Research Outputs for April 2014

Here is a summary of research outputs where authors have acknowledged NeSI. Updates on research outputs are regularly sent to newsletter subscribers. 

New Alphacoronavirus in Mystacina tuberculata Bats, New Zealand

Richard J Hall, Jing Wang, Matthew Peacey, Nicole E Moore, Kate McInnes, Daniel M Tompkins Emerging Infectious Diseases 10.3201/eid2004.131441

Abstract

Because of recent interest in bats as reservoirs of emerging diseases, we investigated the presence of viruses in Mystacina tuberculata bats in New Zealand. A novel alphacoronavirus sequence was detected in guano from roosts of M. tuberculata bats in pristine indigenous forest on a remote offshore island (Codfish Island).

Identifying pathways for managing multiple disturbances to limit plant invasions

Andrew J Tanentzap, William G Lee, Adrian Monks, Kate Ladley, Peter N Johnson, Geoffrey M Rogers, Joy M Comrie, Dean A Clarke, Ella Hayman Journal of Applied Ecology 10.1111/1365-2664.12271

Summary

1. Plant invasions are predicted to accelerate in a world with increased anthropogenic disturbance. Non-native species pre-adapted to these disturbances may especially be poised to invade novel communities. Conservation managers therefore need predictions of how to alter disturbances to maximize the persistence of native biodiversity
2. We tested a multivariate hypothesis about the causal mechanisms underlying plant invasions in an ephemeral wetland in South Island, New Zealand to inform management of this biodiverse but globally imperilled habitat. Our approach details among the first applications in ecology of Bayesian structural equation modelling, demonstrating its potential to inform management by disentangling the relative importance of strongly inter-correlated processes.
3. We found that invasion by non-native plants was lowest in sites where the physical disturbance caused by flooding was both intense and frequent. This effect was stronger than the positive response of non-native species to high soil N supply, which was positively related to flooding.
4. ites flooded over a 4-year period had greater reductions in invasion than those associated with floods in the year prior to plot measurement because non-native species lacked traits for long-term persistence beneath water. Grazer exclusion had a small positive effect on invasion, as non-native species were preferentially selected by the herbivores at our site.
5. Our results show that only species adapted to the dominant disturbance regimes at a site may become successful invaders. Species native to ephemeral wetlands have specially evolved traits that allow them to persist and dominate in these sites.
6. Synthesis and applications. Predictions of invasions in a world of multiple disturbances clearly need to consider whether the evolutionary history of non-native species predisposes them to invade novel communities. Maintaining hydrological and nutrient regimes of ephemeral wetlands will limit the number of introduced species that are pre-adapted to become invasive.

Author-supplied keywords

causal networks, community dynamics, functional traits, invasive species, kettlehole, megafauna, rabbits, restoration, turf plants

Onsager-Kraichnan Condensation in Decaying Two-Dimensional Quantum Turbulence

Thomas P Billam, Matthew T Reeves, Brian P Anderson, Ashton S Bradley Phyiscal Review Letters 10.1103/PhysRevLett.112.145301, arXiv:1307.6374

Abstract

Despite the prominence of Onsager's point-vortex model as a statistical description of 2D classical turbulence, a first-principles development of the model for a realistic superfluid has remained an open problem. Here we develop a mapping of a system of quantum vortices described by the homogeneous 2D Gross-Pitaevskii equation (GPE) to the point-vortex model, enabling Monte-Carlo sampling of the vortex microcanonical ensemble. We use this approach to survey the full range of vortex states in a 2D superfluid, from the vortex-dipole gas at positive temperature to negative-temperature states exhibiting both macroscopic vortex clustering and kinetic energy condensation, which we term an Onsager-Kraichnan condensate (OKC). Damped GPE simulations reveal that such OKC states can emerge dynamically, via aggregation of small-scale clusters into giant OKC-clusters, as the end states of decaying 2D quantum turbulence in a compressible, finite-temperature superfluid. These statistical equilibrium states should be accessible in atomic Bose-Einstein condensate experiments.

A Hydrodynamic and Sediment Transport Model for the Waipaoa Shelf, New Zealand: Sensitivity of Fluxes to Spatially-Varying Erodibility and Model Nesting

Julia M Moriarty 1, Courtney K Harris, Mark G Hadfield Journal of Marine Science and Engineering 10.3390/jmse2020336

Abstract

Numerical models can complement observations in investigations of marine sediment transport and depositional processes. A coupled hydrodynamic and sediment transport model was implemented for the Waipaoa River continental shelf offshore of the North Island of New Zealand, to complement a 13-month field campaign that collected seabed and hydrodynamic measurements. This paper described the formulations used within the model, and analyzed the sensitivity of sediment flux estimates to model nesting and seabed erodibility. Calculations were based on the Regional Ocean Modeling System—Community Sediment Transport Modeling System (ROMS-CSTMS), a primitive equation model using a finite difference solution to the equations for momentum and water mass conservation, and transport of salinity, temperature, and multiple classes of suspended sediment. The three-dimensional model resolved the complex bathymetry, bottom boundary layer, and river plume that impact sediment dispersal on this shelf, and accounted for processes including fluvial input, winds, waves, tides, and sediment resuspension. Nesting within a larger-scale, lower resolution hydrodynamic model stabilized model behavior during river floods and allowed large-scale shelf currents to impact sediment dispersal. To better represent observations showing that sediment erodibility decreased away from the river mouth, the seabed erosion rate parameter was reduced with water depth. This allowed the model to account for the observed spatial pattern of erodibility, though the model held the critical shear stress for erosion constant. Although the model neglected consolidation and swelling processes, use of a spatially-varying erodibility parameter significantly increased export of fluvial sediment from Poverty Bay to deeper areas of the shelf.

Author-supplied keywords

erodibility, model nesting, New Zealand, numerical modeling, sediment transport, Waipaoa shelf

Efficient Parallel Algorithms for the Maximum Subarray Problem

Tadao Takaoka Proceedings of the Twelfth Australasian Symposium on Parallel and Distributed Computing (AusPDC 2014) https://loanhubcanada.org/

Abstract

Parallel algorithm design is generally hard. Parallel program verifcation is even harder. We take an example from the maximum subarray problem and and show those two problems of design and verifcation. The best known communication steps for a mesh architecture for the maximum subarray problem is 2n − 1. We give a formal proof for the parallel algorithm on the mesh architecture based on Hoare logic. The main part of the proof is to establish several space/time invariants with three indices (i; j; k). The indices (i; j) pair specifes the invariant at the (i; j) grid point of the mesh and k specifes the k-th step in the computation. Then ignoring additive constants, the communication steps are improved to (3/2)n steps and fnally n steps, which is optimal in terms of communication steps. Also the first algorithm is implemented on a Blue Gene parallel computer and performance measurements conducted are shown.