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1.
Secondary structure is evaluated for determining evolutionary relationships between catalytic RNA molecules that are so distantly
related they are scarcely alignable. The ribonucleoproteins RNase P (P) and RNase MRP (MRP) have been suggested to be evolutionarily
related because of similarities in both function and secondary structure. However, their RNA sequences cannot be aligned with
any confidence, and this leads to uncertainty in any trees inferred from sequences. We report several approaches to using
secondary structures for inferring evolutionary trees and emphasize quantitative tests to demonstrate that evolutionary information
can be recovered. For P and MRP, three hypotheses for the relatedness are considered. The first is that MRP is derived from
P in early eukaryotes. The next is that MRP is derived from P from an early endosymbiont. The third is that both P and MRP
evolved in the RNA-world (and the need for MRP has since been lost in prokaryotes). Quantitative comparisons of the pRNA and
mrpRNA secondary structures have found that the possibility of an organellar origin of MRP is unlikely. In addition, comparison
of secondary structures support the identity of an RNase P–like sequence in the maize chloroplast genome. Overall, it is concluded
that RNA secondary structure is useful for evaluating evolutionary relatedness, even with sequences that cannot be aligned
with confidence.
Received: 19 July 1999 / Accepted: 3 May 2000 相似文献
2.
Caetano-Anollés G 《Journal of molecular evolution》2002,54(3):333-345
The origin and diversification of RNA secondary structure were traced using cladistic methods. Structural components were
coded as polarized and ordered multi-state characters, following a model of character state transformation outlined by considerations
in statistical mechanics. Several classes of functional RNA were analyzed, including ribosomal RNA (rRNA). Considerable phylogenetic
signal was present in their secondary structure. The intrinsically rooted phylogenies reconstructed from evolved RNA structure
depicted those derived from nucleic acid sequence at all taxonomical levels, and grouped organisms in concordance with traditional
classification, especially in the archaeal and eukaryal domains. Natural selection appears therefore to operate early in the
information flow that originates in sequence and ends in an adapted phenotype. When examining the hierarchical classification
of the living world, phylogenetic analysis of secondary structure of the small and large rRNA subunits reconstructed a universal
tree of life that branched in three monophyletic groups corresponding to Eucarya, Archaea, and Bacteria, and was rooted in
the eukaryotic branch. Ribosomal characters involved in the translational cycle could be easily traced and showed that transfer
RNA (tRNA) binding domains in the large rRNA subunit evolved concurrently with the rest of the rRNA molecule. Results suggest
it is equally parsimonious to consider that ancestral unicellular eukaryotes or prokaryotes gave rise to all extant life forms
and provide a rare insight into the early evolution of nucleic acid and protein biosynthesis.
Received: 13 September 2000 / Accepted: 27 August 2001 相似文献
3.
In addition to characteristic structural properties imposed by evolutionary modification, evolved, single-stranded RNAs also
display characteristic structural properties imposed by intrinsic physical constraints on RNA polymer folding. The balance
of intrinsic and functionally selected characters in the folded conformation of evolved secondary structures was determined
by comparing the predicted secondary structures of evolved and unevolved (random) RNA sequences. Though evolved conformations
are significantly more ordered than conformations of random-sequence RNA, this analysis demonstrates that the majority of
conformational order within evolved structures results not from evolutionary optimization but from constraints imposed by
rules intrinsic to RNA polymer folding.
Received: 25 November 1998 / Accepted: 12 February 1999 相似文献
4.
7S RNA sequences from the hagfish (Myxiniformes) and lamprey (Petromyzontiformes) were cloned and analyzed. In both species,
7S L RNA (also designated SRP RNA, since it represents the RNA constituent of the signal recognition particle) was clearly
detectable. The sequence similarity between the two species was 86%, compared with about 75% similarity between either of
these species and mammals. 7S K RNA was also cloned from the lamprey. The similarity between the 7S K RNA of the lamprey and
that of mammals was 68%. Interestingly, several interspersed elements were found with nearly 100% similarity compared with
mammals. In contrast to the lamprey, no 7S K RNA-related sequences were detectable among hagfish RNA, neither in northern
blots nor with the PCR assay. In view of the significant conservation between the 7S K RNA of lamprey and that of mammals
(human), this unexpected result clearly separates lamprey and hagfish. In addition, the lack of detectable 7S K RNA sequences
in an outgroup, such as amphioxus, indicates that these results do not reflect an autapomorphy of hagfish. Therefore, our
data provide additional support to the notion of a sister group relationship between Petromyzontiformes and gnathostomous
vertebrates to the exclusion of Myxiniformes.
