鼠疫耶尔森氏菌的进化研究:从系统发育学到系统发育基因组学

20世纪90年代末起,基因组学在细菌研究中应用越来越广泛,尤其在进化领域,取得了一系列革命性的发现.本文以鼠疫耶尔森氏菌进化研究为例,介绍了从利用基因组中少数特定片段(等位基因)多态性进行分析的传统系统发育学,到基于大量菌株全基因组序列进行系统发育基因组学的研究发展历程,回顾讨论了基因组学技术的进步为鼠疫菌进化研究领域带来的成果.     

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。     

基因组时代的放线菌系统分类学及其研究进展

由于放线菌在生物技术、医药卫生和环境治理等领域中的实际重要性,已经成为人们研究得最为深入的微生物类群之一。现代放线菌分类学是建立在对16S rRNA基因保守分子序列的系统发育学分析基础上、综合利用多种微生物信息的多相分类学(polyphasic taxonomy)。随着大规模基因测序技术的飞速发展,已经完成了超过100株放线菌的全基因组序列。近年来发展起来的"基因组系统发育学"有助让人们更加系统地理解放线菌类群的发生、演化,以及不同生境类群之间的相互关系。随着越来越多的以系统发育学为指导的基因组测序研究项目,例如"细菌和古菌基因组百科全书(Genomic Encyclopedia of Bacteria andArchaea,GEBA)计划"的出现,标志着放线菌系统学进入了基因组学研究时代。本文对基因组时代的放线菌系统学方法,以及国内外的相关研究成果进行综述。     

关于进化真菌学教学内容的讨论

核酸序列的比较研究使进化真菌学的面貌发生了革命性的变化,分子系统发育揭示的关系反映出真菌进化的复杂性和多样性,真菌系统学反映真菌进化关系的自然系统还有很大的距离,有赖于新物种的不断发现和分子系统发育证据的不断丰富。     

低等六足动物系统学研究进展

低等六足动物包括原尾纲、弹尾纲和双尾纲三个类群,是探讨六足动物起源和进化问题的关键类群,近十年来成为节肢动物系统进化研究中的焦点之一。低等六足动物的系统发育地位以及它们之间的关系一直是备受争论的问题。通过介绍三类低等六足动物最新的分类系统,从经典分类学和系统发育两个方面对低等六足动物近十年来的研究进展进行了综述。迄今,对于三类低等六足动物都建立了比较完备的分类体系,原尾纲划分为3目10科,弹尾纲划分为4目30科,双尾纲划分为2亚目3总科10科。系统发育研究中,大多数的系统发育分析结果不支持传统的缺尾类假说,缺尾纲应摒弃不用。分子数据分析的结果普遍支持原尾纲与双尾纲近缘,但仍需要进一步探讨。线粒体基因组、比较胚胎学和比较精子学的研究结果表明,原尾纲可能经历了长期的趋异进化历史。最近的比较精子学研究支持了双尾纲的单系性。总之,三类低等六足动物系统学研究均取得了长足的发展,但仍然存在诸如研究人员匮乏和研究水平不均衡等问题。系统发育研究中,分子系统学研究成为关注的焦点,而基于核基因和线粒体基因的数据分别建立的系统发育假说存在分歧,亟需开发更优的数据分析方法。此外,需加强低等六足动物比较形态学、比较胚胎学、发育生物学等方面的研究,以便将来进行全证据的系统发育研究。     

植物内生固氮菌系统发育进化新进展

在植物内生固氮菌系统发育进化关系研究中,常用的方法有形态学与蛋白质水平法、数值分类和自动化鉴定法、化学分类法、分子遗传学方法等。本文简要介绍了常用方法的关键技术,并归纳了它们的优缺点。生物学的研究进入基因组时代后,随着高通量DNA测序技术在微生物学领域应用的迅速发展,全基因组测序被应用到微生物系统发育进化研究中,然而目前并未发现对已测全基因组序列的植物内生固氮菌进行系统总结。本文在对已测序植物内生固氮菌进行归纳的基础上,又详细研究了基于基因组数据的几种具有代表性的新方法(ANI分析法、最大唯一匹配指数法、核心基因组分析、组分矢量法、基因流动性分析),并结合目前系统发育进化研究常用方法,对植物内生固氮菌系统发育进化研究趋势进行总结和展望,旨在使植物内生固氮菌的系统发育进化关系研究在精确度、可靠性等方面有所突破。     

