共查询到20条相似文献,搜索用时 15 毫秒
1.
Jon P. Anderson Allen G. Rodrigo Gerald H. Learn Yang Wang Hillard Weinstock Marcia L. Kalish Kenneth E. Robbins Leroy Hood James I. Mullins 《Journal of molecular evolution》2001,53(1):55-62
Phylogenetic analyses frequently rely on models of sequence evolution that detail nucleotide substitution rates, nucleotide
frequencies, and site-to-site rate heterogeneity. These models can influence hypothesis testing and can affect the accuracy
of phylogenetic inferences. Maximum likelihood methods of simultaneously constructing phylogenetic tree topologies and estimating
model parameters are computationally intensive, and are not feasible for sample sizes of 25 or greater using personal computers.
Techniques that initially construct a tree topology and then use this non-maximized topology to estimate ML substitution rates,
however, can quickly arrive at a model of sequence evolution. The accuracy of this two-step estimation technique was tested
using simulated data sets with known model parameters. The results showed that for a star-like topology, as is often seen
in human immunodeficiency virus type 1 (HIV-1) subtype B sequences, a random starting topology could produce nucleotide substitution
rates that were not statistically different than the true rates. Samples were isolated from 100 HIV-1 subtype B infected individuals
from the United States and a 620 nt region of the env gene was sequenced for each sample. The sequence data were used to obtain a substitution model of sequence evolution specific
for HIV-1 subtype B env by estimating nucleotide substitution rates and the site-to-site heterogeneity in 100 individuals from the United States.
The method of estimating the model should provide users of large data sets with a way to quickly compute a model of sequence
evolution, while the nucleotide substitution model we identified should prove useful in the phylogenetic analysis of HIV-1
subtype B env sequences.
Received: 4 October 2000 / Accepted: 1 March 2001 相似文献
2.
A revised evolutionary history of hepatitis B virus (HBV) 总被引:8,自引:0,他引:8
Previous studies of the evolutionary history of hepatitis B virus (HBV) have been compromised by intergenotype recombination
and complex patterns of nucleotide substitution, perhaps caused by differential selection pressures. We examined the phylogenetic
distribution of recombination events among human HBV genotypes and found that genotypes A plus D, and genotypes B plus C,
had distinct patterns of recombination suggesting differing epidemiological relationships among them. By analyzing the nonoverlapping
regions of the viral genome we found strong bootstrap support for some intergenotypic groupings, with evidence of a division
between human genotypes A–E from the viruses sampled from apes and human genotype F. However, the earliest events in the divergence
of HBV remain uncertain. These uncertainties could not be explained by differential selection pressures, as the ratio of nonsynonymous-to-synonymous
substitutions (d
N/d
S) did not vary extensively among lineages and there is no strong evidence for positive selection across the whole tree. Finally,
we provide a new estimate of the mean substitution rate in HBV, 4.2 × 10−5, which suggests that divergence of HBV in humans and apes has occurred only in the last 6000 years. 相似文献
3.
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
4.
Drosophila nuclear introns are commonly assumed to change according to a single rate of substitution, yet little is known about the
evolution of these non-coding sequences. The hypothesis of a uniform substitution rate for introns seems to be at odds with
recent findings that the nucleotide composition of introns varies at a scale unknown before, and that their base content variation
is correlated with that of the adjacent exons. However, no direct attempt at comparing substitution rates in introns seems
to have been addressed so far. We have studied the rate of nucleotide substitution over a region of the Xdh gene containing two adjacent short, constitutively spliced introns, in several species of Drosophila and related genera. The two introns differ significantly in base composition and substitution rate, with one intron evolving
at least twice as fast as the other. In addition, the substitution pattern of the introns is positively associated with that
of the surrounding coding regions, evidencing that the molecular evolution of these introns is impacted by the region in which
they are embedded. The observed differences cannot be attributed to selection acting differently at the level of the secondary
structure of the pre-mRNA. Rather, they are better accounted for by locally heterogeneous patterns of mutation.
Received: 26 July 1999 / Accepted: 21 August 1999 相似文献
5.
Molecular evolution of nitrate reductase genes 总被引:9,自引:0,他引:9
To understand the evolutionary mechanisms and relationships of nitrate reductases (NRs), the nucleotide sequences encoding
19 nitrate reductase (NR) genes from 16 species of fungi, algae, and higher plants were analyzed. The NR genes examined show
substantial sequence similarity, particularly within functional domains, and large variations in GC content at the third codon
position and intron number. The intron positions were different between the fungi and plants, but conserved within these groups.
