Quartet mapping and the extent of lateral transfer in bacterial genomes.

abstract：:Phylogenetic inference from genome-wide data (phylogenomics) has revolutionized the study of evolution because it enables accounting for discordance among evolutionary histories across the genome. To this end, summary methods have been developed to allow accurate and scalable inference of species trees from gene trees...

journal_title：Molecular biology and evolution

authors： Zhang C,Scornavacca C,Molloy EK,Mirarab S

更新日期：2020-11-01 00:00:00

abstract：:A central problem in evolutionary theory concerns the mechanisms by which adaptations requiring multiple mutations emerge in natural populations. We develop a series of expressions that clarify the scaling of the time to establishment of complex adaptations with population size, mutation rate, magnitude of the selecti...

journal_title：Molecular biology and evolution

authors： Lynch M,Abegg A

更新日期：2010-06-01 00:00:00

abstract：:Studies of cichlid evolution have highlighted the importance of visual pigment genes in the spectacular radiation of the African rift lake cichlids. Recent work, however, has also provided strong evidence for adaptive diversification of riverine cichlids in the Neotropics, which inhabit environments of markedly differ...

journal_title：Molecular biology and evolution

authors： Schott RK,Refvik SP,Hauser FE,López-Fernández H,Chang BS

更新日期：2014-05-01 00:00:00

abstract：:The retroid family consists of all genetic elements that encode a potential reverse transcriptase (RT). Members of this family include a diversity of eukaryotic genetic elements (viruses, transposable elements, organelle introns, and plasmids) and the retrons of prokaryotes. Some retroid elements have, in addition to ...

journal_title：Molecular biology and evolution

authors： McClure MA

更新日期：1991-11-01 00:00:00

abstract：:We show how to make appropriate likelihood ratio tests for evolutionary tree models when parameters such as edge (internodes or branches) lengths have nonnegativity constraints. In such cases, under the null model of an edge length being zero, the marginal distribution of this parameter is proven to be a "half-normal"...

journal_title：Molecular biology and evolution

authors： Ota R,Waddell PJ,Hasegawa M,Shimodaira H,Kishino H

更新日期：2000-05-01 00:00:00

abstract：:Single-stranded DNA(ssDNA) viral life cycles must balance double-stranded DNA (dsDNA) and ssDNA biosynthesis. Previously published in vitro results suggest that microvirus C and host cell SSB proteins play antagonistic roles to achieve this balance. To investigate this in vivo, microvirus DNA replication was character...

journal_title：Molecular biology and evolution

authors： Doore SM,Baird CD,2012 University of Arizona Virology Undergraduate Lab.,Roznowski AP,Fane BA

更新日期：2014-06-01 00:00:00

abstract：:With the desire to model population genetic processes under increasingly realistic scenarios, forward genetic simulations have become a critical part of the toolbox of modern evolutionary biology. The SLiM forward genetic simulation framework is one of the most powerful and widely used tools in this area. However, its...

journal_title：Molecular biology and evolution

authors： Haller BC,Messer PW

更新日期：2019-03-01 00:00:00

abstract：:The field of ancient DNA (aDNA) is casting new light on many evolutionary questions. However, problems associated with the postmortem instability of DNA may complicate the interpretation of aDNA data. For example, in population genetic studies, the inclusion of damaged DNA may inflate estimates of diversity. In this p...

journal_title：Molecular biology and evolution

authors： Axelsson E,Willerslev E,Gilbert MT,Nielsen R

更新日期：2008-10-01 00:00:00

abstract：:The environment has profound effects on the expression of many traits and reaction norms describe the expression dynamics of a trait across a broad range of environmental conditions. Here, we analyze gene expression in Drosophila melanogaster across four different developmental temperatures (13-29 °C). Gene expression...

journal_title：Molecular biology and evolution

authors： Chen J,Nolte V,Schlötterer C

更新日期：2015-09-01 00:00:00

abstract：:Ribosomal DNA (rDNA) is one of the most conserved genes in eukaryotes. The multiples copies of rDNA in the genome evolve in a concerted manner, through unequal crossing over and/or gene conversion, two mechanisms related to homologous recombination. Recombination increases local GC content in several organisms through...

