Abstract:
:The kinetics of synonymous codon change and species divergence is described in a matrix formalism that is equally applicable to all levels of codon degeneracy and all levels of codon or nucleotide bias. Based on the formalism it is possible to calculate the sum of all synonymous substitution rate constants from the observed sequence differences between two species. This sum, the relaxation rate, is equivalent to the Log Det transformation that has recently been proposed as a new measure of evolutionary distance (Lockhardt et al. Mol. Biol. Evol. 11(4):605-612, 1994). The relationship between this measure and the average number of base changes per site (Ks) is discussed. The formalism is tested on some sets of simulated sequence divergence data.
journal_name
J Mol Evoljournal_title
Journal of molecular evolutionauthors
Berg OGdoi
10.1007/BF00186546subject
Has Abstractpub_date
1995-09-01 00:00:00pages
345-52issue
3eissn
0022-2844issn
1432-1432journal_volume
41pub_type
杂志文章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::Sequence comparisons of 14 distinct MHC class I cDNA clones isolated from species representing the three major taxonomic lineages of Felidae (domestic cat lineage, ocelot lineage, and pantherine lineage) revealed that feline MHC class I alleles have highly mosaic structures with short polymorphic sequence motifs that ...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/BF00178246
更新日期:1994-07-01 00:00:00
abstract::To get deeper insight into the evolution of phosphoenolpyruvate carboxylase we have identified PEPC fragments (about 1,100 bp) of another 12 plants species not yet investigated in this context. The selected plants include one Chlorophyta, two Bryophyta, four Pteridophyta, and five Spermatophyta species. The obtained p...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/pl00006277
更新日期:1998-01-01 00:00:00
abstract::tRNA with a terminal UCCA-3' forms a structure in which the 3'-sequence folds back. The adenine of glycyl-AMP can base-pair with the uridine of the UCCA-3' region, which places the glycine residue in close proximity to the 3'-terminal adenosine of tRNA, possibly enabling the transfer of glycine from glycyl-AMP to tRNA...
journal_title:Journal of molecular evolution
pub_type: 信件
doi:10.1007/s00239-015-9694-8
更新日期:2015-10-01 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::Covarion processes allow changes in evolutionary rates at sites along the branches of a phylogenetic tree. Covarion-like evolution is increasingly recognized as an important mode of protein evolution. Several recent reports suggest that maximum likelihood estimation employing covarion models may support different opti...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/s00239-007-9062-4
更新日期:2008-01-01 00:00:00
abstract::Liverworts are well supported as the sister group to all other land plants (embryophytes) by molecular data. Observations strongly supporting this earliest dichotomy in embryophyte evolution are the strikingly different introns occurring in the mitochondrial DNAs of liverworts versus non-liverwort embryophytes (NLE), ...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/s00239-010-9348-9
更新日期:2010-05-01 00:00:00
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journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/s00239-007-9013-0
更新日期:2007-09-01 00:00:00
abstract::Photosynthetic eukaryotes can, according to features of their chloroplasts, be divided into two major groups: the red and the green lineage of plastid evolution. To extend the knowledge about the evolution of the red lineage we have sequenced and analyzed the chloroplast genome (cp-genome) of Cyanidium caldarium RK1, ...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/s002390010101
更新日期:2000-10-01 00:00:00
abstract::We obtained and studied HIV-1 sequences with a known sampling year from three outbreaks of the HIV-1 epidemic: 141 env V3 (270 nt) sampled between 1984 and 1992 and 117 pol prot/RT (804 nt) sequences sampled between 1986 and 1999 from Dutch homosexual men and injecting drug users (IDUs), as well as 77 env V3 sequences...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/s00239-001-0070-5
更新日期:2002-05-01 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::We present two new models of protein sequence evolution based on structural properties of mitochondrial proteins. We compare these models with others currently used in phylogenetic analyses, investigating their performance over both short and long evolutionary distances. We find that our models that incorporate second...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/s00239001-0052-7
更新日期:2002-04-01 00:00:00
abstract::Barnacles (Cirripedia) are a subclass of Crustacea. Their peculiar segmentation pattern (few segments, absence of abdominal segments, and, in the parasitic rhizocephalan, loss of segmentation at the adult stage) prompted us to study the engrailed gene, which encodes a homeodomain transcription factor and is expressed ...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/pl00006181
更新日期:1997-06-01 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::Species identification is one of the most important issues in biological studies. Due to recent increases in the amount of genomic information available and the development of DNA sequencing technologies, the applicability of using DNA sequences to identify species (commonly referred to as "DNA barcoding") is being te...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/s00239-010-9380-9
更新日期:2010-10-01 00:00:00
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journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/s002390010148
更新日期:2001-02-01 00:00:00
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journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/BF02099959
更新日期:1986-01-01 00:00:00
abstract::We described previously a family of dispersed palindromic sequences highly repeated in Escherichia coli and Salmonella typhimurium genomes. These sequences, called PU (palindromic units), are located outside structural genes. We report here observations suggesting that PU may have a role in bacterial speciation. ...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/BF02603122
更新日期:1987-01-01 00:00:00
abstract::The phylogenetic relationships among Primates (human), Artiodactyla (cow), Cetacea (whale), Carnivora (seal), and Rodentia (mouse and rat) were estimated from the inferred amino acid sequences of the mitochondrial genomes using Marsupialia (opossum), Aves (chicken), and Amphibia (Xenopus) as an outgroup. The overall e...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/BF00173421
更新日期:1994-11-01 00:00:00
abstract::We analyzed precursor messenger RNAs (pre-mRNAs) of 12 eukaryotic species. In each species, three groups of highly expressed genes, ribosomal proteins, heat shock proteins, and amino-acyl tRNA synthetases, were compared with a control group (randomly selected genes). The purine-pyrimidine (R-Y) composition of pre-mRNA...