The overall and nonsynonymous substitution rates among fungi, algae, and higher plants were estimated to be 4.33 × 10−10 and 3.29 × 10−10 substitutions per site per year. The three functional domains of NR genes evolved at about one-third of the rate of the N-terminal
and the two hinge regions connecting the functional domains. Relative rate tests suggested that the nonsynonymous substitution
rates were constant among different lineages, while the overall nucleotide substitution rates varied between some lineages.
The phylogenetic trees based on NR genes correspond well with the phylogeny of the organisms determined from systematics and
other molecular studies. Based on the nonsynonymous substitution rate, the divergence time of monocots and dicots was estimated
to be about 340 Myr when the fungi–plant or algae–higher plant divergence times were used as reference points and 191 Myr
when the rice–barley divergence time was used as a reference point. These two estimates are consistent with other estimates
of divergence times based on these reference points. The lack of consistency between these two values appears to be due to
the uncertainty of the reference times.
Received: 10 April 1995 / Accepted: 10 September 1995 相似文献
6.
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
7.
Dorota Szczepanik Paweł Mackiewicz Maria Kowalczuk Agnieszka Gierlik Aleksandra Nowicka Mirosław R. Dudek Stanisław Cebrat 《Journal of molecular evolution》2001,52(5):426-433
One of the main causes of bacterial chromosome asymmetry is replication-associated mutational pressure. Different rates of
nucleotide substitution accumulation on leading and lagging strands implicate qualitative and quantitative differences in
the accumulation of mutations in protein coding sequences lying on different DNA strands. We show that the divergence rate
of orthologs situated on leading strands is lower than the divergence rate of those situated on lagging strands. The ratio
of the mutation accumulation rate for sequences lying on lagging strands to that of sequences lying on leading strands is
rather stable and time-independent. The divergence rate of sequences which changed their positions, with respect to the direction
of replication fork movement, is not stable—sequences which have recently changed their positions are the most prone to mutation
accumulation. This effect may influence estimations of evolutionary distances between species and the topology of phylogenetic
trees.
Received: 24 July 2000 / Accepted: 16 January 2001 相似文献
8.
Ivan Laprevotte Sophie Brouillet Christophe Terzian Alain Hénaut 《Journal of molecular evolution》1997,44(2):214-225
A computer-assisted analysis was made of 24 complete nucleotide sequences selected from the vertebrate retroviruses to represent
the ten viral groups. The conclusions of this analysis extend and strengthen the previously made hypothesis on the Moloney
murine leukemia virus: The evolution of the nucleotide sequence appears to have occurred mainly through at least three overlapping
levels of duplication: (1) The distributions of overrepresented (3–6)-mers are consistent with the universal rule of a trend
toward TG/CT excess and with the persistence of a certain degree of symmetry between the two strands of DNA. This suggests
one or several original tandemly repeated sequences and some inverted duplications. (2) The existence of two general core
consensuses at the level of these (3–6)-mers supports the hypothesis of a common evolutionary origin of vertebrate retroviruses.
Consensuses more specific to certain sequences are compatible with phylogenetic trees established independently. The consensuses
could correspond to intermediary evolutionary stages. (3) Most of the (3–6)-mers with a significantly higher than average
frequency appear to be internally repeated (with monomeric or oligomeric internal iterations) and seem to be at least partly
the cause of the bias observed by other researchers at the level of retroviral nucleotide composition. They suggest a third
evolutionary stage by slippage-like stepwise local duplications.
Received: 3 January 1996 / Accepted: 27 March 1996 相似文献
9.
In this study we constructed a bootstrapped distance tree of 500 small subunit ribosomal RNA sequences from organisms belonging
to the so-called crown of eukaryote evolution. Taking into account the substitution rate of the individual nucleotides of
the rRNA sequence alignment, our results suggest that (1) animals, true fungi, and choanoflagellates share a common origin:
The branch joining these taxa is highly supported by bootstrap analysis (bootstrap support [BS] > 90%), (2) stramenopiles
and alveolates are sister groups (BS = 75%), (3) within the alveolates, dinoflagellates and apicomplexans share a common ancestor
BS > 95%), while in turn they both share a common origin with the ciliates (BS > 80%), and (4) within the stramenopiles, heterokont
algae, hyphochytriomycetes, and oomycetes form a monophyletic grouping well supported by bootstrap analysis (BS > 85%), preceded
by the well-supported successive divergence of labyrinthulomycetes and bicosoecids.
