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1.
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
2.
Synonymous and nonsynonymous rate variation in nuclear genes of mammals 总被引:34,自引:6,他引:28
A maximum likelihood approach was used to estimate the synonymous and nonsynonymous substitution rates in 48 nuclear genes
from primates, artiodactyls, and rodents. A codon-substitution model was assumed, which accounts for the genetic code structure,
transition/transversion bias, and base frequency biases at codon positions. Likelihood ratio tests were applied to test the
constancy of nonsynonymous to synonymous rate ratios among branches (evolutionary lineages). It is found that at 22 of the
48 nuclear loci examined, the nonsynonymous/synonymous rate ratio varies significantly across branches of the tree. The result
provides strong evidence against a strictly neutral model of molecular evolution. Our likelihood estimates of synonymous and
nonsynonymous rates differ considerably from previous results obtained from approximate pairwise sequence comparisons. The
differences between the methods are explored by detailed analyses of data from several genes. Transition/transversion rate
bias and codon frequency biases are found to have significant effects on the estimation of synonymous and nonsynonymous rates,
and approximate methods do not adequately account for those factors. The likelihood approach is preferable, even for pairwise
sequence comparison, because more-realistic models about the mutation and substitution processes can be incorporated in the
analysis.
Received: 17 May 1997 / Accepted: 28 September 1997 相似文献
3.
One of the most useful features of molecular phylogenetic analyses is the potential for estimating dates of divergence of
evolutionary lineages from the DNA of extant species. But lineage-specific variation in rate of molecular evolution complicates
molecular dating, because a calibration rate estimated from one lineage may not be an accurate representation of the rate
in other lineages. Many molecular dating studies use a ``clock test' to identify and exclude sequences that vary in rate
between lineages. However, these clock tests should not be relied upon without a critical examination of their effectiveness
at removing rate variable sequences from any given data set, particularly with regard to the sequence length and number of
variable sites. As an illustration of this problem we present a power test of a frequently employed triplet relative rates
test. We conclude that (1) relative rates tests are unlikely to detect moderate levels of lineage-specific rate variation
(where one lineage has a rate of molecular evolution 1.5 to 4.0 times the other) for most commonly used sequences in molecular
dating analyses, and (2) this lack of power is likely to result in substantial error in the estimation of dates of divergence.
As an example, we show that the well-studied rate difference between murid rodents and great apes will not be detected for
many of the sequences used to date the divergence between these two lineages and that this failure to detect rate variation
is likely to result in consistent overestimation the date of the rodent–primate split.
Received: 9 June 1999 / Accepted: 22 October 1999 相似文献
4.
Phylogenetics of Perissodactyla and Tests of the Molecular Clock 总被引:3,自引:0,他引:3
Two mitochondrial genes, the protein-coding cytochrome c oxidase subunit II (COII) gene and a portion of the 12S rRNA gene, were used for phylogenetic investigation of the mammalian
order Perissodactyla. The primary objective of the study was to utilize the extensive fossil record of perissodactyls for
calibrating molecular clocks and comparing estimates of divergence times using both genes and two fossil calibration points.
Secondary objectives included clarification of previously unresolved relationships within Tapiridae and comparison of the
results of separate and combined analyses of two genes. Analyses included several perissodactyl lineages representing all
three families (Tapiridae, Equidae, and Rhinocerotidae), most extant genera, all four species of tapirs, two to four species
of rhinoceros, and two species of Equus. The application of a relatively recent fossil calibration point and a relatively ancient calibration point produced greatly
different estimates of evolutionary rates and divergence times for both genes, even though a relative rates test did not find
significant rate differences among taxa. A likelihood-ratio test, however, rejected a molecular clock for both genes. Neither
calibration point produced estimates of divergence times consistent with paleontological evidence over a range of perissodactyl
radiations. The combined analysis of both genes produces a well-resolved phylogeny with Perissodactyla that conforms to traditional
views of interfamilial relationships and supports monophyly of neotropical tapirs. Combining the data sets increases support
for most nodes but decreases the support for a neotropical tapir clade because the COII and 12S rRNA data sets are in conflict
for tapir relationships.
Received: 6 January 1999 / Accepted: 2 August 1999 相似文献
5.
