叶绿体系统发育基因组学的研究进展

系统发育基因组学是由系统发育研究和基因组学相结合产生的一门崭新的交叉学科。近年来,在植物系统发育研究中,基于叶绿体基因组的系统发育基因组学研究优势渐显端倪,为一些分类困难类群的系统学问题提出了解决方案,但同时也存在某些问题。本文结合近年来叶绿体系统发育基因组学研究中的一些典型实例,讨论了叶绿体系统发育基因组学在植物系统关系重建中的价值和应用前景,并针对其存在问题进行了探讨,其中也涉及了新一代测序技术对叶绿体系统发育基因组学的影响。     

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。     

分子生物学技术在昆虫系统发育地理学研究中的应用

文章对分子生物学技术在系统发育地理学上的应用和研究进展进行综述。介绍mtDNA和ITS等使用最频繁的分子标记,其研究方法最好是测序加上RAPD,RFLP分析,同工酶电泳,SSCP和DSCP中的1种以上或几种方法的组合,数据分析最好是2种方法共同使用,从而确保结果的准确性。     

樟子松人工林一级枝条基径和枝长模型的研究

以东北林业大学帽儿山实验林场樟子松人工林为研究对象,采用枝解析的方法,于2002年、2003年测定了53株林木（年龄17～38a,直径8．61～21．5cm,树高7．48～18．24m）的树冠变量,建立了基于总着枝深度（DINC）和树冠内一级枝条基径（BD）、枝长（BL）的预估模型。对于大小相同树木的一级枝条,这些树冠变量随着DINC的增加而增大,而林木的胸径（DBH）、树高（HT）变量又很好地反映了不同大小树木的基径和枝长的变化。采用独立检验样本对构建的树冠内一级枝条基径和枝长模型进行了拟合统计量和精度检验,结果表明：模型预测效果良好,精度均达到95％以上。构建的一级枝条基径和枝长模型为进一步合理地描述樟子松人工林树冠的形状及其变化以及三维可视化经营提供依据。     

樟子松人工林一级枝条基径和枝长模型的研究

以东北林业大学帽儿山实验林场樟子松人工林为研究对象,采用枝解析的方法,于2002年、2003年测定了53株林木（年龄17~38 a,直径8.61~21.5 cm,树高7.48~18.24 m）的树冠变量,建立了基于总着枝深度（DINC）和树冠内一级枝条基径（BD）、枝长（BL）的预估模型。对于大小相同树木的一级枝条, 这些树冠变量随着DINC的增加而增大,而林木的胸径（DBH）、树高（HT）变量又很好地反映了不同大小树木的基径和枝长的变化。采用独立检验样本对构建的树冠内一级枝条基径和枝长模型进行了拟合统计量和精度检验,结果表明：模型预测效果良好,精度均达到95%以上。构建的一级枝条基径和枝长模型为进一步合理地描述樟子松人工林树冠的形状及其变化以及三维可视化经营提供依据。     

枝孢样枝孢霉的研究概况

引起暗色丝孢霉病的枝孢霉属,属半知菌亚门、丝孢菌纲、暗色孢科。该属50余种。枝孢样枝孢霉为腐生真菌,广泛存在于自然界的土壤、某些动物的粪便、蔬菜、腐木、鸟巢、腐烂水果中。人因皮肤外伤接触后有被感染的机会。它也是真菌过敏症的重要病原菌之一。目前对枝孢样枝孢霉的系统报道较少,现就其生理生化代谢、生态学、病理学及临床和抗真菌研究等方面进行综述。     

中国鸟类的DNA分类及系统发育研究概述

鸟类分类是鸟类学其他研究领域的基础,近年来分子技术的发展,以及计算机技术的应用为鸟类分类学和鸟类系统演化研究提供了新的研究手段,给传统的系统分类研究带来了新的机遇.Tautz等于2002年首先提出运用DNA序列作为生物分类系统的主要平台,即DNA分类学(DNA Taxonomy).而Hebert等于2003年则首次提出了DNA条形码(DNA Barcoding)的概念,并对其物种分类和鉴定意义予以肯定,建议利用线粒体细胞色素C氧化酶亚单位Ⅰ(COI)的特定区段来做DNA条形编码的基础.在鸟类DNA分类方面,国内学者应用线粒体基因Cut b,COI,c-mos,c-myc,12s rRNA,16s rRNA,ND2,ND3,CR,RAG-1以及核基因myoglobin introⅡ等不同片段对很多类群进行了分类探讨和系统发育研究.但是主要集中在鸡形目及雀形目鸟类.中国是鸟类多样性极其丰富的国家,近年来很多亚种、种及以上分类阶元依然存在问题,因此,中国鸟类物种的分类地位、系统发育与演化关系等依然有很多问题等待深入研究.目前国内基于COI的鸟类分类及系统发育研究有了一些报道,但是真正的DNA条形码工作尚需继续、深入地开展.     

