Mitochondrial DNA sequences of primates: tempo and mode of evolution

Summary We cloned and sequenced a segment of mitochondrial DNA from human, chimpanzee, gorilla, orangutan, and gibbon. This segment is 896 bp in length, contains the genes for three transfer RNAs and parts of two proteins, and is homologous in all 5 primates. The 5 sequences differ from one another by base substitutions at 283 positions and by a deletion of one base pair. The sequence differences range from 9 to 19% among species, in agreement with estimates from cleavage map comparisons, thus confirming that the rate of mtDNA evolution in primates is 5 to 10 times higher than in nuclear DNA. The most striking new finding to emerge from these comparisons is that transitions greatly outnumber transversions. Ninety-two percent of the differences among the most closely related species (human, chimpanzee, and gorilla) are transitions. For pairs of species with longer divergence times, the observed percentage of transitions falls until, in the case of comparisons between primates and non-primates, it reaches a value of 45. The time dependence is probably due to obliteration of the record of transitions by multiple substitutions at the same nucleotide site. This finding illustrates the importance of choosing closely related species for analysis of the evolutionary process. The remarkable bias toward transitions in mtDNA evolution necessitates the revision of equations that correct for multiple substitutions at the same site. With revised equations, we calculated the incidence of silent and replacement substitutions in the two protein-coding genes. The silent substitution rate is 4 to 6 times higher than the replacement rate, indicating strong functional constraints at replacement sites. Moreover, the silent rate for these two genes is about 10% per million years, a value 10 times higher than the silent rate for the nuclear genes studied so far. In addition, the mean substitution rate in the three mitochondrial tRNA genes is at least 100 times higher than in nuclear tRNA genes. Finally, genealogical analysis of the sequence differences supports the view that the human lineage branched off only slightly before the gorilla and chimpanzee lineages diverged and strengthens the hypothesis that humans are more related to gorillas and chimpanzees than is the orangutan.Abbreviations mtDNA mitochondrial DNA - bp base pair - URF unidentified reading frame  

Ripley's K(d)函数分析种群空间分布格局的边缘校正

Ripley’sK(d)函数是分析种群空间分布格局最常用的方法，边缘校正是此方法的关键问题。传统的边缘校正包括3种情形：(i)圆完全包含在样地内；(ii)圆与样地的一条边相交；(iii)圆与样地的两条边相交，并有2个或3个交点。实际上，还存在第(iv)种情形，即圆与样地两条边相交有4个交点的情形。本文从数学上证明，传统边缘校正中，当边缘校正属于第(iv)种情形时，仍按第(iii)种情形进行校正，必然导致权重估计偏大，L(d)值偏高，从而影响结果分析。采用我国东北长白山天然云冷杉林样地资料验证了此结论。结果表明，天然云冷杉林中，3个优势种群林木分布格局特点是：鱼鳞云杉和臭冷杉的分布格局曲线非常相近，而与椴木的差异较大。原因是鱼鳞云杉和臭冷杉具有相似的生态学特性。椴木在小尺度显著聚集，因为椴木常在林隙更新。相比较而言，建群种云冷杉分布的均匀程度要比椴木高。  

表观反射率及其在植被遥感中的应用

 由于植被遥感应用定量化和监测等的需求，光学遥感数据的辐射校正更加受到重视。该文论述了辐射校正，辐射定标和大气校正的概念以及它们之间的区别及关系。特别对辐射定标的结果之一，大气层顶表观反射率，简称表观反射率(Apparent reflectance)的定义、概念、计算和它在植被遥感中的应用等方面，进行了详细的论述。  

A new revision of the sequence of plasmid pBR322

A revised sequence in the region immediately upstream from the rop gene of pBR322 is reported. Two base pairs in the accepted sequence do not exist in the plasmid DNA. Specifically, a TA base pair is missing at sequence coordinate 1893 [Sutcliffe, Cold Spring Harbor Symp. Quant. Biol. 43 (1979) 77–90] and an AT base pair is missing at position 1915, giving a total size for pBR322 of 4361 bp. These changes are in a potential translation initiation sequence and probably reflect errors in the original sequence rather than recent evolution of the plasmid.  

