Abstract：
:We examined the codon usages in well-conserved and less-well-conserved regions of vertebrate protein genes and found them to be similar. Despite this similarity, there is a statistically significant decrease in codon bias in the less-well-conserved regions. Our analysis suggests that although those codon changes initially fixed under amino acid replacements tend to follow the overall codon usage pattern, they also reduce the bias in codon usage. This decrease in codon bias leads one to predict that the rate of change of synonymous codons should be greater in those regions that are less well conserved at the amino acid level than in the better-conserved regions. Our analysis supports this prediction. Furthermore, we demonstrate a significantly elevated rate of change of synonymous codons among the adjacent codons 5' to amino acid replacement positions. This provides further support for the idea that there are contextual constraints on the choice of synonymous codons in eukaryotes.
journal_name
J Mol Evoljournal_title
Journal of molecular evolutionauthors
Lipman DJ,Wilbur WJdoi
10.1007/BF02100090subject
Has Abstractpub_date
1984-01-01 00:00:00pages
161-7issue
2eissn
0022-2844issn
1432-1432journal_volume
21pub_type
杂志文章abstract：:The metabolic cycle of Saccharomyces cerevisiae consists of alternating oxidative (respiration) and reductive (glycolysis) energy-yielding reactions. The intracellular concentrations of amino acid precursors generated by these reactions oscillate accordingly, attaining maximal concentration during the middle of their ...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-009-9218-5
更新日期：2009-05-01 00:00:00
abstract：:Male sex genes have shown a pattern of rapid interspecies divergence at both the coding and gene expression level. A common outcome from crosses between closely-related species is hybrid male sterility. Phenotypic and genetic studies in Drosophila sterile hybrid males have shown that spermatogenesis arrest is postmeio...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-010-9404-5
更新日期：2011-01-01 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：:Variation in structure among primate hemoglobins is associated with variation in function. This supports the hypothesis that most substitutions observed among homologous proteins in different species have been fixed by natural selection because they contribute to the fitness of the genotype. It does not support the co...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/BF01653958
更新日期：1972-12-01 00:00:00
abstract：:Available molecular and biochemical data offer conflicting evidence for the origin of the cyanelle of Cyanophora paradoxa. We show that the similarity of cyanelle and green chloroplast sequences is probably a result of these two lineages independently developing the same pattern of directional nucleotide change (subst...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/BF00182392
更新日期：1992-02-01 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：:We present a new approach for analyzing directional mutation pressure and nucleotide content in protein-coding genes. Directional mutation pressure, the heterogenicity in the likelihood of different nucleotide substitutions, is used to explain the increasing or decreasing guanine-cytosine content (GC%) in DNA and is r...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/BF00163805
更新日期：1994-08-01 00:00:00
abstract：:The transposable element mariner occurs widely in the melanogaster species group of Drosophila. However, in drosophilids outside of the melanogaster species group, sequences showing strong DNA hybridization with mariner are found only in the genus Zaprionus. The mariner sequence obtained from Zaprionus tuberculatus is...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/BF02102804
更新日期：1991-12-01 00:00:00
abstract：:DNA sequences representing approximately 40% of the large-subunit rRNA gene from the lower dipteran Chironomus thummi were analyzed. Once aligned with their Drosophila counterparts, sequence and base content comparisons were carried out. Sequence identity was found to be high overall, except for six regions that displ...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/BF00173183
更新日期：1995-12-01 00:00:00
abstract：:Translation termination is catalyzed by release factors that recognize stop codons. However, previous works have shown that in some bacteria, the termination process also involves bases around stop codons. Recently, Ito et al. analyzed release factors and identified the amino acids therein that recognize stop codons. ...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-002-2435-9
更新日期：2003-06-01 00:00:00
abstract：:Hypoxia at deep-sea hydrothermal vents represents one of the most basic challenges for metazoans, which then requires specific adaptations to acquire oxygen to meet their metabolic needs. Hydrothermal vent scale-worms (Polychaeta; Polynoidae) express large amounts of extracellular single- and multi-domain hemoglobins,...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-017-9815-7
更新日期：2017-12-01 00:00:00
abstract：:The evolution of viral genomes has recently attracted considerable attention. We compare the sequences of two large viral genomes, EsV-1 and FirrV-1, belonging to the family of phaeoviruses which infect different species of marine brown algae. Although their genomes differ substantially in size, these viruses share si...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-003-2501-y
更新日期：2003-12-01 00:00:00
abstract：:The entire mitochondrial DNA control region (mtDNA D-loop) was sequenced in the seven extant species of Alectoris partridges. The D-loop length is very conserved (1155 +/- 2 nucleotides), and substitution rates are lower than for the mitochondrial cytochrome b gene of the same species, on average. Comparative analyses...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/pl00006402
更新日期：1998-10-01 00:00:00
abstract：:Spermatogenesis is one of the most complex biological processes undergone by any organism, making it susceptible to perturbations that result in male sterility. Research has demonstrated that mutant phenotypes can be obtained from the disruption of epigenetic modifications, which are commonly microRNA guided. Employin...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-011-9478-8
更新日期：2011-12-01 00:00:00
