贝叶斯推论及其在百合目分子系统学中的应用

贝叶斯推论作为进化生物学的最新进展,在适用复杂模型、大型数据集、计算速度和结果容易解释等方面明显优于其它算法。本文简要介绍了贝叶斯推论原理及其在分子进化和系统发育研究中的重要性,并使用该方法对百合目主要类群的系统发育关系进行了重建。结果显示,百合目rbcL基因最适合的DNA进化模型为GTR I G,贝叶斯法与距离法和最大简约法构建的系统发育树拓扑结构相似,没有显著差异,但是分辨率和支持率明显比后者高。贝叶斯分析结果显示,百合目内划分的7个科,除Smilacaceae科外,其余各科均为高后验概率(PP=1·0)支持的单系类群;文中作者还对各科间的系统关系进行了探讨。     

高危型人乳头瘤病毒基因多态性研究进展

高危型人乳头瘤病毒已被证实是宫颈癌发生发展的必要因素,但不同型别的流行特征存在广泛的区域差异性,且即使是同一型别,其基因组同样存在基因多态性.这些基因多态性可能导致蛋白质功能的差异,进而造成病毒生存能力,致病能力以及与宿主细胞相互作用的差异.现已有大量研究表明HPV16和HPV18型基因多态性在病毒的生物学功能和导致临床疾病进展具有重要意义,因此更多的相关研究围绕着HPV高危型中不同型别的基因多态性相继开展,本文对高危型人乳头瘤病毒HPV16,HPV18,HPV58,HPV52,HPV31和HPV33型的基因多态性研究现状加以综述.     

HPV16型基因变异与宫颈癌发生相关性的研究进展

宫颈癌是女性常见肿瘤之一,严重影响女性健康.研究发现,高危型人乳头瘤病毒感染是宫颈癌发生的重要因素之一.HPV16型是最为常见的一种高危型人乳头瘤病毒,其基因组变异可能具有更大的致癌潜能.本文主要针对HPV16基因型各个区域常见的突变位点与宫颈癌的关系做一总结叙述.     

人乳头瘤病毒核酸检测技术进展及其应用

当今,随着分子学生物技术的不断发展,人们用于人乳头瘤病毒检测的手段也越来越多,其中核酸检测主要包括第2代杂交捕获、聚合酶链反应、原位杂交、Southern杂交和斑点杂交等方法.临床应用的有第2代杂交捕获和荧光定量聚合酶链反应.第2代杂交捕获法为一种半定量方法,是目前美国食品与药物管理局唯一批准能够在临床使用的人乳头瘤病毒DNA检测技术.该法具检测效能高,并可对人乳头瘤病毒进行高危型和低危型分析,为临床人乳头瘤病毒(特别是高危型人乳头瘤病毒)感染的早期诊断和监测提供了新的手段.     

一起荷斯坦奶牛乳头瘤病诊断及其病毒基因型分析

牛乳头瘤病毒是一种能够引起牛发生皮肤乳头状瘤、纤维素瘤、膀胱和食道癌的DNA病毒,现已在牛群中广泛传播,对牛养殖业造成了重大经济损失.为了诊断甘肃某荷斯坦奶牛场300多头泌乳期奶牛乳头突发疣状物的病因,本研究采用流行病学调查、临床观察、组织病理学、分子生物学检测方法和基因测序技术,对患有疣状物的奶牛进行综合诊断.结果 表明,乳头患疣状物奶牛的其它部位无类似生长物,无发烧、疼痛等异常临床症状,组织病理学HE检测疣状物呈现角化过度和细胞空泡化现象,这与牛乳头瘤病毒感染的组织病理变化相似,并且用PCR方法获得了牛乳头状瘤病毒L1基因,测序比对结果显示为乳头瘤病毒7型基因,核苷酸同源性达98％以上.因此,本次荷斯坦奶牛乳头突发疣状物为乳头瘤病毒7型感染引起的,这是甘肃地区首次发现该基因型乳头瘤病毒,应引起奶牛场与防疫部门的重视.     

