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1.
The Root of the Universal Tree of Life Inferred from Anciently Duplicated Genes Encoding Components of the Protein-Targeting Machinery 总被引:5,自引:0,他引:5
The key protein of the signal recognition particle (termed SRP54 for Eucarya and Ffh for Bacteria) and the protein (termed
SRα for Eucarya and Ftsy for bacteria) involved in the recognition and binding of the ribosome SRP nascent polypeptide complex
are the products of an ancient gene duplication that appears to predate the divergence of all extant taxa. The paralogy of
the genes encoding the two proteins (both of which are GTP triphosphatases) is argued by obvious sequence similarities between
the N-terminal half of SRP54(Ffh) and the C-terminal half of SRα(Ftsy). This enables a universal phylogeny based on either
protein to be rooted using the second protein as an outgroup. Phylogenetic trees inferred by various methods from an alignment
(220 amino acid positions) of the shared SRP54(Ffh) and SRα(Ftsy) regions generate two reciprocally rooted universal trees
corresponding to the two genes. The root of both trees is firmly positioned between Bacteria and Archaea/Eucarya, thus providing
strong support for the notion (Iwabe et al. 1989; Gogarten et al. 1989) that the first bifurcation in the tree of life separated
the lineage leading to Bacteria from a common ancestor to Archaea and Eucarya. None of the gene trees inferred from the two
paralogues support a paraphyletic Archaea with the crenarchaeota as a sister group to Eucarya.
Received: 19 March 1998 / Accepted: 5 June 1998 相似文献
2.
Syvanen M 《Journal of molecular evolution》2002,54(2):258-266
The deduced amino acid sequences from 1200 Haemophilus influenzae genes was compared to a data set that contained the orfs from yeast, two different Archaea and the Gram+ and Gram− bacteria,
Bacillus subtilis and Escherichia coli. The results of the comparison yielded a 26 orthologous gene set that had at least one representative from each of the four
groups. A four taxa phylogenetic relationship for these 26 genes was determined. The statistical significance of each minimal
tree was tested against the two alternative four taxa trees. The result was that four genes significantly supported the (Archaea,
Eukaryota) (Gram+, Gram−) topology, two genes supported the one where Gram− and Eukaryota form a clade, and one gene supported
the tree where Gram+ and Eukaryota define one clade. The remaining genes do not uniquely support any phylogeny, thereby collapsing
the two central nodes into a single node. These are referred to as star phylogenies.
I offer a new suggestion for the mechanism that gave rise to the star phylogenies. Namely, these are genes that are younger
than the underlying lineages that currently harbor them. This hypothesis is examined with two proteins that display the star
phylogeny; namely onithine transcarbamylase and tryptophan synthetase. It is shown, using the distance matrix rate test, that
the rate of evolution of these two proteins is comparable to a control gene when rates are determined by comparing closely
related species. This implies that the genes under comparison experience comparable functional constraint. However, when the
genes from remotely related species are compared, a plateau is encountered. Since we see no unusual levels of functional constraint
this plateau cannot be attributed to the divergence of the protein having reached saturation. The simplest explanation is
that the genes displaying the star phylogenies were introduced after Archaea, Eukaryota, and Bacteria had diverged from one
another. They presumably spread through life by horizontal gene transfer.
Received: 12 July 2001 / Accepted: 27 July 2001 相似文献
3.
Maximum likelihood (ML) phylogenies based on 9,957 amino acid (AA) sites of 45 proteins encoded in the plastid genomes of
Cyanophora, a diatom, a rhodophyte (red algae), a euglenophyte, and five land plants are compared with respect to several properties
of the data, including between-site rate variation and aberrant amino acid composition in individual species. Neighbor-joining
trees from AA LogDet distances and ML analyses are seen to be congruent when site rate variability was taken into account.
