Evolutionary Modeling in SLiM 3 for Beginners.

abstract：:Cancer progression is an evolutionary process. During this process, evolving cancer cell populations encounter restrictive ecological niches within the body, such as the primary tumor, circulatory system, and diverse metastatic sites. Efforts to prevent or delay cancer evolution-and progression-require a deep understa...

journal_title：Molecular biology and evolution

authors： Somarelli JA,Gardner H,Cannataro VL,Gunady EF,Boddy AM,Johnson NA,Fisk JN,Gaffney SG,Chuang JH,Li S,Ciccarelli FD,Panchenko AR,Megquier K,Kumar S,Dornburg A,DeGregori J,Townsend JP

更新日期：2020-02-01 00:00:00

abstract：:The nucleotide sequences of the 5'-flanking regions of the duplicated Amy genes in eight sibling species belonging to the melanogaster species subgroup are analyzed. In Drosophila melanogaster, a region of about 450 bp immediately upstream of the translation initiation site of the two paralogous genes (the proximal an...

journal_title：Molecular biology and evolution

authors： Okuyama E,Shibata H,Tachida H,Yamazaki T

更新日期：1996-04-01 00:00:00

abstract：:The internal consistency of the PAM matrix model of protein evolution is here investigated. The 1 PAM matrix has been constructed from amino acid replacements observed in closely related sequences. Such replacements are of two types, those that do not require an intermediate amino acid replacement and those that do. T...

journal_title：Molecular biology and evolution

authors： Wilbur WJ

更新日期：1985-09-01 00:00:00

abstract：:DNA fingerprinting exhibits multilocus genotypes of individuals, detected by the use of a single multilocus probe. Consequently, population data on DNA fingerprinting do not provide a complete characterization of the genetic variation in terms of allele-frequency distributions, since neither the number of loci nor the...

journal_title：Molecular biology and evolution

authors： Jin L,Chakraborty R

更新日期：1994-01-01 00:00:00

abstract：:Hitchhiking effects of advantageous mutations have been invoked to explain reduced polymorphism in regions of low crossing-over in Drosophila. Besides reducing DNA heterozygosity, hitchhiking effects should produce strong linkage disequilibrium and a frequency spectrum skewed toward an excess of rare polymorphisms (co...

journal_title：Molecular biology and evolution

authors： Begun DJ,Aquadro CF

更新日期：1995-05-01 00:00:00

abstract：:The functionality of long noncoding RNAs (lncRNAs) is disputed. In general, lncRNAs are under weak selective pressures, suggesting that the majority of lncRNAs may be nonfunctional. However, although some surveys showed negligible phenotypic effects upon lncRNA perturbation, key biological roles were demonstrated for ...

journal_title：Molecular biology and evolution

authors： Darbellay F,Necsulea A

更新日期：2020-01-01 00:00:00

abstract：:A detailed assessment of the evolution and phylogenetic utility of two genes, ftsZ and wsp, was used to investigate the origin of male-killing Wolbachia, previously isolated from the ladybird Adalia bipunctata and the butterfly Acraea encedon. The analysis included almost all available sequences of B-group Wolbachia a...

journal_title：Molecular biology and evolution

authors： Schulenburg JH,Hurst GD,Huigens TM,van Meer MM,Jiggins FM,Majerus ME

更新日期：2000-04-01 00:00:00

abstract：:There are many more selectively constrained noncoding than coding nucleotides in the mammalian genome, but most mammalian noncoding DNA is subject to weak selection, on average. One of the most striking discoveries to have emerged from comparisons among mammalian genomes is the hundreds of noncoding elements of more t...

journal_title：Molecular biology and evolution

authors： Halligan DL,Oliver F,Guthrie J,Stemshorn KC,Harr B,Keightley PD

更新日期：2011-09-01 00:00:00

abstract：:In chickens, there is a single functional gene (VH1) coding for the heavy chain variable region of immunoglobulins, and immunoglobulin diversity is generated by gene conversion of the VH1 gene by many variable region pseudogenes (psi VH's) that exist on the 5' side of the VH1 gene. To understand the evolution of this ...

journal_title：Molecular biology and evolution

authors： Ota T,Nei M

更新日期：1995-01-01 00:00:00

abstract：:Snake venom gene evolution has been studied intensively over the past several decades, yet most previous studies have lacked the context of complete snake genomes and the full context of gene expression across diverse snake tissues. We took a novel approach to studying snake venom evolution by leveraging the complete ...

