基于核rDNA的ITS序列在种子植物系统发育研究中的应用

种子植物核rDNA是高度重复的串联序列,由于同步进化的力量．大多数物种中这些重复单位间已发生纯合或接近纯合。5．8S rDNA把核rDNA的内转录间隔区分为ITS1和ITS2两部分．在被子植物中ITS1的长度为165～298bp,ITS2的长度为177～266bp,而在裸子植物中ITS片段较长。且其长度变化主要由ITS1的长度变异所致。可对这两个片段PCR产物进行直接测序或克隆测序。由于ITS序列变异较快．能够提供较丰富的变异位点和信息位点,已成为被子植物较低分类阶元的系统发育和分类研究中的重要分子标记,为探讨多倍体复合体网状进化关系,异源多倍体的起源提供了重要的系统学信息．但它一般不适合科以上水平的系统学研究。裸子植物中ITS片段较长,重复序列间的纯合程度不同,测序比较困难．因此对探讨裸子植物系统发育和分类受到了一定的限制,但近年来有所发展。     

山羊草属异源多倍体物种核rDNA ITS区的进化

本文测定了山羊草属Aegilops 3个组中异源多倍体物种的核rDNA ITS区序列,并用邻接法进行了聚类分析。结果表明,多倍体物种的ITS区序列长度为559∽606bp,其中ITS1、ITS2分别有变异位点51、42个,且存在多态位点。多倍体种均与各自的某一祖先种构成稳定分支,说明在杂交-多倍化后,这些多倍体的ITS区在同步进化的作用下已向着其某一祖先种的ITS区进化。对于sect．Vertebrata的异源多倍体物种来说,其ITS区主要向其祖先种Ae．umbellulata(UU)的ITS区进化,这与山羊草属的细胞遗传学研究结果基本一致。在sect．Cylindropyrum和sect．Polyeides中,Ae．cylindrica(CCDD)朝着Ae．caudata (CC)进化;Ae．ventricosa(DDMvMv)朝着Ae．comosa(MM)进化;Ae．vavilovii(DDMMSS)朝着Ae．crassa (DDMM)进化。     

水生被子植物的繁育系统与进化

对植物繁育系统的多样化及其作用模式和机制的研究,是理解植物各类群进化的一个重要基础。这一观点,已被从事植物进化生物学研究的国内外学者普遍接受。本世纪三十年代基因流概念的引人,促使人们在进化研究中,对植物繁育系统的重要性进行了重新评价。在过去的半个多世纪,植物进化生物学也因之而面貌一新,并得到了飞速的发展。时至今日,对植物进化过程中与繁育系统密切相关的一些重要机制,已有了较为深刻的认识（如有性过程中的遗传重组与植物的变异、进而与居群进化之间的关系等）。遗憾的是,这些认识几乎都是建立在对陆生植物研究…     

药用野生稻复合体ITS1和ITS2序列变异及其系统进化分析

通过PCR扩增并测序分析稻属药用野生稻复合体5个野生稻种基因组完整的ITS区及5.8S区,并与栽培稻ITS序列进行比较,构建分子系统进化树,探讨了稻属药用野生稻复合体内不同种间的亲缘关系和系统进化.结果表明,ITS1和ITS2均有较高的G/C含量,ITS1序列的长度多态性相对较高,ITS2序列的碱基突变频率较高.药用野生稻和高秆野生稻亲缘关系很近,而与栽培稻亲缘关系较远;短药野生稻、斑点野生稻、澳洲野生稻与药用野生稻亲缘关系渐近.处于进化的过渡阶段.     

