Abstract:
:We investigate the effect of purifying selection at multiple sites on both the shape of the genealogy and the distribution of mutations on the tree. We find that the primary effect of purifying selection on a genealogy is to shift the distribution of mutations on the tree, whereas the shape of the tree remains largely unchanged. This result is relevant to the large number of coalescent estimation procedures, which generally assume neutrality for segregating polymorphisms--applying these estimators to evolutionarily constrained sequences could lead to a significant degree of bias. We also estimate the statistical power of several neutrality tests in detecting weak to moderate purifying selection and find that the power is quite good for some parameter combinations. This result contrasts with previous studies, which predicted low statistical power because of the minor effect that weak purifying selection has on the shape of a genealogy. Finally, we investigate the effect of Hill-Robertson interference among linked deleterious mutations on patterns of molecular variation. We find that dependence among selected loci can substantially reduce the efficacy of even fairly strong purifying selection.
journal_name
Mol Biol Evoljournal_title
Molecular biology and evolutionauthors
Williamson S,Orive MEdoi
10.1093/oxfordjournals.molbev.a004199subject
Has Abstractpub_date
2002-08-01 00:00:00pages
1376-84issue
8eissn
0737-4038issn
1537-1719journal_volume
19pub_type
杂志文章abstract::The Mlc1 gene of Drosophila melanogaster encodes two MLC1 isoforms via developmentally regulated alternative pre-mRNA splicing. In larval muscle and tubular and abdominal muscles of adults, all of the six exons are included in the spliced mRNA, whereas, in the fibrillar indirect flight muscle of adult, exon 5 is exclu...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a040043
更新日期:1993-07-01 00:00:00
abstract::The chemokine receptor CCR5 can serve as a coreceptor for M-tropic HIV-1 infection and both M-tropic and T-tropic SIV infection. We sequenced the entire CCR5 gene from 10 nonhuman primates: Pongo pygmaeus, Hylobates leucogenys, Trachypithecus francoisi, Trachypithecus phayrei, Pygathrix nemaeus, Rhinopithecus roxellan...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a026205
更新日期:1999-09-01 00:00:00
abstract::Inference of intraspecific population divergence patterns typically requires genetic data for molecular markers with relatively high mutation rates. Microsatellites, or short tandem repeat (STR) polymorphisms, have proven informative in many such investigations. These markers are characterized, however, by high levels...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msh212
更新日期:2004-10-01 00:00:00
abstract::Phenotypes and behaviors respond to resource constraints via adaptation, but the influence of ecological limitations on the composition of eukaryotic genomes is still unclear. We trace connections between plant ecology and genomes through their elemental composition. Inorganic sources of nitrogen (N) are severely limi...
journal_title:Molecular biology and evolution
pub_type: 信件
doi:10.1093/molbev/msp038
更新日期:2009-05-01 00:00:00
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
更新日期:2008-03-01 00:00:00
abstract::We use variation at a set of eight human Y chromosome microsatellite loci to investigate the demographic history of the Y chromosome. Instead of assuming a population of constant size, as in most of the previous work on the Y chromosome, we consider a model which permits a period of recent population growth. We show t...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a026091
更新日期:1999-12-01 00:00:00
abstract::Adaptive evolution at the molecular level can be studied by detecting convergent and parallel evolution at the amino acid sequence level. For a set of homologous protein sequences, the ancestral amino acids at all interior nodes of the phylogenetic tree of the proteins can be statistically inferred. The amino acid sit...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a025789
更新日期:1997-05-01 00:00:00
abstract::The ability to survey polymorphism on a genomic scale has enabled genome-wide scans for the targets of natural selection. Theory that connects patterns of genetic variation to evidence of natural selection most often assumes a diallelic locus and no recurrent mutation. Although these assumptions are suitable to select...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/mss247
更新日期:2013-02-01 00:00:00
abstract::There is increasing evidence that dosage compensation is not a ubiquitous feature following sex chromosome evolution, especially not in organisms where females are the heterogametic sex, like in birds. Even when it occurs, compensation can be incomplete and limited to dosage-sensitive genes. However, previous work has...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msv147
更新日期:2015-10-01 00:00:00
abstract::The high frequency of alternative splicing among the serine/arginine-rich (SR) family of proteins in plants has been linked to important roles in gene regulation during development and in response to environmental stress. In this article, we have searched and manually annotated all the SR proteins in the genomes of ma...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/mst238
更新日期:2014-03-01 00:00:00
abstract::Lichen-forming fungi, in symbiotic associations with algae, frequently have nuclear small subunit ribosomal DNA (SSU rDNA) longer than the 1,800 nucleotides typical for eukaryotes. The lichen-forming ascomycetous fungus Lecanora dispersa contains insertions at eight distinct positions of its SSU rDNA; the lichen-formi...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a040199
更新日期:1995-03-01 00:00:00
abstract::DNA supercoiling is the master function that interconnects chromosome structure and global gene transcription. This function has recently been shown to be under strong selection in Escherichia coli. During the evolution of 12 initially identical populations propagated in a defined environment for 20,000 generations, p...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msq099
