常用系统发育树构建算法和软件鸟瞰

系统发育树又称进化树、生命树等,在达尔文的"进化论"一书中首次出现,之后系统发育树的重构被广大生物学家所接受。该文阐述了构建系统发育树的基本流程,对目前用于构建系统发育树的四类算法(距离法、最大简约法、最大似然法和贝叶斯法)进行了详细地分析和比较,并介绍了一些常用系统发育树构建和分析软件(PHYLIP、MEGA、MrBayes)的特点。     

共同祖先原则和系统发育树的解读

系统发育树是基于共同祖先原则,用于描述生物传代谱系的常用表达方式.可以直观地表达分类群(物种或基因)之间的亲缘关系和进化方向,但这两方面在生物学研究和教学中却常常被误读.通过具体实例,阐释了如何应用共同祖先原则正确解读系统发育树的方法.     

一株野生细菌的16Sr DNA序列分析与系统发育树的构建

以野生细菌F0303的总DNA为模板,采用细菌16Sr DNA的通用引物,通过PCR的方法扩增到一条约1．5Kb的16SrDNA片段。连接到pGEM-T-easy克隆载体上,并用化学法转化E．coli DH5a。用EcoR I对5个随机挑取的转化子进行的酶切分析表明这5个转化子皆为阳性。DNA测序表明该PCR扩增到的16Sr DNA片段长为1475核苷酸。与GenBank上已提交的16Sr DNA进行的比对(BLAST)表明野生细菌F0303归属于沙雷氏属。由Vector NTI Suite 6软件构建的系统发育树表明与深红色沙雷氏细菌(Sematia rubidaea)亲源关系最近,在核苷酸水平有97．8％的相似性。     

系统发育树的构建方法北大核心CSCD

构建系统树是为了鉴定菌株的分类学地位,应该使用正确的方法构建。具体要求如下：1.将鉴定菌的16S rRNA序列递交GenBank,用Blast软件搜索相似的16S rRNA,然后一起构树。2.采用能反应分支长度的软件（如NJ法）,并用Boostrap值分析分支聚类的稳定性。     

系统发育树的构建方法北大核心CSCD

构建系统树是为了鉴定菌株的分类学地位,应该使用正确的方法构建。具体要求如下：1.将鉴定菌的16S rRNA序列递交GenBank,用Blast软件搜索相似的16S rRNA,然后一起构树。     

系统发育树的构建方法北大核心

构建系统树是为了鉴定菌株的分类学地位,应该使用正确的方法构建。具体要求如下： 1.将鉴定菌的16Sr RNA序列递交GenBank,用Blast软件搜索相似的16S rRNA,然后一起构树。 2．采用能反应分支长度的软件（如NJ法）,并用Boostrap值分析分支聚类的稳定性。     

系统发育树的构建方法

构建系统树是为了鉴定菌株的分类学地位,应该使用正确的方法构建。具体要求如下:1.将鉴定菌的16S rRNA序列递交GenBank,用Blast软件搜索相似的16S rRNA,然后一起构树。     

系统发育树的构建方法

构建系统树是为了鉴定菌株的分类学地位,应该使用正确的方法构建。具体要求如下:1.将鉴定菌的16S rRNA序列递交GenBank,用Blast软件搜索相似的16S rRNA,然后一起构树。     

系统发育树的构建方法

<正>构建系统树是为了鉴定菌株的分类学地位,应该使用正确的方法构建。具体要求如下:1.将鉴定菌的16S rRNA序列递交GenBank,用Blast软件搜索相似的16S rRNA,然后一起构树。2.采用能反应分支长度的软件(如NJ法),并用Boostrap值分析分支聚类的稳定性。3.用国际较为通用的一些建树方法,如Neighbour-Joining等,这样结果就更为可靠,更直观。4.请严格按照下列具体要求写作[参见:微生物学报,2004,44(2):143.]     