On the other hand, many evolutionary relationships between crown taxa are still obscure on the basis of 18S rRNA. The branching
order between the animal-fungal-choanoflagellates clade and the chlorobionts, the alveolates and stramenopiles, red algae,
and several smaller groups of organisms remains largely unresolved.
When among-site rate variation is not considered, the inferred tree topologies are inferior to those where the substitution
rate spectrum for the 18S rRNA is taken into account. This is primarily indicated by the erroneous branching of fast-evolving
sequences. Moreover, when different substitution rates among sites are not considered, the animals no longer appear as a monophyletic
grouping in most distance trees.
Received: 11 June 1997 / Accepted: 21 July 1997 相似文献
10.
11.
We have sequenced the cytochrome b gene of Horsfield's tarsier, Tarsius bancanus, to complete a data set of sequences for this gene from representatives of each primate infraorder. These primate cytochrome
b sequences were combined with those from representatives of three other mammalian orders (cat, whale, and rat) in an analysis
of relative evolutionary rates. The nonsynonymous nucleotide substitution rate of the cytochrome b gene has increased approximately twofold along lineages leading to simian primates compared to that of the tarsier and other
primate and nonprimate mammalian species. However, the rate of transversional substitutions at fourfold degenerate sites has
remained uniform among all lineages. This increase in the evolutionary rate of cytochrome b is similar in character and magnitude to that described previously for the cytochrome c oxidase subunit II gene. We propose that the evolutionary rate increase observed for cytochrome b and cytochrome c oxidase subunit II may underlie an episode of coadaptive evolution of these two proteins in the mitochondria of simian primates.
Received: 15 December 1997 / Accepted: 24 February 1998 相似文献
12.
Dadbeh Rouhbakhsh Chi-Yung Lai Carol D. von Dohlen Marta A. Clark Linda Baumann Paul Baumann Nancy A. Moran David J. Voegtlin 《Journal of molecular evolution》1996,42(4):414-421
The bacterial endosymbionts (Buchnera) from the aphids Rhopalosiphum padi, R. maidis, Schizaphis graminum, and Acyrthosiphon pisum contain the genes for anthranilate synthase (trpEG) on plasmids made up of one or more 3.6-kb units. Anthranilate synthase is the first as well as the rate-limiting enzyme
in the tryptophan biosynthetic pathway. The amplification of trpEG on plasmids may result in an increase of enzyme protein and overproduction of this essential amino acid, which is required
by the aphid host. The nucleotide sequence of trpEG from endosymbionts of different species of aphids is highly conserved, as is an approximately 500-bp upstream DNA segment
which has the characteristics of an origin of replication. Phylogenetic analyses were performed using trpE and trpG from the endosymbionts of these four aphids as well as from the endosymbiont of Schlechtendalia chinensis, in which trpEG occurs on the chromosome. The resulting phylogeny was congruent with trees derived from sequences of two chromosome-located
bacterial genes (part of trpB and 16S ribosomal DNA). In turn, trees obtained from plasmid-borne and bacterial chromosome-borne sequences were congruent
with the tree resulting from phylogenetic analysis of three aphid mitochondrial regions (portions of the small and large ribosomal
DNA subunits, as well as cytochrome oxidase II). Congruence of trees based on genes from host mitochondria and from bacteria
adds to previous support for exclusively vertical transmission of the endosymbionts within aphid lineages. Congruence with
trees based on plasmid-borne genes supports the origin of the plasmid-borne trpEG from the chromosomal genes of the same lineage and the absence of subsequent plasmid exchange among endosymbionts of different
species of aphids.
Received: 22 August 1995 / Accepted: 6 September 1995 相似文献
13.
