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1.
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
2.
Hiroshi Wada Mari Kobayashi Riki Sato Nori Satoh Hitoshi Miyasaka Yoshihisa Shirayama 《Journal of molecular evolution》2002,54(1):118-128
To test the validity of intron–exon structure as a phylogenetic marker, the intron–exon structure of EF-1α genes was investigated
for starfish, acornworms, ascidians, larvaceans, and amphioxus and compared with that of vertebrates. Of the 11 distinct intron
insertion sites found within the coding regions of the deuterostome EF-1α genes, 7 are shared by several taxa, while the remainder
are unique to certain taxa. Examination of the shared introns of the deuterostome EF-1α gene revealed that independent intron
loss or intron insertion must have occurred in separate lineages of the deuterostome taxa. Maximum parsimony analysis of the
intron–exon data matrix recovered five parsimonious trees (consistency index = 0.867). From this result, we concluded that
the intron–exon structure of deuterostome EF-1α has evolved more dynamically than previously thought, rendering it unsuitable
as a phylogenetic marker. We also reconstructed an evolutionary history of intron insertion–deletion events on the deuterostome
phylogeny, based on several molecular phylogenetic studies. These analyses revealed that the deuterostome EF-1α gene has lost
individual introns more frequently than all introns simultaneously. 相似文献
3.
A number of proteins have been identified that contain prominent sequence signatures that are uniquely shared by the members
of the Deinococcus-Thermus genera and the cyanobacterial species but which are not found in any of the other eubacterial or archaebacterial homologs.
The proteins containing such sequence signatures include (1) the DnaJ/Hsp40 family of proteins, (2) DNA polymerase I, (3)
the protein synthesis elongation factor EF-Tu, and (4) the elongation factor EF-Ts. A strong affinity of the Deinococcus-Thermus species to cyanobacteria is also seen in the phylogenetic trees based on Hsp70 and DnaJ sequences. These results provide
strong evidence of a close and specific evolutionary relationship between species belonging to these two eubacterial divisions.
Received: 10 September 1997 / Accepted: 15 December 1997 相似文献
4.
Phylogenetic Relationships of Fungi, Plantae, and Animalia Inferred from Homologous Comparison of Ribosomal Proteins 总被引:6,自引:0,他引:6
The complete set of available ribosomal proteins was utilized, at both the peptidic and the nucleotidic level, to establish
that plants and metazoans form two sister clades relative to fungi. Different phylogenetic inference methods are applied to
the sequence data, using archeans as the outgroup. The evolutionary length of the internal branch within the eukaryotic crown
trichotomy is demonstrated to be, at most, one-tenth of the evolutionary length of the branch leading to the cenancester of
these three kingdoms.
Received: 1 November 1997 / Accepted: 7 January 1998 相似文献
5.
6.
The AAA proteins (ATPases Associated with a variety of cellular Activities) are found in eubacterial, archaebacterial, and eukaryotic species and participate in a large number of cellular
processes, including protein degradation, vesicle fusion, cell cycle control, and cellular secretory processes. The AAA proteins
are characterized by the presence of a 230 to 250-amino acid ATPase domain referred to as the Conserved ATPase Domain or CAD. Phylogenetic analysis of 133 CAD sequences from 38 species reveal that AAA CADs are organized into discrete
groups that are related not only in structure but in cellular function. Evolutionary analyses also indicate that the CAD was
present in the last common ancestor of eubacteria, archaebacteria, and eukaryotes. The eubacterial CADs are found in metalloproteases,
while CAD-containing proteins in the archaebacterial and eukaryotic lineages appear to have diversified by a series of gene
duplication events that lead to the establishment of different functional AAA proteins, including proteasomal regulatory,
NSF/Sec, and Pas proteins. The phylogeny of the CADs provides the basis for establishing the patterns of evolutionary change
that characterize the AAA proteins.
Received: 28 January 1997 / Accepted: 8 May 1997 相似文献
7.
