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1.
Molecular sequence data are often aligned on the basis of secondary and/or tertiary structure models. However, these models are regularly updated and sometimes differ depending on the way in which they were constructed. We examined whether the choice of a particular 18S rRNA secondary structure model as alignment basis influences phylogeny inference. We therefore compared 18S rRNA phylogenies derived from alignments based on different models. We used: 1. Maximum parsimony; 2. The neighbour-joining method; 3. The maximum-likelihood approach; and 4. Evolutionary parsimony. This demonstrated that the secondary structure model on which an alignment is based may influence: 1. The tree topologies found by these four methods; 2. The numbers of most parsimonious trees found; and 3. The statistical values calculated by the evolutionary parsimony method.  相似文献   

2.
A fragment of the ammonia monooxygenase gene (amoA) from 31 strains of ammonia-oxidizing bacteria (AOB) was sequenced and analysed phylogenetically. The results were compared with the phylogeny of 16S rDNA from AOB. For most groups of AOB we found a high consistency between the phylogenetic trees based on the 16S rDNA and amoA sequences. Although it is not a phylogenetic marker, using the amoA as a probe when studying microbial diversity will probably reduce the amount of non-AOB detected, compared to using rDNA based probes. The data presented in this paper extend and improve the basis for application of amoA in studies of AOB in the environment.  相似文献   

3.
The phylogeny of the family Tephritidae (Diptera: Tephritidae) was reconstructed from mitochondrial 12S, 16S, and COII gene fragments using 87 species, including 79 tephritid and 8 outgroup species. Minimum evolution and Bayesian trees suggested the following phylogenetic relationships: (1) A sister group relationship between Ortalotrypeta and Tachinisca, and their basal phylogenetic position within Tephritidae; (2) a sister group relationship between the tribe Acanthonevrini and Phytalmiini; (3) monophyly of Plioreocepta, Taomyia and an undescribed new genus, and their sister group relationship with the subfamily Tephritinae; (4) a possible sister group relationship of Cephalophysa and Adramini; and (5) reconfirmation of monophyly for Trypetini, Carpomyini, Tephritinae, and Dacinae. The combination of 12S, 16S, and COII data enabled resolution of phylogenetic relationships among the higher taxa of Tephritidae.  相似文献   

4.
5S rRNAs from 12 species of free living and parasitic platyhelminthes were sequenced. In the phylogenetic analysis, attention was focused on the statistical estimates of the trees corresponding to existing phylogenetic hypotheses. The available 5S rRNA data agree well with widely accepted views on the relationships between the Acoela, Polycladida, Tricladida, and Neorhabdocoela; our analysis of the published 18S rRNA sequences also demonstrated good correspondence between these views and molecular data. With available 5S rRNA data the hypothesis that the dalyellioid turbellarians is the sister group of the Neodermata is less convincing than the hypotheses proposing the Neodermata as the sister group of the Neorhabdocoela, or of the Seriata, or of the branch uniting them. A relatively low rate of base replacement in parasitic flatworms, probably, accounts for the uncertain position of the Neodermata, while a relatively high rate in planarians may explain a relatively too early divergence of the Tricladida in several published phylogenetic trees constructed from various rRNA data.  相似文献   

5.
Phylogenetic relationships within the group of molting protostomes were reconstructed by comparing the sets of 18S and 28S rRNA gene sequences considered either separately or in combination. The reliability of reconstructions was estimated from the bootstrap indices for major phylogenetic tree nodes and from the degree of congruence of phylogenetic trees obtained by different methods. By either criterion, the phylogenetic trees reconstructed on the basis of both 18 and 28S rRNA gene sequences were better than those based on the 18S or 28S sequences alone. The results of reconstruction are consistent with the phylogenetic hypothesis classifying protostomes into two major clades: molting Ecdysozoa (Priapulida + Kinorhyncha, Nematoda + Nematomorpha, Onychophora + Tardigrada, Myriapoda + Chelicerata, and Crustacea + Hexapoda) and nonmolting Lophotrochozoa (Plathelminthes, Nemertini, Annelida, Mollusca, Echiura, and Sipuncula). Nematomorphs (Nematomorpha) do not belong to the clade Cephalorhyncha (Priapulida + Kinorhyncha). It is concluded that combined data on the 18S and 28S rRNA gene sequences provide a more reliable basis for phylogenetic inferences.__________Translated from Molekulyarnaya Biologiya, Vol. 39, No. 4, 2005, pp. 590–601.Original Russian Text Copyright © 2005 by Petrov, Vladychenskaya.  相似文献   

