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1.
Weinreich DM 《Journal of molecular evolution》2001,52(1):40-50
A higher rate of molecular evolution in rodents than in primates at synonymous sites and, to a lesser extent, at amino acid
replacement sites has been reported previously for most nuclear genes examined. Thus in these genes the average ratio of amino
acid replacement to synonymous substitution rates in rodents is lower than in primates, an observation at odds with the neutral
model of molecular evolution. Under Ohta's mildly deleterious model of molecular evolution, these observations are seen as
the consequence of the combined effects of a shorter generation time (driving a higher mutation rate) and a larger effective
population size (resulting in more effective selection against mildly deleterious mutations) in rodents. The present study
reports the results of a maximum-likelihood analysis of the ratio of amino acid replacements to synonymous substitutions for
genes encoded in mitochondrial DNA (mtDNA) in these two lineages. A similar pattern is observed: in rodents this ratio is
significantly lower than in primates, again consistent only with the mildly deleterious model. Interestingly the lineage-specific
difference is much more pronounced in mtDNA-encoded than in nuclear-encoded proteins, an observation which is shown to run
counter to expectation under Ohta's model. Finally, accepting certain fossil divergence dates, the lineage-specific difference
in amino acid replacement-to-synonymous substitution ratio in mtDNA can be partitioned and is found to be entirely the consequence
of a higher mutation rate in rodents. This conclusion is consistent with a replication-dependent model of mutation in mtDNA.
Received: 24 September 1999 / Accepted: 18 September 2000 相似文献
2.
Bickel DR 《Journal of molecular evolution》2000,50(4):381-390
Many tests of the lineage dependence of substitution rates, computations of the error of evolutionary distances, and simulations
of molecular evolution assume that the rate of evolution is constant in time within each lineage descended from a common ancestor.
However, estimates of the index of dispersion of numbers of mammalian substitutions suggest that the rate has time-dependent
variations consistent with a fractal-Gaussian-rate Poisson process, which assumes common descent without assuming rate constancy.
While this model does not affect certain relative-rate tests, it substantially increases the uncertainty of branch lengths.
Thus, fluctuations in the rate of substitution cannot be neglected in calculations that rely on evolutionary distances, such
as the confidence intervals of divergence times and certain phylogenetic reconstructions. The fractal-Gaussian-rate Poisson
process is compared and contrasted with previous models of molecular evolution, including other Poisson processes, the fractal
renewal process, a Lévy-stable process, a fractional-difference process, and a log-Brownian process. The fractal models are
more compatible with mammalian data than the nonfractal models considered, and they may also be better supported by Darwinian
theory. Although the fractal-Gaussian-rate Poisson process has not been proven to have better agreement with data or theory
than the other fractal models, its Gaussian nature simplifies the exploration of its impact on evolutionary distance errors
and relative-rate tests.
Received: 29 September 1999 / Accepted: 20 January 2000 相似文献
3.
Considerable controversy has surrounded the application of mitochondrial DNA data to reconstruction of evolutionary relationships
among the endemic cichlids of Lake Malawi. Central to this debate has been the issue of whether lineage sorting is complete,
and thus whether these data actually reflect species phylogeny, or simply gene genealogy. Review of all mtDNA control region
sequences available for members of one monophyletic subset of this species flock, the Malawi rockfishes, or mbuna, strongly indicates that lineage sorting is incomplete: Character-based analyses of these sequences reconstruct gene, not
species, interrelationships. Analysis of the pattern of nucleotide substitutions differentiating these mtDNA alleles suggests
that pyrimidine residues undergo transition substitutions more often than do purines. Estimation of the magnitude of derived
sequence differentiation in light of the reconstructed gene genealogy suggests that the mbuna may be of considerably more recent vintage than previous molecular characterizations have indicated.
Received: 6 April 1996 / Accepted: 3 March 1997 相似文献
4.
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
5.
6.
