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 explain variation in phenotypic error rates and in abundance of error mitigation mechanisms? Translational read-through provides a model to investigate both issues as it is common, mostly nonadaptive, and has good proxy for rate (TAA being the least leaky stop codon) and potential error mitigation via "fail-safe" 3' additional stop codons (ASCs). Prior theory of translational read-through has suggested that when population sizes are high, weak selection for local mitigation can be effective thus predicting a positive correlation between ASC enrichment and Ne. Contra to prediction, we find that ASC enrichment is not correlated with Ne. ASC enrichment, although highly phylogenetically patchy, is, however, more common both in unicellular species and in genes expressed in unicellular modes in multicellular species. By contrast, Ne does positively correlate with TAA enrichment. These results imply that local phenotypic error rates, not local mitigation rates, are consistent with a drift barrier/nearly neutral model.
journal_name
Mol Biol Evoljournal_title
Molecular biology and evolutionauthors
Ho AT,Hurst LDdoi
10.1093/molbev/msaa210subject
Has Abstractpub_date
2021-01-04 00:00:00pages
244-262issue
1eissn
0737-4038issn
1537-1719pii
5892771journal_volume
38pub_type
杂志文章abstract::Previous studies have shown that splicing efficiency, and thus maturation of pre-mRNA, depends on the correct folding of the RNA molecule into a secondary or higher order structure. When disrupted by a mutation, aberrant folding may result in a lower splicing efficiency. However, the structure can be restored by a sec...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msn195
更新日期:2008-11-01 00:00:00
abstract::The most frequent measure of phylogenetic uncertainty for splits is bootstrap support. Although large bootstrap support intuitively suggests that a split in a tree is well supported, it has not been clear how large bootstrap support needs to be to conclude that there is significant evidence that a hypothesized split i...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msq048
更新日期:2010-07-01 00:00:00
abstract::Several new families of DNA transposons were identified by computer-assisted searches in a wide range of animal species that includes nematodes, flat worms, mosquitoes, sea squirt, zebrafish, and humans. Many of these elements have coding capacity for transposases, which are related to each other and to those encoded ...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msh188
更新日期:2004-09-01 00:00:00
abstract::The plant pathogen Phytophthora infestans emerged in Europe in 1845, triggering the Irish potato famine and massive European potato crop losses that continued until effective fungicides were widely employed in the 20th century. Today the pathogen is ubiquitous, with more aggressive and virulent strains surfacing in re...
journal_title:Molecular biology and evolution
pub_type: 历史文章,信件
doi:10.1093/molbev/msu086
更新日期:2014-06-01 00:00:00
abstract::Analysis of evolution of paralogous genes in a genome is central to our understanding of genome evolution. Comparison of closely related bacterial genomes, which has provided clues as to how genome sequences evolve under natural conditions, would help in such an analysis. With species Staphylococcus aureus, whole-geno...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msk013
更新日期:2006-06-01 00:00:00
abstract::Debate on the adaptive origins of primates has long focused on the functional ecology of the primate visual system. For example, it is hypothesized that variable expression of short- (SWS1) and middle-to-long-wavelength sensitive (M/LWS) opsins, which confer color vision, can be used to infer ancestral activity patter...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msv346
更新日期:2016-04-01 00:00:00
abstract::Eutrema salsugineum and Schrenkiella parvula are salt-tolerant relatives of the salt-sensitive species Arabidopsis thaliana. An important component of salt tolerance is the regulation of Na(+) ion homeostasis, which occurs in part through proteins encoded by the Cation/Proton Antiporter-1 (CPA1) gene family. We used a...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msu152
更新日期:2014-08-01 00:00:00
abstract::The plant MADS-box regulatory gene family includes several loci that control different aspects of inflorescence and floral development. Orthologs to the Arabidopsis thaliana MADS-box floral meristem genes APETALA1 and CAULIFLOWER and the floral organ identity genes APETALA3 and PISTILLATA were isolated from the congen...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a026193
更新日期:1999-08-01 00:00:00
abstract::Viral genome integration provides a complex route to biological innovation that has rarely but repeatedly occurred in one of the most diverse lineages of organisms on the planet, parasitoid wasps. We describe a novel endogenous virus in braconid wasps derived from pathogenic alphanudiviruses. Limited to a subset of th...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msy148
更新日期:2018-10-01 00:00:00
abstract::Alternative splicing (AS) contributes to increased transcriptome and proteome diversity in various eukaryotic lineages. Previous studies showed low levels of conservation of alternatively spliced (cassette) exons within mammals and within dipterans. We report a strikingly different pattern in Caenorhabditis nematodes-...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msm262
更新日期:2008-02-01 00:00:00
abstract::We report the genomic organization and deduced protein sequence of a cephalochordate member of the Otx homeobox gene family (AmphiOtx) and show its probable single-copy state in the genome. We also present molecular phylogenetic analysis indicating that there was single ancestral Otx gene in the first chordates which ...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a025961
更新日期:1998-05-01 00:00:00
