Strong asymmetric mutation bias in endosymbiont genomes coincide with loss of genes for replication restart pathways.

abstract：:The Sm family of proteins is closely associated with RNA metabolism throughout all life. These proteins form homomorphic and heteromorphic rings consisting of six or seven subunits with a characteristic central pore, the presence of which is critical for binding U-rich regions of single-stranded RNA. Eubacteria and Ar...

journal_title：Molecular biology and evolution

authors： Scofield DG,Lynch M

更新日期：2008-11-01 00:00:00

abstract：:MrBayes, using Metropolis-coupled Markov chain Monte Carlo (MCMCMC or (MC)(3)), is a popular program for Bayesian inference. As a leading method of using DNA data to infer phylogeny, the (MC)(3) Bayesian algorithm and its improved and parallel versions are now not fast enough for biologists to analyze massive real-wor...

journal_title：Molecular biology and evolution

authors： Bao J,Xia H,Zhou J,Liu X,Wang G

更新日期：2013-06-01 00:00:00

abstract：:Alcohol dehydrogenase genes were amplified by PCR, cloned, and sequenced from 11 putative nonhybrid species of the angiosperm genus Paeonia. Sequences of five exons and six intron regions of the Adh gene were used to reconstruct the phylogeny of these species. Two paralogous genes, Adh1A, and Adh2, were found; an addi...

journal_title：Molecular biology and evolution

authors： Sang T,Donoghue MJ,Zhang D

更新日期：1997-10-01 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：:Traditionally, living cetaceans (order Cetacea) are classified into two highly distinct suborders: the echolocating toothed whales, Odontoceti, and the filter-feeding baleen whales, Mysticeti. A molecular phylogeny based on 1,352 base pairs of two mitochondrial ribosomal gene segments and the mitochondrial cytochrome ...

journal_title：Molecular biology and evolution

authors： Milinkovitch MC,Meyer A,Powell JR

更新日期：1994-11-01 00:00:00

abstract：:In a striking contrast, matK is one of the most rapidly evolving plastid genes and also one of the few plastid genes to be retained in all nonphotosynthetic plants examined to date. DNA sequences of this region were obtained from photosynthetic and nonphotosynthetic plants of Orobanchaceae and their relatives. The res...

journal_title：Molecular biology and evolution

authors： Young ND,dePamphilis CW

更新日期：2000-12-01 00:00:00

abstract：:We measured nucleotide variability within and between the three semispecies of the Drosophila athabasca complex, at the period (per) gene by using a polymerase chain reaction-based four-cutter restriction-enzyme analysis. The levels of polymorphism varied considerably between the three semispecies. Our results for per...

journal_title：Molecular biology and evolution

authors： Ford MJ,Yoon CK,Aquadro CF

更新日期：1994-03-01 00:00:00

abstract：:With growing amounts of genome data and constant improvement of models of molecular evolution, phylogenetic reconstruction became more reliable. However, our knowledge of the real process of molecular evolution is still limited. When enough large-sized data sets are analyzed, any subtle biases in statistical models ca...

journal_title：Molecular biology and evolution

authors： Kitazoe Y,Kishino H,Okabayashi T,Watabe T,Nakajima N,Okuhara Y,Kurihara Y

更新日期：2005-03-01 00:00:00

abstract：:Wolbachia bacteria infect about half of all arthropods, with diverse and extreme consequences ranging from sex-ratio distortion and mating incompatibilities to protection against viruses. These phenotypic effects, combined with efficient vertical transmission from mothers to offspring, satisfactorily explain the invas...

journal_title：Molecular biology and evolution

authors： Bailly-Bechet M,Martins-Simões P,Szöllosi GJ,Mialdea G,Sagot MF,Charlat S

更新日期：2017-05-01 00:00:00

abstract：:When bacteria evolve resistance against a particular antibiotic, they may simultaneously gain increased sensitivity against a second one. Such collateral sensitivity may be exploited to develop novel, sustainable antibiotic treatment strategies aimed at containing the current, dramatic spread of drug resistance. To da...

journal_title：Molecular biology and evolution

authors： Barbosa C,Trebosc V,Kemmer C,Rosenstiel P,Beardmore R,Schulenburg H,Jansen G

更新日期：2017-09-01 00:00:00

abstract：:Statistical methods for computing the standard errors of the branching points of an evolutionary tree are developed. These methods are for the unweighted pair-group method-determined (UPGMA) trees reconstructed from molecular data such as amino acid sequences, nucleotide sequences, restriction-sites data, and electrop...

journal_title：Molecular biology and evolution

authors： Nei M,Stephens JC,Saitou N

更新日期：1985-01-01 00:00:00

abstract：:The fully sequenced chloroplast genomes of maize (subfamily Panicoideae), rice (subfamily Bambusoideae), and wheat (subfamily Pooideae) provide the unique opportunity to investigate the evolution of chloroplast genes and genomes in the grass family (Poaceae) by whole-genome comparison. Analyses of nucleotide sequence ...

journal_title：Molecular biology and evolution

authors： Matsuoka Y,Yamazaki Y,Ogihara Y,Tsunewaki K

更新日期：2002-12-01 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：:The serial coalescent extends traditional coalescent theory to include genealogies in which not all individuals were sampled at the same time. Inference in this framework is powerful because population size and evolutionary rate may be estimated independently. However, when the sequences in question are affected by se...

journal_title：Molecular biology and evolution

authors： O'Fallon BD

更新日期：2011-11-01 00:00:00

abstract：:Debate on the adaptive origins of primates has long focused on the functional ecology of the primate visual system. For example, it is hypothesized that variable expression of short- (SWS1) and middle-to-long-wavelength sensitive (M/LWS) opsins, which confer color vision, can be used to infer ancestral activity patter...