山羊草属二倍体物种核rDNA ITS区序列及其系统发育关系分析

测定了山羊草属（Ａｅｇｉｌｏｐｓ）二倍物种核ｒＤＮＡ ＩＴＳ区序列,发现其碱基粉介于６０１－６０７之间,比报道的小ｒｉｕｃｅａｅ）其他属的ＩＴＳ区我略长,Ｇ＋Ｃ含量达６１．１％～６２．９％,序列间的分化距离为０．００５０～０．０４６８。用ＰＨＹＬＩＰ３．５ｅ软件包对所测得的ＤＮＡ数据进行聚类分析,结果显示：１．Ａｅ．ｓｐｅｌｔｏｉｄｅｓ与该组其他种相距很远,支持将其从Ｓｉｔｏｐｓｉｓ组中独立出来,     

核糖体rDNA ITS序列在真菌学研究中的应用

rDNA序列的同源性和变化性使其用于真菌各级水平的系统学研究,其中ITS区进化速率较快、长度适中,广泛用于属内种间或种内群体的系统学研究。该文就rDNA序列结构特点、ITS序列在真菌分子系统学及病原学中的应用等方面进行综述。     

贵州桐梓何首乌rDNA ITS序列分析

以改进的CTAB法对何首乌总基因组DNA进行提取,采用通用引物对不同来源的何首乌rDNA ITS序列进行PCR扩增、测序和序列分析.结果表明,何首乌rDNA完全序列片段长度共约652 bp,其中ITS1的长度为202 bp,5.8S的长度为161 bp,ITS2长度为232 bp,与其近缘种ITS序列间存在明显差异.其rDNA ITS序列在分子水平上为鉴别何首乌提供了参考依据.     

福建青梅rDNA ITS区克隆与序列分析

利用PCR法对青梅ITS1、5.8S、ITS2序列扩增后克隆测序,用软件DNAMAN和MEGA3.1分析测序结果,研究18个福建青梅样品的核糖体ITS碱基序列差异。获得青梅18个样品rDNA中的ITS和5.8S完全序列,ITS1、5.8S和ITS2序列长度分别为223~224bp、164bp和241~246bp,5.8S较为保守。根据测序结果,以UPGMA法建立系统发生树,从分子水平说明18个样品间的变异程度,并将福建青梅差异较大的14条rDNA ITS序列登录GenBank,获得登录号:EF523482-EF523493、EF529435和EF529436。     

珠母贝属的系统发育: 核rDNA ITS序列证据

珠母贝属（pinctada）的一些种类是生产海水珍珠的重要母贝,个别种类已濒临灭绝。本文利用核糖体DNA内部转录间隔区1（ITS1）和2（ITS2）序列对珠母贝属常见种类的系统发育和分类地位进行了分析。结果表明：ITS1长410-482bp,其中Pinctada maxima最长,P.fucata,P.fucata martensii,P.imbricata和P.nigra最短。ITS2长210-249bp,其中P.albina和P.nigra最长,P.maxima和P.margaritifera最短。碱基替换的同质性检测发现,P.maxima、P.margaritifera和P.chemnitzi的碱基替换格局存在显著性差异,前二者的GC含量显著高于其他种,在进化上可能比较原始;而P．chemnitzi可能发生过染色体重排事件,可能是新近形成的种。系统发育分析表明,所研究的种类可分成3个类群：类群Ⅰ包含P.fucata、P.fucatamartensii和P．imbricata;类群Ⅱ包含P.albina、P.nigra、P.chemnitzi和P.radiata;类群Ⅲ包含P.maxima和P.margaritifera。在类群Ⅰ中,我国的P．fucata、日本的P．fucatamartensii和澳大利亚的P．imbricata的种间遗传分化不明显,可能为同种,根据命名优先原则应以P.imbricata命名该种为宜。类群Ⅱ中P.albina和P．nigra可能是两个亚种,而GenBank中的P.radiata（AY144603）可能是P.chemnitzi的误定。类群Ⅲ（P.maxima和P.margaritifera）分化较早,与碱基替换格局的检测结果相符。     

