共查询到8条相似文献,搜索用时 15 毫秒
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Tests and efficiencies of separate regression models 总被引:1,自引:0,他引:1
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David Posada 《Journal of molecular evolution》2001,52(5):434-444
Models of sequence evolution play an important role in molecular evolutionary studies. The use of inappropriate models of
evolution may bias the results of the analysis and lead to erroneous conclusions. Several procedures for selecting the best-fit
model of evolution for the data at hand have been proposed, like the likelihood ratio test (LRT) and the Akaike (AIC) and
Bayesian (BIC) information criteria. The relative performance of these model-selecting algorithms has not yet been studied
under a range of different model trees. In this study, the influence of branch length variation upon model selection is characterized.
This is done by simulating sequence alignments under a known model of nucleotide substitution, and recording how often this
true model is recovered by different model-fitting strategies. Results of this study agree with previous simulations and suggest
that model selection is reasonably accurate. However, different model selection methods showed distinct levels of accuracy.
Some LRT approaches showed better performance than the AIC or BIC information criteria. Within the LRTs, model selection is
affected by the complexity of the initial model selected for the comparisons, and only slightly by the order in which different
parameters are added to the model. A specific hierarchy of LRTs, which starts from a simple model of evolution, performed
overall better than other possible LRT hierarchies, or than the AIC or BIC.
Received: 2 October 2000 / Accepted: 4 January 2001 相似文献
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Serotonin (5-HT) and its receptors have been involved in critical signal transduction mechanism and deregulation implicated in mood-related disorders. 5-HT activities are mediated through a family of transmembrane spanning serotonin receptors. Both within the family and species, 5-HT receptor protein sequence diversity and 7-transmembrane structural homogeneity have long been intriguing. In this study, we have analyzed the codon site constraint in 5-HT1 subclass receptors from 13 orthologous mammalian mRNA coding sequence. Further, the study was extended to computationally investigate the impact of non-synonymous sites with respect to function and structural significance through sequence homology algorithm and molecular dynamics simulation (MDS). Codon sites with significant posterior probability were observed in 5-HT1A, 5‐HT1B and 5-HT1D receptor indicating variations in site constraint within the 5‐HT1 sub-class genes. In 5-HT1A receptor, seven sites were detected at the functional intracellular loop3 (ICL3) with higher substitution rate through Codeml program. Sequence homology algorithm identifies that these sites were functionally tolerant within the mammals representing a selectively relaxed constraint at this domain. On the other hand, the root mean square deviation (rmsd) values from MDS suggest differences in structural conformation of ICL3 models among the species. Specifically, the human ICL3 model fluctuation was comparatively more stable than other species. Hence, we argue that these sites may have varying influence in G-proteins coupling and activation of effectors systems through downstream interacting accessory proteins of cell among the species. However, further experimental studies are required to elucidate the precise role and the seeming difference of these sites in 5-HT receptors between species. 相似文献