Abstract:
:This paper concludes that the statistical properties of protein evolution are compatible with a particular model of evolution by natural selection. The argument begins with a statistical description of the molecular clock based on a Poisson process with a randomly varying tick rate. If the time scale of the change of the tick rate of the molecular clock is assumed to be much less than the average time between substitutions, then it is shown that the substitution process must be episodic, with bursts of substitutions being separated by long periods of time with no substitutions. This analysis generalizes the recent work of Gillespie (1984a). The second part of the argument shows that a simple model of evolution by natural selection--one that incorporates a changing environment, the molecular landscape, and a simple form of epistasis--exhibits dynamics that are identical to those inferred from the statistical analysis. This leads to the conclusion that natural selection is a viable explanation for protein evolution. In addition, a correction formula for multiple substitutions is given that does not require that the substitution process be a Poisson process, and some comments on the inability of the neutral allele theory to account for the dynamics of the substitution process are presented.
journal_name
Mol Biol Evoljournal_title
Molecular biology and evolutionauthors
Gillespie JHdoi
10.1093/oxfordjournals.molbev.a040382subject
Has Abstractpub_date
1986-03-01 00:00:00pages
138-55issue
2eissn
0737-4038issn
1537-1719journal_volume
3pub_type
杂志文章abstract::Rubisco, the primary photosynthetic carboxylase, evolved 3-4 billion years ago in an anaerobic, high CO(2) atmosphere. The combined effect of low CO(2) and high O(2) levels in the modern atmosphere, and the inability of Rubisco to distinguish completely between CO(2) and O(2), leads to the occurrence of an oxygenation...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msq335
更新日期:2011-04-01 00:00:00
abstract::Two recent studies have presented conflicting views on variation present within the 294 base third domain of the 12S rRNA gene in the genus Drosophila, and in D. pseudoobscura in particular. One study suggested that this gene is highly invariant across the genus, while another recovered 22 distinct haplotypes from 22 ...
journal_title:Molecular biology and evolution
pub_type: 评论,杂志文章
doi:10.1093/oxfordjournals.molbev.a026374
更新日期:2000-06-01 00:00:00
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
更新日期:2007-05-01 00:00:00
abstract::The evolution of DNA base composition evolution is simplified to a six-parameter model when there are no strand biases for mutation and selection. We analyzed the dynamics of this model with special attention to the influence of a change in substitution rates. The G + C content of the DNA sequence tends to an equilibr...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a026156
更新日期:1999-06-01 00:00:00
abstract::This study describes the distribution of hobo-hybridizing sequences in the genus Drosophila. Southern blot analysis of 134 species revealed that hobo sequences are limited to the melanogaster and montium subgroups of the melanogaster-species group. Of the hobo-bearing species, only D. melanogaster and two of its sibli...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a040625
更新日期:1990-11-01 00:00:00
abstract::Standard methods of phylogenetic reconstruction are based on models that assume homogeneity of nucleotide composition among taxa. However, this assumption is often violated in biological data sets. In this study, we examine possible effects of nucleotide heterogeneity among lineages on the phylogenetic reconstruction ...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msi036
更新日期:2005-03-01 00:00:00
abstract::Bacterial plasmids substantially contribute to the rapid spread of antibiotic resistance, which is a crisis in healthcare today. Coevolution of plasmids and their hosts promotes this spread of resistance by ameliorating the cost of plasmid carriage. However, our knowledge of plasmid-bacteria coevolution is solely base...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msaa024
更新日期:2020-06-01 00:00:00
abstract::Lineage-specific gene duplications contribute to a large variation in specialized metabolites among different plant species. There is also considerable variability in the specialized metabolites within a single plant species. However, it is unclear whether copy number variations (CNVs) derived from gene duplication ev...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msx234
更新日期:2017-12-01 00:00:00
abstract::A highly abundant satellite DNA comprising 17% of the Tribolium castaneum (Insecta, Coleoptera) genome was cloned and sequenced. The satellite monomer is 360 bp long, has a high A+T content of 73%, and lacks significant internal substructures. The sequence variability is 3.6%, essentially due to random distribution of...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a025668
更新日期:1996-10-01 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
pub_type: 杂志文章
doi:10.1093/molbev/msv348
更新日期:2016-04-01 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
pub_type: 杂志文章
doi:10.1093/molbev/msv091
更新日期:2015-08-01 00:00:00
abstract::Phylogeny estimation is extremely crucial in the study of molecular evolution. The increase in the amount of available genomic data facilitates phylogeny estimation from multilocus sequence data. Although maximum likelihood and Bayesian methods are available for phylogeny reconstruction using multilocus sequence data,...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msn043
更新日期:2008-05-01 00:00:00
abstract::It is well known that molecular data "saturates" with increasing sequence divergence (thereby losing phylogenetic information) and that in addition the accumulation of misleading information due to chance similarities or to systematic bias may accompany saturation as well. Exploratory data analysis methods that can qu...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msm139
