Abstract:
:Heuristic approaches were used to quantify the influence that sequencing errors have on estimates of nucleotide diversity, substitution rate, and the construction of genealogies. Error rates of less than 1 nucleotide/kb probably have little affect on conclusions about the evolutionary history of highly polymorphic organisms such as Drosophila and Escherichia coli, but organisms with very low nucleotide diversity, such as humans, require greater sequencing accuracy. A scan of GenBank for corrections of previous errors reveals that sequencing errors are highly nonrandom.
journal_name
Mol Biol Evoljournal_title
Molecular biology and evolutionauthors
Clark AG,Whittam TSdoi
10.1093/oxfordjournals.molbev.a040756subject
Has Abstractpub_date
1992-07-01 00:00:00pages
744-52issue
4eissn
0737-4038issn
1537-1719journal_volume
9pub_type
杂志文章abstract::During the course of a random sequencing project of the genome of the dimorphic yeast Yarrowia lipolytica, we have identified sequences that were repeated in the genome and that matched the reverse transcriptase (RT) sequence of non-long terminal repeat (non-LTR) retrotransposons. Extension of sequencing on each side ...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a004125
更新日期:2002-05-01 00:00:00
abstract::We show how to make appropriate likelihood ratio tests for evolutionary tree models when parameters such as edge (internodes or branches) lengths have nonnegativity constraints. In such cases, under the null model of an edge length being zero, the marginal distribution of this parameter is proven to be a "half-normal"...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a026358
更新日期:2000-05-01 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::The marine cyanobacterium Prochlorococcus MED4 has the smallest sequenced genome of any photosynthetic organism. Prochlorococcus MED4 shares many genomic characteristics with chloroplasts and bacterial endosymbionts, including a reduced coding capacity, missing DNA repair genes, a minimal transcriptional regulatory ne...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msn217
更新日期:2009-01-01 00:00:00
abstract::Drosophila melanogaster, unlike mammals, has seven insulin-like peptides (DILPS). In Drosophila, all seven genes (dilp1-7) are single copy in the 12 species studied, except for D. grimshawi with two tandem copies of dilp2. Our comparative analysis revealed that genes dilp1-dilp7 exhibit differential functional constra...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msq353
更新日期:2011-05-01 00:00:00
abstract::Polytoma obtusum and Polytoma uvella are members of a clade of nonphotosynthetic chlorophyte algae closely related to Chlamydomonas humicola and other photosynthetic members of the Chlamydomonadaceae. Descended from a nonphotosynthetic mutant, these obligate heterotrophs retain a plastid (leucoplast) with a functional...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a003968
更新日期:2001-09-01 00:00:00
abstract::Inaccurate inference of positional homologies in multiple sequence alignments and systematic errors introduced by alignment heuristics obfuscate phylogenetic inference. Alignment masking, the elimination of phylogenetically uninformative or misleading sites from an alignment before phylogenetic analysis, is a common p...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/mss264
更新日期:2013-03-01 00:00:00
abstract::Estimation of evolutionary distances from coding sequences must take into account protein-level selection to avoid relative underestimation of longer evolutionary distances. Current modeling of selection via site-to-site rate heterogeneity generally neglects another aspect of selection, namely position-specific amino ...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a025995
更新日期:1998-07-01 00:00:00
abstract::Simple models of molecular evolution assume that sequences evolve by a Poisson process in which nucleotide or amino acid substitutions occur as rare independent events. In these models, the expected ratio of the variance to the mean of substitution counts equals 1, and substitution processes with a ratio greater than ...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msn112
更新日期:2008-08-01 00:00:00
abstract::As the oomycete pathogen causing potato late blight disease, Phytophthora infestans triggered the famous 19th-century Irish potato famine and remains the leading cause of global commercial potato crop destruction. But the geographic origin of the genotype that caused this devastating initial outbreak remains disputed,...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msv241
更新日期:2016-02-01 00:00:00
abstract::Nonsense-mediated decay (NMD) pathways for detection and degradation of transcripts containing premature termination (stop) codons (PTCs) are ubiquitous among the eukaryotes. NMD uses the presence of a second signal downstream of a termination codon to distinguish a PTC from a true stop codon. In mammals and perhaps o...