journal_title：Molecular biology and evolution

authors： Reyes-Velasco J,Card DC,Andrew AL,Shaney KJ,Adams RH,Schield DR,Casewell NR,Mackessy SP,Castoe TA

更新日期：2015-01-01 00:00:00

abstract：:Although there is substantial evidence that, in animals, male-inherited neutral DNA evolves at a higher rate than female-inherited DNA, the relative evolutionary rate of male- versus female-inherited DNA has not been investigated in plants. We compared the substitution rates at neutral sites of maternally and paternal...

journal_title：Molecular biology and evolution

authors： Whittle CA,Johnston MO

更新日期：2002-06-01 00:00:00

abstract：:Alpha-defensins are a family of mammalian antimicrobial peptides that exhibit variable activity against a panel of microbes, including bacteria, fungi, and enveloped viruses. We have employed a maximum-likelihood approach to detect evidence of positive selection (adaptive evolution) in the evolution of these important...

journal_title：Molecular biology and evolution

authors： Lynn DJ,Lloyd AT,Fares MA,O'Farrelly C

更新日期：2004-05-01 00:00:00

abstract：:Multipartite genomes, containing at least two large replicons, are found in diverse bacteria; however, the advantage of this genome structure remains incompletely understood. Here, we perform comparative genomics of hundreds of finished β-proteobacterial genomes to gain insights into the role and emergence of multipar...

journal_title：Molecular biology and evolution

authors： diCenzo GC,Mengoni A,Perrin E

更新日期：2019-03-01 00:00:00

abstract：:The origin of novel traits is recognized as an important process underlying many major evolutionary radiations. We studied the genetic basis for the evolution of haustoria, the novel feeding organs of parasitic flowering plants, using comparative transcriptome sequencing in three species of Orobanchaceae. Around 180 g...

journal_title：Molecular biology and evolution

authors： Yang Z,Wafula EK,Honaas LA,Zhang H,Das M,Fernandez-Aparicio M,Huang K,Bandaranayake PC,Wu B,Der JP,Clarke CR,Ralph PE,Landherr L,Altman NS,Timko MP,Yoder JI,Westwood JH,dePamphilis CW

更新日期：2015-03-01 00:00:00

abstract：:The roles of selection and horizontal transfer in the evolution of the canonical subfamily of P: elements were studied in the saltans and willistoni species groups of the genus Drosophila (subgenus Sophophora). We estimate that the common ancestor of the canonical P: subfamily dates back 2-3 Myr at the most, despite t...

journal_title：Molecular biology and evolution

authors： Silva JC,Kidwell MG

更新日期：2000-10-01 00:00:00

abstract：:Analysis of evolution of paralogous genes in a genome is central to our understanding of genome evolution. Comparison of closely related bacterial genomes, which has provided clues as to how genome sequences evolve under natural conditions, would help in such an analysis. With species Staphylococcus aureus, whole-geno...

journal_title：Molecular biology and evolution

authors： Tsuru T,Kawai M,Mizutani-Ui Y,Uchiyama I,Kobayashi I

更新日期：2006-06-01 00:00:00

abstract：:Blooms that are formed by cyanobacteria consist of toxic and nontoxic strains. The mechanisms that result in the occurrence of nontoxic strains are enigmatic. All the nontoxic strains of the filamentous cyanobacterium Planktothrix that were isolated from 9 European countries were found to have lost 90% of a large micr...

journal_title：Molecular biology and evolution

authors： Christiansen G,Molitor C,Philmus B,Kurmayer R

更新日期：2008-08-01 00:00:00

abstract：:Measuring natural selection on genomic elements involved in the cis-regulation of gene expression--such as transcriptional enhancers and promoters--is critical for understanding the evolution of genomes, yet it remains a major challenge. Many studies have attempted to detect positive or negative selection in these non...

journal_title：Molecular biology and evolution

authors： Smith JD,McManus KF,Fraser HB

更新日期：2013-11-01 00:00:00

abstract：:The plant pathogen Phytophthora infestans emerged in Europe in 1845, triggering the Irish potato famine and massive European potato crop losses that continued until effective fungicides were widely employed in the 20th century. Today the pathogen is ubiquitous, with more aggressive and virulent strains surfacing in re...

