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。     

食肉目哺乳动物的系统发育学研究概述

追溯生物界不同生物类型的起源及进化关系,即重建生物类群的系统发育树是进化生物学领域中一个十分重要的内容。食肉目哺乳动物位于食物链顶端,很多成员不仅在我国野生动物保护工作中占有重要地位,而且还是研究动物适应性进化遗传机制的重要模式生物。因而,食肉目物种作为物种资源中的一个重要类群,其系统发育学一直是国内外研究的热门课题。构建可靠的食肉目分子系统树,无疑将具有重要的进化理论意义和保护生物学价值。鉴于目前食肉目各科间系统发育关系仍然处于“广泛争论”的状态,本文将针对食肉目科水平上的系统发育学研究进展,包括来自于形态学特征、细胞学及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。这对今后食肉目系统发育方面的进一步研究工作具有指导意义,并为以该类群作为模式生物开展适应性进化研究奠定基础。     

食肉目哺乳动物的系统发育学研究概述

追溯生物界不同生物类型的起源及进化关系，即重建生物类群的系统发育树是进化生物学领域中一个十分重要的内容。食肉目哺乳动物位于食物链顶端，很多成员不仅在我国野生动物保护工作中占有重要地位，而且还是研究动物适应性进化遗传机制的重要模式生物。因而，食肉目物种作为物种资源中的一个重要类群，其系统发育学一直是国内外研究的热门课题。构建可靠的食肉目分子系统树，无疑将具有重要的进化理论意义和保护生物学价值。鉴于目前食肉目各科间系统发育关系仍然处于“广泛争论”的状态，本文将针对食肉目科水平上的系统发育学研究进展，包括来自于形态学特征、细胞学及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。这对今后食肉目系统发育方面的进一步研究工作具有指导意义，并为以该类群作为模式生物开展适应性进化研究奠定基础。     

哺乳动物系统发育基因组学研究进展

哺乳动物是一类最进化并在地球上占主导地位的动物类群,重建其系统发育关系一直是分子系统学的研究热点。随着越来越多物种全基因组测序的完成,在基因组水平上探讨该类动物的系统发育关系与进化成为研究的热点。本文从全基因组序列,稀有基因组变异及染色体涂染等几个方面简要介绍了当前系统发育基因组学在现生哺乳动物分子系统学中的应用,综合已有的研究归纳整理了胎盘亚纲的总目及目间的系统发育关系,给出了胎盘动物19 个目的系统发育树。本文还分析了哺乳动物系统发育基因组学目前所面临的主要问题及未来的发展前景。     

系统与进化植物学开放研究实验室1999年进展与成果简介

中国科学院植物研究所系统与进化植物学开放研究实验室经中国科学院批准,于1987年8月13日正式成立。从成立至今,本室的学术方向是以生物学各学科为手段,从分子、细胞、组织、个体和居群各层次揭示植物物种形成、进化过程和机制,重建系统发育。同时进行生物多样性、特别是保护生     

系统与进化植物学国家重点实验室

系统与进化植物学国家重点实验室的历史可追溯到1928年在北平成立的静生生物调查研究所植物部和1929年成立的国立北平研究院植物研究所。1987年经中国科学院批准正式成立了中国科学院植物研究所系统与进化植物学开放研究实验室,2001年更名为“系统与进化植物学重点实验室”。2005年3月国家科技部正式发文批准成立“系统与进化植物学国家重点实验室”,依托单位是中国科学院植物研究所。实验室的总体定位和研究方向是利用多学科研究手段,开展植物物种多样性的起源和演化、系统发育重建以及进化机制等重大基础理论研究,取得具有重要国际影响的原创性研究成果,培养该领域的高层次人才。主要研究领域为植物分类、区系和生物地理学,植物的起源和系统发育重建,居群生物学和保护遗传学,进化发育和进化基因组学。     

短散在元件的筛选方法及其在鲸类和爬行类系统发育与进化研究中的应用

短散在元件(short interspersed repetitive elements,SINEs)是广泛分布于真核生物基因组中的一种反转录转座子。近年来越来越多的研究表明SINEs对基因组的结构、功能和进化起着重要作用,是研究物种系统发育和种群生物学的一个良好分子标记。本文简单介绍了SINEs的特征、基本结构、分离和鉴定,以及近年来SINEs标记在系统发育与进化研究中的应用。     

rDNA在昆虫纲系统发育研究中的应用

昆虫纲是动物界种类最丰富的一个类群,研究昆虫的系统发育对了解生物进化历程及进化机制都有重要意义。传统的系统发育研究主要依赖于物种的生物学性状、形态解剖特征、以及生物地理学信息等。但是,随着学科的发展,也遇到了一些传统方法难以解决的困难,例如：由于物种间可供比较的形态学性状是有限的,一些进化距离较远的类群难以统一分析,这对于高级分类阶元的研究尤为突出;由于超同进化的存在,不同类群的物种可能表现出相似的形态特征;用形态特征定义一个分类阶元,就必须对标本的完整性、性别、生长阶段有严格的要求;此外,对形…     

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.     

