The mosaic nature of the eukaryotic nucleus.


:The phylogenies for each of the protein-coding genes from the Methanococcus jannaschii genome were surveyed to determine the history of the major groups of life. For each gene, homologous sequences from other archaea, eucarya, and Gram-positive and Gram-negative bacteria were collected and aligned, and a phylogeny was reconstructed with a maximum-likelihood algorithm. The majority of significant phylogenies favor the eucarya and the archaca as sister groups. A smaller, but still substantial, portion of these significant phylogenies favor an eucarya/Gram-negative clade. These results indicate that support for the early history of life is not unequivocal. A chimeric origin of eukaryotes or an ancient, massive horizontal transfer of genes from Gram-negative bacteria to eucarya can explain many of the observed phylogenies.


Mol Biol Evol


Ribeiro S,Golding GB




Has Abstract


1998-07-01 00:00:00












  • Non-African populations of Drosophila melanogaster have a unique origin.

    abstract::Drosophila melanogaster is widely used as a model in DNA variation studies. Patterns of polymorphism have, however, been affected by the history of this species, which is thought to have recently spread out of Africa to the rest of the world. We analyzed DNA sequence variation in 11 populations, including four contine...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Baudry E,Viginier B,Veuille M

    更新日期:2004-08-01 00:00:00

  • The Footprint of Polygenic Adaptation on Stress-Responsive Cis-Regulatory Divergence in the Arabidopsis Genus.

    abstract::Adaptation of a complex trait often requires the accumulation of many modifications to finely tune its underpinning molecular components to novel environmental requirements. The investigation of cis-acting regulatory modifications can be used to pinpoint molecular systems partaking in such complex adaptations. Here, w...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: He F,Arce AL,Schmitz G,Koornneef M,Novikova P,Beyer A,de Meaux J

    更新日期:2016-08-01 00:00:00

  • Functional compensation of primary and secondary metabolites by duplicate genes in Arabidopsis thaliana.

    abstract::It is well known that knocking out a gene in an organism often causes no phenotypic effect. One possible explanation is the existence of duplicate genes; that is, the effect of knocking out a gene is compensated by a duplicate copy. Another explanation is the existence of alternative pathways. In terms of metabolic pr...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Hanada K,Sawada Y,Kuromori T,Klausnitzer R,Saito K,Toyoda T,Shinozaki K,Li WH,Hirai MY

    更新日期:2011-01-01 00:00:00

  • The dynamic nature of eukaryotic genomes.

    abstract::Analyses of diverse eukaryotes reveal that genomes are dynamic, sometimes dramatically so. In numerous lineages across the eukaryotic tree of life, DNA content varies within individuals throughout life cycles and among individuals within species. Discovery of examples of genome dynamism is accelerating as genome seque...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Parfrey LW,Lahr DJ,Katz LA

    更新日期:2008-04-01 00:00:00

  • Discovery of cyanophage genomes which contain mitochondrial DNA polymerase.

    abstract::DNA polymerase γ is a family A DNA polymerase responsible for the replication of mitochondrial DNA in eukaryotes. The origins of DNA polymerase γ have remained elusive because it is not present in any known bacterium, though it has been hypothesized that mitochondria may have inherited the enzyme by phage-mediated non...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Chan YW,Mohr R,Millard AD,Holmes AB,Larkum AW,Whitworth AL,Mann NH,Scanlan DJ,Hess WR,Clokie MR

    更新日期:2011-08-01 00:00:00

  • Is Mutation Random or Targeted?: No Evidence for Hypermutability in Snail Toxin Genes.

    abstract::Ever since Luria and Delbruck, the notion that mutation is random with respect to fitness has been foundational to modern biology. However, various studies have claimed striking exceptions to this rule. One influential case involves toxin-encoding genes in snails of the genus Conus, termed conotoxins, a large gene fam...

    journal_title:Molecular biology and evolution

    pub_type: 信件


    authors: Roy SW

    更新日期:2016-10-01 00:00:00

  • Extensive Differential Splicing Underlies Phenotypically Plastic Aphid Morphs.

