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












  • Heads or tails: a simple reliability check for multiple sequence alignments.

    abstract::The question of multiple sequence alignment quality has received much attention from developers of alignment methods. Less forthcoming, however, are practical measures for addressing alignment quality issues in real life settings. Here, we present a simple methodology to help identify and quantify the uncertainties in...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Landan G,Graur D

    更新日期:2007-06-01 00:00:00

  • Short repetitive sequences in green algal mitochondrial genomes: potential roles in mitochondrial genome evolution.

    abstract::Current data on green algal mitochondrial genomes suggest an unexpected dichotomy within the group with respect to genome structure, organization, and sequence affiliations. The present study suggests that there is a correlation between this dichotomy on one hand and the differences in the abundance, base composition,...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Nedelcu AM,Lee RW

    更新日期:1998-06-01 00:00:00

  • The involucrin genes of the white-fronted capuchin and cottontop tamarin: the platyrrhine middle region.

    abstract::In all anthropoid species, the coding region of the involucrin gene contains a segment of short tandem repeats that were added sequentially, beginning in a common anthropoid ancestor. The involucrin coding region of each of two platyrrhine species, the white-fronted capuchin (Cebus albifrons) and the cottontop tamarin...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Phillips M,Rice RH,Djian P,Green H

    更新日期:1991-09-01 00:00:00

  • Distribution of hobo transposable elements in the genus Drosophila.

    abstract::This study describes the distribution of hobo-hybridizing sequences in the genus Drosophila. Southern blot analysis of 134 species revealed that hobo sequences are limited to the melanogaster and montium subgroups of the melanogaster-species group. Of the hobo-bearing species, only D. melanogaster and two of its sibli...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Daniels SB,Chovnick A,Boussy IA

    更新日期:1990-11-01 00:00:00

  • mtDNA tandem repeats in domestic dogs and wolves: mutation mechanism studied by analysis of the sequence of imperfect repeats.

    abstract::The mitochondrial (mt) DNA control region (CR) of dogs and wolves contains an array of imperfect 10 bp tandem repeats. This region was studied for 14 domestic dogs representing the four major phylogenetic groups of nonrepetitive CR and for 5 wolves. Three repeat types were found among these individuals, distributed so...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Savolainen P,Arvestad L,Lundeberg J

    更新日期:2000-04-01 00:00:00

  • Insights from the Shell Proteome: Biomineralization to Adaptation.

    abstract::Bivalves have evolved a range of complex shell forming mechanisms that are reflected by their incredible diversity in shell mineralogy and microstructures. A suite of proteins exported to the shell matrix space plays a significant role in controlling these features, in addition to underpinning some of the physical pro...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Arivalagan J,Yarra T,Marie B,Sleight VA,Duvernois-Berthet E,Clark MS,Marie A,Berland S

    更新日期:2017-01-01 00:00:00

  • Molecular evolution and population genetics of duplicated accessory gland protein genes in Drosophila.

    abstract::To investigate the potential importance of gene duplication in D. melanogaster accessory gland protein (Acp) gene evolution we carried out a computational analysis comparing annotated D. melanogaster Acp genes to the entire D. melanogaster genome. We found that two known Acp genes are actually members of small multige...

    journal_title:Molecular biology and evolution

    pub_type: 信件


    authors: Holloway AK,Begun DJ

    更新日期:2004-09-01 00:00:00

  • Testing hypotheses about the sister group of the passeriformes using an independent 30-locus data set.

    abstract::Although many phylogenetic studies have focused on developing hypotheses about relationships, advances in data collection and computation have increased the feasibility of collecting large independent data sets to rigorously test controversial hypotheses or carefully assess artifacts that may be misleading. One such r...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Wang N,Braun EL,Kimball RT

    更新日期:2012-02-01 00:00:00

  • Proceedings of the SMBE Tri-National Young Investigators' Workshop 2005. Genome-wide search of gene conversions in duplicated genes of mouse and rat.

    abstract::Gene conversion is considered to play important roles in the formation of genomic makeup such as homogenization of multigene families and diversification of alleles. We devised two statistical tests on quartets for detecting gene conversion events. Each "quartet" consists of two pairs of orthologous sequences supposed...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Ezawa K,OOta S,Saitou N,SMBE Tri-National Young Investigators.