Rates of Conservative and Radical Nonsynonymous Nucleotide Substitutions in Mammalian Nuclear Genes 总被引:28,自引:0,他引:28
Zhang J 《Journal of molecular evolution》2000,50(1):56-68
To understand the process and mechanism of protein evolution, it is important to know what types of amino acid substitutions
are more likely to be under selection and what types are mostly neutral. An amino acid substitution can be classified as either
conservative or radical, depending on whether it involves a change in a certain physicochemical property of the amino acid.
Assuming Kimura's two-parameter model of nucleotide substitution, I present a method for computing the numbers of conservative
and radical nonsynonymous (amino acid altering) nucleotide substitutions per site and estimate these rates for 47 nuclear
genes from mammals. The results are as follows. (1) The average radical/conservative rate ratio is 0.81 for charge changes,
0.85 for polarity changes, and 0.49 when both polarity and volume changes are considered. (2) The radical/conservative rate
ratio is positively correlated with the nonsynonymous/synonymous rate ratio for charge changes or when both polarity and volume
changes are considered. (3) Both the conservative/synonymous rate ratio and the radical/synonymous rate ratio are lower in
the rodent lineage than in the primate or artiodactyl lineage, suggesting more intense purifying selection in the rodent lineage,
for both conservative and radical nonsynonymous substitutions. (4) Neglecting transition/transversion bias would cause an
underestimation of both radical and conservative rates and the ratio thereof. (5) Transversions induce more dramatic genetic
alternations than transitions in that transversions produce more amino acid altering changes and among which, more radical
changes.
Received: 6 April 1999 / Accepted: 16 August 1999 相似文献
7.
Eduardo Eizirik Sandro L. Bonatto Warren E. Johnson Peter G. Crawshaw Jr. Jean Cristophe Vié Dulce M. Brousset Stephen J. O'Brien Francisco M. Salzano 《Journal of molecular evolution》1998,47(5):613-624
The ocelot (Leopardus pardalis) and margay (L. wiedii) are sister-species of Neotropical cats which evolved from a lineage that migrated into South America during the formation
of the Panamanian land bridge 3–5 million years ago. Patterns of population genetic divergence of each species were studied
by phylogenetic analyses of mitochondrial DNA (mtDNA) control region sequences in individuals sampled across the distribution
of these taxa. Abundant genetic diversity and remarkably concordant phylogeographic partitions for both species were observed,
identifying parallel geographic regions which likely reflect historical faunal barriers. Inferred aspects of phylogeography,
population genetic structure, and demographic history were used to formulate conservation recommendations for these species.
In addition, observed patterns of sequence variation provided insight into the molecular evolution of the mtDNA control region
in closely related felids.
Received: 26 January 1998 / Accepted: 14 May 1998 相似文献
8.
Nucleotide Substitution Rate of Mammalian Mitochondrial Genomes 总被引:22,自引:0,他引:22
We present here for the first time a comprehensive study based on the analysis of closely related organisms to provide an
accurate determination of the nucleotide substitution rate in mammalian mitochondrial genomes. This study examines the evolutionary
pattern of the different functional mtDNA regions as accurately as possible on the grounds of available data, revealing some
important ``genomic laws.' The main conclusions can be summarized as follows. (1) High intragenomic variability in the evolutionary
dynamic of mtDNA was found. The substitution rate is strongly dependent on the region considered, and slow- and fast-evolving
regions can be identified. Nonsynonymous sites, the D-loop central domain, and tRNA and rRNA genes evolve much more slowly
than synonymous sites and the two peripheral D-loop region domains. The synonymous rate is fairly uniform over the genome,
whereas the rate of nonsynonymous sites depends on functional constraints and therefore differs considerably between genes.
(2) The commonly accepted statement that mtDNA evolves more rapidly than nuclear DNA is valid only for some regions, thus
it should be referred to specific mitochondrial components. In particular, nonsynonymous sites show comparable rates in mitochondrial
and nuclear genes; synonymous sites and small rRNA evolve about 20 times more rapidly and tRNAs about 100 times more rapidly
in mitochondria than in their nuclear counterpart. (3) A species-specific evolution is particularly evident in the D-loop
region. As the divergence times of the organism pairs under consideration are known with sufficient accuracy, absolute nucleotide
substitution rates are also provided.