Physiological variation in metabolic phenotyping and functional genomic studies: use of orthogonal signal correction and PLS-DA

Metabolic phenotyping, or metabotyping, is increasingly being used as a probe in functional genomics studies. However, such profiling is subject to intrinsic physiological variation found in all animal populations. Using a nuclear magnetic resonance-based metabonomic approach, we show that diurnal variations in metabolism can obscure the interpretation of strain-related metabolic differences in two phenotypically normal mouse strains (C57BL10J and Alpk:ApfCD). To overcome this problem, diurnal-related metabolic variation was removed from these spectral data by application of orthogonal signal correction (OSC), a data filtering method. Interpretation of the removed orthogonal variation indicated that diurnal-related variation had been removed and that the AM samples contained higher levels of creatine, hippurate, trimethylamine, succinate, citrate and 2-oxo-glutarate and lower levels of taurine, trimethylamine-N-oxide, spermine and 3-hydroxy-iso-valerate relative to the PM samples. We propose OSC will have great potential removing confounding variation obscuring subtle changes in metabolism in functional genomic studies and will be of benefit to optimising interpretation of proteomic and genomic datasets.  

近视眼激光角膜切除术原理及控制方法

本文从理论上研究了激光人眼角膜切除术的原理和控制方法。详细分析了角膜前表面的曲率半径对近发消融深度和治疗结果的影响。  

生态系统服务价值的生态区位修正方法——以北京市为例

生态系统服务价值评估是当前生态经济学和环境经济学的研究热点和焦点，生态区位是影响生态系统服务价值的重要因子。以北京市为例，对北京市进行生态区位的划分，遵循资源稀缺性原理，将不同生态区位赋予不同的生态区位系数，并以北京市1980年、1995年和2000年土地利用图为例，以生态区位系数对北京市用地类型的生态服务价值进行修正，以体现不同生态区位单位面积生态系统服务价值的不同。研究得到了北京市3期土地利用单位面积生态系统服务价值分布图。分析发现:北京市的生态系统服务价值组成中，水田、有林地、灌木林和水体的生态系统服务价值占的比重较高；各生态区位生态系统服务总价值从城区到近郊平原区到近郊半山区到远郊山区依次增加;从1980年到1995年，北京市的生态系统服务价值减少了1.21×107元，而且各生态区位的生态系统服务价值也大都减少；从1995年到2000年，北京市的生态系统服务价值有所提高，但与1980年相比还是减少了3.07×106元。  

Statistical strategies for avoiding false discoveries in metabolomics and related experiments

Many metabolomics, and other high-content or high-throughput, experiments are set up such that the primary aim is the discovery of biomarker metabolites that can discriminate, with a certain level of certainty, between nominally matched ‘case’ and ‘control’ samples. However, it is unfortunately very easy to find markers that are apparently persuasive but that are in fact entirely spurious, and there are well-known examples in the proteomics literature. The main types of danger are not entirely independent of each other, but include bias, inadequate sample size (especially relative to the number of metabolite variables and to the required statistical power to prove that a biomarker is discriminant), excessive false discovery rate due to multiple hypothesis testing, inappropriate choice of particular numerical methods, and overfitting (generally caused by the failure to perform adequate validation and cross-validation). Many studies fail to take these into account, and thereby fail to discover anything of true significance (despite their claims). We summarise these problems, and provide pointers to a substantial existing literature that should assist in the improved design and evaluation of metabolomics experiments, thereby allowing robust scientific conclusions to be drawn from the available data. We provide a list of some of the simpler checks that might improve one’s confidence that a candidate biomarker is not simply a statistical artefact, and suggest a series of preferred tests and visualisation tools that can assist readers and authors in assessing papers. These tools can be applied to individual metabolites by using multiple univariate tests performed in parallel across all metabolite peaks. They may also be applied to the validation of multivariate models. We stress in particular that classical p-values such as “p < 0.05”, that are often used in biomedicine, are far too optimistic when multiple tests are done simultaneously (as in metabolomics). Ultimately it is desirable that all data and metadata are available electronically, as this allows the entire community to assess conclusions drawn from them. These analyses apply to all high-dimensional ‘omics’ datasets.  

Quantifying phylogenetically structured environmental variation

Comparative analysis methods control for the variation linked to phylogeny before attempting to correlate the remaining variation of a trait to present-day conditions (i.e., ecology and/or environment). A portion of the phylogenetic variation of the trait may be related to ecology, however; this portion is called "phylogenetic niche conservatism." We propose a method of variation partitioning that allows users to quantify this portion of the variation, called the "phylogenetically structured environmental variation." The new method is applied to published data to study, in a phylogenetic framework, the link between body mass and population density in 79 species of mammals. The results suggest that an important part of the variation of mammal body mass is related to the common influence of phylogeny and population density.