当前位置： SCI文献检索 > MOLECULAR BIOLOGY AND EVOLUTION期刊下所有文献 > Codon Usage Bias in Animals: Disentangling the Effects of Natural Selection, Effective Population Size, and GC-Biased Gene Conversion.

Codon Usage Bias in Animals: Disentangling the Effects of Natural Selection, Effective Population Size, and GC-Biased Gene Conversion.

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 in a handful of model organisms so far, and can be affected by confounding, nonadaptive processes such as GC-biased gene conversion and experimental artefacts. Using population transcriptomics data, we analyzed the relationship between codon usage, gene expression, allele frequency distribution, and recombination rate in 30 nonmodel species of animals, each from a different family, covering a wide range of effective population sizes. We disentangled the effects of translational selection and GC-biased gene conversion on codon usage by separately analyzing GC-conservative and GC-changing mutations. We report evidence for effective translational selection on codon usage in large-Ne species of animals, but not in small-Ne ones, in agreement with the nearly neutral theory of molecular evolution. C- and T-ending codons tend to be preferred over synonymous G- and A-ending ones, for reasons that remain to be determined. In contrast, we uncovered a conspicuous effect of GC-biased gene conversion, which is widespread in animals and the main force determining the fate of AT↔GC mutations. Intriguingly, the strength of its effect was uncorrelated with Ne.

journal_name

Mol Biol Evol

journal_title

Molecular biology and evolution

authors

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

doi

10.1093/molbev/msy015

subject

Has Abstract

pub_date

2018-05-01 00:00:00

pages

1092-1103

issue

5

eissn

0737-4038

issn

1537-1719

pii

4829954

journal_volume

35

pub_type

杂志文章

相关文献

MOLECULAR BIOLOGY AND EVOLUTION文献大全
  • Constraints on the evolution of plastid introns: the group II intron in the gene encoding tRNA-Val(UAC).

    abstract：:The evolution of the group II intron in the plastid gene encoding tRNA(Val)UAC (trnV) from seven plant taxa was studied by aligning secondary and other structural features. Levels of evolutionary divergence between six angiosperms and a liverwort, Marchantia polymorpha, were compared for the six domains commonly demon...

    journal_title：Molecular biology and evolution

    pub_type： 杂志文章

    doi：10.1093/oxfordjournals.molbev.a040765

    authors： Learn GH Jr,Shore JS,Furnier GR,Zurawski G,Clegg MT

    更新日期：1992-09-01 00:00:00

  • The application of a molecular clock based on molecular sequences and the fossil record to explain biogeographic distributions within the Alexandrium tamarense "species complex" (Dinophyceae).

    abstract：:The cosmopolitan dinoflagellate genus Alexandrium, and especially the A. tamarense species complex, contain both toxic and nontoxic strains. An understanding of their evolution and paleogeography is a necessary precursor to unraveling the development and spread of toxic forms. The inclusion of more strains into the ex...

    journal_title：Molecular biology and evolution

    pub_type： 杂志文章

    doi：10.1093/molbev/msg105

    authors： John U,Fensome RA,Medlin LK

    更新日期：2003-07-01 00:00:00

  • Mitochondrial DNA in the sea urchin Arbacia lixula: evolutionary inferences from nucleotide sequence analysis.

    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

    pub_type： 杂志文章

    doi：10.1093/oxfordjournals.molbev.a040661

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

    更新日期：1991-07-01 00:00:00

  • Evaluation of methods for determination of a reconstructed history of gene sequence evolution.

    abstract：:With whole-genome sequences being completed at an increasing rate, it is important to develop and assess tools to analyze them. Following annotation of the protein content of a genome, one can compare sequences with previously characterized homologous genes to detect novel functions within specific proteins in the evo...

    journal_title：Molecular biology and evolution

    pub_type： 杂志文章

    doi：10.1093/oxfordjournals.molbev.a003745

    authors： Liberles DA

    更新日期：2001-11-01 00:00:00

  • Analysis of piRNA-mediated silencing of active TEs in Drosophila melanogaster suggests limits on the evolution of host genome defense.

    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

    pub_type： 杂志文章

    doi：10.1093/molbev/mst081

    authors： Kelleher ES,Barbash DA

    更新日期：2013-08-01 00:00:00

  • Ancestral Function and Diversification of a Horizontally Acquired Oomycete Carboxylic Acid Transporter.

    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

    pub_type： 杂志文章

    doi：10.1093/molbev/msy082

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

    更新日期：2018-08-01 00:00:00

  • Divergence and Remarkable Diversity of the Y Chromosome in Guppies.