食肉目猫科物种的系统发育学研究概述

猫科动物(Felidae)是食肉目中肉食性最强的一科, 其中许多成员是人们最熟悉、最引人注目的动物, 也是各地的顶级食肉动物。目前37个现存猫科物种中有36个已经被列为濒危和稀有对象。食肉目猫科物种的进化历史是一个快速辐射和较近时期发生的物种形成事件, 使得猫科物种之间系统发育关系的重建非常困难, 一直处于广泛争论的状态。构建可靠的猫科系统发育关系, 具有重要的进化理论意义和保护生物学价值。文章对猫科物种的系统发育学研究进展, 包括来自于形态学特征、细胞学和分子生物学方面的证据做简要概述, 并提出目前研究中存在的问题。以期对今后猫科物种的系统发育方面的进一步研究工作具有指导意义, 并为该类群的生物多样性资源保护提供科学依据。     

东洋区枝长跗摇蚊属一新组合种——细长枝长跗摇蚊(双翅目:摇蚊科)

Datta等于1992年依据印度标本建立1新种,命名为Tanytarsus gracilistylus （Chaudhuri ＆ Datta）,,本文作者在中国长跗摇蚊族研究中发现了采自福建省的同一种类,依据Ekrem（1999）和Cranstonetn,（1989）提出的属级鉴别特征,对该种性状进行比较分析,确认该种除中附器不分枝外,其余特征均符合枝长跗摇蚊属Cladotanytarsus的属征,而与长跗摇蚊属Tanytarsus的属征不符。该种中附器不具分枝应属于枝长跗摇蚊属内种间的一个特殊变异。本文将该种由长跗摇蚊属移入枝长跗摇蚊属作为新组合,同时依据中国标本对该种进行了详细描述,制作了本属中国13种雄成虫分种检索表。     

长枝木霉eg1基因的克隆及表达

从长枝木霉3.1029基因组中克隆了内切葡聚糖酶EGI基因,该基因全长1 566 bp,由3个外显子2个内含子组成,编码461个氨基酸,编码蛋白的N端为22aa组成的信号肽。采用重叠PCR法获得无内含子的内切葡聚糖酶基因eg1,构建成pYE-Leg1重组质粒;同时将其成熟肽编码序列插入酿酒酵母分泌型表达载体pYEα中,构建成pYEα-Leg1重组质粒;分别转化酿酒酵母。重组转化子经β-半乳糖诱导,检测表达产物的酶活,结果表明,pYE-Leg1转化子无明显胞外酶活;而pYEα-Leg1转化子在刚果红平板上可产生明显的水解圈,酶活检测显示pYEα载体可有效地将该基因在酿酒酵母中表达并分泌到胞外,发酵液中的酶活在培养96 h达到最高1.16 U/mL,最适酶解温度为50℃,最适pH值为5.6。以上研究将为利用酿酒酵母生产胞外纤维素酶提供依据。     

The Labeninae (Hymenoptera: Ichneumonidae): a study in phylogenetic reconstruction and evolutionary biology

The internal phylogenetic relationships of the ichneumonid subfamily Labeninae (Hymenoptera) are re‐assessed using 136 characters for 54 species representing all currently known species‐groups. New character sets are used. These include a new form of seta (named the grossulariform setae) which are present on the inner surface of the hind coxa of some females, and the extensive structural modifications of the terminal segments of the female metasoma, which are described and structural homologies established. The monophyly of the Labeninae and of the four component tribes, Groteini, Poecilocryptini, Xenothyrini and Labenini, is demonstrated. The Groteini is shown to be the sister‐group to the Poecilocryptini + (Xenothyrini + Labenini). Monophyletic genera are established, including three new genera: Ozlabium gen. nov. Gauld & Wahl (type‐species 0. arcadium sp. nov.) in the Groteini from Australia; Torquinsha gen. nov. Gauld & Wahl (type‐species Certonotus invictus Porter) in the Labenini from Chile, and Gauldianus gen. nov. Lanfranco (type‐species Gauldianus chilensis sp. nov. Lanfranco) in the Labenini from Chile. Apechoneura is removed from synonymy and re‐instated as a valid genus for a complex of tropical American species. The biogeographic patterns shown by the Labeninae are discussed. Evidence suggests that the group radiated on Gondwanaland after the separation of Africa/India/Madagascar, but prior to the separation of Australia. Species occurring off the southern continental fragments, in North America, are shown to be members of highly derived lineages, a result consistent with the hypothesis that labenines colonized North America recently through Mesoamerica. Patterns of host utilization and mating behaviour are examined for the group. Members of the more derived lineages show progressively more female specializations for attacking hosts deeply concealed in woody substrates. Males in the more specialized lineages are shown to have a wider array of secondary sexual characteristics and genitalic ornamentations than more plesiomorphic taxa.     

