25 Works

Data from: On-shelf larval retention limits population connectivity in a coastal broadcast spawner

Peter R. Teske, Jonathan Sandoval-Castillo, Erik Van Sebille, Jonathan Waters, Luciano B. Beheregaray, LB Beheregaray &
Broadcast-spawning marine organisms with long pelagic larval duration are often expected to be genetically homogeneous throughout their ranges. When genetic structure is found in such taxa, it may be in the form of chaotic genetic patchiness: i.e. patterns that might seem independent of any underlying environmental variation. The joint analysis of population genetic data and marine environmental data can elucidate factors driving such spatial genetic diversity patterns. Using meso-scale sampling (at a scale of 10s...

Data from: The scaling of parasite biomass with host biomass in lake ecosystems: are parasites limited by host resources?

Clément Lagrue & Robert Poulin
The standing crop biomass of different populations or trophic levels reflects patterns of energy flow through an ecosystem. The contribution of parasites to total biomass is often considered negligible; recent evidence suggests otherwise, although it comes from a narrow range of natural systems. Quantifying how local parasite biomass, whether that of a single species or an assemblage of species sharing the same host, varies across localities with host population biomass, is critical to determine what...

Data from: Evidence for Bergmann's rule and not allopatric subspeciation in the threatened kaka (Nestor meridionalis)

Nic Dussex, James Sainsbury, Ron Moorhouse, Ian G. Jamieson & Bruce C. Robertson
Species of conservation concern characterized by small and declining populations greatly benefit from proactive management approaches such as population translocations. Because they often show intra-specific genetic and phenotypic variation, which can result from drift or differential selective pressures between habitats, understanding the distribution of such variation and its underlying processes is a prerequisite to develop effective management guidelines. Indeed, translocations among genetically differentiated populations potentially locally adapted are discouraged in order to avoid outbreeding depression,...

Data from: Heterozygote advantage at MHC DRB may influence response to infectious disease epizootics

Amy J. Osborne, John Pearson, Sandra S. Negro, B. Louise Chilvers, Martin A. Kennedy & Neil J. Gemmell
The effect of MHC polymorphism on individual fitness variation in the wild remains equivocal; however, much evidence suggests that heterozygote advantage is a major determinant. To understand the contribution of MHC polymorphism to individual disease resistance or susceptibility in natural populations, we investigated two MHC class II B loci, DQB and DRB, in the New Zealand sea lion (NZSL, Phocarctos hookeri). The NZSL is a threatened species which is unusually susceptible to death by bacterial...

Data from: Are molecular markers useful predictors of adaptive potential?

Elizabeth A. Mittell, Shinichi Nakagawa & Jarrod D. Hadfield
Estimates of molecular genetic variation are often used as a cheap and simple surrogate for a population's adaptive potential, yet empirical evidence suggests they are unlikely to be a valid proxy. However, this evidence is based on molecular genetic variation poorly predicting estimates of adaptive potential rather than how well it predicts true values. As a consequence, the relationship has been systematically underestimated and the precision with which it could be measured severely overstated. By...

Data from: Kinetic estimation of GFR improves prediction of dialysis and recovery after kidney transplantation

Timothy J. Pianta, Zoltan H. Endre, John W. Pickering, Nicholas A. Buckley & Philip W. Peake
Background: The early prediction of delayed graft function (DGF) would facilitate patient management after kidney transplantation. Methods: In a single-centre retrospective analysis, we investigated kinetic estimated GFR under non-steady-state conditions, KeGFR, in prediction of DGF. KeGFRsCr was calculated at 4h, 8h and 12h in 56 recipients of deceased donor kidneys from initial serum creatinine (sCr) concentrations, estimated creatinine production rate, volume of distribution, and the difference between consecutive sCr values. The utility of KeGFRsCr for...

Data from: The genomes of two key bumblebee species with primitive eusocial organisation

Ben M. Sadd, Seth M. Barribeau, Guy Bloch, Dirk C. De Graaf, Peter Dearden, Christine Elsik, Jurgen Gadau, Cornelius Grimmelikhuijzen, Martin Hasselmann, Jeffrey Lozier, Hugh Robertson, Guy Smagghe, Eckart Stolle, Matthias Van Vaerenbergh, Robert Waterhouse, Erich Bornberg-Bauer, Steffan Klasberg, Anna Bennett, Francisco Camara, Roderic Guigo, Katharina Hoff, Marco Mariotti, Monica Munos-Torres, Terence Murphy, Didac Santesmasses … & Kim C. Worley
Background: The shift from solitary to social behavior is one of the major evolutionary transitions. Primitively eusocial bumblebees are uniquely placed to illuminate the evolution of highly eusocial insect societies. Bumblebees are also invaluable natural and agricultural pollinators, and there is widespread concern over recent population declines in some species. High-quality genomic data will inform key aspects of bumblebee biology, including susceptibility to implicated population viability threats. Results: We report the high quality draft genome...