    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

    pub_type： 杂志文章

    doi：10.1093/molbev/msaa257

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

    更新日期：2021-01-23 00:00:00

  • Heads or tails: a simple reliability check for multiple sequence alignments.

    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

    pub_type： 杂志文章

    doi：10.1093/molbev/msm060

    authors： Landan G,Graur D

    更新日期：2007-06-01 00:00:00

  • Detecting Signatures of Positive Selection along Defined Branches of a Population Tree Using LSD.

    abstract：:Identifying the genomic basis underlying local adaptation is paramount to evolutionary biology, and bears many applications in the fields of conservation biology, crop, and animal breeding, as well as personalized medicine. Although many approaches have been developed to detect signatures of positive selection within ...

    journal_title：Molecular biology and evolution

    pub_type： 杂志文章

    doi：10.1093/molbev/msy053

    authors： Librado P,Orlando L

    更新日期：2018-06-01 00:00:00

  • A method of alignment masking for refining the phylogenetic signal of multiple sequence alignments.

    abstract：:Inaccurate inference of positional homologies in multiple sequence alignments and systematic errors introduced by alignment heuristics obfuscate phylogenetic inference. Alignment masking, the elimination of phylogenetically uninformative or misleading sites from an alignment before phylogenetic analysis, is a common p...

    journal_title：Molecular biology and evolution

    pub_type： 杂志文章

    doi：10.1093/molbev/mss264

    authors： Rajan V

    更新日期：2013-03-01 00:00:00

  • Investigation of loss and gain of introns in the compact genomes of pufferfishes (Fugu and Tetraodon).

    abstract：:We have investigated intron evolution in the compact genomes of 2 closely related species of pufferfishes, Fugu rubripes and Tetraodon nigroviridis, that diverged about 32 million years ago (MYA). Analysis of 148,028 aligned intron positions in 13,547 gene pairs using human as an outgroup identified 57 and 24 intron l...

    journal_title：Molecular biology and evolution

    pub_type： 杂志文章

    doi：10.1093/molbev/msm278

    authors： Loh YH,Brenner S,Venkatesh B

    更新日期：2008-03-01 00:00:00

  • Diminishing Returns on Intragenic Repeat Number Expansion in the Production of Signaling Peptides.

    abstract：:Signaling peptides enable communication between cells, both within and between individuals, and are therefore key to the control of complex physiological and behavioral responses. Since their small sizes prevent direct transmission to secretory pathways, these peptides are often produced as part of a larger polyprotei...

    journal_title：Molecular biology and evolution

    pub_type： 杂志文章

    doi：10.1093/molbev/msx243

    authors： Rogers DW,McConnell E,Miller EL,Greig D

    更新日期：2017-12-01 00:00:00

  • Translational selection on codon usage in Xenopus laevis.

    abstract：:A correspondence analysis of codon usage in Xenopus laevis revealed that the first axis is strongly correlated with the base composition at third codon positions. The second axis discriminates between putatively highly expressed genes and the other coding sequences, with expression levels being confirmed by the analys...

    journal_title：Molecular biology and evolution

    pub_type： 杂志文章

    doi：10.1093/oxfordjournals.molbev.a003958

    authors： Musto H,Cruveiller S,D'Onofrio G,Romero H,Bernardi G

    更新日期：2001-09-01 00:00:00

  • Global patterns of human DNA sequence variation in a 10-kb region on chromosome 1.

    abstract：:Human DNA variation is currently a subject of intense research because of its importance for studying human origins, evolution, and demographic history and for association studies of complex diseases. A approximately 10-kb region on chromosome 1, which contains only four small exons (each <155 bp), was sequenced for 6...

    journal_title：Molecular biology and evolution

    pub_type： 杂志文章

    doi：10.1093/oxfordjournals.molbev.a003795

    authors： Yu N,Zhao Z,Fu YX,Sambuughin N,Ramsay M,Jenkins T,Leskinen E,Patthy L,Jorde LB,Kuromori T,Li WH

    更新日期：2001-02-01 00:00:00

  • Adaptive Radiation of the Flukes of the Family Fasciolidae Inferred from Genome-Wide Comparisons of Key Species.

    abstract：:Liver and intestinal flukes of the family Fasciolidae cause zoonotic food-borne infections that impact both agriculture and human health throughout the world. Their evolutionary history and the genetic basis underlying their phenotypic and ecological diversity are not well understood. To close that knowledge gap, we c...