Marco Salemi Anne-Mieke Vandamme Chiara Gradozzi Kristel Van Laethem Ercole Cattaneo Graham Taylor Claudio Casoli Patrick Goubau Jan Desmyter Umberto Bertazzoni 《Journal of molecular evolution》1998,46(5):602-611
Seven new Italian and two new British HTLV-II isolates were obtained from injecting drug users and the entire long terminal
repeat (LTR) region was sequenced. Restriction analysis showed that all the Italian isolates are of the IIb subtype, whereas
the British isolates are of the IIa subtype. To understand whether the further differentiation of each two principal HTLV-II
subtypes in several subgroups could be statistically supported by phylogenetic analysis, the neighbor-joining, parsimony,
and maximum likelihood methods were used. The separation between IIa and IIb is very well supported by all three methods.
At least two phylogenetic subgroups exist within the HTLV-IIa and at least three within the HTLV-IIb subtype. In the present
analysis, no statistical support was obtained for additional phylogroups. Two particular subgroups seem interesting because
they include all European and North American injecting drug user strains within the IIa and IIb subtypes, respectively. These
data confirm that European HTLV-II infection among drug users is probably derived from North America. They also suggest that
though a certain differentiation by restriction analysis in different subgroups is possible, carefully interpreted phylogenetic
analyses remain necessary. Using the likelihood ratio test, a molecular clock for the drug user strains was calibrated. A
fixation rate between 1.08 × 10−4 and 2.7 × 10−5 nucleotide substitutions per site per year was calculated for the IIa and IIb injecting drug user strains. This is the lowest
fixation rate so far reported for RNA viruses, including for HIV, which typically range between 10−2 and 10−4. 相似文献
6.
Joseph Felsenstein 《Journal of molecular evolution》2001,53(4-5):447-455
As methods of molecular phylogeny have become more explicit and more biologically realistic following the pioneering work
of Thomas Jukes, they have had to relax their initial assumption that rates of evolution were equal at all sites. Distance
matrix and likelihood methods of inferring phylogenies make this assumption; parsimony, when valid, is less limited by it.
Nucleotide sequences, including RNA sequences, can show substantial rate variation; protein sequences show rates that vary
much more widely. Assuming a prior distribution of rates such as a gamma distribution or lognormal distribution has deservedly
been popular, but for likelihood methods it leads to computational difficulties. These can be resolved using hidden Markov
model (HMM) methods which approximate the distribution by one with a modest number of discrete rates. Generalized Laguerre
quadrature can be used to improve the selection of rates and their probabilities so as to more nearly approach the desired
gamma distribution. A model based on population genetics is presented predicting how the rates of evolution might vary from
locus to locus. Challenges for the future include allowing rates at a given site to vary along the tree, as in the ``covarion'
model, and allowing them to have correlations that reflect three-dimensional structure, rather than position in the coding
sequence. Markov chain Monte Carlo likelihood methods may be the only practical way to carry out computations for these models.
Received: 8 February 2001 / Accepted: 20 May 2001 相似文献
7.
David C. Nickle Gerald H. Learn Matthew W. Rain James I. Mullins John E. Mittler 《Journal of molecular evolution》2002,54(1):134-137
Studies of ancient DNA have attracted considerable attention in scientific journals and the popular press. Several of the
more extreme claims for ancient DNA have been questioned on biochemical grounds (i.e., DNA surviving longer than expected)
and evolutionary grounds (i.e., nucleotide substitution patterns not matching theoretical expectations for ancient DNA). A
recent letter to Nature from Vreeland et al. (2000), however, tops all others with respect to age and condition of the specimen. These researchers
extracted and cultured a bacterium from an inclusion body from what they claim is a 250 million-year (Myr)-old salt crystal.
If substantiated, this observation could fundamentally alter views about bacterial physiology, ecology and evolution. Here
we report on molecular evolutionary analyses of the 16S rDNA from this specimen. We find that 2-9-3 differs from a modern
halophile, Salibacillus marismortui, by just 3 unambiguous bp in 16S rDNA, versus the ∼59 bp that would be expected if these bacteria evolved at the same rate
as other bacteria. We show, using a Poisson distribution, that unless it can be shown that S. marismortui evolves 5 to 10 times more slowly than other bacteria for which 16S rDNA substitution rates have been established, Vreeland
et al.'s claim would be rejected at the 0.05 level. Also, a molecular clock test and a relative rates test fail to substantiate
Vreeland et al.'s claim that strain 2-9-3 is a 250-Myr-old bacterium. The report of Vreeland et al. thus falls into a long
series of suspect ancient DNA studies.