    abstract::Phenotypic plasticity results in a diversity of phenotypes from a single genotype in response to environmental cues. To understand the molecular basis of phenotypic plasticity, studies have focused on differential gene expression levels between environmentally determined phenotypes. The extent of alternative splicing ...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Grantham ME,Brisson JA

    更新日期:2018-08-01 00:00:00

  • Cross-Study Comparison Reveals Common Genomic, Network, and Functional Signatures of Desiccation Resistance in Drosophila melanogaster.

    abstract::Repeated attempts to map the genomic basis of complex traits often yield different outcomes because of the influence of genetic background, gene-by-environment interactions, and/or statistical limitations. However, where repeatability is low at the level of individual genes, overlap often occurs in gene ontology categ...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Telonis-Scott M,Sgrò CM,Hoffmann AA,Griffin PC

    更新日期:2016-04-01 00:00:00

  • The "domino theory" of gene death: gradual and mass gene extinction events in three lineages of obligate symbiotic bacterial pathogens.

    abstract::During the adaptation of an organism to a parasitic lifestyle, various gene functions may be rendered superfluous due to the fact that the host may supply these needs. As a consequence, obligate symbiotic bacterial pathogens tend to undergo reductive genomic evolution through gene death (nonfunctionalization or pseudo...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Dagan T,Blekhman R,Graur D

    更新日期:2006-02-01 00:00:00

  • Rapid functional divergence of a newly evolved polyubiquitin gene in Drosophila and its role in the trade-off between male fecundity and lifespan.

    abstract::The cost of reproduction is a pivotal trade-off with various biological processes during the evolution of organisms. However, the genes and molecular mechanisms underlying the evolution of balancing reproductive capacity and its cost are still largely unknown. Here, we present a comprehensive study on the evolution, e...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Zhan Z,Ding Y,Zhao R,Zhang Y,Yu H,Zhou Q,Yang S,Xiang H,Wang W

    更新日期:2012-05-01 00:00:00

  • Extreme reconfiguration of plastid genomes in the angiosperm family Geraniaceae: rearrangements, repeats, and codon usage.

    abstract::Geraniaceae plastid genomes (plastomes) have experienced a remarkable number of genomic changes. The plastomes of Erodium texanum, Geranium palmatum, and Monsonia speciosa were sequenced and compared with other rosids and the previously published Pelargonium hortorum plastome. Geraniaceae plastomes were found to be hi...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Guisinger MM,Kuehl JV,Boore JL,Jansen RK

    更新日期:2011-01-01 00:00:00

  • Detecting Signatures of Positive Selection along Defined Branches of a Population Tree Using LSD.

    abstract::Identifying the genomic basis underlying local adaptation is paramount to evolutionary biology, and bears many applications in the fields of conservation biology, crop, and animal breeding, as well as personalized medicine. Although many approaches have been developed to detect signatures of positive selection within ...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Librado P,Orlando L

    更新日期:2018-06-01 00:00:00

  • Euarchontan Opsin Variation Brings New Focus to Primate Origins.

    abstract::Debate on the adaptive origins of primates has long focused on the functional ecology of the primate visual system. For example, it is hypothesized that variable expression of short- (SWS1) and middle-to-long-wavelength sensitive (M/LWS) opsins, which confer color vision, can be used to infer ancestral activity patter...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Melin AD,Wells K,Moritz GL,Kistler L,Orkin JD,Timm RM,Bernard H,Lakim MB,Perry GH,Kawamura S,Dominy NJ

    更新日期:2016-04-01 00:00:00

  • The genealogy of a sequence subject to purifying selection at multiple sites.

    abstract::We investigate the effect of purifying selection at multiple sites on both the shape of the genealogy and the distribution of mutations on the tree. We find that the primary effect of purifying selection on a genealogy is to shift the distribution of mutations on the tree, whereas the shape of the tree remains largely...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Williamson S,Orive ME

    更新日期:2002-08-01 00:00:00

  • Population genetics of speciation in nonmodel organisms: I. Ancestral polymorphism in mangroves.

