70 Works

Data from: Sexual conflict in action: an antagonistic relationship between maternal and paternal sex allocation in the tammar wallaby, Notamacropus eugenii

Amy M. Edwards, Elissa Z. Cameron, Janine E. Deakin, Tariq Ezaz, Jorge C. Pereira, Malcolm A. Ferguson-Smith & Kylie A. Robert
Sex ratio biases are often inconsistent, both among and within species and populations. While some of these inconsistencies may be due to experimental design, much of the variation remains inexplicable. Recent research suggests that an exclusive focus on mothers may account for some of the inconsistency, with an increasing number of studies showing variation in sperm sex ratios and seminal fluids. Using fluorescent in-situ hybridization we show a significant population level Y-chromosome bias in the...

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: 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...

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: 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: \"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: 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: 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: 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: 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: 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: 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...

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...

Anthropogenic disturbance impacts ectomycorrhizal communities and abiotic soil properties: implications for an endemic forest disease

Sarah Sapsford
In forest ecosystems, habitat fragmentation negatively impacts stand structure and biodiversity; the resulting fragmented patches of forest have distinct, disturbed edge habitats that experience different environmental conditions than the interiors of the fragments. In southwest Western Australia, there is a large-scale decline of the keystone tree species Corymbia calophylla following fragmentation and land use change. These changes have altered stand structure and increased their susceptibility to an endemic fungal pathogen, Quambalaria coyrecup, which causes chronic...

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...

Data from: Sperm competition risk drives rapid ejaculate adjustments mediated by seminal fluid

Michael J. Bartlett, Tammy E. Steeves, Neil J. Gemmell & Patrice C. Rosengrave
In many species, males can make rapid adjustments to ejaculate performance in response to sperm competition risk; however, the mechanisms behind these changes are not understood. Here, we manipulate male social status in an externally fertilising fish, chinook salmon (Oncorhynchus tshawytscha), and find that in less than 48 hr, males can upregulate sperm velocity when faced with an increased risk of sperm competition. Using a series of in vitro sperm manipulation and competition experiments, we...

Data from: paco: implementing Procrustean Approach to Cophylogeny in R

Matthew C. Hutchinson, Edgar Fernando Cagua, Juan A. Balbuena, Daniel B. Stouffer & Timothée Poisot
1. The concordance of evolutionary histories and extant species interactions provides a useful metric for addressing questions of how the structure of ecological communities is influenced by macro-evolutionary processes. 2. We introduce paco (v.0.3.1), an R package to perform Procrustean Approach to Cophylogeny. This method assesses the phylogenetic congruence, or evolutionary dependence, of two groups of interacting species using both ecological interaction networks and their phylogenetic history. 3. We demonstrate the functionality of paco through...

Data from: Plant, herbivore and parasitoid community composition in native Nothofagaceae forests vs. exotic pine plantations

Guadalupe Peralta, Carol M. Frost & Raphael K. Didham
1.Converting natural areas into land used for production causes dramatic changes in the configuration of landscapes. Both the loss and fragmentation of native habitats contribute to biodiversity loss worldwide and the consequent creation of artificial edges can have a significant influence on community assembly. The conservation value of plantation forests has been identified for specific species, but it is not clear whether exotic pine plantations can also be used for the preservation of native communities...

Data from: Explaining large mitochondrial sequence differences within a population sample

Mary Morgan-Richards, Mariana Bulgarella, Louisa Sivyer, Edwina J. Dowle, Marie Hale, Rachael Van Heugten, Natasha E. McKean & Steven A. Trewick
Mitochondrial DNA sequence is frequently used to infer species' boundaries, as divergence is relatively rapid when populations are reproductively isolated. However, the shared history of a non-recombining gene naturally leads to correlation of pairwise differences, resulting in mtDNA clusters that might be mistaken for evidence of multiple species. There are four distinct processes that can explain high levels of mtDNA sequence difference within a single sample. Here, we examine one case in detail as an...