Received: 24 September 1999 / Accepted: 9 February 2000 相似文献
5.
Relics from the RNA World 总被引:1,自引:0,他引:1
An RNA world is widely accepted as a probable stage in the early evolution of life. Two implications are that proteins have
gradually replaced RNA as the main biological catalysts and that RNA has not taken on any major de novo catalytic function
after the evolution of protein synthesis, that is, there is an essentially irreversible series of steps RNA → RNP → protein.
This transition, as expected from a consideration of catalytic perfection, is essentially complete for reactions when the
substrates are small molecules. Based on these principles we derive criteria for identifying RNAs in modern organisms that
are relics from the RNA world and then examine the function and phylogenetic distribution of RNA for such remnants of the
RNA world. This allows an estimate of the minimum complexity of the last ribo-organism—the stage just preceding the advent
of genetically encoded protein synthesis. Despite the constraints placed on its size by a low fidelity of replication (the
Eigen limit), we conclude that the genome of this organism reached a considerable level of complexity that included several
RNA-processing steps. It would include a large protoribosome with many smaller RNAs involved in its assembly, pre-tRNAs and
tRNA processing, an ability for recombination of RNA, some RNA editing, an ability to copy to the end of each RNA strand,
and some transport functions. It is harder to recognize specific metabolic reactions that must have existed but synthetic
and bio-energetic functions would be necessary. Overall, this requires that such an organism maintained a multiple copy, double-stranded
linear RNA genome capable of recombination and splicing. The genome was most likely fragmented, allowing each ``chromosome'
to be replicated with minimum error, that is, within the Eigen limit. The model as developed serves as an outgroup to root
the tree of life and is an alternative to using sequence data for inferring properties of the earliest cells.
Received: 14 January 1997 / Accepted: 19 May 1997 相似文献
6.
Axel Janke Ola Magnell Georg Wieczorek Michael Westerman Ulfur Arnason 《Journal of molecular evolution》2002,54(1):71-80
The monotremes, the duck-billed platypus and the echidnas, are characterized by a number of unique morphological characteristics,
which have led to the common belief that they represent the living survivors of an ancestral stock of mammals. Analysis of
new data from the complete mitochondrial (mt) genomes of a second monotreme, the spiny anteater, and another marsupial, the
wombat, yielded clear support for the Marsupionta hypothesis. According to this hypothesis marsupials are more closely related
to monotremes than to eutherians, consistent with a basal split between eutherians and marsupials/monotremes among extant
mammals. This finding was also supported by analysis of new sequences from a nuclear gene—18S rRNA. The mt genome of the wombat
shares some unique features with previously described marsupial mtDNAs (tRNA rearrangement, a missing tRNALys, and evidence for RNA editing of the tRNAAsp). Molecular estimates of genetic divergence suggest that the divergence between the platypus and the spiny anteater took
place ≈34 million years before present (MYBP), and that between South American and Australian marsupials ≈72 MYBP.
Received: 28 October 2000 / Accepted: 23 March 2001 相似文献
7.
Martijn A. Huynen 《Journal of molecular evolution》1996,43(3):165-169
RNA secondary-structure folding algorithms predict the existence of connected networks of RNA sequences with identical secondary
structures. Fitness landscapes that are based on the mapping between RNA sequence and RNA secondary structure hence have many
neutral paths. A neutral walk on these fitness landscapes gives access to a virtually unlimited number of secondary structures
that are a single point mutation from the neutral path. This shows that neutral evolution explores phenotype space and can
play a role in adaptation.
Received: 23 December 1995 / Accepted: 17 March 1996 相似文献
8.
Alexander P. Gultyaev F.H.D. van Batenburg Cornelis W.A. Pleij 《Journal of molecular evolution》2002,54(1):1-8
Comparison of the most stable potential hairpins in the sequences of natural ribozymes with those in the randomized sequences
has revealed that the hairpin loop energies are lower than expected by chance. Although these hairpins are not necessarily
parts of functional structures, there is a selective pressure to diminish the destabilizing free energies of the hairpin loops.