Received: 12 April 2001 / Accepted: 9 June 2001 相似文献
8.
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
9.
The transition/transversion (ti/tv) rate ratios are estimated by pairwise sequence comparison and joint likelihood analysis
using mitochondrial cytochrome b genes of 28 primate species, representing both the Strepsirrhini (lemurs and lories) and the Anthropoidea (monkeys, apes,
and humans). Pairwise comparison reveals a strong negative correlation between estimates of the ti/tv ratio and the sequence
distance, even when both are corrected for multiple substitutions. The maximum-likelihood estimate of the ti/tv ratio changes
with the species included in the analysis. The ti/tv bias within the lemuriform taxa is found to be as strong as in the anthropoids,
in contradiction to an earlier study which sampled only one lemuriform. Simulations show the surprising result that both the
pairwise correction method and the joint likelihood analysis tend to overcorrect for multiple substitutions and overestimate
the ti/tv ratio, especially at low sequence divergence. The bias, however, is not large enough to account for the observed
patterns. Nucleotide frequency biases, variation of substitution rates among sites, and different evolutionary dynamics at
the three codon positions can be ruled out as possible causes. The likelihood-ratio test suggests that the ti/tv rate ratios
may be variable among evolutionary lineages. Without any biological evidence for such a variation, however, we are left with
no plausible explanations for the observed patterns other than a possible saturation effect due to the unrealistic nature
of the model assumed.
Received: 1 October 1997 / Accepted: 29 September 1998 相似文献
10.
Austin L. Hughes 《Journal of molecular evolution》2002,54(1):90-101
Phylogenies of gene families including members in both vertebrates and DNA viruses of the poxvirus and/or herpesvirus families
showed that the viral genes originated at widely different times over the history of life. Certain of these viral genes (for
example, the genes encoding the large and small subunits of ribonucleoside–diphosphate reductase) originated before animals
diverged from fungi, while others originated much more recently. The most striking examples of recent origin involved viral
genes encoding the cytokine interleukin-10 (IL-10), which originated independently in viruses at least three times since the
divergence of the orders of eutherian mammals, presumably by viral capture of host genes. In certain domains, viral IL-10
genes showed significantly higher rates of nonsynonymous substitution than their nearest mammalian homologues. Though the
mutation rate in these viral genes is up to 20 times that of the corresponding mammalian genes, a high mutation rate alone
did not account for these differences because they were not seen in all domains. Rather, in certain domains it appears that
functional constraints present in the case of mammalian IL-10 are relaxed in the case of the viral homologues. Furthermore,
a nonrandom pattern of change with respect to amino acid residue charge in the N-terminal portion of the mature protein has
occurred repeatedly in independently derived viral IL-10 genes, strongly suggesting that positive selection has led to divergence
of this functionally important domain in viral IL-10.
Received: 11 January 2001 / Accepted: 23 May 2001 相似文献
11.
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
12.
Berg OG 《Journal of molecular evolution》1999,48(4):398-407
The synonymous divergence between Escherichia coli and Salmonella typhimurium is explained in a model where there is a large variation between mutation rates at different nucleotide sites in the genome.
The model is based on the experimental observation that spontaneous mutation rates can vary over several orders of magnitude
at different sites in a gene. Such site-specific variation must be taken into account when studying synonymous divergence
and will result in an apparent saturation below the level expected from an assumption of uniform rates. Recently, it has been
suggested that codon preference in enterobacteria has a very large site-specific variation and that the synonymous divergence
between different species, e.g., E. coli and Salmonella, is saturated. In the present communication it is shown that when site-specific variation in mutation rates is introduced,
there is no need to invoke assumptions of saturation and a large variability in codon preference. The same rate variation
will also bring average mutation rates as estimated from synonymous sequence divergence into numerical agreement with experimental
values.
Received: 10 July 1998 / Accepted: 20 August 1998 相似文献
13.
14.
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
15.
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
16.
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
17.