    abstract::The level of DNA polymorphism in the ancestral species at the time of speciation can be estimated using DNA sequences from many loci sampled from 2 or more extant species. The comparison between ancestral and extant polymorphism can be informative about the population genetics of speciation. In this study, we collecte...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Zhou R,Zeng K,Wu W,Chen X,Yang Z,Shi S,Wu CI

    更新日期:2007-12-01 00:00:00

  • Out of America to Africa or Asia: inference of dispersal histories using nuclear and plastid DNA and the S-RNase self-incompatibility locus.

    abstract::The plant genus Lycium (Solanaceae) originated in the Americas and includes approximately 85 species that are distributed worldwide. The vast majority of Old World species occur in southern Africa and eastern Asia. In this study, we examine biogeographic relationships among Old World species using a phylogenetic appro...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Miller JS,Kamath A,Damashek J,Levin RA

    更新日期:2011-01-01 00:00:00

  • Molecular adaptation of a leaf-eating bird: stomach lysozyme of the hoatzin.

    abstract::This report describes a lysozyme expressed at high levels in the stomach of the hoatzin, the only known foregut-fermenting bird. Evolutionary comparison places it among the calcium-binding lysozymes rather than among the conventional types. Conventional lysozymes were recruited as digestive enzymes twice in the evolut...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Kornegay JR,Schilling JW,Wilson AC

    更新日期:1994-11-01 00:00:00

  • Theoretical foundation of the balanced minimum evolution method of phylogenetic inference and its relationship to weighted least-squares tree fitting.

    abstract::Due to its speed, the distance approach remains the best hope for building phylogenies on very large sets of taxa. Recently (R. Desper and O. Gascuel, J. Comp. Biol. 9:687-705, 2002), we introduced a new "balanced" minimum evolution (BME) principle, based on a branch length estimation scheme of Y. Pauplin (J. Mol. Evo...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Desper R,Gascuel O

    更新日期:2004-03-01 00:00:00

  • Evolutionary dynamics of tandem repeats in the mitochondrial DNA control region of the minnow Cyprinella spiloptera.

    abstract::Length variation due to tandem repeats is now recognized as a common feature of animal mitochondrial DNA; however, the evolutionary dynamics of repeated sequences are not well understood. Using phylogenetic analysis, predictions of three models of repeat evolution were tested for arrays of 260-bp repeats in the cyprin...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Broughton RE,Dowling TE

    更新日期:1997-12-01 00:00:00

  • Evolution of closely linked gene pairs in vertebrate genomes.

    abstract::The orientation of closely linked genes in mammalian genomes is not random: there are more head-to-head (h2h) gene pairs than expected. To understand the origin of this enrichment in h2h gene pairs, we have analyzed the phylogenetic distribution of gene pairs separated by less than 600 bp of intergenic DNA (gene duos)...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Franck E,Hulsen T,Huynen MA,de Jong WW,Lubsen NH,Madsen O

    更新日期:2008-09-01 00:00:00

  • Rare variation facilitates inferences of fine-scale population structure in humans.

    abstract::Understanding the genetic structure of human populations has important implications for the design and interpretation of disease mapping studies and reconstructing human evolutionary history. To date, inferences of human population structure have primarily been made with common variants. However, recent large-scale re...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: O'Connor TD,Fu W,NHLBI GO Exome Sequencing Project.,ESP Population Genetics and Statistical Analysis Working Group, Emily Turner.,Mychaleckyj JC,Logsdon B,Auer P,Carlson CS,Leal SM,Smith JD,Rieder MJ,Bamshad MJ,Nickerson DA,Ake

    更新日期:2015-03-01 00:00:00

  • Bayesian Analysis of Evolutionary Divergence with Genomic Data under Diverse Demographic Models.

    abstract::We present a new Bayesian method for estimating demographic and phylogenetic history using population genomic data. Several key innovations are introduced that allow the study of diverse models within an Isolation-with-Migration framework. The new method implements a 2-step analysis, with an initial Markov chain Monte...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Chung Y,Hey J

    更新日期:2017-06-01 00:00:00

  • Asymmetric Context-Dependent Mutation Patterns Revealed through Mutation-Accumulation Experiments.