In contrast, no significant bias is observed in the stacking values of the most stable stems. In the ribozymes isolated in
vitro the loops of potential hairpins are closer to random values, which can result in less efficient folding rates. Furthermore,
the effects of kinetic traps seem to be more significant in the folding pathways of the in vitro isolates due to a potential
to form stable stacks incompatible with the functional folds. Similarly to natural ribozyme sequences, the untranslated regions
of viral RNAs also form hairpins with relatively low loop free energies. These evolutionary trends suggest ways for efficient
engineering of improved RNA constructs on the basis of analysis of in vitro isolates and approaches for the search of regions
coding for functional RNA structures in large genome sequences.
Received: 12 January 2001 / Accepted: 21 May 2001 相似文献
9.
A Phylogenetic Study of the Origin of the Domestic Pig Estimated from the Near-Complete mtDNA Genome 总被引:18,自引:0,他引:18
The near-complete pig mtDNA genome sequence (15,997 bp) was determined from two domestic pigs (one Chinese Meishan and one
Swedish Landrace) and two European wild boars. The sequences were analyzed together with a previously published sequence representing
a Swedish domestic pig. The sequences formed three distinct clades, denoted A, E1, and E2, with considerable sequence divergence
between them (0.8–1.2%). The results confirm our previous study (based on the sequence of the cytochrome B gene and the control
region only) and provide compelling evidence that domestication of pigs must have occurred from both an Asian and a European
subspecies of the wild boar. We estimated the time since the divergence of clade A (found in Chinese Meishan pigs) and E1
(found in European domestic pigs) at about 900,000 years before present, long before domestication about 9000 years ago. The
pattern of nucleotide substitutions among the sequences was in good agreement with previous interspecific comparisons of mammalian
mtDNA; the lowest substitution rates were observed at nonsynonymous sites in protein-coding genes, in the tRNA and rRNA genes,
while the highest rates were observed at synonymous sites and in the control region. The presence of Asian clade A in some
major European breeds (Large White and Landrace) most likely reflects the documented introgression of Asian germplasm into
European stocks during the 18th and 19th centuries. The coexistence of such divergent mtDNA haplotypes for 100+ generations
is expected to lead to the presence of recombinant haplotypes if paternal transmission and recombination occur at a low frequency.
We found no evidence of such recombination events in the limited sample studied so far.
Received: 19 April 2000; Accepted: 15 November 2000 相似文献
10.
The mitochondrial DNA-encoded cytochrome oxidase subunit I (COI) gene and the nuclear DNA-encoded hsp60 gene from the euglenoid
protozoan Euglena gracilis were cloned and sequenced. The COI sequence represents the first example of a mitochondrial genome-encoded gene from this
organism. This gene contains seven TGG tryptophan codons and no TGA tryptophan codons, suggesting the use of the universal
genetic code. This differs from the situation in the mitochondrion of the related kinetoplastid protozoa, in which TGA codes
for tryptophan. In addition, a complete absence of CGN triplets may imply the lack of the corresponding tRNA species. COI
cDNAs from E. gracilis possess short 5′ and 3′ untranslated transcribed sequences and lack a 3′ poly[A] tail.
The COI gene does not require uridine insertion/deletion RNA editing, as occurs in kinetoplastid mitochondria, to be functional,
and no short guide RNA-like molecules could be visualized by labeling total mitochondrial RNA with [α-32P]GTP and guanylyl transferase. In spite of the differences in codon usage and the 3′ end structures of mRNAs, phylogenetic
analysis using the COI and hsp60 protein sequences suggests a monophyletic relationship between the mitochondrial genomes
of E. gracilis and of the kinetoplastids, which is consistent with the phylogenetic relationship of these groups previously obtained using
nuclear ribosomal RNA sequences.
Received: 5 March 1996 / Accepted: 31 July 1996 相似文献
11.
In Lactococcus lactis there is a protein, HisZ, in the histidine-biosynthetic operon that exhibits significant sequence identity with histidyl-tRNA
synthetase (HisRS) but does not aminoacylate tRNA. HisRS homologs that, like HisZ, cannot aminoacylate tRNA are represented
in a highly divergent set of bacteria (including an aquificale, cyanobacteria, firmicutes, and proteobacteria), yet are missing
from other bacteria, including mycrobacteria and certain proteobacteria. Phylogenetic analysis of the HisRS and HisRS-like
family suggests that the HisZ proteins form a monophyletic group that attaches outside the predominant bacterial HisRS clade.
