MATLAB 7.X 生物信息工具箱的应用-- 专用分析工具（ 六）*

序列分析可以获取蕴藏在简单序列中的生物信息,是生物信息分析的基础。通过生物大分子序列差异分析构建的系统树则可为我们提供可视化的物种间的进化关系。MATLAB7.X生物信息工具箱包含了几个图形用户界面设计的专用分析工具,这些专用分析工具交互性好,易于使用。借助于这些分析工具,用户不仅可以对基因序列进行分析查看并能进行相对应的氨基酸序列分析,还可以方便快捷地构建系统发育树。即使用户不会编程也可以进行序列分析和系统发育分析的研究,大大地提高了分析的效率。本文详细介绍了序列分析工具Seqtool和系统发育分析工具Phytreetool在序列分析及系统发育树构建方面的应用,所有操作方便快捷,分析结果可视化程度高。     

等位基因杂合子现象及其在系统发育学分析中的研究概述

系统发育研究已是澄清所有进化历史问题的必由之路。选择合适的分子标记以及最大限度地挖掘和利用其所包含的系统发育信息是构建可靠的系统发育树的关键。等位基因杂合子(Intra-individual allele heterozygotes, IIAHs)是核基因内含子作为系统发育研究中的分子标记时常常出现的现象。如何挖掘并利用其中所包含的系统发育信息成为近年来系统发育学的研究热点。文章从此现象的产生、杂合子的分离以及现有的研究方法3个方面详尽概述, 阐述了IIAHs及其在系统发育分析中的最新研究进展。     

线粒体nad1基因内含子在稻族系统学研究中的价值——兼论Porteresia的系统位置

在植物的系统与进化研究中,相对于叶绿体和核基因片段来说,线粒体基因片段由于其分辨率较低、结构复杂而较少应用到系统学研究中。本研究选用nad1基因的第2内含子序列探讨了稻族Oryzeae的系统发育关系,并着重分析了单型属Porteresia的系统学位置,并在此基础上探讨了nad1基因内含子序列的系统学意义以及空位性状在系统发育重建中的价值。本研究结果支持将稻族分为两个亚族（Oryzinae和Zizaniinae）的处理,稻族中假稻属Leersia与稻属Oryza最近缘,Porteresia coarctata不应该单独成属而应处理为稻属的成员。本研究表明,nad1第2内含子具有一定的系统发育信息,尤其是在较高分类等级的系统发育重建中具有较大价值;同时表明空位的合理利用将在已有序列信息基础上提供更多的系统发育信息。     

简单INDEL编码与其它空位编码方法的比较

不同的系统发育重建算法以不同的方式编码空位,但是不同的编码方式对系统发育分析结果的影响并不清楚.介绍了一种新的空位编码方式--简单indel编码,并将它与将空位编码成丢失的数据和编码成第5性状作了比较.统计分析表明,简单indel编码的确比将空位编码成丢失的数据更有效,但是与将空位编码成第5性状相比两者结果差异不大.而且,随着空位含量的降低,简单indel编码发挥的作用也减少.     

微生物系统发育多样性及其保护生物学意义

近年来,分子系统发育分析方法,特别是rBNA基因同源性分析方法,在微生物多样性的研究中发挥着越来越重要的作用．它克服了传统的微生物分离培养方法的限制,极大地促进了人们对微生物多样性的理解．在遗传信息同源性分析基础上得出的微生物系统发育多样性为多样性的保护提供了新的视点．它不但可以作为微生物多样性评价的手段,而且为多样性保护中优先秩序的确定提供了依据．同时也为生物多样性保护确定了目标,即最大程度地保护系统发育关系中所包含的信息．本文对微生物系统发育多样性的特点及其保护生物学意义进行了简要评述．     

小麦WOX转录因子基因的全基因组鉴定与分析

小麦是全球主要粮食作物之一.本研究运用生物信息学技术手段对普通小麦(Triticum aestivum L.)的WOX基因进行了全基因组鉴定、系统发育树构建、序列分析.结果显示:小麦基因组一共包含了26个WOX基因,其中在Phytozome数据库中收录有序列信息的有20个,可分为3个亚族,各亚族内的WOX基因具有相似的...     