Four feasible trees are identified in these analyses, one of which is preferred, and one of which is almost excluded by statistical
criteria. A transition probability matrix for the general reversible Markov model of amino acid substitutions is estimated
from the data, assuming each of these four trees. In all cases, the tree with diatom and rhodophyte as sister taxa was clearly
favored. The new transition matrix based on the best tree, called cpREV, takes into account distinct substitution patterns
in plastid-encoded proteins and should be useful in future ML inferences using such data. A second rate matrix, called cpREV*,
based on a weighted sum of rate matrices from different trees, is also considered.
Received: 3 June 1999 / Accepted: 26 November 1999 相似文献
4.
It is now well-established that compositional bias in DNA sequences can adversely affect phylogenetic analysis based on those
sequences. Phylogenetic analyses based on protein sequences are generally considered to be more reliable than those derived
from the corresponding DNA sequences because it is believed that the use of encoded protein sequences circumvents the problems
caused by nucleotide compositional biases in the DNA sequences. There exists, however, a correlation between AT/GC bias at
the nucleotide level and content of AT- and GC-rich codons and their corresponding amino acids. Consequently, protein sequences
can also be affected secondarily by nucleotide compositional bias. Here, we report that DNA bias not only may affect phylogenetic
analysis based on DNA sequences, but also drives a protein bias which may affect analyses based on protein sequences. We present
a striking example where common phylogenetic tools fail to recover the correct tree from complete animal mitochondrial protein-coding
sequences. The data set is very extensive, containing several thousand sites per sequence, and the incorrect phylogenetic
trees are statistically very well supported. Additionally, neither the use of the LogDet/paralinear transform nor removal
of positions in the protein alignment with AT- or GC-rich codons allowed recovery of the correct tree. Two taxa with a large
compositional bias continually group together in these analyses, despite a lack of close biological relatedness. We conclude
that even protein-based phylogenetic trees may be misleading, and we advise caution in phylogenetic reconstruction using protein
sequences, especially those that are compositionally biased.
Received: 19 February 1998 / Accepted: 28 August 1998 相似文献
5.
Bernard Labedan Anne Boyen Margot Baetens Daniel Charlier Pingguo Chen Raymond Cunin Virginie Durbeco Nicolas Glansdorff Guy Herve Christianne Legrain Ziyuan Liang Christina Purcarea Martine Roovers Rony Sanchez Thia-Lin Toong Marc Van de Casteele Françoise van Vliet Ying Xu Yuan-Fu Zhang 《Journal of molecular evolution》1999,49(4):461-473
Forty-four sequences of ornithine carbamoyltransferases (OTCases) and 33 sequences of aspartate carbamoyltransferases (ATCases)
representing the three domains of life were multiply aligned and a phylogenetic tree was inferred from this multiple alignment.
The global topology of the composite rooted tree (each enzyme family being used as an outgroup to root the other one) suggests
that present-day genes are derived from paralogous ancestral genes which were already of the same size and argues against
a mechanism of fusion of independent modules. A closer observation of the detailed topology shows that this tree could not
be used to assess the actual order of organismal descent. Indeed, this tree displays a complex topology for many prokaryotic
sequences, with polyphyly for Bacteria in both enzyme trees and for the Archaea in the OTCase tree. Moreover, representatives
of the two prokaryotic Domains are found to be interspersed in various combinations in both enzyme trees. This complexity
may be explained by assuming the occurrence of two subfamilies in the OTCase tree (OTC α and OTC β) and two other ones in
the ATCase tree (ATC I and ATC II). These subfamilies could have arisen from duplication and selective losses of some differentiated
copies during the successive speciations. We suggest that Archaea and Eukaryotes share a common ancestor in which the ancestral
copies giving the present-day ATC II/OTC β combinations were present, whereas Bacteria comprise two classes: one containing
the ATC II/OTC α combination and the other harboring the ATC I/OTC β combination. Moreover, multiple horizontal gene transfers
could have occurred rather recently amongst prokaryotes. Whichever the actual history of carbamoyltransferases, our data suggest
that the last common ancestor to all extant life possessed differentiated copies of genes coding for both carbamoyltransferases,
indicating it as a rather sophisticated organism. 相似文献
6.