Torres C Piñeiro y Leone FG Pezzano SC Mbayed VA Campos RH 《Molecular phylogenetics and evolution》2011,59(1):114-122
Hepatitis B virus (HBV) is a globally distributed human pathogen. The aim of this work was to analyze the evolutionary history of HBV genotype F, emphasizing on the study of subgenotypes prevalent in the Southern area of South America. Complete genomes of HBV genotype F from 36 samples from Argentina and Chile were sequenced and analyzed by phylogenetic and Bayesian coalescent methods along with sequences obtained from GenBank database. The phylogeography separated not only Central American from South American isolates but also revealed that different subgenotypes are distributed in constrained although not exclusive areas of the continent. The result obtained with time-stamped complete genomes failed to explain the wide geographical distribution and the clustering observed in this genotype. Conversely, the use of Bayesian coalescent analyses with substitution rates as priors, instead of the co-estimation of tMRCA and substitution rate, allowed us to propose a far origin for the HBV genotype F based on the phylogeographical and epidemiological data. 相似文献
14.
Graziano Pesole Luigi R. Ceci Carmela Gissi Cecilia Saccone Carla Quagliariello 《Journal of molecular evolution》1996,43(5):447-452
We have analyzed the nad3-rps12 locus for eight angiosperms in order to compare the utility of mitochondrial DNA and edited mRNA sequences in phylogenetic
reconstruction. The two coding regions, containing from 25 to 35 editing sites in the various plants, have been concatenated
in order to increase the significance of the analysis. Differing from the corresponding chloroplast sequences, unedited mitochondrial
DNA sequences seem to evolve under a quasi-neutral substitution process which undifferentiates the nucleotide substitution
rates for the three codon positions. By using complete gene sequences (all codon positions) we found that genomic sequences
provide a classical angiosperm phylogenetic tree with a clear-cut grouping of monocotyledons and dicotyledons with Magnoliidae
at the basal branch of the tree. Conversely, owing to their low nucleotide substitution rates, edited mRNA sequences were
found not to be suitable for studying phylogenetic relationships among angiosperms.
Received: 24 January 1996 / Accepted: 5 June 1996 相似文献
15.
The morphologically uniform species Gonium pectorale is a colonial green flagellate of worldwide distribution. The affinities of 25 isolates from 18 sites on five continents
were assessed by both DNA sequence comparisons and sexual compatibility. Complete sequences were obtained (i) for the internal
transcribed spacer ITS-1 and ITS-2 regions of ribosomal DNA and (ii) for each of three single-copy spliceosomal introns, two
in a small G protein and one in the actin gene. ITS sequences appeared to homogenize sufficiently rapidly to behave as a single
copy gene. Intron sequence differences between isolates in this species reached nucleotide substitution saturation, while
ITS sequences did not. Parsimony and evolutionary distance analysis of the two types of DNA data gave essentially the same
tree conformation. By all these criteria, the group of G. pectorale isolates fell into two main clades, A and B. Clade A, with isolates from four continents, was comprised of four subclades
of quite closely related isolates, plus one strain of ambiguous affinity. Clade B was comprised of two subclades represented
by South African and South American isolates, respectively; thus, only subclades of clade B showed geographical localization.
With respect to mating, all isolates except one homothallic strain and one apparently sterile strain fell into either one
or the other of two mating types. Pairings in all possible combinations revealed that isolates from the same site formed abundant
zygotes, which germinated to produce new, sexually active organisms. Zygotes were also formed in many pairings of other combinations,
including crosses of clade A with clade B organisms, but none of the latter produced viable germlings. The ability to mate
and produce viable progeny that were themselves capable of sexual reproduction was restricted to members of subclades established
on the basis of DNA sequence similarities. Thus, the grades of difference in both nuclear intron sequences and rDNA ITS sequences
paralleled those observed in the sexual analysis.
Received: 9 March 1998 / Accepted: 1 June 1998 相似文献
16.
The Origin of Chlorarachniophyte Plastids, as Inferred from Phylogenetic Comparisons of Amino Acid Sequences of EF-Tu 总被引:4,自引:0,他引:4
Ken-ichiro Ishida Ying Cao Masami Hasegawa Norihiro Okada Yoshiaki Hara 《Journal of molecular evolution》1997,45(6):682-687
A molecular phylogenetic analysis of elongation factor Tu (EF-Tu) proteins from plastids was performed in an attempt to identify
the origin of chlorarachniophyte plastids, which are considered to have evolved from the endosymbiont of a photosynthetic
eukaryote. Partial sequences of the genes for plastid EF-Tu proteins (1,080–1,089 bp) were determined for three algae that
contain chlorophyll b, namely, Gymnochlora stellata (Chlorarachniophyceae), Bryopsis maxima (Ulvophyceae), and Pyramimonas disomata (Prasinophyceae). The deduced amino acid sequences were used to construct phylogenetic trees of the plastid and bacterial
EF-Tu proteins by the maximum likelihood, the maximum parsimony, and the neighbor joining methods.
