Statistical tests for taxonomic distinctiveness from observations of monophyly

The observation of monophyly for a specified set of genealogical lineages is often used to place the lineages into a distinctive taxonomic entity. However, it is sometimes possible that monophyly of the lineages can occur by chance as an outcome of the random branching of lineages within a single taxon. Thus, especially for small samples, an observation of monophyly for a set of lineages--even if strongly supported statistically--does not necessarily indicate that the lineages are from a distinctive group. Here I develop a test of the null hypothesis that monophyly is a chance outcome of random branching. I also compute the sample size required so that the probability of chance occurrence of monophyly of a specified set of lineages lies below a prescribed tolerance. Under the null model of random branching, the probability that monophyly of the lineages in an index group occurs by chance is substantial if the sample is highly asymmetric, that is, if only a few of the sampled lineages are from the index group, or if only a few lineages are external to the group. If sample sizes are similar inside and outside the group of interest, however, chance occurrence of monophyly can be rejected at stringent significance levels (P < 10(-5)) even for quite small samples (approximately 20 total lineages). For a fixed total sample size, rejection of the null hypothesis of random branching in a single taxon occurs at the most stringent level if samples of nearly equal size inside and outside the index group--with a slightly greater size within the index group--are used. Similar results apply, with smaller sample sizes needed, when reciprocal monophyly of two groups, rather than monophyly of a single group, is of interest. The results suggest minimal sample sizes required for inferences to be made about taxonomic distinctiveness from observations of monophyly.     

VPMCD: variable interaction modeling approach for class discrimination in biological systems

Data classification algorithms applied for class prediction in computational biology literature are data specific and have shown varying degrees of performance. Different classes cannot be distinguished solely based on interclass distances or decision boundaries. We propose that inter-relations among the features be exploited for separating observations into specific classes. A new variable predictive model based class discrimination (VPMCD) method is described here. Three well established and proven data sets of varying statistical and biological significance are utilized as benchmark. The performance of the new method is compared with advanced classification algorithms. The new method performs better during different tests and shows higher stability and robustness. The VPMCD is observed to be a potentially strong classification approach and can be effectively extended to other data mining applications involving biological systems.     

Sequence analysis and rule development of predicting protein stability change upon mutation using decision tree model

Understanding the mechanism of the protein stability change is one of the most challenging tasks. Recently, the prediction of protein stability change affected by single point mutations has become an interesting topic in molecular biology. However, it is desirable to further acquire knowledge from large databases to provide new insights into the nature of them. This paper presents an interpretable prediction tree method (named iPTREE-2) that can accurately predict changes of protein stability upon mutations from sequence based information and analyze sequence characteristics from the viewpoint of composition and order. Therefore, iPTREE-2 based on a regression tree algorithm exhibits the ability of finding important factors and developing rules for the purpose of data mining. On a dataset of 1859 different single point mutations from thermodynamic database, ProTherm, iPTREE-2 yields a correlation coefficient of 0.70 between predicted and experimental values. In the task of data mining, detailed analysis of sequences reveals the possibility of the compositional specificity of residues in different ranges of stability change and implies the existence of certain patterns. As building rules, we found that the mutation residues in wild type and in mutant protein play an important role. The present study demonstrates that iPTREE-2 can serve the purpose of predicting protein stability change, especially when one requires more understandable knowledge.     

街谷绿化消减机动车排放污染物的研究方法与进展

随着街道两侧建筑群向高密度、高层化发展,传统“树越多越好”的绿化模式在应对城市街谷空气污染时是否适用受到广泛关注。明晰街谷绿化植物特征及其种植设计模式对机动车排放污染物消减的调控机理是发挥其提升街谷空气品质的重要前提。本文通过对近年国内外相关文献的梳理,比较分析了现场观测、风洞试验和数值模拟3种研究方法的适用性及局限性,详细剖析了行道树、绿篱两类绿化模式对街谷空气污染物扩散与沉降的影响机制,提出了一套面向空气质量提升的街谷绿化适应性设计工作框架。最后,分别从典型街谷绿化设计图示语言研制、街谷空气污染暴露评估技术指南编制、计算机流体力学模型中街谷绿化效应物理过程参数化方案优化等方面进行探讨,以期为后续研究提供思路和借鉴。     

Roosting requirements of Helmeted Guineafowl Numida meleagris on Highveld grain and livestock farms with alien tree groves,Gauteng province,South Africa