The symbiotic protists of the lower termite have been regarded as a model of early-branched eukaryotes because of their simple cellular systems and morphological features. However, cultivation of these symbiotic protists is very difficult. For this reason, these interesting protists have not been well characterized in terms of their molecular biology. In research on these organisms which have not yet been cultivated, we developed a method for retrieving specific genes from a small number of cells, through micromanipulation without axenic cultivation, and we obtained EF-1 alpha and alpha-tubulin genes from members of the Hypermastigida--the parabasalid protist Trichonympha agilis and the oxymonad protists Pyrsonympha grandis and Dinenympha exilis--from the termite Reticulitermes speratus gut community. Results of phylogenetic analysis of the amino acid sequences of both proteins, EF-1 alpha and alpha-tubulin, indicate that the hypermastigid, parabasalid, and oxymonad protists do not share a close common ancestor. In addition, although the EF-1 alpha phylogeny indicates that these two groups of protists branched at an early stage of eukaryotic evolution, the alpha-tubulin phylogeny indicates that these protists can be assigned to two diversified clades. As shown in a recent investigation of alpha-tubulin phylogeny, eukaryotic organisms can be divided into three classes: an animal--parabasalids clade, a plant--protists clade, and the diplomonads. In this study, we show that parabasalids, including hypermastigids, can be classified as belonging to the animal--parabasalids clade and the early-branching eukaryote oxymonads can be classified as belonging to the plant--protists clade. Our findings suggest that these protists have a cellular microtubule system that has diverged considerably, and it seems that such divergence of the microtubule system occurred in the earliest stage of eukaryotic evolution. 相似文献
8.
Patrick J. Keeling Naomi M. Fast Geoff I. McFadden 《Journal of molecular evolution》1998,47(6):649-655
Eubacterial and eukaryotic translation initiation systems have very little in common, and therefore the evolutionary events
that gave rise to these two disparate systems are difficult to ascertain. One common feature is the presence of initiation,
elongation, and release factors belonging to a large GTPase superfamily. One of these initiation factors, the γ subunit of
initiation factor 2 (eIF-2γ), is found only in eukaryotes and archaebacteria. We have sequenced eIF-2γ gene fragments from
representative diplomonads, parabasalia, and microsporidia and used these new sequences together with new archaebacterial
homologues to examine the phylogenetic position of eIF-2γ within the GTPase superfamily. The archaebacterial and eukaryotic
eIF-2γ proteins are found to be very closely related, and are in turn related to SELB, the selenocysteine-specific elongation
factor from eubacteria. The overall topology of the GTPase tree further suggests that the eIF-2γ/SELB group may represent
an ancient subfamily of GTPases that diverged prior to the last common ancestor of extant life.
Received: 2 January 1998 / Accepted: 1 June 1998 相似文献
9.
The relative rates of change for eight sets of ubiquitous proteins were determined by a test in which anciently duplicated
paralogs are used to root the universal tree and distances are calculated between each taxonomic group and the last common
ancestor. The sets included ATPase subunits, elongation factors, signal recognition particle and its receptor, three sets
of tRNA synthetases, transcarbamoylases, and an internal duplication in carbamoyl phosphate synthase. In each case phylogenetic
trees were constructed and the distances determined for all pairs. Taken over the period of time since their last common ancestor,
average evolutionary rates are remarkably similar for Bacteria and Eukarya, but Archaea exhibit a significantly slower average
rate.
Received: 30 December 1999 / Accepted: 5 April 2000 相似文献
10.
We studied the evolutionary history of two homologous proteins of the human complement system, factor H (FH) and the α chain
of the C4b binding protein (C4bpα), and included in this study the related proteins from the barred sand bass (P. nebulifer) and the nematode C. elegans. Phylogenetic trees inferred from individual short consensus repeats (SCRs) and divergence among repeats from different genes
suggest that human FH has a much closer evolutionary relationship to putative complement components from P. nebulifer and C. elegans than does the C4bpα. This indicates that a member of the alternative pathway of the complement system (FH) has an ancient
origin, while a homologous member of the classical pathway (C4bpα) appeared later in evolutionary history as a result of gene
duplication. The ancient evolutionary position of FH is in agreement with the suggestion that the alternative pathway of the
complement system is older than the classical pathway. Phylogenetic analysis also shows that the sand bass cofactor protein
SBP1 and cofactor related protein SBCRP-1 have diverged very recently.
