Abstract:
:A systematic way of inferring evolutionary relatedness of microbial organisms from the oligopeptide content, i.e., frequency of amino acid K-strings in their complete proteomes, is proposed. The new method circumvents the ambiguity of choosing the genes for phylogenetic reconstruction and avoids the necessity of aligning sequences of essentially different length and gene content. The only "parameter" in the method is the length K of the oligopeptides, which serves to tune the "resolution power" of the method. The topology of the trees converges with K increasing. Applied to a total of 109 organisms, including 16 Archaea, 87 Bacteria, and 6 Eukarya, it yields an unrooted tree that agrees with the biologists' "tree of life" based on SSU rRNA comparison in a majority of basic branchings, and especially, in all lower taxa.
journal_name
J Mol Evoljournal_title
Journal of molecular evolutionauthors
Qi J,Wang B,Hao BIdoi
10.1007/s00239-003-2493-7keywords:
subject
Has Abstractpub_date
2004-01-01 00:00:00pages
1-11issue
1eissn
0022-2844issn
1432-1432journal_volume
58pub_type
杂志文章abstract::The DNA sequences of three members of the Alu family of repeated sequences located 5' to the chimpanzee alpha 2 gene have been determined. The base sequences of the three corresponding human Alu family repeats have been previously determined, permitting the comparison of identical Alu family members in human and chimp...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/BF02115687
更新日期:1985-01-01 00:00:00
abstract::RNA editing affecting chloroplast and mitochondrial genomes has been identified in all major clades of land plants. The frequency of edited sites varies greatly between lineages but hornworts represent an extreme in propensity for editing in both their chloroplast and mitochondrial genomes. cDNA sequences from seven t...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/s00239-004-0146-0
更新日期:2005-11-01 00:00:00
abstract::Nucleotide sequences for the kappa-casein precursor proteins have been determined from the genomic DNAs or hair roots of the Ruminantia. The coding regions, exons 2, 3, and 4, were amplified separately via the three kinds of PCRs and then directly sequenced. The primers were designed from the sequence of bovine kappa-...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/BF00173165
更新日期:1995-12-01 00:00:00
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journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/BF00160152
更新日期:1994-09-01 00:00:00
abstract::A few years ago we presented a stationary Markov model of gene evolution according to which only homologous genes from not too divergent species obeying the condition of being stationary may behave as reliable molecular clocks. A compartmentalized model of the nuclear genome in which the genes are distributed in compa...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/BF02602910
更新日期:1989-11-01 00:00:00
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journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/pl00006406
更新日期:1998-11-01 00:00:00
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journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/s00239-018-9846-8
更新日期:2018-06-01 00:00:00
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journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/BF02202111
更新日期:1996-12-01 00:00:00
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journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/s002390010129
更新日期:2001-01-01 00:00:00
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journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/BF02100013
更新日期:1987-01-01 00:00:00
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journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/BF00167109
更新日期:1995-02-01 00:00:00
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journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/BF02101640
更新日期:1983-01-01 00:00:00
abstract::Four cloned unique sequences from the human Y chromosome, two of which are found only on the Y chromosome and two of which are on both the X and Y chromosomes, were hybridized to restriction enzyme-treated DNA samples of a male and a female chimpanzee (Pan troglodytes), gorilla (Gorilla gorilla), and pig-tailed macaqu...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/BF02603114
更新日期:1987-01-01 00:00:00
abstract::This study examines the diverse maximum wavelength absorption (lambdamax) found in crayfishes (Decapoda: Cambaridae and Parastacidae) and the associated genetic variation in their opsin locus. We measured the wavelength absorption in the photoreceptors of six species that inhabit environments of different light intens...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/pl00006257
更新日期:1997-11-01 00:00:00
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journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/s00239-010-9340-4
更新日期:2010-05-01 00:00:00