LZ complexity distance of DNA sequences and its application in phylogenetic tree reconstruction

DNA sequences can be treated as finite-length symbol strings over a four-letter alphabet （A, C, T, G）. As a universal and computable complexity measure, LZ complexity is valid to describe the complexity of DNA sequences. In this study, a concept of conditional LZ complexity between two sequences is proposed according to the principle of LZ complexity measure. An LZ complexity distance metric between two nonnull sequences is defined by utilizing conditional LZ complexity. Based on LZ complexity distance, a phylogenetic tree of 26 species of placental mammals （Eutheria） with three outgroup species was reconstructed from their complete mitochondrial genomes. On the debate that which two of the three main groups of placental mammals, namely Primates, Ferungulates, and Rodents, are more closely related, the phylogenetic tree reconstructed based on LZ complexity distance supports the suggestion that Primates and Ferungulates are more closely related.     

The use of colour characters in phylogenetic reconstruction

The use of coloration as a source of characters in phylogenetic reconstruction is investigated using 54 published data sets. Studies were divided into two categories based on a priori postulated roles of the coloration: (1) aposematic and mimetic coloration and (2) nonaposematic, nonmimetic coloration plus dual signals. Colour characters superficially appear to provide similar phylogenetic signal to morphological ones in the case of aposematic and mimetic coloration but significantly less in other situations. However, the data indicated that the apparent signal in the aposematic/mimetic studies tends to be in greater conflict with the morphological signal. It is proposed that this reflects constraints in the evolution of colour characters that are part of aposematic/mimetic patterns and not that they are necessarily good indicators of phylogeny.  © 2006 The Linnean Society of London, Biological Journal of the Linnean Society , 2006, 88 , 193–202.     

Comparing phylogenetic signal in intraspecific and interspecific body size datasets

Phylogenetic comparative methods have become a standard statistical approach for analysing interspecific data, under the assumption that traits of species are more similar than expected by chance (i.e. phylogenetic signal is present). Here I test for phylogenetic signal in intraspecific body size datasets to evaluate whether intraspecific datasets may require phylogenetic analysis. I also compare amounts of phylogenetic signal in intraspecific and interspecific body size datasets. Some intraspecific body size datasets contain significant phylogenetic signal. Detection of significant phylogenetic signal was dependant upon the number of populations (n) and the amount of phylogenetic signal (K) for a given dataset. Amounts of phylogenetic signal do not differ between intraspecific and interspecific datasets. Further, relationships between significance of phylogenetic signal and sample size and amount of phylogenetic signal are similar for intraspecific and interspecific datasets. Thus, intraspecific body size datasets are similar to interspecific body size datasets with respect to phylogenetic signal. Whether these results are general for all characters requires further study.     

phylosem: A fast and simple R package for phylogenetic inference and trait imputation using phylogenetic structural equation models

Phylogenetic comparative methods (PCMs) can be used to study evolutionary relationships and trade-offs among species traits. Analysts using PCM may want to (1) include latent variables, (2) estimate complex trait interdependencies, (3) predict missing trait values, (4) condition predicted traits upon phylogenetic correlations and (5) estimate relationships as slope parameters that can be compared with alternative regression methods. The Comprehensive R Archive Network (CRAN) includes well-documented software for phylogenetic linear models (phylolm), phylogenetic path analysis (phylopath), phylogenetic trait imputation (Rphylopars) and structural equation models (sem), but none of these can simultaneously accomplish all five analytical goals. We therefore introduce a new package phylosem for phylogenetic structural equation models (PSEM) and summarize features and interface. We also describe new analytical options, where users can specify any combination of Ornstein-Uhlenbeck, Pagel's-δ and Pagel's-λ transformations for species covariance. For the first time, we show that PSEM exactly reproduces estimates (and standard errors) for simplified cases that are feasible in sem, phylopath, phylolm and Rphylopars and demonstrate the approach by replicating a well-known case study involving trade-offs in plant energy budgets.     

