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1.
Fernando Alvarez-Valin Kamel Jabbari Nicolas Carels Giorgio Bernardi 《Journal of molecular evolution》1999,49(3):330-342
In this work, we have investigated the relationships between synonymous and nonsynonymous rates and base composition in coding
sequences from Gramineae to analyze the factors underlying the variation in substitutional rates. We have shown that in these genes the rates of nucleotide
divergence, both synonymous and nonsynonymous, are, to some extent, dependent on each other and on the base composition. In
the first place, the variation in nonsynonymous rate is related to the GC level at the second codon position (the higher the
GC2 level, the higher the amino acid replacement rate). The correlation is especially strong with T2, the coefficients being significant in the three data sets analyzed. This correlation between nonsynonymous rate and base
composition at the second codon position is also detectable at the intragenic level, which implies that the factors that tend
to increase the intergenic variance in nonsynonymous rates also affect the intragenic variance. On the other hand, we have
shown that the synonymous rate is strongly correlated with the GC3 level. This correlation is observed both across genes and at the intragenic level. Similarly, the nonsynonymous rate is also
affected at the intragenic level by GC3 level, like the silent rate. In fact, synonymous and nonsynonymous rates exhibit a parallel behavior in relation to GC3 level, indicating that the intragenic patterns of both silent and amino acid divergence rates are influenced in a similar
way by the intragenic variation of GC3. This result, taken together with the fact that the number of genes displaying intragenic correlation coefficients between
synonymous and nonsynonymous rates is not very high, but higher than random expectation (in the three data sets analyzed),
strongly suggests that the processes of silent and amino acid replacement divergence are, at least in part, driven by common
evolutionary forces in genes from Gramineae.
Received: 2 July 1998 / Accepted: 18 April 1999 相似文献
2.
A Survey of the Molecular Evolutionary Dynamics of Twenty-Five Multigene Families from Four Grass Taxa 总被引:10,自引:0,他引:10
We surveyed the molecular evolutionary characteristics of 25 plant gene families, with the goal of better understanding general
processes in plant gene family evolution. The survey was based on 247 GenBank sequences representing four grass species (maize,
rice, wheat, and barley). For each gene family, orthology and paralogy relationships were uncertain. Recognizing this uncertainty,
we characterized the molecular evolution of each gene family in four ways. First, we calculated the ratio of nonsynonymous
to synonymous substitutions (d
N/d
S) both on branches of gene phylogenies and across codons. Our results indicated that the d
N/d
S ratio was statistically heterogeneous across branches in 17 of 25 (68%) gene families. The vast majority of d
N/d
S estimates were <<1.0, suggestive of selective constraint on amino acid replacements, and no estimates were >1.0, either across
phylogenetic lineages or across codons. Second, we tested separately for nonsynonymous and synonymous molecular clocks. Sixty-eight
percent of gene families rejected a nonsynonymous molecular clock, and 52% of gene families rejected a synonymous molecular
clock. Thus, most gene families in this study deviated from clock-like evolution at either synonymous or nonsynonymous sites.
Third, we calculated the effective number of codons and the proportion of G+C synonymous sites for each sequence in each gene
family. One or both quantities vary significantly within 18 of 25 gene families. Finally, we tested for gene conversion, and
only six gene families provided evidence of gene conversion events. Altogether, evolution for these 25 gene families is marked
by selective constraint that varies among gene family members, a lack of molecular clock at both synonymous and nonsynonymous
sites, and substantial variation in codon usage.
Received: 25 May 2000 / Accepted: 16 October 2000 相似文献
3.
Ballard JW 《Journal of molecular evolution》2000,51(1):64-75
The current study compares the nucleotide variation among 22 complete mitochondrial genomes of the three distinct Drosophila simulans haplotypes with intron 1 of the alcohol dehydrogenase-related locus. This is the first study to investigate the sequence variation of multiple complete mitochondrial genomes within distinct
mitochondrial haplotypes of a single species. Patterns of variation suggest distinct forces are influencing the evolution
of mitochondrial DNA (mtDNA) and autosomal DNA in D. simulans. First, there is little variation within each mtDNA haplotype but strong differentiation among them. In contrast, there is
no support for differentiation of the mitochondrial haplotypes at the autosomal locus. Second, there is a significant deficiency
of mitochondrial variation in each haplotype relative to the autosomal locus. Third, the ratio of nonsynonymous to synonymous
substitutions is not equal in all branches of the well-resolved phylogeny. There is an excess of nonsynonymous substitutions
relative to synonymous substitutions within each D. simulans haplotype. This result is similar to that previously observed within the mtDNA of distinct species. A single evolutionary
force may be causally linked to the observed patterns of mtDNA variation—a rickettsia-like microorganism, Wolbachia pipientis, which is known to directly influence mitochondrial evolution but have a less direct influence on autosomal loci.