journal_title：Molecular biology and evolution

authors： Escobar JS,Glémin S,Galtier N

更新日期：2011-09-01 00:00:00

abstract：:Effective population size is fundamental in population genetics and characterizes genetic diversity. To infer past population dynamics from molecular sequence data, coalescent-based models have been developed for Bayesian nonparametric estimation of effective population size over time. Among the most successful is a G...

journal_title：Molecular biology and evolution

authors： Gill MS,Lemey P,Faria NR,Rambaut A,Shapiro B,Suchard MA

更新日期：2013-03-01 00:00:00

abstract：:We investigated global patterns of variation in 157 whole-genome sequences of Vibrio parahaemolyticus, a free-living and seafood associated marine bacterium. Pandemic clones, responsible for recent outbreaks of gastroenteritis in humans, have spread globally. However, there are oceanic gene pools, one located in the o...

journal_title：Molecular biology and evolution

authors： Cui Y,Yang X,Didelot X,Guo C,Li D,Yan Y,Zhang Y,Yuan Y,Yang H,Wang J,Wang J,Song Y,Zhou D,Falush D,Yang R

更新日期：2015-06-01 00:00:00

abstract：:Transposable elements (TEs) make up around 10%-15% of the Drosophila melanogaster genome, but its sibling species Drosophila simulans carries only one third as many such repeat sequences. We do not, however, have an overall view of copy numbers of the various classes of TEs (long terminal repeat [LTR] retrotransposons...

journal_title：Molecular biology and evolution

authors： Vieira C,Lepetit D,Dumont S,Biémont C

更新日期：1999-09-01 00:00:00

abstract：:Operons coding for the enzyme arsenite oxidase have been detected in the genomes from Archaea and Bacteria by Blast searches using the amino acid sequences of the respective enzyme characterized in two different beta-proteobacteria as templates. Sequence analyses show that in all these species, arsenite oxidase is tra...

journal_title：Molecular biology and evolution

authors： Lebrun E,Brugna M,Baymann F,Muller D,Lièvremont D,Lett MC,Nitschke W

更新日期：2003-05-01 00:00:00

abstract：:In order to investigate divergence of immune regulation among Drosophila species, we have engaged in a study of innate immune function in F1 hybrids of Drosophila melanogaster and D. simulans. If pathways have diverged between the species such that incompatibilities have arisen between interacting components of the im...

journal_title：Molecular biology and evolution

authors： Hill-Burns EM,Clark AG

更新日期：2010-11-01 00:00:00

abstract：:Good phylogenetic trees are required to test hypotheses about evolutionary processes. We report four new avian mitochondrial genomes, which together with an improved method of phylogenetic analysis for vertebrate mt genomes give results for three questions in avian evolution. The new mt genomes are: magpie goose (Anse...

journal_title：Molecular biology and evolution

authors： Harrison GL,McLenachan PA,Phillips MJ,Slack KE,Cooper A,Penny D

更新日期：2004-06-01 00:00:00

abstract：:Several authors have postulated that genetic divergence between populations could result in genomic incompatibilities that would cause an increase in transposition in their hybrids, producing secondary effects such as sterility and therefore starting a speciation process. It has been demonstrated that transposition la...

journal_title：Molecular biology and evolution

authors： Labrador M,Farré M,Utzet F,Fontdevila A

更新日期：1999-07-01 00:00:00

abstract：:Gene orders have been shown to be generally unstable by comprehensive analyses in several complete genomes. In this study, we examined instability of genome structures within operons, where functionally related genes are clustered. We compared gene orders of known operons obtained from Escherichia coli and Bacillus su...

journal_title：Molecular biology and evolution

authors： Itoh T,Takemoto K,Mori H,Gojobori T

更新日期：1999-03-01 00:00:00

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

authors： Williamson S,Orive ME

更新日期：2002-08-01 00:00:00

abstract：:Estimation of population parameters for the common ancestors of humans and the great apes is important in understanding our evolutionary history. In particular, inference of population size for the human-chimpanzee common ancestor may shed light on the process by which the 2 species separated and on whether the human ...

