Tripartitions do not always discriminate phylogenetic networks

Phylogenetic networks are a generalization of phylogenetic trees that allow for the representation of non-treelike evolutionary events, like recombination, hybridization, or lateral gene transfer. In a recent series of papers devoted to the study of reconstructibility of phylogenetic networks, Moret, Nakhleh, Warnow and collaborators introduced the so-called tripartition metric for phylogenetic networks. In this paper we show that, in fact, this tripartition metric does not satisfy the separation axiom of distances (zero distance means isomorphism, or, in a more relaxed version, zero distance means indistinguishability in some specific sense) in any of the subclasses of phylogenetic networks where it is claimed to do so. We also present a subclass of phylogenetic networks whose members can be singled out by means of their sets of tripartitions (or even clusters), and hence where the latter can be used to define a meaningful metric.     

Effect of lethality on the extinction and on the error threshold of quasispecies

In this paper the effect of lethality on error threshold and extinction has been studied in a population of error-prone self-replicating molecules. For given lethality and a simple fitness landscape, three dynamic regimes can be obtained: quasispecies, error catastrophe, and extinction. Using a simple model in which molecules are classified as master, lethal and non-lethal mutants, it is possible to obtain the mutation rates of the transitions between the three regimes analytically. The numerical resolution of the extended model, in which molecules are classified depending on their Hamming distance to the master sequence, confirms the results obtained in the simple model and shows how an error catastrophe regime changes when lethality is taken in account.     

基于生态系统演变机理的生态系统脆弱性、适应性与突变理论

随着气候变化影响广度与深度的增加,生态系统脆弱性、适应性与突变理论逐渐被广泛应用到生态学研究领域中,探讨和评估各类生态系统对气候变化的敏感性、脆弱性和适应性,可谋求更好的方式来应对气候变化对区域生态系统带来的深远影响,服务于国家生态系统可持续管理及生态安全建设.虽然相关研究已获取许多进展,区分了气候敏感区和某些生态系统...     

南方红壤侵蚀区土壤肥力质量的突变——以福建省长汀县为例

以南方红壤侵蚀区典型区域福建省长汀县为研究区,将土壤肥力质量10个因子作为内部因子,坡度、植被覆盖度、水土流失强度等作为外部因子,构建土壤肥力质量演变的尖点突变模型,并分析土壤肥力质量演变分别与土壤肥力质量等级、水土流失强度、坡度和植被覆盖度的关系.研究结果表明:1)90个样点中,突变的样点共27个,占30％,稳定的样点共63个,占70％;2)突变样点主要对应于土壤肥力质量等级1和等级2(分别占突变样点总数的48.15％和33.33％)、水土流失微度和轻度(分别占37.04％和44.44％)、坡度5-10.和10-15.(分别占37.04％和40.74％)、植被覆盖度＞0.4和0.3-0.4(分别占48.15％和37.04％);分叉集△与土壤肥力质量等级、水土流失强度、坡度和植被覆盖度都呈极显著(P＜0.01)相关关系,皮尔逊相关系数绝对值的大小顺序为:水土流失强度＞植被覆盖度＞土壤肥力质量等级＞坡度;突变主要发生于土壤肥力质量等级较高、水土流失强度较轻、坡度中等、植被覆盖较好的地点;3)土壤肥力质量演变时间相对较长,应根据中间过渡状态来判断是否产生突变;土壤肥力质量处于突变状态时可用较小投入产生较大效益,在关注严重水土流失区生态恢复与重建的同时,不应忽视突变区的治理.     

Organic solvent tolerance and thermostability of a β-glucosidase co-engineered by random mutagenesis

Random mutagenesis was applied for development of organic solvent tolerant β-glucosidase I (BGLI) of Pichia etchellsii to extend its use for glyco-conjugate synthesis in non-aqueous medium. Previously cloned BGL1 encoding β-glucosidase I (BGLI) was subjected to error prone PCR and the mutant library was cloned in pPIC9 followed by transformation into Pichia pastoris. Transformants were first selected for functional β-glucosidase phenotype followed by screening for organic solvent tolerance in acetonitrile, dimethylformamide, dimethyl sulfoxide, methanol, 2-propanol. One of the enzyme variants, named, OT-BGLI exhibited 1.7- to 10-fold higher stability in 20–30% (v/v) methanol, 2-propanol, dimethylformamide compared to the wild type enzyme. This property was also accompanied by higher thermostability of the enzyme in aqueous buffer solution. Three of the six mutations (other 3 being silent) were mapped in the non-conserved regions of the gene. Modeled structure of the enzyme pin pointed increased hydrogen bonds, intra-ionic interactions (contributed by G414D and N789D replacements), facilitated proton exchange in organic solvents (contributed by Y722H) to be the causative agents for enhanced organic solvent stability and thermostability. Secondary structure of the mutant enzyme was similar to the wild type enzyme. Simultaneous enhanced organic solvent and thermal stability makes this enzyme an ideal candidate for glycoconjugate synthesis in aqueous-organic solvent systems.     

Statistical characteristics of the density-independent population fluctuation and the evaluation of density-dependence and regulation in animal populations

In this study it was proved that the “density-independent population” shows the following characteristics if the analysis is made using time-series samples:

1. The slope b in the density-on-density regression between successive developmental stages has a general tendency to become smaller than 1, though the bias approaches zero if one or more of the following three conditions are satisfied: (a) the data cover a large number of generations, (b) the variance of the rate of population change for the period concerned is small relative to that for the residual period in a whole generation, and (c) the population has a distinct trend to either increase or decrease over generations.
2. The variance for the generation-to-generation population fluctuation increases continually as the number of generations is increased, even if the population has no inherent trend to increase or decrease. For a fixed number of generations, however, the variance remains constant among different developmental stages.

On the basis of these theoretical results, a modified method for detecting density-dependence from time-series samples was presented, together with a new, tentative technique of variance analysis to evaluate the regulation of numbers directly. The results of applying these methods to some sets of data from both hypothetical and actual populations illustrated their validity for use in population studies.     

A practical guide to mitochondrial DNA error prevention in clinical, forensic, and population genetics

Several suggestions have been made for avoiding errors in mitochondrial DNA (mtDNA) sequencing and documentation. Unfortunately, the current clinical, forensic, and population genetic literature on mtDNA still delivers a large number of studies with flawed sequence data, which, in extreme cases, damage the whole message of a study. The phylogenetic approach has been shown to be useful for pinpointing most of the errors. However, many geneticists, especially in the forensic and medical fields, are not familiar with either effective search strategies or the evolutionary terminology. We here provide a manual that should help prevent errors at any stage by re-examining data fresh from the sequencer in the light of previously published data. A fictitious case study of a European mtDNA data set (albeit composed from the literature) then demonstrates the steps one has to go through in order to assess the quality of sequencing and documentation.     

An error catastrophe in cancer?

A comparison between the evolution of cancer cell populations and RNA viruses reveals a number of remarkable similarities. Both display high levels of plasticity and adaptability as a consequence of high degrees of genetic variation. It has been suggested that, as it occurs with RNA viruses, there is a threshold in the levels of genetic instability affordable by cancer cells in order to be able to overcome selection barriers (Trends Genet. 15 (1999) M57). Here we explore this concept by means of a simple mathematical model. It is shown that an error threshold exists in this model, which investigates both competition between cancer cell populations and its impact on overall tumor growth dynamics. Once the threshold is reached, the highly unstable tumor cell populations, which were sustaining malignant growth, become unable to maintain their genetic information, which in turn triggers a slowed down overall tumor growth regime.