James R. Brown Frank T. Robb Robert Weiss W. Ford Doolittle 《Journal of molecular evolution》1997,45(1):9-16
Each amino acid is attached to its cognate tRNA by a distinct aminoacyl-tRNA synthetase (aaRS). The conventional evolutionary
view is that the modern complement of synthetases existed prior to the divergence of eubacteria and eukaryotes. Thus comparisons
of prokaryotic and eukaryotic aminoacyl-tRNA synthetases of the same type (charging specificity) should show greater sequence
similarities than comparisons between synthetases of different types—and this is almost always so. However, a recent study
[Ribas de Pouplana L, Furgier M, Quinn CL, Schimmel P (1996) Proc Natl Acad Sci USA 93:166–170] suggested that tryptophanyl- (TrpRS) and tyrosyl-tRNA (TyrRS) synthetases of the Eucarya (eukaryotes) are more
similar to each other than either is to counterparts in the Bacteria (eubacteria). Here, we reexamine the evolutionary relationships
of TyrRS and TrpRS using a broader range of taxa, including new sequence data from the Archaea (archaebacteria) as well as
species of Eucarya and Bacteria. Our results differ from those of Ribas de Pouplana et al.: All phylogenetic methods support
the separate monophyly of TrpRS and TyrRS. We attribute this result to the inclusion of the archaeal data which might serve
to reduce long branch effects possibly associated with eukaryotic TrpRS and TyrRS sequences. Furthermore, reciprocally rooted
phylogenies of TrpRS and TyrRS sequences confirm the closer evolutionary relationship of Archaea to eukaryotes by placing
the root of the universal tree in the Bacteria.
Received: 7 December 1996 / Accepted: 11 February 1997 相似文献
7.
The phylogenetic position of hagfishes in vertebrate evolution is currently controversial. The 18S and 28S rRNA trees support
the monophyly of hagfishes and lampreys. In contrast, the mitochondrial DNAs suggest the close association of lampreys and
gnathostomes. To clarify this controversial issue, we have conducted cloning and sequencing of the four nuclear DNA–coded
single-copy genes encoding the triose phosphate isomerase, calreticulin, and the largest subunit of RNA polymerase II and
III. Based on these proteins, together with the Mn superoxide dismutase for which hagfish and lamprey sequences are available
in database, phylogenetic trees have been inferred by the maximum likelihood (ML) method of protein phylogeny. It was shown
that all the five proteins prefer the monophyletic tree of cyclostomes, and the total log-likelihood of the five proteins
significantly supports the cyclostome monophyly at the level of ±1 SE. The ML trees of aldolase family comprising three nonallelic
isoforms and the complement component group comprising C3, C4, and C5, both of which diverged during vertebrate evolution
by gene duplications, also suggest the cyclostome monophyly.
Received: 28 April 1999 / Accepted: 30 June 1999 相似文献
8.
Mitochondrial Genes Collectively Suggest the Paraphyly of Crustacea with Respect to Insecta 总被引:9,自引:0,他引:9
Erik García-Machado Malgorzata Pempera Nicole Dennebouy Mario Oliva-Suarez Jean-Claude Mounolou Monique Monnerot 《Journal of molecular evolution》1999,49(1):142-149
Complete sequences of seven protein coding genes from Penaeus notialis mitochondrial DNA were compared in base composition and codon usage with homologous genes from Artemia franciscana and four insects. The crustacean genes are significantly less A + T-rich than their counterpart in insects and the pattern
of codon usage (ratio of G + C-rich versus A + T-rich codon) is less biased. A phylogenetic analysis using amino acid sequences
of the seven corresponding polypeptides supports a sister-taxon status for mollusks–annelid and arthropods. Furthermore, a
distance matrix-based tree and two most-parsimonious trees both suggest that crustaceans are paraphyletic with respect to
insects. This is also supported by the inclusion of Panulirus argus COII (complete) and COI and COIII (partial) sequence data. From analysis of single and combined genes to infer phylogenies,
it is observed that obtained from single genes are not well supported in most topologies cases and notably differ from that
of the tree based on all seven genes.