Received: 16 September 1999 / Accepted: 14 March 2000 相似文献
4.
Singhania NA Dyer KD Zhang J Deming MS Bonville CA Domachowske JB Rosenberg HF 《Journal of molecular evolution》1999,49(6):721-728
The two eosinophil ribonucleases, eosinophil-derived neurotoxin (EDN/RNase 2) and eosinophil cationic protein (ECP/RNase
3), are among the most rapidly evolving coding sequences known among primates. The eight mouse genes identified as orthologs
of EDN and ECP form a highly divergent, species-limited cluster. We present here the rat ribonuclease cluster, a group of
eight distinct ribonuclease A superfamily genes that are more closely related to one another than they are to their murine
counterparts. The existence of independent gene clusters suggests that numerous duplications and diversification events have
occurred at these loci recently, sometime after the divergence of these two rodent species (∼10–15 million years ago). Nonsynonymous
substitutions per site (d
N) calculated for the 64 mouse/rat gene pairs indicate that these ribonucleases are incorporating nonsilent mutations at accelerated
rates, and comparisons of nonsynonymous to synonymous substitution (d
N / d
S) suggest that diversity in the mouse ribonuclease cluster is promoted by positive (Darwinian) selection. Although the pressures
promoting similar but clearly independent styles of rapid diversification among these primate and rodent genes remain uncertain,
our recent findings regarding the function of human EDN suggest a role for these ribonucleases in antiviral host defense.
Received: 8 April 1999 / Accepted: 22 June 1999 相似文献
5.
We have determined the nucleotide sequences of sevenlacY alleles isolated from natural isolates ofEscherichia coli. Nucleotide heterozygosity estimates for this locus were compared to those obtained from previous studies of intraspecific variation at chromosomal loci, revealing thatlacY has unusually low synonymous site variation. The average pairwise heterozygosity of synonymous sites (Ks=0.0112+/-0.0100) is the second lowest reported and the lowest for loci that have an equivalent level of nonsynonymous variation. We consider several hypotheses to explain how different forces in evolution could act to create the observed pattern of polymorphism, including selection for translational efficiency and positive selection. Our analysis most strongly supports the hypothesis that positive selection has acted on thelacY locus inE. coli. 相似文献
6.
Wei Wu Morris Goodman Margaret I. Lomax Lawrence I. Grossman 《Journal of molecular evolution》1997,44(5):477-491
Cytochrome c oxidase (COX) is a multi-subunit enzyme complex that catalyzes the final step of electron transfer through the respiratory
chain on the mitochondrial inner membrane. Up to 13 subunits encoded by both the mitochondrial (subunits I, II, and III) and
nuclear genomes occur in eukaryotic organisms ranging from yeast to human. Previously, we observed a high number of amino
acid replacements in the human COX IV subunit compared to mouse, rat, and cow orthologues. Here we examined COX IV evolution
in the two groups of anthropoid primates, the catarrhines (hominoids, cercopithecoids) and platyrrhines (ceboids), as well
as one prosimian primate (lorisiform), by sequencing PCR-amplified portions of functional COX4 genes from genomic DNAs. Phylogenetic analysis of the COX4 sequence data revealed that accelerated nonsynonymous substitution rates were evident in the early evolution of both catarrhines
and, to a lesser extent, platyrrhines. These accelerated rates were followed later by decelerated rates, suggesting that positive
selection for adaptive amino acid replacement became purifying selection, preserving replacements that had occurred. The evidence
for positive selection was especially pronounced along the catarrhine lineage to hominoids in which the nonsynonymous rate
was first faster than the synonymous rate, then later much slower. The rates of three types of ``neutral DNA' nucleotide
substitutions (synonymous substitutions, pseudogene nucleotide substitutions, and intron nucleotide substitutions) are similar
and are consistent with previous observations of a slower rate of such substitutions in the nuclear genomes of hominoids than
in the nuclear genomes of other primate and mammalian lineages.
