Phylogenetic utility of the mitochondrial cytochrome oxidase gene: molecular evolution of the Drosophila buzzatii species complex.


:Phylogenetic relationships among eight species of the Drosophila buzzatii species complex (D. mulleri subgroup; D. repleta species group) and D. hamatofila were determined by sequencing the mitochondrial cytochrome oxidase subunit I, II, and III genes. The species examined included members of the martensis cluster (D. martensis, D. starmeri, D. venezolana), the buzzatii cluster (D. buzzatii, D. serido, D. borborema), and the stalkeri cluster (D. stalkeri, D. richardsoni). The molecular phylogeny was found to be congruent with the chromosomal inversion phylogeny. Analyzing the cytochrome oxidase subunits separately revealed that not all the subunits seem to have the same phylogenetic information content. Parameters are discussed that might explain these differences.


J Mol Evol


Spicer GS




Has Abstract


1995-12-01 00:00:00












  • Horizontal gene transfer contributes to the wide distribution and evolution of type II restriction-modification systems.

    abstract::Restriction modification (RM) systems serve to protect bacteria against bacteriophages. They comprise a restriction endonuclease activity that specifically cleaves DNA and a corresponding methyltransferase activity that specifically methylates the DNA, thereby protecting it from cleavage. Such systems are very common ...

    journal_title:Journal of molecular evolution

    pub_type: 杂志文章


    authors: Jeltsch A,Pingoud A

    更新日期:1996-02-01 00:00:00

  • Analyses of ribosomal RNA sequences from glaucocystophyte cyanelles provide new insights into the evolutionary relationships of plastids.

    abstract::Glaucocystophyte algae (sensu Kies, Berl. Deutsch. Bot. Ges. 92, 1979) contain plastids (cyanelles) that retain the peptidoglycan wall of the putative cyano-bacterial endosymbiont; this and other ultrastructural characters (e.g., unstacked thylakoids, phycobilisomes) have suggested that cyanelles are "primitive" plast...

    journal_title:Journal of molecular evolution

    pub_type: 杂志文章


    authors: Helmchen TA,Bhattacharya D,Melkonian M

    更新日期:1995-08-01 00:00:00

  • Allelic variation of HERV-K(HML-2) endogenous retroviral elements in human populations.

    abstract::Human endogenous retroviruses (HERVs) are the remnants of ancient germ cell infection by exogenous retroviruses and occupy up to 8% of the human genome. It has been suggested that HERV sequences have contributed to primate evolution by regulating the expression of cellular genes and mediating chromosome rearrangements...

    journal_title:Journal of molecular evolution

    pub_type: 杂志文章


    authors: Macfarlane C,Simmonds P

    更新日期:2004-11-01 00:00:00

  • Molecular genetics and evolution of stomach and nonstomach lysozymes in the hoatzin.

    abstract::Multiple genes of the hoatzin encoding stomach lysozyme c and closely related members of this calcium-binding lysozyme c group were cloned from a genomic DNA library and sequenced. There are a minimum of five genes represented among these sequences that encode two distinct groups of protein sequences. One group of thr...

    journal_title:Journal of molecular evolution

    pub_type: 杂志文章


    authors: Kornegay JR

    更新日期:1996-06-01 00:00:00

  • The photolytic degradation and oxidation of organic compounds under simulated Martian conditions.

    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


    authors: Oró J,Holzer G

    更新日期:1979-12-01 00:00:00

  • Phylogenetic analysis of the Friedreich ataxia GAA trinucleotide repeat.

    abstract::Friedreich ataxia is an autosomal recessive neurodegenerative disorder associated with a GAA repeat expansion in the first intron of the gene (FRDA) encoding a novel, highly conserved, 210 amino acid protein known as frataxin. Normal variation in repeat size was determined by analysis of more than 600 DNA samples from...

    journal_title:Journal of molecular evolution

    pub_type: 杂志文章


    authors: Justice CM,Den Z,Nguyen SV,Stoneking M,Deininger PL,Batzer MA,Keats BJ

    更新日期:2001-03-01 00:00:00

  • The "Origin-of-Life Reactor" and Reduction of CO2 by H2 in Inorganic Precipitates.

    abstract::It has been suggested that inorganic membranes were forerunners of organic membranes at the origin of life. Such membranes, interposed between alkaline fluid in submarine vents and the more acidic Hadean ocean, were thought to house inorganic molecular machines. H+ flowed down the pH gradient (ΔpH) from ocean to vent ...

    journal_title:Journal of molecular evolution

    pub_type: 信件,评审


    authors: Jackson JB

    更新日期:2017-08-01 00:00:00

  • The effect of local nucleotides on synonymous codon usage in the honeybee (Apis mellifera L.) genome.