    更新日期:2006-05-01 00:00:00

  • Estimating gene gain and loss rates in the presence of error in genome assembly and annotation using CAFE 3.

    abstract::Current sequencing methods produce large amounts of data, but genome assemblies constructed from these data are often fragmented and incomplete. Incomplete and error-filled assemblies result in many annotation errors, especially in the number of genes present in a genome. This means that methods attempting to estimate...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Han MV,Thomas GW,Lugo-Martinez J,Hahn MW

    更新日期:2013-08-01 00:00:00

  • Parallel evolution of nacre building gene sets in molluscs.

    abstract::The capacity to biomineralize is closely linked to the rapid expansion of animal life during the early Cambrian, with many skeletonized phyla first appearing in the fossil record at this time. The appearance of disparate molluscan forms during this period leaves open the possibility that shells evolved independently a...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Jackson DJ,McDougall C,Woodcroft B,Moase P,Rose RA,Kube M,Reinhardt R,Rokhsar DS,Montagnani C,Joubert C,Piquemal D,Degnan BM

    更新日期:2010-03-01 00:00:00

  • Organellar RNA editing and plant-specific extensions of pentatricopeptide repeat proteins in jungermanniid but not in marchantiid liverworts.

    abstract::The pyrimidine exchange type of RNA editing in land plant (embryophyte) organelles has largely remained an enigma with respect to its biochemical mechanisms, the underlying specificities, and its raison d'être. Apparently arising with the earliest embryophytes, RNA editing is conspicuously absent in one clade of liver...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Rüdinger M,Polsakiewicz M,Knoop V

    更新日期:2008-07-01 00:00:00

  • The covariation between TpA deficiency, CpG deficiency, and G+C content of human isochores is due to a mathematical artifact.

    abstract::CpG and TpA dinucleotides are underrepresented in the human genome. The CpG deficiency is due to the high mutation rate from C to T in methylated CpG's. The TpA suppression was thought to reflect a counterselection against TpA's destabilizing effect in RNA. Unexpectedly, the TpA and CpG deficiencies vary according to ...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Duret L,Galtier N

    更新日期:2000-11-01 00:00:00

  • The fate of mutations surfing on the wave of a range expansion.

    abstract::Many species, including humans, have dramatically expanded their range in the past, and such range expansions had certainly an impact on their genetic diversity. For example, mutations arising in populations at the edge of a range expansion can sometimes surf on the wave of advance and thus reach a larger spatial dist...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Klopfstein S,Currat M,Excoffier L

    更新日期:2006-03-01 00:00:00

  • Rampant Parasexuality Evolves in a Hospital Pathogen during Antibiotic Selection.

    abstract::Horizontal gene transfer threatens the therapeutic success of antibiotics by facilitating the rapid dissemination of resistance alleles among bacterial species. The conjugative mobile element Tn916 provides an excellent context for examining the role of adaptive parasexuality as it carries the tetracycline-resistance ...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Beabout K,Hammerstrom TG,Wang TT,Bhatty M,Christie PJ,Saxer G,Shamoo Y

    更新日期:2015-10-01 00:00:00

  • Sequencing errors and molecular evolutionary analysis.

    abstract::Heuristic approaches were used to quantify the influence that sequencing errors have on estimates of nucleotide diversity, substitution rate, and the construction of genealogies. Error rates of less than 1 nucleotide/kb probably have little affect on conclusions about the evolutionary history of highly polymorphic org...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Clark AG,Whittam TS

    更新日期:1992-07-01 00:00:00

  • Parallel evolution of opsin gene expression in African cichlid fishes.

    abstract::Phenotypic evolution may occur either through alterations to the structure of protein-coding genes or their expression. Evidence for which of these two mechanisms more commonly contribute to the evolution of a phenotype can be garnered from examples of parallel and convergent evolution. The visual system of East Afric...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: O'Quin KE,Hofmann CM,Hofmann HA,Carleton KL

    更新日期:2010-12-01 00:00:00

  • Evolution of dinoflagellate unigenic minicircles and the partially concerted divergence of their putative replicon origins.

    abstract::Dinoflagellate chloroplast genes are unique in that each gene is on a separate minicircular chromosome. To understand the origin and evolution of this exceptional genomic organization we completely sequenced chloroplast psbA and 23S rRNA gene minicircles from four dinoflagellates: three closely related Heterocapsa spe...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Zhang Z,Cavalier-Smith T,Green BR

    更新日期:2002-04-01 00:00:00

  • Diversity in degrees of freedom of mitochondrial transit peptides.

    abstract::Most mitochondrial proteins are synthesized in the cytosol of eukaryotic cells as precursor proteins carrying N-terminal extensions called transit peptides or presequences, which mediate their specific transport into mitochondria. However, plant cells possess a second potential target organelle for such transit peptid...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Staiger C,Hinneburg A,Klösgen RB

    更新日期:2009-08-01 00:00:00

  • Frequent Retroviral Gene Co-option during the Evolution of Vertebrates.

    abstract::Endogenous retroviruses are ubiquitous in the vertebrate genomes. On occasion, hosts recruited retroviral genes to mediate their own biological functions, a process formally known as co-option or exaptation. Much remains unknown about the extent of retroviral gene co-option in vertebrates, although more than ten retro...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Wang J,Han GZ

    更新日期:2020-11-01 00:00:00

  • The elevated GC content at exonic third sites is not evidence against neutralist models of isochore evolution.