journal_title：Molecular biology and evolution

authors： Melin AD,Wells K,Moritz GL,Kistler L,Orkin JD,Timm RM,Bernard H,Lakim MB,Perry GH,Kawamura S,Dominy NJ

更新日期：2016-04-01 00:00:00

abstract：:The activation peptide of mammalian trypsinogens contains a highly conserved tetra-aspartate sequence (D19-D20-D21-D22) preceding the K23-I24 scissile peptide bond, which is hydrolyzed as the first step in the activation process. Here, we examined the evolution and function of trypsinogen activation peptides through i...

journal_title：Molecular biology and evolution

authors： Chen JM,Kukor Z,Le Maréchal C,Tóth M,Tsakiris L,Raguénès O,Férec C,Sahin-Tóth M

更新日期：2003-11-01 00:00:00

abstract：:The detection of selection, both positive and negative, acting on a DNA sequence or class of nucleotide sites requires comparison with a reference sequence that is unaffected by selection. In Drosophila, recent findings of widespread selective constraint, as well as adaptive evolution, in both coding and noncoding reg...

journal_title：Molecular biology and evolution

authors： Parsch J,Novozhilov S,Saminadin-Peter SS,Wong KM,Andolfatto P

更新日期：2010-06-01 00:00:00

abstract：:Untangling the root of the evolutionary tree of placental mammals has been nearly an impossible task. The good news is that only three possibilities are seriously considered. The bad news is that all three possibilities are seriously considered. Paleontologists favor a root anchored by Xenarthra (e.g., sloths and ante...

journal_title：Molecular biology and evolution

authors： Teeling EC,Hedges SB

更新日期：2013-09-01 00:00:00

abstract：:A cDNA that encodes the heart-type lactate dehydrogenase (LDH-B) from the teleost fish Fundulus heteroclitus was cloned and sequenced. The protein encoded by the cDNA was analyzed in relation to 13 LDH proteins from a variety of taxa. One of the deductions from this analysis is that LDH-B proteins have residues in the...

journal_title：Molecular biology and evolution

authors： Crawford DL,Constantino HR,Powers DA

更新日期：1989-07-01 00:00:00

abstract：:Previous studies have shown that genes that are expressed predominantly or exclusively in males tend to evolve rapidly in comparison to other genes. In most cases, however, it is unknown whether this rapid evolution is the result of increased positive (or sexual) selection on male-expressed traits or if it is due to a...

journal_title：Molecular biology and evolution

authors： Zhang Z,Parsch J

更新日期：2005-10-01 00:00:00

abstract：:The orientation of closely linked genes in mammalian genomes is not random: there are more head-to-head (h2h) gene pairs than expected. To understand the origin of this enrichment in h2h gene pairs, we have analyzed the phylogenetic distribution of gene pairs separated by less than 600 bp of intergenic DNA (gene duos)...

journal_title：Molecular biology and evolution

authors： Franck E,Hulsen T,Huynen MA,de Jong WW,Lubsen NH,Madsen O

更新日期：2008-09-01 00:00:00

abstract：:Detecting positive selection in species with heterogeneous habitats and complex demography is notoriously difficult and prone to statistical biases. The model plant Arabidopsis thaliana exemplifies this problem: In spite of the large amounts of data, little evidence for classic selective sweeps has been found. Moreove...

journal_title：Molecular biology and evolution

authors： Huber CD,Nordborg M,Hermisson J,Hellmann I

更新日期：2014-11-01 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：:Here, we present a study of the molecular evolution of the pheromone receptor genes (pre-1 and pre-2) in Neurospora taxa with different mating systems. We focus on comparisons between heterothallic and homothallic taxa, reproducing sexually by outcrossing and by intrahaploid selfing, respectively. Our general aim was ...

journal_title：Molecular biology and evolution

authors： Nygren K,Strandberg R,Gioti A,Karlsson M,Johannesson H

更新日期：2012-12-01 00:00:00

abstract：:A phylogenetic analysis of sex-chromosomal zinc-finger genes (Zfx and Zfy) indicates that the genes have not evolved completely independently since their initial separation. The sequence similarities suggest gene conversion in the last exon between the duplicated Y-chromosomal genes Zfy-1 and Zfy-2 in the mouse. There...

journal_title：Molecular biology and evolution

authors： Pamilo P,Bianchi NO

更新日期：1993-03-01 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

abstract：:Whole-genome duplications (WGDs) have contributed to gene-repertoire enrichment in many eukaryotic lineages. However, most duplicated genes are eventually lost and it is still unclear why some duplicated genes are evolutionary successful whereas others quickly turn to pseudogenes. Here, we show that dosage constraints...

journal_title：Molecular biology and evolution

authors： Gout JF,Lynch M

更新日期：2015-08-01 00:00:00

abstract：:4.5SH RNA is a 94-nt small RNA with unknown function. This RNA is known to be present in the mouse, rat, and hamster cells; however, it is not found in human, rabbit, and chicken. In the mouse genome, the 4.5SH RNA gene is a part of a long (4.2 kb) tandem repeat ( approximately 800 copies) unit. Here, we found that 4....

journal_title：Molecular biology and evolution

authors： Gogolevskaya IK,Koval AP,Kramerov DA

更新日期：2005-07-01 00:00:00

abstract：:The complete mitochondrial genome of Tupaia belangeri, a representative of the eutherian order Scandentia, was determined and compared with full-length mitochondrial sequences of other eutherian orders described to date. The complete mitochondrial genome is 16, 754 nt in length, with no obvious deviation from the gene...

journal_title：Molecular biology and evolution

authors： Schmitz J,Ohme M,Zischler H

更新日期：2000-09-01 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