journal_title:Molecular biology and evolution
pub_type: 信件
doi:10.1093/molbev/msm010
更新日期:2007-04-01 00:00:00
abstract::Here, a model allowing covarion-like evolution of DNA sequences is introduced. In contrast to standard representation of the distribution of evolutionary rates, this model allows the site-specific rate to vary between lineages. This is achieved by adding as few as two parameters to the widely used among-site rate vari...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a003868
更新日期:2001-05-01 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::The heat shock protein (Hsp) sequences, because of their ubiquity and high degree of conservation, provide useful models for phylogenetic analysis. In this paper I have carried out a global alignment of all available sequences (a total of 31) for the 90-kD heat shock protein (Hsp90) family. The minimum amino acid iden...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a040281
更新日期:1995-11-01 00:00:00
abstract::Blooms that are formed by cyanobacteria consist of toxic and nontoxic strains. The mechanisms that result in the occurrence of nontoxic strains are enigmatic. All the nontoxic strains of the filamentous cyanobacterium Planktothrix that were isolated from 9 European countries were found to have lost 90% of a large micr...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msn120
更新日期:2008-08-01 00:00:00
abstract::Since the discovery of ING1 class II tumor suppressors in 1996, five different ING genes (ING1 to ING5) encoding proteins with highly conserved plant homeodomain (PHD) motifs and several splicing isoforms of the ING1 and ING2 gene have been identified. The ING family functions in DNA repair and apoptosis in response t...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msh256
更新日期:2005-01-01 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::Ever since Luria and Delbruck, the notion that mutation is random with respect to fitness has been foundational to modern biology. However, various studies have claimed striking exceptions to this rule. One influential case involves toxin-encoding genes in snails of the genus Conus, termed conotoxins, a large gene fam...
journal_title:Molecular biology and evolution
pub_type: 信件
doi:10.1093/molbev/msw140
更新日期:2016-10-01 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::Understanding how pathogens acquire resistance to drugs is important for the design of treatment strategies, particularly for rapidly evolving viruses such as HIV-1. Drug treatment can exert strong selective pressures and sites within targeted genes that confer resistance frequently evolve far more rapidly than the ne...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msm021
更新日期:2007-04-01 00:00:00
abstract::Single-stranded DNA(ssDNA) viral life cycles must balance double-stranded DNA (dsDNA) and ssDNA biosynthesis. Previously published in vitro results suggest that microvirus C and host cell SSB proteins play antagonistic roles to achieve this balance. To investigate this in vivo, microvirus DNA replication was character...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msu089
更新日期:2014-06-01 00:00:00
abstract::The spread of farming out of the Balkans and into the rest of Europe followed two distinct routes: An initial expansion represented by the Impressa and Cardial traditions, which followed the Northern Mediterranean coastline; and another expansion represented by the LBK (Linearbandkeramik) tradition, which followed the...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msv181
更新日期:2015-12-01 00:00:00
abstract::We have followed, in glucose-limited chemostats, the evolution of natural isolates of Escherichia coli possessing maximal growth rates of 0.48-1.43 doublings/h. Under these conditions a rapid-growth phenotype similar to that of standard laboratory wild-type strains was selected so that after 280 generations all of the...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a040731
更新日期:1992-05-01 00:00:00
abstract::We report the complete sequence of a paralogous copy of elongation factor-1 alpha (EF-1 alpha) in the honeybee, Apis mellifera (Hymenoptera: Apidae). This copy differs from a previously described copy in the positions of five introns and in 25% of the nucleotide sites in the coding regions. The existence of two paralo...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a025920
更新日期:1998-03-01 00:00:00
abstract::DNA fingerprinting exhibits multilocus genotypes of individuals, detected by the use of a single multilocus probe. Consequently, population data on DNA fingerprinting do not provide a complete characterization of the genetic variation in terms of allele-frequency distributions, since neither the number of loci nor the...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a040086
更新日期:1994-01-01 00:00:00
abstract::Hybridization in plants may result in hybrid speciation or introgression and, thus, is now widely understood to be an important mechanism of species diversity on an evolutionary timescale. Hybridization is particularly common in ferns, as is polyploidy, which often results from hybrid crosses. Nevertheless, hybrid spe...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msaa097
更新日期:2020-09-01 00:00:00
abstract::Evolutionary parsimony is an easy-to-use method of phylogenetic inference that is based on nucleic acid sequences and that does not require the assumption that evolutionary processes in the various sites on the molecule are identical. It does, however, require a parameter constraint, known as the "balanced transversio...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a040784
更新日期:1992-11-01 00:00:00
abstract::Mouse has emerged as the most common model organism in biomedicine. Here, we analyzed the tolerance to the loss-of-function (LoF) of selenoprotein genes, estimated from mouse knockouts and the frequency of LoF variants in humans. We found not only a general correspondence in tolerance (e.g., GPX1, GPX2) and intoleranc...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msz218
更新日期:2020-02-01 00:00:00
abstract::Traditionally, living cetaceans (order Cetacea) are classified into two highly distinct suborders: the echolocating toothed whales, Odontoceti, and the filter-feeding baleen whales, Mysticeti. A molecular phylogeny based on 1,352 base pairs of two mitochondrial ribosomal gene segments and the mitochondrial cytochrome ...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a040164
更新日期:1994-11-01 00:00:00
abstract::Barley (Hordeum vulgare) is a major crop, grown worldwide and in a wide range of climatic conditions. Despite its importance as a crop species, little is known about the population genetics of barley and the effects of bottlenecks, adaptation, and gene flow on genetic diversity within and between landrace populations....
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msp308
更新日期:2010-04-01 00:00:00