Data from: An assessment of ancient DNA preservation in Holocene-Pleistocene fossil bone excavated from the world heritage Naracoorte Caves, South Australia

Alicia Grealy, Amy Macken, Morten E. Allentoft, Nicolas J. Rawlence, Elizabeth Reed & Michael Bunce
Although there is a long history of research into the fossil deposits of the Naracoorte Caves (South Australia), ancient DNA (aDNA) has not been integrated into any palaeontological study from this World Heritage site. Here, we provide the first evidence of aDNA preservation in Holocene- and Pleistocene-aged fossil bone from a deposit inside Robertson Cave. Using a combination of metabarcoding and shotgun next-generation sequencing approaches, we demonstrate that aDNA from diverse taxa can be retrieved...

Data from: Are extra-pair males different from cuckolded males? An empirical and meta-analytic examination

Yu-Hsun Hsu, Julia Schroeder, Isabel Winney, Terry Burke & Shinichi Nakagawa
Traditional models for female extra-pair matings assume that females benefit indirectly from extra-pair mating behaviour. Under these so-called adaptive models, extra-pair males are hypothesized to have more compatible genotypes, larger body size, exaggerated ornaments or to be older than cuckolded males. Alternatively, (‘nonadaptive’) models that consider female extra-pair matings to be a by-product posit that female extra-pair mating can be maintained even if there is no benefit to females. This could happen if, for example,...

Data from: Population structure within an alpine archipelago: strong signature of past climate change in the New Zealand rock wren (Xenicus gilviventris)

Kerry A. Weston & B. C. Robertson
Naturally subdivided populations such as those occupying high-altitude habitat patches of the ‘alpine archipelago’ can provide significant insight into past biogeographical change and serve as useful models for predicting future responses to anthropogenic climate change. Among New Zealand's alpine taxa, phylogenetic studies support two major radiations: the first correlating with geological forces (Pliocene uplift) and the second with climatic processes (Pleistocene glaciations). The rock wren (Xenicus gilviventris) is a threatened alpine passerine belonging to the...

Data from: The Trojan Female Technique for pest control: a candidate mitochondrial mutation confers low male fertility across diverse nuclear backgrounds in Drosophila melanogaster

Damian K. Dowling, Daniel M. Tompkins & Neil J. Gemmell
Pest species represent a major ongoing threat to global biodiversity. Effective management approaches are required that regulate pest numbers, while minimizing collateral damage to nontarget species. The Trojan Female Technique (TFT) was recently proposed as a prospective approach to biological pest control. The TFT draws on the evolutionary hypothesis that maternally inherited mitochondrial genomes are prone to the accumulation of male, but not female, harming mutations. These mutations could be harnessed to provide trans-generational fertility-based...

Data from: PopART: full-feature software for haplotype network construction

Jessica W. Leigh & David Bryant
1. Haplotype networks are an intuitive method for visualising relationships between individual genotypes at the population level. 2. Here, we present popart, an integrated software package that provides a comprehensive implementation of haplotype network methods, phylogeographic visualisation tools and standard statistical tests, together with publication-ready figure production. 3. popart also provides a platform for the implementation and distribution of new network-based methods – we describe one such new method, integer neighbour-joining. 4. The software is...

Data from: Bottom-up regulation of parasite population densities in freshwater ecosystems

Clément Lagrue & Robert Poulin
Theory predicts the bottom–up coupling of resource and consumer densities, and epidemiological models make the same prediction for host–parasite interactions. Empirical evidence that spatial variation in local host density drives parasite population density remains scarce, however. We test the coupling of consumer (parasite) and resource (host) populations using data from 310 populations of metazoan parasites infecting invertebrates and fish in New Zealand lakes, spanning a range of transmission modes. Both parasite density (no. parasites per...