6.
嗜盐古细菌的系统发育分析   总被引:9,自引:0,他引:9       下载免费PDF全文
用“Clustalw”和“PHYLIP”程序包分析嗜盐古细菌16S rRNA序列,建立了嗜盐古细菌的系统发育树。比较分析的结果进一步支持了以前的结论,即嗜盐古细菌在自然系统分类上应被分成嗜盐菌科的6个属。此系统发育分析方法不仅体现了在嗜盐古细菌属一级分类上的优势,而且还可能被用作一种相应于以《伯杰氏细菌系统分类手册》(第三卷)为基础的嗜盐古细菌种一级分类上的代换方法。实际上,这种系统发育分析方法比其他建立在表型特性基础上的分类系统更真实地反映了嗜盐古细菌内的亲缘关系。该方法的其他运算细节在本文中也进行了讨论。  相似文献   

7.
Summary The effects of temporal (among different branches of a phylogeny) and spatial (among different nucleotide sites within a gene) nonuniformities of nucleotide substitution rates on the construction of phylogenetic trees from nucleotide sequences are addressed. Spatial nonuniformity may be estimated by using Shannon's (1948) entropy formula to measure the Relative Nucleotide Variability (RNV) at each nucleotide site in an aligned set of sequences; this is demonstrated by a comparative analysis of 5S rRNAs. New methods of constructing phylogenetic trees are proposed that augment the Unweighted Pair-Group Using Arithmetic Averages (UPGMA) algorithm by estimating and compensating for both spatial and temporal nonuniformity in substitution rates. These methods are evaluated by computer simulations of 5S rRNA evolution that include both kinds of nonuniformities. It was found that the proposed Reference Ratio Method improved both the ability to reconstruct the correct topology of a tree and also the estimation of branch lengths as compared to UPGMA. A previous method (Farris et al. 1970; Klotz et al. 1979; Li 1981) was found to be less successful in reconstructing topologies when there is high probability of multiple mutations at some sites. Phylogenetic analyses of 5S rRNA sequences support the endosymbiotic origins of both chloroplasts and mitochondria, even though the latter exhibit an accelerated rate of nucleotide substitution. Phylogenetic trees also reveal an adaptive radiation within the eubacteria and another within the eukaryotes for the origins of most major phyla within each group during the Precambrian era.  相似文献   

8.
数种昆虫5S rRNA结构特点的比较   总被引:1,自引:0,他引:1       下载免费PDF全文
比较已知结构的昆虫5S rRNA的核苷酸顺序,发现同科、同目的昆虫比不同科、不同目的昆虫有较少的核苷酸差别.根据Kimura和Ohta(1972)提出的经验公式,绘制了数种昆虫的系统发育图.结果表明,从分子进化得到的结论和经典分类基本上是一致的.根据DeWachter等(1982)提出的二级结构模型,归纳分析这些昆虫5S rRNA,发现保守位点与半保守位点(同一位点仅出现二种核苷酸残基)之和几乎占整个5S rRNA分子的100%.  相似文献   

9.
The genes of ribosomal RNA are the most popular and frequently used markers for bacterial phylogeny and reconstruction of insect-symbiont coevolution. In primary symbionts, such as Buchnera and Wigglesworthia, genome economization leads to the establishment of a single copy of these sequences. In phylogenetic studies, they provide sufficient information and yield phylogenetic trees congruent with host evolution. In contrast, other symbiotic lineages (e.g., the genus Arsenophonus) carry a higher number of rRNA copies in their genomes, which may have serious consequences for phylogenetic inference. In this study, we show that in Arsenophonus triatominarum the degree of heterogeneity can affect reconstruction of phylogenetic relationships and mask possible coevolution between the symbiont and its host. Phylogenetic arrangement of individual rRNA copies was used, together with a calculation of their divergence time, to demonstrate that the incongruent 16S rDNA trees and low nucleotide diversity in the secondary symbiont could be reconciled with the coevolutionary scenario.  相似文献   

10.
Chloroplast 4.5 S rRNAs of the monocotAcorus calamus and the dicotLigularia calthifolia have been sequenced. Phylogenetic trees for the chloroplast 4.5 S and 5 S rRNAs and also for cytosol 5 S rRNAs have been constructed by several methods. They are compared with previous studies. Evidently, it is necessary to consider the inequality of nucleotide substitution rates in different lines for adequate phylogenetic reconstructions. Some relevant conclusions are presented. The possibilities and prospects for using data on low-molecular-weight rRNAs from cytosol and organelles for deducing phylogenetic relationships in plants are discussed.Dedicated to the memory ofS. V. Meyen, Vice-president of the International Organization of Palaeobotany (Dec. 17, 1935–March 30, 1987).  相似文献   

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