系统发育树的构建方法

构建系统树是为了鉴定菌株的分类学地位,应该使用正确的方法构建。具体要求如下:1.将鉴定菌的16S rRNA序列递交GenBank,用Blast软件搜索相似的16S rRNA,然后一起构树。2.采用能反应分支长度的软件(如NJ法),并用Boostrap值分析分支聚类的稳定性。3.用国际较为通用的一些建树方法,如Neighbour-Joining等,这样结果就更为可靠,更直观。     

基于k-mer组分信息的系统发生树构建方法

随着越来越多基因组的测序完成,基于全基因组的非比对的系统发生分析已成为研究热点。不同的生物物种或个体基因组之间的核酸组分不完全相同。遗传语言-DNA序列的信息很大程度上反映在其k—mer频数中。基于基因组序列k-mer频数的系统发生树则从新的角度为我们提供物种之间的亲缘关系。本文定义基于k-mer,频数的信息参数,并用它表征基因组序列,计算不同基因组之间信息参数的距离,用邻接法对84个病毒构建了系统发生树,发现构建的系统发生树很大程度上与已有的系统发生树相吻合。     

Characterization and phylogenetic analysis of the complete mitogenome of Allactaga sibirica (Rodentia: Dipodidae)

Allactaga sibirica (Dipodidae) is widely distributed in the northwestern arid regions of China. The complete mitochondrial genome (mitogenome) of A. sibirica was 16,685 bp in length; included 13 protein-coding genes, 2 ribosome genes, 22 tRNA genes, and one control region; and had a structure that was typical of vertebrates. The base composition and codon usage of the mitogenome are described, and the structure of the non-coding sequence in the A. sibirica is reported for the first time. The putative origin of replication for the light strand of A. sibirica was approximately 45 bp long, and was highly conserved in the stem-loop and adjacent sequences. Phylogenetic analyses showed high resolution in each of the main divergent clades within Dipodoidea using mitogenomes data. The results indicated that the Zapodidae group was a representative of very basal taxon in Dipodoidea, and shared a common ancestor with Dipodidae species. Within Dipodidae clade, Allactaginae species was at basal position, and this result was in line with previous molecular systematic and morphological studies. Furthermore, Euchoreutes naso and A. sibirica had a close relationship could implicate a sister-group relationship between Euchoreutinae and Allactaginae. Meanwhile, this work also provided a set of useful data on phylogeny and molecular evolution in Dipodidae species.     

A standard operating procedure for phylogenetic inference (SOPPI) using (rRNA) marker genes

Phylogenetic analysis is currently used worldwide for taxonomic classification and identification of microorganisms. However, despite the countless trees that have been reconstructed and published in recent decades, so far, no user-friendly compilation of recommendations to standardize the data analysis and tree reconstruction process has been published. Consequently, this standard operating procedure for phylogenetic inference (SOPPI) offers a helping hand for working through the process from sampling in the field to phylogenetic tree reconstruction and publication. It is not meant to be authoritative or comprehensive, but should help to make phylogenetic inference and diversity analysis more reliable and comparable between different laboratories. It is mainly focused on using the ribosomal RNA as a universal phylogenetic marker, but the principles and recommendations can be applied to any valid marker gene. Feedback and suggestions from the scientific community are welcome in order to improve these guidelines further. Any updates will be made available on the SILVA webpage at http://www.arb-silva.de/projects/soppi.     

Orthonormal transform to decompose the variance of a life-history trait across a phylogenetic tree

In recent years, there has been an increased interest in studying the variability of a quantitative life-history trait across a set of species sharing a common phylogeny. However, such studies have suffered from an insufficient development of statistical methods aimed at decomposing the trait variance with respect to the topological structure of the tree. Here we propose a new and generic approach that expresses the topological properties of the phylogenetic tree via an orthonormal basis, which is further used to decompose the trait variance. Such a decomposition provides a structure function, referred to as an "orthogram," which is relevant to characterize in both graphical and statistical aspects the dependence of trait values on the topology of the tree ("phylogenetic dependence"). We also propose four complementary test statistics to be computed from orthogram values that help to diagnose both the intensity and the nature of phylogenetic dependence. The relevance of the method is illustrated by the analysis of three phylogenetic data sets, drawn from the literature and typifying contrasted levels and aspects of phylogenetic dependence. Freely available routines which have been programmed in the R framework are also proposed.     

