Phylogenetic depth of Thermotoga maritima inferred from analysis of the fus gene: amino acid sequence of elongation factor G and organization of the Thermotoga str operon.

abstract：:While studies of the evolutionary histories of protein families are commonplace, little is known on noncoding RNAs beyond microRNAs and some snoRNAs. Here we investigate in detail the evolutionary history of the nine spliceosomal snRNA families (U1, U2, U4, U5, U6, U11, U12, U4atac, and U6atac) across the completely o...

journal_title：Journal of molecular evolution

authors： Marz M,Kirsten T,Stadler PF

更新日期：2008-12-01 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

authors： Schmidt W

更新日期：1995-10-01 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

authors： Crain WR Jr,Boshar MF,Cooper AD,Durica DS,Nagy A,Steffen D

更新日期：1987-01-01 00:00:00

abstract：:There have been two distinct phases of evolution of the genetic code: an ancient phase--prior to the divergence of the three domains of life, during which the standard genetic code was established--and a modern phase, in which many alternative codes have arisen in specific groups of genomes that differ only slightly f...

journal_title：Journal of molecular evolution

authors： Sengupta S,Higgs PG

更新日期：2015-06-01 00:00:00

abstract：:Computational analysis of the hypothetical open reading frame MJ0236 from Methanococcus jannaschii reveals its membership to a family of bacterial and eukaryotic proteins, predicted to be the HMP-P kinases involved in thiamin biosyntheis (ThiD). The eukaryotic members of this family contain a C-terminal extension simi...

journal_title：Journal of molecular evolution

authors： Ouzounis CA,Kyrpides NC

更新日期：1997-12-01 00:00:00

abstract：:The codon assignment of the quasi-universal genetic code can be assumed to have resulted from the evolutionary pressures that prevailed when the code was still evolving. Here, we review studies of the structure of the genetic code based on optimization models. We also review studies that, from the structure of the cod...

journal_title：Journal of molecular evolution

authors： Jestin JL,Kempf A

更新日期：2009-11-01 00:00:00

abstract：:The size and diversity of bacteriophage populations require methodologies to quantitatively study the landscape of phage differences. Statistical approaches are confronted with small genome sizes forbidding significant single-phage analysis, and comparative methods analyzing full phage genomes represent an alternative...

journal_title：Journal of molecular evolution

authors： Carbone A

更新日期：2008-03-01 00:00:00

abstract：:The neutral theory of molecular evolution states that most mutations are deleterious or neutral. It results that the evolutionary rate of a given position in an alignment is a function of the level of constraint acting on this position. Inferring evolutionary rates from a set of aligned sequences is hence a powerful m...

journal_title：Journal of molecular evolution

authors： Dutheil J

更新日期：2008-09-01 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

authors： Carmon A,Larson M,Wayne M,MacIntyre R

更新日期：2010-03-01 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

authors： Van de Peer Y,Baldauf SL,Doolittle WF,Meyer A

更新日期：2000-12-01 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

authors： Liò P,Goldman N

更新日期：2002-04-01 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

authors： Grimaldi MC,Crouau-Roy B

更新日期：1997-03-01 00:00:00

abstract：:Evolutionary divergence times can be inferred from molecular distances if a molecular clock can be assumed and if the substitution rate can be estimated. We present new evidence from relative rate tests that the rate of substitution at fourfold degenerate sites of nuclear genome-coding DNA is uniform in primate and ro...

journal_title：Journal of molecular evolution

authors： Easteal S,Herbert G

更新日期：1997-01-01 00:00:00

abstract：:Heat induces a number of premutational lesions (for example, the deamination of cytosine to uracil) in DNA and RNA. These kinds of errors occur in resting as well as replicating polynucleotides. However, an increase in temperature also raises the probability of copying error occurring in nucleic acids because of incre...

journal_title：Journal of molecular evolution

authors： Reanney DC,Pressing J

更新日期：1984-01-01 00:00:00

abstract：:This study was designed to characterize further the nontranscribed intergenic spacers (NTSs) of the 5S rRNA genes of fish and evaluate this marker as a tool for comparative studies. Two members of the closely related North American Great Lakes cisco species complex (Coregonus artedi and C. zenithicus) were chosen for ...

journal_title：Journal of molecular evolution

authors： Sajdak SL,Reed KM,Phillips RB

更新日期：1998-06-01 00:00:00

abstract：:A 2550-bp portion of the mitochondrial genome of a Demosponge, genus Tetilla, was amplified from whole genomic DNA extract and sequenced. The sequence was found to code for the 3' end of the 16S rRNA gene, cytochrome c oxidase subunit II, a lysine tRNA, ATPase subunit 8, and a 5' portion of ATPase subunit 6. The Porif...

journal_title：Journal of molecular evolution

authors： Watkins RF,Beckenbach AT

更新日期：1999-05-01 00:00:00

abstract：:Using all currently predicted coding regions in the honeybee genome, a novel form of synonymous codon bias is presented that affects the usage of particular codons dependent on the surrounding nucleotides in the coding region. Nucleotides at the third codon site are correlated, dependent on their weak (adenine [A] or ...

