Maximum-likelihood phylogenetic analysis under a covarion-like model.

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

abstract：:An attempt to use phylogenetic invariants for tree reconstruction was made at the end of the 80s and the beginning of the 90s by several researchers (the initial idea due to Lake [1987] and Cavender and Felsenstein [1987]). However, the efficiency of methods based on invariants is still in doubt (Huelsenbeck 1995; Jin...

journal_title：Molecular biology and evolution

authors： Casanellas M,Fernández-Sánchez J

更新日期：2007-01-01 00:00:00

abstract：:The structural genes for nitrogenase, nifK, nifD, and nifH, are crucial for nitrogen fixation. Previous phylogenetic analysis of the amino acid sequence of nifH suggested that this gene had been horizontally transferred from a proteobacterium to the gram-positive/cyanobacterial clade, although the confounding effects ...

journal_title：Molecular biology and evolution

authors： Hirsch AM,McKhann HI,Reddy A,Liao J,Fang Y,Marshall CR

更新日期：1995-01-01 00:00:00

abstract：:A large majority of bacterial genomes show strand asymmetry, such that G and T preferentially accumulate on the leading strand. The mechanisms are unknown, but cytosine deaminations are thought to play an important role. Here, we have examined DNA strand asymmetry in three strains of the aphid endosymbiont Buchnera ap...

journal_title：Molecular biology and evolution

authors： Klasson L,Andersson SG

更新日期：2006-05-01 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：: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：:The genotypic signature of spatially varying selection is ubiquitous across the Drosophila melanogaster genome. Spatially structured adaptive phenotypic differences are also commonly found, particularly along New World and Australian latitudinal gradients. However, investigation of gene expression variation in one or ...

journal_title：Molecular biology and evolution

authors： Levine MT,Eckert ML,Begun DJ

更新日期：2011-01-01 00:00:00

abstract：:Whole genome duplications (WGDs) have been hypothesized to be responsible for major transitions in evolution. However, the effects of WGD and subsequent gene loss on cellular behavior and metabolism are still poorly understood. Here we develop a genome scale evolutionary model to study the dynamics of gene loss and me...

journal_title：Molecular biology and evolution

authors： van Hoek MJ,Hogeweg P

更新日期：2009-11-01 00:00:00

abstract：:A major theoretical consequence of selection at a locus is the genetic hitchhiking of linked sites (selective sweep). The extent of hitchhiking around a gene is related to the strength of selection and the rate of recombination, with its impact diminishing with distance from the selected site. At the Rop-1 locus of th...

journal_title：Molecular biology and evolution

authors： Rose CJ,Chapman JR,Marshall SD,Lee SF,Batterham P,Ross HA,Newcomb RD

更新日期：2011-06-01 00:00:00

abstract：:Horizontal gene transfer (HGT) can equip organisms with novel genes, expanding the repertoire of genetic material available for evolutionary innovation and allowing recipient lineages to colonize new environments. However, few studies have characterized the functions of HGT genes experimentally or examined postacquisi...

journal_title：Molecular biology and evolution

authors： Savory FR,Milner DS,Miles DC,Richards TA

更新日期：2018-08-01 00:00:00

abstract：:We present the first molecular phylogenetic examination of the evolutionary position of retortamonads, a group of mitochondrion-lacking flagellates usually found as commensals of the intestinal tracts of vertebrates. Our phylogenies include small subunit ribosomal gene sequences from six retortamonad isolates-four fro...

journal_title：Molecular biology and evolution

authors： Silberman JD,Simpson AG,Kulda J,Cepicka I,Hampl V,Johnson PJ,Roger AJ

更新日期：2002-05-01 00:00:00

abstract：:The Piwi-interacting RNA (piRNA) pathway defends animal genomes against the harmful consequences of transposable element (TE) infection by imposing small-RNA-mediated silencing. Because silencing is targeted by TE-derived piRNAs, piRNA production is posited to be central to the evolution of genome defense. We harnesse...

journal_title：Molecular biology and evolution

authors： Kelleher ES,Barbash DA

更新日期：2013-08-01 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

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：:From the stirodont Arbacia lixula we determined the sequence of 5,127 nucleotides of mitochondrial DNA (mtDNA) encompassing 18 tRNAs, two complete coding genes, parts of three other coding genes, and part of the 12S ribosomal RNA (rRNA). The sequence confirms that the organization of mtDNA is conserved within echinoid...

journal_title：Molecular biology and evolution

authors： De Giorgi C,Lanave C,Musci MD,Saccone C

更新日期：1991-07-01 00:00:00

abstract：:Most phylogenetic models assume that the evolutionary process is stationary and reversible. In addition to being biologically improbable, these assumptions also impair inference by generating models under which the likelihood does not depend on the position of the root. Consequently, the root of the tree cannot be inf...