Data from: Interspecies interference and monitoring duration affect detection rates in chew cards

Olivia R. Burge, Dave Kelly & Janet M. Wilmshurst
Pest monitoring methods should provide unbiased accurate estimates of pest densities and locations, while also minimizing time-in-field and costs. Recent pest mammal monitoring studies have found that chew cards are more effective than conventional mammal monitoring methods, but little experimental work has been done to determine optimal experimental duration or quantify the risks of saturation by one species biasing detections of other species. Here, we used chew cards in three sites within Awarua wetland (Southland,...

Data from: Forest disturbance and seasonal food availability influence a conditional seed dispersal mutualism

Babale Aliyu, Joshua A. Thia, Elena Moltchanova, Pierre-Michel Forget & Hazel M. Chapman
The interaction between granivorous scatter-hoarding mammals and plants is a conditional mutualism: scatter-hoarders consume seeds (acting as predators), but the movement of seed by scatter-hoarders may contribute to dispersal (acting as mutualists). Understanding the ecological factors that shape this relationship is highly relevant in anthropogenically disturbed tropical forests where large-bodied frugivores are extirpated. In such forests, large-seeded trees that once depended on these frugivores for dispersal may now only have scatter-hoarders as prospective dispersers. We...

Data from: Improvement of non-key traits in radiata pine breeding programme when long-term economic importance is uncertain

Yongjun Li, Heidi Dungey, Alvin Yanchuk & Luis A. Apiolaza
Diameter at breast height (DBH), wood density (DEN) and predicted modulus of elasticity (PME) are considered as ‘key traits’ (KT) in the improvement in radiata pine breeding programmes in New Zealand. Any other traits which are also of interest to radiata pine breeders and forest growers are called ‘non-key traits’ (NKTs). External resin bleeding (ERB), internal checking (IC), number of heartwood rings (NHR) are three such non-key traits which affect wood quality of radiata pine...

Data from: Bayesian phylogenetic estimation of clade ages supports trans-atlantic dispersal of cichlid fishes

Michael Matschiner, Zuzana Musilová, Julia M.I. Barth, Zuzana Starostová, Walter Salzburger, Mike Steel & Remco Bouckaert
Divergence-time estimation based on molecular phylogenies and the fossil record has provided insights into fundamental questions of evolutionary biology. In Bayesian node dating, phylogenies are commonly time calibrated through the specification of calibration densities on nodes representing clades with known fossil occurrences. Unfortunately, the optimal shape of these calibration densities is usually unknown and they are therefore often chosen arbitrarily, which directly impacts the reliability of the resulting age estimates. As possible solutions to this...

Data from: Swapping birth and death: symmetries and transformations in phylodynamic models

Tanja Stadler & Mike Steel
Stochastic birth--death models provide the foundation for studying and simulating evolutionary trees in phylodynamics. A curious feature of such models is that they exhibit fundamental symmetries when the birth and death rates are interchanged. In this paper, we first provide intuitive reasons for these known transformational symmetries. We then show that these transformational symmetries (encoded in algebraic identities) are preserved even when individuals at the present are sampled with some probability. However, these extended symmetries...

An invasive species erodes the performance of coastal wetland protected areas

Junlin Ren, Jianshe Chen, Changlin Xu, Johan Van De Koppel, Mads Thomsen, Shi-Yun Qiu, Fangyan Cheng, Wanjuan Song, Quan-Xing Liu, Chi Xu, Junhong Bai, Yihui Zhang, Baoshan Cui, Mark Bertness, Brian Silliman, Bo Li & Qiang He
The world has increasingly relied upon protected areas (PAs) to rescue highly valued ecosystems from human activities, but whether PAs will fare well with bioinvasions remains unknown. By analyzing three decades of seven largest coastal PAs in China, including multiple World Natural Heritage and/or Wetlands of International Importance sites, we show that although PAs are achieving success in rescuing iconic wetlands and critical shorebird habitats from once widespread reclamation, this success is counteracted by escalating...

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