain unknown. We test for the influence of edge effects and matrix habitat restoration on the reassembly of dung beetle communities and consequent recovery of dung removal rates across tropical forest edges. Using path modelling, we disentangle the relative importance of community-weighted trait means and functional trait dispersion from total biomass...

Data from: The scaling of population persistence with carrying capacity does not asymptote in populations of a fish experiencing extreme climate variability

Richard S.A. White, Brendan A. Wintle, Peter A. McHugh, Douglas J. Booker, Angus R. McIntosh & Richard S. A. White
Despite growing concerns regarding increasing frequency of extreme climate events and declining population sizes, the influence of environmental stochasticity on the relationship between population carrying capacity and time-to-extinction has received little empirical attention. While time-to-extinction increases exponentially with carrying capacity in constant environments, theoretical models suggest increasing environmental stochasticity causes asymptotic scaling, thus making minimum viable carrying capacity vastly uncertain in variable environments. Using empirical estimates of environmental stochasticity in fish metapopulations, we showed that...

Data from: Minimally invasive estimation of ventricular dead space volume through use of Frank-Starling curves

Shaun Davidson, Chris Pretty, Antoine Pironet, Thomas Desaive, Nathalie Janssen, Bernard Lambermont, Philippe Morimont & J. Geoffrey Chase
This paper develops a means of more easily and less invasively estimating ventricular dead space volume (Vd), an important, but difficult to measure physiological parameter. Vd represents a subject and condition dependent portion of measured ventricular volume that is not actively participating in ventricular function. It is employed in models based on the time varying elastance concept, which see widespread use in haemodynamic studies, and may have direct diagnostic use. The proposed method involves linear...

Data from: \"Disentangling nestedness\" disentangled

Serguei Saavedra & Daniel B. Stouffer
Analytical research indicates that the ‘nestedness’ of mutualistic networks facilitates the coexistence of species by minimizing the costs of competition relative to the benefits of facilitation. In contrast, James et al. recently argued that a more parsimonious explanation exists: the persistence of a community and its constituent species depends more on their having many interactions (high connectance and high degree, respectively) than for these interactions to be organized in any particular manner. Here we demonstrate...

Data from: Capacity to support predators scales with habitat size

Angus R. McIntosh, Peter A. McHugh, Michael J. Plank, Phillip G. Jellyman, Helen J. Warburton, Hamish S. Grieg & Hamish S. Greig
Habitat reduction could drive biodiversity loss if the capacity of food webs to support predators is undermined by habitat-size constraints on predator body size. Assuming that (i) available space restricts predator body size, (ii) mass-specific energy needs of predators scale with their body size, and (iii) energy availability scales with prey biomass, we predicted that predator biomass per unit area would scale with habitat size (quarter-power exponent) and prey biomass (three-quarter–power exponent). We found that...

Data from: Accurate predictions of coexistence in natural systems require the inclusion of facilitative interactions and environmental dependency

Malyon D. Bimler, Daniel B. Stouffer, Hao Ran Lai & Margaret M. Mayfield
1. Coexistence between plant species is well known to depend on the outcomes of species interactions within an environmental context. The incorporation of environmental variation into empirical studies of coexistence are rare, however, due to the complex experiments needed to do so and the lack of feasible modelling approaches for determining how environmental factors alter specific coexistence mechanisms. 2. In this paper, we present a simple modelling framework for assessing how variation in species interactions...

Data from: Analysis of the genome of the New Zealand giant collembolan (Holacanthella duospinosa) sheds light on hexapod evolution

Chen Wu, Melissa D. Jordan, Richard D. Newcomb, Neil J. Gemmell, Sarah Bank, Karen Meusemann, Peter K. Dearden, Elizabeth J. Duncan, Sefanie Grosser, Kim Rutherford, Paul P. Gardner, Ross N. Crowhurst, Bernd Steinwender, Leah K. Tooman, Mark I. Stevens & Thomas R. Buckley
Background: The New Zealand collembolan genus Holacanthella contains the largest species of springtails (Collembola) in the world. Using Illumina technology we have sequenced and assembled a draft genome and transcriptome from Holacanthella duospinosa (Salmon). We have used this annotated assembly to investigate the genetic basis of a range of traits critical to the evolution of the Hexapoda, the phylogenetic position of H. duospinosa and potential horizontal gene transfer events. Results: Our genome assembly was ~375...

Data from: Phylogenetic diversity and coevolutionary signals among trophic levels change across a habitat edge

Guadalupe Peralta, Carol M. Frost, Raphael K. Didham, Arvind Varsani & Jason M. Tylianakis
1. Incorporating the evolutionary history of species into community ecology enhances understanding of community composition, ecosystem functioning and responses to environmental changes. 2. Phylogenetic history might partly explain the impact of fragmentation and land-use change on assemblages of interacting organisms, and even determine potential cascading effects across trophic levels. However, it remains unclear whether phylogenetic diversity of basal resources is reflected at higher trophic levels in the food web. In particular, phylogenetic determinants of community...

Data from: Cyclic population dynamics and density-dependent intransitivity as pathways to coexistence between co-occurring annual plants

Daniel B. Stouffer, Claire E. Wainwright, Thomas Flanagan & Margaret M. Mayfield
1. Recent studies have brought renewed attention to the importance of complex species interactions - notably intransitive interactions - to patterns of plant community diversity. One underappreciated avenue through which intransitivity can occur is through cyclic population dynamics. Though such cyclic intransitive relationships have been extensively studied in predator-prey systems, evidence of their importance in competitive communities, notably plant communities, is more limited. Most studies of coexistence in plant communities assume fixed-point coexistence even while...

Data from: Genetic analyses reveal hybridization but no hybrid swarm in one of the world's rarest birds

Tammy E Steeves, Richard F Maloney, Marie L Hale, Jason M Tylianakis & Neil J Gemmell
Abstract: Hybridization facilitated by human activities has dramatically altered the evolutionary trajectories of threatened taxa around the globe. Whereas introduced mammalian predators and widespread habitat loss and degradation clearly imperil the recovery and survival of the New Zealand endemic black stilt or kakī (Himantopus novaezelandiae), the risk associated with hybridization between this critically endangered endemic and its self-introduced congener, the pied stilt or poaka (H. himantopus leucocephalus) is less clear. Here we combine Bayesian admixture...

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