Abstract:
:This paper constructs a temporal scale for bacterial evolution by tying ecological events that took place at known times in the geological past to specific branch points in the genealogical tree relating the 16S ribosomal RNAs of eubacteria, mitochondria, and chloroplasts. One thus obtains a relationship between time and bacterial RNA divergence which can be used to estimate times of divergence between other branches in the bacterial tree. According to this approach, Salmonella typhimurium and Escherichia coli diverged between 120 and 160 million years (Myr) ago, a date which fits with evidence that the chief habitats occupied now by these two enteric species became available that long ago. The median extent of divergence between S. typhimurium and E. coli at synonymous sites for 21 kilobases of protein-coding DNA is 100%. This implies a silent substitution rate of 0.7-0.8%/Myr--a rate remarkably similar to that observed in the nuclear genes of mammals, invertebrates, and flowering plants. Similarities in the substitution rates of eucaryotes and procaryotes are not limited to silent substitutions in protein-coding regions. The average substitution rate for 16S rRNA in eubacteria is about 1%/50 Myr, similar to the average rate for 18S rRNA in vertebrates and flowering plants. Likewise, we estimate a mean rate of roughly 1%/25 Myr for 5S rRNA in both eubacteria and eucaryotes. For a few protein-coding genes of these enteric bacteria, the extent of silent substitution since the divergence of S. typhimurium and E. coli is much lower than 100%, owing to extreme bias in the usage of synonymous codons. Furthermore, in these bacteria, rates of amino acid replacement were about 20 times lower, on average, than the silent rate. By contrast, for the mammalian genes studied to date, the average replacement rate is only four to five times lower than the rate of silent substitution.
journal_name
J Mol Evoljournal_title
Journal of molecular evolutionauthors
Ochman H,Wilson ACdoi
10.1007/BF02111283subject
Has Abstractpub_date
1987-01-01 00:00:00pages
74-86issue
1-2eissn
0022-2844issn
1432-1432journal_volume
26pub_type
杂志文章abstract::Horizontal gene transfer (HGT) has a major impact on the evolution of prokaryotic genomes, as it allows genes evolved in different contexts to be combined in a single genome, greatly enhancing the ways evolving organisms can explore the gene content space and adapt to the environment. A systematic analysis of HGT in a...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/s00239-018-9836-x
更新日期:2018-04-01 00:00:00
abstract::Recombination has been suggested to be an important factor for the genetic variation of bacterial genes, but few studies have dealt with intragenic recombination between the same or closely related species of cyanobacteria. Here we provide strong evidence for recombination in the microcystin synthetase (mcy) gene clus...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/s00239-004-2583-1
更新日期:2004-06-01 00:00:00
abstract::Catalyzed polymerization reactions represent a primary anabolic activity of all cells. It can be assumed that early cells carried out such reactions, in which macromolecular catalysts were encapsulated within some type of boundary membrane. In the experiments described here, we show that a template-independent RNA pol...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/BF00160400
更新日期:1994-12-01 00:00:00
abstract::As the origin(s) of life on Earth remains an open question, detailed characteristics about the "last universal ancestor" (LUA) continue to be obscured. Here we provide arguments that strengthen the bacterial-like nature of the LUA. Our view attempts to recreate the evolution of archaeal lipids, the major components of...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/s00239-006-0141-8
更新日期:2007-03-01 00:00:00
abstract::We have used three reference sequences representative of bacterial drug resistance pumps and sugar transport proteins to collect the 91 most closely related sequences from a composite, nonredundant protein sequence database. Having eliminated certain very close relatives, the remainder were subjected to analysis and a...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/BF02198855
更新日期:1996-02-01 00:00:00
