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1.
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
2.
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
3.
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
4.
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
5.
Mitochondrial small-subunit (19S) rDNA sequences were obtained from 10 angiosperms to further characterize sequence divergence
levels and structural variation in this molecule. These sequences were derived from seven holoparasitic (nonphotosynthetic)
angiosperms as well as three photosynthetic plants. 19S rRNA is composed of a conservative core region (ca. 1450 nucleotides)
as well as two variable regions (V1 and V7). In pairwise comparisons of photosynthetic angiosperms to Glycine, the core 19S rDNA sequences differed by less than 1.4%, thus supporting the observation that variation in mitochondrial rDNA
is 3–4 times lower than seen in protein coding and rDNA genes of other subcellular organelles. Sequences representing four
distinct lineages of nonasterid holoparasites showed significantly increased numbers of substitutions in their core 19S rDNA
sequences (2.3–7.6%), thus paralleling previous findings that showed accelerated rates in nuclear (18S) and plastid (16S)
rDNA from the same plants. Relative rate tests confirmed the accelerated nucleotide substitution rates in the holoparasites
whereas rates in nonparasitic plants were not significantly increased. Among comparisons of both parasitic and nonparasitic
plants, transversions outnumbered transitions, in many cases more than two to one. The core 19S rRNA is conserved in sequence
and structure among all nonparasitic angiosperms whereas 19S rRNA from members of holoparasitic Balanophoraceae have unique
extensions to the V5 and V6 variable domains. Substitution and insertion/deletion mutations characterized the V1 and V7 regions
of the nonasterid holoparasites. The V7 sequence of one holoparasite (Scybalium) contained repeat motifs. The cause of substitution rate increases in the holoparasites does not appear to be a result of
RNA editing, hence the underlying molecular mechanism remains to be fully documented.
Received: 18 May 1997 / Accepted: 11 July 1997 相似文献
6.
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
7.
Sequence differences in the tRNA-proline (tRNApro) end of the mitochondrial control-region of three species of Pacific butterflyfishes accumulated 33–43 times more rapidly
than did changes within the mitochondrial cytochrome b gene (cytb). Rapid evolution in this region was accompanied by strong
transition/transversion bias and large variation in the probability of a DNA substitution among sites. These substitution
constraints placed an absolute ceiling on the magnitude of sequence divergence that could be detected between individuals.
This divergence ``ceiling' was reached rapidly and led to a decay in the relative rate of control-region/cytb b evolution.
A high rate of evolution in this section of the control-region of butterflyfishes stands in marked contrast to the patterns
reported in some other fish lineages. Although the mechanism underlying rate variation remains unclear, all taxa with rapid
evolution in the 5′-end of the control-region showed extreme transition biases. By contrast, in taxa with slower control-region
evolution, transitions accumulated at nearly the same rate as transversions. More information is needed to understand the
relationship between nucleotide bias and the rate of evolution in the 5′-end of the control-region.
Despite strong constraints on sequence change, phylogenetic information was preserved in the group of recently differentiated
species and supported the clustering of sequences into three major mtDNA groupings. Within these groups, very similar control-region
sequences were widely distributed across the Pacific Ocean and were shared between recognized species, indicating a lack of
mitochondrial sequence monophyly among species.
Received: 30 June 1996 / Accepted: 15 May 1997 相似文献
8.
A Phylogenetic Study of the Origin of the Domestic Pig Estimated from the Near-Complete mtDNA Genome 总被引:18,自引:0,他引:18
The near-complete pig mtDNA genome sequence (15,997 bp) was determined from two domestic pigs (one Chinese Meishan and one
Swedish Landrace) and two European wild boars. The sequences were analyzed together with a previously published sequence representing
a Swedish domestic pig. The sequences formed three distinct clades, denoted A, E1, and E2, with considerable sequence divergence
between them (0.8–1.2%). The results confirm our previous study (based on the sequence of the cytochrome B gene and the control
region only) and provide compelling evidence that domestication of pigs must have occurred from both an Asian and a European
subspecies of the wild boar. We estimated the time since the divergence of clade A (found in Chinese Meishan pigs) and E1
(found in European domestic pigs) at about 900,000 years before present, long before domestication about 9000 years ago. The
pattern of nucleotide substitutions among the sequences was in good agreement with previous interspecific comparisons of mammalian
mtDNA; the lowest substitution rates were observed at nonsynonymous sites in protein-coding genes, in the tRNA and rRNA genes,
while the highest rates were observed at synonymous sites and in the control region. The presence of Asian clade A in some
major European breeds (Large White and Landrace) most likely reflects the documented introgression of Asian germplasm into
European stocks during the 18th and 19th centuries. The coexistence of such divergent mtDNA haplotypes for 100+ generations
is expected to lead to the presence of recombinant haplotypes if paternal transmission and recombination occur at a low frequency.