山茱萸不同栽培品种的 rDNA ITS 序列分析

为测定山茱萸（Cornus officinalis Sieb.et.Zucc.）核糖体DNA的ITS序列,对山茱萸不同栽培品种进行了ITS序列分析。通过实验筛选出一对引物,进行PCR扩增,对扩增产物提取纯化,双脱氧链终止法DNA测序。然后,利用DNAssist Version 2.0软件加手工校正确定ITS1-5.8S-ITS2序列,并进行ITS序列分析。获得了山茱萸的ITS1-5.8S-ITS2完全序列,ITS1为253bp,5.8S为156bp,ITS2为273bp,总共682bp。7种果型的山茱萸其5.8S基因序列显示高度的一致性,圆柱形果型、长梨形果型、椭圆形果型和纺锤形果型的ITS区序列完全一致,短圆柱形果型在ITS1区3′端及ITS2区5′端各有1个变异位点;短梨形果型在ITS1区5′端有3个变异位点;长圆柱形果型在ITS1区有5个变异位点。结果表明,ITS序列在山茱萸种内比较保守,有的栽培品种之间有较小的差异,此研究为中药山茱萸分子鉴定提供了科学依据。     

Deciphering species complexes: Puccinia andropogonis and Puccinia coronata, examples of differing modes of speciation

Species of macrocyclic, heteroecious grass rusts often have been defined with wide host ranges and variation in spore morphology. Consequently, some are species complexes and contain genetically distinct forms. Molecular analyses, together with morphological and biological methods, provide powerful means to dissect these complexes. Puccinia coronata is a complex species that has a broad telial host range including more than 45 genera of grasses and a narrow aecial host range. Phylogenetic analysis of nuclear ribosomal internal transcribed spacer (ITS) DNA sequences from 15 aecial and telial collections grouped P. coronata into six distinct clades supporting separation of this complex into four distinct species. Puccinia andropogonis, a common rust of tall prairie grasses in North America, is also a complex species. However, in contrast to P. coronata, P. andropogonis has a narrow telial host range and a broad aecial host range. DNA sequence analysis grouped 15 collections of P. andropogonis into six distinct clades representing at least four distinct species. Speciation of P. coronata appears to have occurred primarily by radiation onto new telial hosts, whereas in P. andropogonis speciation appears to have occurred primarily by radiation onto new aecial hosts.     

The mycorrhiza of <Emphasis Type="Italic">Schizocodon soldanelloides</Emphasis> var. <Emphasis Type="Italic">magnus</Emphasis> (Diapensiaceae) is regarded as ericoid mycorrhiza from its structure and fungal identities

Structure and fungal identities were examined in the mycorrhizal roots of Schizocodon soldanelloides var. magnus (Diapensiaceae) to determine the mycorrhizal category. Previous studies had suggested the mycorrhizae of Diapensiaceae could be categorized as ericoid, but the mycorrhizal fungi have never been identified. The diameter of the fine lateral roots, in which coiled hyphae were found in epidermal cells, was mostly less than 100 μm. Molecular analyses identified the fungal isolates to be Helotiales and Oidiodendron. From the structure and fungal identities, we confirmed that the mycorrhiza of S. soldanelloides is an ericoid mycorrhiza.     

水霉菌的形态及ITS区分子鉴定

研究利用形态学和分子生物学相结合的方法, 对从患病黄颡鱼病灶处分离的水霉菌株(HSY)的分类地位进行了研究。结果显示, 该菌在18—23℃均能形成游动孢子囊, 但只在20℃才大量释放游动孢子; 在15℃培养约3 周出现大量的藏卵器, 多数顶生, 形态与Saprolegnia litoralis 和Saprolegnia ferax 的均非常相似。序列比对分析显示, HSY 菌株与S. litoralis、S. bulbosa、S. oliviae、S. longicaulis、S. ferax、S. mixta 和S.anomalies 的ITS 区(包括5.8S rDNA)序列相似性均高于99%。系统发育分析显示, 所选的真菌分为3 个群,HSY 落于第一个群, MP 树显示HSY 菌株与S. litoralis、S. bulbosa、S. oliviae、S. longicaulis、S. ferax 以及S. mixta 枝系均互相平行, 而NJ 树显示其与S. ferax 和S. mixta 更近。综合形态学、ITS 区序列及系统发育分析, 将HSY 菌株暂定为多子水霉(Saprolegnia ferax)。     