abstract::Here we report DNA sequences from mitochondrial cytochrome b gene segments (1,005 base pairs per species) for the extinct woolly mammoth (Mammuthus primigenius) and Steller's sea cow (Hydrodamalis gigas) and the extant Asian elephant (Elephas maximus), the Western Indian manatee (Trichechus manatus), and the hyrax (Pr...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/pl00006160
更新日期:1997-04-01 00:00:00
abstract::The amino acid sequences of the largest subunits of the RNA polymerases I, II, and III from eukaryotes were compared with those of archaebacterial and eubacterial homologs, and their evolutionary relationships were analyzed in detail by a recently developed tree-making method, the likelihood method of protein phylogen...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/BF02099931
更新日期:1991-01-01 00:00:00
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 align...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/s00239-003-2493-7
更新日期:2004-01-01 00:00:00
abstract::Circadian clock genes are remarkably conserved between eucoelomates. Although Drosophila has one copy of each major component, vertebrates have two or (in the case of the Period genes) three paralogs (Per1-3). We investigated the possibility that the vertebrate Per genes arose through two genome duplications during th...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/s00239-005-0185-1
更新日期:2006-06-01 00:00:00
abstract::The PIGSFEAST (PF) exon of the Drosophila dumpy gene is undergoing concerted evolution by the process of unequal crossing over. We have developed a long-range PCR-based assay to amplify the approximately 12 kb long exon which contains variable numbers of 303 or 306 nt long repeats in a tandem array. We applied this pr...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/s00239-010-9327-1
更新日期:2010-03-01 00:00:00
abstract::Orphan genes, lacking detectable homologs in outgroup species, typically represent 10-30% of eukaryotic genomes. Efforts to find the source of these young genes indicate that de novo emergence from non-coding DNA may in part explain their prevalence. Here, we investigate the roots of orphan gene emergence in the Droso...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/s00239-020-09939-z
更新日期:2020-05-01 00:00:00
abstract::A long-standing hypothesis posits that morphological changes may be more likely to result from changes in regulation of gene expression than from changes in the protein coding sequences of genes. We have compared the expression pattern of the twisted gastrulation (tsg) gene among five Drosophila species: D. melanogast...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/pl00006293
更新日期:1998-02-01 00:00:00
abstract::A reaction which oligomerizes nucleotides under possible prebiotic conditions has been characterized. Nucleoside monophosphate in the presence of cyanamide at acid pH condenses to form dithymideine pyrophosphate and phosphodiester bonded compounds. Imidazole compounds and activated precursors such as nucleoside tripho...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/BF01732356
更新日期:1975-11-04 00:00:00
abstract::Analysis of mitochondrial DNAs (mtDNAs) from parthenogenetic lizards of the Heteronotia binoei complex with restriction enzymes revealed an approximately 5-kb addition present in all 77 individuals. Cleavage site mapping suggested the presence of a direct tandem duplication spanning the 16S and 12S rRNA genes, the con...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/BF02103135
更新日期:1991-11-01 00:00:00
abstract::Marine mussels of the genus Mytilus have two types of mitochondrial DNA with separate paternal and maternal inheritance. Females are homoplasmic for an F genome that is transmitted to all offspring, whereas males are heteroplasmic for this F genome and for a highly diverged (> 20%) M genome that is transmitted only to...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/s00239-003-0019-y
更新日期:2003-01-01 00:00:00
abstract::The heterotrophic theory of the origin of life is the only proposal available with experimental support. This comes from the ease of prebiotic synthesis under strongly reducing conditions. The prebiotic synthesis of organic compounds by reduction of CO(2) to monomers used by the first organisms would also be considere...
