A New Formulation of Random Genetic Drift and Its Application to the Evolution of Cell Populations.

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 drift is defined by the WF model, it becomes stronger as the population size, N, decreases. However, the intensity of competition decreases when N decreases and, hence, drift might become weaker. To resolve the paradox, we propose that random drift be defined by the variance of "individual output", V(k) [k being the progeny number of each individual with the mean of E(k)], rather than by the WF sampling. If the distribution of k is known for any population, its strength of drift relative to a WF population of the same size, N, can be calculated. Generally, E(k) and V(k) should be density dependent but their relationships are different with or without competition, leading to opposite predictions on the efficiency of random drift as N changes. We apply the "individual output" model to asexual cell populations that are either unregulated (such as tumors) or negatively density-dependent (e.g., bacteria). In such populations, the efficiency of drift could be as low as <10% of that in WF populations. Interestingly, when N is below the carrying capacity, random drift could in fact increase as N increases. Growing asexual populations, especially tumors, may therefore be genetically even more heterogeneous than the high diversity estimated by some conventional models.

journal_name

Mol Biol Evol

authors

Chen Y,Tong D,Wu CI

doi

10.1093/molbev/msx161

subject

Has Abstract

pub_date

2017-08-01 00:00:00

pages

2057-2064

issue

8

eissn

0737-4038

issn

1537-1719

pii

3835633

journal_volume

34

pub_type

杂志文章
  • Alu-mediated acquisition of unstable ATTCT pentanucleotide repeats in the human ATXN10 gene.

    abstract::Spinocerebellar ataxia type 10 is caused by ATTCT repeat expansion in the ATXN10 gene in humans. We studied the evolutionary history of the human genome to determine the time and mechanism of the acquisition of unstable ATTCT repeats in the genome. We found that long interspersed element-1 (LINE-1) was inserted into A...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章

    doi:10.1093/molbev/msp172

    authors: Kurosaki T,Matsuura T,Ohno K,Ueda S

    更新日期:2009-11-01 00:00:00

  • Rampant Parasexuality Evolves in a Hospital Pathogen during Antibiotic Selection.

    abstract::Horizontal gene transfer threatens the therapeutic success of antibiotics by facilitating the rapid dissemination of resistance alleles among bacterial species. The conjugative mobile element Tn916 provides an excellent context for examining the role of adaptive parasexuality as it carries the tetracycline-resistance ...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章

    doi:10.1093/molbev/msv133

    authors: Beabout K,Hammerstrom TG,Wang TT,Bhatty M,Christie PJ,Saxer G,Shamoo Y

    更新日期:2015-10-01 00:00:00

  • Maintenance and Loss of Duplicated Genes by Dosage Subfunctionalization.

    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

    pub_type: 杂志文章

    doi:10.1093/molbev/msv095

    authors: Gout JF,Lynch M

    更新日期:2015-08-01 00:00:00

  • The Influence of Polyploidy on the Evolution of Yeast Grown in a Sub-Optimal Carbon Source.

    abstract::Polyploidization events have occurred during the evolution of many fungi, plant, and animal species and are thought to contribute to speciation and tumorigenesis, however little is known about how ploidy level contributes to adaptation at the molecular level. Here we integrate whole genome sequencing, RNA expression a...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章

    doi:10.1093/molbev/msx205

    authors: Scott AL,Richmond PA,Dowell RD,Selmecki AM

    更新日期:2017-10-01 00:00:00

  • A graphical method for detecting recombination in phylogenetic data sets.

    abstract::Current phylogenetic tree reconstruction methods assume that there is a single underlying tree topology for all sites along the sequence. The presence of mosaic sequences due to recombination violates this assumption and will cause phylogenetic methods to give misleading results due to the imposition of a single tree ...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章

    doi:10.1093/oxfordjournals.molbev.a025722

    authors: McGuire G,Wright F,Prentice MJ

    更新日期:1997-11-01 00:00:00

  • Predicting the Landscape of Recombination Using Deep Learning.

    abstract::Accurately inferring the genome-wide landscape of recombination rates in natural populations is a central aim in genomics, as patterns of linkage influence everything from genetic mapping to understanding evolutionary history. Here, we describe recombination landscape estimation using recurrent neural networks (ReLERN...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章

    doi:10.1093/molbev/msaa038

    authors: Adrion JR,Galloway JG,Kern AD

    更新日期:2020-06-01 00:00:00

  • Population structure in the American oyster as inferred by nuclear gene genealogies.