Worldwide evidence of a unimodal relationship between productivity and plant species richness

Lauchlan H. Fraser, Jason Pither, Anke Jentsch, Marcelo Sternberg, Martin Zobel, Diana Askarizadeh, Sandor Bartha, Carl Beierkuhnlein, Jonathan A. Bennett, Alex Bittel, Bazartseren Boldgiv, Ilsi I. Boldrini, Edward Bork, Leslie Brown, Marcelo Cabido, James Cahill, Cameron N. Carlyle, Giandiego Campetella, Stefano Chelli, Ofer Cohen, Anna-Maria Csergo, Sandra Diaz, Lucas Enrico, David Ensing, Alessandra Fidelis … & Szilárd Szentes
The search for predictions of species diversity across environmental gradients has challenged ecologists for decades. The humped-back model (HBM) suggests that plant diversity peaks at intermediate productivity; at low productivity few species can tolerate the environmental stresses, and at high productivity a few highly competitive species dominate. Over time the HBM has become increasingly controversial, and recent studies claim to have refuted it. Here, by using data from coordinated surveys conducted throughout grasslands worldwide and...

Data from: Broad-scale genetic patterns of New Zealand abalone, Haliotis iris, across a distribution spanning 13° latitude and major oceanic water masses

Margaret Will, Tom McCowan & Neil J. Gemmell
The New Zealand black-foot abalone, Haliotis iris, or pāua, is endemic to the rocky reefs surrounding New Zealand, whose main land mass spans 13° of latitude and separates the Tasman Sea from the Pacific Ocean. In this study, we examined the population genetic structure of this important commercial, cultural and recreational species by genotyping nine microsatellite loci in 485 pāua from 27 locations distributed across mainland New Zealand and the Chatham Islands. We found low,...

Data from: Geographically contrasting biodiversity reductions in a widespread New Zealand seabird

Nicolas J. Rawlence, Martyn Kennedy, Christian N. K. Anderson, Stefan Prost, Charlotte E. Till, Ian Smith, R. Paul Scofield, Alan J. D. Tennyson, Jill Hamel, Chris Lalas, Elizabeth A. Matisoo-Smith, Jonathan M. Waters & Ian W. G. Smith
Unravelling prehistoric anthropogenic impacts on biodiversity represents a key challenge for biologists and archaeologists. New Zealand's endemic Stewart Island Shag (Leucocarbo chalconotus) comprises two distinct phylogeographic lineages, currently restricted to the country's south and southeast. However, fossil and archaeological remains suggest a far more widespread distribution at the time of Polynesian settlement ca. 1280 AD, encompassing much of coastal South Island. We used modern and ancient DNA, radiocarbon dating, and Bayesian modelling, to assess the...

Data from: Genome-wide SNPs reveal fine-scale differentiation among wingless alpine stonefly populations, and introgression between winged and wingless forms

Nicolas Dussex, Aaron Chuah & Jonathan M. Waters
Insect flight-loss is a repeated phenomenon in alpine habitats, where wing reduction is thought to enhance local recruitment and increase fecundity. One predicted consequence of flight loss is reduced dispersal ability, which should lead to population genetic differentiation and perhaps ultimately to speciation. Using a dataset of 15,123 SNP loci, we present comparative analyses of fine-scale population structure in co-distributed Zelandoperla stonefly species, across three parallel altitudinal transects in New Zealand's Rock and Pillar mountain...

Data from: Monte Carlo Strategies for selecting parameter values in simulation experiments

Jessica W. Leigh & David Bryant
Simulation experiments are used widely throughout evolutionary biology and bioinformatics to compare models, promote methods, and test hypotheses. The biggest practical constraint on simulation experiments is the computational demand, particularly as the number of parameters increases. Given the extraordinary success of Monte Carlo methods for conducting inference in phylogenetics, and indeed throughout the sciences, we investigate ways in which Monte Carlo framework can be used to carry out simulation experiments more efficiently. The key idea...

Data from: Light limitation within southern New Zealand kelp forest communities

Matthew J. Desmond, Daniel W. Pritchard & Christopher D. Hepburn
Light is the fundamental driver of primary productivity in the marine environment. Reduced light availability has the potential to alter the distribution, community composition, and productivity of key benthic primary producers, potentially reducing habitat and energy provision to coastal food webs. We compared the underwater light environment of macroalgal dominated shallow subtidal rocky reef habitats on a coastline modified by human activities with a coastline of forested catchments. Key metrics describing the availability of photosynthetically...

