Abstract:
:Substitution rates at the three codon positions (r1, r2, and r3) of mammalian mitochondrial genes are in the order of r3 > r1 > r2, and the rate heterogeneity at the three positions, as measured by the shape parameter of the gamma distribution (alpha 1, alpha 2, and alpha 3), is in the order of alpha 3 > alpha 1 > alpha 2. The causes for the rate heterogeneity at the three codon positions remain unclear and, in particular, there has been no satisfactory explanation for the observation of alpha 1 > alpha 2. I attempted to dissect the causes of rate heterogeneity by studying the pattern of nonsynonymous substitutions with respect to codon positions in 10 mitochondrial genes from 19 mammalian species. Nonsynonymous substitutions involve more different amino acid replacements at the second than at the first codon position, which results in r1 > r2. The difference between r1 and r2 increases with the intensity of purifying selection, and so does the rate heterogeneity in nonsynonymous substitutions among sites at the same codon position. All mitochondrial genes appear to have functionally important and unimportant codons, with the latter having all three codon positions prone to nonsynonymous substitutions. Within the functionally important codons, the second codon position is much more conservative than the codon position. This explains why alpha 1 > alpha 2. The result suggests that overweighting of the second codon position in phylogenetic analysis may be a misguided practice.
journal_name
Mol Biol Evoljournal_title
Molecular biology and evolutionauthors
Xia Xdoi
10.1093/oxfordjournals.molbev.a025930subject
Has Abstractpub_date
1998-03-01 00:00:00pages
336-44issue
3eissn
0737-4038issn
1537-1719journal_volume
15pub_type
杂志文章abstract::Alpha-defensins are a family of mammalian antimicrobial peptides that exhibit variable activity against a panel of microbes, including bacteria, fungi, and enveloped viruses. We have employed a maximum-likelihood approach to detect evidence of positive selection (adaptive evolution) in the evolution of these important...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msh084
更新日期:2004-05-01 00:00:00
abstract::Molluscs in general, and bivalves in particular, exhibit an extraordinary degree of mitochondrial gene order variation when compared with other metazoans. Two factors inhibiting our understanding the evolution of gene rearrangement in bivalves are inadequate taxonomic sampling and failure to examine gene order in a ph...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msg218
更新日期:2003-11-01 00:00:00
abstract::The genomes are folded in a complex three-dimensional (3D) structure. Some features of this organization are common for all eukaryotes, but little is known about its evolution. Here, we have studied the 3D organization and regulation of zebrafish globin gene domain and compared its organization and regulation with tho...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msx100
更新日期:2017-06-01 00:00:00
abstract::A 32-kb region including the Adh structural gene was analyzed with six restriction endonucleases in 20 lines of Drosophila pseudoobscura, one line of D. persimilis, and one line of D. miranda. Nineteen lines of D. pseudoobscura from a single population were estimated to be polymorphic at one in every 15 nucleotides (p...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a040438
更新日期:1987-05-01 00:00:00
abstract::Understanding genome and chromosome evolution is important for understanding genetic inheritance and evolution. Universal events comprising DNA replication, transcription, repair, mobile genetic element transposition, chromosome rearrangements, mitosis, and meiosis underlie inheritance and variation of living organism...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msr011
更新日期:2011-06-01 00:00:00
abstract::Heterotachy occurs when the relative evolutionary rates among sites are not the same across lineages. Sequence alignments are likely to exhibit heterotachy with varying severity because the intensity of purifying selection and adaptive forces at a given amino acid or DNA sequence position is unlikely to be the same in...