牛乳头瘤病毒基因2型新疆南疆Aks-01流行株全基因组序列测定及其特征分析

为从分子水平了解牛乳头瘤病毒(Bovine papillomavirus,BPV)新疆南疆Aks-01株全基因组序列、结构特征及遗传变异情况。本研究选取新疆南疆患病牛皮肤肿瘤样物,以乳头瘤病毒L1基因的简并引物FAP59/FAP64进行PCR法基因分型鉴定并确定其基因型,根据GenBank中BPV参考株设计扩增引物和测序引物,对Aks-01株进行全基因组扩增、测序及序列分析。序列分析表明,新疆南疆Aks-01株为BPV-2基因型,其全基因组长为7944bp,具有BPV-2基因型的结构特征,与GenBank收录的BPV-2基因型参考株核苷酸比较,同源性高达98%。与BPV-1、BPV-13的基因型参考株进化关系最近,同属Delta属。该Aks-01株为新疆南疆地区首次检测确认并测定全基因组序列的牛乳头瘤病毒。     

《柳叶刀-肿瘤学》：高危HPV DNA检测可初筛宫颈癌

高危型人乳头瘤病毒（HPV）DNA检测可作为宫颈癌初筛方法,用于中国及其他发展中国家宫颈癌的二级预防。这一结论来自题为《高危型人乳头瘤病毒DNA检测作为宫颈癌初筛方法的有效性研究——中国以人群为基础的17个筛查研究综合分析》的论文。     

人乳头瘤病毒与宫颈癌前病变的相关性研究

目的：探讨人乳头瘤病毒感染与宫颈癌前病变两者之间的相关性。方法：选择2009年11月～2011年12月来我院就诊的220例宫颈病变患者为研究对象,将患者分成4组,即炎症组、CINl组、CIN2组和CIN3组,各组进行人乳头瘤病毒检出率及病毒载量的比较。结果：炎症组、CINl、CIN2和CIN34组人乳头瘤病毒的检出率分别为67．2％、80％、87．3％和91．4％且4组之间比较差异有显著统计学意义（P〈O．001）。炎症组HPV感染的阳性率与CIN组比较显著降低（P〈0．005）,宫颈癌前病变各组HPV感染呈阳性的病毒载量差异有统计学意义（P〈0．05）。结论：宫颈癌前病变的严重程度和感染高危型HPV病毒载量呈正相关,随着感染高危型HPV病毒载量越高,宫颈癌前病变的程度越严重。     

乳头瘤病毒E2蛋白的分子生物学研究进展

乳头瘤病毒Ｅ２蛋白是一种多功能蛋白,在乳头瘤病毒的生活史中处于核心的枢纽地位。Ｅ２蛋白可在ＤＮＡ复制水平,ＲＮＡ转录水平上对基因表达进行调控,Ｅ２蛋白可启动,凶制乳头瘤病毒早期启动子的表达。研究Ｅ２蛋白的功能有助于揭开乳头瘤病毒的生活史及其致病的分子机理。     

人乳头瘤病毒16型和11型L1基因双价重组杆状病毒转移质粒的构建及鉴定

目的：构建人乳头瘤病毒16型与11型L1基因双价重组杆状病毒转移质粒并对其进行鉴定。方法：采用：PCR法从尖锐湿疣组织标本中扩增人乳头瘤病毒11型晚期基因L1,并对其进行克隆测序;利用基因重组技术将人乳头瘤病毒16型和11型L1晚期基因共同装入杆状病毒转移载体中,分别位于强启动子Ppolh和弱启动子P10之下;利用酶切和PCR技术对双价重组杆状病毒转移质粒进行鉴定。结果：PCR扩增法获得尖税湿疣组织中感染的人乳头瘤病毒11型的L1基因,得到人乳头瘤病毒16型L1和11型L1基因双价重组杆状病毒转移质粒,经酶切电泳鉴定验证重组成功。结论：本研究成功构建了双价重组杆状病毒转移质粒,为进一步构建双价L1蛋白表达系统进而建立双价基因工程亚单位疫苗打下基础。     