abstract::Most mitochondrial proteins are synthesized in the cytosol of eukaryotic cells as precursor proteins carrying N-terminal extensions called transit peptides or presequences, which mediate their specific transport into mitochondria. However, plant cells possess a second potential target organelle for such transit peptid...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msp087
更新日期:2009-08-01 00:00:00
abstract::Drosophila melanogaster is widely used as a model in DNA variation studies. Patterns of polymorphism have, however, been affected by the history of this species, which is thought to have recently spread out of Africa to the rest of the world. We analyzed DNA sequence variation in 11 populations, including four contine...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msh089
更新日期:2004-08-01 00:00:00
abstract::Phylogenetic reconstruction of the evolutionary history of closely related organisms may be difficult because of the presence of unsorted lineages and of a relatively high proportion of heterozygous sites that are usually not handled well by phylogenetic programs. Genomic data may provide enough fixed polymorphisms to...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/mst271
更新日期:2014-04-01 00:00:00
abstract::Enzyme function is strongly affected by temperature, and orthologs from species adapted to different thermal environments often show temperature compensation in kinetic properties. Antarctic notothenioid fishes live in a habitat of constant, extreme cold (-1.86 +/- 2 degrees C), and orthologs of the enzyme A4-lactate ...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msh237
更新日期:2004-12-01 00:00:00
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...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a004199
更新日期:2002-08-01 00:00:00
abstract::Transposable elements (TEs) make up around 10%-15% of the Drosophila melanogaster genome, but its sibling species Drosophila simulans carries only one third as many such repeat sequences. We do not, however, have an overall view of copy numbers of the various classes of TEs (long terminal repeat [LTR] retrotransposons...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a026215
更新日期:1999-09-01 00:00:00
abstract::Due to its speed, the distance approach remains the best hope for building phylogenies on very large sets of taxa. Recently (R. Desper and O. Gascuel, J. Comp. Biol. 9:687-705, 2002), we introduced a new "balanced" minimum evolution (BME) principle, based on a branch length estimation scheme of Y. Pauplin (J. Mol. Evo...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msh049
更新日期:2004-03-01 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::Nei and Gojobori (1986) developed a simple method to estimate the numbers of synonymous (ds) and nonsynonymous (dN) substitutions per site. In the present paper, we have developed a method for computing variances and covariances of ds's and dN's and of the proportions of synonymous (ps) and nonsynonymous (pN) differen...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a040140
更新日期:1994-07-01 00:00:00
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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
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journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a026388
更新日期:2000-07-01 00:00:00
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journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msr008
更新日期:2011-06-01 00:00:00
abstract::Positive selection sites (PSSs), a class of amino acid sites with an excess of nonsynonymous to synonymous substitutions, are indicators of adaptive molecular evolution and have been detected in many protein families involved in a diversity of biological processes by statistical approaches. However, few studies are co...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msw065
更新日期:2016-08-01 00:00:00
abstract::Variation at the FADS1/FADS2 gene cluster is functionally associated with differences in lipid metabolism and is often hypothesized to reflect adaptation to an agricultural diet. Here, we test the evidence for this relationship using both modern and ancient DNA data. We show that almost all the inhabitants of Europe c...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msy180
更新日期:2018-12-01 00:00:00
abstract::It is widely accepted that evolutionary changes in conserved developmental signaling pathways play an important role in morphological evolution. However, few in silico studies were interested in tracking such changes in a signaling pathway. The Ectodysplasin (EDA) pathway provides an opportunity to fill this gap becau...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msn038
更新日期:2008-05-01 00:00:00
abstract::We performed a genealogical analysis of the ionotropic glutamate receptor (iGluR) gene family, which includes the animal iGluRs and the newly isolated glutamate receptor-like genes (GLR) of plants discovered in Arabidopsis. Distance measures firmly placed the plant GLR genes within the iGluR clade as opposed to other ...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a026167
更新日期:1999-06-01 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::Duplication, resulting in gene redundancy, is well known to be a driving force of evolutionary change. Gene families are therefore useful targets for approaching genome evolution. To address the gene death process, we examined the fate of the 10-member-large S288C DUP240 family in 15 Saccharomyces cerevisiae strains. ...
journal_title:Molecular biology and evolution
pub_type: 历史文章,杂志文章
doi:10.1093/molbev/msi170
更新日期:2005-09-01 00:00:00
abstract::There are three common alleles (A, B, and O) at the human ABO blood group locus. We compared nucleotide sequences of these alleles, and relatively large numbers of nucleotide differences were found among them. These differences correspond to the divergence time of at least a few million years, which is unusually large...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a025776
更新日期:1997-04-01 00:00:00