更新日期:2010-09-01 00:00:00
abstract::Transfer RNA (tRNA) is essential for the translation of genetic information into proteins, and understanding its molecular evolution is important if we are to understand the genetic code. In general, long variable-arm (V-arm) structures form in tRNA(Leu), tRNA(Ser), and bacterial and organellar tRNA(Tyr). However, as ...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msv253
更新日期:2016-02-01 00:00:00
abstract::Polymerases are essential for life, being responsible for replication, transcription, and the repair of nucleic acid molecules. Those that share a right-hand-shaped fold and catalytic site structurally similar to the DNA polymerase I of Escherichia coli may catalyze RNA- or DNA-dependent RNA polymerization, reverse tr...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msu219
更新日期:2014-10-01 00:00:00
abstract::The increased interest in asexual organisms calls for in-depth studies of asexual complexes that actively give rise to new clones. We present an extensive molecular study of the Otiorhynchus scaber (Coleoptera, Curculionidae) weevil system. Three forms have traditionally been recognized: diploid sexuals, triploid, and...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msg180
更新日期:2003-10-01 00:00:00
abstract::Restriction site variations in nuclear ribosomal DNA (rDNA) spacers and mitochondrial DNA (mtDNA) were examined in several populations of mole rats with variable numbers of chromosomes, which represented the two superspecies Spalax leucodon (2n = 38, 54, or 62) and Spalax ehrenbergi (2n = 52, 54, 58, or 60). Sequence ...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a025574
更新日期:1996-01-01 00:00:00
abstract::Directional evolution in microsatellites is the tendency for microsatellites either to increase or to decrease in size over time between populations. We analyzed 99 microsatellite loci in a sample of 193 maize plants representing the entire pre-Columbian range of this crop for evidence of directional evolution. We too...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msg156
更新日期:2003-09-01 00:00:00
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
更新日期:2000-12-01 00:00:00
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
更新日期:2011-05-01 00:00:00
abstract::We describe a stochastic birth-and-death model of evolution of horizontally transferred genes in microbial populations. The model is a generalization of the stochastic model described by Berg and Kurland and includes five parameters: the rate of mutational inactivation, selection coefficient, invasion rate (i.e., rate...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msi167
更新日期:2005-08-01 00:00:00
abstract::When bacteria evolve resistance against a particular antibiotic, they may simultaneously gain increased sensitivity against a second one. Such collateral sensitivity may be exploited to develop novel, sustainable antibiotic treatment strategies aimed at containing the current, dramatic spread of drug resistance. To da...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msx158
更新日期:2017-09-01 00:00:00
abstract::The ParaHox and Hox gene clusters control aspects of animal anterior-posterior development and are related as paralogous evolutionary sisters. Despite this relationship, it is not clear if the clusters operate in similar ways, with similar constraints. To compare clusters, we examined the transposable-element (TE) con...
journal_title:Molecular biology and evolution
pub_type: 信件
doi:10.1093/molbev/msp235
更新日期:2010-02-01 00:00:00
abstract::In chickens, there is a single functional gene (VH1) coding for the heavy chain variable region of immunoglobulins, and immunoglobulin diversity is generated by gene conversion of the VH1 gene by many variable region pseudogenes (psi VH's) that exist on the 5' side of the VH1 gene. To understand the evolution of this ...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a040194
更新日期:1995-01-01 00:00:00
abstract::Horizontal gene transfer (HGT) has been described as a common mechanism of transferring genetic material between prokaryotes, whereas genetic transfers from eukaryotes to prokaryotes have been rarely documented. Here we report a rare case of HGT in which plant expansin genes that code for plant cell-wall loosening pro...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/mst206
更新日期:2014-02-01 00:00:00
abstract::Although many phylogenetic studies have focused on developing hypotheses about relationships, advances in data collection and computation have increased the feasibility of collecting large independent data sets to rigorously test controversial hypotheses or carefully assess artifacts that may be misleading. One such r...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msr230
更新日期:2012-02-01 00:00:00
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
更新日期:1997-07-01 00:00:00
abstract::The fully sequenced chloroplast genomes of maize (subfamily Panicoideae), rice (subfamily Bambusoideae), and wheat (subfamily Pooideae) provide the unique opportunity to investigate the evolution of chloroplast genes and genomes in the grass family (Poaceae) by whole-genome comparison. Analyses of nucleotide sequence ...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a004033
更新日期:2002-12-01 00:00:00
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
更新日期:2004-09-01 00:00:00
abstract::Males and females often have marked phenotypic differences, and the expression of these dissimilarities invariably involves sex differences in gene expression. Sex-biased gene expression has been well characterized in animal species, where a high proportion of the genome may be differentially regulated in males and fe...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msv049
更新日期:2015-06-01 00:00:00
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
更新日期:2021-01-04 00:00:00