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
abstract::Processes exhibiting diversity and selection would have been necessary to promote chemical evolution on early Earth. In this work, a model process was developed using non-kinetic selection to synthesize and isolate small molecule imidazolium catalysts. These catalysts were purified by affinity chromatography and recyc...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/s00239-015-9687-7
更新日期:2015-08-01 00:00:00
abstract::We characterized the organization of mitochondrial genes from a diverse range of hymenopterans. Of the 21 taxa characterized, 12 had distinct, derived organizations. Some rearrangements were consistent with the duplication-random loss mechanism, while others were not. Local inversions were relatively common, i.e., rea...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/s00239-002-2420-3
更新日期:2003-05-01 00:00:00
abstract::Parsimony is commonly used to infer the direction of substitution and mutation. However, it is known that parsimony is biased when the base composition of the DNA sequence is skewed. Here I quantify this effect for several simple cases. The analysis demonstrates that parsimony can be misleading even when levels of seq...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/pl00006427
更新日期:1998-12-01 00:00:00
abstract::Twenty-seven protein sequence elements, six to nine amino acids long, were extracted from 15 phylogenetically diverse complete prokaryotic proteomes. The elements are present in all of these proteomes, with at least one copy each (omnipresent elements), and have presumably been conserved since the last universal commo...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/s00239-007-9032-x
更新日期:2007-12-01 00:00:00
abstract::Cosmochemical considerations suggest various potential sources for the accumulation of organic matter on Mars. However the Viking Molecular Analysis did not indicate any indigenous organic compounds on the surface of Mars. Their disappearance from the top layer is most likely caused by the combined action of the high ...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/BF01732374
更新日期:1979-12-01 00:00:00
abstract::Synonymous codon usage in yeast appears to be influenced by natural selection on gene expression, as well as regional variation in compositional bias. Because of the large number of potential targets of selection (i.e., most of the codons in the genome) and presumed small selection coefficients, codon usage is an exce...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/s00239-003-2459-9
更新日期:2003-07-01 00:00:00
abstract::The mitochondrial genetic variability in European rabbit (Oryctolagus cuniculus) populations present in Europe and North Africa from 11,000 years ago to the present day has been analyzed using ancient DNA techniques. DNA was extracted from 90 rabbit bones found in 22 archaeological sites dated between the Mesolithic a...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/BF00163228
更新日期:1995-03-01 00:00:00
abstract::We have studied the relative contribution of inversions, transpositions, deletions, and nucleotide substitutions to the evolution of Chlamydia trachomatis and Chlamydia pneumoniae. The minimal number of rearrangement events required for converting the gene order structure of one genome into that of the other was estim...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/s00239-001-0087-9
更新日期:2002-07-01 00:00:00
abstract::Microsatellite DNA sequences have become the dominant source of nuclear genetic markers for most applications. It is important to investigate the basis of variation between alleles and to know if current assumptions about the mechanisms of microsatellite mutation (that is to say, variations involving simple changes in...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/pl00006151
更新日期:1997-03-01 00:00:00
abstract::Characterization of sequences homologous to the Drosophila melanogaster gypsy transposable element was carried out in Drosophila subobscura (gypsyDS). They were found to be widely distributed among natural populations of this species. From Southern blot and in situ analyses, these sequences appear to be mobile in this...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/BF00166248
更新日期:1993-02-01 00:00:00