Received: 25 August 1998 / Accepted: 8 March 1999 相似文献
9.
The cytochrome b gene as a phylogenetic marker: the limits of resolution for analyzing relationships among cichlid fishes 总被引:12,自引:0,他引:12
The mitochondrial cytochrome b (cyt-b) gene is widely used in systematic studies to resolve divergences at many taxonomic levels. The present study focuses mainly
on the utility of cyt-b as a molecular marker for inferring phylogenetic relationship at various levels within the fish family Cichlidae. A total
of 78 taxa were used in the present analysis, representing all the major groups in the family Cichlidae (72 taxa) and other
families from the suborders Labroidei and Percoidei. Gene trees obtained from cyt-b are compared to a published total evidence tree derived from previous studies. Minimum evolution trees based on cyt-b data resulted in topologies congruent with all previous analyses. Parsimony analyses downweighting transitions relative to
transversions (ts1:tv4) or excluding transitions at third codon positions resulted in more robust bootstrap support for recognized
clades than unweighted parsimony. Relative rate tests detected significantly long branches for some taxa (LB taxa) which were
composed mainly by dwarf Neotropical cichlids. An improvement of the phylogenetic signal, as shown by the four-cluster likelihood
mapping analysis, and higher bootstrap values were obtained by excluding LB taxa. Despite some limitations of cyt-b as a phylogenetic marker, this gene either alone or in combination with other data sets yields a tree that is in agreement
with the well-established phylogeny of cichlid fish.
Received: 11 October 2000 / Accepted: 26 February 2001 相似文献
10.
Goremykin VV Holland B Hirsch-Ernst KI Hellwig FH 《Molecular biology and evolution》2005,22(9):1813-1822
Determining the phylogenetic relationships among the major lines of angiosperms is a long-standing problem, yet the uncertainty as to the phylogenetic affinity of these lines persists. While a number of studies have suggested that the ANITA (Amborella-Nymphaeales-Illiciales-Trimeniales-Aristolochiales) grade is basal within angiosperms, studies of complete chloroplast genome sequences also suggested an alternative tree, wherein the line leading to the grasses branches first among the angiosperms. To improve taxon sampling in the existing chloroplast genome data, we sequenced the chloroplast genome of the monocot Acorus calamus. We generated a concatenated alignment (89,436 positions for 15 taxa), encompassing almost all sequences usable for phylogeny reconstruction within spermatophytes. The data still contain support for both the ANITA-basal and grasses-basal hypotheses. Using simulations we can show that were the ANITA-basal hypothesis true, parsimony (and distance-based methods with many models) would be expected to fail to recover it. The self-evident explanation for this failure appears to be a long-branch attraction (LBA) between the clade of grasses and the out-group. However, this LBA cannot explain the discrepancies observed between tree topology recovered using the maximum likelihood (ML) method and the topologies recovered using the parsimony and distance-based methods when grasses are deleted. Furthermore, the fact that neither maximum parsimony nor distance methods consistently recover the ML tree, when according to the simulations they would be expected to, when the out-group (Pinus) is deleted, suggests that either the generating tree is not correct or the best symmetric model is misspecified (or both). We demonstrate that the tree recovered under ML is extremely sensitive to model specification and that the best symmetric model is misspecified. Hence, we remain agnostic regarding phylogenetic relationships among basal angiosperm lineages. 相似文献
11.
