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41.
Approximate methods for estimating the pattern of nucleotide substitution and the variation of substitution rates among sites 总被引:13,自引:6,他引:7
We propose two approximate methods (one based on parsimony and one on
pairwise sequence comparison) for estimating the pattern of nucleotide
substitution and a parsimony-based method for estimating the gamma
parameter for variable substitution rates among sites. The matrix of
substitution rates that represents the substitution pattern can be
recovered through its relationship with the observable matrix of site
pattern frequences in pairwise sequence comparisons. In the parsimony
approach, the ancestral sequences reconstructed by the parsimony algorithm
were used, and the two sequences compared are those at the ends of a branch
in the phylogenetic tree. The method for estimating the gamma parameter was
based on a reinterpretation of the numbers of changes at sites inferred by
parsimony. Three data sets were analyzed to examine the utility of the
approximate methods compared with the more reliable likelihood methods. The
new methods for estimating the substitution pattern were found to produce
estimates quite similar to those obtained from the likelihood analyses. The
new method for estimating the gamma parameter was effective in reducing the
bias in conventional parsimony estimates, although it also overestimated
the parameter. The approximate methods are computationally very fast and
appear useful for analyzing large data sets, for which use of the
likelihood method requires excessive computation.
相似文献
42.
Comparison of models for nucleotide substitution used in maximum- likelihood phylogenetic estimation 总被引:31,自引:15,他引:16
Using real sequence data, we evaluate the adequacy of assumptions made in
evolutionary models of nucleotide substitution and the effects that these
assumptions have on estimation of evolutionary trees. Two aspects of the
assumptions are evaluated. The first concerns the pattern of nucleotide
substitution, including equilibrium base frequencies and the
transition/transversion-rate ratio. The second concerns the variation of
substitution rates over sites. The maximum-likelihood estimate of tree
topology appears quite robust to both these aspects of the assumptions of
the models, but evaluation of the reliability of the estimated tree by
using simpler, less realistic models can be misleading. Branch lengths are
underestimated when simpler models of substitution are used, but the
underestimation caused by ignoring rate variation over nucleotide sites is
much more serious. The goodness of fit of a model is reduced by ignoring
spatial rate variation, but unrealistic assumptions about the pattern of
nucleotide substitution can lead to an extraordinary reduction in the
likelihood. It seems that evolutionary biologists can obtain accurate
estimates of certain evolutionary parameters even with an incorrect
phylogeny, while systematists cannot get the right tree with confidence
even when a realistic, and more complex, model of evolution is assumed.
相似文献
43.
Pot experiments were conducted with a calcareous soil (Inceptisol) to elucidate the effects of bicarbonate (0 and 20 mM) and root zone temperature (15° and 25°C) on the uptake of Zn, Fe, Mn and Cu by "Zn-efficient" and "Zn-inefficient" rice cultivars. Bicarbonate decreased concentrations and total uptake of Zn in shoots of "Zn-inefficient" cultivars, especially of IR 26 at 25°C, but not in Zn-efficient cultivars. Bicarbonate decreased concentrations and uptake of Fe in shoots of Zn inefficient cultivars, particularly in IR 26. Concentrations and total uptake of Mn were lower in bicarbonate treatment in the Zn-inefficient cultivars at 15°C, and in all cultivars at 25°C. However, concentration and uptake of Cu were not affected by bicarbonate in all cultivars. Compared to the 25°C root zone temperature, the concentrations and total uptake of both Zn and Cu in shoots at 15°C were lower in Zn-inefficient than in the Zn-efficient cultivars. The results indicate that Zn-efficiency in rice is causally related to high tolerance of plant to elavated bicarbonate concentrations in soil solution. 相似文献
44.
T. C. Pan T. H. Lin C. L. Tseng M. H. Yang C. W. Huang 《Biological trace element research》1993,39(2-3):117-128
Blackfoot disease is a peripheral vascular disease resulting in gangrene of the lower extremities. Though extensive epidemiological
study has implicated that high arsenic content in artesian well water of the endemic area, bears some important connection
with the disease, the etiology of the disease is still unknown. In this study, attention is paid to multielement determination
in order to find out whether the trace elements in hair of Blackfoot disease patients are different from those of the controls.
Experimental results indicate that the concentrations of As and Se in hair of patients are significantly higher than those
of the controls, but Ca and Zn are significantly lower than those of the controls. The possible connection of these elements
with the etiology of the disease is discussed. 相似文献
45.
Yang S. P.; Bergo G. W.; Krasney E.; Krasney J. A. 《Journal of applied physiology》1994,76(1):303-313
46.
The effect of hydration on the dynamics of trimethoprim bound to dihydrofolate reductase. A deuterium NMR study. 下载免费PDF全文
To determine the effect of hydration on the dynamics of a protein complex, we used deuterium nuclear magnetic resonance (NMR) techniques to examine a trimethoprim (TMP)/E. coli dihydrofolate reductase (DHFR) complex in its lyophilized, partially hydrated, polycrystalline, and ammonium sulfate-precipitated states. The results indicate that TMP is rigid in the lyophilized powder state. The dynamic behavior could be restored by partial rehydration. At 30 wt% hydration the deuterium spectrum of the partially hydrated sample was indistinguishable from that of the polycrystalline and ammonium sulfate-precipitated samples, suggesting that the structure of the protein/TMP complex is similar in the three physical states. Furthermore, we found that the para- and meta-methoxyl groups have very different dynamical behavior. 相似文献
47.
本文报道在我国广西隆林壮族中发现一个罕見的HbQ复合α,β地中海贫血家系。先证者女,18岁,贫血面容,肝脾肿大。化学结构分析确证本Hb变异体为HbQ Thailand[α74(EF3)Asp→His]。血红蛋白组成以及α和β珠蛋白基因分析结果表明,先证者的珠蛋白基因型为-α~Q/-α~T复合β°/β°(IVSI-1G→T/Codon17A→T);先证者父的基因型为-‘α~Q/-复合β~O/β~A(IVSI-1G→T/β~A);先证母的基因型为-α~T/αα复合β~O/β~A(Codon17A→T/β~A)。 相似文献
48.
49.
50.
广西、云南的PSEUDOSCHWAGERINA化石及其地层意义 总被引:8,自引:4,他引:4
该文记述了广西宜山马脑山剖面及云南八宝小独山剖面Pseudoschwaserina属34种(亚种),分析了两剖面Pseudoschwagerina动物群的面貌,讨论了Pseudoschwagerina的地层意义。研究表明,两剖面Pseudoschwagerina动物群具有地方性种稀少的共同特点,大多数种皆为广相型分子。从动物群的组成上看,广西、云南Pseudoschwagerina动物群与我国贵州、北美及俄罗斯等地的Pseudoschwagerina动物群有较大的相似性。但是,目前归入 Pseudoschwagerina名下的各种在形态上有着较大的差异,造成不同地区合Pseudoschwagerina地层带化石难以直接对比。根据对两剖面Pseudoschwagerina地层分布规律的研究以及国内、外Pseudochwagerina地理分布的资料,笔者建议选用 Pseudoschwagerina uddeni,P.beedei,P.robusta等 Pseudoschwagerina的典型分子做为含Pseudoschwagerina地层划分、对比的首要标准类群,选用P.uddeni和P.robusta分别做为确定Pseudoschwagerina带底、顶界线的首要标准种,以便于含Pseudoschwagerina地层的全球性的对比。 相似文献