最大似然法和贝叶斯推论与似然比检验探讨泽泻目系统发育关系

应用最大似然法(ML)、贝叶斯推论(BI)、邻接法(NJ)和似然比检验(hLRTs)进行泽泻目分子系统学研究。所用的rbcL基因序列代表了泽泻目14科46属以及作为外类群的6相关属。研究结果表明,*等级制似然比检验表明泽泻目rbcL序列最适合的DNA进化模型为GTR+I+G,最大似然法、贝叶斯法和邻接法构建的系统发育树拓扑结构相似,没有显著的差异,但贝叶斯树支持率较高;泽泻目为一单系类群,由两个主要谱系分支构成,深层分布格局由5个主要分支构成。基于分子系统发育树,文中对泽泻目科间、水鳖科+茨藻科、泽泻科+花蔺科+黄花蔺科、和"Cymodoeaceae complex"的系统发育关系进行了讨论。研究结果还表明,泽泻目系统发育关系可能还需要更多的证据进一步的澄清。     

以雾灵山夜蛾科为材料评估进化模型对DNA条码分类的影响

为了探究进化模型对DNA条形码分类的影响, 本研究以雾灵山夜蛾科44个种的标本为材料, 获得COI基因序列。使用邻接法（neighbor-joining）、 最大简约法（maximum parsimony）、 最大似然法（maximum likelihood）以及贝叶斯法（Bayesian inference）构建系统发育树, 并且对邻接法的12种模型、 最大似然法的7种模型、 贝叶斯法的2种模型进行模型成功率的评估。结果表明, 邻接法的12种模型成功率相差不大, 较稳定; 最大似然法及贝叶斯法的不同模型成功率存在明显差异, 不稳定; 最大简约法不基于模型, 成功率比较稳定。邻接法及最大似然法共有6种相同的模型, 这6种模型在不同的方法中成功率存在差异。此外, 分子数据中存在单个物种仅有一条序列的情况, 显著降低了模型成功率, 表明在DNA条形码研究中, 每个物种需要有多个样本。     

Genomic diversity and evolution of papillomaviruses in rhesus monkeys.

We are studying the diversity of and relationships among papillomaviruses (PVs) to understand the modes and timescales of PV evolution and in the hope of finding animal PVs that may serve as model systems for disease caused by human PVs (HPVs). Toward this goal, we have examined 326 genital samples from rhesus monkeys and long-tailed macaques with a PCR protocol optimized for detecting genital HPV types. In 28 of the rhesus monkey samples, we found amplicons derived from 12 different and novel PV genomes, RhPV-a to RhPV-m, with the likely taxonomic status of "type." The frequency with which novel RhPVs were detected suggests that rhesus monkeys may play host to PVs with a diversity similar to that of humans. In phylogenetic trees, all 12 of the different RhPVs and the previously described type RhPV-1 were members of the genital HPV supergroup and formed three minor branches distinct from the 11 branches formed by genital HPVs. We also identified a novel PV amplicon, MfPV-a, from a long-tailed macaque, a species belonging to the same genus as rhesus monkeys. MfPV-a turned out to be a close relative of five RhPVs. It appears that the evolution of primate lineages leading to the genus Macaca and to humans created transmission barriers for PVs, resulting in viral evolution closely linked to the host. Additional support for the linked-evolution hypothesis comes from considering the phylogenetic association of two other ape and monkey PVs with the genital HPVs, the supergroup formed by at least seven ungulate PVs, and the isolated phylogenetic position of the only known bird PV.     