Received: 11 May 1998 / Accepted: 2 September 1998 相似文献
9.
A model of nucleotide substitution that allows the transition/transversion rate bias to vary across sites was constructed.
We examined the fit of this model using likelihood-ratio tests by analyzing 13 protein coding genes and 1 pseudogene. Likelihood-ratio
testing indicated that a model that allows variation in the transition/transversion rate bias across sites provided a significant
improvement in fit for most protein coding genes but not for the pseudogene. When the analysis was repeated with parameters
estimated separately for first, second, and third codon positions, strong heterogeneity was uncovered for the first and second
codon positions; the variation in the transition/transversion rate was generally weaker at the third codon position. The transition
rate bias and branch lengths are underestimated when variation in the transition/transversion rate was not accommodated, suggesting
that it may be important to accommodate variation in the pattern of nucleotide substitution for accurate estimation of evolutionary
parameters.
Received: 4 November 1997 / Accepted: 19 May 1998 相似文献
10.
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
11.
Gwenaël Piganeau Dominique Mouchiroud Laurent Duret Christian Gautier 《Journal of molecular evolution》2002,54(1):129-133
The relationship between the silent substitution rate (K
s) and the GC content along the genome is a focal point of the debate about the origin of the isochore structure in vertebrates.
Recent estimation of the silent substitution rate showed a positive correlation between K
s and GC content, in contradiction with the predictions of both the regional mutation bias model and the selection or biased
gene conversion model. The aim of this paper is to help resolve this contradiction between theoretical studies and data. We
analyzed the relationship between K
s and GC content under (1) uniform mutation bias, (2) a regional mutation bias, and (3) mutation bias and selection. We report
that an increase in K
s with GC content is expected under mutation bias because of either nonequilibrium of the isochore structure or an increasing
mutation rate from AT toward GC nucleotides in GC-richer isochores. We show by simulations that CpG deamination tends to increase
the mutation rate with GC content in a regional mutation bias model. We also demonstrate that the relationship between K
s and GC under the selectionist or biased gene conversion model is positive under weak selection if the mutation selection
equilibrium GC frequency is less than 0.5.
Received: 28 March 2001 / Accepted: 16 May 2001 相似文献
12.
A detailed analysis of the evolutionary history of hepatitis B virus (HBV) was undertaken using 39 mammalian hepadnaviruses
for which complete genome sequences were available, including representatives of all six human genotypes, as well as a large
sample of small S gene sequences. Phylogenetic trees of these data were ambiguous, supporting no single place of origin for
HBV, and depended heavily on the underlying model of DNA substitution. In some instances genotype F, predominant in the Americas,
was the first to diverge, suggesting that the virus arose in the New World. In other trees, however, sequences from genotype
B, prevalent in East Asia, were the most divergent. An attempt was also made to determine the rate of nucleotide substitution
in the C open reading frame and then to date the origin of HBV. However, no relationship between time and number of substitutions
was found in two independent data sets, indicating that a reliable molecular clock does not exist for these data. Both the
pattern and the rate of nucleotide substitution are therefore complex phenomena in HBV and hinder any attempt to reconstruct
the past spread of this virus.
Received: 5 December 1998 / Accepted: 23 February 1999 相似文献
13.
Charles M. Matthews Cassandra J. Vandenberg Clive N.A. Trotman 《Journal of molecular evolution》1998,46(6):729-733
The Artemia hemoglobin is a dimer comprising two nine-domain covalent polymers in quaternary association. Each polymer is encoded by
a gene representing nine successive globin domains which have different sequences and are presumed to have been copied originally
from a single-domain gene. Two different polymers exist as the result of a complete duplication of the nine-domain gene, allowing
the formation of either homodimers or the heterodimer. The total population size of 18 domains comprising nine corresponding
pairs, coupled with the probability that they reflect several hundred million years of evolution in the same lineage, provides
a unique model in which the process of gene multiplication can be analyzed. The outcome has important implications for the
reliability of local molecular clocks.