journal_title：Molecular biology and evolution

authors： Martin MD,Ho SY,Wales N,Ristaino JB,Gilbert MT

更新日期：2014-06-01 00:00:00

abstract：:A statistical analysis of the nucleotide sequence variability in 14 published hepatitis B virus (HBV) genomes was carried out using parametric and nonparametric methods. A parametric statistical model revealed that the different regions of the genome differed significantly in their variability. The conclusion was supp...

journal_title：Molecular biology and evolution

authors： Lauder IJ,Lin HJ,Lau JY,Siu TS,Lai CL

更新日期：1993-03-01 00:00:00

abstract：:Discrepancies in phylogenetic trees of bacteria and archaea are often explained as lateral gene transfer events. However, such discrepancies may also be due to phylogenetic artifacts or orthology assignment problems. A first step that may help to resolve this dilemma is to estimate the extent of phylogenetic inconsist...

journal_title：Molecular biology and evolution

authors： Soria-Carrasco V,Castresana J

更新日期：2008-11-01 00:00:00

abstract：:How is adaptability generated in a system composed of interacting cellular machineries, each with a separate and functionally critical job to perform? The machinery for organelle inheritance is precisely one such system, requiring coordination between robust and ancient cellular modules, including the cell cycle, cyto...

journal_title：Molecular biology and evolution

authors： Mast FD,Rachubinski RA,Dacks JB

更新日期：2012-03-01 00:00:00

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

authors： Parfrey LW,Lahr DJ,Katz LA

更新日期：2008-04-01 00:00:00

abstract：:Genetic studies of Tibetans, an ethnic group with a long-lasting presence on the Tibetan Plateau which is known as the highest plateau in the world, may offer a unique opportunity to understand the biological adaptations of human beings to high-altitude environments. We conducted a genome-wide study of 1,000,000 genet...

journal_title：Molecular biology and evolution

authors： Xu S,Li S,Yang Y,Tan J,Lou H,Jin W,Yang L,Pan X,Wang J,Shen Y,Wu B,Wang H,Jin L

更新日期：2011-02-01 00:00:00

abstract：:Herpes simplex virus types 1 and 2 (HSV-1 and HSV-2) are ubiquitous human pathogens. Both viruses evolved from simplex viruses infecting African primates and they are thus thought to have left Africa during early human migrations. We analyzed the population structure of HSV-1 and HSV-2 circulating strains. Results ind...

journal_title：Molecular biology and evolution

authors： Forni D,Pontremoli C,Clerici M,Pozzoli U,Cagliani R,Sironi M

更新日期：2020-05-01 00:00:00

abstract：:There are many examples of groups (such as birds, bees, mammals, multicellular animals, and flowering plants) that have undergone a rapid radiation. In such cases, where there is a combination of short internal and long external branches, correctly estimating and rooting phylogenetic trees is known to be a difficult p...

journal_title：Molecular biology and evolution

authors： Shavit L,Penny D,Hendy MD,Holland BR

更新日期：2007-11-01 00:00:00

abstract：:Deciphering invasion routes from molecular data is crucial to understanding biological invasions, including identifying bottlenecks in population size and admixture among distinct populations. Here, we unravel the invasion routes of the invasive pest Drosophila suzukii using a multi-locus microsatellite dataset (25 lo...

journal_title：Molecular biology and evolution

authors： Fraimout A,Debat V,Fellous S,Hufbauer RA,Foucaud J,Pudlo P,Marin JM,Price DK,Cattel J,Chen X,Deprá M,François Duyck P,Guedot C,Kenis M,Kimura MT,Loeb G,Loiseau A,Martinez-Sañudo I,Pascual M,Polihronakis Richmond M,

更新日期：2017-04-01 00:00:00

abstract：:The order of genes on eukaryotic chromosomes is nonrandom. Some neighboring genes show order conservation among species, while some neighboring genes separate during evolution. Here, we investigated whether neighboring genes show interactions after their separation. We found that neighboring gene pairs tend to show in...

journal_title：Molecular biology and evolution

authors： Dai Z,Xiong Y,Dai X

更新日期：2014-05-01 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：:For populations to maintain optimal fitness, harmful mutations must be efficiently purged from the genome. Yet, under circumstances that diminish the effectiveness of natural selection, such as the process of plant and animal domestication, deleterious mutations are predicted to accumulate. Here, we compared the load ...

journal_title：Molecular biology and evolution

authors： Renaut S,Rieseberg LH

更新日期：2015-09-01 00:00:00