    abstract::Multiple haplotypes from each of three nuclear loci were isolated and sequenced from geographic populations of the American oyster, Crassostrea virginica. In tests of alternative phylogeographic hypotheses for this species, nuclear gene genealogies constructed for these haplotypes were compared to one another, to a mi...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章

    doi:10.1093/oxfordjournals.molbev.a025908

    authors: Hare MP,Avise JC

    更新日期:1998-02-01 00:00:00

  • Proteomics and comparative genomic investigations reveal heterogeneity in evolutionary rate of male reproductive proteins in mice (Mus domesticus).

    abstract::Male reproductive fitness is strongly affected by seminal fluid. In addition to interacting with the female environment, seminal fluid mediates important physiological characteristics of sperm, including capacitation and motility. In mammals, the male reproductive tract shows a striking degree of compartmentalization,...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章

    doi:10.1093/molbev/msp094

    authors: Dean MD,Clark NL,Findlay GD,Karn RC,Yi X,Swanson WJ,MacCoss MJ,Nachman MW

    更新日期:2009-08-01 00:00:00

  • A model of directional selection applied to the evolution of drug resistance in HIV-1.

    abstract::Understanding how pathogens acquire resistance to drugs is important for the design of treatment strategies, particularly for rapidly evolving viruses such as HIV-1. Drug treatment can exert strong selective pressures and sites within targeted genes that confer resistance frequently evolve far more rapidly than the ne...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章

    doi:10.1093/molbev/msm021

    authors: Seoighe C,Ketwaroo F,Pillay V,Scheffler K,Wood N,Duffet R,Zvelebil M,Martinson N,McIntyre J,Morris L,Hide W

    更新日期:2007-04-01 00:00:00

  • Endogenous lentiviral elements in the weasel family (Mustelidae).

    abstract::Endogenous retroviruses provide molecular fossils for studying the ancient evolutionary history of retroviruses. Here, we report our independent discovery and analysis of endogenous lentiviral insertions (Mustelidae endogenous lentivirus [MELV]) within the genomes of weasel family (Mustelidae). Genome-scale screening ...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章

    doi:10.1093/molbev/mss126

    authors: Han GZ,Worobey M

    更新日期:2012-10-01 00:00:00

  • Effective Population Size Predicts Local Rates but Not Local Mitigation of Read-through Errors.

    abstract::In correctly predicting that selection efficiency is positively correlated with the effective population size (Ne), the nearly neutral theory provides a coherent understanding of between-species variation in numerous genomic parameters, including heritable error (germline mutation) rates. Does the same theory also exp...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章

    doi:10.1093/molbev/msaa210

    authors: Ho AT,Hurst LD

    更新日期:2021-01-04 00:00:00

  • Tracing the evolutionary history of Drosophila regulatory regions with models that identify transcription factor binding sites.

    abstract::Much of evolutionary change is mediated at the level of gene expression, yet our understanding of regulatory evolution remains unsatisfying. In light of recent data indicating that transcription factor binding sites undergo substantial turnover between species, we attempt to quantify the process of binding site turnov...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章

    doi:10.1093/molbev/msg077

    authors: Dermitzakis ET,Bergman CM,Clark AG

    更新日期:2003-05-01 00:00:00

  • Divergence time of porcine reproductive and respiratory syndrome virus subtypes.

    abstract::Porcine reproductive and respiratory syndrome virus (PRRSV) recently emerged in domestic pigs of Western Europe and North America. Although time of emergence was identical on the two continents, genetic composition was markedly different with a clear geographical subtype structure, indicating that subtypes diverged in...

    journal_title:Molecular biology and evolution

    pub_type: 评论,信件

    doi:10.1093/molbev/msi208

    authors: Forsberg R

    更新日期:2005-11-01 00:00:00

  • Molecular phylogeny, biogeography, and habitat preference evolution of marsupials.

