一种序列系统发育研究策略。
A strategy for sequence phylogeny research.
作者信息
Sankoff D, Cedergren R J, McKay W
出版信息
Nucleic Acids Res. 1982 Jan 11;10(1):421-31. doi: 10.1093/nar/10.1.421.
Abstract
Minimal mutation trees, and almost minimal trees, are constructed from two data sets, one of phenylalanine tRNA sequences, and the other of 5S RNA sequences, from a diverse range of organisms. The two sets of results are mutually consistent. Trees representing previous evolutionary hypotheses are compared using a total weighted mutational distance criterion. The importance of sequence data from relatively little-studed phylogenetic lines is stressed. A procedure is illustrated which circumvents the computational difficulty of evaluating the astronomically large number of possible trees, without resorting to suboptimal methods.
摘要
最小突变树和几乎最小的树是根据两个数据集构建的，一个是来自多种生物的苯丙氨酸tRNA序列数据集，另一个是5S RNA序列数据集。两组结果相互一致。使用总加权突变距离标准比较代表先前进化假说的树。强调了来自研究较少的系统发育谱系的序列数据的重要性。阐述了一种程序，该程序无需采用次优方法就能规避评估数量庞大得惊人的可能树的计算难题。
相似文献
1
A strategy for sequence phylogeny research.
Nucleic Acids Res. 1982 Jan 11;10(1):421-31. doi: 10.1093/nar/10.1.421.
2
Phylogeny of transfer RNA.
Orig Life. 1984;14(1-4):547-55. doi: 10.1007/BF00933703.
3
Transfer-RNA: the early adaptor.
Naturwissenschaften. 1981 May;68(5):217-28. doi: 10.1007/BF01047323.
4
Nucleotide sequence of the pea chloroplast tRNA-Thr(GGU) gene and flanking regions. Comparison to the Vicia faba sequence.
Nucleic Acids Res. 1987 Jan 26;15(2):854. doi: 10.1093/nar/15.2.854.
5
Compilation of sequences of tRNA genes.
Nucleic Acids Res. 1985;13 Suppl(Suppl):r51-104. doi: 10.1093/nar/13.suppl.r51.
6
Conservation of plant cytoplasmic tRNA structure. Nucleotide sequence of rape tRNAPhe.
Biochimie. 1984 Jun;66(6):483-6. doi: 10.1016/0300-9084(84)90084-1.
7
The anticodon of the maize chloroplast gene for tRNA Leu UAA is split by a large intron.
Nucleic Acids Res. 1982 May 25;10(10):3027-37. doi: 10.1093/nar/10.10.3027.
8
The nucleotide sequence of phenylalanine tRNA from the cytoplasm of Neurospora crassa.
Nucleic Acids Res. 1980 Mar 11;8(5):1023-32. doi: 10.1093/nar/8.5.1023.
9
Nucleotide sequence of the spinach chloroplast tRNA(CAALeu) gene and its flanking regions.
Nucleic Acids Res. 1987 Apr 24;15(8):3621. doi: 10.1093/nar/15.8.3621.
10
[The human mitochondrial genome and evolution of transfer methionine RNA].
Mol Biol (Mosk). 1984 Mar-Apr;18(2):323-31.
引用本文的文献
1
Quantifying the mechanisms of domain gain in animal proteins.
Genome Biol. 2010;11(7):R74. doi: 10.1186/gb-2010-11-7-r74. Epub 2010 Jul 15.
2
Stable tRNA-based phylogenies using only 76 nucleotides.
RNA. 2010 Aug;16(8):1469-77. doi: 10.1261/rna.726010. Epub 2010 Jun 17.
3
A multiple sequence comparison method.
Bull Math Biol. 1993 Mar;55(2):465-86. doi: 10.1007/BF02460892.
4
Phylogeny reconstruction for protein sequences based on amino acid properties.
J Mol Evol. 1995 Oct;41(4):522-30. doi: 10.1007/BF00160324.
5
5S RNA sequence from the Philosamia silkworm: evidence for variable evolutionary rates in insect 5S RNA.
Nucleic Acids Res. 1982 Sep 25;10(18):5711-6. doi: 10.1093/nar/10.18.5711.
6
The nucleotide sequences of the 5S rRNAs of four mushrooms and their use in studying the phylogenetic position of basidiomycetes among the eukaryotes.
Nucleic Acids Res. 1983 May 11;11(9):2871-80. doi: 10.1093/nar/11.9.2871.
7
Nucleotide sequences of 5s rRNAs from sponge Halichondria japonica and tunicate Halocynthia roretzi and their phylogenetic positions.
Nucleic Acids Res. 1983 Apr 11;11(7):1969-74. doi: 10.1093/nar/11.7.1969.
8
Unusual structural features of the 5S ribosomal RNA from Streptococcus cremoris.
Nucleic Acids Res. 1983 Nov 11;11(21):7569-77. doi: 10.1093/nar/11.21.7569.
9
Simplified computer programs for search of homology within nucleotide sequences.
Nucleic Acids Res. 1984 Jan 11;12(1 Pt 1):193-201. doi: 10.1093/nar/12.1part1.193.
10
On the evolutionary descent of organisms and organelles: a global phylogeny based on a highly conserved structural core in small subunit ribosomal RNA.
Nucleic Acids Res. 1984 Jul 25;12(14):5837-52. doi: 10.1093/nar/12.14.5837.
本文引用的文献
1
The evolving tRNA molecule.
CRC Crit Rev Biochem. 1981;11(1):35-104. doi: 10.3109/10409238109108699.
2
Collection of published 5S and 5.8S RNA sequences and their precursors.
Nucleic Acids Res. 1981 Jan 10;9(1):r25-42. doi: 10.1093/nar/9.1.213-a.
3
Phylogenetic tree derived from bacterial, cytosol and organelle 5S rRNA sequences.
Nucleic Acids Res. 1981 Mar 25;9(6):1451-61. doi: 10.1093/nar/9.6.1451.
4
The phylogeny of prokaryotes.
Science. 1980 Jul 25;209(4455):457-63. doi: 10.1126/science.6771870.
5
3' Terminal labelling of RNA of RNA with beta-32P-pyrophosphate group and its application to the sequence analysis of 5S RNA from Streptomyces griseus.
Nucleic Acids Res. 1980 Sep 25;8(18):4111-24. doi: 10.1093/nar/8.18.4111.
6
Frequency of insertion-deletion, transversion, and transition in the evolution of 5S ribosomal RNA.
J Mol Evol. 1976 Mar 29;7(2):133-49. doi: 10.1007/BF01732471.
7
Evolution of methionine initiator and phenylalanine transfer RNAs.
J Mol Evol. 1979 Dec;14(4):287-300. doi: 10.1007/BF01732496.
8
Evolutionary change in 5S RNA secondary structure and a phylogenic tree of 54 5S RNA species.
Proc Natl Acad Sci U S A. 1979 Jan;76(1):381-5. doi: 10.1073/pnas.76.1.381.
9
Origins of prokaryotes, eukaryotes, mitochondria, and chloroplasts.
Science. 1978 Jan 27;199(4327):395-403. doi: 10.1126/science.202030.
Zotero 插件