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1.
Kei-ichi Kuma Naruo Nikoh Naoyuki Iwabe Takashi Miyata 《Journal of molecular evolution》1995,41(2):238-246
The phylogenetic position of Dictyostelium inferred from 18S rRNA data contradicts that from protein data. Protein trees always show the close affinity of Dictyostelium with animals, fungi, and plants, whereas in 18S rRNA trees the branching of Dictyostelium is placed at a position before the massive radiation of protist groups including the divergence of the three kingdoms. To settle this controversial issue and to determine the correct position of Dictyostelium, we inferred the phylogenetic relationship among Dictyostelium and the three kingdoms Animalia, Fungi, and Plantae by a maximum-likelihood method using 19 different protein data sets. It was shown at the significance level of 1 SE that the branching of Dictyostelium antedates the divergence of Animalia and Fungi, and Plantae is an outgroup of the Animalia-Fungi-Dictyostelium clade.Correspondence to: T. Miyata 相似文献
2.
Primary structure of theParamecium tetraurelia small-subunit rRNA coding region: Phylogenetic relationships within the caliophora 总被引:8,自引:0,他引:8
We have sequenced the coding region for the small-subunit rRNA gene from Paramecium tetraurelia. Similarity comparisons between small-subunit rRNAs from representatives of the Metazoa, the Plantae, the Fungi and four other members of the Ciliophora were used to construct phylogenetic trees. In these phylogenies the Ciliophora diverged from the eukaryotic line of descent as a loose phylogenetic grouping during a radiative period that gave rise to the Fungi, the Plantae and the Metazoa. 相似文献
3.
Phylogenetic relationship of the kingdoms Animalia, Plantae, and Fungi, inferred from 23 different protein species 总被引:6,自引:3,他引:3
The phylogenetic relationship among the kingdoms Animalia, Plantae, and
Fungi remains uncertain, because of lack of solid fossil evidence. In spite
of the extensive molecular phylogenetic analyses since the early report,
this problem is a longstanding controversy; the proposed phylogenetic
relationships differ for different authors, depending on the molecules and
methods that they use. To settle this problem, we have accumulated 23
different protein species from the three kingdoms and have inferred the
phylogenetic trees by three different methods-- the maximum-likelihood
method, the neighbor-joining method, and the maximum-parsimony method--for
each data set. Although inferred tree topologies differ for different
protein species and methods used, both the maximum-likelihood analysis
based on the difference (delta l) between the total log-likelihood of a
tree and that of the maximum- likelihood tree and bootstrap probability (P)
of 23 proteins consisting of 10,051 amino acid sites in total have shown
that a tree ((A,F),P), in which Plantae (P) is an outgroup to an Animalia
(A)-Fungi (F) clade, is the maximum-likelihood tree; the delta l (= 0.0)
and P (94%) of ((A,F),P) are significantly larger than those of ((A,P),F)
(delta l = - 54.4 +/- 36.3; and P = 6%) and ((F,P),A) (delta l = -141.1 +/-
30.9; and P = 0%).(ABSTRACT TRUNCATED AT 250 WORDS)
相似文献
4.
Early branchings in the evolution of eukaryotes: Ancient divergence of entamoeba that lacks mitochondria revealed by protein sequence data 总被引:11,自引:0,他引:11
Masami Hasegawa Tetsuo Hashimoto Jun Adachi Naoyuki Iwabe Takashi Miyata 《Journal of molecular evolution》1993,36(4):380-388
Summary Phylogenetic analyses of ribosomal RNA sequences have played an important role in the study of early evolution of life. However, Loomis and Smith suggested that the ribosomal RNA tree is sometimes misleading—especially when G+C content differs widely among lineages—and that a protein tree from amino acid sequences may be more reliable. In this study, we analyzed amino acid sequence data of elongation factor-1 by a maximum likelihood method to clarify branching orders in the early evolution of eukaryotes. Contrary to Sogin et al.'s tree of small-subunit ribosomal RNA, a protozoan species, Entamoeba histolytica, that lacks mitochondria was shown to have diverged from the line leading to eukaryotes with mitochondria before the latter separated into several kingdoms. This indicates that Entamoeba is a living relic of the earliest phase of eukaryotic evolution before the symbiosis of protomitochondria occurred. Furthermore, this suggests that, among eukaryotic kingdoms with mitochondria, Fungi is the closest relative of Animalia, and that a cellular slime mold, Dictyostelium discoideum, had not diverged from the line leading to Plantae-Fungi-Animalia before these three kingdoms separated.