The phylogeny of Iberian Aphodiini species (Coleoptera, Scarabaeoidea, Scarabaeidae, Aphodiinae) based on morphology

Abstract.  The phylogeny of Iberian Aphodiini species was reconstructed based on morphology. Wing venation, mouthparts, male and female genitalia, and external morphology provided ninety-four characters scored for ninety-three Aphodiini species. Phylogenetic analyses were based on maximum parsimony and Bayesian inference criteria. Maximum parsimony consensus trees recovered Acrossus species as a sister group of the remaining Aphodiini, followed by two other branches, one including Neagolius , Plagiogonus , Ahermodontus and Ammoecius species, and the other including Oxyomus , Nimbus , Heptaulacus and Euheptaulacus species. The remaining studied taxa clustered in an unresolved group. Bayesian inference trees recovered Acrossus as the sister group of the remaining Iberian Aphodiini, followed by Colobopterus erraticus and the rest of the Iberian Aphodiini, but this latter branch was unresolved. The general lack of statistical support for the inferred phylogenetic relationships at terminal nodes using both maximum parsimony and Bayesian inference suggests that variation in morphological characters useful for phylogenetic inference in the present study is small, perhaps as a consequence of a radiation event occurring at the origin of the tribe. A probable evolutionary pattern for Aphodiini is proposed which infers six groups, namely Acrossian, Ammoecian, Oxyomian, Aphodian s.str., Colobopteran and Aphodian s.l. clades.     

The accuracy of species tree estimation under simulation: a comparison of methods

Numerous simulation studies have investigated the accuracy of phylogenetic inference of gene trees under maximum parsimony, maximum likelihood, and Bayesian techniques. The relative accuracy of species tree inference methods under simulation has received less study. The number of analytical techniques available for inferring species trees is increasing rapidly, and in this paper, we compare the performance of several species tree inference techniques at estimating recent species divergences using computer simulation. Simulating gene trees within species trees of different shapes and with varying tree lengths (T) and population sizes (), and evolving sequences on those gene trees, allows us to determine how phylogenetic accuracy changes in relation to different levels of deep coalescence and phylogenetic signal. When the probability of discordance between the gene trees and the species tree is high (i.e., T is small and/or is large), Bayesian species tree inference using the multispecies coalescent (BEST) outperforms other methods. The performance of all methods improves as the total length of the species tree is increased, which reflects the combined benefits of decreasing the probability of discordance between species trees and gene trees and gaining more accurate estimates for gene trees. Decreasing the probability of deep coalescences by reducing also leads to accuracy gains for most methods. Increasing the number of loci from 10 to 100 improves accuracy under difficult demographic scenarios (i.e., coalescent units ≤ 4N(e)), but 10 loci are adequate for estimating the correct species tree in cases where deep coalescence is limited or absent. In general, the correlation between the phylogenetic accuracy and the posterior probability values obtained from BEST is high, although posterior probabilities are overestimated when the prior distribution for is misspecified.     

Comparison of Bayesian and maximum likelihood bootstrap measures of phylogenetic reliability

Owing to the exponential growth of genome databases, phylogenetic trees are now widely used to test a variety of evolutionary hypotheses. Nevertheless, computation time burden limits the application of methods such as maximum likelihood nonparametric bootstrap to assess reliability of evolutionary trees. As an alternative, the much faster Bayesian inference of phylogeny, which expresses branch support as posterior probabilities, has been introduced. However, marked discrepancies exist between nonparametric bootstrap proportions and Bayesian posterior probabilities, leading to difficulties in the interpretation of sometimes strongly conflicting results. As an attempt to reconcile these two indices of node reliability, we apply the nonparametric bootstrap resampling procedure to the Bayesian approach. The correlation between posterior probabilities, bootstrap maximum likelihood percentages, and bootstrapped posterior probabilities was studied for eight highly diverse empirical data sets and were also investigated using experimental simulation. Our results show that the relation between posterior probabilities and bootstrapped maximum likelihood percentages is highly variable but that very strong correlations always exist when Bayesian node support is estimated on bootstrapped character matrices. Moreover, simulations corroborate empirical observations in suggesting that, being more conservative, the bootstrap approach might be less prone to strongly supporting a false phylogenetic hypothesis. Thus, apparent conflicts in topology recovered by the Bayesian approach were reduced after bootstrapping. Both posterior probabilities and bootstrap supports are of great interest to phylogeny as potential upper and lower bounds of node reliability, but they are surely not interchangeable and cannot be directly compared.     