线蚓科分类学研究进展

线蚓科隶属于环节动物门环带纲,迄今共记录32属650余种,是该纲的第二大科。它们广泛分布于土壤、海洋、淡水、河口和冰川等。其中,约2/3的线蚓科物种(近500种)为陆生种类,100余种仅分布在海洋中。尽管经历了200多年的探索,线蚓科仍然是认知最少的类群之一。尝试回顾人类对线蚓科环带动物分类学和系统发育学方面的认知历程和积累的知识体系,描述线蚓科关键的形态学分类特征以及线蚓科分类研究遇到的主要问题和障碍,展望了线蚓科分类学未来的研究方向。线蚓科的分类研究尚处于α分类阶段,体现在以物种探索为主和大量的已描述的物种需要验证等。而基于生物学物种概念(生殖隔离)的线蚓科物种探索,虽然有一些合理的逻辑解释,但缺乏严格的科学验证。线蚓科内多数属为复系,表明已建立的线蚓科分类系统仍然不能很好的反映线蚓科的自然进化历史。线蚓科分类面临的主要问题和障碍是未描述种类亟待发掘、已描述的物种需要验证、属/种的厘定以及现代属级概念的建立、DNA分类在线蚓科的应用和线蚓科内的系统发育关系研究亟待开展,以及物种探索的不平衡、经费和研究人才匮乏以及网络分类的缺失等。将分子学数据和系统发育物种概念纳入线蚓科的分类学研究,应该是线蚓科分类的一个方向。通过解读保守基因的信息,可以揭示线蚓科的祖先与它们生活的古环境长期斗争的历史,以及将优良的性状遗传给后代的过程和驱动力。而系统发育物种概念认为物种是拥有共同祖先的,物种仅能通过生殖隔离与系统发育重建一起加以验证。基于系统发育物种概念而构建的线蚓科分类系统,必将能真实的反映线蚓科内各分类单元的亲缘关系和进化轨迹。而将最新的线蚓科分类学知识传播于分类学知识的终端使用者,是线蚓分类学家的职责。这些知识将有助于提高人们对线蚓类在生态系统中功能的了解,如土壤有机质分解、养分矿化和健康评价以及评估气候变化等。     

Analysis of Acorus calamus chloroplast genome and its phylogenetic implications

Determining the phylogenetic relationships among the major lines of angiosperms is a long-standing problem, yet the uncertainty as to the phylogenetic affinity of these lines persists. While a number of studies have suggested that the ANITA (Amborella-Nymphaeales-Illiciales-Trimeniales-Aristolochiales) grade is basal within angiosperms, studies of complete chloroplast genome sequences also suggested an alternative tree, wherein the line leading to the grasses branches first among the angiosperms. To improve taxon sampling in the existing chloroplast genome data, we sequenced the chloroplast genome of the monocot Acorus calamus. We generated a concatenated alignment (89,436 positions for 15 taxa), encompassing almost all sequences usable for phylogeny reconstruction within spermatophytes. The data still contain support for both the ANITA-basal and grasses-basal hypotheses. Using simulations we can show that were the ANITA-basal hypothesis true, parsimony (and distance-based methods with many models) would be expected to fail to recover it. The self-evident explanation for this failure appears to be a long-branch attraction (LBA) between the clade of grasses and the out-group. However, this LBA cannot explain the discrepancies observed between tree topology recovered using the maximum likelihood (ML) method and the topologies recovered using the parsimony and distance-based methods when grasses are deleted. Furthermore, the fact that neither maximum parsimony nor distance methods consistently recover the ML tree, when according to the simulations they would be expected to, when the out-group (Pinus) is deleted, suggests that either the generating tree is not correct or the best symmetric model is misspecified (or both). We demonstrate that the tree recovered under ML is extremely sensitive to model specification and that the best symmetric model is misspecified. Hence, we remain agnostic regarding phylogenetic relationships among basal angiosperm lineages.     