Data from: Performance and accuracy of lightweight and low-cost GPS data loggers according to antenna positions, fix intervals, habitats and animal movements

Marie-Amélie Forin-Wiart, Pauline Hubert, Pascal Sirguey & Marie-Lazarine Poulle
Recently developed low-cost Global Positioning System (GPS) data loggers are promising tools for wildlife research because of their affordability for low-budget projects and ability to simultaneously track a greater number of individuals compared with expensive built-in wildlife GPS. However, the reliability of these devices must be carefully examined because they were not developed to track wildlife. This study aimed to assess the performance and accuracy of commercially available GPS data loggers for the first time...

Data from: Stoichiometric imbalances between detritus and detritivores are related to shifts in ecosystem functioning

André Frainer, Jérémy Jabiol, Mark O. Gessner, Andreas Bruder, Eric Chauvet, Brendan McKie & Brendan G. McKie
How are resource consumption and growth rates of litter-consuming detritivores affected by imbalances between consumer and litter C:N:P ratios? To address this question, we offered leaf litter as food to three aquatic detritivore species, which represent a gradient of increasing body N:P ratios: a crustacean, a caddisfly and a stonefly. The detritivores were placed in microcosms and submerged in a natural stream. Four contrasting leaf species were offered, both singly and in two-species mixtures, to...

Data from: Troubleshooting the potential pitfalls of cross-fostering

Isabel S. Winney, Shinichi Nakagawa, Yu-Hsun Hsu, Terry Burke, Julia Schroeder & Isabel Winney
1. Cross-fostering is the transfer of offspring between their natal environment and a new social environment. This method allows researchers to disentangle the genetic and interacting environmental effects that influence phenotypes, and is popular in both wild and laboratory studies. Here, we discuss three factors that might bias cross-fostering and influence ecological and evolutionary conclusions if not accommodated. 2. First, cross-fostering tends to be spatially and temporally non-random because heterogeneous breeding conditions can result in...

Data from: Multiple-stressor effects on leaf litter decomposition and fungal decomposers in agricultural streams contrast between litter species

Andreas Bruder, Romana K. Salis, Nicola J. McHugh & Christoph D. Matthaei
Agricultural land use commonly exerts multiple stressors on the functioning of stream ecosystems, including leaf litter decomposition and the utilization of this resource in stream food webs. If stressors interact, their cumulative effects on biotic responses cannot be predicted from knowledge of individual stressor effects, posing challenges for management and restoration of these ecosystems. We examined the individual and interactive effects of four common agricultural stressors and the role of litter quality on leaf litter...

Data from: Unexpected positive and negative effects of continuing inbreeding in one of the world’s most inbred wild animals

Emily L. Weiser, Catherine E. Grueber, Euan S. Kennedy & Ian G. Jamieson
Inbreeding depression, the reduced fitness of offspring of related individuals, is a central theme in evolutionary biology. Inbreeding effects are influenced by the genetic makeup of a population, which is driven by any history of genetic bottlenecks and genetic drift. The Chatham Island black robin represents a case of extreme inbreeding following two severe population bottlenecks. We tested whether inbreeding measured by a 20-year pedigree predicted variation in fitness among individuals, despite the high mean...

Data from: Population differentiation and behavioural association of the two ‘personality’ genes DRD4 and SERT in dunnocks (Prunella modularis)

Benedikt Holtmann, Stefanie Grosser, Malgorzata Lagisz, Sheri R. Johnson, Eduardo S. A. Santos, Carlos E. Lara, Bruce Robertson, Shinichi Nakagawa, S. L. Johnson & B. C. Robertson
Quantifying the variation in behaviour-related genes within and between populations provides insight into how evolutionary processes shape consistent behavioural traits (i.e. personality). Deliberate introductions of non-native species offer opportunities to investigate how such genes differ between native and introduced populations and how polymorphisms in the genes are related to variation in behaviour. Here, we compared the genetic variation of the two ‘personality’ genes, DRD4 and SERT, between a native (United Kingdom, UK) and an introduced...

Registration Year

  • 2015
    25

Resource Types

  • Dataset
    25

Affiliations

  • University of Otago
    25
  • Department of Conservation
    3
  • UNSW Sydney
    3
  • Max Planck Institute for Ornithology
    2
  • Sao Paulo State University
    2
  • Flinders University
    2
  • French National Centre for Scientific Research
    2
  • University of Copenhagen
    2
  • University of Sydney
    2
  • University of Camerino
    1