The two polymers differ from each other at 11.7% of amino acid sites; however when corresponding individual domains are compared
between polymers, amino acid substitution fluctuates by a factor of 2.7-fold from lowest to highest. This variation is not
obvious at the DNA level: Domain pair identity values fluctuate by 1.3-fold. Identity values are, however, uncorrected for
multiple substitutions, and both silent and nonsilent changes are pooled. Therefore, to determine the variability in relative
substitution rates at the DNA level, we have used the method of Li (1993, J Mol Evol 36:96–99) to determine estimates of nonsynonymous (K
A
) and synonymous (K
S
) substitutions per site for the nine pairs of domains. As expected, the overall level of silent substitutions (K
S
of 56.9%) far exceeded nonsilent substitutions (K
A
of 6.7%); however, for corresponding domain pairs, K
A
fluctuates by 2.3-fold and K
S
by 1.7-fold. The large discrepancies reflected in the expressed protein have accrued within a single lineage and the implication
is that divergence dates of different genera based on amino acid sequences, even with well-studied proteins of reasonable
size, can be wrong by a factor well in excess of 2.
Received: 4 June 1997 / Accepted: 17 December 1997 相似文献
14.
The primary and secondary structure of the small-subunit ribosomal RNA (ssrRNA) gene from the naked, marine amoeba, Vannella anglica (subclass Gymnamoebia), was determined. The ssrRNA is 1962 nucleotides in length, with a low G+C content of 37.1%. The ssrRNA
is composed of several uncommon secondary structure features including helix E8-1, which may be a useful target for rRNA probes
for the direct identification of isolates in mixed culture. Phylogenetic analysis of sequence data showed that V. anglica branched prior to the rapid diversification of the eukaryotes. It did not associate with the other naked, lobose amoebae
represented by Acanthamoeba and Hartmannella, indicating that Vannella represents a separate amoeboid lineage and the subclass Gymnamoebia is polyphyletic.
Received: 9 July 1998 / Accepted: 16 November 1998 相似文献
15.
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
16.
Bacteriophage of the family Leviviridae have played an important role in molecular biology where representative species,
such as Qβ and MS2, have been studied as model systems for replication, translation, and the role of secondary structure in
gene regulation. Using nucleotide sequences from the coat and replicase genes we present the first statistical estimate of
phylogeny for the family Leviviridae using maximum-likelihood and Bayesian estimation. Our analyses reveal that the coliphage
species are a monophyletic group consisting of two clades representing the genera Levivirus and Allolevivirus. The Pseudomonas species PP7 diverged from its common ancestor with the coliphage prior to the ancient split between these genera and their
subsequent diversification. Differences in genome size, gene composition, and gene expression are shown with a high probability
to have changed along the lineage leading to the Allolevivirus through gene expansion. The change in genome size of the Allolevivirus ancestor may have catalyzed subsequent changes that led to their current genome organization and gene expression.
Received: 3 March 2000 / Accepted: 17 October 2000 相似文献
17.
The very high AT content of hymenopteran mtDNA has warranted speculation about nucleotide substitution processes in this
group. Here we investigate the pattern of honeybee, Apis mellifera, mtDNA nucleotide polymorphisms inferred from phylogeny in terms of differences between the ATPase6, COI, COII, COIII, cytochrome
b, and ND2 genes and strand asymmetry in mutation rates. The observed transition/transversion ratios and the distribution of
nonsynonymous substitutions between regions differed significantly. The pattern of differences between genes leading to these
heterogeneities (the ATPase6 and COIII genes group apart from the rest) differed markedly from that predicted on the basis
of long-term evolutionary change and may indicate differences between current and long-term dynamics of sequence evolution.
Also, there is strong strand asymmetry in substitutions, which probably results in a mutability of G and C sufficiently high
to account for the AT-richness of honeybee mtDNA.
