最大节俭
生物
系统发育学
系统发育树
现存分类群
氨基酸
遗传学
树(集合论)
序列(生物学)
进化生物学
组合数学
数学
基因
克莱德
作者
Zefeng Yang,Sudhir Kumar,M Nei
出处
期刊:Genetics
[Oxford University Press]
日期:1995-12-01
卷期号:141 (4): 1641-1650
被引量:725
标识
DOI:10.1093/genetics/141.4.1641
摘要
Abstract A statistical method was developed for reconstructing the nucleotide or amino acid sequences of extinct ancestors, given the phylogeny and sequences of the extant species. A model of nucleotide or amino acid substitution was employed to analyze data of the present-day sequences, and maximum likelihood estimates of parameters such as branch lengths were used to compare the posterior probabilities of assignments of character states (nucleotides or amino acids) to interior nodes of the tree; the assignment having the highest probability was the best reconstruction at the site. The lysozyme c sequences of six mammals were analyzed by using the likelihood and parsimony methods. The new likelihood-based method was found to be superior to the parsimony method. The probability that the amino acids for all interior nodes at a site reconstructed by the new method are correct was calculated to be 0.91, 0.86, and 0.73 for all, variable, and parsimony-informative sites, respectively, whereas the corresponding probabilities for the parsimony method were 0.84, 0.76, and 0.51, respectively. The probability that an amino acid in an ancestral sequence is correctly reconstructed by the likelihood analysis ranged from 91.3 to 98.7% for the four ancestral sequences.
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