    abstract::The human genome is divided into isochores, large stretches (>300 kb) of genomic DNA with more or less consistent GC content. Mutational/neutralist and selectionist models have been put forward to explain their existence. A major criticism of the mutational models is that they cannot account for the higher GC content ...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Duret L,Hurst LD

    更新日期:2001-05-01 00:00:00

  • Automated structural comparisons clarify the phylogeny of the right-hand-shaped polymerases.

    abstract::Polymerases are essential for life, being responsible for replication, transcription, and the repair of nucleic acid molecules. Those that share a right-hand-shaped fold and catalytic site structurally similar to the DNA polymerase I of Escherichia coli may catalyze RNA- or DNA-dependent RNA polymerization, reverse tr...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Mönttinen HA,Ravantti JJ,Stuart DI,Poranen MM

    更新日期:2014-10-01 00:00:00

  • Mitochondrial Mutation Rate, Spectrum and Heteroplasmy in Caenorhabditis elegans Spontaneous Mutation Accumulation Lines of Differing Population Size.

    abstract::Mitochondrial genomes of metazoans, given their elevated rates of evolution, have served as pivotal markers for phylogeographic studies and recent phylogenetic events. In order to determine the dynamics of spontaneous mitochondrial mutations in small populations in the absence and presence of selection, we evolved mut...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Konrad A,Thompson O,Waterston RH,Moerman DG,Keightley PD,Bergthorsson U,Katju V

    更新日期:2017-06-01 00:00:00

  • Population Parameters Underlying an Ongoing Soft Sweep in Southeast Asian Malaria Parasites.

    abstract::Multiple kelch13 alleles conferring artemisinin resistance (ART-R) are currently spreading through Southeast Asian malaria parasite populations, providing a unique opportunity to observe an ongoing soft selective sweep, investigate why resistance alleles have evolved multiple times and determine fundamental population...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Anderson TJ,Nair S,McDew-White M,Cheeseman IH,Nkhoma S,Bilgic F,McGready R,Ashley E,Pyae Phyo A,White NJ,Nosten F

    更新日期:2017-01-01 00:00:00

  • Rapid evolution and gene-specific patterns of selection for three genes of spermatogenesis in Drosophila.

    abstract::Hybrid males resulting from crosses between closely related species of Drosophila are sterile. The F1 hybrid sterility phenotype is mainly due to defects occurring during late stages of development that relate to sperm individualization, and so genes controlling sperm development may have been subjected to selective d...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Civetta A,Rajakumar SA,Brouwers B,Bacik JP

    更新日期:2006-03-01 00:00:00

  • Accuracy and power of the likelihood ratio test in detecting adaptive molecular evolution.

    abstract::The selective pressure at the protein level is usually measured by the nonsynonymous/synonymous rate ratio (omega = dN/dS), with omega < 1, omega = 1, and omega > 1 indicating purifying (or negative) selection, neutral evolution, and diversifying (or positive) selection, respectively. The omega ratio is commonly calcu...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Anisimova M,Bielawski JP,Yang Z

    更新日期:2001-08-01 00:00:00

  • Positively selected disease response orthologous gene sets in the cereals identified using Sorghum bicolor L. Moench expression profiles and comparative genomics.

    abstract::Disease response genes (DRGs) diverge under recurrent positive selection as a result of a molecular arms race between hosts and pathogens. Most of these studies were conducted in animals, and few defense genes have been shown to evolve adaptively in plants. To test for adaptation in the molecules mediating disease res...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Zamora A,Sun Q,Hamblin MT,Aquadro CF,Kresovich S

    更新日期:2009-09-01 00:00:00

  • Whole-genome expression plasticity across tropical and temperate Drosophila melanogaster populations from Eastern Australia.

    abstract::The genotypic signature of spatially varying selection is ubiquitous across the Drosophila melanogaster genome. Spatially structured adaptive phenotypic differences are also commonly found, particularly along New World and Australian latitudinal gradients. However, investigation of gene expression variation in one or ...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Levine MT,Eckert ML,Begun DJ

    更新日期:2011-01-01 00:00:00

  • The transition to self-compatibility in Arabidopsis thaliana and evolution within S-haplotypes over 10 Myr.

    abstract::A recent investigation found evidence that the transition of Arabidopsis thaliana from ancestral self-incompatibility (SI) to full self-compatibility occurred very recently and suggested that this occurred through a selective fixation of a nonfunctional allele (PsiSCR1) at the SCR gene, which determines pollen specifi...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Bechsgaard JS,Castric V,Charlesworth D,Vekemans X,Schierup MH

    更新日期:2006-09-01 00:00:00

  • Evolutionary distances for protein-coding sequences: modeling site-specific residue frequencies.

    abstract::Estimation of evolutionary distances from coding sequences must take into account protein-level selection to avoid relative underestimation of longer evolutionary distances. Current modeling of selection via site-to-site rate heterogeneity generally neglects another aspect of selection, namely position-specific amino ...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Halpern AL,Bruno WJ

    更新日期:1998-07-01 00:00:00