    journal_title：Molecular biology and evolution

    pub_type： 杂志文章

    doi：10.1093/molbev/msz204

    authors： Choi YJ,Fontenla S,Fischer PU,Le TH,Costábile A,Blair D,Brindley PJ,Tort JF,Cabada MM,Mitreva M

    更新日期：2020-01-01 00:00:00

  • FGF signaling emerged concomitantly with the origin of Eumetazoans.

    abstract：:Complex metazoan bodies require cell-to-cell communication for development, a process often mediated by signaling molecules binding to specific receptors. Relatively few signaling pathways have been recruited during evolution to build multicellular animals from unicellular zygotes. Of these few signaling pathways, one...

    journal_title：Molecular biology and evolution

    pub_type： 杂志文章

    doi：10.1093/molbev/mst222

    authors： Bertrand S,Iwema T,Escriva H

    更新日期：2014-02-01 00:00:00

  • Conserved motifs reveal details of ancestry and structure in the small TIM chaperones of the mitochondrial intermembrane space.

    abstract：:The mitochondrial inner and outer membranes are composed of a variety of integral membrane proteins, assembled into the membranes posttranslationally. The small translocase of the inner mitochondrial membranes (TIMs) are a group of approximately 10 kDa proteins that function as chaperones to ferry the imported protein...

    journal_title：Molecular biology and evolution

    pub_type： 杂志文章

    doi：10.1093/molbev/msm031

    authors： Gentle IE,Perry AJ,Alcock FH,Likić VA,Dolezal P,Ng ET,Purcell AW,McConnville M,Naderer T,Chanez AL,Charrière F,Aschinger C,Schneider A,Tokatlidis K,Lithgow T

    更新日期：2007-05-01 00:00:00

  • Phylogenetics in Caenorhabditis elegans: an analysis of divergence and outcrossing.

    abstract：:This study establishes a phylogenetic framework for the natural geographic isolates of the widely studied nematode species Caenorhabditis elegans. Virtually complete mitochondrial genomes are sequenced from 27 C. elegans natural isolates to characterize mitochondrial divergence patterns and to investigate the evolutio...

    journal_title：Molecular biology and evolution

    pub_type： 杂志文章

    doi：10.1093/molbev/msg044

    authors： Denver DR,Morris K,Thomas WK

    更新日期：2003-03-01 00:00:00

  • BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data.

    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

    pub_type： 杂志文章

    doi：10.1093/oxfordjournals.molbev.a025808

    authors： Gascuel O

    更新日期：1997-07-01 00:00:00

  • Hydrogen peroxide-induced gene expression across kingdoms: a comparative analysis.

    abstract：:Cells react to oxidative stress conditions by launching a defense response through the induction of nuclear gene expression. The advent of microarray technologies allowed monitoring of oxidative stress-dependent changes of transcript levels at a comprehensive and genome-wide scale, resulting in a series of inventories...

    journal_title：Molecular biology and evolution

    pub_type： 杂志文章,meta分析

    doi：10.1093/molbev/msm276

    authors： Vandenbroucke K,Robbens S,Vandepoele K,Inzé D,Van de Peer Y,Van Breusegem F

    更新日期：2008-03-01 00:00:00

  • Relative efficiencies of the maximum parsimony and distance-matrix methods in obtaining the correct phylogenetic tree.

    abstract：:The relative efficiencies of the maximum parsimony (MP) and distance-matrix methods in obtaining the correct tree (topology) were studied by using computer simulation. The distance-matrix methods examined are the neighbor-joining, distance-Wagner, Tateno et al. modified Farris, Faith, and Li methods. In the computer s...

    journal_title：Molecular biology and evolution

    pub_type： 杂志文章

    doi：10.1093/oxfordjournals.molbev.a040497

    authors： Sourdis J,Nei M

    更新日期：1988-05-01 00:00:00

  • Comparison of regulatory and structural regions of genes of tryptophan metabolism.

    abstract：:The genes of tryptophan biosynthesis are arranged and regulated differently in many microorganisms. Comparison of the transcription regulatory regions of the trp operons of several species of enterobacteria reveals that those sequences and structures believed to be essential for repression and attenuation control are ...

    journal_title：Molecular biology and evolution

    pub_type： 杂志文章

    doi：10.1093/oxfordjournals.molbev.a040307

    authors： Yanofsky C

    更新日期：1984-02-01 00:00:00

  • Tracing the Austronesian footprint in Mainland Southeast Asia: a perspective from mitochondrial DNA.

    abstract：:As the relic of the ancient Champa Kingdom, the Cham people represent the major Austronesian speakers in Mainland Southeast Asia (MSEA) and their origin is evidently associated with the Austronesian diffusion in MSEA. Hitherto, hypotheses stemming mainly from linguistic and cultural viewpoints on the origin of the Cha...