Received: 22 May 1996 / Accepted: 24 November 1996 相似文献
7.
Capsular polysaccharides are important virulence factors both in Gram-positive and Gram-negative bacteria. A similar cluster
organization of the genes involved in the synthesis of bacterial exopolysaccharides has been postulated in both cases, suggesting
that these clusters evolved by module assembly. Horizontal gene transfer has been postulated to explain the polymorphism found
in these cellular polymers. The cap1K and cap3A genes coding for the pneumococcal type 1 and type 3 UDP-glucose dehydrogenases, respectively, have been compared with other
UDP-sugar dehydrogenases. We have observed that the evolutionary distance between Cap1K and Cap3A is approximately equal to
that found between Cap1K (or Cap3A) and other UDP-GlcDH of families evolutionarily distant like KfiD, the dehydrogenase from
Escherichia coli K5. On the basis of comparisons of G + C content, patterns of synonymous and nonsynonymous substitutions, dinucleotide frequencies,
and codon usage bias, we conclude that the kfiD gene has been introduced into E. coli from an exogenous source, probably from a streptococcal species.
Received: 26 May 1997 / Accepted: 30 July 1997 相似文献
8.
9.
Sequence variation at the major histocompatibility complex DRB loci in beluga (Delphinapterus leucas) and narwhal (Monodon monoceros) 总被引:2,自引:2,他引:0
The variation at loci with similarity to DRB class II major histocompatibility complex loci was assessed in 313 beluga collected from 13 sampling locations across North
America, and 11 narwhal collected in the Canadian high Arctic. Variation was assessed by amplification of exon 2, which codes
for the peptide binding region, via the polymerase chain reaction, followed by either cloning and DNA sequencing or single-stranded
conformation polymorphism analysis. Two DRB loci were identified in beluga: DRB1, a polymorphic locus, and, DRB2, a monomorphic locus. Eight alleles representing five distinct lineages (based on sequence similarity) were found at the
beluga DRB1 locus. Although the relative number of alleles is low when compared with terrestrial mammals, the amino acid variation found
among the lineages is moderate. At the DRB1 locus, the average number of nonsynonymous substitutions per site is greater than the average number of synonymous substitutions
per site (0.0806 : 0.0207, respectively;P<0.01). Most of the 31 amino acid substitutions do not conserve the physiochemical properties of the residue, and 21 of these
are located at positions implicated as forming pockets responsible for the selective binding of foreign peptide side chains.
Only DRB1 variation was examined in 11 narwhal, revealing a low amount of variation. These data are consistent with an important role
for the DRB1 locus in the cellular immune response of beluga. In addition, the ratio of nonsynonymous to synonymous substitutions is similar
to that among primate alleles, arguing against a reduction in the balancing selection pressure in the marine environment.
Two hypotheses may explain the modest amount of Mhc variation when compared with terrestrial mammals: small population sizes at speciation or a reduced neutral substitution
rate in cetaceans.
Received: 15 July 1997 / Revised: 24 March 1998 相似文献
10.
McClellan DA 《Journal of molecular evolution》2000,51(2):131-140
Mitochondrial genetic codons can be categorized by four patterns of nucleotide-site degeneracy based on varying combinations
of twofold- or nondegenerate sites at first codon positions and twofold- or fourfold-degenerate sites at third codon positions.
Herein, a model of molecular evolution is introduced that uses these patterns to calculate expected substitution frequencies
for each codon position and substitution type relative to overall number of synonymous or nonsynonymous substitutions. Regions
of the pocket gopher cytochrome oxidase subunit I (COI) and cytochrome b (cyt-b) genes are analyzed using this model. Chi-square distributions are used to produce relative goodness-of-fit (GF) scores for
measuring the difference between substitution frequencies predicted by the codon-degeneracy model (CDM), and frequencies inferred
using a well-supported phylogenetic tree of closely related species. The GF scores for expected and observed synonymous (GFsyn= 0.429, p= 0.807) and nonsynonymous (GFns= 2.309, p= 0.679) substitution frequencies resulted in a failure to reject the CDM as a null hypothesis for the molecular evolution
of COI and cyt-b in pocket gophers. Alternative tree topologies and calculations of transition bias for these data result in higher GF scores.
Received: 25 March 1999 / Accepted: 17 September 1999 相似文献
11.