Recent invader or indicator of environmental change? A phylogenetic and ecological study of Cylindrospermopsis raciborskii in New Zealand

Cylindrospermopsis raciborskii is a diazotrophic and potentially toxic cyanobacterium that was initially thought to be confined to tropical freshwaters. Recently it appears to have expanded its range to more temperate regions of the globe. There are contrasting hypotheses to explain this spread including; dispersal of highly adapted strains or localised spread from warm refuges as climatic or environmental conditions change. C. raciborskii was first detected in the isolated island nation of New Zealand in 2003, providing a unique opportunity to explore whether this recent identification is due to a new incursion or resultant from climatic or environmental change. Phylogenetic analysis (nifH, ITS1-L, ITS1-S, and rpoC1) of six strains isolated from two New Zealand lakes showed they were most closely related to those from South America, and suggest that the recent detection of this species was not due to a new incursion. Ten years of environmental data from three lakes (Waaki, Waikare and Whangape) experiencing blooms were analysed to identify potential reasons for recent C. raciborskii blooms. This analysis showed that the relatively recent (within the last 20–30 years) collapses of extensive macrophyte stands in lakes Waaki, Waikare and Whangape have resulted in increased turbidity’, low water column dissolved reactive phosphorus and seasonal shifts in the dissolved inorganic nitrogen availability, all conditions known to facilitate C. raciborskii dominance. Collectively these data indicate that C. raciborskii has always been present in New Zealand, and that recent changes in environmental conditions in these lakes are now facilitating bloom events.     

A multi-locus analysis of phylogenetic relationships within cheilostome bryozoans supports multiple origins of ascophoran frontal shields

Phylogenetic relationships within the bryozoan order Cheilostomata are currently uncertain, with many morphological hypotheses proposed but scarcely tested by independent means of molecular analysis. This research uses DNA sequence data across five loci of both mitochondrial and nuclear origin from 91 species of cheilostome Bryozoa (34 species newly sequenced). This vastly improved the taxonomic coverage and number of loci used in a molecular analysis of this order and allowed a more in-depth look into the evolutionary history of Cheilostomata. Maximum likelihood and Bayesian analyses of individual loci were carried out along with a partitioned multi-locus approach, plus a range of topology tests based on morphological hypotheses. Together, these provide a comprehensive set of phylogenetic analyses of the order Cheilostomata. From these results inferences are made about the evolutionary history of this order and proposed morphological hypotheses are discussed in light of the independent evidence gained from the molecular data.Infraorder Ascophorina was demonstrated to be non-monophyletic, and there appears to be multiple origins of the ascus and associated structures involved in lophophore extension. This was further supported by the lack of monophyly within each of the four ascophoran grades (acanthostegomorph/spinocystal, hippothoomorph/gymnocystal, umbonulomorph/umbonuloid, lepraliomorph/lepralioid) defined by frontal-shield morphology. Chorizopora, currently classified in the ascophoran grade Hippothoomorpha, is phylogenetically distinct from Hippothoidae, providing strong evidence for multiple origins of the gymnocystal frontal shield type. Further evidence is produced to support the morphological hypothesis of multiple umbonuloid origins of lepralioid frontal shields, using a step-wise set of topological hypothesis tests combined with examination of multi-locus phylogenies.     

Counting labeled transitions in continuous-time Markov models of evolution

Counting processes that keep track of labeled changes to discrete evolutionary traits play critical roles in evolutionary hypothesis testing. If we assume that trait evolution can be described by a continuous-time Markov chain, then it suffices to study the process that counts labeled transitions of the chain. For a binary trait, we demonstrate that it is possible to obtain closed-form analytic solutions for the probability mass and probability generating functions of this evolutionary counting process. In the general, multi-state case we show how to compute moments of the counting process using an eigen decomposition of the infinitesimal generator, provided the latter is a diagonalizable matrix. We conclude with two examples that demonstrate the utility of our results. V.N.M. was supported by a Dissertation Year Fellowship from the UCLA Graduate Division. M.A.S. is an Alfred P. Sloan Research Fellow.