Effects of taxon sampling and tree reconstruction methods on phylodiversity metrics

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Joint reconstruction of divergence times and life-history evolution in placental mammals using a phylogenetic covariance model

Violation of the molecular clock has been amply documented, and is now routinely taken into account by molecular dating methods. Comparative analyses have revealed a systematic component in rate variation, relating it to the evolution of life-history traits, such as body size or generation time. Life-history evolution can be reconstructed using Brownian models. However, the resulting estimates are typically uncertain, and potentially sensitive to the underlying assumptions. As a way of obtaining more accurate ancestral trait and divergence time reconstructions, correlations between life-history traits and substitution rates could be used as an additional source of information. In this direction, a Bayesian framework for jointly reconstructing rates, traits, and dates was previously introduced. Here, we apply this model to a 17 protein-coding gene alignment for 73 placental taxa. Our analysis indicates that the coupling between molecules and life history can lead to a reevaluation of ancestral life-history profiles, in particular for groups displaying convergent evolution in body size. However, reconstructions are sensitive to fossil calibrations and to the Brownian assumption. Altogether, our analysis suggests that further integrating inference of rates and traits might be particularly useful for neontological macroevolutionary comparative studies.     

Evolutionary disequilibrium and activity period in primates: a bayesian phylogenetic approach

Activity period plays a central role in studies of primate origins and adaptations, yet fundamental questions remain concerning the evolutionary history of primate activity period. Lemurs are of particular interest because they display marked variation in activity period, with some species exhibiting completely nocturnal or diurnal lifestyles, and others distributing activity throughout the 24-h cycle (i.e., cathemerality). Some lines of evidence suggest that cathemerality in lemurs is a recent and transient evolutionary state (i.e., the evolutionary disequilibrium hypothesis), while other studies indicate that cathemerality is a stable evolutionary strategy with a more ancient history. Debate also surrounds activity period in early primate evolution, with some recent studies casting doubt on the traditional hypothesis that basal primates were nocturnal. Here, we used Bayesian phylogenetic methods to reconstruct activity period at key points in primate evolution. Counter to the evolutionary disequilibrium hypothesis, the most recent common ancestor of Eulemur was reconstructed as cathemeral at ～9-13 million years ago, indicating that cathemerality in lemurs is a stable evolutionary strategy. We found strong evidence favoring a nocturnal ancestor for all primates, strepsirrhines and lemurs, which adds to previous findings based on parsimony by providing quantitative support for these reconstructions. Reconstructions for the haplorrhine ancestor were more equivocal, but diurnality was favored for simian primates. We discuss the implications of our models for the evolutionary disequilibrium hypothesis, and we identify avenues for future research that would provide new insights into the evolution of cathemerality in lemurs.     

Rapid maximum likelihood ancestral state reconstruction of continuous characters: A rerooting‐free algorithm

Ancestral state reconstruction is a method used to study the evolutionary trajectories of quantitative characters on phylogenies. Although efficient methods for univariate ancestral state reconstruction under a Brownian motion model have been described for at least 25 years, to date no generalization has been described to allow more complex evolutionary models, such as multivariate trait evolution, non‐Brownian models, missing data, and within‐species variation. Furthermore, even for simple univariate Brownian motion models, most phylogenetic comparative R packages compute ancestral states via inefficient tree rerooting and full tree traversals at each tree node, making ancestral state reconstruction extremely time‐consuming for large phylogenies. Here, a computationally efficient method for fast maximum likelihood ancestral state reconstruction of continuous characters is described. The algorithm has linear complexity relative to the number of species and outperforms the fastest existing R implementations by several orders of magnitude. The described algorithm is capable of performing ancestral state reconstruction on a 1,000,000‐species phylogeny in fewer than 2 s using a standard laptop, whereas the next fastest R implementation would take several days to complete. The method is generalizable to more complex evolutionary models, such as phylogenetic regression, within‐species variation, non‐Brownian evolutionary models, and multivariate trait evolution. Because this method enables fast repeated computations on phylogenies of virtually any size, implementation of the described algorithm can drastically alleviate the computational burden of many otherwise prohibitively time‐consuming tasks requiring reconstruction of ancestral states, such as phylogenetic imputation of missing data, bootstrapping procedures, Expectation‐Maximization algorithms, and Bayesian estimation. The described ancestral state reconstruction algorithm is implemented in the Rphylopars functions anc.recon and phylopars.