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。     

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。     

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。     

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。     

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。     

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。     

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。     

Techniques and statistical data analysis in molecular population genetics

Following the development of PCR methods, molecular techniques have become widely used for detecting genetic variation in natural populations. Most nucleotide changes can be detected by these techniques. Many of these changes probably reflect silent substitutions that are likely to be selectively neutral, making them particularly suitable to population genetic studies. In this paper, we review the published literature on molecular population genetics, with respect to the genome assayed (nuclear, mitochondrial or chloroplast), the organisms studied, the molecular techniques used, and the biological problems addressed. Several molecular techniques are then compared using experimental results obtained from a population genetic study of the Mytilus complex in the North Atlantic and Mediterranean. Finally, the most appropriate theoretical tools to analyse molecular population genetic data are discussed.     

The best of both worlds: Phylogenetic eigenvector regression and mapping

Eigenfunction analyses have been widely used to model patterns of autocorrelation in time, space and phylogeny. In a phylogenetic context, Diniz-Filho et al. (1998) proposed what they called Phylogenetic Eigenvector Regression (PVR), in which pairwise phylogenetic distances among species are submitted to a Principal Coordinate Analysis, and eigenvectors are then used as explanatory variables in regression, correlation or ANOVAs. More recently, a new approach called Phylogenetic Eigenvector Mapping (PEM) was proposed, with the main advantage of explicitly incorporating a model-based warping in phylogenetic distance in which an Ornstein-Uhlenbeck (O-U) process is fitted to data before eigenvector extraction. Here we compared PVR and PEM in respect to estimated phylogenetic signal, correlated evolution under alternative evolutionary models and phylogenetic imputation, using simulated data. Despite similarity between the two approaches, PEM has a slightly higher prediction ability and is more general than the original PVR. Even so, in a conceptual sense, PEM may provide a technique in the best of both worlds, combining the flexibility of data-driven and empirical eigenfunction analyses and the sounding insights provided by evolutionary models well known in comparative analyses.     

The role of chromosome changes in the diversification of Passiflora L. (Passifloraceae)

Passiflora L. has more than 575 species distributed especially in the Neotropics. The chromosome number variation in the genus is highly congruent with its main subgenera, but its basic chromosome number (x) and the underlying events responsible for this variation have remained controversial. Here, we provide a robust and well-resolved time-calibrated phylogeny that includes 102 taxa, and by means of phylogenetic comparative methods (PCM) we tested the relative importance of polyploidy and dysploidy events to Passiflora karyotype evolution and diversification. Passiflora arose 42.9 Mya, with subgenus diversification at the end of the Palaeogene (Eocene-Oligocene). The basic chromosome number of the genus is proposed as x?=?6, and a strong recent diversification found in the Passiflora subgenus (Miocene) correlated to genome size increase and a chromosome change from n?=?6 to n?=?9 by ascending dysploidy. Polyploidy, conversely, appeared restricted to few lineages, such as Astrophea and Deidamioides subgenera, and did not lead to diversification increases. Our findings suggest that ascending dysploidy provided a great advantage for generating long-term persistent lineages and promoting species diversification. Thus, chromosome numbers/genome size changes may have contributed to morphological/ecological traits that explain the pattern of diversification observed in the genus Passiflora.     

Among cradles and museums: seasonally dry forest promotes lineage exchanges between rain forest and savanna

ABSTRACT

Background: Cerrado comprises heterogeneous vegetation types. The flora of the vegetation types has distinct biogeographic origins and thus can be hypothesised to have distinct evolutionary imprints.

Aims: We hypothesised that the flora of riparian forest was phylogenetically overdispersed, whereas those of more open habitats were phylogenetically clustered.

Methods: We built a species-level phylogeny for 1,663 species of trees, shrubs and palms and analysed the pattern of lineage distribution, alpha and beta phylogenetic diversity among Cerrado vegetation types (riparian forest, rocky savana, savana and seasonally dry forest - SDTF).

Results: We found a gradient of high phylogenetic diversity and overdispersion from riparian forests towards phylogenetic clustering in vegetation in more open and drier habitats. Habitat shifts were common along the evolutionary history of all families analysed and most families showed a high frequency of shifts from SDTF to riparian forest and savanna.

Conclusions: SDTF seems to be a transitional habitat in evolutionary terms, promoting lineage exchanges between stands of riparian forest and savanna. While riparian forest can be seen as a ‘museum’, that harbours ancient lineages, savanna and rocky savanna are a ‘cradle’ of derived lineages. Habitat shifts are an important underlying drive of high present-day Cerrado flora diversity.