We found no evidence of such recombination events in the limited sample studied so far.
Received: 19 April 2000; Accepted: 15 November 2000 相似文献
9.
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
10.
Analysis of nucleotide substitutions of mitochondrial DNAs in Drosophila melanogaster and its sibling species 总被引:4,自引:0,他引:4
To study the rate and pattern of nucleotide substitution in mitochondrial
DNA (mtDNA), we cloned and sequenced a 975-bp segment of mtDNA from
Drosophila melanogaster, D. simulans, and D. mauritiana containing the
genes for three transfer RNAs and parts of two protein- coding genes, ND2
and COI. Statistical analysis of synonymous substitutions revealed a
predominance of transitions over transversions among the three species, a
finding differing from previous results obtained from a comparison of D.
melanogaster and D. yakuba. The number of transitions observed was nearly
the same for each species comparison, including D. yakuba, despite the
differences in divergence times. However, transversions seemed to increase
steadily with increasing divergence time. By contrast, nonsynonymous
substitutions in the ND2 gene showed a predominance of transversions over
transitions. Most transversions were between A and T and seemed to be due
to some kind of mutational bias to which the A + T-rich mtDNA of Drosophila
species may be subject. The overall rate of nucleotide substitution in
Drosophila mtDNA appears to be slightly faster (approximately 1.4 times)
than that of the Adh gene. This contrasts with the result obtained for
mammals, in which the mtDNA evolves approximately 10 times faster than
single-copy nuclear DNA. We have also shown that the start codon of the COI
gene is GTGA in D. simulans and GTAA in D. mauritiana. These codons are
different from that of D. melanogaster (ATAA).
相似文献
11.
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
12.
A full-length cytochrome b pseudogene was found in rodents; it has apparently been translocated from a mitochondrion to the nuclear genome in the subfamily
Arvicolinae. The pseudogene (ψcytb) differed from its mitochondrial counterpart at 201 of 1143 sites (17.6%) and by four indels. Cumulative evidence suggests
that the pseudogene has been translocated to the nucleus. Phylogenetic reconstruction indicates that the pseudogene arose
before the diversification of M. arvalis/M. rossiaemeridionalis from M. oeconomus, but after the divergence of the peromyscine/sigmodontine/arvicoline clades some ∼10 MYA. Published rates of divergence between
mitochondrial genes and their nuclear pseudogenes suggest that the translocation of this mitochondrial gene to the nuclear
genome occurred some 6 MYA, in agreement with the phylogenetic evidence.
Received: 16 January 1998 / Accepted: 18 July 1998 相似文献
13.
The mitochondrial genomes of the Chlorophyta exhibit significant diversity with respect to gene content and genome compactness; however, quantitative data on the rates of nucleotide substitution in mitochondrial DNA, which might help explain the origin of this diversity, are lacking. To gain insight into the evolutionary forces responsible for mitochondrial genome diversification, we sequenced to near completion the mitochondrial genome of the chlorophyte Chlamydomonas incerta, estimated the evolutionary divergence between Chlamydomonas reinhardtii and C. incerta mitochondrial protein-coding genes and rRNA-coding regions, and compared the relative evolutionary rates in mitochondrial and nuclear genes. Synonymous and nonsynonymous substitution rates do not differ significantly between the mitochondrial and nuclear protein-coding genes. The mitochondrial rRNA-coding regions, however, are evolving much faster than their nuclear counterparts, and this difference might be explained by relaxed functional constraints on the mitochondrial translational apparatus due to the small number of proteins synthesized in Chlamydomonas mitochondria. Substitution rates at synonymous sites in a nonstandard mitochondrial gene (rtl) and at intronic and synonymous sites in nuclear genes expressed at low levels suggest that the mutation rate is similar in these two genetic compartments. Potential evolutionary forces shaping mitochondrial genome evolution in Chlamydomonas are discussed. 相似文献
14.
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
15.
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
16.
Ballard JW 《Journal of molecular evolution》2000,51(1):48-63
In this study, a comparative genomics approach is employed to investigate the forces that shape evolutionary change in the
mitochondrial DNA (mtDNA) of members of the Drosophila melanogaster subgroup. This approach facilitates differentiation of the patterns of variation resulting from processes acting at a higher
level from those acting on a single gene. The mitochondrial genomes of three isofemale lines of D. simulans (siI, -II, and -III), two of D. melanogaster (Oregon R and a line from Zimbabwe), and D. mauritiana (maI and -II), and one of D. sechellia were sequenced and compared with that derived from D. yakuba. Data presented here indicate that at least three broad mechanisms shape the evolutionary dynamics of mtDNA in these taxa.