Offprint requests to: M. Hasegawa 相似文献
5.
Molecular phylogeny of the kingdoms Animalia, Plantae, and Fungi 总被引:7,自引:2,他引:5
The branching order of the kingdoms Animalia, Plantae, and Fungi has been a controversial issue. Using the transformed distance method and the maximum parsimony method, we investigated this problem by comparing the sequences of several kinds of macromolecules in organisms spanning all three kingdoms. The analysis was based on the large-subunit and small-subunit ribosomal RNAs, 10 isoacceptor transfer RNA families, and six highly conserved proteins. All three sets of sequences support the same phylogenetic tree: plants and animals are sibling kingdoms that have diverged more recently than the fungi. The ribosomal RNA and protein data sets are large enough so that in both cases the inferred phylogeny is statistically significant. The present report appears to be the first to provide statistically conclusive molecular evidence for the phylogeny of the three kingdoms. The determination of this phylogeny will help us to understand the evolution of various molecular, cellular, and developmental characters shared by any two of the three kingdoms. Noting that the large-subunit rRNA sequences have evolved at similar rates in the three kingdoms, we estimated the ratio of the time since the animal-plant split to the time since the fungal divergence to be 0.90. 相似文献
6.
A revised six-kingdom system of life 总被引:10,自引:0,他引:10
T. CAVALIER-SMITH 《Biological reviews of the Cambridge Philosophical Society》1998,73(3):203-266
7.
Comparison of the nucleotide sequence of soybean 18S rRNA with the sequences of other small-subunit rRNAs 总被引:16,自引:0,他引:16
Virginia K. Eckenrode Jonathan Arnold Richard B. Meagher 《Journal of molecular evolution》1985,21(3):259-269
Summary We present the sequence of the nuclearencoded ribosomal small-subunit RNA from soybean. The soybean 18S rRNA sequence of 1807 nucleotides (nt) is contained in a gene family of approximately 800 closely related members per haploid genome. This sequence is compared with the ribosomal small-subunit RNAs of maize (1805 nt), yeast (1789 nt),Xenopus (1825 nt), rat (1869 nt), andEscherichia coli (1541 nt). Significant sequence homology is observed among the eukaryotic small-subunit rRNAs examined, and some sequence homology is observed between eukaryotic and prokaryotic small-subunit rRNAs. Conserved regions are found to be interspersed among highly diverged sequences. The significance of these comparisons is evaluated using computer simulation of a random sequence model. A tentative model of the secondary structure of soybean 18S rRNA is presented and discussed in the context of the functions of the various conserved regions within the sequence. On the basis of this model, the short basepaired sequences defining the four structural and functional domains of all 18S rRNAs are seen to be well conserved. The potential roles of other conserved soybean 18S rRNA sequences in protein synthesis are discussed. 相似文献
8.
Summary Epixenosomes live on the dorsal surface of their ciliate host,Euplotidium itoi. They lack a nuclear envelope and divide like prokaryotes. On the other hand they have a morphological and functional cell compartmentalization and possess tubules that are sensible to tubulin inhibitors and positively react with different antitubulin antibodies. In the present paper, as a first step to investigate their real nature, the in situ hybridization technique was applied at the ultrastructural level. Different prokaryotic and eukaryotic probes suitable for detecting rRNA genes were used. An additional test was performed with the gene encoding for tubulin in the ciliateEuplotes crassus. Positive results, evidenced by a precise localization of gold particles, were obtained with all the eukaryotic probes used. These probes were obtained from organisms belonging to three different kingdoms (Protista, Animalia, Plantae). On the contrary, no hybridization was obtained with prokaryotic probes, not even when the probe used was an oligonucleotide complementary to all bacterial 16S rRNA so far sequenced. On the basis of these results and of the other observations so far accumulated, the possible eukaryotic nature of epixenosomes is discussed.Abbreviations BSA
bovine serum albumin
- DZ
dome-shaped zone
- EDTA
ethylenediaminetetracetic acid
- PCR
polymerase chain reaction
- SEM
scanning electron microscope
- UV
ultraviolet 相似文献
9.