番石榴实蝇和瓜实蝇的线粒体L-rRNA基因测序及双翅目昆虫L-rRNA基因的结构特征与系统发育关系分析

RNA二级结构比一级结构包含更多的信息, 在物种系统发育分析中更能反应真实情况。因而, 本研究对番石榴实蝇Bactrocera correcta和瓜实蝇B. cucurbitae的L-rRNA全基因进行了测序, 构建了双翅目L-rRNA基因二级结构的模式图, 并分析了其结构特征, 而后基于H45~H47茎环结构参数和结构序列及L-rRNA结构序列对双翅目13科的系统发育关系进行了初步分析。结果表明： 双翅目昆虫具有保守的L-rRNA二级结构; 不同结构区碱基组成和分布不均匀, Ⅳ区和Ⅴ区的完全保守碱基含量最高, GC含量最高, 绝大部分科Ⅵ区的AT斜率均小于0; 科内特有碱基和科间少数保守碱基大部分为G或C。瘿蚊科与双翅目其他科具有较远的系统发育关系, 而丽蝇科、 寄蝇科和食蚜蝇科有相近的系统发育关系; 虻科与网翅虻科同在一个小分支; 蠓科与蚊科同在一个大的系统发育分支。利用单方面参数不易得到理想的进化结果, 准确系统发育分析需要结合多方面的参数。     

系统发育分析中的最大简约法及其优化

随着生物技术的不断发展和系统发育学的深入研究, 在重构系统发育树时, 研究人员往往要面对更多的挑战和困难, 比如： (1)需要分析的样本数（物种数或个体数）不断增加; (2)需要分析的数据量迅速扩大。尤其在基因组测序技术的推动下, 基于分子信息的系统发育重建需要极大的计算量, 因此数学方法、 计算机技术以及其他辅助工具对于系统发育重建的效率和精确度起着至关重要的作用。最大简约法（maximum parsimony）是一种重要的系统发育重建方法, 提高其计算效率对系统发育学研究具有重要意义, 针对该算法的优化改进需要生物学家和计算机专家的共同努力。本文通过详细地阐述最大简约法的计算流程, 分析其参数选择对计算效率的影响, 帮助更多的计算机使用者, 在并不了解系统发育学基础的情况下, 更方便地针对实际的系统发育算法问题给出更好、 更快、 更精准的解决方案; 同时为系统发育研究工作者, 较为清晰地解释最大简约法的构树思想和计算逻辑, 推动针对最大简约法的不断改进与优化。     

植物系统发育区系地理学研究:以云南植物区系为例

传统植物区系地理学研究主要以植物区系的分类群组成及其分布区类型的分析为主,忽视了进化历史的分析。本文根据前期云南植物区系的分区研究,基于云南种子植物1,983个属的系统发育关系,结合其地理分布,从进化历史的角度分析不同地理单元的分类群组成、系统发育组成及其相似性,探讨各个地理单元的系统发育结构及地理单元间的系统发育相似性。结果表明:云南植物区系不同地理单元的系统发育多样性与科或属的丰富度显著相关,其系统发育结构为非随机型;不同地理单元间的系统发育组成相似性与分类群组成相似性显著相关,二者的聚类分析均表明具有热带植物区系性质的地理单元与具有温带植物区系性质的地理单元各自聚为一类。由此可见,融合进化历史信息的植物区系分析有助于更加深入地理解植物区系的性质和来源。     

核基因在两栖爬行动物分子系统学中的研究进展

从DNA水平探索生物进化的理论、生物类群的演化历史具有重要的意义,应用DNA序列研究生物的系统发育和进化规律成为当前分子系统学研究的热点,与线粒体DNA相比,核基因由于包含有更加丰富的生物学信息,运用核基因序列或将核基因序列与线粒体基因序列相结合研究两栖爬行动物的系统发育,正成为分子系统学领域的新的发展趋势.Rag-1、Rag-2、tyrosinase、rhodopsin、C-mos等核基因已在两栖爬行动物分子系统学中得到了广泛的应用.由于目前的技术手段等诸多因素,限制了更多的核基因用于两栖爬行动物分子系统学研究.为此简要介绍了目前核基因在两栖爬行动物分子系统学方面的研究进展,并分析了核基因序列在分子系统学应用上面临的问题和应用前景.     

The relative performance of indel-coding methods in simulations

We used simulations to compare the performance of 10 approaches that have been used for treating unambiguously aligned gaps in phylogenetic analyses. We examined how these approaches perform under the ideal conditions of correct alignments, as well as how robust they are to errors caused by use of inferred alignments. Our results indicate that 5th-state coding dramatically outperformed all other coding methods, which in turn all outperformed treating gaps as missing data or excluding gapped positions. Simple indel coding (SIC) and modified complex indel coding (MCIC) performed about the same, and generally outperformed the other indel-coding methods. The high performance of 5th-state coding was largely found to be a weighting artifact. We suggest that MCIC-coded gap characters be scored for all unambiguously aligned gaps in parsimony-based molecular phylogenetic analyses. When the number of terminals sampled precludes the use of MCIC, SIC may be used as an effective substitute.     