    journal_title：Molecular biology and evolution

    pub_type： 杂志文章

    doi：10.1093/molbev/msq131

    authors： Peng MS,Quang HH,Dang KP,Trieu AV,Wang HW,Yao YG,Kong QP,Zhang YP

    更新日期：2010-10-01 00:00:00

  • Model-based verification of hypotheses on the origin of modern Japanese revisited by Bayesian inference based on genome-wide SNP data.

    abstract：:Various hypotheses for the peopling of the Japanese archipelago have been proposed, which can be classified into three models: transformation, replacement, and hybridization. In recent years, one of the hybridization models ("dual-structure model") has been widely accepted. According to this model, Neolithic hunter-ga...

    journal_title：Molecular biology and evolution

    pub_type： 杂志文章

    doi：10.1093/molbev/msv045

    authors： Nakagome S,Sato T,Ishida H,Hanihara T,Yamaguchi T,Kimura R,Mano S,Oota H,Asian DNA Repository Consortium.

    更新日期：2015-06-01 00:00:00

  • Nucleotide sequence analysis of the human salivary protein genes HIS1 and HIS2, and evolution of the STATH/HIS gene family.

    abstract：:Human histatins are a family of low-M(r), neutral to very basic, histidine-rich salivary polypeptides. They probably function as part of the nonimmune host defense system in the oral cavity. A 39-kb region of DNA containing the HIS1 and HIS2 genes was isolated from two human genomic phage libraries as a series of over...

    journal_title：Molecular biology and evolution

    pub_type： 杂志文章

    doi：10.1093/oxfordjournals.molbev.a040022

    authors： Sabatini LM,Ota T,Azen EA

    更新日期：1993-05-01 00:00:00

  • Tracing the Archaeal Origins of Eukaryotic Membrane-Trafficking System Building Blocks.

    abstract：:In contrast to prokaryotes, eukaryotic cells are characterized by a complex set of internal membrane-bound compartments. A subset of these, and the protein machineries that move material between them, define the membrane-trafficking system (MTS), the emergence of which represents a landmark in eukaryotic evolution. Un...

    journal_title：Molecular biology and evolution

    pub_type： 杂志文章

    doi：10.1093/molbev/msw034

    authors： Klinger CM,Spang A,Dacks JB,Ettema TJ

    更新日期：2016-06-01 00:00:00

  • Evolution of CRISPs associated with toxicoferan-reptilian venom and mammalian reproduction.

    abstract：:Cysteine-rich secretory proteins (CRISPs) are glycoproteins found exclusively in vertebrates and have broad diversified functions. They are hypothesized to play important roles in mammalian reproduction and in reptilian venom, where they disrupt homeostasis of the prey through several mechanisms, including among other...

    journal_title：Molecular biology and evolution

    pub_type： 杂志文章

    doi：10.1093/molbev/mss058

    authors： Sunagar K,Johnson WE,O'Brien SJ,Vasconcelos V,Antunes A

    更新日期：2012-07-01 00:00:00

  • IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era.

    abstract：:IQ-TREE (http://www.iqtree.org, last accessed February 6, 2020) is a user-friendly and widely used software package for phylogenetic inference using maximum likelihood. Since the release of version 1 in 2014, we have continuously expanded IQ-TREE to integrate a plethora of new models of sequence evolution and efficien...

    journal_title：Molecular biology and evolution

    pub_type： 杂志文章

    doi：10.1093/molbev/msaa015

    authors： Minh BQ,Schmidt HA,Chernomor O,Schrempf D,Woodhams MD,von Haeseler A,Lanfear R

    更新日期：2020-05-01 00:00:00

  • Evolution at the tip and base of the X chromosome in an African population of Drosophila melanogaster.

    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

    pub_type： 杂志文章

    doi：10.1093/oxfordjournals.molbev.a040213

    authors： Begun DJ,Aquadro CF

    更新日期：1995-05-01 00:00:00

  • Molecular evolution and population genetics of duplicated accessory gland protein genes in Drosophila.

    abstract：:To investigate the potential importance of gene duplication in D. melanogaster accessory gland protein (Acp) gene evolution we carried out a computational analysis comparing annotated D. melanogaster Acp genes to the entire D. melanogaster genome. We found that two known Acp genes are actually members of small multige...

    journal_title：Molecular biology and evolution

    pub_type： 信件

    doi：10.1093/molbev/msh195

    authors： Holloway AK,Begun DJ

    更新日期：2004-09-01 00:00:00