Abstract
The primary diversification of eukaryotes involved protozoa, especially zooflagellates—flagellate protozoa without plastids.
Understanding the origins of the higher eukaryotic kingdoms (two purely heterotrophic, Animalia and Fungi, and two primarily
photosynthetic, Plantae and Chromista) depends on clarifying evolutionary relationships among the phyla of the ancestral kingdom
Protozoa. We therefore sequenced 18S rRNA genes from 10 strains from the protozoan phyla Choanozoa and Apusozoa. Eukaryote
diversity is encompassed by three early-radiating, arguably monophyletic groups: Amoebozoa, opisthokonts, and bikonts. Our
taxon-rich rRNA phylogeny for eukaryotes allowing for intersite rate variation strongly supports the opisthokont clade (animals,
Choanozoa, Fungi). It agrees with the view that Choanozoa are sisters of or ancestral to animals and reveals a novel nonflagellate
choanozoan lineage, Ministeriida, sister either to choanoflagellates, traditionally considered animal ancestors, or to animals.
Maximum likelihood trees suggest that within animals Placozoa are derived from medusozoan Cnidaria (we therefore place Placozoa
as a class within subphylum Medusozoa of the Cnidaria) and hexactinellid sponges evolved from demosponges. The bikont and
amoebozoan radiations are both very ill resolved. Bikonts comprise the kingdoms Plantae and Chromista and three major protozoan
groups: alveolates, excavates, and Rhizaria. Our analysis weakly suggests that Apusozoa, represented by Ancyromonas and the apusomonads (Apusomonas and the highly diverse and much more ancient genus Amastigomonas, from which it evolved), are not closely related to other Rhizaria and may be the most divergent bikont lineages. Although
Ancyromonas and apusomonads appear deeply divergent in 18S rRNA trees, the trees neither refute nor support the monophyly of Apusozoa.
The bikont phylum Cercozoa weakly but consistently appears as sister to Retaria (Foraminifera; Radiolaria), together forming
a hitherto largely unrecognized major protozoan assemblage (core Rhizaria) in the eukaryote tree. Both 18S rRNA sequence trees
and a rare deletion show that nonciliate haplosporidian and paramyxid parasites of shellfish (together comprising the Ascetosporea)
are not two separate phyla, as often thought, but part of the Cercozoa, and may be related to the plant-parasitic plasmodiophorids
and phagomyxids, which were originally the only parasites included in the Cercozoa. We discuss rRNA trees in relation to other
evidence concerning the basal diversification and root of the eukaryotic tree and argue that bikonts and opisthokonts, at
least, are holophyletic. Amoebozoa and bikonts may be sisters—jointly called anterokonts, as they ancestrally had an anterior
cilium, not a posterior one like opisthokonts; this contrasting ciliary orientation may reflect a primary divergence in feeding
mode of the first eukaryotes. Anterokonts also differ from opisthokonts in sterol biosynthesis (cycloartenol versus lanosterol
pathway), major exoskeletal polymers (cellulose versus chitin), and mitochondrial cristae (ancestrally tubular not flat),
possibly also primary divergences. 相似文献
10.
Are red algae plants? 总被引:3,自引:0,他引:3
MARK A. RAGAN ROBIN R. GUTELL 《Botanical journal of the Linnean Society. Linnean Society of London》1995,118(2):81-105
For 200 years prior to the 1938 publication of H. F. Copeland, all authorities (with one exception) classified red algae (Rhodophyta) within Kingdom Plantae or its equivalent. Copeland's reclassification of red algae within Kingdom Protista or Protoctista drew from an alternative tradition, dating to Cohn in 1867, in which red algae were viewed as the earliest or simplest eukaryotes. Analyses of ribosomal RNA (rRNA) sequence data initially favoured Copeland's reclassification. Many more rRNA gene (rDNA) sequences are now available from the eukaryote lineages most closely related to red algae, and based on these data, the hypothesis that red algae and green plants are sister groups cannot be rejected. An increasing body of sequence, intron-location and functional data from nuclear- and mitochondrially encoded proteins likewise supports a sister-group relationship between red algae and green plants. Submerging Kingdoms Plantae, Animalia and Fungi into Eukarya would provide a more natural framework for the eventual resolution of whether red algae are plants or prorists. 相似文献
11.