Ziheng Yang 《Journal of molecular evolution》1996,42(5):587-596
Models of nucleotide substitution were constructed for combined analyses of heterogeneous sequence data (such as those of
multiple genes) from the same set of species. The models account for different aspects of the heterogeneity in the evolutionary
process of different genes, such as differences in nucleotide frequencies, in substitution rate bias (for example, the transition/transversion
rate bias), and in the extent of rate variation across sites. Model parameters were estimated by maximum likelihood and the
likelihood ratio test was used to test hypotheses concerning sequence evolution, such as rate constancy among lineages (the
assumption of a molecular clock) and proportionality of branch lengths for different genes. The example data from a segment
of the mitochondrial genome of six hominoid species (human, common and pygmy chimpanzees, gorilla, orangutan, and siamang)
were analyzed. Nucleotides at the three codon positions in the protein-coding regions and from the tRNA-coding regions were
considered heterogeneous data sets. Statistical tests showed that the amount of evolution in the sequence data reflected in
the estimated branch lengths can be explained by the codon-position effect and lineage effect of substitution rates. The assumption
of a molecular clock could not be rejected when the data were analyzed separately or when the rate variation among sites was
ignored. However, significant differences in substitution rate among lineages were found when the data sets were combined
and when the rate variation among sites was accounted for in the models. Under the assumption that the orangutan and African
apes diverged 13 million years ago, the combined analysis of the sequence data estimated the times for the human-chimpanzee
separation and for the separation of the gorilla as 4.3 and 6.8 million years ago, respectively. 相似文献
18.
Kazuhisa Tsunoyama Matthew I. Bellgard Takashi Gojobori 《Journal of molecular evolution》2001,53(4-5):456-464
It has been observed that synonymous substitution rates vary among genes in various organisms, although the cause of the
variation is unresolved. At the intragenic level, however, the variation of synonymous substitutions is somewhat controversial.
By developing a rigorous statistical test and applying the test to 418 homologous gene pairs between mouse and rat, we found
that more than 90% of gene pairs showed a statistical significance in intragenic variation of synonymous substitution rates.
Moreover, by examining all conceivable possibilities for the cause of the variation, we successfully found that intragenic
variation of synonymous substitutions in mammalian genes is caused mainly by a nonrandom mutation due to the methylation of
CpG dinucleotides rather than by functional constraints.
Received: 12 January 2001 / Accepted: 28 February 2001 相似文献
19.
The large subunit ribosomal RNA sequences from the heterokont algae Ochromonas danica, Nannochloropsis salina, and Tribonema aequale were determined. These sequences were combined with small subunit ribosomal RNA sequences in order to carry out a phylogenetic
analysis based on neighbor-joining, maximum parsimony, and maximum likelihood methods. Our results indicate that heterokont
fungi and heterokont algae each are monophyletic, and confirm that they together form a monophyletic group called ``stramenopiles.'
Within the heterokont algae, the eustigmatophyte Nannochloropsis salina either clusters with the chrysophyte Ochromonas danica or forms a sister group to a cluster comprising the phaeophyte Scytosiphon lomentaria and the xanthophyte Tribonema aequale. The alveolates were identified as the closest relatives of the stramenopiles, but the exact order of divergence between the
eukaryotic crown taxa could not be established with confidence.
Received: 22 November 1996 / Accepted: 14 February 1997 相似文献
20.
Synonymous substitution rates in mitochondrial and nuclear genes of Drosophila were compared. To make accurate comparisons, we considered the following: (1) relative synonymous rates, which do not require
divergence time estimates, should be used; (2) methods estimating divergence should take into account base composition; (3)
only very closely related species should be used to avoid effects of saturation; (4) the heterogeneity of rates should be
examined. We modified the methods estimating synonymous substitution numbers to account for base composition bias. By using
these methods, we found that mitochondrial genes have 1.7–3.4 times higher synonymous substitution rates than the fastest
nuclear genes or 4.5–9.0 times higher rates than the average nuclear genes. The average rate of synonymous transversions was
2.7 (estimated from the melanogaster species subgroup) or 2.9 (estimated from the obscura group) times higher in mitochondrial genes than in nuclear genes. Synonymous transversions in mitochondrial genes occurred
at an approximately equivalent rate to those in the fastest nuclear genes. This last result is not consistent with the hypothesis
that the difference in turnover rates between mitochondrial and nuclear genomes is the major factor determining higher synonymous
substitution rates in mtDNA. We conclude that the difference in synonymous substitution rates is due to a combination of two
factors: a higher transitional mutation rate in mtDNA and constraints on nuclear genes due to selection for codon usage.
Received: 27 November 1996 / Accepted: 8 May 1997 相似文献