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...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/BF02099932
更新日期：1991-01-01 00:00:00
abstract：:Polymerization of various nucleoside-5'-phosphorimidazolides has been conducted in neutral aqueous solution using divalent metal ions as catalysts. Oligonucleotide formation took place from each of the ribonucleoside-5'-phosphorimidazolides, ImpC, ImpU, ImpA, ImpG, and ImpI. The yields and distributions of the resulti...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/BF02100072
更新日期：1988-01-01 00:00:00
abstract：:The sequence of the mitochondrial DNA (mtDNA) molecule of the European hedgehog (Erinaceus europaeus) was determined. The length of the sequence presented is 17,442 nucleotides (nt). The molecule is thus the largest eutherian mtDNA molecule so far reported. The organization of the molecule conforms with that of other ...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/BF00173175
更新日期：1995-12-01 00:00:00
abstract：:A problem with studying evolutionary dynamics of mitochondrial (mt) DNA is that classical population genetic techniques cannot identify selected substitutions because of genetic hitchhiking. We circumvented this problem by employing a candidate complex approach to study sequence variation in cytochrome c oxidase (COX)...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-008-9078-4
更新日期：2008-03-01 00:00:00
abstract：:In the previous three reports in this series we demonstrated that the EF-hand family of proteins evolved by a complex pattern of gene duplication, transposition, and splicing. The dendrograms based on exon sequences are nearly identical to those based on protein sequences for troponin C, the essential light chain myos...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/BF02406723
更新日期：1993-05-01 00:00:00
abstract：:We examined the cis- vs. trans-splicing status of the mitochondrial group II intron nad1i728 in 439 species (427 genera) of land plants, using both Southern hybridization results (for 416 species) and intron sequence data from the literature. A total of 164 species (157 genera), all angiosperms, was found to have a tr...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-004-2606-y
更新日期：2004-07-01 00:00:00
abstract：:We have analyzed the gene that encodes receptor tyrosine kinase (RTK) from the marine sponge Geodia cydonium, which belongs to the most ancient and simple metazoan groups, the Porifera. RTKs are enzymes found only in metazoa. The sponge gene contains two introns in the extracellular part of the protein. However, the r...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/pl00006141
更新日期：1997-03-01 00:00:00
abstract：:Comparisons of the sequence divergence of three species of Hawaiian Drosophila have been made by hybridization of single-copy tracer DNA of each of the species with driver DNA from each species, and measurement of the average melting temperature (Tma) in a chaotropic solvent (2.4 M tetraethylammonium chloride) which m...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/BF01734358
更新日期：1981-01-01 00:00:00
abstract：:The diversity of functional genes and the related processes are important issues for conservation biology. This is especially relevant for populations that have suffered from demographic reduction as a consequence of the processes of postglacial colonization. In this perspective, the aims of the present study are (1) ...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-011-9456-1
更新日期：2011-08-01 00:00:00
abstract：:We report the nucleotide sequence of the single muscle actin gene of the sea urchin Strongylocentrotus purpuratus. Comparison of the protein-coding sequence of this muscle actin gene (pSpG28) with that of two linked sea urchin cytoskeletal actin genes (pSpG17 and CyIIa) reveals a region of exceptional sequence conserv...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/BF02100039
更新日期：1987-01-01 00:00:00
abstract：:cDNA encoding the adhesive protein of the mussel Mytilus coruscus (Mcfp1) was isolated. The coding region encoded 848 amino acids (a.a.) comprising the 20-a.a. signal peptide, the 21-a.a. nonrepetitive linker, and the 805-a.a. repetitive domain. Although the first 204 nucleotides and the 3'-untranslated region of Mcfp...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/BF02339009
更新日期：1996-10-01 00:00:00
abstract：:Unravelling gene structure requires the identification and understanding of the constraints that are often associated with the evolutionary history and functional domains of genes. We speculated in this manuscript with the possibility of the existence in orthologs of an emergent highly conserved gene structure that mi...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-019-09889-1
更新日期：2019-04-01 00:00:00
abstract：:The activated dimonophosphate of 3'-deoxyadenosine (cordycepin) undergoes oligomerization to produce a new family of pyrophosphate-linked oligomers in which the average repeating unit involves a nine-atom structural group. The presence of a poly(U) template increases the relative yields of higher oligomers, although t...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/BF02101146
更新日期：1987-01-01 00:00:00
abstract：:TT virus (TTV) has a remarkable genetic heterogeneity. To study TTV evolution, phylogenetic analyses were performed on 739 DNA sequences mapping in the N22 region of ORF1. Analysis of neighbor-joining consensus trees shows significant differences between DNA and protein phylogeny. Median joining networks phylogenetic ...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-002-2352-y
更新日期：2002-11-01 00:00:00
abstract：:It has recently been argued that living metazoans diverged over 800 million years ago, based on evidence from 22 nuclear genes for such a deep divergence between vertebrates and arthropods (Gu 1998). Two "internal" calibration points were used. However, only one fossil divergence date (the mammal-bird split) was direc...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/pl00006562
更新日期：1999-09-01 00:00:00
abstract：:Single-fly polymerase chain reaction amplification and direct DNA sequencing revealed high levels of length polymorphism in the threonine-glycine encoding repeat region of the period (per) gene in natural populations of Drosophila melanogaster. DNA comparison of two alleles of identical lengths gave a high number of s...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/BF02342746
更新日期：1991-03-01 00:00:00