This study describes the relationship between Helmeted Guineafowl Numida meleagris and invasive alien trees on livestock and maize farms south-east of Johannesburg, Gauteng province, South Africa. The dependence of the birds on alien trees affects strategies for the removal of these trees. During June to December 2014, Helmeted Guineafowl were recorded weekly on maps along a 42 km transect. Since Helmeted Guineafowl live in cohesive social groups of 15–20 birds, they roost communally in one or two trees during winter rather than spreading across an entire tree grove. The distribution of alien trees across the landscape in patches has enabled Helmeted Guineafowl flocks to reach new feeding patches near to roosting trees, as old feeding patches are depleted. One Helmeted Guineafowl flock of 15–20 birds requires ～0.09 ha covered with mature alien trees for roosting. Suggestions are presented relating to the reduction of alien trees in compliance with the Conservation of Agricultural Resources Act 43 of 1983 and conservation of Helmeted Guineafowl.     

Direct comparison of four methods to construct xylem vulnerability curves: Differences among techniques are linked to vessel network characteristics

During periods of dehydration, water transport through xylem conduits can become blocked by embolism formation. Xylem embolism compromises water supply to leaves and may lead to losses in productivity or plant death. Vulnerability curves (VCs) characterize plant losses in conductivity as xylem pressures decrease. VCs are widely used to characterize and predict plant water use at different levels of water availability. Several methodologies for constructing VCs exist and sometimes produce different results for the same plant material. We directly compared four VC construction methods on stems of black cottonwood (Populus trichocarpa), a model tree species: dehydration, centrifuge, X‐ray–computed microtomography (microCT), and optical. MicroCT VC was the most resistant, dehydration and centrifuge VCs were intermediate, and optical VC was the most vulnerable. Differences among VCs were not associated with how cavitation was induced but were related to how losses in conductivity were evaluated: measured hydraulically (dehydration and centrifuge) versus evaluated from visual information (microCT and optical). Understanding how and why methods differ in estimating vulnerability to xylem embolism is important for advancing knowledge in plant ecophysiology, interpreting literature data, and using accurate VCs in water flux models for predicting plant responses to drought.     

Stable genetic transformation of white pine (Pinus strobus L.) after cocultivation of embryogenic tissues with Agrobacterium tumefaciens

A genetic transformation procedure for white pine has been developed after cocultivation of embryogenic tissues with Agrobacterium tumefaciens. This efficient transformation procedure led to an average of four independent transformed lines per gram of cocultivated embryogenic tissue and up to 50 transformed lines can be obtained in a routine experiment. Constructs bearing the uidA gene or the green fluorescent protein (GFP) gene were introduced and -glucuronidase (GUS) activity was followed over time. The expression of the uidA gene was lowest with a 35S-gus-intron construct and was 20-fold higher with a 35S-35S-AMVgus::nptII construct. The addition of scaffold attachment region (SAR) sequences surrounding the gus::nptII fusion did not significantly enhance the GUS activity. Transformed mature somatic embryos have been germinated and plantlets are presently being acclimatized.     

Quartet mapping and the extent of lateral transfer in bacterial genomes

Several recent analyses have used quartet-based methods to assess the congruence among phylogenies derived for large sets of genes from prokaryotic genomes. The principal conclusion from these studies is that lateral gene transfer (LGT) has blurred prokaryotic phylogenies to such a degree that the darwinian scheme of treelike evolution might be abandoned in favor of a net or web. Here, we focus on one of these methods, quartet mapping, and show that its application can lead to overestimation of the extent of inferred LGT in prokaryotes, particularly when applied to distantly related taxa.     

Temperature sensitivity of nitrogen productivity for Scots pine and Norway spruce

Environmental conditions control physiological processes in plants and thus their growth. The predicted global warming is expected to accelerate tree growth. However, the growth response is a complex function of several processes with both direct and indirect effects. To analyse this problem we have used needle nitrogen productivity, which is an aggregate parameter for production of new foliage. Data on needle dry matter, production, and nitrogen content in needles of Scots pine ( Pinus sylvestris) and Norway spruce ( Picea abies) from a wide range of climatic conditions were collected and needle nitrogen productivities, defined as dry matter production of needles per unit of nitrogen in the needle biomass, were calculated. Our results show that the nitrogen productivity for spruce is insensitive to temperature. However, for pine, temperature affects both the magnitude of nitrogen productivity at low needle biomass and the response to self-shading but the temperature response is small at the high end of needle biomass. For practical applications it may be sufficient to use a species-specific nitrogen productivity that is independent of temperature. Because temperature affects tree growth indirectly as well as through soil processes, the effects of temperature change on tree growth and ecosystem carbon storage should mainly be derived from effects on nitrogen availability through changes in nitrogen mineralization. In addition, this paper summarises data on dry matter, production and nitrogen content of needles of conifers along a temperature gradient.