Recovering phylogenetic signal from frog mating calls

Goicoechea, N., De La Riva, I. & Padial, J. M. (2010). Recovering phylogenetic signal from frog mating calls. —Zoologica Scripta, 39, 411–154. Few studies have tried to analyse the phylogenetic information contained in frog mating calls. While some of those studies suggest that sexual selection deletes any phylogenetic signal, others indicate that frog calls do retain phylogenetic informative characters. Discordant results can be the outcome of disparate rates of character evolution and evolutionary plasticity of call characters in different groups of frogs, but also the result of applying different coding methods. No study to date has compared the relative performance of different coding methods in detecting phylogenetic signal in calls, hampering thus potential consilience between previous results. In this study, we analyse the strength of phylogenetic signal in 10 mating call characters of 11 related species of frogs belonging to three genera of Andean and Amazonian frogs (Anura: Terrarana: Strabomantidae). We use six quantitative characters (number of notes per call, note length, call length, number of pulses per note, fundamental frequency and dominant frequency) and four qualitative ones (presence/absence of: pseudopulses, frequency modulation in notes, amplitude modulation in notes and amplitude modulation in pulses). We code quantitative characters using four different coding and scaling methods: (i) gap‐coding, (ii) fixed‐scale, (iii) step‐matrix gap‐weighting with between‐characters scaling, and (iv) step‐matrix gap‐weighting with between‐states scaling. All four coding methods indicate that frog calls contain phylogenetic information. These results suggest that divergent selection on frog mating calls may not always be strong enough to eliminate phylogenetic signal. However, coding methods strongly affect the amount of recoverable information. Step‐matrix gap‐weighting with between‐characters scaling and gap‐coding are suggested as the best methods available for coding quantitative characters of frog calls. Also, our results indicate that the arbitrariness in selecting character states and the method for scaling transitions weights, rather than the number of character states, is what potentially biases phylogenetic analyses with quantitative characters.     

Coding of insertion-deletion events of the chloroplastic intergene atp beta-rbcL for the phylogeny of the Valerianeae tribe (Valerianaceae)

A preliminary analysis of the sequence alignment of the chloroplast intergene atp beta-rbcL in tribe Valerianeae reveals that insertion-deletion evolutionary events ('indels'), combined with nucleotide substitutions, have occurred in large zones in some of the studied taxa. Due to the frequent occurrence and large size of indels within this tribe, intergene length varies from 531 to 788 base pairs within the studied species. This situation poses gap coding problems that we had to tackle before phylogenetic analysis. Four methods of gap coding were used: elimination of gapped sites ('complete omission'), 'missing data', 'fifth base' and Barriel's coding method, which translates indels into new multistate characters in the data matrix. After application of these four methods of data treatment, phylogenetic analyses (maximum parsimony) did not lead to very different results. Three robust clades emerged in each case, corresponding to the Centranthinae subtribe (genus Centranthus), the Fediinae subtribe (genera Fedia and Valerianella), and the American species of Valeriana. The theoretical basis and biological significance of these four methods are discussed in order to apply the best ones in future studies.     

Uninode coding vs gene tree parsimony for phylogenetic reconstruction using duplicate genes

Two different methods of using paralogous genes for phylogenetic inference have been proposed: reconciled trees (or gene tree parsimony) and uninode coding. Gene tree parsimony suffers from 10 serious problems, including differential weighting of nucleotide and gap characters, undersampling which can be misinterpreted as synapomorphy, all of the characters not being allowed to interact, and conflict between gene trees being given equal weight, regardless of branch support. These problems are largely avoided by using uninode coding. The uninode coding method is elaborated to address multiple gene duplications within a single gene tree family and handle problems caused by lack of gene tree resolution. An example of vertebrate phylogeny inferred from nine genes is reanalyzed using uninode coding. We suggest that uninode coding be used instead of gene tree parsimony for phylogenetic inference from paralogous genes.     

Incorporating indels as phylogenetic characters: Impact for interfamilial relationships within Arctoidea (Mammalia: Carnivora)

Insertion and deletion events (indels) provide a suite of markers with enormous potential for molecular phylogenetics. Using many more indel characters than those in previous studies, we here for the first time address the impact of indel inclusion on the phylogenetic inferences of Arctoidea (Mammalia: Carnivora). Based on 6843 indel characters from 22 nuclear intron loci of 16 species of Arctoidea, our analyses demonstrate that when the indels were not taken into consideration, the monophyly of Ursidae and Pinnipedia tree and the monophyly of Pinnipedia and Musteloidea tree were both recovered, whereas inclusion of indels by using three different indel coding schemes give identical phylogenetic tree topologies supporting the monophyly of Ursidae and Pinnipedia. Our work brings new perspectives on the previously controversial placements among Arctoidea families, and provides another example demonstrating the importance of identifying and incorporating indels in the phylogenetic analyses of introns. In addition, comparison of indel incorporation methods revealed that the three indel coding methods are all advantageous over treating indels as missing data, given that incorporating indels produces consistent results across methods. This is the first report of the impact of different indel coding schemes on phylogenetic reconstruction at the family level in Carnivora, which indicates that indels should be taken into account in the future phylogenetic analyses.     

