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1.
The mitochondrial DNA (mtDNA) control region was sequenced in 37 sperm
whales from a large part of the global range of the species. Nucleotide
diversity was several-fold lower than that reported for control regions of
abundant and outbred mammals, but similar to that for populations known to
have experienced bottlenecks. Relative neck tests did not suggest that the
low diversity is due to a lower substitution rate in sperm whale mtDNA.
Rather, it is more likely that demographic factors have reduced diversity.
The pattern of nucleotide substitutions was examined by cladistic methods,
facilitated by the apparent monophyly of lineages from the Southern
Hemisphere, as defined by a single base pair deletion. Substitutions were
nonrandom in nature, confined to a few "hot spots," and parallel
substitutions constituted a majority of the inferred changes. The
substitution pattern fitted a negative binomial distribution better than a
Poisson distribution, and the bias in number of substitutions among sites
was considerably higher than previously reported for the mtDNA control
region of any species. A novel method of estimating time since common
ancestry was developed, which utilizes the transition/transversion ratio R
and the number of substitutions inferred from a parsimony analysis. Using
this method, we estimated the age of sperm whale mtDNA diversity to be
about 6,000-25,000 years, and when the uncertainty of R was accounted for,
a range of about 1,000- 100,000 years was obtained.
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2.
We sequenced the NADH dehydrogenase subunit 3 (ND3) gene from a sample of 61 humans, five common chimpanzees, and one gorilla to test whether patterns of mitochondrial DNA (mtDNA) variation are consistent with a neutral model of molecular evolution. Within humans and within chimpanzees, the ratio of replacement to silent nucleotide substitutions was higher than observed in comparisons between species, contrary to neutral expectations. To test the generality of this result, we reanalyzed published human RFLP data from the entire mitochondrial genome. Gains of restriction sites relative to a known human mtDNA sequence were used to infer unambiguous nucleotide substitutions. We also compared the complete mtDNA sequences of three humans. Both the RFLP data and the sequence data reveal a higher ratio of replacement to silent nucleotide substitutions within humans than is seen between species. This pattern is observed at most or all human mitochondrial genes and is inconsistent with a strictly neutral model. These data suggest that many mitochondrial protein polymorphisms are slightly deleterious, consistent with studies of human mitochondrial diseases. 相似文献
3.
Human Mitochondrial DNA Variation and Evolution: Analysis of Nucleotide Sequences from Seven Individuals 总被引:36,自引:8,他引:28
We have analyzed nucleotide sequence variation in an approximately 900-base pair region of the human mitochondrial DNA molecule encompassing the heavy strand origin of replication and the D-loop. Our analysis has focused on nucleotide sequences available from seven humans. Average nucleotide diversity among the sequences is 1.7%, several-fold higher than estimates from restriction endonuclease site variation in mtDNA from these individuals and previously reported for other humans. This disparity is consistent with the rapidly evolving nature of this noncoding region. However, several instances of convergent or parallel gain and loss of restriction sites due to multiple substitutions were observed. In addition, other results suggest that restriction site (as well as pairwise sequence) comparisons may underestimate the total number of substitutions that have occurred since the divergence of two mtDNA sequences from a common ancestral sequence, even at low levels of divergence. This emphasizes the importance of recognizing the large standard errors associated with estimates of sequence variability, particularly when constructing phylogenies among closely related sequences. Analysis of the observed number and direction of substitutions revealed several significant biases, most notably a strand dependence of substitution type and a 32-fold bias favoring transitions over transversions. The results also revealed a significantly nonrandom distribution of nucleotide substitutions and sequence length variation. Significantly more multiple substitutions were observed than expected for these closely related sequences under the assumption of uniform rates of substitution. The bias for transitions has resulted in predominantly convergent or parallel changes among the observed multiple substitutions. There is no convincing evidence that recombination has contributed to the mtDNA sequence diversity we have observed. 相似文献
4.