Genomic trees have been constructed based on the presence and absence of families of protein-encoding genes observed in 27
complete genomes, including genomes of 15 free-living organisms. This method does not rely on the identification of suspected
orthologs in each genome, nor the specific alignment used to compare gene sequences because the protein-encoding gene families
are formed by grouping any protein with a pairwise similarity score greater than a preset value. Because of this all inclusive
grouping, this method is resilient to some effects of lateral gene transfer because transfers of genes are masked when the
recipient genome already has a homolog (not necessarily an ortholog) of the incoming gene. Of 71 genes suspected to have been
laterally transferred to the genome of Aeropyrum pernix, only approximately 7 to 15 represent genes where a lateral gene transfer appears to have generated homoplasy in our character
dataset. The genomic tree of the 15 free-living taxa includes six different bacterial orders, six different archaeal orders,
and two different eukaryotic kingdoms. The results are remarkably similar to results obtained by analysis of rRNA. Inclusion
of the other 12 genomes resulted in a tree only broadly similar to that suggested by rRNA with at least some of the differences
due to artifacts caused by the small genome size of many of these species. Very small genomes, such as those of the two Mycoplasma genomes included, fall to the base of the Bacterial domain, a result expected due to the substantial gene loss inherent to
these lineages. Finally, artificial ``partial genomes' were generated by randomly selecting ORFs from the complete genomes
in order to test our ability to recover the tree generated by the whole genome sequences when only partial data are available.
The results indicated that partial genomic data, when sampled randomly, could robustly recover the tree generated by the whole
genome sequences.
Received: 30 May 2001 / Accepted: 10 October 2001 相似文献
12.
Bocchetta M Gribaldo S Sanangelantoni A Cammarano P 《Journal of molecular evolution》2000,50(4):366-380
The phylogenetic placement of the Aquifex and Thermotoga lineages has been inferred from (i) the concatenated ribosomal proteins S10, L3, L4, L23, L2, S19, L22, and S3 encoded in
the S10 operon (833 aa positions); (ii) the joint sequences of the elongation factors Tu(1α) and G(2) coded by the str operon tuf and fus genes (733 aa positions); and (iii) the joint RNA polymerase β- and β′-type subunits encoded in the rpoBC operon (1130 aa positions). Phylogenies of r-protein and EF sequences support with moderate (r-proteins) to high statistical confidence (EFs) the placement of the two hyperthermophiles at the base of the bacterial clade
in agreement with phylogenies of rRNA sequences. In the more robust EF-based phylogenies, the branching of Aquifex and Thermotoga below the successive bacterial lineages is given at bootstrap proportions of 82% (maximum likelihood; ML) and 85% (maximum
parsimony; MP), in contrast to the trees inferred from the separate EF-Tu(1α) and EF-G(2) data sets, which lack both resolution
and statistical robustness. In the EF analysis MP outperforms ML in discriminating (at the 0.05 level) trees having A. pyrophilus and T. maritima as the most basal lineages from competing alternatives that have (i) mesophiles, or the Thermus genus, as the deepest bacterial radiation and (ii) a monophyletic A. pyrophilus–T. maritima cluster situated at the base of the bacterial clade. RNAP-based phylogenies are equivocal with respect to the Aquifex and Thermotoga placements. The two hyperthermophiles fall basal to all other bacterial phyla when potential artifacts contributed by the
compositionally biased and fast-evolving Mycoplasma genitalium and Mycoplasma pneumoniae sequences are eschewed. However, the branching order of the phyla is tenuously supported in ML trees inferred by the exhaustive
search method and is unresolved in ML trees inferred by the quartet puzzling algorithm. A rooting of the RNA polymerase-subunit
tree at the mycoplasma level seen in both the MP trees and the ML trees reconstructed with suboptimal amino acid substitution
models is not supported by the EF-based phylogenies which robustly affiliate mycoplasmas with low-G+C gram-positives and,
most probably, reflects a ``long branch attraction' artifact.
Received: 22 September 1999 / Accepted: 11 January 2000 相似文献
13.
