Abstract:
:The similarity of certain reported angiosperm rDNA internal transcribed spacer (ITS) region sequences to those of green algae prompted our analysis of the deep-level phylogenetic signal in the highly conserved but short 5.8S and hypervariable ITS2 sequences. We found that 5.8S sequences yield phylogenetic trees similar to but less well supported than those generated by a ca. 10-fold longer alignment from rDNA-18S sequences, as well as independent evidence. We attribute this result to our finding that, compared to 18S, the 5.8S has a higher proportion of sites subject to vary and greater among-site substitution rate homogeneity. We also determined that our phylogenetic results are not likely affected by intramolecular compensatory mutation to maintain RNA secondary structure nor by evident systematic biases in base composition. Despite historical homology, there appears to be no ITS2 primary sequence similarity shared sufficient similarity to cluster correctly on the basis of alignability. Our results indicate that groups, however, share sufficient similarity to cluster correctly on the basis of alignability. Our results indicate that ITS region sequences can diagnose organismal origins and phylogenetic relationships at many phylogenetic levels and provide a useful paradigm for molecular evolutionary study.
journal_name
Mol Biol Evoljournal_title
Molecular biology and evolutionauthors
Hershkovitz MA,Lewis LAdoi
10.1093/oxfordjournals.molbev.a025693subject
Has Abstractpub_date
1996-11-01 00:00:00pages
1276-95issue
9eissn
0737-4038issn
1537-1719journal_volume
13pub_type
杂志文章abstract::Novel coronaviruses, including SARS-CoV-2, SARS, and MERS, often originate from recombination events. The mechanism of recombination in RNA viruses is template switching. Coronavirus transcription also involves template switching at specific regions, called transcriptional regulatory sequences (TRS). It is hypothesize...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msaa281
更新日期:2020-11-04 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 geographic origin and time of dispersal of Austroasiatic (AA) speakers, presently settled in south and southeast Asia, remains disputed. Two rival hypotheses, both assuming a demic component to the language dispersal, have been proposed. The first of these places the origin of Austroasiatic speakers in southeast A...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msq288
更新日期:2011-02-01 00:00:00
abstract::Several authors have postulated that genetic divergence between populations could result in genomic incompatibilities that would cause an increase in transposition in their hybrids, producing secondary effects such as sterility and therefore starting a speciation process. It has been demonstrated that transposition la...
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::Microarray platforms are used increasingly to make comparative inferences through genome-wide surveys of gene expression. Although recent studies focus on describing the evidence for natural selection using estimates of the within- and between-taxa mutational variances, these methods do not explicitly or flexibly acco...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msp149
更新日期:2009-10-01 00:00:00
abstract::Evolution at silent sites is often used to estimate the pace of selectively neutral processes or to infer differences in divergence times of genes. However, silent sites are subject to selection in favor of preferred codons, and the strength of such selection varies dramatically across genes. Here, we use the relation...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msh265
更新日期:2005-01-01 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::Recent studies of mitochondrial DNA (mtDNA) variation in mammals and Drosophila have shown an excess of amino acid variation within species (replacement polymorphism) relative to the number of silent and replacement differences fixed between species. To examine further this pattern of nonneutral mtDNA evolution, we pr...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a025634
更新日期:1996-07-01 00:00:00
abstract::Despite its poorly adapted codon usage, HIV-1 replicates and is expressed extremely well in human host cells. HIV-1 has recently been shown to package non-lysyl transfer RNAs (tRNAs) in addition to the tRNA(Lys) needed for priming reverse transcription and integration of the HIV-1 genome. By comparing the codon usage ...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msr005
更新日期:2011-06-01 00:00:00
abstract::Full-length L1 elements have been shown to possess, at their 5' end, tandem repeats called "A" or "F" types. By sequencing the 5' region of two large L1 copies that did not hybridize to A or F probes, we have identified a new sequence that is found at the 5' end of many L1 elements and that we call "V." The element ch...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a040707
更新日期:1992-01-01 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::Much of evolutionary change is mediated at the level of gene expression, yet our understanding of regulatory evolution remains unsatisfying. In light of recent data indicating that transcription factor binding sites undergo substantial turnover between species, we attempt to quantify the process of binding site turnov...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msg077
更新日期:2003-05-01 00:00:00
abstract::We determine the phylogenetic backbone of the East Asian mtDNA tree by using published complete mtDNA sequences and assessing both coding and control region variation in 69 Han individuals from southern China. This approach assists in the interpretation of published mtDNA data on East Asians based on either control re...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a003996
更新日期:2002-10-01 00:00:00