L N Seravin 《Tsitologiia》1992,34(5):3-33
Comparative evidence on the lack of three important organelles (flagella, Golgi-complex, mitochondria) in cells and organisms at the cellular level of organization has been summarized for all the four eukaryotic kingdoms--Protista, Fungi, Plantae and Animalia (Metazoa). It is established that in the course of evolution these organelles may undergo the total reduction. There is no cellular organelle to be regarded as universal, indispensable. There are only three main obligatory cell components--the plasmalemma, nucleus and cytoplasm (with applied cytoskeleton, cytomembranes and ribosomes). The reduction of flagella (cilia) is occurring in different taxa independent of the transition of protists from the flagellate type of locomotion to the amoeboid, gliding of metabolizing ones, and in the number of metazoan cells. The members of Protista and Fungi, which line in microaerobic or anaerobic conditions, nearly inevitably lose their mitochondria. The tendency to lose Golgi-complex is demonstrated in protists with parasitic mode of life, especially in combination with anaerobiosis. There is so far no satisfied morphological criterium that could say with certainty whether the lacking of flagella, Golgi complex or mitochondria in the low eukaryotes may be primary or secondary (as the result of reduction). Data on the composition, structure and RNA nucleotide sequences cannot be either the straight evidence. A comparative analysis of these data shows that the ribosomes of the primary eukaryotes were, presumably, of a prokaryotic type. Their eukaryotization was carried out for a long time during the evolution of the low eukaryotes (Protista and Fungi), probably, independently in different phylogenetic lines. It is unknown at what steps and in what main phylogenetic lines the three above mentioned organelles may have appeared. It is proposed to single out a special division of cytology--organellology (organoidology)--as an individual science whose main purpose may be investigation of the origination, evolution and disappearance of organelles. 相似文献
12.
Thomas Cavalier-Smith 《European journal of protistology》2013,49(2):115-178
I discuss how different feeding modes and related cellular structures map onto the eukaryote evolutionary tree. Centrally important for understanding eukaryotic cell diversity are Loukozoa: ancestrally biciliate phagotrophic protozoa possessing a posterior cilium and ventral feeding groove into which ciliary currents direct prey. I revise their classification by including all anaerobic Metamonada as a subphylum and adding Tsukubamonas. Loukozoa, often with ciliary vanes, are probably ancestral to all protozoan phyla except Euglenozoa and Percolozoa and indirectly to kingdoms Animalia, Fungi, Plantae, and Chromista. I make a new protozoan phylum Sulcozoa comprising subphyla Apusozoa (Apusomonadida, Breviatea) and Varisulca (Diphyllatea; Planomonadida, Discocelida, Mantamonadida; Rigifilida). Understanding sulcozoan evolution clarifies the origins from them of opisthokonts (animals, fungi, Choanozoa) and Amoebozoa, and their evolutionary novelties; Sulcozoa and their descendants (collectively called podiates) arguably arose from Loukozoa by evolving posterior ciliary gliding and pseudopodia in their ventral groove. I explain subsequent independent cytoskeletal modifications, accompanying further shifts in feeding mode, that generated Amoebozoa, Choanozoa, and fungi. I revise classifications of Choanozoa, Conosa (Amoebozoa), and basal fungal phylum Archemycota. I use Choanozoa, Sulcozoa, Loukozoa, and Archemycota to emphasize the need for simply classifying ancestral (paraphyletic) groups and illustrate advantages of this for understanding step-wise phylogenetic advances. 相似文献
13.