    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

    pub_type: 杂志文章


    authors: Cutler RW,Chantawannakul P

    更新日期:2007-06-01 00:00:00

  • Detecting site-specific biochemical constraints through substitution mapping.

    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

    pub_type: 杂志文章


    authors: Dutheil J

    更新日期:2008-09-01 00:00:00

  • Functional constraints of 6-phosphogluconate dehydrogenase (6-PGD) based on sequence and structural information.

    abstract::The pentose phosphate cycle is considered as a major source of NADPH and pentose needed for nucleic acid biosynthesis. 6-Phosphogluconate dehydrogenase (6PGD), an enzyme participating in this cycle, catalyzes the oxidative decarboxylation of 6PGD to ribulose 5-phosphate with the subsequent release of CO2 and the reduc...

    journal_title:Journal of molecular evolution

    pub_type: 杂志文章


    authors: Goulielmos GN,Eliopoulos E,Loukas M,Tsakas S

    更新日期:2004-09-01 00:00:00

  • Role of everlasting triplet expansions in protein evolution.

    abstract::Analysis of occurrence of simple amino acid repeats in large ensemble of prokaryotic and eukaryotic sequences reveals that nearly all amino acids found in the repeats belong to those which have in their codon repertoires aggressively expanding triplets, all of three known pathologically expanding classes GCU (GCU, CUG...

    journal_title:Journal of molecular evolution

    pub_type: 杂志文章


    authors: Koren Z,Trifonov EN

    更新日期:2011-02-01 00:00:00

  • Amplification and phylogenetic relationships of a subfamily of blood, a retrotransposable element of Drosophila.

    abstract::To get a better understanding of the effect of interelement selection on the variation of long terminal repeat retrotransposon families, we have investigated the evolutionary history of blood in the Drosophila melanogaster species complex. We carried out a PCR approach to amplify the 5' untranslated region from blood ...

    journal_title:Journal of molecular evolution

    pub_type: 杂志文章


    authors: Costas J,Valadé E,Naveira H

    更新日期:2001-04-01 00:00:00

  • Divergence and polymorphism under the nearly neutral theory of molecular evolution.

    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


    authors: Welch JJ,Eyre-Walker A,Waxman D

    更新日期:2008-10-01 00:00:00

  • Experimental indication in favor of the introns-late theory: the receptor tyrosine kinase gene from the sponge Geodia cydonium.

    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


    authors: Gamulin V,Skorokhod A,Kavsan V,Müller IM,Müller WE

    更新日期:1997-03-01 00:00:00

  • Evidence for recombination in the microcystin synthetase (mcy) genes of toxic cyanobacteria Microcystis spp.

    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


    authors: Tanabe Y,Kaya K,Watanabe MM

    更新日期:2004-06-01 00:00:00

  • Autocatalytic Sets and RNA Secondary Structure.

    abstract::The dominant paradigm in origin of life research is that of an RNA world. However, despite experimental progress towards the spontaneous formation of RNA, the RNA world hypothesis still has its problems. Here, we introduce a novel computational model of chemical reaction networks based on RNA secondary structure and a...

    journal_title:Journal of molecular evolution

    pub_type: 杂志文章


    authors: Hordijk W

    更新日期:2017-04-01 00:00:00

  • The interaction of protein structure, selection, and recombination on the evolution of the type-1 fimbrial major subunit (fimA) from Escherichia coli.

    abstract::Fimbrial adhesins allow bacteria to interact with and attach to their environment. The bacteria possibly benefit from these interactions, but all external structures including adhesins also allow bacteria to be identified by other organisms. Thus adhesion molecules might be under multiple forms of selection including ...

    journal_title:Journal of molecular evolution

    pub_type: 杂志文章


    authors: Peek AS,Souza V,Eguiarte LE,Gaut BS

    更新日期:2001-02-01 00:00:00

  • Interaction of silent and replacement changes in eukaryotic coding sequences.

    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 initi...

    journal_title:Journal of molecular evolution

    pub_type: 杂志文章


    authors: Lipman DJ,Wilbur WJ

    更新日期:1984-01-01 00:00:00

  • Computational identification and evolutionary relationships of the microRNA gene cluster miR-71/2 in protostomes.

    abstract::MicroRNAs (miRNAs) are small noncoding RNA molecules which are processed into ~20-24 nt molecules that can regulate the gene expression post-transcriptionally. MiRNA gene clusters have been identified in a range of species, where in miRNAs are often processed from polycistronic transcripts. In this study, a computatio...

    journal_title:Journal of molecular evolution

    pub_type: 信件


    authors: de Souza Gomes M,Donoghue MT,Muniyappa M,Pereira RV,Guerra-Sá R,Spillane C

    更新日期:2013-06-01 00:00:00

  • What can 18S rDNA do for bivalve phylogeny?

    abstract::Molecular characteristics, especially 18S rDNA sequences, may be of great value for the study of bivalve evolution and its numerous morphological convergencies once the reliability of these data can be evaluated. The analysis of 11 published complete molluscan sequences and two new ones, Arca noae and Atrina pectinata...

    journal_title:Journal of molecular evolution

    pub_type: 杂志文章


    authors: Steiner G,Müller M

    更新日期:1996-07-01 00:00:00

  • Detecting recombination in TT virus: a phylogenetic approach.

