Evolution of closely linked gene pairs in vertebrate genomes.

abstract：:Photosystem II, the water oxidizing enzyme, altered the course of evolution by filling the atmosphere with oxygen. Here, we reconstruct the origin and evolution of water oxidation at an unprecedented level of detail by studying the phylogeny of all D1 subunits, the main protein coordinating the water oxidizing cluster...

journal_title：Molecular biology and evolution

authors： Cardona T,Murray JW,Rutherford AW

更新日期：2015-05-01 00:00:00

abstract：:Previous studies on human mitochondrial genomes showed that the ratio of intra-specific diversities at nonsynonymous-to-synonymous positions was two to ten times higher than the ratio of interspecific divergences at these positions, suggesting an excess of slightly deleterious nonsynonymous polymorphisms. However, suc...

journal_title：Molecular biology and evolution

authors： Subramanian S

更新日期：2011-01-01 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：:Convergent and parallel amino acid substitutions in protein evolution, collectively referred to as molecular convergence here, have small probabilities under neutral evolution. For this reason, molecular convergence is commonly viewed as evidence for similar adaptations of different species. The surge in the number of...

journal_title：Molecular biology and evolution

authors： Zou Z,Zhang J

更新日期：2015-08-01 00:00:00

abstract：:Cellular Ca(2+) homeostasis is tightly regulated and is pivotal to life. Inositol 1,4,5-trisphosphate receptors (IP3Rs) and ryanodine receptors (RyRs) are the major ion channels that regulate Ca(2+) release from intracellular stores. Although these channels have been extensively investigated in multicellular organisms...

journal_title：Molecular biology and evolution

authors： Alzayady KJ,Sebé-Pedrós A,Chandrasekhar R,Wang L,Ruiz-Trillo I,Yule DI

更新日期：2015-09-01 00:00:00

abstract：:Drosophila melanogaster, unlike mammals, has seven insulin-like peptides (DILPS). In Drosophila, all seven genes (dilp1-7) are single copy in the 12 species studied, except for D. grimshawi with two tandem copies of dilp2. Our comparative analysis revealed that genes dilp1-dilp7 exhibit differential functional constra...

journal_title：Molecular biology and evolution

authors： Guirao-Rico S,Aguadé M

更新日期：2011-05-01 00:00:00

abstract：:The third chromosome of Drosophila pseudoobscura is polymorphic for numerous gene arrangements that form classical clines in North America. The polytene salivary chromosomes isolated from natural populations revealed changes in gene order that allowed the different gene arrangements to be linked together by paracentri...

journal_title：Molecular biology and evolution

authors： Wallace AG,Detweiler D,Schaeffer SW

更新日期：2011-08-01 00:00:00

abstract：:Human c-Myb proto-oncogene is highly expressed in hematopoietic progenitors as well as leukemia and certain solid tumor. However, the regulatory mechanisms of its expression and biological functions remain largely unclear. Recently, c-Myb has been shown to be targeted by microRNA-150 (miR-150) which thereby controls B...

journal_title：Molecular biology and evolution

authors： Lin YC,Kuo MW,Yu J,Kuo HH,Lin RJ,Lo WL,Yu AL

更新日期：2008-10-01 00:00:00

abstract：:Whether coding or regulatory sequence change is more important to the evolution of phenotypic novelty is one of biology's major unresolved questions. The field of evo-devo has shown that in early development changes to regulatory regions are the dominant mode of genetic change, but whether this extends to the evolutio...

journal_title：Molecular biology and evolution

authors： Jasper WC,Linksvayer TA,Atallah J,Friedman D,Chiu JC,Johnson BR

更新日期：2015-02-01 00:00:00

abstract：:We have followed, in glucose-limited chemostats, the evolution of natural isolates of Escherichia coli possessing maximal growth rates of 0.48-1.43 doublings/h. Under these conditions a rapid-growth phenotype similar to that of standard laboratory wild-type strains was selected so that after 280 generations all of the...

journal_title：Molecular biology and evolution

authors： Mikkola R,Kurland CG

更新日期：1992-05-01 00:00:00

abstract：:To explore the origin of the diversity observed in natural populations, many studies have investigated the relationship between genotype and phenotype. In yeast species, especially in Saccharomyces cerevisiae, these studies are mainly conducted using recombinant offspring derived from two genetically diverse isolates,...

journal_title：Molecular biology and evolution

authors： Brion C,Caradec C,Pflieger D,Friedrich A,Schacherer J

更新日期：2020-09-01 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：:Male sexual behavior in the fruit fly Drosophila melanogaster is regulated by fruitless (fru), a sex-determination gene specifying the synthesis of BTB-Zn finger proteins that likely function as male-specific transcriptional regulators. Expression of fru in the nervous system specifies male sexual behavior and the mus...