On the estimation of the rate of nucleotide substitution for the control region of human mitochondrial DNA 总被引:2,自引:0,他引:2
To apply molecular clock for studying human evolution, the pattern of nucleotide substitution for the control region of human mtDNA was analyzed in detail. It is well known that the rate of nucleotide substitution for the control region is much higher than that for any other part of mtDNA. In this study, the higher substitution rate was attributed to the higher rate of transition-type substitution between pyrimidines within the D-loop part, whereas the rates of other types of substitution were essentially the same over the entire mtDNA molecule. Even within the control region, the rate and pattern of nucleotide substitution were different between the D-loop part and the rest. The rate and pattern for the non-D-loop part were very similar to those for fourfold-degenerate sites in the protein-coding region. In contrast, the D-loop and non-D-loop parts showed similarities in the base composition, whereas the base composition of fourfold-degenerate sites slightly different from that of the both parts of the control region. It is concluded, therefore, that the nucleotide frequencies of the control region should be used to estimate the number of substitutions (d) between the control region sequences. However, a method to verify the accuracy of the estimation of d by means of the transition/transversion (s/v) ratio was theoretically studied. It was suggested that the s/v ratio becomes constant over a wide range of d values only when the estimation of d is unbiased. On the basis of this result, the estimates of d previously obtained between human sequences were evaluated. 相似文献
5.
Satoshi Horai Yoko Satta Kenji Hayasaka Rumi Kondo Tadashi Inoue Takafumi Ishida Seiji Hayashi Naoyuki Takahata 《Journal of molecular evolution》1992,35(1):32-43
Summary Molecular biology has resurrected C. Darwin and T.H. Huxley's question about the origin of humans, but the precise branching pattern and dating remain controversial. To settle this issue, a large amount of sequence information is required. We determined mitochondrial (mt) DNA sequences for five hominoids; pygmy and common chimpanzees, gorilla, orangutan, and siamang. The common region compared with the known human sequence is 4759 by long, encompassing genes for 11 transfer RNAs and 6 proteins. Because of the high substitution rates in mammalian mtDNA and an unprecedentedly large region compared, the sequence differences clearly indicate that the closest relatives to human are chimpanzees rather than gorilla. For dating the divergences of human, chimpanzee, and gorilla, we used only unsaturated parts of sequence differences in which the mtDNA genealogy is not obscured by multiple substitutions. The result suggests that gorilla branched off 7.7 ± 0.7 million years (Myr) ago and human 4.7 ± 0.5 Myr ago; the time difference between these divergences being as long as 3 Myr.Offprint requests to: S. Horai 相似文献
6.
Nucleotide substitutions of the four-fold degenerate sites and the total
third codon positions of mitochondrial DNA from human, common chimpanzee,
bonobo, gorilla, and orangutan were examined in detail by three alternative
Markov models; (1) Hasegawa, Kishino, and Yano's (1985) model, (2) Tamura
and Nei's (1993) model, and (3) the general reversible Markov model. These
sites are expected to be relatively free from constraint, and therefore
their tempo and mode in evolution should reflect those of mutation. It
turned out that, among the alternative models, the general reversible
Markov model best approximates the nucleotide substitutions of the
four-fold degenerate sites and the total third codon positions, while the
maximum likelihood estimates of the numbers of nucleotide substitutions
along each branch do not differ significantly among the three models. It
was further shown that the transition rate of these sites during evolution,
and therefore transitional mutation rate of mtDNA, are higher in humans
than in chimpanzees and gorillas probably by about two times. However,
transversional mutation rate and amino acid substitution rate do not differ
significantly between humans and the African apes. These and additional
observations suggest heterogeneity of the mutation rate as well as of the
constraint operating on the mtDNA-encoded proteins among different lineages
of Hominoidea.
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7.