The first set of mechanisms is intrinsic to the molecule. Dominant processes may be interpreted as selection for an increased
rate of replication of the mtDNA molecule, biases in DNA repair, and differences in the pattern of nucleotide substitution
among strands. In the genes encoded on the major strand (62% of the coding DNA) changes to or from C predominate, whereas
on the minor changes to or from G predominate. The second set of mechanisms affects distinct lineages. There are evolutionary
rate differences among lineages, possibly owing to population demographic changes or changes in mutational biases. This is
supported by the heterogeneity found in synonymous, nonsynonymous, and silent substitutions. The third set of mechanisms differentially
affects distinct genes. A maximum-likelihood sliding-window analysis detected four disjunct regions that have a significantly
different nucleotide substitution process from that derived from the complete sequence. These data show the potential for
comparative genomics to tease apart subtle forces that shape the evolution of DNA.
Received: 30 July 1999 / Accepted: 16 March 2000 相似文献
17.
Molecular Timing of Primate Divergences as Estimated by Two Nonprimate Calibration Points 总被引:13,自引:0,他引:13
The complete mitochondrial DNA (mtDNA) molecule of the hamadryas baboon, Papio hamadryas, was sequenced and included in a molecular analysis of 24 complete mammalian mtDNAs. The particular aim of the study was to
time the divergence between Cercopithecoidea and Hominoidea. That divergence, set at 30 million years before present (MYBP)
was a fundamental reference for the original proposal of recent hominoid divergences, according to which the split among gorilla,
chimpanzee, and Homo took place 5 MYBP. In the present study the validity of the postulated 30 MYBP dating of the Cercopithecoidea/Hominoidea
divergence was examined by applying two independent nonprimate molecular references, the divergence between artiodactyls and
cetaceans set at 60 MYBP and that between Equidae and Rhinocerotidae set at 50 MYBP. After calibration for differences in
evolutionary rates, application of the two references suggested that the Cercopithecoidea/Hominoidea divergence took place
>50 MYBP. Consistent with the marked shift in the dating of the Cercopithecoidea/Hominoidea split, all hominoid divergences
receive a much earlier dating. Thus the estimated date of the divergence between Pan (chimpanzee) and Homo is 10–13 MYBP and that between Gorilla and the Pan/Homo linage ≈17 MYBP. The same datings were obtained in an analysis of clocklike evolving genes. The findings show that recalculation
is necessary of all molecular datings based directly or indirectly on a Cercopithecoidea/Hominoidea split 30 MYBP.
Received: 1 April 1998 / Accepted: 1 July 1998 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.
Synonymous substitution rates have been shown to vary among evolutionary
lineages of both nuclear and organellar genes across a broad range of
taxonomic groups. In animals, rate heterogeneity does not appear to be
correlated across nuclear and mitochondrial genes. In this paper, we
contrast substitution rates in two plant groups and show that grasses
evolve more rapidly than palms at synonymous sites in a mitochondrial, a
nuclear, and a plastid gene. Furthermore, we show that the relative rates
of synonymous substitution between grasses and palms are similar at the
three loci. The correlation in synonymous substitution rates across genes
is particularly striking because the three genes evolve at very different
absolute rates. In contrast, relative rates of nonsynonymous substitution
are not conserved among the three genes.
相似文献
20.
We compared nonsynonymous substitution rates (Ka) of nuclear coding genes between four major groups of living sauropsids
(reptiles): birds, squamates, crocodiles, and turtles. Since only 9 orthologous genes are known in all the four taxonomic
groups, we searched for orthologous genes known in chicken and at least one of any representative of poikilotherm sauropsids.
Thus, we analyzed three additional data sets: 28 genes identified in chicken and various squamates, 24 genes identified in
chicken and crocodilians, and 20 genes identified in chicken and turtles. To compare nonsynonymous substitution rates between
all lineages of sauropsids, we used the relative-rate test with human genes as the outgroup. We show that 22/28 nuclear coding
genes of squamates, especially snakes (15/16), have an higher evolutionary rate than those in chicken (in mean, 30–40% faster).
However, no such difference is detected between crocodiles, turtles and chicken. Higher substitution rate in squamates nuclear
coding genes than in chicken, and probably than in other sauropsids, could explain some of the difficulties in resolving the
molecular phylogeny of reptiles.
Received: 5 July 2000 / Accepted: 13 February 2001 相似文献