Received: 21 October 1998 / Accepted: 27 January 1999 相似文献
18.
The complete mitochondrial DNA (mtDNA) of the donkey and mtDNA comparisons among four closely related mammalian species-pairs 总被引:7,自引:0,他引:7
The nucleotide sequence of the complete mitochondrial genome of the donkey, Equus asinus, was determined. The length of the molecule is 16,670 bp. The length, however, is not absolute due to pronounced heteroplasmy
caused by variable numbers of two types of repetitive motifs in the control region. The sequence of the repeats is (a) 5′-CACACCCA
and (b) 5′-TGCGCGCA, respectively. The order of (a) and (b) can be expressed as {n[2(a)+(b)]+m(a)}. In 32 different clones analyzed the number of n and m ranged from 0 to 9 and 1 to 7. The two rRNA genes, the 13 peptide-coding genes, and the 22 tRNA genes of the donkey and the
horse, Equus caballus, were compared in detail. Total nucleotide difference outside the control region was 6.9%. Nucleotide difference between peptide-coding
genes ranged from 6.4% to 9.4% with a mean of 8.0%. In the inferred protein sequences of the 13 peptide-coding genes the amino
acid difference was 0.2–8.8%, and the mean for the 13 concatenated amino acid sequences was 1.9%. In the 22 tRNA genes, the
mean difference was 3.5%, and that in the two rRNA genes was 4.1%. The mtDNA differences between the donkey and the horse
suggest that the evolutionary separation of the two species occurred ≈9 million years ago. Analyses of differences among the
mtDNAs of three other species-pairs, harbor seal/grey seal, fin whale/blue whale, and Homo/common chimpanzee, showed that the relative evolutionary rate of individual peptide-coding genes varies among different species-pairs
and modes of comparison. The findings show that the superimposition of sequence data of one lineage for resolving and dating
evolutionary divergences of other lineages should be performed with caution unless based on comprehensive data.
Received: 15 October 1995 / Accepted: 15 April 1996 相似文献
19.
We suggest a nucleotide substitution model that takes correlation between base-paired nucleotides into account. The model
includes the estimation of the transition–transversion ratio and allows inference of the shape parameter of a discrete gamma
distribution to include rate heterogeneity. A Cox-test statistic, applied to a diatom ribosomal RNA alignment, shows that
the suggested correlation model explains evolution of the stem region better than usual independence models. Moreover, the
Cox-test procedure is extended to shed some light upon the problem of assigning helical regions in a secondary structure based
alignment. This approach provides an estimate of the percentage of stem positions that do not appear to be correlated.
Received: 4 March 1999 / Accepted: 10 May 1999 相似文献
20.
The Drosophila fat body protein 2 gene (Fbp2) is an ancient duplication of the alcohol dehydrogenase gene (Adh) which encodes a protein that differs substantially from ADH in its methionine content. In D. melanogaster, there is one methionine in ADH, while there are 51 (20% of all amino acids) in FBP2. Methionine is involved in 46% of amino
acid replacements when Fbp2 DNA sequences are compared between D. melanogaster and D. pseudoobscura. Methionine accumulation does not affect conserved residues of the ADH-ADHr-FBP2 multigene family. The multigene family has evolved by replacement of mildly hydrophobic amino acids by methionine with
no apparent reversion. Its short-term evolution was compared between two Drosophila species, while its long-term evolution was compared between two genera belonging respectively to acalyptrate and calyptrate
Diptera, Drosophila and Sarcophaga. The pattern of nucleotide substitution was consistent with an independent accumulation of methionines at the Fbp2 locus in each lineage. Under a steady-state model, the rate of methionine accumulation was constant in the lineage leading
to Drosophila, and was twice as fast as that in the calyptrate lineage. Substitution rates were consistent with a slight positive selective
advantage for each methionine change in about one-half of amino acid sites in Drosophila. This shows that selection can potentially account for a large proportion of amino acid replacements in the molecular evolution
of proteins.
Received: 12 December 1994 / Accepted: 15 April 1996 相似文献