MtDNA substitution rate and segregation of heteroplasmy in coding and noncoding regions 总被引:3,自引:0,他引:3
The mitochondrial DNA (mtDNA) substitution rate and segregation of heteroplasmy were studied for the non-coding control region (D-loop) and 500 bp of the coding region between nucleotide positions 5550 and 6050, by sequence analysis of blood samples from 194 individuals, representing 33 maternal lineages. No homoplasmic nucleotide substitutions were detected in a total of 292 transmissions. The estimated substitution rate per nucleotide per million years for the control region (micro>0.21, 95% CI 0-0.6) was not significantly different from that for the coding region (micro>0.54, 95% CI 0-1.0). Variation in the length of homopolymeric C streches was observed at three sites in the control region (positions 65, 309 and 16,189), all of which were in the heteroplasmic state. Segregation of heteroplasmic genotypes between generations was observed in several maternal pedigrees. At position 309, a longer poly C tract length was strongly associated with a higher probability for heteroplasmy and rapid segregation between generations. The length heteroplasmy at positions 65 and 16,189 was found at low frequency and was confined to a few families. 相似文献
8.
We have investigated the pattern and extent of nucleotide diversityin 10 X-chromosomal genes where mutations are known to causemental retardation in humans. For each gene, we sequenced theentire coding region from cDNA in humans, chimpanzees, and orangutans,as well as about 3 kb of genomic DNA in 20 humans sampled worldwideand in 10 chimpanzees representing two "subspecies." Overallnucleotide diversity in these genes is about twofold lower inhumans than in chimpanzees, and nucleotide diversity withinand between species is low, suggesting that a high level offunctional constraint acts on these genes. Strikingly, we findthat a summary of the allele frequency spectrum is significantlycorrelated in humans and chimpanzees, perhaps reflecting verysimilar levels of constraint at these genes in the two species.A possible exception is FMR2, which shows a higher number ofnonsynonymous than synonymous substitutions on the human lineage,suggesting the action of positive selection. 相似文献
9.
Summary A molecular clock analysis was carried out on the nucleotide sequences of parts of the major noncoding region of mitochondrial DNA (mtDNA) from the major geographic populations of humans. Dates of branchings in the mtDNA tree among humans were estimated with an improved maximum likelihood method. Two species of chimpanzees were used as an outgroup, and the mtDNA clock was calibrated by assuming that the chimpanzee/human split occurred 4 million years ago, following our earlier works. A model of homogeneous evolution among sites does not fit well with the data even within hypervariable segments, and hence an additional parameter that represents a proportion of variable sites was introduced. Taking account of this heterogeneity among sites, the date for the deepest root of the mtDNA tree among humans was estimated to be 280,000±50,000 years old (±1 SE), although there remains uncertainty about the constancy of the evolutionary rate among lineages. The evolutionary rate of the most rapidly evolving sites in mtDNA was estimated to be more than 100 times greater than that of a nuclear pseudogene. 相似文献
10.
Mitochondrial D-loop hypervariable region I (HVI) sequences are widely used in human molecular evolutionary studies, and therefore accurate assessment of rate heterogeneity among sites is essential. We used the maximum-likelihood method to estimate the gamma shape parameter alpha for variable substitution rates among sites for HVI from humans and chimpanzees to provide estimates for future studies. The complete data of 839 humans and 224 chimpanzees, as well as many subsets of these data, were analyzed to examine the effect of sequence sampling. The effects of the genealogical tree and the nucleotide substitution model were also examined. The transition/transversion rate ratio (kappa) is estimated to be about 25, although much larger and biased estimates were also obtained from small data sets at low divergences. Estimates of alpha were 0.28-0.39 for human data sets of different sizes and 0.20-0.39 for data sets including different chimpanzee subspecies. The combined data set of both species gave estimates of 0.42-0.45. While all those estimates suggest highly variable substitution rates among sites, smaller samples tend to give smaller estimates of alpha. Possible causes for this pattern were examined, such as biases in the estimation procedure and shifts in the rate distribution along certain lineages. Computer simulations suggest that the estimation procedure is quite reliable for large trees but can be biased for small samples at low divergences. Thus, an alpha of 0.4 appears suitable for both humans and chimpanzees. Estimates of alpha can be affected by the nucleotide sites included in the data, the overall tree length (the amount of sequence divergence), the number of rate classes used for the estimation, and to a lesser extent, the included sequences. The genealogical tree, the substitution model, and demographic processes such as population expansion do not have much effect. 相似文献