Received: 1 December 1997 / Accepted: 3 June 1998 相似文献
11.
Olivier Verneau François Catzeflis Anthony V. Furano 《Journal of molecular evolution》1997,45(4):424-436
We determined ∼215 bp of DNA sequence from the 3′-untranslated region (UTR) of 240 cloned L1 (LINE-1) elements isolated from
22 species of Rattus sensu lato and Rattus sensu stricto murine rodents. The sequences were sorted into different L1 subfamilies, and oligonucleotides cognate to them
were hybridized to genomic DNA of various taxa. From the distribution of the L1 subfamilies in the various species, we inferred
the partial phylogeny of Rattus sensu lato. The four Maxomys species comprise a well-defined clade separate from a monophyletic cluster that contains the two Leopoldamys and four Niviventer species. The Niviventer/Leopoldamys clade, in turn, shares a node with the clade that contains Berylmys, Sundamys, Bandicota, and Rattus sensu stricto. The evolutionary relationships that we deduced agree with and significantly extend the phylogeny of Rattus sensu lato established by other molecular criteria. Furthermore, the L1 amplification events scored here produced a unique
phylogenetic tree, that is, in no case did a character (a given L1 amplification event) appear on more than one branch. The
lack of homoplasy found in this study supports the robustness of L1 amplification events as phylogenetic markers for the study
of mammalian evolution.
Received: 8 November 1996 / Accepted: 11 April 1997 相似文献
12.
The evolutionary patterns of hepatitis C virus (HCV), including the best-fitting nucleotide substitution model and the molecular
clock hypothesis, were investigated by analyzing full-genome sequences available in the HCV database. The likelihood ratio
test allowed us to discriminate among different evolutionary hypotheses. The phylogeny of the six major HCV types was accurately
inferred, and the final tree was rooted by reconstructing the hypothetical HCV common ancestor with the maximum likelihood
method. The presence of phylogenetic noise and the relative nucleotide substitution rates in the different HCV genes were
also examined. These results offer a general guideline for the future of HCV phylogenetic analysis and also provide important
insights on HCV origin and evolution.
Received: 13 January 2001 / Accepted: 21 June 2001 相似文献
13.
Phylogenetic studies based on DNA sequences typically ignore the potential occurrence of recombination, which may produce different alignment regions with different evolutionary histories. Traditional phylogenetic methods assume that a single history underlies the data. If recombination is present, can we expect the inferred phylogeny to represent any of the underlying evolutionary histories? We examined this question by applying traditional phylogenetic reconstruction methods to simulated recombinant sequence alignments. The effect of recombination on phylogeny estimation depended on the relatedness of the sequences involved in the recombinational event and on the extent of the different regions with different phylogenetic histories. Given the topologies examined here, when the recombinational event was ancient, or when recombination occurred between closely related taxa, one of the two phylogenies underlying the data was generally inferred. In this scenario, the evolutionary history corresponding to the majority of the positions in the alignment was generally recovered. Very different results were obtained when recombination occurred recently among divergent taxa. In this case, when the recombinational breakpoint divided the alignment in two regions of similar length, a phylogeny that was different from any of the true phylogenies underlying the data was inferred. 相似文献
14.
Berry S 《Journal of molecular evolution》2002,54(5):595-613
All organisms rely on chemiosmotic membrane systems for energy transduction; the great variety of participating proteins
and pathways can be reduced to a few universal principles of operation. This chemical basis of bioenergetics is reviewed with
respect to the origin and early evolution of life. For several of the cofactors which play important roles in bioenergetic
reactions, plausible prebiotic sources have been proposed, and it seems likely that these cofactors were present before elaborate
protein structures. In particular, the hydrophobic quinones require only a membrane-enclosed compartment to yield a minimum
chemiosmotic system, since they can couple electron transport and proton translocation in a simple way. It is argued that
the central features of modern bioenergetics, such as the coupling of redox reactions and ion translocation at the cytoplasmic
membrane, probably are ancient features which arose early during the process of biogenesis. The notion of a thermophile root
of the universal phylogenetic tree has been discussed controversially, nevertheless, thermophiles are interesting model organisms
for reconstructing the origin of chemiosmotic systems, since they are often acidophiles and anaerobic respirers exploiting
iron–sulfur chemistry. This perspective can help to explain the prominent role of iron–sulfur proteins in extant biochemistry
as well as the origin of both respiration and proton extrusion within the context of a possible origin of life in the vicinity
of hot vents.