Phylogenomics of Fargesia and Yushania reveals a history of reticulate evolution

Reticulate evolution is a common and important driving force in angiosperm evolution. In this study, we analyzed the phylogenetic signals of genomic regions with different inheritance patterns to understand the evolutionary process of organisms using species-rich Himalaya–Hengduan taxa of bamboos (Fargesia Franchet and Yushania Keng). We constructed phylogenetic trees using different sampling strategies and reconstruction methods based on genome skimming and double digest restriction-site-associated DNA sequencing data. We assessed the congruence of topologies generated from different datasets and employed several approaches to reveal the causes of phylogenetic incongruence, including the detection of hybridization and introgression using PhyloNetworks and the D-statistic test (ABBA-BABA test). We found that, in the plastome-based phylogeny, Fargesia bamboos can be clustered into three groups and Yushania was nested within one of them, which contradicts the nuclear–double digest restriction-site-associated DNA sequencing-based phylogeny. Moreover, the genetic variation of chloroplast DNA is significantly correlated with geographical distribution. The strong signal of incomplete lineage sorting, hybridization, introgression, and cytoplasmic gene flow found among genera and species suggests that reticulate evolution is the main cause for the phylogenetic incongruence between nuclear and chloroplast datasets. Our results add evidence that genomes with different inheritance patterns can reveal distinct evolutionary histories of species and suggest that reticulate evolution is prevalent in rapidly diversifying groups.     

Inferring phylogenetic networks by the maximum parsimony criterion: a case study

Horizontal gene transfer (HGT) may result in genes whose evolutionary histories disagree with each other, as well as with the species tree. In this case, reconciling the species and gene trees results in a network of relationships, known as the "phylogenetic network" of the set of species. A phylogenetic network that incorporates HGT consists of an underlying species tree that captures vertical inheritance and a set of edges which model the "horizontal" transfer of genetic material. In a series of papers, Nakhleh and colleagues have recently formulated a maximum parsimony (MP) criterion for phylogenetic networks, provided an array of computationally efficient algorithms and heuristics for computing it, and demonstrated its plausibility on simulated data. In this article, we study the performance and robustness of this criterion on biological data. Our findings indicate that MP is very promising when its application is extended to the domain of phylogenetic network reconstruction and HGT detection. In all cases we investigated, the MP criterion detected the correct number of HGT events required to map the evolutionary history of a gene data set onto the species phylogeny. Furthermore, our results indicate that the criterion is robust with respect to both incomplete taxon sampling and the use of different site substitution matrices. Finally, our results show that the MP criterion is very promising in detecting HGT in chimeric genes, whose evolutionary histories are a mix of vertical and horizontal evolution. Besides the performance analysis of MP, our findings offer new insights into the evolution of 4 biological data sets and new possible explanations of HGT scenarios in their evolutionary history.     

DISCORDANCE BETWEEN NUCLEAR AND CHLOROPLAST PHYLOGENIES IN THE HEUCHERA GROUP (SAXIFRAGACEAE)

Various factors, including taxon density, sampling error, convergence, and heterogeneity of evolutionary rates, can potentially lead to incongruence between phylogenetic trees based on different genomes. Particularly at the generic level and below, chloroplast capture resulting from hybridization may distort organismal relationships in phylogenetic analyses based on the chloroplast genome, or genes included therein. However, the extent of such discord between chloroplast DNA (cpDNA) trees and those trees based on nuclear genes has rarely been assessed. We therefore used sequences of the internal transcribed spacer regions (ITS-1 and ITS-2) of nuclear ribosomal DNA (rDNA) to reconstruct phylogenetic relationships among members of the Heuchera group of genera (Saxifragaceae). The Heuchera group presents an important model for the analysis of chloroplast capture and its impact on phylogenetic reconstruction because hybridization is well documented within genera (e.g., Heuchera), and intergeneric hybrids involving six of the nine genera have been reported. An earlier study provided a well-resolved phylogenetic hypothesis for the Heuchera group based on cpDNA restriction-site variation. However, trees based on ITS sequences are discordant with the cpDNA-based tree. Evidence from both morphology and nuclear-encoded allozymes is consistent with the ITS trees, rather than the cpDNA tree, and several points of phylogenetic discord can clearly be attributed to chloroplast capture. Comparison of the organellar and ITS trees also raises the strong likelihood that ancient events of chloroplast capture occurred between lineages during the early diversification of the Heuchera group. Thus, despite the many advantages and widespread use of cpDNA data in phylogeny reconstruction, comparison of relationships based on cpDNA and ITS sequences for the Heuchera group underscores the need for caution in the use of organellar variation for retrieving phylogeny at lower taxonomic levels, particularly in groups noted for hybridization.     

Revaluation of deuterostome phylogeny and evolutionary relationships among chordate subphyla using mitogenome data

The traditional knowledge in textbooks indicated that cephalochordates were the closest relatives to vertebrates among all extant organisms. However, this opinion was challenged by several recent phylogenetic studies using hundreds of nuclear genes. The researchers suggested that urochordates, but not cephalochordates, should be the closest living relatives to vertebrates. In the present study, by using data generated from hundreds of mtDNA sequences, we revalue the deuterostome phylogeny in terms of whole mitochondrial genomes （mitogenomes）. Our results firmly demonstrate that each of extant deuterostome phyla and chordate subphyla is monophyletic. But the results present several alternative phylogenetic trees depending on different sequence datasets used in the analysis. Although no clear phylogenetic relationships are obtained, those trees indicate that the ancient common ancestor diversified rapidly soon after their appearance in the early Cambrian and generated all major deuterostome lineages during a short historical period, which is consistent with ＂Cambrian explosion＂ revealed by paleontologists. It was the 520-million-year＇s evolution that obscured the phylogenetic relationships of extant deuterostomes. Thus, we conclude that an integrative analysis approach rather than simply using more DNA sequences should be employed to address the distant evolutionary relationship.     