六足动物分子系统学研究进展

对近期国内外六足总纲动物的原尾纲、弹尾纲、双尾纲和昆虫纲在种群遗传变异及进化、种及种下阶元的分类鉴定、种上阶元的系统发育分析等分子系统学方面的研究进展进行了综述。多基因的联合分子数据研究日益增加。随着分子技术的日益推广,不同类型的基因序列甚至全基因组的联合使用将引导分子系统学走向辉煌的未来。     

直翅目昆虫分子系统学研究新进展

对1994年以来国内外在直翅目昆虫种群遗传变异及进化、种及种下阶元的分类鉴定、种上阶元的系统发育分析及分子进化等分子系统学方面的研究进展进行了综述。近年来,蝗亚目昆虫分子系统学方面的研究成果较为丰富,而有关螽亚目的分子系统学研究较少。线粒体基因和核基因序列联合分析、整个基因组全序列分析以及分子数据与形态学的密切结合将是分子系统学未来发展的主要研究手段。     

昆虫比较线粒体基因组学研究进展

动物线粒体基因组因其基因组成稳定、基因排列相对保守、普遍为母系遗传、极少发生重组等而被广泛应用于进化与系统发育等研究。目前,昆虫中已有356个线粒体基因组序列被测定,代表了33个目中的28个目。大量比较基因组学研究使得我们对昆虫线粒体基因组的特征与进化方式有了较为清晰的认识。本文对昆虫线粒体基因组的测序进展、基因组的结构特征、碱基组成、控制区的特征、基因重排及其机理、进化速率及其在昆虫系统发育研究中的应用等方面的研究进展进行介绍。     

比较基因组学在哺乳动物进化研究中的应用

哺乳动物经过长期进化,使其基因组在结构和功能上存在着明显的差异,构成了表型进化的基础。随着人类、部分哺乳动物基因组测序的完成,以比较基因组学为主要研究手段的哺乳动物进化研究应运而生,从而为在基因组水平上深入认识哺乳动物进化关系、揭示生命的起源和进化提供依据。对比较基因组学的主要研究方法进行了综述,进而探讨其在哺乳动物进化研究中的应用,并对哺乳动物比较基因组学的发展进行了展望。     

Evolution of the genomic rate of recombination in mammals

Rates of recombination vary considerably between species. Despite the significance of this observation for evolutionary biology and genetics, the evolutionary mechanisms that contribute to these interspecific differences are unclear. On fine physical scales, recombination rates appear to evolve rapidly between closely related species, but the mode and tempo of recombination rate evolution on the broader scale is poorly understood. Here, we use phylogenetic comparative methods to begin to characterize the evolutionary processes underlying average genomic recombination rates in mammals. We document a strong phylogenetic effect in recombination rates, indicating that more closely related species tend to have more similar average rates of recombination. We demonstrate that this phylogenetic signal is not an artifact of errors in recombination rate estimation and show that it is robust to uncertainty in the mammalian phylogeny. Neutral evolutionary models present good fits to the data and we find no evidence for heterogeneity in the rate of evolution in recombination across the mammalian tree. These results suggest that observed interspecific variation in average genomic rates of recombination is largely attributable to the steady accumulation of neutral mutations over evolutionary time. Although single recombination hotspots may live and die on short evolutionary time scales, the strong phylogenetic signal in genomic recombination rates indicates that the pace of evolution on this scale may be considerably slower.     

A practical approach to phylogenomics: the phylogeny of ray-finned fish (Actinopterygii) as a case study

Background  

Molecular systematics occupies one of the central stages in biology in the genomic era, ushered in by unprecedented progress in DNA technology. The inference of organismal phylogeny is now based on many independent genetic loci, a widely accepted approach to assemble the tree of life. Surprisingly, this approach is hindered by lack of appropriate nuclear gene markers for many taxonomic groups especially at high taxonomic level, partially due to the lack of tools for efficiently developing new phylogenetic makers. We report here a genome-comparison strategy to identifying nuclear gene markers for phylogenetic inference and apply it to the ray-finned fishes – the largest vertebrate clade in need of phylogenetic resolution.     