    abstract::Marsupials exhibit great diversity in ecology and morphology. However, compared with their sister group, the placental mammals, our understanding of many aspects of marsupial evolution remains limited. We use 101 mitochondrial genomes and data from 26 nuclear loci to reconstruct a dated phylogeny including 97% of exta...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章

    doi:10.1093/molbev/msu176

    authors: Mitchell KJ,Pratt RC,Watson LN,Gibb GC,Llamas B,Kasper M,Edson J,Hopwood B,Male D,Armstrong KN,Meyer M,Hofreiter M,Austin J,Donnellan SC,Lee MS,Phillips MJ,Cooper A

    更新日期:2014-09-01 00:00:00

  • Out of America to Africa or Asia: inference of dispersal histories using nuclear and plastid DNA and the S-RNase self-incompatibility locus.

    abstract::The plant genus Lycium (Solanaceae) originated in the Americas and includes approximately 85 species that are distributed worldwide. The vast majority of Old World species occur in southern Africa and eastern Asia. In this study, we examine biogeographic relationships among Old World species using a phylogenetic appro...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章

    doi:10.1093/molbev/msq253

    authors: Miller JS,Kamath A,Damashek J,Levin RA

    更新日期:2011-01-01 00:00:00

  • A test for heterotachy using multiple pairs of sequences.

    abstract::Heterotachy is a general term to describe positions that evolve at different rates in different lineages. Heterotachy also can generally be viewed as multivariate rates-across-sites variation, which can be described as randomly drawing rates (or branch lengths) from a multivariate distribution for each branch at each ...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章

    doi:10.1093/molbev/msq346

    authors: Wu J,Susko E

    更新日期:2011-05-01 00:00:00

  • Meiotic recombination dramatically decreased in thelytokous queens of the little fire ant and their sexually produced workers.

    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

    pub_type: 杂志文章

    doi:10.1093/molbev/msr082

    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

  • Effects of sequence alignment and structural domains of ribosomal DNA on phylogeny reconstruction for the protozoan family sarcocystidae.

    abstract::Finding correct species relationships using phylogeny reconstruction based on molecular data is dependent on several empirical and technical factors. These include the choice of DNA sequence from which phylogeny is to be inferred, the establishment of character homology within a sequence alignment, and the phylogeny a...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章

    doi:10.1093/oxfordjournals.molbev.a026285

    authors: Mugridge NB,Morrison DA,Jäkel T,Heckeroth AR,Tenter AM,Johnson AM

    更新日期:2000-12-01 00:00:00

  • Origin of a giant sex chromosome.

    abstract::Chromosome size and morphology vary within and among species, but little is known about the proximate or ultimate causes of these differences. Cichlid fish species in the tribe Oreochromini share an unusual giant chromosome that is ∼3 times longer than the other chromosomes. This giant chromosome functions as a sex ch...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章

    doi:10.1093/molbev/msaa319

    authors: Conte MA,Clark FE,Roberts RB,Xu L,Tao W,Zhou Q,Wang D,Kocher TD

    更新日期:2020-12-10 00:00:00

  • Loss of Heterozygosity Drives Adaptation in Hybrid Yeast.

    abstract::Hybridization is often considered maladaptive, but sometimes hybrids can invade new ecological niches and adapt to novel or stressful environments better than their parents. The genomic changes that occur following hybridization that facilitate genome resolution and/or adaptation are not well understood. Here, we exam...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章

    doi:10.1093/molbev/msx098

    authors: Smukowski Heil CS,DeSevo CG,Pai DA,Tucker CM,Hoang ML,Dunham MJ

    更新日期:2017-07-01 00:00:00

  • Efficient implementation of MrBayes on multi-GPU.

    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

    pub_type: 杂志文章

    doi:10.1093/molbev/mst043

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

    更新日期:2013-06-01 00:00:00

  • Characterization of the Cadherin-Catenin Complex of the Sea Anemone Nematostella vectensis and Implications for the Evolution of Metazoan Cell-Cell Adhesion.

    abstract::The cadherin-catenin complex (CCC) mediates cell-cell adhesion in bilaterian animals by linking extracellular cadherin-based adhesions to the actin cytoskeleton. However, it is unknown whether the basic organization of the complex is conserved across all metazoans. We tested whether protein interactions and actin-bind...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章

    doi:10.1093/molbev/msw084

    authors: Clarke DN,Miller PW,Lowe CJ,Weis WI,Nelson WJ

    更新日期:2016-08-01 00:00:00

  • Purifying selection detected in the plastid gene matK and flanking ribozyme regions within a group II intron of nonphotosynthetic plants.