Molecular systematics of the Eastern Fence Lizard (Sceloporus undulatus): a comparison of Parsimony, Likelihood, and Bayesian approaches

Phylogenetic analysis of large datasets using complex nucleotide substitution models under a maximum likelihood framework can be computationally infeasible, especially when attempting to infer confidence values by way of nonparametric bootstrapping. Recent developments in phylogenetics suggest the computational burden can be reduced by using Bayesian methods of phylogenetic inference. However, few empirical phylogenetic studies exist that explore the efficiency of Bayesian analysis of large datasets. To this end, we conducted an extensive phylogenetic analysis of the wide-ranging and geographically variable Eastern Fence Lizard (Sceloporus undulatus). Maximum parsimony, maximum likelihood, and Bayesian phylogenetic analyses were performed on a combined mitochondrial DNA dataset (12S and 16S rRNA, ND1 protein-coding gene, and associated tRNA; 3,688 bp total) for 56 populations of S. undulatus (78 total terminals including other S. undulatus group species and outgroups). Maximum parsimony analysis resulted in numerous equally parsimonious trees (82,646 from equally weighted parsimony and 335 from weighted parsimony). The majority rule consensus tree derived from the Bayesian analysis was topologically identical to the single best phylogeny inferred from the maximum likelihood analysis, but required approximately 80% less computational time. The mtDNA data provide strong support for the monophyly of the S. undulatus group and the paraphyly of "S. undulatus" with respect to S. belli, S. cautus, and S. woodi. Parallel evolution of ecomorphs within "S. undulatus" has masked the actual number of species within this group. This evidence, along with convincing patterns of phylogeographic differentiation suggests "S. undulatus" represents at least four lineages that should be recognized as evolutionary species.     

<Emphasis Type="Italic">Protocruzia</Emphasis>, a highly ambiguous ciliate (Protozoa; Ciliophora): Very likely an ancestral form for Heterotrichea,Colpodea or Spirotrichea? With reevaluation of its evolutionary position based on multigene analyses

The ciliate genus Protocruzia belongs to one of the most ambiguous taxa considering its systematic position,possibly as a member of the classes Heterotrichea,Spirotrichea or Karyorelictea,which is tentatively placed into Spirotrichea in Lynn's 2008 system.To test these hypotheses,multigene trees(Bayesian inference,evolutionary distance,maximum parsimony,and maximum likelihood) were constructed using the small subunit rRNA(SSU rRNA) gene,internal transcribed spacer 2(ITS2) and a protein coding gene(histone H...     

利用DNA序列构建系统树的方法介绍

利用DNA序列进行系统发生分析是分子进化研究的必要手段。构建系统树的方法有距离法、简约法、最大似然法以及贝叶斯推断法等。要解决特定的系统发生问题,首先要挑选合理的分类群及序列,尽量减少数据的偏倚,然后选择构树方法,最后还要对结果进行评价并给出进化学上的解释。本文讨论了挑选数据的原则及存在的问题,介绍了几种构树方法的基本原理及步骤,并列举了它们的优缺点。Abstract: Construction of phylogenetic trees is a key means in molecular evolutionary studies. The methods of constructing phylogenetic trees include the distance-based methods, parsimony, maximum likelihood, and Bayesian inference methods. To resolve a special problem about phylogeny, several notices are necessary: first, to select the reasonable data at less bias as possible; second, to choose the proper method to reconstruct phylogenetic tree; third, to evaluate the conclusions and explain them on the field of evolution. The present paper provides a brief introduction of the principles of data selection and tree-construction methods, and discusses about their advantage and disadvantage points.