IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies.

abstract：:Random genetic drift, or stochastic change in gene frequency, is a fundamental evolutionary force that is usually defined within the ideal Wright-Fisher (WF) population. However, as the theory is increasingly applied to populations that deviate strongly from the ideal model, a paradox of random drift has emerged. When...

journal_title：Molecular biology and evolution

authors： Chen Y,Tong D,Wu CI

更新日期：2017-08-01 00:00:00

abstract：:We performed a genealogical analysis of the ionotropic glutamate receptor (iGluR) gene family, which includes the animal iGluRs and the newly isolated glutamate receptor-like genes (GLR) of plants discovered in Arabidopsis. Distance measures firmly placed the plant GLR genes within the iGluR clade as opposed to other ...

journal_title：Molecular biology and evolution

authors： Chiu J,DeSalle R,Lam HM,Meisel L,Coruzzi G

更新日期：1999-06-01 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：:A novel family of non-long-terminal-repeat (non-LTR) retrotransposons, named MosquI, was discovered in the yellow fever mosquito, Aedes aegypti. There were approximately 14 copies of MosquI in the A. aegypti genome. Four of the five analyzed MosquI elements were truncated at the 5' ends while one of them, MosquI-Aa2, ...

journal_title：Molecular biology and evolution

authors： Tu Z,Hill JJ

更新日期：1999-12-01 00:00:00

abstract：:About half of the mammalian genome is composed of retroposons. Long interspersed elements (LINEs) and short interspersed elements (SINEs) are the most abundant repetitive elements and account for about 21% and 13% of the human genome, respectively. SINEs have been detected in all major mammalian lineages, except for t...

journal_title：Molecular biology and evolution

authors： Churakov G,Smit AF,Brosius J,Schmitz J

更新日期：2005-04-01 00:00:00

abstract：:The malaria parasite's chloroquine resistance transporter (CRT) is an integral membrane protein localized to the parasite's acidic digestive vacuole. The function of CRT is not known and the protein was originally described as a transporter simply because it possesses 10 transmembrane domains. In wild-type (chloroquin...

journal_title：Molecular biology and evolution

authors： Martin RE,Kirk K

更新日期：2004-10-01 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 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：:Approximately 100 strains derived from natural populations of Drosophila melanogaster were tested for the presence or absence of P-element sequences by using two molecular probes derived from internal regions of a full-sized P element. Strains that had been collected from several continents at varying times during the...

journal_title：Molecular biology and evolution

authors： Anxolabéhère D,Kidwell MG,Periquet G

更新日期：1988-05-01 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：: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：:Parasitoid wasps use venom to manipulate the immunity and metabolism of their host insects in a variety of ways to provide resources for their offspring. Yet, how genes are recruited and evolve to perform venom functions remain open questions. A recently recognized source of eukaryotic genome innovation is lateral gen...

journal_title：Molecular biology and evolution

authors： Martinson EO,Martinson VG,Edwards R,Mrinalini,Werren JH

更新日期：2016-04-01 00:00:00

abstract：:Multilocus sequence typing (MLST) is a recently developed nucleotide sequence-based method for the definitive assignment of isolates within bacterial populations to specific clones. MLST uses the same principles as multilocus enzyme electrophoresis and provides data that can be used to investigate aspects of the popul...

journal_title：Molecular biology and evolution

authors： Feil EJ,Maiden MC,Achtman M,Spratt BG

更新日期：1999-11-01 00:00:00

abstract：:Serum response factor (SRF) and myocyte enhancer factor 2 (MEF2) represent two types of members of the MCM1, AGAMOUS, DEFICIENS, and SRF (MADS)-box transcription factor family present in animals and fungi. Each type has distinct biological functions, which are reflected by the distinct specificities of the proteins bo...

journal_title：Molecular biology and evolution

authors： Wu W,Huang X,Cheng J,Li Z,de Folter S,Huang Z,Jiang X,Pang H,Tao S

更新日期：2011-01-01 00:00:00

abstract：:The capacity to biomineralize is closely linked to the rapid expansion of animal life during the early Cambrian, with many skeletonized phyla first appearing in the fossil record at this time. The appearance of disparate molluscan forms during this period leaves open the possibility that shells evolved independently a...

journal_title：Molecular biology and evolution

authors： Jackson DJ,McDougall C,Woodcroft B,Moase P,Rose RA,Kube M,Reinhardt R,Rokhsar DS,Montagnani C,Joubert C,Piquemal D,Degnan BM

更新日期：2010-03-01 00:00:00

abstract：:Positive selection sites (PSSs), a class of amino acid sites with an excess of nonsynonymous to synonymous substitutions, are indicators of adaptive molecular evolution and have been detected in many protein families involved in a diversity of biological processes by statistical approaches. However, few studies are co...

journal_title：Molecular biology and evolution

authors： Zhu L,Peigneur S,Gao B,Zhang S,Tytgat J,Zhu S

更新日期：2016-08-01 00:00:00

abstract：:Copy number variants (CNVs) within humans can have both adaptive and deleterious effects. Because of their phenotypic significance, researchers have attempted to find single nucleotide polymorphisms (SNPs) in high linkage disequilibrium (LD) with CNVs to use in genomewide association studies. However, studies have fou...