Relative benefits of amino‐acid,codon, degeneracy,DNA, and purine‐pyrimidine character coding for phylogenetic analyses of exons

Both traditional as well as 10 more recent methods of coding characters from exons of protein‐coding genes are reviewed. The more recent methods collectively blur the distinction between nucleotide and amino‐acid coding and enable investigators to carefully quantify the effects of different sources of phylogenetic signal as well as their potential biases. Codon models, which explicitly model silent and replacement substitutions, are a major advance and are expected to be broadly useful for simultaneously inferring recent and ancient divergences, unlike amino‐acid coding. Degeneracy coding, wherein ambiguity codes are used to eliminate silent substitutions at the individual‐nucleotide level, has clear advantages over scoring amino‐acid characters. Nucleotide, codon, and amino‐acid models are now directly comparable with easy‐to‐use programs, and widely used phylogenetics programs can analyze partitioned supermatrices that incorporate all three types of model. Therefore, it should become standard practice to test among these alternative model types before conducting parametric phylogenetic analyses. An earlier study of 78 protein‐coding genes from 360 green‐plant plastid genomes is used as an empirical example with which to quantify the relative performance of alternative character‐coding methods using five quantification measures. Codon models were selected as having the best fit to the data, yet were outperformed by nucleotide models for all five quantification measures. Third‐codon positions were found to be an important source of phylogenetic signal and even outperformed analyses of first and second positions for some measures. Degeneracy coding generally performed at least as well as amino‐acid coding and is an arguably more effective alternative.     

The Logical Basis for the use of Continuous Characters in Phylogenetic Systematics

It has been argued that continuous characteristics should be excluded from cladistic analysis for two reasons: because the data are considered inappropriate; and because the methods for the conversion of these data into codes are considered arbitrary. Metric data, however, fulfill the sole criterion for inclusion in phylogenetic analysis, the presence of homologous character states, and thus cannot be excluded as a class of data. The second line of reasoning, that coding methods are arbitrary, applies to gap and segment coding, but quantitative data can be coded in a nonarbitrary manner by means of tests of statistical significance. These procedures, which are both objective and repeatable, determine the probability that two taxa possess an homologous character state; that is, if they have inherited a particular central tendency and distribution of individual variates unchanged from a common ancestor. Thus, the application of statistical tests to quantitative data empirically detects the presence of evolu tionary change, the raw material of phylogenetic reconstruction.     

Problematic character coding methods in morphology and their effects

The effects of different coding practices in morphological phylogenetic analysis are well documented. In many cases, we can determine that certain practices can be regarded as undesirable and should be avoided. Certain coding practices do not correctly translate the expected information to the cladistic algorithm. It may go unnoticed that expressions of character information in character lists, which may be entirely logical to any reader, do not necessarily reflect the mathematics employed by a phylogenetic algorithm. Despite a wealth of literature on coding procedures and documentation of these issues, problematic character coding practices are still common. A review is provided of different coding and character formulation practices, particularly relating to multistate character information that may either: (1) lead to a failure to capture grouping information implied in the character list; (2) cause problematic weighting or spuriously high certainty in particular optimizations; and (3) impose congruence artificially, by linking more than one variable character to a particular state. Each of these is reviewed and presented with a hypothetical example. Recommendations for avoiding these pitfalls are described in light of how parsimony algorithms work with character data. Character lists must be drawn up not only to present character variation logically, but also with consideration for how computer algorithms implement cladistic logic. The widespread use of problematic character coding procedures may account for some of the perceived problems with morphological data. Therefore, an exploration of the effects of these methods and standardization of methods should be a goal for the very near future. © 2011 The Linnean Society of London, Biological Journal of the Linnean Society, 2011, 104 , 489–498.     

Are Third Positions Really That Bad? A Test Using Vertebrate Cytochrome b

In the analysis of coding DNA sequences for phylogenetic purposes 3rd positions are commonly downweighted, or excluded, and 2nd positions are likewise given high weight. The basis of this is a belief that the larger numbers of 3rd position substitutions imply a larger amount of misleading information than the slowly evolving 2nd positions. This paper tests this assertion by splitting 10 vertebrate data sets into three parts consisting of 1st, 2nd, and 3rd positions only. The relative performance of these data sets was tested by a number of suggested methods for assessing the phylogenetic content in a data set. Contrary to the prediction, the relative performance was 3rd > 1st > 2nd. This implies that a downweighting of 3rd positions in favour of 2nd positions is not supported by the analyses of their phylogenetic content. There are several reasons to believe that the overall amount of change is a poor predictor of the level of homoplasy and these are discussed. The overall conclusion is that unless there is solid evidence that 3rd positions really are misleading, they should not be treated so by default.