Wen-Hsiung Li 《Journal of molecular evolution》1993,36(1):96-99
Summary The current convention in estimating the number of substitutions per synonymous site (K
S
) and per nonsynonymous site (K
A
) between two protein-coding genes is to count each twofold degenerate site as one-third synonymous and two-thirds nonsynonymous
because one of the three possible changes at such a site is synonymous and the other two are nonsynonymous. This counting
rule can considerably overestimate theK
S
value because transitional mutations tend to occur more often than transversional mutations and because most transitional
mutations at twofold degenerate sites are synonymous. A new method that gives unbiased estimates is proposed. An application
of the new and the old method to 14 pairs of mouse and rat genes shows that the new method gives aK
S
value very close to the number of substitutions per fourfold degenerate site whereas the old method gives a value 30% higher.
Both methods give aK
A
value close to the number of substitutions per nondegenerate site. 相似文献
12.
There are two tightly linked loci (D and CE) for the human Rh blood group. Their gene products are membrane proteins having
12 transmembrane domains and form a complex with Rh50 glycoprotein on erythrocytes. We constructed phylogenetic networks of
human and nonhuman primate Rh genes, and the network patterns suggested the occurrences of gene conversions. We therefore
used a modified site-by-site reconstruction method by using two assumed gene trees and detected 9 or 11 converted regions.
After eliminating the effect of gene conversions, we estimated numbers of nonsynonymous and synonymous substitutions for each
branch of both trees. Whichever gene tree we selected the branch connecting hominoids and Old World monkeys showed significantly
higher nonsynonymous than synonymous substitutions, an indication of positive selection. Many other branches also showed higher
nonsynonymous than synonymous substitutions; this suggests that the Rh genes have experienced some kind of positive selection.
Received: 16 March 1999 / Accepted: 17 June 1999 相似文献
13.
In an effort to detect factors which may be under positive selection, a survey for such genes in two pathogenic strains of
Helicobacter pylori (J99 and 26695) was performed. Based on an analysis of synonymous and nonsynonymous substitutions, we identified 19 candidate
genes under positive selection. A search for homologues with known crystallographic structures revealed Escherichia coli carbomoyl phosphate synthetase as a homologue of H. pylori carbamoyl phosphate synthetase. Carbamoyl phosphate synthetase as isolated from E. coli is a heterodimeric enzyme that possesses two different but coupled functionalities and is involved in the first committed
step in the separate biosynthetic pathways for arginine and pyrimidine nucleotides. In this study, we provide evidence indicating
that one of these functionalities appears to be under selective pressure. Reports from previously published site-directed
mutagenesis studies point to a decoupling of amidotransferase and synthetase activities. Implications of these findings for
a metabolic enzyme under positive selection are discussed in terms of the mechanisms of H. pylori pathogenesis.
Received: 11 June 2001 / Accepted: 12 September 2001 相似文献
14.
Fimbrial adhesins allow bacteria to interact with and attach to their environment. The bacteria possibly benefit from these
interactions, but all external structures including adhesins also allow bacteria to be identified by other organisms. Thus
adhesion molecules might be under multiple forms of selection including selection to constrain functional interactions or
evolve novel epitopes to avoid recognition. We address these issues by studying genetic diversity in the Escherichia coli type-1 fimbrial major subunit, fimA. Overall, sequence diversity in fimA is high (π= 0.07) relative to that in other E. coli genes. High diversity is a function of positive diversifying selection, as detected by d
N/d
S ratios higher than 1.0, and amino acid residuces subject to diversifying selection are nonrandomly clustered on the exterior
surface of the peptide. In addition, McDonald and Kreitman tests suggest that there has been historical but not current directional
selection at fimA between E. coli and Salmonella. Finally, some regions of the fimA peptide appear to be under strong structural constraint within E. coli, particularly the interior regions of the molecule that is involved in subunit to subunit interaction. Recombination also
plays a major role contributing to E. coli fimA allelic variation and estimates of recombination (2N
e
c) and mutation (2N
eμ) are about the same. Recombination may act to separate the diverse evolutionary forces in different regions of the fimA peptide.
Received: 13 April 2000 / Accepted: 28 October 2000 相似文献
15.
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
16.