Mitochondrial DNA (mtDNA) sequences are widely used for inferring the phylogenetic relationships among species. Clearly,
the assumed model of nucleotide or amino acid substitution used should be as realistic as possible. Dependence among neighboring
nucleotides in a codon complicates modeling of nucleotide substitutions in protein-encoding genes. It seems preferable to
model amino acid substitution rather than nucleotide substitution. Therefore, we present a transition probability matrix of
the general reversible Markov model of amino acid substitution for mtDNA-encoded proteins. The matrix is estimated by the
maximum likelihood (ML) method from the complete sequence data of mtDNA from 20 vertebrate species. This matrix represents
the substitution pattern of the mtDNA-encoded proteins and shows some differences from the matrix estimated from the nuclear-encoded
proteins. The use of this matrix would be recommended in inferring trees from mtDNA-encoded protein sequences by the ML method.
Received: 3 May 1995 / Accepted: 31 October 1995 相似文献
14.
We investigated the occurrence of gene conversions between paralogous sequences of Salmoninae derived from ancestral tetraploidization
and their effect on the evolutionary history of DNA sequences. A microsatellite with long flanking regions (750 bp) including
both coding and noncoding sequences was analyzed. Microsatellite size polymorphism was used to detect the alleles of both
paralogous counterparts and infer linkage arrangement between loci. DNA sequencing of seven Salmoninae species revealed that
paralogous sequences were highly differentiated within species, especially for noncoding regions. Ten gene conversion events
between paralogous sequences were inferred. While these events appears to have homogenized regions of otherwise highly differential
paralogous sequences, they amplified the differentiation among orthologous sequences. Their effects were larger on coding
than on noncoding regions. As a consequence, noncoding sequences grouped by orthologous lineages in phylogenetic trees, whereas
coding regions grouped by taxa. Based upon these results, we present a model showing how gene conversion events may also result
in the PCR amplification of nonorthologous sequences in different taxa, with obvious complications for phylogenetic inferences,
comparative mapping, and population genetic studies.
Received: 11 October 2000 / Accepted: 18 September 2001 相似文献
15.
We have investigated the phylogenetic relationships of monotremes and marsupials using nucleotide sequence data from the
neurotrophins; nerve growth factor (NGF), brain-derived neurotrophic factor (BDNF), and neurotrophin-3 (NT-3). The study included
species representing monotremes, Australasian marsupials and placentals, as well as species representing birds, reptiles,
and fish. PCR was used to amplify fragments encoding parts of the neurotrophin genes from echidna, platypus, and eight marsupials
from four different orders. Phylogenetic trees were generated using parsimony analysis, and support for the different tree
structures was evaluated by bootstrapping. The analysis was performed with NGF, BDNF, or NT-3 sequence data used individually
as well as with the three neurotrophins in a combined matrix, thereby simultaneously considering phylogenetic information
from three separate genes. The results showed that the monotreme neurotrophin sequences associate to either therian or bird
neurotrophin sequences and suggests that the monotremes are not necessarily related closer to therians than to birds. Furthermore,
the results confirmed the present classification of four Australasian marsupial orders based on morphological characters,
and suggested a phylogenetic relationship where Dasyuromorphia is related closest to Peramelemorphia followed by Notoryctemorphia
and Diprotodontia. These studies show that sequence data from neurotrophins are well suited for phylogenetic analysis of mammals
and that neurotrophins can resolve basal relationships in the evolutionary tree.
Received: 27 January 1997 / Accepted: 20 March 1997 相似文献
16.
