A systematic survey of loss-of-function variants in human protein-coding genes

Genome-sequencing studies indicate that all humans carry many genetic variants predicted to cause loss of function (LoF) of protein-coding genes, suggesting unexpected redundancy in the human genome. Here we apply stringent filters to 2951 putative LoF variants obtained from 185 human genomes to determine their true prevalence and properties. We estimate that human genomes typically contain ~100 genuine LoF variants with ~20 genes completely inactivated. We identify rare and likely deleterious LoF alleles, including 26 known and 21 predicted severe disease-causing variants, as well as common LoF variants in nonessential genes. We describe functional and evolutionary differences between LoF-tolerant and recessive disease genes and a method for using these differences to prioritize candidate genes found in clinical sequencing studies.     

Selection of Eucalypt Plus Trees with Regard to Splitting in the Sawn Timber / SELEKSIE VAN EUCALYPTUS-PLUSBOME MET BETREKKING TOT SPLITSING IN DIE GESAAGDE HOUT

A practical method in use in South Africa for quantifying the extent of splitting in the timber of the genus Eucalyptus in order to determine minimum standards for selection purposes, is explained. The standards are used to assist in the choice of phenotypes, the progeny of which it is hoped will produce timber which splits less.     

Landscape,fire and habitat: which features of recently burned heathland influence site occupancy of an early successional specialist?

Context

Multiple ecological drivers generate spatial patterns in species’ distributions. Changes to natural disturbance regimes can place early successional habitat specialists at an increased risk of extinction by altering landscape patterns of habitat suitability.

Objectives

We developed a series of hypotheses to evaluate the effects of landscape structure, fire history, and site-level habitat quality on site occupancy by an early successional specialist, the eastern chestnut mouse (Pseudomys gracilicaudatus).

Methods

We obtained eight years of monitoring data from 26 sites in recently burned heathland in southeast Australia. We used generalised linear models to determine which explanatory variables were related to occupancy. We also explored predictability in patterns of small mammal species co-occurrence.

Results

Landscape structure (patch area, landscape heterogeneity) was strongly related to site occupancy. Site occupancy was associated with dead shrubs in the understory and rock cover on ground layer, but was not directly influenced by recent or historical fire. Contrary to contemporary ecological theory, we found no predictable species associations in our early successional community.

Conclusions

We recommend surveys take account of landscape configuration and proximity to suitable habitat for optimal results. Fire regimes expected to promote eastern chestnut mouse population growth should encourage the retention of critical habitat features rather than be based on temporal rates of successional stages. For management to adequately account for post-disturbance patterns in early successional communities, a species-by-species, multi-scaled approach to research is necessary.

     

Grain dormancy in fixed lines of white-grained wheat (<Emphasis Type="Italic">Triticum aestivum</Emphasis> L.) grown under controlled environmental conditions

Pre-harvest sprouting (PHS) in wheat (Triticum aestivum L.) can be a significant problem, causing deleterious effects on grain quality. However, the adverse impacts of PHS can be reduced by introgressing genes controlling grain dormancy into white-grained bread wheat. Screening for grain dormancy typically involves germination testing of harvest-ripe grain grown in a glasshouse or field. However, the more uniform environmental conditions provided by temperature controlled glasshouses (i.e. controlled environmental conditions—CEC) may provide significant benefits for the assessment of grain dormancy. In this study, the dormancy phenotype of grain grown under CEC incorporating an extended photoperiod, was compared with 2 years of data from field grown material. Four dormant double haploid lines (derived from SW95-50213 and AUS1408) and two locally adapted non-dormant cultivars EGA Gregory and EGA Wills were compared in three replicated experiments grown under CEC (22 ± 3°C and 24 h photoperiod). The germination response of harvest-ripe grain was examined to assess the expression of grain dormancy. Two measures of germination, the predicted time to 50% germination (G ₅₀) and a weighted germination index, both clearly differentiated dormant and non-dormant lines grown under CEC. In addition, levels of grain dormancy were similar to field-grown plants. These results demonstrated that CEC with an extended photoperiod can be used for rapid and reliable characterisation of grain dormancy in fixed lines of bread wheat.     

Invasions of the Portuguese millipede,Ommatoiulus moreleti,in southern Australia

The Portuguese millipede, Ommatoiulus moreleti, was first recorded in Australia on Eyre Peninsula, South Australia in 1953. By the early 1980s, O. moreleti had spread to several sites across southern Australia where it had become a significant nuisance pest invading houses in large numbers in autumn and spring. At that time, it was predicted that O. moreleti would further expand its distribution to occupy most areas of southern Australia with mean annual rainfall of 300–2400 mm (excluding areas with summer rain maxima), mean daily minimum air temperatures in winter of 0–15 °C and mean daily maximum temperatures in summer of 18–33 °C, based on climatic matching of where it had already spread to. This paper reports the known distribution of O. moreleti in Australia in 2013 and confirms the earlier prediction. Whilst stadial age and body size (width) of O. moreleti now vary greatly between individual sites in Australia, geographic scale patterns in these traits are slight, with both age and size only weakly correlated with rainfall and temperature. Millipedes are smaller in Australia compared with Portugal. The importance of this size variation is discussed with reference to its likely influence on fecundity and the success of an introduced biological control agent (Pelidnoptera nigripennis: Diptera, Sciomyzidae).     

Understanding ‘resource’ conflicts in Papua New Guinea

Abstract: Papua New Guinea, with its heavy dependence on natural resources, limited economic development in the past two decades, poor record of governance and high‐profile separatist conflicts such as the Bougainville civil war, appears to be an exemplar of the ‘Resource Curse’ theory – the notion that natural resources actively undermine economic development. Using a number of examples from a range of scales, this paper argues that what appear to be ‘resource’ conflicts in Papua New Guinea are actually better conceived as conflicts around identity and social relationships. The very different conceptualisation of natural resources in most Melanesian societies – as elements of the social world as much as any external environmental sphere – means that resources become a conduit for local social and political agendas and tensions to be expressed. The nature of traditional conflict in Melanesian societies is discussed as a guide to the better management and resolution of what appear to be ‘resource’ conflicts in Papua New Guinea.