    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


    authors: Manni F,Rotola A,Caselli E,Bertorelle G,Di Luca D

    更新日期:2002-11-01 00:00:00

  • Evolution of RNA polymerases and branching patterns of the three major groups of Archaebacteria.

    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


    authors: Iwabe N,Kuma K,Kishino H,Hasegawa M,Miyata T

    更新日期:1991-01-01 00:00:00

  • Cotranscriptional 3'-End Processing of T7 RNA Polymerase Transcripts by a Smaller HDV Ribozyme.

    abstract::In vitro run-off transcription by T7 RNA polymerase generates heterogeneous 3'-ends because the enzyme tends to add untemplated adenylates. To generate homogeneous 3'-termini, HDV ribozymes have been used widely. Their sequences are added to the 3'-terminus such that co-transcriptional self-cleavage generates homogene...

    journal_title:Journal of molecular evolution

    pub_type: 杂志文章


    authors: Akoopie A,Müller UF

    更新日期:2018-08-01 00:00:00

  • Classification of nucleotide sequences using support vector machines.

    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


    authors: Seo TK

    更新日期:2010-10-01 00:00:00

  • Codon usage and selection on proteins.

    abstract::Selection pressures on proteins are usually measured by comparing homologous nucleotide sequences (Zuckerkandl and Pauling 1965). Recently we introduced a novel method, termed volatility, to estimate selection pressures on proteins on the basis of their synonymous codon usage (Plotkin and Dushoff 2003; Plotkin et al. ...

    journal_title:Journal of molecular evolution

    pub_type: 杂志文章


    authors: Plotkin JB,Dushoff J,Desai MM,Fraser HB

    更新日期:2006-11-01 00:00:00

  • Triple helices formed by polyuridylic acid with some amino deoxyadenosine derivatives.

    abstract::The stability of helical structures formed by polyuridylic acid with nucleosides and nucleotides derived from adenosine is not significantly affected by replacing hydroxyl groups by hydrogen, amino, or azido functions. Stability is affected by the position of the phosphate group. ...

    journal_title:Journal of molecular evolution

    pub_type: 杂志文章


    authors: Gibbs DE,Orgel LE

    更新日期:1976-06-23 00:00:00

  • Comparative structure analysis of vertebrate U17 small nucleolar RNA (snoRNA).

    abstract::Intron-encoded U17 RNA is a member of the H/ACA box class of small nucleolar RNAs (snoRNAs) involved in ribosomal RNA (rRNA) maturation. U17 snoRNA shows typical characteristics of guide RNAs, which specify sites of pseudouridylation on the precursor rRNA (pre-rRNA). However, in spite of the presence of H and ACA boxe...

    journal_title:Journal of molecular evolution

    pub_type: 杂志文章


    authors: Cervelli M,Cecconi F,Giorgi M,Annesi F,Oliverio M,Mariottini P

    更新日期:2002-02-01 00:00:00

  • Fungal origin by horizontal transfer of a plant mitochondrial group I intron in the chimeric CoxI gene of Peperomia.

    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

    pub_type: 杂志文章


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

    更新日期:1995-11-01 00:00:00

  • The Central Symbiosis of Molecular Biology: Molecules in Mutualism.

    abstract::As illustrated by the mitochondrion and the eukaryotic cell, little in biology makes sense except in light of mutualism. Mutualisms are persistent, intimate, and reciprocal exchanges; an organism proficient in obtaining certain benefits confers those on a partner, which reciprocates by conferring different benefits. M...

    journal_title:Journal of molecular evolution

    pub_type: 杂志文章,评审


    authors: Lanier KA,Petrov AS,Williams LD

    更新日期:2017-08-01 00:00:00

  • A graph theoretic approach to the development of minimal phylogenetic trees.

    abstract::The problem of determining the minimal phylogenetic tree is discussed in relation to graph theory. It is shown that this problem is an example of the Steiner problem in graphs which is to connect a set of points by a minimal length network where new points can be added. There is no reported method of solving realistic...

    journal_title:Journal of molecular evolution

    pub_type: 杂志文章


    authors: Foulds LR,Hendy MD,Penny D

    更新日期:1979-07-18 00:00:00