Received: 6 June 2001 / Accepted: 16 October 2001 相似文献
15.
Ayako Yamamoto Tetsuo Hashimoto Emiko Asaga Masami Hasegawa Nobuichi Goto 《Journal of molecular evolution》1997,44(1):98-105
Major parts of amino-acid-coding regions of elongation factor (EF)-1α and EF-2 in Trichomonas tenax were amplified by PCR from total genomic DNA and the products were cloned into a plasmid vector, pGEM-T. The three clones
from each of the products of the EF-1α and EF-2 were isolated and sequenced. The insert DNAs of the clones containing EF-1α
coding regions were each 1,185 bp long with the same nucleotide sequence and contained 53.1% of G + C nucleotides. Those of
the clones containing EF-2 coding regions had two different sequences; one was 2,283 bp long and the other was 2,286 bp long,
and their G + C contents were 52.5 and 52.9%, respectively. The copy numbers of the EF-1α and EF-2 gene per chromosome were
estimated as four and two, respectively.
The deduced amino acid sequences obtained by the conceptual translation were 395 residues from EF-1α and 761 and 762 residues
from the EF-2s. The sequences were aligned with the other eukaryotic and archaebacterial EF-1αs and EF-2s, respectively.
The phylogenetic position of T. tenax was inferred by the maximum likelihood (ML) method using the EF-1α and EF-2 data sets. The EF-1α analysis suggested that
three mitochondrion-lacking protozoa, Glugea plecoglossi, Giardia lamblia, and T. tenax, respectively, diverge in this order in the very early phase of eukaryotic evolution. The EF-2 analysis also supported the
divergence of T. tenax to be immediately next to G. lamblia.
Received: 15 February 1996 / Accepted: 28 June 1996 相似文献
16.
The ribosomal protection proteins (RPPs) mediate the resistance to tetracycline (TC) in Gram-positive and Gram-negative bacteria.
The RPPs display sequence similarity to translation elongation factors, EF-G/EF-2 and EF-Tu/EF-1α. To determine the evolutionary
origin of the RPPs, we constructed a composite phylogenetic tree of the RPPs, EF-G/EF-2 and EF-Tu/EF-1α. This tree includes
two universal trees for the EF-G/EF-2 and EF-Tu/EF-1α, which form clusters corresponding to the respective two groups of proteins
from three superkingdoms. The cluster of RPPs was placed at a point between the EF-G/EF-2 and EF-Tu/EF-1α clusters. The branch
length (substitutions/site) between the node for the RPP cluster and the primary divergence of the RPPs was statistically
shorter than that between the node for this cluster and the primary divergence in the EF-G/EF-2 cluster. This indicates that
the RPPs derived through duplication and divergence of the ancient GTPase before the divergence of the three superkingdoms.
Furthermore, this suggests the RPPs’ extant function occurred before the streptomycetes that include the TC-producing strains.
Therefore, the RPPs evolved independent of the presence of TCs and serve a function other than antibiotic resistance. The
RPPs may provide ribosomal protection against other chemical substances in the environment.
Reviewing
Editor: Dr. Margaret Riley
Takeshi Kobayashi, Lisa Nonaka have contributed significantly to the research and preparation of this article. 相似文献
17.
18.
