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Christchurch, New Zealand

Scion, officially registered as New Zealand Forest Research Institute Limited, is a New Zealand Crown Research Institute with its primary areas of research, science and technology development being in the areas of forestry, wood products, wood-derived materials and other biomaterials sectors. Wikipedia.

Ball R.D.,New Zealand Forest Research Institute

In genome-wide association studies hundreds of thousands of loci are scanned in thousands of cases and controls, with the goal of identifying genomic loci underpinning disease. This is a challenging statistical problem requiring strong evidence. Only a small proportion of the heritability of common diseases has so far been explained. This "dark matter of the genome" is a subject of much discussion. It is critical to have experimental design criteria that ensure that associations between genomic loci and phenotypes are robustly detected. To ensure associations are robustly detected we require good power (e.g., 0.8) and sufficiently strong evidence [i.e., a high Bayes factor (e.g., 10 6, meaning the data are 1 million times more likely if the association is real than if there is no association)] to overcome the low prior odds for any given marker in a genome scan to be associated with a causal locus. Power calculations are given for determining the sample sizes necessary to detect effects with the required power and Bayes factor for biallelic markers in linkage disequilibrium with causal loci in additive, dominant, and recessive genetic models. Significantly stronger evidence and larger sample sizes are required than indicated by traditional hypothesis tests and power calculations. Many reported putative effects are not robustly detected and many effects including some large moderately low-frequency effects may remain undetected. These results may explain the dark matter in the genome. The power calculations have been implemented in R and will be available in the R package ldDesign. Source

Bertheau C.,University of Orleans | Brockerhoff E.G.,New Zealand Forest Research Institute | Roux-Morabito G.,University of Orleans | Lieutier F.,University of Orleans | Jactel H.,French National Institute for Agricultural Research
Ecology Letters

The translocation of species beyond their native range is a major threat to biodiversity. Invasions by tree-feeding insects attacking native trees and the colonization of introduced trees by native insects result in new insect-tree relationships. To date there is uncertainty about the key factors that influence the outcome of these novel interactions. We report the results of a meta-analysis of 346 pairwise comparisons of forest insect fitness on novel and ancient host tree species from 31 publications. Host specificity of insects and phylogenetic relatedness between ancient and novel host trees emerged as key factors influencing insect fitness. Overall, fitness was significantly lower on novel host species than on ancient hosts. However, in some cases, fitness increased on novel hosts, mainly in polyphagous insects or when close relatives of ancient host trees were colonized. Our synthesis enables greatly improved impact prediction and risk assessment of biological invasions. © 2010 Blackwell Publishing Ltd/CNRS. Source

Suckling D.M.,The New Zealand Institute for Plant and Food Research Ltd | Brockerhoff E.G.,New Zealand Forest Research Institute
Annual Review of Entomology

Epiphyas postvittana (Walker) (Lepidoptera: Tortricidae), the light brown apple moth (LBAM), is an important leafroller pest with an exceptionally wide host range that includes many horticultural crops and other woody and herbaceous plants. LBAM is native to southeastern Australia but has invaded Western Australia, New Zealand, Hawaii, much of England, and in 2007, it was confirmed as established in California. The discovery of this pest in California has led to a major detection and regulatory effort because of concerns about economic and environmental impacts. Its recent discovery in Sweden is also of note. LBAM has often been intercepted on imports of fruit and other plant parts, and it has the potential to become a successful invader in temperate and subtropical regions worldwide. The importance of the insect has prompted development of classical biological control programs together with a wide variety of other management interventions that can be used in integrated pest management or integrated pest eradication. © 2010 by Annual Reviews All rights reserved. Source

Ball R.D.,New Zealand Forest Research Institute
Methods in Molecular Biology

In this chapter we describe a novel Bayesian approach to designing GWAS studies with the goal of ensuring robust detection of effects of genomic loci associated with trait variation. The goal of GWAS is to detect loci associated with variation in traits of interest. Finding which of 500,000 - 1,000,000 loci has a practically significant effect is a difficult statistical problem, like finding a needle in a haystack. We address this problem by designing experiments to detect effects with a given Bayes factor, where the Bayes factor is chosen sufficiently large to overcome the low prior odds for genomic associations. Methods are given for various possible data structures including random population samples, case-control designs, transmission disequilibrium tests, sib-based transmission disequilibrium tests, and other family-based designs including designs for plants with clonal replication. We also consider the problem of eliciting prior information from experts, which is necessary to quantify prior odds for loci. We advocate a "subjective" Bayesian approach, where the prior distribution is considered as a mathematical representation of our prior knowledge, while also giving generic formulae that allow conservative computations based on low prior information, e.g., equivalent to the information in a single sample point. Examples using R and the R packages ldDesign are given throughout. © Springer Science+Business Media, LLC 2013. Source

Wingfield M.J.,University of Pretoria | Brockerhoff E.G.,New Zealand Forest Research Institute | Wingfield B.D.,University of Pretoria | Slippers B.,University of Pretoria

Several key tree genera are used in planted forests worldwide, and these represent valuable global resources. Planted forests are increasingly threatened by insects and microbial pathogens, which are introduced accidentally and/or have adapted to new host trees. Globalization has hastened tree pest emergence, despite a growing awareness of the problem, improved understanding of the costs, and an increased focus on the importance of quarantine. To protect the value and potential of planted forests, innovative solutions and a better-coordinated global approach are needed. Mitigation strategies that are effective only in wealthy countries fail to contain invasions elsewhere in the world, ultimately leading to global impacts. Solutions to forest pest problems in the future should mainly focus on integrating management approaches globally, rather than single-country strategies. A global strategy to manage pest issues is vitally important and urgently needed. Source

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