Satoru Kanai Reiko Kikuno Hiroyuki Toh Haruko Ryo Takeshi Todo 《Journal of molecular evolution》1997,45(5):535-548
The photolyase–blue-light photoreceptor family is composed of cyclobutane pyrimidine dimer (CPD) photolyases, (6-4) photolyases,
and blue-light photoreceptors. CPD photolyase and (6-4) photolyase are involved in photoreactivation for CPD and (6-4) photoproducts,
respectively. CPD photolyase is classified into two subclasses, class I and II, based on amino acid sequence similarity. Blue-light
photoreceptors are essential light detectors for the early development of plants. The amino acid sequence of the receptor
is similar to those of the photolyases, although the receptor does not show the activity of photoreactivation. To investigate
the functional divergence of the family, the amino acid sequences of the proteins were aligned. The alignment suggested that
the recognition mechanisms of the cofactors and the substrate of class I CPD photolyases (class I photolyases) are different
from those of class II CPD photolyases (class II photolyases). We reconstructed the phylogenetic trees based on the alignment
by the NJ method and the ML method. The phylogenetic analysis suggested that the ancestral gene of the family had encoded
CPD photolyase and that the gene duplication of the ancestral proteins had occurred at least eight times before the divergence
between eubacteria and eukaryotes.
Received: 23 October 1996 / Accepted: 1 April 1997 相似文献
17.
Among Bacteria the carA and carB genes encoding the small (CarA) and large (CarB) subunits of carbamoylphosphate synthase (CPS) have been lost in certain
symbionts (Haemophylus influenzae) and in most obligate intracellular parasites (Chlamydiae, Spirochaetes, Mycoplasmatales, Rickettsiae) having genome sizes in the 0.7- to 1.1-Mb range. Compared to Bacteria, Archaea exhibit a more varied pattern of CPS gene
losses and an unusual propensity to incorporate CPS genes derived from both Bacteria and other Archaea. Schematically they
fall into three groups. Group 1 taxa (the crenarchaeon Aeropyrum pernix and the euryarchaea Pyrococcus horikoshi and Pyrococcus abyssii) lack CPS genes altogether. Group 2 taxa (comprising Halobacteriales, Thermoplasmales, Methanococcales, Methanomicrobiales,
Archaeoglobales) harbor CPS genes whose encoded CarB and CarA subunit proteins are ostensibly bacterial in origin; that is,
they are intermixed with bacterial homologues on a phylogeny of concatenated CarA and CarB sequences and are not distinguishable
from bacterial sequences after searching for domain-specific amino acid residue positions. Group 3 taxa (the crenarchaea Pyrobaculum aerophilum, Sulfolobus solfataricus, and Sulfolobus tokodaii and the euryarchaeon Pyrococcus furiosus) harbor CPS genes whose encoded proteins appear to be archaeal: consistent with an archaeal origin, the CarA and CarB sequences
in this group possess both unique signatures and signatures affiliating them to Eukarya. Based on the topology of the clade
comprising the four Group 3 taxa, we argue that CPS genes of P. furiosus (a euryarchaeon) and those of the crenarchaea P. aerophilum, S. solfataricus, and S. tokodaii are of a single type, resulting from the two genes being laterally transferred from a crenarchaeon to P. furiosus. 相似文献
18.
Kleineidam RG Pesole G Breukelman HJ Beintema JJ Kastelein RA 《Journal of molecular evolution》1999,48(3):360-368
Mammalian secretory ribonucleases (RNases 1) form a family of extensively studied homologous proteins that were already used
for phylogenetic analyses at the protein sequence level previously. In this paper we report the determination of six ribonuclease
gene sequences of Artiodactyla and two of Cetacea. These sequences have been used with ruminant homologues in phylogenetic
analyses that supported a group including hippopotamus and toothed whales, a group of ruminant pancreatic and brain-type ribonucleases,
and a group of tylopod sequences containing the Arabian camel pancreatic ribonuclease gene and Arabian and Bactrian camel
and alpaca RNase 1 genes of unknown function. In all analyses the pig was the first diverging artiodactyl. This DNA-based
tree is compatible to published trees derived from a number of other genes. The differences to those trees obtained with ribonuclease
protein sequences can be explained by the influence of convergence of pancreatic RNases from hippopotamus, camel, and ruminants
and by taking into account the information from third codon positions in the DNA-based analyses. The evolution of sequence
features of ribonucleases such as the distribution of positively charged amino acids and of potential glycosylation sites
is described with regard to increased double-stranded RNA cleavage that is observed in several cetacean and artiodactyl RNases
which may have no role in ruminant or ruminant-like digestion.