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.     

生命之树及其应用

生命之树的概念由达尔文在1859年提出, 用以反映分类群的亲缘关系和进化历史。近30年来, 随着建树性状种类的多样化、数据量的快速增长以及建树方法的不断发展和完善, 生命之树的规模越来越大, 可信度也越来越高。分子生物学、生态学、基因组学、生物信息学及计算机科学等的快速发展, 使得生命之树成为开展学科间交叉研究的桥梁, 其用途日益广泛。本文综述了生命之树研究的历史和现状, 介绍了生命之树在以下几个方面的应用: (1)通过构建不同尺度的生命之树, 理解生物类群间的系统发育关系; (2)通过时间估算和地理分布区重建, 推测现存生物的起源和地理分布格局及其成因; (3)基于时间树, 结合生态、环境因子及关键创新性状, 探讨生物的多样化进程和成因; (4)揭示生物多样性的来源和格局, 预测生物多样性动态变化, 并提出相应的保护策略。最后, 本文评估了生命之树在目前海量数据情况下遇到的序列比对困难、基因树冲突、“流浪类群”干扰等建树难题, 并指出了构建“超大树”的发展趋势。     

Whole genome-based phylogenetic analysis of free-living microorganisms.

A phylogenetic 'tree of life' has been constructed based on the observed presence and absence of families of protein-encoding genes observed in 11 complete genomes of free-living microorganisms. Past attempts to reconstruct the evolutionary relation-ships of microorganisms have been limited to sets of genes rather than complete genomes. Despite apparent rampant lateral gene transfer among microorganisms, these results indicate a single robust underlying evolutionary history for these organisms. Broadly, the tree produced is very similar to the small subunit rRNA tree although several additional phylogenetic relationships appear to be resolved, including the relationship of Archaeoglobus to the methanogens studied. This result is in contrast to notions that a robust phylogenetic reconstruction of microorganisms is impossible due to their genomes being composed of an incomprehensible amalgam of genes with complicated histories and suggests that this style of genome-wide phylogenetic analysis could become an important method for studying the ancient diversification of life on Earth. Analyses using informational and operational subsets of the genes showed that this 'tree of life' is not dependent on the phylogenetically more consistent informational genes.     

Phylogenetic niche conservatism, phylogenetic signal and the relationship between phylogenetic relatedness and ecological similarity among species

Ecologists are increasingly adopting an evolutionary perspective, and in recent years, the idea that closely related species are ecologically similar has become widespread. In this regard, phylogenetic signal must be distinguished from phylogenetic niche conservatism. Phylogenetic niche conservatism results when closely related species are more ecologically similar that would be expected based on their phylogenetic relationships; its occurrence suggests that some process is constraining divergence among closely related species. In contrast, phylogenetic signal refers to the situation in which ecological similarity between species is related to phylogenetic relatedness; this is the expected outcome of Brownian motion divergence and thus is necessary, but not sufficient, evidence for the existence of phylogenetic niche conservatism. Although many workers consider phylogenetic niche conservatism to be common, a review of case studies indicates that ecological and phylogenetic similarities often are not related. Consequently, ecologists should not assume that phylogenetic niche conservatism exists, but rather should empirically examine the extent to which it occurs.     

The foot-and-mouth disease RNA virus as a model in experimental phylogenetics.

Phylogenetic reconstruction methods are subject to two types of limitations: our knowledge about the true history of organisms and the gross simplification implied in the numerical simulation models of the relationships between them. In such a situation, experimental phylogenetics provides a way to assess the accuracy of the phylogenetic reconstruction methods. Nonetheless, this capacity is only feasible for organisms in which replication and mutation rates are high enough to provide valuable data. On the other hand, experimental phylogenetics also provides insights on the main evolutionary processes acting on viral variability under different population dynamics. Our study with the foot-and-mouth disease virus (FMDV) strongly suggests that the phylogenetic reconstruction methods can infer erroneous phylogenies due to nucleotide convergences between isolates belonging to different experimental lineages. We also point out that the diverse evolutionary mechanisms acting in different experimental dynamics generate alterations and change the frequencies of genetic variants, which can lead to the misinterpretation of the real evolutionary history.