    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

    pub_type: 杂志文章

    doi:10.1093/oxfordjournals.molbev.a026295

    authors: Young ND,dePamphilis CW

    更新日期:2000-12-01 00:00:00

  • Molecular population genetics of the alcohol dehydrogenase locus in the Hawaiian drosophilid D. mimica.

    abstract::Sequence variation among 10 alleles of the alcohol dehydrogenase (Adh) gene of the Hawaiian drosophilid D. mimica was analyzed with reference to the evolutionary history of the Hawaiian subgroup as well as to levels and patterns of polymorphism of the Adh gene in continental drosophilid species. The Adh gene of D. mim...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章

    doi:10.1093/oxfordjournals.molbev.a025582

    authors: Ayala FJ,Campbell CD,Selander RK

    更新日期:1996-12-01 00:00:00

  • Functional regulatory divergence of the innate immune system in interspecific Drosophila hybrids.

    abstract::In order to investigate divergence of immune regulation among Drosophila species, we have engaged in a study of innate immune function in F1 hybrids of Drosophila melanogaster and D. simulans. If pathways have diverged between the species such that incompatibilities have arisen between interacting components of the im...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章

    doi:10.1093/molbev/msq146

    authors: Hill-Burns EM,Clark AG

    更新日期:2010-11-01 00:00:00

  • Symbiotic origin of a novel actin gene in the cryptophyte Pyrenomonas helgolandii.

    abstract::Cryptophytes are photosynthetic protists that have acquired their plastids through the secondary symbiotic uptake of a red alga. A remarkable feature of cryptophytes is that they maintain a reduced form of the red algal nucleus, the nucleomorph, between the second and third plastid membranes (periplastidial compartmen...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章

    doi:10.1093/oxfordjournals.molbev.a026271

    authors: Stibitz TB,Keeling PJ,Bhattacharya D

    更新日期:2000-11-01 00:00:00

  • Statistical evaluation of the Rodin-Ohno hypothesis: sense/antisense coding of ancestral class I and II aminoacyl-tRNA synthetases.

    abstract::We tested the idea that ancestral class I and II aminoacyl-tRNA synthetases arose on opposite strands of the same gene. We assembled excerpted 94-residue Urgenes for class I tryptophanyl-tRNA synthetase (TrpRS) and class II Histidyl-tRNA synthetase (HisRS) from a diverse group of species, by identifying and catenating...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章

    doi:10.1093/molbev/mst070

    authors: Chandrasekaran SN,Yardimci GG,Erdogan O,Roach J,Carter CW Jr

    更新日期:2013-07-01 00:00:00

  • Evidence for positive selection on Drosophila melanogaster seminal fluid protease homologs.

    abstract::Proteins present in the seminal fluid of Drosophila melanogaster (accessory gland proteins Acps) contribute to female postmating behavioral changes, sperm storage, sperm competition, and immunity. Consequently, male-female coevolution and host-pathogen interactions are thought to underlie the rapid, adaptive evolution...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章

    doi:10.1093/molbev/msm270

    authors: Wong A,Turchin MC,Wolfner MF,Aquadro CF

    更新日期:2008-03-01 00:00:00

  • On the origins and admixture of Malagasy: new evidence from high-resolution analyses of paternal and maternal lineages.

    abstract::The Malagasy have been shown to be a genetically admixed population combining parental lineages with African and South East Asian ancestry. In the present paper, we fit the Malagasy admixture history in a highly resolved phylogeographic framework by typing a large set of mitochondrial DNA and Y DNA markers in unrelate...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章

    doi:10.1093/molbev/msp120

    authors: Tofanelli S,Bertoncini S,Castrì L,Luiselli D,Calafell F,Donati G,Paoli G

    更新日期:2009-09-01 00:00:00

  • Evolutionary origin and diversification of epidermal barrier proteins in amniotes.

    abstract::The evolution of amniotes has involved major molecular innovations in the epidermis. In particular, distinct structural proteins that undergo covalent cross-linking during cornification of keratinocytes facilitate the formation of mechanically resilient superficial cell layers and help to limit water loss to the envir...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章

    doi:10.1093/molbev/msu251

    authors: Strasser B,Mlitz V,Hermann M,Rice RH,Eigenheer RA,Alibardi L,Tschachler E,Eckhart L

    更新日期:2014-12-01 00:00:00