Received: 2 June 1998 / Accepted: 31 August 1998 相似文献
19.
Piero Cammarano Roberta Creti Anna M. Sanangelantoni Peter Palm 《Journal of molecular evolution》1999,49(4):524-537
A global alignment of EF-G(2) sequences was corrected by reference to protein structure. The selection of characters eligible
for construction of phylogenetic trees was optimized by searching for regions arising from the artifactual matching of sequence
segments unique to different phylogenetic domains. The spurious matchings were identified by comparing all sections of the
global alignment with a comprehensive inventory of significant binary alignments obtained by BLAST probing of the DNA and
protein databases with representative EF-G(2) sequences. In three discrete alignment blocks (one in domain II and two in domain
IV), the alignment of the bacterial sequences with those of Archaea–Eucarya was not retrieved by database probing with EF-G(2)
sequences, and no EF-G homologue of the EF-2 sequence segments was detected by using partial EF-G(2) sequences as probes in
BLAST/FASTA searches. The two domain IV regions (one of which comprises the ADP-ribosylatable site of EF-2) are almost certainly
due to the artifactual alignment of insertion segments that are unique to Bacteria and to Archaea–Eucarya. Phylogenetic trees
have been constructed from the global alignment after deselecting positions encompassing the unretrieved, spuriously aligned
regions, as well as positions arising from misalignment of the G′ and G″ subdomain insertion segments flanking the ``fifth'
consensus motif of the G domain (?varsson, 1995). The results show inconsistencies between trees inferred by alternative methods
and alternative (DNA and protein) data sets with regard to Archaea being a monophyletic or paraphyletic grouping. Both maximum-likelihood
and maximum-parsimony methods do not allow discrimination (by log-likelihood difference and difference in number of inferred
substitutions) between the conflicting (monophyletic vs. paraphyletic Archaea) topologies. No specific EF-2 insertions (or
terminal accretions) supporting a crenarchaeal–eucaryal clade are detectable in the new EF-G(2) sequence alignment. 相似文献
20.
Nuclear and Nucleomorph SSU rDNA Phylogeny in the Cryptophyta and the Evolution of Cryptophyte Diversity 总被引:5,自引:0,他引:5
The plastid-bearing members of the Cryptophyta contain two functional eukaryotic genomes of different phylogenetic origin,
residing in the nucleus and in the nucleomorph, respectively. These widespread and diverse protists thus offer a unique opportunity
to study the coevolution of two different eukaryotic genomes within one group of organisms. In this study, the SSU rRNA genes
of both genomes were PCR-amplified with specific primers and phylogenetic analyses were performed on different data sets using
different evolutionary models. The results show that the composition of the principal clades obtained from the phylogenetic
analyses of both genes was largely congruent, but striking differences in evolutionary rates were observed. These affected
the topologies of the nuclear and nucleomorph phylogenies differently, resulting in long-branch attraction artifacts when
simple evolutionary models were applied. Deletion of long-branch taxa stabilized the internal branching order in both phylogenies
and resulted in a completely resolved topology in the nucleomorph phylogeny. A comparison of the tree topologies derived from
SSU rDNA sequences with characters previously used in cryptophyte systematics revealed that the biliprotein type was congruent,
but the type of inner periplast component incongruent, with the molecular trees. The latter is indicative of a hidden cellular
dimorphism (cells with two periplast types present in a single clonal strain) of presumably widespread occurrence throughout
cryptophyte diversity, which, in consequence, has far-reaching implications for cryptophyte systematics as it is practiced
today. 相似文献