Relationships within the family Actiniidae (Cnidaria,Actiniaria) based on molecular characters

Current sea anemone systematics is based on relatively few morphological characters, and potentially could benefit from the use of molecular characters. In this paper, the phylogenetic relationships of 12 species from 6 genera in the family Actiniidae have been investigated using electrophoretically separated isozymes. A numerical cladistic analysis has produced an estimated phylogeny. The implications of this phylogeny for the taxonomic use of certain morphological characters are discussed.     

The reform of palaeontology and the rise of biogeography – 25 years after 'ontogeny, phylogeny, paleontology and the biogenetic law' (Nelson, 1978)

Aim To document the historical development of cladistics and the roles palaeontology and biogeography played in establishing coherent concepts of phylogenetic relationships focusing on some aspects of the contributions of Gareth Nelson. Conclusions Nelson's reformulation of the threefold parallelism provides a rationale for investigating phylogeny, replacing the central role palaeontology once played with biogeography, adding a spatial dimension to the concept of phylogeny. This approach to phylogeny replaces the old ‘transformationist’ view with the cladistic view, the latter dependent on discovering relationships among taxa. Numerical phylogenetic methods are inherently ‘transformationist’ and have replaced stratigraphy as the key to phylogenetic relationships. Numerical methods in systematics and biogeography are inherently transformational and suffer the same problems as the old palaeontology.     

Claims and limits of phylogenetic systematics1

Within the methodology of phylogenetic systematics four hierarchic levels are distinguished: the “Central Claim” (to reconstruct phylogeny), methodoloical postulate (to conclude analysis with a purely dichotomous cladogram if ever possible), method (search for sister-group relationships by character analysis), and “Taxonomic Principle” (establishment of a classification reflecting merely the recognized genealoy). Certain limits of applicability and reliability of traditional phylogenetic systematics are specified: genealogy can only be analysed among taxa with perceptible evolutionary novelties; reticulated genealogy is not yet regarded; events other than cladogenetic ones cannot be recognised. Phylogenetic systematics is an independent method which has not been absorbed by any type of “pattern” or “transformed” cladism. Phylogenetic systematics relies on the theory of evolution, which does not lead into circularity, since phylogenetic systematics does not claim to prove or to explain evolution whatsoever.     

Validity of the Diplostomoidea and Diplostomida (Digenea,Platyhelminthes) upheld in phylogenomic analysis

Higher systematics within the Digenea, Carus 1863 have been relatively stable since a phylogenetic analysis of partial nuclear ribosomal markers (rDNA) led to the erection of the Diplostomida Olson, Cribb, Tkach, Bray, and Littlewood, 2003. However, recent mitochondrial (mt) genome phylogenies suggest this order might be paraphyletic. These analyses show members of two diplostomidan superfamilies are more closely related to the Plagiorchiida La Rue, 1957 than to other members of the Diplostomida. A recent phylogeny based on partial cytochrome c oxidase I also indicates one of the groups implicated, the Diplostomoidea Poirier, 1886, is non-monophyletic. To determine if these results were robust to additional taxon sampling, we analyzed mt genomes from seven diplostomoids in three families. To choose between phylogenetic alternatives based on mt genomes and the prior rDNA-based topology, we analyzed hundreds of ultra-conserved genomic elements assembled from shotgun sequencing. The Diplostomida was paraphyletic in the mt genome phylogeny but supported in the ultra-conserved genomic element phylogeny. We speculate this mitonuclear discordance is related to ancient, rapid radiation in the Digenea. Both ultra-conserved genomic elements and mt genomes support the monophyly of the Diplostomoidea and show congruent relationships within it. The Cyathocotylidae Mühling, 1898 are early diverging descendants of a paraphyletic clade of Diplostomidae Poirier, 1886, in which are nested members of the Strigeidae Railliet, 1919; the results support prior suggestions that the Crassiphialinae Sudarikov, 1960 will rise to the family level. Morphological traits of diplostomoid metacercariae appear to be more useful for differentiating clades than those of adults. We describe a new species of Cotylurus Szidat, 1928, resurrect a species of Hysteromorpha Lutz, 1931, and find support for a species of Alaria Schrank, 1788 of contested validity. Complete rDNA operons from seven diplostomoid species are provided as a resource for future studies.     

