Homoplasy and distribution of AFLP fragments: an analysis in silico of the genome of different species.

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

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

abstract：:A simple model for the evolution of the rate of molecular evolution is presented. With a Bayesian approach, this model can serve as the basis for estimating dates of important evolutionary events even in the absence of the assumption of constant rates among evolutionary lineages. The method can be used in conjunction ...

journal_title：Molecular biology and evolution

authors： Thorne JL,Kishino H,Painter IS

更新日期：1998-12-01 00:00:00

abstract：:The spontaneous deamination of cytosine produces uracil mispaired with guanine in DNA, which will produce a mutation, unless repaired. In all domains of life, uracil-DNA glycosylases (UDGs) are responsible for the elimination of uracil from DNA. Thus, UDGs contribute to the integrity of the genetic information and the...

journal_title：Molecular biology and evolution

authors： Lucas-Lledó JI,Maddamsetti R,Lynch M

更新日期：2011-03-01 00:00:00

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

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

abstract：:The AID/APOBEC family (comprising AID, APOBEC1, APOBEC2, and APOBEC3 subgroups) contains members that can deaminate cytidine in RNA and/or DNA and exhibit diverse physiological functions (AID and APOBEC3 deaminating DNA to trigger pathways in adaptive and innate immunity; APOBEC1 mediating apolipoprotein B RNA editing...

journal_title：Molecular biology and evolution

authors： Conticello SG,Thomas CJ,Petersen-Mahrt SK,Neuberger MS

更新日期：2005-02-01 00:00:00

abstract：:Polyploidization events have occurred during the evolution of many fungi, plant, and animal species and are thought to contribute to speciation and tumorigenesis, however little is known about how ploidy level contributes to adaptation at the molecular level. Here we integrate whole genome sequencing, RNA expression a...

journal_title：Molecular biology and evolution

authors： Scott AL,Richmond PA,Dowell RD,Selmecki AM

更新日期：2017-10-01 00:00:00

abstract：:Proteins present in the seminal fluid of Drosophila melanogaster (accessory gland proteins Acps) contribute to female postmating behavioral changes, sperm storage, sperm competition, and immunity. Consequently, male-female coevolution and host-pathogen interactions are thought to underlie the rapid, adaptive evolution...

journal_title：Molecular biology and evolution

authors： Wong A,Turchin MC,Wolfner MF,Aquadro CF

更新日期：2008-03-01 00:00:00

abstract：:Novel coronaviruses, including SARS-CoV-2, SARS, and MERS, often originate from recombination events. The mechanism of recombination in RNA viruses is template switching. Coronavirus transcription also involves template switching at specific regions, called transcriptional regulatory sequences (TRS). It is hypothesize...

journal_title：Molecular biology and evolution

authors： Yang Y,Yan W,Hall AB,Jiang X

更新日期：2020-11-04 00:00:00

abstract：:Several recent analyses have used quartet-based methods to assess the congruence among phylogenies derived for large sets of genes from prokaryotic genomes. The principal conclusion from these studies is that lateral gene transfer (LGT) has blurred prokaryotic phylogenies to such a degree that the darwinian scheme of ...

journal_title：Molecular biology and evolution

authors： Daubin V,Ochman H

更新日期：2004-01-01 00:00:00

abstract：:Interbreeding between hatchery-reared and wild fish, through deliberate stocking or escapes from fish farms, can result in rapid phenotypic and gene expression changes in hybrids, but the underlying mechanisms are unknown. We assessed if one generation of captive breeding was sufficient to generate inter- and/or trans...

journal_title：Molecular biology and evolution

authors： Rodriguez Barreto D,Garcia de Leaniz C,Verspoor E,Sobolewska H,Coulson M,Consuegra S

更新日期：2019-10-01 00:00:00

abstract：:We report the presence of four nuclear paralogs of a 380-bp segment of cytochrome b in callitrichine primates (marmosets and tamarins). The mitochondrial cytochrome b sequence and each nuclear paralog were obtained from several species, allowing multiple comparisons of rates and patterns of substitution both between m...

journal_title：Molecular biology and evolution

authors： Mundy NI,Pissinatti A,Woodruff DS

更新日期：2000-07-01 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：:During the last 60 years, the inversion polymorphism on the third chromosome of Drosophila pseudoobscura has become a case study of the evolution of linked blocks of genes, isolated from each other by the suppression of recombination in heterozygotes for different inversions. Due to its location within inverted region...

journal_title：Molecular biology and evolution

authors： Popadić A,Popadić D,Anderson WW

更新日期：1995-09-01 00:00:00

abstract：:A novel algorithm, GS-Aligner, that uses bit-level operations was developed for aligning genomic sequences. GS-Aligner is efficient in terms of both time and space for aligning two very long genomic sequences and for identifying genomic rearrangements such as translocations and inversions. It is suitable for aligning ...

journal_title：Molecular biology and evolution

authors： Shih AC,Li WH

更新日期：2003-08-01 00:00:00

abstract：:That natural selection affects molecular evolution at synonymous sites in protein-coding sequences is well established and is thought to predominantly reflect selection for translational efficiency/accuracy mediated through codon bias. However, a recently developed maximum likelihood framework, when applied to 18 codi...

journal_title：Molecular biology and evolution

authors： Singh ND,Bauer DuMont VL,Hubisz MJ,Nielsen R,Aquadro CF

更新日期：2007-12-01 00:00:00

abstract：:The DnaK-DnaJ-GrpE (KJE) chaperone system functions at the fulcrum of protein homeostasis in bacteria. It interacts both with nascent polypeptides and with proteins that have become unfolded, either funneling its clients toward the native state or ushering misfolded proteins into degradation. In line with its key role...