journal_title：Molecular biology and evolution

authors： Gailey DA,Billeter JC,Liu JH,Bauzon F,Allendorfer JB,Goodwin SF

更新日期：2006-03-01 00:00:00

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

authors： Heineman RH,Bull JJ,Molineux IJ

更新日期：2009-06-01 00:00:00

abstract：:The guppy sex chromosomes show an extraordinary diversity in divergence across populations and closely related species. In order to understand the dynamics of the guppy Y chromosome, we used linked-read sequencing to assess Y chromosome evolution and diversity across upstream and downstream population pairs that vary ...

journal_title：Molecular biology and evolution

authors： Almeida P,Sandkam BA,Morris J,Darolti I,Breden F,Mank JE

更新日期：2021-01-23 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：: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：: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

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

abstract：:Genetic incompatibilities are commonly observed between hybridizing species. Although this type of isolating mechanism has received considerable attention, we have few examples describing how genetic incompatibilities evolve. We investigated the evolution of two loci involved in a classic example of a Bateson-Dobzhans...

journal_title：Molecular biology and evolution

authors： Scarpino SV,Hunt PJ,Garcia-De-Leon FJ,Juenger TE,Schartl M,Kirkpatrick M

更新日期：2013-10-01 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：:Comparing newly obtained and previously known nucleotide and amino-acid sequences underpins modern biological research. BLAST is a well-established tool for such comparisons but is challenging to use on new data sets. We combined a user-centric design philosophy with sustainable software development approaches to crea...

journal_title：Molecular biology and evolution

authors： Priyam A,Woodcroft BJ,Rai V,Moghul I,Munagala A,Ter F,Chowdhary H,Pieniak I,Maynard LJ,Gibbins MA,Moon H,Davis-Richardson A,Uludag M,Watson-Haigh NS,Challis R,Nakamura H,Favreau E,Gómez EA,Pluskal T,Leonard G,Rump

更新日期：2019-12-01 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：: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

authors： Clark MA,Moran NA,Baumann P

更新日期：1999-11-01 00:00:00

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

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

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

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

更新日期：2016-04-01 00:00:00

abstract：:We propose an improved version of the neighbor-joining (NJ) algorithm of Saitou and Nei. This new algorithm, BIONJ, follows the same agglomerative scheme as NJ, which consists of iteratively picking a pair of taxa, creating a new mode which represents the cluster of these taxa, and reducing the distance matrix by repl...

journal_title：Molecular biology and evolution

authors： Gascuel O

更新日期：1997-07-01 00:00:00

abstract：:We have evaluated the molecular evolution of the chemokine receptor CCR5 in primates. The chemokine receptor CCR5 serves as a major co-receptor for human immunodeficiency virus/simian immunodeficiency virus (HIV/SIV) infection. Knowledge of evolution of the CCR5 molecule and selection on the CCR5 gene may shed light o...

journal_title：Molecular biology and evolution

authors： Zhang YW,Ryder OA,Zhang YP

更新日期：2003-10-01 00:00:00

abstract：:The mitoribosome, as known from studies in model organisms, deviates considerably from its ancestor, the bacterial ribosome. Deviations include substantial reduction of the mitochondrial ribosomal RNA (mt-rRNA) structure and acquisition of numerous mitochondrion-specific (M) mitoribosomal proteins (mtRPs). A broadly a...

journal_title：Molecular biology and evolution

authors： Valach M,Alcazar JAG,Sarrasin M,Lang BF,Gray MW,Burger G

更新日期：2020-09-04 00:00:00

abstract：:Partial 18S rRNA sequence of the nemertine Cerebratulus lacteus was obtained and compared with those of coelomate metazoans and acoelomate platyhelminths to test whether nemertines share a most recent common ancestor with the platyhelminths, as traditionally has been implied, or whether nemertines lie within a protost...

journal_title：Molecular biology and evolution

authors： Turbeville JM,Field KG,Raff RA

更新日期：1992-03-01 00:00:00

abstract：:The similarity of certain reported angiosperm rDNA internal transcribed spacer (ITS) region sequences to those of green algae prompted our analysis of the deep-level phylogenetic signal in the highly conserved but short 5.8S and hypervariable ITS2 sequences. We found that 5.8S sequences yield phylogenetic trees simila...

journal_title：Molecular biology and evolution

authors： Hershkovitz MA,Lewis LA

更新日期：1996-11-01 00:00:00