journal_title：Journal of molecular evolution

authors： Cutler RW,Chantawannakul P

更新日期：2007-06-01 00:00:00

abstract：:The C-terminal domain of methionyl-tRNA synthetase (MetRS-C) from Nanoarchaeum equitans is homologous to a tRNA-binding protein consisting of 111 amino acids (Trbp111) from Aquifex aeolicus. The crystal structure of MetRS-C showed that it existed as a homodimer, and that each monomer possessed an oligonucleotide/oligo...

journal_title：Journal of molecular evolution

authors： Suzuki H,Kaneko A,Yamamoto T,Nambo M,Hirasawa I,Umehara T,Yoshida H,Park SY,Tamura K

更新日期：2017-06-01 00:00:00

abstract：:Sequences were obtained from five species of rodents that are orthologous to an H2a histone pseudogene from Mus musculus. The pseudogene is part of the cluster of replication-dependent histone genes found on Mus musculus chromosome 13. Comparative analysis of these five sequences together with the previously published...

journal_title：Journal of molecular evolution

authors： DeBry RW

更新日期：1998-03-01 00:00:00

abstract：:Phospholipid vesicles (liposomes) were subjected to dehydration-hydration cycles in the presence of 6-carboxyfluorescein or salmon sperm DNA. We found that the vesicles fused into multilamellar structures during dehydration with solutes trapped between the lamellae. Upon rehydration the lamellae swelled and formed lar...

journal_title：Journal of molecular evolution

authors： Deamer DW,Barchfeld GL

更新日期：1982-01-01 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

authors： Weber AL,Miller SL

更新日期：1981-01-01 00:00:00

abstract：:The accuracies and efficiencies of three different methods of making phylogenetic trees from gene frequency data were examined by using computer simulation. The methods examined are UPGMA, Farris' (1972) method, and Tateno et al.'s (1982) modified Farris method. In the computer simulation eight species (or populations...

journal_title：Journal of molecular evolution

authors： Nei M,Tajima F,Tateno Y

更新日期：1983-01-01 00:00:00

abstract：:Computer analyses of various genome sequences revealed the existence of certain periodical patterns of adenine-adenine dinucleotides (ApA). For each genome sequence of 13 eubacteria, 3 archaebacteria, 10 eukaryotes, 60 mitochondria, and 9 chloroplasts, we counted frequencies of ApA dinucleotides at each downstream pos...

journal_title：Journal of molecular evolution

authors： Tomita M,Wada M,Kawashima Y

更新日期：1999-08-01 00:00:00

abstract：:Heterokonts are evolutionarily important as the most nutritionally diverse eukaryote supergroup and the most species-rich branch of the eukaryotic kingdom Chromista. Ancestrally photosynthetic/phagotrophic algae (mixotrophs), they include several ecologically important purely heterotrophic lineages, all grossly unders...

journal_title：Journal of molecular evolution

authors： Cavalier-Smith T,Chao EE

更新日期：2006-04-01 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

authors： Wang HC,Susko E,Spencer M,Roger AJ

更新日期：2008-01-01 00:00:00

abstract：:We present phylogenetic evidence that a group I intron in an angiosperm mitochondrial gene arose recently by horizontal transfer from a fungal donor species. A 1,716-bp fragment of the mitochondrial coxI gene from the angiosperm Peperomia polybotrya was amplified via the polymerase chain reaction and sequenced. Compar...

journal_title：Journal of molecular evolution

authors： Vaughn JC,Mason MT,Sper-Whitis GL,Kuhlman P,Palmer JD

更新日期：1995-11-01 00:00:00

abstract：:Runs of identical amino acids encoded by triplet repeats (homopolymers) are components of numerous proteins, yet their role is poorly understood. Large numbers of homopolymers are present in the Drosophila melanogaster mastermind (mam) protein surrounding several unique charged amino acid clusters. Comparison of mam s...

journal_title：Journal of molecular evolution

authors： Newfeld SJ,Schmid AT,Yedvobnick B

更新日期：1993-11-01 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

authors： Crandall KA,Cronin TW

更新日期：1997-11-01 00:00:00

abstract：:An assay based on derivative analysis of thermal denaturation (melting) behavior of reassociated DNA was developed in an attempt to characterize the sequence relationships in repeated DNA families according to the homogeneous or heterogeneous models of Bendich and Anderson (1977). The validity of the technique was con...

journal_title：Journal of molecular evolution

authors： Preisler RS,Thompson WF

更新日期：1981-01-01 00:00:00

abstract：:Eukaryotic Nramp genes encode divalent metal ion permeases important for nutrition and resistance to microbial infection. Bacterial homologs encode proton-dependent transporters of manganese (MntH), and other divalent metal ions. Bacterial MntH were classified in three homology groups (A, B, C) and MntH C further subd...

journal_title：Journal of molecular evolution

authors： Richer E,Courville P,Bergevin I,Cellier MF

更新日期：2003-10-01 00:00:00