journal_title：Molecular biology and evolution

authors： Warnecke T

更新日期：2012-11-01 00:00:00

abstract：:Two longstanding issues on the molecular clock hypothesis are studied in this article. First, is there a global molecular clock in mammals? Although many authors have observed unequal rates of nucleotide substitution among mammalian lineages, some authors have proposed a global clock for all eutherians, i.e., a single...

journal_title：Molecular biology and evolution

authors： Yi S,Ellsworth DL,Li WH

更新日期：2002-12-01 00:00:00

abstract：:Insertions and deletions (indels) in protein-coding genes are important sources of genetic variation. Their role in creating new proteins may be especially important after gene duplication. However, little is known about how indels affect the divergence of duplicate genes. We here study thousands of duplicate genes in...

journal_title：Molecular biology and evolution

authors： Guo B,Zou M,Wagner A

更新日期：2012-10-01 00:00:00

abstract：:In Arabidopsis, stem cell homeostasis in the shoot apical meristem (SAM) is controlled by a feedback loop between WUS and CLV functions. We have identified WUS orthologues in maize and rice by a detailed phylogenetic analysis of the WOX gene family and subsequent cloning. A single WUS orthologue is present in the rice...

journal_title：Molecular biology and evolution

authors： Nardmann J,Werr W

更新日期：2006-12-01 00:00:00

abstract：:Taxonomic congruence and total evidence are competing paradigms in phylogenetic inference. Taxonomic congruence focuses on deriving a consensus from the results obtained from separately analyzed data sets, whereas total evidence uses character congruence in the search for the best-fitting hypothesis for all of the ava...

journal_title：Molecular biology and evolution

authors： Eernisse DJ,Kluge AG

更新日期：1993-11-01 00:00:00

abstract：:The number of subunits of RNA polymerases (RNAPs) increases during evolution from 5 in eubacteria to 12 in archaea. In eukaryotes, which have at least three RNAPs, the number of subunits has expanded from 12 in RNA polymerase II (RNAPII) to 14 in RNA polymerase I (RNAPI) and to 17 in RNA polymerase III (RNAPIII). It w...

journal_title：Molecular biology and evolution

authors： Carter R,Drouin G

更新日期：2010-05-01 00:00:00

abstract：:Cryptophytes are photosynthetic protists that have acquired their plastids through the secondary symbiotic uptake of a red alga. A remarkable feature of cryptophytes is that they maintain a reduced form of the red algal nucleus, the nucleomorph, between the second and third plastid membranes (periplastidial compartmen...

journal_title：Molecular biology and evolution

authors： Stibitz TB,Keeling PJ,Bhattacharya D

更新日期：2000-11-01 00:00:00

abstract：:The ribosome is responsible for protein synthesis in all living organisms. It is best known to exist around 3.5-3.7 Ga whereat life on Earth inhabited anoxic environment with abundant soluble irons. The RNAs and proteins are the two biopolymers that constitute the ribosome. However, both proteins and RNAs require meta...

journal_title：Molecular biology and evolution

authors： Lin SY,Wang YC,Hsiao C

更新日期：2019-05-01 00:00:00

abstract：:Rubisco (ribulose-1,5-bisphosphate carboxylase/oxygenase; EC 4.1.1.39), the most abundant protein in nature, catalyzes the assimilation of CO(2) (worldwide about 10(11) t each year) by carboxylation of ribulose-1,5-bisphosphate. It is a hexadecamer consisting of eight large and eight small subunits. Although the Rubis...

journal_title：Molecular biology and evolution

authors： Schwarte S,Tiedemann R

更新日期：2011-06-01 00:00:00

abstract：:A 32-kb region including the Adh structural gene was analyzed with six restriction endonucleases in 20 lines of Drosophila pseudoobscura, one line of D. persimilis, and one line of D. miranda. Nineteen lines of D. pseudoobscura from a single population were estimated to be polymorphic at one in every 15 nucleotides (p...

journal_title：Molecular biology and evolution

authors： Schaeffer SW,Aquadro CF,Anderson WW

更新日期：1987-05-01 00:00:00

abstract：:Selection on codon usage bias is well documented in a number of microorganisms. Whether codon usage is also generally shaped by natural selection in large organisms, despite their relatively small effective population size (Ne), is unclear. In animals, the population genetics of codon usage bias has only been studied ...

journal_title：Molecular biology and evolution

authors： Galtier N,Roux C,Rousselle M,Romiguier J,Figuet E,Glémin S,Bierne N,Duret L

更新日期：2018-05-01 00:00:00

abstract：:Analysis of mitochondrial DNA restriction fragment length polymorphism in European anchovy (Engraulis encrasicolus) revealed a large number of mitotypes that form two distinct clusters (phylads). Phylad A consists of one common mitotype and many rare secondary mitotypes that are one mutational step removed from the ma...

journal_title：Molecular biology and evolution

authors： Magoulas A,Tsimenides N,Zouros E

更新日期：1996-01-01 00:00:00

abstract：:Lichen-forming fungi, in symbiotic associations with algae, frequently have nuclear small subunit ribosomal DNA (SSU rDNA) longer than the 1,800 nucleotides typical for eukaryotes. The lichen-forming ascomycetous fungus Lecanora dispersa contains insertions at eight distinct positions of its SSU rDNA; the lichen-formi...

journal_title：Molecular biology and evolution

authors： Gargas A,DePriest PT,Taylor JW

更新日期：1995-03-01 00:00:00

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

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

更新日期：2006-05-01 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