abstract::An exhaustive computer-assisted analysis of the Moloney murine leukemia virus nucleotide sequence shows numerous deviations in the oligomeric distribution, suggesting three overlapping levels of a stepwise duplicative evolution. (1) The sequence fits the universal rule of TG/CT excess which has been proposed as the co...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/BF00171820
更新日期:1992-11-01 00:00:00
abstract::The evolutionary speed and the consequent immune escape of H3N2 influenza A virus make it an interesting evolutionary system. Charged amino acid residues are often significant contributors to the free energy of binding for protein-protein interactions, including antibody-antigen binding and ligand-receptor binding. We...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/s00239-010-9405-4
更新日期:2011-01-01 00:00:00
abstract::Darwinian theory requires that mutations be produced in a nonanticipatory manner; it is nonetheless consistent to suggest that mutations that have repeatedly led to nonviable phenotypes would be introduced less frequently than others-if under appropriate genetic control. Immunoglobulins produced during infection acqui...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/pl00006530
更新日期:1999-07-01 00:00:00
abstract::In this article, we investigated the structural and dynamical evolutionary behaviour of a set of ten thioredoxin proteins as formed by three extant forms and seven resurrected ones in laboratory. Starting from the crystallographic structures, we performed all-atom molecular dynamics simulations and compare the traject...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/s00239-019-09894-4
更新日期:2019-07-01 00:00:00
abstract::The weight-averaged observed/expected dinucleotide frequencies for the sum total of the coding regions of five Toxoplasma genes were compared with the same parameters previously determined for the coding regions of 21 Plasmodium genes. In addition, codon usage in the five Toxoplasma genes was compared with that in the...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/BF02101892
更新日期:1990-04-01 00:00:00
abstract::The gene content of a mitochondrial (mt) genome, i.e., 37 genes and a large noncoding region (LNR), is usually conserved in Metazoa. The arrangement of these genes and the LNR is generally conserved at low taxonomic levels but varies substantially at high levels. We report here a variation in mt gene content and gene ...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/s00239-005-0196-y
更新日期:2006-08-01 00:00:00
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journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/BF02101791
更新日期:1990-07-01 00:00:00
abstract::We have implemented a routine procedure for screening protein sequences for evidence of intragenic duplications. We tested 163 protein sequences representing 116 superfamilies of unrelated proteins. Twenty superfamilies contain proteins with internal gene duplications. The intragenic duplications detected can be divid...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/BF01734217
更新日期:1978-02-21 00:00:00
abstract::We have sequenced the nuclear and mitochondrial small subunit rRNA genes (rns) and the mitochondrial genes coding for subunits 1 and 3 of the cytochrome oxidase (cox1 and cox3, respectively) of the chytridiomycete Allomyces macrogynus. Phylogenetic trees inferred from the derived COX1 and COX3 proteins and the nuclear...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/BF00175824
更新日期:1995-11-01 00:00:00
abstract::Factors involved in the selection of the 20 protein L-alpha-amino acids during chemical evolution and the early stages of Darwinian evolution are discussed. The selection is considered on the basis of the availability in the primitive ocean, function in proteins, the stability of the amino acid and its peptides, stabi...
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
abstract::Ornithine decarboxylase (ODC) is the first enzyme in the polyamine biosynthetic pathway. We have studied the evolutionary history of the mammalian ODC mRNA, focusing on the rate of accumulation of sequence divergence within specific subregions of the molecule. The phylogenetic relationships among the mRNAs from severa...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/BF00556360
更新日期:1993-06-01 00:00:00
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journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/BF01732678
更新日期:1981-01-01 00:00:00
abstract::Statistical and biochemical studies of the genetic code have found evidence of nonrandom patterns in the distribution of codon assignments. It has, for example, been shown that the code minimizes the effects of point mutation or mistranslation: erroneous codons are either synonymous or code for an amino acid with chem...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/pl00006381
更新日期:1998-09-01 00:00:00
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journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/s00239-006-0135-6
更新日期:2007-02-01 00:00:00
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journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/BF02602925
更新日期:1989-12-01 00:00:00