The trees obtained in the present analysis suggest that all plastids that contain chlorophyll b are monophyletic and that the chlorarachniophyte plastids are closely related to those of the Ulvophyceae. The phylogenetic
trees also suggest that euglenophyte plastids are closely related to prasinophycean plastids. The results indicate that the
chlorarachniophyte plastids evolved from a green algal endosymbiont that was closely related to the Ulvophyceae and that at
least two secondary endosymbiotic events have occurred in the lineage of algae with plastids that contain chlorophyll b.
Received: 10 March 1997 / Accepted: 28 July 1997 相似文献
17.
We obtained 16 nucleotide sequences (∼1400 bp each) of the first intron of the mitochondrial (mt) gene for NADH subunit 4
(nad4) from 10 species of Brassicaceae. Using these new sequences and five published sequences from GenBank, we constructed
a phylogenetic tree of the Brassicaceae species under study and showed that the rate of nucleotide substitution in the first
intron of nad4 is very low, about 0.16–0.23 × 10−9 substitution per site per year, which is about half of the silent rate in exons of nad4. The ratios of substitution rates
in this intron, ITS, and IGS are approximately 1:23:73, where ITS is the nuclear intergenic spacer between 18S and 25S rRNA
genes and IGS is the intergenic spacer of 5S rRNA genes. A segment (335 bp) in the first intron of nad4 in Brassicaceae species
that is absent in wheat was considered as a nonfunctional sequence and used to estimate the neutral rate (the rate of mutation)
in mtDNA to be 0.5–0.7 × 10−9 substitution per site per year, which is about three times higher than the substitution rate in the rest of the first intron
of nad4. We estimated that the dates of divergence are 170–235 million years (Myr) for the monocot–dicot split, 112–156 Myr
for the Brassicaceae–Lettuce split, 14.5–20.4 Myr for the Brassica–Arabidopsis split, and 14.5–20.4 Myr for the Arabidopsis–Arabideae split.
Received: 14 July 1998 / Accepted: 1 October 1998 相似文献
18.
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
19.
Suzuki Y Katayama K Fukushi S Kageyama T Oya A Okamura H Tanaka Y Mizokami M Gojobori T 《Journal of molecular evolution》1999,48(4):383-389
With the aim of elucidating evolutionary features of GB virus C/hepatitis G virus (GBV-C/HGV), molecular evolutionary analyses
were conducted using the entire coding region of this virus. In particular, the rate of nucleotide substitution for this virus
was estimated to be less than 9.0 × 10−6 per site per year, which was much slower than those for other RNA viruses. The phylogenetic tree reconstructed for GBV-C/HGV,
by using GB virus A (GBV-A) as outgroup, indicated that there were three major clusters (the HG, GB, and Asian types) in GBV-C/HGV,
and the divergence between the ancestor of GB- and Asian-type strains and that of HG-type strains first took place more than
7000–10,000 years ago. The slow evolutionary rate for GBV-C/HGV suggested that this virus cannot escape from the immune response
of the host by means of producing escape mutants, implying that it may have evolved other systems for persistent infection.
Received: 2 June 1998 / Accepted: 8 August 1998 相似文献
20.
Horizontal transfer of genes coding for the photosynthetic reaction centers of purple bacteria 总被引:11,自引:0,他引:11
Kenji V. P. Nagashima Akira Hiraishi Keizo Shimada Katsumi Matsuura 《Journal of molecular evolution》1997,45(2):131-136
Phylogenetic trees were drawn and analyzed based on the nucleotide sequences of the 1.5-kb gene fragment coding for the L
and M subunits of the photochemical reaction center of various purple photosynthetic bacteria. These trees are mostly consistent
with phylogenetic trees based on 16S rRNA and soluble cytochrome c, but differ in some significant details. This inconsistency implies horizontal transfer of the genes that code for the photosynthetic
apparatus in purple bacteria. Possibilities of similar transfers of photosynthesis genes during the evolution of photosynthesis
are discussed especially for the establishment of oxygenic photosynthesis.
Received: 8 July 1996 / Accepted: 12 March 1997 相似文献