Abstract:
:In the maximum likelihood (ML) method for estimating a molecular phylogenetic tree, the pattern of nucleotide substitutions for computing likelihood values is assumed to be simpler than that of the actual evolutionary process, simply because the process, considered to be quite devious, is unknown. The problem, however, is that there has been no guarantee to endorse the simplification. To study this problem, we first evaluated the robustness of the ML method in the estimation of molecular trees against different nucleotide substitution patterns, including Jukes and Cantor's, the simplest ever proposed. Namely, we conducted computer simulations in which we could set up various evolutionary models of a hypothetical gene, and define a true tree to which an estimated tree by the ML method was to be compared. The results show that topology estimation by the ML method is considerably robust against different ratios of transitions to transversions and different GC contents, but branch length estimation is not so. The ML tree estimation based on Jukes and Cantor's model is also revealed to be resistant to GC content, but rather sensitive to the ratio of transitions to transversions. We then applied the ML method with different substitution patterns to nucleotide sequence data on tax gene from T-cell leukemia viruses whose evolutionary process must have been more complicated than that of the hypothetical gene. The results are in accordance with those from the simulation study, showing that Jukes and Cantor's model is as useful as a more complicated one for making inferences about molecular phylogeny of the viruses.
journal_name
J Mol Evoljournal_title
Journal of molecular evolutionauthors
Fukami-Kobayashi K,Tateno Ydoi
10.1007/BF02099932subject
Has Abstractpub_date
1991-01-01 00:00:00pages
79-91issue
1eissn
0022-2844issn
1432-1432journal_volume
32pub_type
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journal_title:Journal of molecular evolution
pub_type: 杂志文章
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journal_title:Journal of molecular evolution
pub_type: 杂志文章
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更新日期:1998-10-01 00:00:00
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journal_title:Journal of molecular evolution
pub_type: 杂志文章
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更新日期:2007-07-01 00:00:00
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journal_title:Journal of molecular evolution
pub_type: 杂志文章
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journal_title:Journal of molecular evolution
pub_type: 杂志文章
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更新日期:2001-09-01 00:00:00
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journal_title:Journal of molecular evolution
pub_type: 杂志文章
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journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/s00239-007-9026-8
更新日期:2007-10-01 00:00:00
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journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/BF02100636
更新日期:1986-01-01 00:00:00
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journal_title:Journal of molecular evolution
pub_type: 杂志文章
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更新日期:1988-01-01 00:00:00
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journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/BF02352300
更新日期:1996-07-01 00:00:00
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journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/s00239-014-9648-6
更新日期:2014-12-01 00:00:00
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journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/s00239-004-2640-9
更新日期:2004-10-01 00:00:00
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journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/s002390010049
更新日期:2000-05-01 00:00:00
abstract::Langley and Fitch (1974, 1976) have shown that the pattern of nucleotide substitutions in proteins is inconsistent with a Poisson process with constant rate. From this they conclude that the rate is temporally heterogeneous. It is pointed out in this note that a process which is temporally homogeneous but not a Poisso...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/BF01732751
更新日期:1979-06-08 00:00:00
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journal_title:Journal of molecular evolution
pub_type: 杂志文章
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journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/BF01795749
更新日期:1981-01-01 00:00:00
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journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/pl00006208
更新日期:1997-07-01 00:00:00
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journal_title:Journal of molecular evolution
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journal_title:Journal of molecular evolution
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journal_title:Journal of molecular evolution
pub_type: 杂志文章
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更新日期:1989-07-01 00:00:00
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journal_title:Journal of molecular evolution
pub_type: 杂志文章
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更新日期:1996-09-01 00:00:00
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journal_title:Journal of molecular evolution
pub_type: 杂志文章
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更新日期:2004-06-01 00:00:00
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journal_title:Journal of molecular evolution
pub_type: 杂志文章
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