These observations are consistent with a model in which the absences of HisZ from bacteria are due to its loss during evolution.
It has recently been shown that HisZ from L. lactis binds to the ATP-PRPP transferase (HisG) and that both HisZ and HisG are required for catalyzing the first reaction in histidine
biosynthesis. Phylogenetic analysis of HisG sequences shows conclusively that proteobacterial HisG and histidinol dehydrogenase
(HisD) sequences are paraphyletic and that the partition of the Proteobacteria associated with the presence/absence of HisZ corresponds to that based on HisG and HisD paraphyly. Our results suggest that
horizontal gene transfer played an important role in the evolution of the regulation of histidine biosynthesis.
Received: 16 July 1999 / Accepted: 4 January 2000 相似文献
12.
Modified purines are found in all organisms in the tRNA, rRNA, and even DNA, raising the possibility of an early role for
these compounds in the evolution of life. These include N
6-methyladenine, 1-methyladenine, N
6,N
6-dimethyladenine, 1-methylhypoxanthine, 1-methylguanine, and N
2-methylguanine. We find that these bases as well as a number of nonbiological modified purines can be synthesized from adenine
and guanine by the simple reaction of an amine or an amino group with adenine and guanine under the concentrated conditions
of the drying-lagoon or drying-beach model of prebiotic synthesis with yields as high as 50%. These compounds are therefore
as prebiotic as adenine and guanine and could have played an important role in the RNA world by providing additional functional
groups in ribozymes, especially for the construction of hydrophobic binding pockets.
Received: 7 August 1998 / Accepted: 31 December 1998 相似文献
13.
To date, the small nuclear 4.5SI RNA has only been studied in the rat (Rattus norvegicus). Combining PCR and hybridization analyses, we have revealed 4.5SI RNA homologues sequences in the genomes of four myomorph rodent families (Muridae, Cricetidae, Spalicidae, and Rhizomyidae),
and not in other myomorph families (Dipodidae, Zapodidae, Geomyidae, and Heteromyidae) or sciuromorph and caviomorph rodents.
By Northern-hybridization, 4.5SI RNA has been detected in the common rat (R. norvegicus, Muridae), golden hamster (Mesocricetus auratus, Cricetidae), and Russian mole rat (Spalax microphthalmus, Spalacidae), but not in the related great jerboa (Allactaga jaculus, Dipodidae) or in four non-myomorph rodent species tested. cDNA derived from 4.5SI RNA of M. auratus and S. microphthalmus has been cloned and sequenced. The hamster RNA is found to differ from rat 4.5SI RNA by only one nucleotide substitution. For the mole rat, two variants of 4.5SI RNA are detected: short (S) and long (L) with length 101 and 108 nt, respectively. The L variant differs from the S variant
as well as from murid and cricetid 4.5SI RNAs by both a 7 nt insertion and a varying number of nucleotide substitutions. The sequence similarity between the spalacid
S-variant and murid/crecitid variants of 4.5SI RNA is 90%. Judging from species distribution, 4.5SI RNA genes emerged during the same period of time as the related short interspersed element B2 arose. This occurred after
the divergence of Dipodidae lineage but before the branching of Spalicidae/Rhizomyidae lineage from a common myomorph rodent
stem. S variant genes seemed to emerge in a common ancestor of spalacids and rhizomyds whereas L variant genes formed in spalacids
following the divergence of these two families. The low rate of evolutionary changes of 4.5SI RNA, at least, in murids and cricetids (6 × 10−4 substitutions per site per million years), suggests that this RNA is under selection constraint and have a function. This
is a remarkable fact if the recent origin and narrow species distribution range of 4.5SI RNA genes is taken into account. Genes with narrow species distribution are proposed to be referred to as stenogenes.
Received: 11 December 2000 / Accepted: 27 August 2001 相似文献
14.
The heterotrophic theory of the origin of life is the only proposal available with experimental support. This comes from
the ease of prebiotic synthesis under strongly reducing conditions. The prebiotic synthesis of organic compounds by reduction
of CO2 to monomers used by the first organisms would also be considered an heterotrophic origin. Autotrophy means that the first
organisms biosynthesized their cell constituents as well as assembling them. Prebiotic synthetic pathways are all different
from the biosynthetic pathways of the last common ancestor (LCA). The steps leading to the origin of the metabolic pathways
are closer to prebiotic chemistry than to those in the LCA. There may have been different biosynthetic routes between the
prebiotic and the LCAs that played an early role in metabolism but have disappeared from extant organisms. The semienzymatic
theory of the origin of metabolism proposed here is similar to the Horowitz hypothesis but includes the use of compounds leaking
from preexisting pathways as well as prebiotic compounds from the environment. 相似文献
15.