更新日期:2007-09-01 00:00:00
abstract::Crabs of the infra-order Brachyura are one of the most diverse groups of crustaceans with approximately 7,000 described species in 98 families, occurring in marine, freshwater, and terrestrial habitats. The relationships among the brachyuran families are poorly understood due to the high morphological complexity of th...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msu068
更新日期:2014-05-01 00:00:00
abstract::The RIIIS/J inbred mouse strain is a model for type 1 von Willebrand disease (VWD), a common human bleeding disorder. Low von Willebrand factor (VWF) levels in RIIIS/J are due to a regulatory mutation, Mvwf1, which directs a tissue-specific switch in expression of a glycosyltransferase, B4GALNT2, from intestine to blo...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msn284
更新日期:2009-03-01 00:00:00
abstract::Plasticity and robustness of signaling pathways partly rely on genetic redundancy, although the precise mechanism that provides functional specificity to the different redundant elements in a given process is often unknown. In Arabidopsis, functional redundancy in gibberellin signaling has been largely attributed to t...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msq012
更新日期:2010-06-01 00:00:00
abstract::Herpes simplex virus types 1 and 2 (HSV-1 and HSV-2) are ubiquitous human pathogens. Both viruses evolved from simplex viruses infecting African primates and they are thus thought to have left Africa during early human migrations. We analyzed the population structure of HSV-1 and HSV-2 circulating strains. Results ind...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msaa001
更新日期:2020-05-01 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
pub_type: 杂志文章
doi:10.1093/molbev/msl153
更新日期:2007-01-01 00:00:00
abstract::In all anthropoid species, the coding region of the involucrin gene contains a segment of short tandem repeats that were added sequentially, beginning in a common anthropoid ancestor. The involucrin coding region of each of two platyrrhine species, the white-fronted capuchin (Cebus albifrons) and the cottontop tamarin...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a040674
更新日期:1991-09-01 00:00:00
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
更新日期:2008-03-01 00:00:00
abstract::Herpesviruses have been infecting and codiverging with their vertebrate hosts for hundreds of millions of years. The primate simplex viruses exemplify this pattern of virus-host codivergence, at a minimum, as far back as the most recent common ancestor of New World monkeys, Old World monkeys, and apes. Humans are the ...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msu185
更新日期:2014-09-01 00:00:00
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
更新日期:2009-08-01 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
pub_type: 杂志文章
doi:10.1093/molbev/msu247
更新日期:2014-11-01 00:00:00
abstract::Chemosensory genes are frequently the target of positive selection and are often present in large gene families, but little is known about heterogeneity of selection in these cases and its relation to function. Here, we use the vomeronasal-1 receptor (V1R) repertoire of mouse lemurs (Microcebus spp.) as a model system...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/mss188
更新日期:2012-12-01 00:00:00
abstract::Cytochrome c oxidase (COX) consists of 13 subunits, 3 encoded in the mitochondrial genome and 10 in the nucleus. Little is known of the role of the nuclear-encoded subunits, some of which exhibit tissue-specific isoforms. Subunit VIa is unique in having tissue-specific isoforms in all mammalian species examined. We ex...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a025798
更新日期:1997-06-01 00:00:00
abstract::Analysis of mitochondrial DNA restriction fragment length polymorphism in European anchovy (Engraulis encrasicolus) revealed a large number of mitotypes that form two distinct clusters (phylads). Phylad A consists of one common mitotype and many rare secondary mitotypes that are one mutational step removed from the ma...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a025554
更新日期:1996-01-01 00:00:00
abstract::Here we use phylogenomics with expressed sequence tag (EST) data from the ecologically important coccolithophore-forming alga Emiliania huxleyi and the plastid-lacking cryptophyte Goniomonas cf. pacifica to establish their phylogenetic positions in the eukaryotic tree. Haptophytes and cryptophytes are members of the p...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msm089
更新日期:2007-08-01 00:00:00
abstract::The spontaneous deamination of cytosine produces uracil mispaired with guanine in DNA, which will produce a mutation, unless repaired. In all domains of life, uracil-DNA glycosylases (UDGs) are responsible for the elimination of uracil from DNA. Thus, UDGs contribute to the integrity of the genetic information and the...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msq318
更新日期:2011-03-01 00:00:00
abstract::Recent studies have linked demographic changes and epidemiological patterns in bacterial populations using coalescent-based approaches. We identified 26 studies using skyline plots and found that 21 inferred overall population expansion. This surprising result led us to analyze the impact of natural selection, recombi...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msw048
更新日期:2016-07-01 00:00:00
abstract::This review explores features of the origin and evolution of colicins in Escherichia coli. First, the evolutionary relationships of 16 colicin and colicin-related proteins are inferred from amino acid and DNA sequence comparisons. These comparisons are employed to detail the evolutionary mechanisms involved in the ori...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a040081
更新日期:1993-11-01 00:00:00