Genosystematics and new insight into the phylogeny and taxonomy of liverworts

The current state of molecular studies in liverworts, including original data, was considered. The traditional concepts of the liverwort phylogeny and systematics have greatly changed as a result of recent molecular researches. The phylogenetic inferences from studies of different DNA loci of different species sampling are mainly congruent. The phylogeny and systematics of the suborder Jungermaniineae, one of the largest and taxonomically difficult groups, is discussed on the basis of nucleotide sequence analyses of internal transcribed spacers 1 and 2 (ITS1-2) of nuclear rDNA and chloroplast trnL-F in a representative species sampling.     

The current status of chemical systematics

Chemical systematics sets out to interpret the phylogenetic implications of the occurrence and distribution of secondary metabolites. In this review, a number of the major contributions from the 1960's and 1970's are identified and re-assessed in the light of recent evidence gained from DNA studies. It is shown that for the most part conclusions drawn on the basis of secondary metabolite distribution have been confirmed by the new techniques and it is concluded that chemical systematics can continue to provide useful insights into plant phylogeny.     

被子植物系统发育深层关系研究: 进展与挑战

被子植物系统发育学是研究被子植物及其各类群间亲缘关系与进化历史的学科。从20世纪90年代起, 核苷酸和氨基酸序列等分子数据开始被广泛运用于被子植物系统发育研究, 经过20多年的发展, 从使用单个或联合少数几个细胞器基因, 到近期应用整个叶绿体基因组来重建被子植物的系统发育关系, 目、科水平上的被子植物系统发育框架已被广泛接受。在这个框架中, 基部类群、主要的5个分支(即真双子叶植物、单子叶植物、木兰类、金粟兰目和金鱼藻目)、每个分支所包含的目以及几个大分支包括的核心类群等都具有高度支持。与此同时, 细胞器基因还存在一些固有的问题, 例如单亲遗传、系统发育信息量有限等, 因此近年来双亲遗传的核基因在被子植物系统发育研究中的重要性逐渐得到关注, 并在不同分类阶元的研究中都取得了一定进展。但是, 被子植物系统发育中仍然存在一些难以确定的关系, 例如被子植物5个分支之间的关系、真双子叶植物内部某些类群的位置等。本文简述了20多年来被子植物系统发育深层关系的主要研究进展, 讨论了被子植物系统发育学常用的细胞器基因和核基因的选用, 已经确定和尚未确定系统发育位置的主要类群, 以及研究中尚存在的问题和可能的解决方法。     

Poor taxon sampling, poor character sampling, and non-repeatable analyses of a contrived dataset do not provide a more credible estimate of insect phylogeny: a reply to Kjer

The wealth of data available for phylogenetic analysis of the insect orders, from both morphological and molecular sources, is steadily increasing. However, controversy exists among the methodologies one can use to reconstruct ordinal relationships. Recently, Kjer (2004 ) presented an analysis of insect ordinal relationships based exclusively on a single source of information: 18S rDNA sequence data. Kjer claims that his analysis resulted in a more “credible” phylogeny for the insect orders and strongly criticized our previous phylogenetic results. However, Kjer only used a subset of the data that are currently available for insect ordinal phylogeny, misrepresented our analyses, and omitted other analyses we have published on insect ordinal phylogeny. In our estimation, Kjer did a poor job of representing the current state of affairs in insect ordinal phylogenetics. Furthermore, we examine a number of analytical issues that are relevant not only for insect phylogeny, but systematics as a science, such as: repeatability and objectivity, locating alignment boundaries, secondary structure, goodness of fit measure, epistemological coherence, practicality and homology. © The Willi Hennig Society 2005.