journal_title:Journal of molecular evolution
pub_type: 杂志文章,评审
doi:
更新日期:1999-10-01 00:00:00
abstract::Hemoglobin Vancouver is a new abnormal hemoglobin with an amino acid substitution of the normal aspartyl residue 73 of the beta chain by a tyrosyl residue. It was discovered in a man of Chinese descent in association with beta thalassemia. It was subsequently detected in a sister in association with normal Hb A. The o...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/BF01796121
更新日期:1976-12-31 00:00:00
abstract::This report describes the distribution of P-element sequences among members of the closely related willistoni and saltans species groups of the subgenus Sophophora. Gel-blotting analyses showed that many, but not all, species from each of these groups possess sequences with homology to the P transposable element of Dr...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/BF02099908
更新日期:1986-01-01 00:00:00
abstract::The complete mitochondrial DNA (mtDNA) sequence of the brine shrimp Artemia franciscana has been determined. It extends the present knowledge of mitochondrial genomes to the crustacean class and supplies molecular markers for future comparative studies in this large branch of the arthropod phylum. Artemia mtDNA is 15,...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/BF00160272
更新日期:1994-10-01 00:00:00
abstract::Gene duplication creates a second copy of a gene either in tandem to the ancestral locus or dispersed to another chromosomal location. When the ancestral copy of a dispersed duplicate is lost from the genome, it creates the appearance that the gene was "relocated" from the ancestral locus to the derived location. Gene...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/s00239-018-9849-5
更新日期:2018-07-01 00:00:00
abstract::Studies during the last 20 years have shown that the chromosomes of many organisms, especially those of higher vertebrates, consist of a series of segments having different properties. These can be recognized as, for example, G- and R-bands. Recent studies have indicated that genes tend to lie in the R-bands rather th...
journal_title:Journal of molecular evolution
pub_type: 杂志文章,评审
doi:10.1007/BF02407346
更新日期:1993-08-01 00:00:00
abstract::The helix-turn-helix domain-containing family of transcriptional regulators is of ancient origin and has been incorporated into numerous disparate biological processes. As a consequence, the forces shaping its early evolution have been difficult to reconstruct. Herein, we analyze this large and diverse family with a c...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/pl00006552
更新日期:1999-09-01 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
abstract::Recent experience with molecular phylogeny has shown that all molecular markers have strengths and weaknesses. Nonetheless, despite several notable discrepancies with phylogenies obtained from protein data, the merits of the small subunit ribosomal RNA (SSU rRNA) as a molecular phylogenetic marker remain indisputable....
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/s002390010120
更新日期:2000-12-01 00:00:00
abstract::Molecular domestication of a transposable element is defined as its functional recruitment by the host genome. To date, two independent events of molecular domestication of the P transposable element have been described: in the Drosophila obscura species group and in the Drosophila montium species subgroup. These P ne...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/s00239-004-0324-0
更新日期:2005-10-01 00:00:00
abstract::Two families of high-cysteine chorion proteins in Bombyx mori are encoded in 15 tandemly arranged nonidentical gene pairs. It is assumed that this locus arose by duplication with subsequent sequence divergence. We have compared DNA sequences from two such neighboring pairs of genes in an attempt to understand the mann...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/BF02104732
更新日期:1984-01-01 00:00:00
abstract::The nearly neutral theory attributes most nucleotide substitution and polymorphism to genetic drift acting on weakly selected mutants, and assumes that the selection coefficients for these mutants are drawn from a continuous distribution. This means that parameter estimation can require numerical integration, and this...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/s00239-008-9146-9
更新日期:2008-10-01 00:00:00
abstract::The alpha-esterase cluster of D. melanogaster contains 11 esterase genes dispersed over 60 kb. Embedded in the cluster are two unrelated open reading frames that have sequence similarity with genes encoding ubiquitin-conjugating enzyme and tropomyosin. The esterase amino acid sequences show 37-66% identity with one an...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/BF02338832
更新日期:1996-09-01 00:00:00
abstract::RNA has a myriad of biological roles in contemporary life. We use the RNA paradigm for genotype-phenotype mappings to study the evolution of multiple coding in dependence to mutation rates. We study three different one-to-many genotype-phenotype mappings which have the potential to encode the information for multiple ...
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
abstract::This paper presents an essentially new method used to construct phylogenetic trees from related amino acid sequences. The method is based on a new distance measure which describes sequence relationships by means of typical steric and physicochemical properties of the amino acids and is advantageous in some essential p...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/BF00160324
更新日期:1995-10-01 00:00:00