Summary The nucleotide sequences of 5S rRNAs from three protozoa,Bresslaua vorax, Euplotes woodruffi andChlamydomonas sp. have been determined and aligned together with the sequences of 12 protozoa species including unicellular green algae already reported by the authors and others. Using this alignment, a phylogenic tree of the 15 species of protozoa has been constructed. The tree suggests that the ancestor for protozoa evolved at an early time of eukaryotic evolution giving two major groups of organisms. One group, which shares a common ancestor with vascular plants, contains a unicellular green flagellate (Chlamydomonas) and unicellular green algae. The other group, which shares a common ancestor with the multicellular animals, includes various flagellated protozoa (includingEuglena), ciliated protozoa and slime molds. Most of these protozoa appear to have separated from one another at a fairly early period of eukaryotic evolution. 相似文献
14.
15.
Matus-Ortega MG Salmerón-Santiago KG Flores-Herrera O Guerra-Sánchez G Martínez F Rendón JL Pardo JP 《Comparative biochemistry and physiology. Part D, Genomics & proteomics》2011,6(3):256-263
The distribution of the alternative NADH dehydrogenase (NDH-2) in the living world was explored. The enzyme, although present in representatives of all living kingdoms, does not have a universal distribution. With the exception of ε-proteobacteria, the enzyme was found in all eubacterial groups. In contrast with the known presence of the NDH-2 in Archaea, the alternative oxidase (AOX) is absent in this group. With regard to the Eukarya domain, the NDH-2 was found in representatives of Protista, Fungi, Plantae, and Animalia. In the latter, however, the presence of the enzyme was restricted to some primitive Metazoa (Placozoa and Cnidaria), and two members of the Deuterostomate lineage of the Bilateria (Echinodermata and Urochordata). No evidence for the presence of the NDH-2 was found in any representative of the Protostomate branch of the Bilateria, contrasting with the existence of the AOX in this same group. It is worth mentioning that those animal species containing the NDH-2 also have an AOX. The actual distribution of the NDH-2 in the various living kingdoms is discussed within the framework of the endosymbiotic theory; in addition, a hypothesis is proposed to explain the disappearance of the alternative NDH-2 and AOX from the majority of the animals. 相似文献
16.
Evolutionary relationships of eukaryotic kingdoms 总被引:5,自引:0,他引:5
The evolutionary relationships of four eukaryotic kingdoms—Animalia, Plantae, Fungi, and Protista—remain unclear. In particular, statistical support for the closeness of animals to fungi rather than to plants is lacking, and a preferred branching order of these and other eukaryotic lineages is still controversial even though molecular sequences from diverse eukaryotic taxa have been analyzed. We report a statistical analysis of 214 sequences of nuclear small-subunit ribosomal RNA (srRNA) gene undertaken to clarify these evolutionary relationships. We have considered the variability of substitution rates and the nonindependence of nucleotide substitution across sites in the srRNA gene in testing alternative hypotheses regarding the branching patterns of eukaryote phylogeny. We find that the rates of evolution among sites in the srRNA sequences vary substantially and are approximately gamma distributed with size and shape parameter equal to 0.76. Our results suggest that (1) the animals and true fungi are indeed closer to each other than to any other crown group in the eukaryote tree, (2) red algae are the closest relatives of animals, true fungi, and green plants, and (3) the heterokonts and alveolates probably evolved prior to the divergence of red algae and animal-fungus-green-plant lineages. Furthermore, our analyses indicate that the branching order of the eukaryotic lineages that diverged prior to the evolution of alveolates may be generally difficult to resolve with the srRNA sequence data. 相似文献
17.
Traditional views about the origin of eukaryotes and relationshipsbetween major "kingdoms" reflect interpretations of the fossilrecord and comparisons of phenotypic characters. This perspectiveis challenged by phylogenetic frameworks inferred from comparisonsof macromolecular sequences which share a common ancestry. Similaritiesbetween ribosomal RNA genes demonstrate that instead of beingrelatively recent biological inventions, eukaryotes representa discrete lineage that may be as old as the archaebacterialand eubacterial lines of descent. The diversity of protistansmall subunit rRNA sequences exceeds that seen within the entireprokaryotic world. The earliest branching lineages include diplomonads,microsporidians, and tritrichomonads. Yet, other major protistangroups diverged relatively late in the evolutionary historyof nucleated cells. Rather than being a concise evolutionaryassemblage, the Protista should be regarded as a collectionof paraphyletic lineages. In contrast, the Fungi, Plantae, andAnimalia are independent monophyletic groupings. They originatednearly simultaneously during a relatively recent period characterizedby a massive diversification of forms. This novel view of eukaryoticevolution suggests that a reliance upon large phenotypic differencesin delineating kingdoms can obscure true genealogical relationships.Instead of dividing eukaryotes into four or more major divisions,they should be considered as a single kingdom that encompassesa progression of independently diverging lineages. 相似文献
18.
