Abstract:
:Previous studies on human mitochondrial genomes showed that the ratio of intra-specific diversities at nonsynonymous-to-synonymous positions was two to ten times higher than the ratio of interspecific divergences at these positions, suggesting an excess of slightly deleterious nonsynonymous polymorphisms. However, such an overabundance of nonsynonymous single nucleotide polymorphisms (SNPs) was not found in human nuclear genomes. Here, genome-wide estimates using >14,000 human-chimp nuclear genes and 1 million SNPs from four human genomes showed a significant proportion of deleterious nonsynonymous SNPs (∼ 15%). Importantly, this study reveals a negative correlation between the magnitude of selection pressure and the proportion of deleterious SNPs on human genes. The proportion of deleterious amino acid replacement polymorphisms is 3.5 times higher in genes under high purifying selection compared with that in less constrained genes (28% vs. 8%). These results are explained by differences in the extent of contribution of mildly deleterious mutations to diversity and substitution.
journal_name
Mol Biol Evoljournal_title
Molecular biology and evolutionauthors
Subramanian Sdoi
10.1093/molbev/msq287subject
Has Abstractpub_date
2011-01-01 00:00:00pages
49-52issue
1eissn
0737-4038issn
1537-1719pii
msq287journal_volume
28pub_type
信件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
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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
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doi:10.1093/molbev/msp038
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abstract::Human c-Myb proto-oncogene is highly expressed in hematopoietic progenitors as well as leukemia and certain solid tumor. However, the regulatory mechanisms of its expression and biological functions remain largely unclear. Recently, c-Myb has been shown to be targeted by microRNA-150 (miR-150) which thereby controls B...
journal_title:Molecular biology and evolution
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doi:10.1093/molbev/msn165
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abstract::Phylogenetic inference from genome-wide data (phylogenomics) has revolutionized the study of evolution because it enables accounting for discordance among evolutionary histories across the genome. To this end, summary methods have been developed to allow accurate and scalable inference of species trees from gene trees...
journal_title:Molecular biology and evolution
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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
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abstract::This study is a geographically systematic genetic survey of the easternmost subspecies of chimpanzee, Pan troglodytes schweinfurthii. DNA was noninvasively collected in the form of shed hair from chimpanzees of known origin in Uganda, Rwanda, Tanzania, and Zaïre. Two hundred sixty-two DNA sequences from hypervariable ...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a025841
更新日期:1997-09-01 00:00:00
abstract::Copy number variants (CNVs) within humans can have both adaptive and deleterious effects. Because of their phenotypic significance, researchers have attempted to find single nucleotide polymorphisms (SNPs) in high linkage disequilibrium (LD) with CNVs to use in genomewide association studies. However, studies have fou...
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journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a026182
更新日期:1999-07-01 00:00:00
abstract::With the desire to model population genetic processes under increasingly realistic scenarios, forward genetic simulations have become a critical part of the toolbox of modern evolutionary biology. The SLiM forward genetic simulation framework is one of the most powerful and widely used tools in this area. However, its...
journal_title:Molecular biology and evolution
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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::The roles of selection and horizontal transfer in the evolution of the canonical subfamily of P: elements were studied in the saltans and willistoni species groups of the genus Drosophila (subgenus Sophophora). We estimate that the common ancestor of the canonical P: subfamily dates back 2-3 Myr at the most, despite t...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a026253
更新日期:2000-10-01 00:00:00
abstract::Interbreeding between hatchery-reared and wild fish, through deliberate stocking or escapes from fish farms, can result in rapid phenotypic and gene expression changes in hybrids, but the underlying mechanisms are unknown. We assessed if one generation of captive breeding was sufficient to generate inter- and/or trans...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msz135
更新日期:2019-10-01 00:00:00
abstract::To investigate DNA variation in natural plant populations, a 1.8-kb region of the acidic chitinase locus (ChiA)was analyzed for 17 ecotypes of Arabidopsis thaliana sampled worldwide and 3 Arabis species in Japan. As in the Adh region, dimorphism was detected throughout the investigated ChiA region, suggesting the poss...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a025740
更新日期:1997-12-01 00:00:00
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
更新日期:2014-02-01 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::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::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
更新日期:2013-06-01 00:00:00
abstract::The genotypic signature of spatially varying selection is ubiquitous across the Drosophila melanogaster genome. Spatially structured adaptive phenotypic differences are also commonly found, particularly along New World and Australian latitudinal gradients. However, investigation of gene expression variation in one or ...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msq197
更新日期:2011-01-01 00:00:00
abstract::The phylogenetic relationships of the biflagellate protist group Apusomonadidae have been unclear despite the availability of some molecular data. We analyzed sequences from 6 nuclear encoded genes-small-subunit rRNA, large-subunit rRNA, alpha-tubulin, beta-tubulin, actin, and heat shock protein 90-to infer the phylog...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msl120
更新日期:2006-12-01 00:00:00
abstract::The mitochondrial (mt) DNA control region (CR) of dogs and wolves contains an array of imperfect 10 bp tandem repeats. This region was studied for 14 domestic dogs representing the four major phylogenetic groups of nonrepetitive CR and for 5 wolves. Three repeat types were found among these individuals, distributed so...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a026328
更新日期:2000-04-01 00:00:00
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journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msi140
更新日期:2005-07-01 00:00:00
abstract::The mitochondrial genome has undergone radical changes in both the Chlorophyta and Streptophyta, yet little is known about the dynamics of mtDNA evolution in either of these lineages. In the Chlorophyta, which comprises four of the five recognized classes of green algae (Prasinophyceae, Trebouxiophyceae, Ulvophyceae, ...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msh099
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journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msp163
更新日期:2009-11-01 00:00:00
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journal_title:Molecular biology and evolution
pub_type: 杂志文章
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更新日期:2020-09-01 00:00:00
abstract::Environmental or genomic changes during evolution can relax negative selection pressure on specific loci, permitting high frequency polymorphisms at previously conserved sites. Here, we jointly analyze population genomic and comparative genomic data to search for functional processes showing relaxed negative selection...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/mst098
更新日期:2013-08-01 00:00:00
abstract::Noncoding DNA sequences, which play various roles in gene expression and regulation, are under evolutionary pressure. Gene regulation requires specific protein-DNA binding events, and our previous studies showed that both DNA sequence and shape readout are employed by transcription factors (TFs) to achieve DNA binding...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msy099
更新日期:2018-08-01 00:00:00
abstract::A combination of three independent biological features, genomic organization, diagnostic amino acid sites, and rare indels, was used to elucidate the phylogeny of the vertebrate serpin (serine protease inhibitor) superfamily. A strong correlation between serpin gene families displaying (1) a conserved exon-intron patt...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a003838
更新日期:2001-04-01 00:00:00
abstract::Knotted-like (KNOX) proteins constitute a group of homeodomain proteins involved in pattern formation in developing tissues of angiosperms and other green plants. We conducted phylogenetic analyses of nucleotide and amino acid sequences of all known KNOX proteins in order to examine their evolution. Our analyses revea...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a026136
更新日期:1999-04-01 00:00:00
abstract::Molar content of guanine plus cytosine (G + C) and optimal growth temperature (OGT) are main factors characterizing the frequency distribution of amino acids in prokaryotes. Previous work, using multivariate exploratory methods, has emphasized ascertainment of biological factors underlying variability between genomes,...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msj023
更新日期:2006-01-01 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