journal_title：Molecular biology and evolution

authors： Cherlin S,Heaps SE,Nye TMW,Boys RJ,Williams TA,Embley TM

更新日期：2018-04-01 00:00:00

abstract：:Large phylogenomics data sets require fast tree inference methods, especially for maximum-likelihood (ML) phylogenies. Fast programs exist, but due to inherent heuristics to find optimal trees, it is not clear whether the best tree is found. Thus, there is need for additional approaches that employ different search st...

journal_title：Molecular biology and evolution

authors： Nguyen LT,Schmidt HA,von Haeseler A,Minh BQ

更新日期：2015-01-01 00:00:00

abstract：:We present a new Bayesian method for estimating demographic and phylogenetic history using population genomic data. Several key innovations are introduced that allow the study of diverse models within an Isolation-with-Migration framework. The new method implements a 2-step analysis, with an initial Markov chain Monte...

journal_title：Molecular biology and evolution

authors： Chung Y,Hey J

更新日期：2017-06-01 00:00:00

abstract：:The giant extracellular hexagonal bilayer hemoglobin (HBL-Hb) of the deep-sea hydrothermal vent tube worm Riftia pachyptila is able to transport simultaneously O(2) and H(2)S in the blood from the gills to a specific organ: the trophosome that harbors sulfide-oxidizing endosymbionts. This vascular HBL-Hb is made of 14...

journal_title：Molecular biology and evolution

authors： Bailly X,Jollivet D,Vanin S,Deutsch J,Zal F,Lallier F,Toulmond A

更新日期：2002-09-01 00:00:00

abstract：:The diversity and evolution of bitter taste perception in mammals is not well understood. Recent discoveries of bitter taste receptor (T2R) genes provide an opportunity for a genetic approach to this question. We here report the identification of 10 and 30 putative T2R genes from the draft human and mouse genome seque...

journal_title：Molecular biology and evolution

authors： Shi P,Zhang J,Yang H,Zhang YP

更新日期：2003-05-01 00:00:00

abstract：:The elongation factor 1 alpha (EF-1 alpha) has become widely employed as a phylogenetic marker for studying eukaryotic evolution. However, a disturbing problem, the artifactual polyphyly of ciliates, is always observed. It has been suggested that the addition of new sequences will help to circumvent this problem. Thus...

journal_title：Molecular biology and evolution

authors： Moreira D,Le Guyader H,Philippe H

更新日期：1999-02-01 00:00:00

abstract：:Assessing the influence of three-dimensional protein structure on sequence evolution is a difficult task, mainly because of the assumption of independence between sites required by probabilistic phylogenetic methods. Recently, models that include an explicit treatment of protein structure and site interdependencies ha...

journal_title：Molecular biology and evolution

authors： Kleinman CL,Rodrigue N,Lartillot N,Philippe H

更新日期：2010-07-01 00:00:00

abstract：:The question of multiple sequence alignment quality has received much attention from developers of alignment methods. Less forthcoming, however, are practical measures for addressing alignment quality issues in real life settings. Here, we present a simple methodology to help identify and quantify the uncertainties in...

journal_title：Molecular biology and evolution

authors： Landan G,Graur D

更新日期：2007-06-01 00:00:00

abstract：:C repeats constitute the predominant family of short interspersed repeats (SINEs) in the rabbit genome. Determination of the nucleotide sequence 5' to rabbit zeta-globin genes reveals clusters of C repeats, and analysis of these and other sequenced regions of rabbit chromosomes shows that the C repeats have a strong t...

journal_title：Molecular biology and evolution

authors： Krane DE,Clark AG,Cheng JF,Hardison RC

更新日期：1991-01-01 00:00:00

abstract：:Based on previous observations that newly inserted LINEs and SINEs have particularly long 3' A-tails, which shorten rapidly during evolutionary time, we have analyzed the rat and mouse genomes for evidence of recently inserted SINEs and LINEs. We find that the youngest predicted subfamilies of rodent identifier (ID) e...

journal_title：Molecular biology and evolution

authors： Odom GL,Robichaux JL,Deininger PL

更新日期：2004-11-01 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 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

abstract：:The genomes are folded in a complex three-dimensional (3D) structure. Some features of this organization are common for all eukaryotes, but little is known about its evolution. Here, we have studied the 3D organization and regulation of zebrafish globin gene domain and compared its organization and regulation with tho...

journal_title：Molecular biology and evolution

authors： Kovina AP,Petrova NV,Gushchanskaya ES,Dolgushin KV,Gerasimov ES,Galitsyna AA,Penin AA,Flyamer IM,Ioudinkova ES,Gavrilov AA,Vassetzky YS,Ulianov SV,Iarovaia OV,Razin SV

更新日期：2017-06-01 00:00:00

abstract：:Many methods exist for detecting introgression between nonsister species, but the most commonly used require either a single sequence from four or more taxa or multiple sequences from each of three taxa. Here, we present a test for introgression that uses only a single sequence from three taxa. This test, denoted D3, ...

journal_title：Molecular biology and evolution

authors： Hahn MW,Hibbins MS

更新日期：2019-12-01 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