Many of the biosynthetic pathways, especially those leading to the coenzymes, must have originated very early, perhaps before
enzymes were available to catalyze their synthesis. While a number of enzymatic reactions in metabolism are known to proceed
nonenzymatically, there are no examples of entire metabolic sequences that can be achieved in this manner. The most primitive
pathway for nicotinic acid biosynthesis is the reaction of aspartic acid with dihydroxyacetone phosphate. We report here that
nicotinic acid (NAc) and its metabolic precursor, quinolinic acid (QA), are produced in yields as high as 7% in a six-step
nonenzymatic sequence from aspartic acid and dihydroxyacetone phosphate (DHAP). The biosynthesis of ribose phosphate could
have produced DHAP and other three carbon compounds. Aspartic acid could have been available from prebiotic synthesis or from
the ribozyme synthesis of pyrimidines. These results suggest that NAD could have originated in the RNA world and that the
nonenzymatic biosynthesis of the cofactor nicotinamide could have been an inevitable consequence of life based on carbohydrates
and amino acids. The enzymes of the modern pathway were later added in any order.
Received: 22 May 2000 / Accepted: 7 August 2000 相似文献
16.
Complete sequences of mitochondrial DNA (mtDNA) are useful for the reconstruction of phylogenetic trees of mammals and, in
particular, for inferring higher-order relationships in mammals. In this study, we determined the complete sequence (16,705
bp) of the mtDNA of a Japanese megabat, the Ryukyu flying fox (Pteropus dasymallus). We analyzed this sequence phylogenetically by comparing it with the complete sequence of mtDNAs of 35 mammals in an effort
to reevaluate the enigmatic relationship between Megachiroptera and Microchiroptera and the relationships between them and
other mammals. Maximum-likelihood analysis of 12 concatenated mitochondrial proteins from 36 mammals strongly suggested the
monophyly of the order Chiroptera and its close relationship to Fereuungulata (Carnivora + Perissodactyla + Cetartiodactyla).
We estimated that megabats and microbats diverged approximately 58 MyrBP and discussed the origin and early evolution of Chiroptera
based on our findings.
Received: 28 January 2000 / Accepted: 30 June 2000 相似文献
17.
The secondary structure of rRNA internal transcribed spacer 2 is important in the process of ribosomal biogenesis. Trematode
ITS sequences are poorly conserved and difficult to align for phylogenetic comparisons above a family level. If a conserved
secondary structure can be identified, it can be used to guide primary sequence alignments. ITS2 sequences from 39 species
were compared. These species span four orders of trematodes (Echinostomiformes, Plagiorchiformes, Strigeiformes, and Paramphistomiformes)
and one monogenean (Gyrodactyliformes). The sequences vary in length from 251 to 431 bases, with an average GC content of
48%. The monogenean sequence could not be aligned with confidence to the trematodes. Above the family level trematode sequences
were alignable from the 5′ end for 139 bases. Secondary structure foldings predicted a four-domain model. Three folding patterns
were required for the apex of domain B. The folding pattern of domains C and D varies for each family. The structures display
a high GC content within stems. Bases A and U are favored in unpaired regions and variable sites cluster. This produces a
mosaic of conserved and variable regions with a structural conformation resistant to change. Two conserved strings were identified,
one in domain B and the other in domain C. The first site can be aligned to a processing site identified in yeast and rat.
The second site has been found in plants, and structural location appears to be important. A phylogenetic tree of the trematode
sequences, aligned with the aid of secondary structures, distinguishes the four recognized orders.
Received: 21 November 1997 / Accepted: 9 February 1998 相似文献
18.