Phylogenetic Relationships of the Glycolytic Enzyme, Glyceraldehyde-3-Phosphate Dehydrogenase, from Parabasalid Flagellates 总被引:4,自引:0,他引:4
Over 90% of the open reading frame of gap genes for glycolytic glyceraldehyde-3-phosphate dehydrogenase (GAPDH; EC 1.2.1.12) was obtained with PCR from five species
of Parabasala. With gap1 from Trichomonas vaginalis obtained earlier, the data include two sequences each for three species. All sequences were colinear with T. vaginalis gap1 and shared with it as a synapomorphy a 10- to 11-residue insertion not found in any other gap and an S-loop with characteristic features of eubacterial GAPDH. All residues known to be highly conserved in this enzyme
were present. The parabasalid sequences formed a robust monophyletic group in phylogenetic reconstructions with distance-based,
maximum-parsimony, and maximum-likelihood methods. The two genes of the amphibian commensal, Trichomitus batrachorum, shared a common ancestor with the rest, which separate into two well-supported lineages. T. vaginalis and Tetratrichomonas gallinarum (both representatives of Trichomonadinae) formed one, while Monocercomonas sp. and Tritrichomonas foetus formed the other. These data agreed with and/or were close to published reconstructions based on other macromolecules. They
did not support the ancestral position of Monocercomonas sp. proposed on the basis of morphological characteristics but confirmed an early emergence of Trichomitus batrachorum. The sequence pairs obtained from three species indicated either gene duplications subsequent to the divergence of the corresponding
lineages or a strong gene conversion later in these lineages. The parabasalid clade was a robust part of the eubacterial radiation
of GAPDH and showed no relationships to the clade that contained all other eukaryotic gap genes. The data clearly reveal that the members of this lineage use in their glycolytic pathway a GAPDH species with properties
and an evolutionary history that are unique among all eukaryotes studied so far.
Received: 28 April 1997 / Accepted: 14 October 1997 相似文献
19.
Primary Structure and Phylogenetic Relationships of a Malate Dehydrogenase Gene from Giardia lamblia
The lactate and malate dehydrogenases comprise a complex protein superfamily with multiple enzyme homologues found in eubacteria,
archaebacteria, and eukaryotes. In this study we describe the sequence and phylogenetic relationships of a malate dehydrogenase
(MDH) gene from the amitochondriate diplomonad protist, Giardia lamblia. Parsimony, distance, and maximum-likelihood analyses of the MDH protein family solidly position G. lamblia MDH within a eukaryote cytosolic MDH clade, to the exclusion of chloroplast, mitochondrial, and peroxisomal homologues. Furthermore,
G. lamblia MDH is specifically related to a homologue from Trichomonas vaginalis. This MDH topology, together with published phylogenetic analyses of β-tubulin, chaperonin 60, valyl-tRNA synthetase, and
EF-1α, suggests a sister-group relationship between diplomonads and parabasalids. Since these amitochondriate lineages contain
genes encoding proteins which are characteristic of mitochondria and α-proteobacteria, their shared ancestry suggests that
mitochondrial properties were lost in the common ancestor of both groups.
Received: 14 September 1998 / Accepted: 29 December 1998 相似文献
20.
Covarion shifts cause a long-branch attraction artifact that unites microsporidia and archaebacteria in EF-1alpha phylogenies 总被引:1,自引:0,他引:1
Microsporidia branch at the base of eukaryotic phylogenies inferred from translation elongation factor 1alpha (EF-1alpha) sequences. Because these parasitic eukaryotes are fungi (or close relatives of fungi), it is widely accepted that fast-evolving microsporidian sequences are artifactually "attracted" to the long branch leading to the archaebacterial (outgroup) sequences ("long-branch attraction," or "LBA"). However, no previous studies have explicitly determined the reason(s) why the artifactual allegiance of microsporidia and archaebacteria ("M + A") is recovered by all phylogenetic methods, including maximum likelihood, a method that is supposed to be resistant to classical LBA. Here we show that the M + A affinity can be attributed to those alignment sites associated with large differences in evolutionary site rates between the eukaryotic and archaebacterial subtrees. Therefore, failure to model the significant evolutionary rate distribution differences (covarion shifts) between the ingroup and outgroup sequences is apparently responsible for the artifactual basal position of microsporidia in phylogenetic analyses of EF-1alpha sequences. Currently, no evolutionary model that accounts for discrete changes in the site rate distribution on particular branches is available for either protein or nucleotide level phylogenetic analysis, so the same artifacts may affect many other "deep" phylogenies. Furthermore, given the relative similarity of the site rate patterns of microsporidian and archaebacterial EF-1alpha proteins ("parallel site rate variation"), we suggest that the microsporidian orthologs may have lost some eukaryotic EF-1alpha-specific nontranslational functions, exemplifying the extreme degree of reduction in this parasitic lineage. 相似文献