Differential homogenization and amplification of two satellite DNAs in the genus Cucurbita (Cucurbitaceae)

Two different satellite DNAs exist in the genus Cucurbita which are different with respect to repeat length (350 by and 170 bp), array size, and sequence homogenization. Whereas the 350-bp satellite DNA is prominent and very homogeneous in all species investigated except for C. maxima and C. lundelliana, the 170-bp satellite is rather evenly distributed in all species. In C. maxima and C. lundelliana the 350-bp satellite is present only in small amounts, but detectable by the sensitive PCR method. These repeats are also very homogeneous, reflecting a silent stage of satellite DNA. In contrast, the 170-bp satellite DNA is intra- and interspecifically heterogeneous. It is striking that the species with no detectable amount of 350-bp satellite contain 170-bp satellite DNA clusters with the highest degree of homogeneity. The evolution of satellite DNA repeats within cultivated and wild species in the genus Cucurbita is elucidated using the sequence data of both satellite DNAs from all species investigated. The value of satellite DNA for phylogenetic analysis between closely related species is discussed. Correspondence to: V. Hemleben     

Diaulota koreana,new species on Korean coasts with a discussion of its phylogenetic relationships (Coleoptera: Staphylinidae: Aleocharinae)

Diaulota koreana Yoo and Ahn new species is described in the intertidal zones of the southern part of the Korean peninsula and illustrations of diagnostic characters are presented. A cladistic analysis of the Liparocephalini based on 50 adult characters suggests that the new species belongs to the genus Diaulota Casey within the Liparocephalini. Similarities and differences among the liparocephaline genera are presented. Phylogenetic relationships of Diaulota koreana Yoo and Ahn new species among the Liparocephalini are briefly discussed.     

Systematics of Cafius corallicola (Fairmaire) (Coleoptera: Staphylinidae) with a discussion of its phylogenetic relationships

A systematic review of the marine littoral Cafius corallicola (Fairmaire), widely distributed along the coasts from the Indian Ocean to the western Atlantic Ocean through the southern Pacific Ocean, is presented based on morphological and molecular characters (COI and 28S). Specimens of the two species [C. corallicola and C. caribeanus Bierig] are extremely similar to each other including the form of the aedeagus. The molecular analyses support the validity of C. corallicola with one synonymy based on morphological characters. Genetic divergence of COI using uncorrected p-distance among these two species ranged from 0.35% to 4.49%. Cafius caribeanus Bierig syn. nov. is synonymized under C. corallicola. Phylogenetic relationships of C. corallicola with similar congeners are resolved as (C. corallicola (C. rufescens (C. filum + C. sericeus))). Cafius corallicola is redescribed with illustrations of diagnostic characters.     

Using a mega-phylogeny of seed plants to test for non-random patterns of areal-types across the Chinese tree of life

The species composition of plant assemblages can in large part be explained by a long history of biogeographic and evolutionary events. Over the past decade, botanists and plant ecologists have increasingly sought to quantify phylogenetic signal in ecological traits to help inform their inferences regarding the mechanisms driving plant assemblages. However, most studies with a test of phylogenetic signal in the ecological traits have focused on a local scale, while comparatively few studies have been carried out on a regional scale. In this study, I presented a family-level phylogeny and a genus-level phylogeny that included all families and genera of extant seed plants in China, and use both phylogenies to examine whether areal-types or distribution patterns of families and genera of seed plants are non-randomly distributed across the Chinese tree of life. My study shows that the areal-types of families and genera of seed plants exhibit significant phylogenetic signal across the family- or genus-level phylogeny of seed plants in China.