Ding F Sharma S Chalasani P Demidov VV Broude NE Dokholyan NV 《RNA (New York, N.Y.)》2008,14(6):1164-1173
RNA molecules with novel functions have revived interest in the accurate prediction of RNA three-dimensional (3D) structure and folding dynamics. However, existing methods are inefficient in automated 3D structure prediction. Here, we report a robust computational approach for rapid folding of RNA molecules. We develop a simplified RNA model for discrete molecular dynamics (DMD) simulations, incorporating base-pairing and base-stacking interactions. We demonstrate correct folding of 150 structurally diverse RNA sequences. The majority of DMD-predicted 3D structures have <4 A deviations from experimental structures. The secondary structures corresponding to the predicted 3D structures consist of 94% native base-pair interactions. Folding thermodynamics and kinetics of tRNA(Phe), pseudoknots, and mRNA fragments in DMD simulations are in agreement with previous experimental findings. Folding of RNA molecules features transient, non-native conformations, suggesting non-hierarchical RNA folding. Our method allows rapid conformational sampling of RNA folding, with computational time increasing linearly with RNA length. We envision this approach as a promising tool for RNA structural and functional analyses. 相似文献
19.
Steinhauser S Beckert S Capesius I Malek O Knoop V 《Journal of molecular evolution》1999,48(3):303-312
RNA editing affects messenger RNAs and transfer RNAs in plant mitochondria by site-specific exchange of cytidine and uridine
bases in both seed and nonseed plants. Distribution of the phenomenon among bryophytes has been unclear since RNA editing
has been detected in some but not all liverworts and mosses. A more detailed understanding of RNA editing in plants required
extended data sets for taxa and sequences investigated. Toward this aim an internal region of the mitochondrial nad5 gene
(1104 nt) was analyzed in a large collection of bryophytes and green algae (Charales). The genomic nad5 sequences predict
editing in 30 mosses, 2 hornworts, and 7 simple thalloid and leafy liverworts (Jungermanniidae). No editing is, however, required
in seven species of the complex thalloid liverworts (Marchantiidae) and the algae. RNA editing among the Jungermanniidae,
on the other hand, reaches frequencies of up to 6% of codons being modified. Predictability of RNA editing from the genomic
sequences was confirmed by cDNA analysis in the mosses Schistostega pennata and Rhodobryum roseum, the hornworts Anthoceros husnotii and A. punctatus, and the liverworts Metzgeria conjugata and Moerckia flotoviana. All C-to-U nucleotide exchanges predicted to reestablish conserved codons were confirmed. Editing in the hornworts includes
the removal of genomic stop codons by frequent reverse U-to-C edits. Expectedly, no RNA editing events were identified by
cDNA analysis in the marchantiid liverworts Ricciocarpos natans, Corsinia coriandra, and Lunularia cruciata. The findings are discussed in relation to models on the phylogeny of land plants.
Received: 2 April 1998 / Accepted: 4 August 1998 相似文献
20.
The Rooting of the Universal Tree of Life Is Not Reliable 总被引:19,自引:0,他引:19
Several composite universal trees connected by an ancestral gene duplication have been used to root the universal tree of
life. In all cases, this root turned out to be in the eubacterial branch. However, the validity of results obtained from comparative
sequence analysis has recently been questioned, in particular, in the case of ancient phylogenies. For example, it has been
shown that several eukaryotic groups are misplaced in ribosomal RNA or elongation factor trees because of unequal rates of
evolution and mutational saturation. Furthermore, the addition of new sequences to data sets has often turned apparently reasonable
phylogenies into confused ones. We have thus revisited all composite protein trees that have been used to root the universal
tree of life up to now (elongation factors, ATPases, tRNA synthetases, carbamoyl phosphate synthetases, signal recognition
particle proteins) with updated data sets. In general, the two prokaryotic domains were not monophyletic with several aberrant
groupings at different levels of the tree. Furthermore, the respective phylogenies contradicted each others, so that various
ad hoc scenarios (paralogy or lateral gene transfer) must be proposed in order to obtain the traditional Archaebacteria–Eukaryota
sisterhood. More importantly, all of the markers are heavily saturated with respect to amino acid substitutions. As phylogenies
inferred from saturated data sets are extremely sensitive to differences in evolutionary rates, present phylogenies used to
root the universal tree of life could be biased by the phenomenon of long branch attraction. Since the eubacterial branch
was always the longest one, the eubacterial rooting could be explained by an attraction between this branch and the long branch
of the outgroup. Finally, we suggested that an eukaryotic rooting could be a more fruitful working hypothesis, as it provides,
for example, a simple explanation to the high genetic similarity of Archaebacteria and Eubacteria inferred from complete genome
analysis. 相似文献