Comparison of the nucleotide sequence of soybean 18S rRNA with the sequences of other small-subunit rRNAs 总被引:1,自引:0,他引:1
We present the sequence of the nuclear-encoded ribosomal small-subunit RNA from soybean. The soybean 18S rRNA sequence of 1807 nucleotides (nt) is contained in a gene family of approximately 800 closely related members per haploid genome. This sequence is compared with the ribosomal small-subunit RNAs of maize (1805 nt), yeast (1789 nt), Xenopus (1825 nt), rat (1869 nt), and Escherichia coli (1541 nt). Significant sequence homology is observed among the eukaryotic small-subunit rRNAs examined, and some sequence homology is observed between eukaryotic and prokaryotic small-subunit rRNAs. Conserved regions are found to be interspersed among highly diverged sequences. The significance of these comparisons is evaluated using computer simulation of a random sequence model. A tentative model of the secondary structure of soybean 18S rRNA is presented and discussed in the context of the functions of the various conserved regions within the sequence. On the basis of this model, the short base-paired sequences defining the four structural and functional domains of all 18S rRNAs are seen to be well conserved. The potential roles of other conserved soybean 18S rRNA sequences in protein synthesis are discussed. 相似文献
19.
Homology between actin coding and its adjacent sequences in widely divergent species 总被引:1,自引:0,他引:1
Eco RI restriction endonuclease DNA fragments from several representatives of the kingdoms Protista and Animalia were electrophoretically separated and transferred to the nitrocellulose filters. These DNA's were hybridized with [32p]-labelled actin coding sequence from Drosophila melanogaster (Dm). The results indicate that the nucleic acid sequences of the genes coding for actin(s) has been highly conserved throughout evolution. Similar experiments were performed using the sequence derived from the 5' end of Drosophila actin gene as a probe. Cross-hybridization was observed between Drosophila and Acanthamoeba castellanii. This may indicate a functionally important region at the 5' end which has been conserved. 相似文献
20.
Annexin homologues in the kingdoms of Planta and Protista were characterized by molecular sequence analysis to determine
their phylogenetic and structural relationship with annexins of Animalia. Sequence fragments from 19 plant annexins were identified
in sequence databases and composite sequences were also assembled from expressed sequence tags for Arabidopsis thaliana. Length differences in protein amino-termini and evidence for unique exon splice sites indicated that plant annexins were
distinct from those of animals. A third annexin gene of Giardia lamblia (Anx21-Gla) was identified as a distant relative to other protist annexins and to those of higher eukaryotes, thus providing a suitable
outgroup for evolutionary reconstruction of the family tree. Rooted evolutionary trees portrayed protist, plant, and Dictyostelium annexins as early, monophyletic ramifications prior to the appearance of closely related animal annexin XIII. Molecular phylogenetic
analyses of DNA and protein sequence alignments revealed at least seven separate plant subfamilies, represented by Anx18 (alfalfa, previously classified), Anx22 (thale cress), Anx23 (thale cress, cotton, rape and cabbage), Anx24 (bell pepper and tomato p34), Anx25 (strawberry, horseradish, pea, soybean, and castor bean), Anx26-Zma, and Anx27-Zma (maize). Other unique subfamilies may exist for rice, tomato p35, apple, and celery annexins. Consensus sequences compiled
for each eukaryotic kingdom showed some breakdown of the ``annexin-fold' motif in repeats 2 and 3 of protist and plant annexins
and a conserved codon deletion in repeat 3 of plants. The characterization of distinct annexin genes in plants and protists
reflects their comparable diversity among animal species and offers alternative models for the comparative study of structure–function
relationships within this important gene family.
Received: 30 May 1996 / Accepted: 20 August 1996 相似文献