journal_title:Molecular biology and evolution
pub_type: 信件
doi:10.1093/molbev/msi212
更新日期:2005-11-01 00:00:00
abstract::Transcriptional control of gene expression is regulated by biochemical interactions between cis-regulatory DNA sequences and trans-acting factors that form complex regulatory networks. Genetic changes affecting both cis- and trans-acting sequences in these networks have been shown to alter patterns of gene expression ...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msx068
更新日期:2017-06-01 00:00:00
abstract::Most "tests of neutrality" assess whether particular data sets depart from the predictions of a standard neutral model with no recombination. For Drosophila, where nuclear polymorphism data routinely show evidence of genetic exchange, the assumption of no recombination is often unrealistic. In addition, while conserva...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a003805
更新日期:2001-03-01 00:00:00
abstract::One of the most fundamental questions for understanding the origin of species is why genes that function to cause fertility in a pure-species genetic background fail to produce fertility in a hybrid genetic background. A related question is why the sex that is most often sterile or inviable in hybrids is the heterogam...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msg119
更新日期:2003-07-01 00:00:00
abstract::The number of subunits of RNA polymerases (RNAPs) increases during evolution from 5 in eubacteria to 12 in archaea. In eukaryotes, which have at least three RNAPs, the number of subunits has expanded from 12 in RNA polymerase II (RNAPII) to 14 in RNA polymerase I (RNAPI) and to 17 in RNA polymerase III (RNAPIII). It w...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msp316
更新日期:2010-05-01 00:00:00
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
更新日期:2020-06-01 00:00:00
abstract::The retroid family consists of all genetic elements that encode a potential reverse transcriptase (RT). Members of this family include a diversity of eukaryotic genetic elements (viruses, transposable elements, organelle introns, and plasmids) and the retrons of prokaryotes. Some retroid elements have, in addition to ...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a040686
更新日期:1991-11-01 00:00:00
abstract::Identifying the genomic basis underlying local adaptation is paramount to evolutionary biology, and bears many applications in the fields of conservation biology, crop, and animal breeding, as well as personalized medicine. Although many approaches have been developed to detect signatures of positive selection within ...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msy053
更新日期:2018-06-01 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
更新日期:2004-05-01 00:00:00
abstract::Cyanobacteria are among the most ancient organisms known to have circadian rhythms. The cpmA gene is involved in controlling the circadian output signal. We studied polymorphism and divergence of this gene in six populations of a stress-tolerant cyanobacterium, Chroococcidiopsis sp., sampled in extreme habitats across...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/mss191
更新日期:2012-12-01 00:00:00
abstract::Male sexual behavior in the fruit fly Drosophila melanogaster is regulated by fruitless (fru), a sex-determination gene specifying the synthesis of BTB-Zn finger proteins that likely function as male-specific transcriptional regulators. Expression of fru in the nervous system specifies male sexual behavior and the mus...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msj070
更新日期:2006-03-01 00:00:00
abstract::We present a new Bayesian method for estimating demographic and phylogenetic history using population genomic data. Several key innovations are introduced that allow the study of diverse models within an Isolation-with-Migration framework. The new method implements a 2-step analysis, with an initial Markov chain Monte...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msx070
更新日期:2017-06-01 00:00:00
abstract::Various nucleotide substitution models have been developed to accommodate among lineage rate heterogeneity, thereby relaxing the assumptions of the strict molecular clock. Recently developed "uncorrelated relaxed clock" and "random local clock" (RLC) models allow decoupling of nucleotide substitution rates between des...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msr228
更新日期:2012-02-01 00:00:00
abstract::Although evolutionary studies of gene function often rely on RNA interference, the ideal approach would use reverse genetics to create null mutations for cross-species comparisons and forward genetics to identify novel genes in each species. We have used transcription activator-like effector nucleases (TALENs) to faci...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/mst213
更新日期:2014-02-01 00:00:00
abstract::Rearrangements of mitochondrial DNA gene order have been suggested as a tool for defining the pattern of evolutionary divergence in arthropod taxa. We have employed a combination of highly conserved insect-based polymerase chain reaction (PCR) primers with long-PCR to survey 14 noninsect arthropods for mitochondrial g...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a004141
更新日期:2002-06-01 00:00:00
abstract::Dinoflagellate chloroplast genes are unique in that each gene is on a separate minicircular chromosome. To understand the origin and evolution of this exceptional genomic organization we completely sequenced chloroplast psbA and 23S rRNA gene minicircles from four dinoflagellates: three closely related Heterocapsa spe...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a004104
更新日期:2002-04-01 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::Photosystem II, the water oxidizing enzyme, altered the course of evolution by filling the atmosphere with oxygen. Here, we reconstruct the origin and evolution of water oxidation at an unprecedented level of detail by studying the phylogeny of all D1 subunits, the main protein coordinating the water oxidizing cluster...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msv024
更新日期:2015-05-01 00:00:00
abstract::In the age of whole-genome population genetics, so-called genomic scan studies often conclude with a long list of putatively selected loci. These lists are then further scrutinized to annotate these regions by gene function, corresponding biological processes, expression levels, or gene networks. Such annotations are ...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/mss136
更新日期:2012-10-01 00:00:00
abstract::Influenza A viruses from wild aquatic birds, their natural reservoir species, are thought to have reached a form of stasis, characterized by low rates of evolutionary change. We tested this hypothesis by estimating rates of nucleotide substitution in a diverse array of avian influenza viruses (AIV) and allowing for ra...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msl102
更新日期:2006-12-01 00:00:00
abstract::We have investigated intron evolution in the compact genomes of 2 closely related species of pufferfishes, Fugu rubripes and Tetraodon nigroviridis, that diverged about 32 million years ago (MYA). Analysis of 148,028 aligned intron positions in 13,547 gene pairs using human as an outgroup identified 57 and 24 intron l...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msm278
更新日期:2008-03-01 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::Cancer progression is an evolutionary process. During this process, evolving cancer cell populations encounter restrictive ecological niches within the body, such as the primary tumor, circulatory system, and diverse metastatic sites. Efforts to prevent or delay cancer evolution-and progression-require a deep understa...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msz242
更新日期:2020-02-01 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 organization of the mitochondrial genome is generally very conserved among vertebrates. Because of this, examination of the rare rearrangements which do occur has been suggested as offering a powerful alternative to phylogenetic analyses of mitochondrial DNA sequences. Here, we report on an avian mitochondrial rea...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a026223
更新日期:2000-01-01 00:00:00