journal_title：Molecular biology and evolution

authors： Schrider DR,Hahn MW

更新日期：2010-01-01 00:00:00

abstract：:TATA box, the core promoter element, exists in a broad range of eukaryotes, and the expression of TATA-containing genes usually responds to various environmental stresses. Hence, the evolution of TATA-box in duplicate genes may provide some clues for the interrelationship among environmental stress, expression differe...

journal_title：Molecular biology and evolution

authors： Zou Y,Huang W,Gu Z,Gu X

更新日期：2011-10-01 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：:The little fire ant, Wasmannia auropunctata, displays a peculiar breeding system polymorphism. Classical haplo-diploid sexual reproduction between reproductive individuals occurs in some populations, whereas, in others, queens and males reproduce clonally. Workers are produced sexually and are sterile in both clonal a...

journal_title：Molecular biology and evolution

authors： Rey O,Loiseau A,Facon B,Foucaud J,Orivel J,Cornuet JM,Robert S,Dobigny G,Delabie JH,Mariano Cdos S,Estoup A

更新日期：2011-09-01 00:00:00

abstract：:Animal venoms have evolved many times. Venomous species are especially common in three of the four main groups of arthropods (Chelicerata, Myriapoda, and Hexapoda), which together represent tens of thousands of species of venomous spiders, scorpions, centipedes, and hymenopterans. Surprisingly, despite their great div...

journal_title：Molecular biology and evolution

authors： von Reumont BM,Blanke A,Richter S,Alvarez F,Bleidorn C,Jenner RA

更新日期：2014-01-01 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：:The SLiM forward genetic simulation framework has proved to be a powerful and flexible tool for population genetic modeling. However, as a complex piece of software with many features that allow simulating a diverse assortment of evolutionary models, its initial learning curve can be difficult. Here we provide a step-...

journal_title：Molecular biology and evolution

authors： Haller BC,Messer PW

更新日期：2019-05-01 00:00:00

abstract：:TYRO3, AXL, and MERTK (TAM) receptors are a family of receptor tyrosine kinases that maintain homeostasis through the clearance of apoptotic cells, and when defective, contribute to chronic inflammatory and autoimmune diseases such as atherosclerosis, multiple sclerosis, systemic lupus erythematosus, rheumatoid arthri...

journal_title：Molecular biology and evolution

authors： Evans AL,Blackburn JWD,Taruc K,Kipp A,Dirk BS,Hunt NR,Barr SD,Dikeakos JD,Heit B

更新日期：2017-07-01 00:00:00

abstract：:The nuclear large subunit (LSU) rRNA gene is a rich source of phylogenetic characters because of its large size, mosaic of slowly and rapidly evolving regions, and complex secondary structure variation. Nevertheless, many studies have indicated that inconsistency, bias, and gene-specific error (e.g., within-individual...

journal_title：Molecular biology and evolution

authors： Omilian AR,Taylor DJ

更新日期：2001-12-01 00:00:00

abstract：:Chromosomal DNA from 23 closely related, pathogenic strains of Escherichia coli was digested and probed for the insertion sequences IS1, IS2, IS4, IS5, and IS30. Under the assumption that elements residing in DNA restriction fragments of the same apparent length are identical by descent, parsimony analysis of these ch...

journal_title：Molecular biology and evolution

authors： Lawrence JG,Dykhuizen DE,DuBose RF,Hartl DL

更新日期：1989-01-01 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 emergence of islands has been linked to spectacular radiations of diverse organisms. Although penguins spend much of their lives at sea, they rely on land for nesting, and a high proportion of extant species are endemic to geologically young islands. Islands may thus have been crucial to the evolutionary diversifi...

journal_title：Molecular biology and evolution

authors： Cole TL,Ksepka DT,Mitchell KJ,Tennyson AJD,Thomas DB,Pan H,Zhang G,Rawlence NJ,Wood JR,Bover P,Bouzat JL,Cooper A,Fiddaman SR,Hart T,Miller G,Ryan PG,Shepherd LD,Wilmshurst JM,Waters JM

更新日期：2019-04-01 00:00:00

abstract：:Disease response genes (DRGs) diverge under recurrent positive selection as a result of a molecular arms race between hosts and pathogens. Most of these studies were conducted in animals, and few defense genes have been shown to evolve adaptively in plants. To test for adaptation in the molecules mediating disease res...

journal_title：Molecular biology and evolution

authors： Zamora A,Sun Q,Hamblin MT,Aquadro CF,Kresovich S

更新日期：2009-09-01 00:00:00

abstract：:We examine rate heterogeneity among evolutionary lineages of the grass family at two plasmid loci, ndhF and rbcL, and we introduce a method to determine whether patterns of rate heterogeneity are correlated between loci. We show both that rates of synonymous evolution are heterogeneous among grass lineages and that ar...

journal_title：Molecular biology and evolution

authors： Gaut BS,Clark LG,Wendel JF,Muse SV

更新日期：1997-07-01 00:00:00