Rates of synonymous and nonsynonymous nucleotide substitutions and codon usage bias (ENC) were estimated for a number of
nuclear and chloroplast genes in a sample of centric and pennate diatoms. The results suggest that DNA evolution has taken
place, on an average, at a slower rate in the chloroplast genes than in the nuclear genes: a rate variation pattern similar
to that observed in land plants. Synonymous substitution rates in the chloroplast genes show a negative association with the
degree of codon usage bias, suggesting that genes with a higher degree of codon usage bias have evolved at a slower rate.
While this relationship has been shown in both prokaryotes and multicellular eukaryotes, it has not been demonstrated before
in diatoms.
Received: 3 June 1998 / Accepted: 11 August 1998 相似文献
17.
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
18.
Tomoko Ohta 《Journal of molecular evolution》1998,46(6):633-638
The pattern of polymorphisms at major histocompatibility complex loci was studied by computer simulations and by DNA sequence
analysis. Two types of selection, overdominance plus short-term selection and maternal–fetal incompatibility, were simulated
for a gene family with intra- and interlocus gene conversion. Both types of selection were found to be consistent with the
observed patterns of polymorphisms. It was also found that the more interlocus conversion occurs, the higher the divergence
becomes at both nonsynonymous and synonymous sites. The ratio of nonsynonymous-to-synonymous divergence among alleles decreases
as the interlocus conversion rate increases. These results agree with the interpretation that the rate of interlocus conversion
is lower in human genes than in genes of other nonprimate mammals. This is because, in the latter, synonymous divergence at
the ARS (antigen recognition site) is often higher than that at the non-ARS, whereas in the former, this is not so. Also,
the ratio of nonsynonymous to synonymous substitutions at the ARS tends to be higher in human genes than in other mammalian
genes. The main difference between overdominance plus short-term selection and maternal–fetal interaction is that the number
of alleles and heterozygosity per locus are higher in the latter than in the former under the presumed selection intensities.
However, the average divergence among alleles tends to be lower in the latter than in the former under similar conditions.
Received: 30 September 1997 / Accepted: 15 December 1997 相似文献
19.
de Miranda AB Alvarez-Valin F Jabbari K Degrave WM Bernardi G 《Journal of molecular evolution》2000,50(1):45-55
Mycobacterium tuberculosis and Mycobacterium leprae are the ethiological agents of tuberculosis and leprosy, respectively. After performing extensive comparisons between genes
from these two GC-rich bacterial species, we were able to construct a set of 275 homologous genes. Since these two bacterial
species also have a very low growth rate, translational selection could not be so determinant in their codon preferences as
it is in other fast-growing bacteria. Indeed, principal-components analysis of codon usage from this set of homologous genes
revealed that the codon choices in M. tuberculosis and M. leprae are correlated not only with compositional constraints and translational selection, but also with the degree of amino acid
conservation and the hydrophobicity of the encoded proteins. Finally, significant correlations were found between GC3 and synonymous distances as well as between synonymous and nonsynonymous distances.
Received: 30 October 1998 / Accepted: 16 August 1999 相似文献
20.
The class I genes of the major histocompatibility complex (Mhc) are here investigated for the first time in a passerine bird. The great reed warbler is a rare species in Sweden with a
few semi-isolated populations. Yet, we found extensive Mhc class I variation in the study population. The variable exon 3, corresponding to the α2 domain, was amplified from genomic DNA with degenerated primers. Seven different genomic class I sequences were detected
in a single individual. One of the sequences had a deletion leading to a shift in the reading frame, indicating that it was
not a functional gene. A randomly selected clone was used as a probe for restriction fragment length polymorphism (RFLP) studies
in combination with the restriction enzyme Pvu II. The RFLP pattern was complex with 21–25 RFLP fragments per individual and extensive variation. Forty-nine RFLP genotypes
were detected in 55 tested individuals. To study the number of transcribed genes, we isolated 14 Mhc class I clones from a cDNA library from a single individual. We found eight different sequences of four different lengths
(1.3–2.2 kilobases), suggesting there are at least four transcribed loci. The number of nonsynonymous substitutions (d
N
) in the peptide binding region of exon 3 were higher than the number of synonymous substitutions (d
S
), indicating balancing selection in this region. The number of transcribed genes and the numerous RFLP fragments found so
far suggest that the great reed warbler does not have a "minimal essential Mhc" as has been suggested for the chicken.
Received: 13 May 1998 / Revised: 18 August 1998 相似文献