    abstract::Despite the general assumption that site-specific mutation rates are independent of the local sequence context, a growing body of evidence suggests otherwise. To further examine context-dependent patterns of mutation, we amassed 5,645 spontaneous mutations in wild- type (WT) and mismatch-repair deficient (MMR(-)) muta...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Sung W,Ackerman MS,Gout JF,Miller SF,Williams E,Foster PL,Lynch M

    更新日期:2015-07-01 00:00:00

  • Adaptive evolution of hepcidin genes in antarctic notothenioid fishes.

    abstract::Hepcidin is a small bioactive peptide with dual roles as an antimicrobial peptide and as the principal hormonal regulator of iron homeostasis in human and mouse. Hepcidin homologs of very similar structures are found in lower vertebrates, all comprise approximately 20-25 amino acids with 8 highly conserved cysteines f...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Xu Q,Cheng CH,Hu P,Ye H,Chen Z,Cao L,Chen L,Shen Y,Chen L

    更新日期:2008-06-01 00:00:00

  • Selection against deleterious LINE-1-containing loci in the human lineage.

    abstract::We compared sex chromosomal and autosomal regions of similar GC contents and found that the human Y chromosome contains nine times as many full-length (FL) ancestral LINE-1 (L1) elements per megabase as do autosomes and that the X chromosome contains three times as many. In addition, both sex chromosomes contain a ca....

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Boissinot S,Entezam A,Furano AV

    更新日期:2001-06-01 00:00:00

  • Excess amino acid polymorphism in mitochondrial DNA: contrasts among genes from Drosophila, mice, and humans.

    abstract::Recent studies of mitochondrial DNA (mtDNA) variation in mammals and Drosophila have shown an excess of amino acid variation within species (replacement polymorphism) relative to the number of silent and replacement differences fixed between species. To examine further this pattern of nonneutral mtDNA evolution, we pr...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Rand DM,Kann LM

    更新日期:1996-07-01 00:00:00

  • Nucleotide polymorphism in the acidic chitinase locus (ChiA) region of the wild plant Arabidopsis thaliana.

    abstract::To investigate DNA variation in natural plant populations, a 1.8-kb region of the acidic chitinase locus (ChiA)was analyzed for 17 ecotypes of Arabidopsis thaliana sampled worldwide and 3 Arabis species in Japan. As in the Adh region, dimorphism was detected throughout the investigated ChiA region, suggesting the poss...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Kawabe A,Innan H,Terauchi R,Miyashita NT

    更新日期:1997-12-01 00:00:00

  • Sequence evolution in bacterial endosymbionts having extreme base compositions.

    abstract::A major limitation on ability to reconstruct bacterial evolution is the lack of dated ancestors that might be used to evaluate and calibrate molecular clocks. Vertically transmitted symbionts that have cospeciated with animal hosts offer a firm basis for calibrating sequence evolution in bacteria, since fossils of the...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Clark MA,Moran NA,Baumann P

    更新日期:1999-11-01 00:00:00

  • HIV-1 modulates the tRNA pool to improve translation efficiency.

    abstract::Despite its poorly adapted codon usage, HIV-1 replicates and is expressed extremely well in human host cells. HIV-1 has recently been shown to package non-lysyl transfer RNAs (tRNAs) in addition to the tRNA(Lys) needed for priming reverse transcription and integration of the HIV-1 genome. By comparing the codon usage ...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: van Weringh A,Ragonnet-Cronin M,Pranckeviciene E,Pavon-Eternod M,Kleiman L,Xia X

    更新日期:2011-06-01 00:00:00

  • Layers of evolvability in a bacteriophage life history trait.

    abstract::Functional redundancy in genomes arises from genes with overlapping functions, allowing phenotypes to persist after gene knockouts. Evolutionary redundancy or evolvability of a genome is one step removed, in that functional redundancy is absent but the genome has the potential to evolve to restore a lost phenotype. Ex...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Heineman RH,Bull JJ,Molineux IJ

    更新日期:2009-06-01 00:00:00