journal_title：Molecular biology and evolution

authors： Burgess R,Yang Z

更新日期：2008-09-01 00:00:00

abstract：:Most of the well-characterized mitochondrial genomes from diverse green algal lineages are circular mapping DNA molecules; however, Chlamydomonas reinhardtii has a linear 15.8 kb unit mitochondrial genome with 580 or 581 bp inverted repeat ends. In mitochondrial-enriched fractions prepared from Polytomella parva (=P. ...

journal_title：Molecular biology and evolution

authors： Fan J,Lee RW

更新日期：2002-07-01 00:00:00

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

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

更新日期：2006-09-01 00:00:00

abstract：:The spacer between the 16S and 23S rRNA genes of the chloroplast DNA has been implicated as an origin of replication in several species of plants. In the evening primrose, Oenothera, this site was found to vary greatly in size, with plastid genomes (plastomes) being readily distinguished. To determine whether plastome...

journal_title：Molecular biology and evolution

authors： Sears BB,Stoike LL,Chiu WL

更新日期：1996-07-01 00:00:00

abstract：:Mitochondrial protein translation requires interactions between transfer RNAs encoded by the mitochondrial genome (mt-tRNAs) and mitochondrial aminoacyl tRNA synthetase proteins (mt-aaRS) encoded by the nuclear genome. It has been argued that animal mt-tRNAs have higher deleterious substitution rates relative to their...

journal_title：Molecular biology and evolution

authors： Adrion JR,White PS,Montooth KL

更新日期：2016-01-01 00:00:00

abstract：:Many intron positions are conserved in varying subsets of eukaryotic genomes and, consequently, comprise a potentially informative class of phylogenetic characters. Roy and Gilbert developed a method of phylogenetic reconstruction using the patterns of intron presence-absence in eukaryotic genes and, applying this met...

journal_title：Molecular biology and evolution

authors： Zheng J,Rogozin IB,Koonin EV,Przytycka TM

更新日期：2007-11-01 00:00:00

abstract：:As human populations dispersed throughout the world, they were subjected to new selective forces, which must have led to local adaptation via natural selection and hence altered patterns of genetic variation. Yet, there are very few examples known in which such local selection has clearly influenced human genetic vari...

journal_title：Molecular biology and evolution

authors： Kayser M,Brauer S,Stoneking M

更新日期：2003-06-01 00:00:00

abstract：:Modifications to transcriptional regulators play a major role in adaptation. Here, we compared the effects of multiple beneficial mutations within and between Escherichia coli rpoB, the gene encoding the RNA polymerase β subunit, and rho, which encodes a transcriptional terminator. These two genes have harbored adapti...

journal_title：Molecular biology and evolution

authors： González-González A,Hug SM,Rodríguez-Verdugo A,Patel JS,Gaut BS

更新日期：2017-11-01 00:00:00

abstract：:Simple models of molecular evolution assume that sequences evolve by a Poisson process in which nucleotide or amino acid substitutions occur as rare independent events. In these models, the expected ratio of the variance to the mean of substitution counts equals 1, and substitution processes with a ratio greater than ...

journal_title：Molecular biology and evolution

authors： Bedford T,Hartl DL

更新日期：2008-08-01 00:00:00

abstract：:One of the most fundamental questions for understanding the origin of species is why genes that function to cause fertility in a pure-species genetic background fail to produce fertility in a hybrid genetic background. A related question is why the sex that is most often sterile or inviable in hybrids is the heterogam...

journal_title：Molecular biology and evolution

authors： Michalak P,Noor MA

更新日期：2003-07-01 00:00:00

abstract：:Understanding genome and chromosome evolution is important for understanding genetic inheritance and evolution. Universal events comprising DNA replication, transcription, repair, mobile genetic element transposition, chromosome rearrangements, mitosis, and meiosis underlie inheritance and variation of living organism...

journal_title：Molecular biology and evolution

authors： Li X,Zhu C,Lin Z,Wu Y,Zhang D,Bai G,Song W,Ma J,Muehlbauer GJ,Scanlon MJ,Zhang M,Yu J

更新日期：2011-06-01 00:00:00