abstract::Most of the well-characterized mitochondrial genomes from diverse green algal lineages are circular mapping DNA molecules; however, Chlamydomonas reinhardtii has a linear 15.8 kb unit mitochondrial genome with 580 or 581 bp inverted repeat ends. In mitochondrial-enriched fractions prepared from Polytomella parva (=P. ...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a004180
更新日期:2002-07-01 00:00:00
abstract::Direct sequencing of polymerase chain reaction products is now an expanding area of plant systematics and evolution. Within angiosperms the rbcL gene has been widely sequenced and used for inferring plant phylogenies at higher taxonomic levels. Unfortunately rbcL does not usually contain enough information to resolve ...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a040157
更新日期:1994-09-01 00:00:00
abstract::The adaptive radiation of cichlid fishes in East African Lake Malawi encompasses over 500 species that are believed to have evolved within the last 800,000 years from a common founder population. It has been proposed that hybridization between ancestral lineages can provide the genetic raw material to fuel such except...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msz294
更新日期:2020-04-01 00:00:00
abstract::alpha 1-Proteinase inhibitor (alpha 1-PI), a member of the serine proteinase inhibitor superfamily, has a primary role in controlling neutrophil elastase activity within the mammalian circulation. Several studies have indicated that the reactive center region of alpha 1-PI, the amino acid sequence of which is critical...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a025594
更新日期:1996-02-01 00:00:00
abstract::How is adaptability generated in a system composed of interacting cellular machineries, each with a separate and functionally critical job to perform? The machinery for organelle inheritance is precisely one such system, requiring coordination between robust and ancient cellular modules, including the cell cycle, cyto...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msr264
更新日期:2012-03-01 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::IQ-TREE (http://www.iqtree.org, last accessed February 6, 2020) is a user-friendly and widely used software package for phylogenetic inference using maximum likelihood. Since the release of version 1 in 2014, we have continuously expanded IQ-TREE to integrate a plethora of new models of sequence evolution and efficien...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msaa015
更新日期:2020-05-01 00:00:00
abstract::Many species, including humans, have dramatically expanded their range in the past, and such range expansions had certainly an impact on their genetic diversity. For example, mutations arising in populations at the edge of a range expansion can sometimes surf on the wave of advance and thus reach a larger spatial dist...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msj057
更新日期:2006-03-01 00:00:00
abstract::Vitamin B(12) (cobalamin) is a dietary requirement for humans because it is an essential cofactor for two enzymes, methylmalonyl-CoA mutase and methionine synthase (METH). Land plants and fungi neither synthesize or require cobalamin because they do not contain methylmalonyl-CoA mutase, and have an alternative B(12)-i...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msr124
更新日期:2011-10-01 00:00:00
abstract::Random genetic drift, or stochastic change in gene frequency, is a fundamental evolutionary force that is usually defined within the ideal Wright-Fisher (WF) population. However, as the theory is increasingly applied to populations that deviate strongly from the ideal model, a paradox of random drift has emerged. When...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msx161
更新日期:2017-08-01 00:00:00
abstract::The relative efficiencies of the maximum parsimony (MP) and distance-matrix methods in obtaining the correct tree (topology) were studied by using computer simulation. The distance-matrix methods examined are the neighbor-joining, distance-Wagner, Tateno et al. modified Farris, Faith, and Li methods. In the computer s...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a040497
更新日期:1988-05-01 00:00:00
abstract::Repeated attempts to map the genomic basis of complex traits often yield different outcomes because of the influence of genetic background, gene-by-environment interactions, and/or statistical limitations. However, where repeatability is low at the level of individual genes, overlap often occurs in gene ontology categ...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msv349
更新日期:2016-04-01 00:00:00
abstract::Septate junctions (SJs) insure barrier properties and control paracellular diffusion of solutes across epithelia in invertebrates. However, the origin and evolution of their molecular constituents in Metazoa have not been firmly established. Here, we investigated the genomes of early branching metazoan representatives...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msu265
更新日期:2015-01-01 00:00:00
abstract::Isoprene is the most abundant biogenic volatile hydrocarbon compound naturally emitted by plants and plays a major role in atmospheric chemistry. It has been proposed that isoprene synthases (IspS) may readily evolve from other terpene synthases, but this hypothesis has not been experimentally investigated. We isolate...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msx178
更新日期:2017-10-01 00:00:00
abstract::CpG and TpA dinucleotides are underrepresented in the human genome. The CpG deficiency is due to the high mutation rate from C to T in methylated CpG's. The TpA suppression was thought to reflect a counterselection against TpA's destabilizing effect in RNA. Unexpectedly, the TpA and CpG deficiencies vary according to ...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a026261
更新日期:2000-11-01 00:00:00
abstract::Current phylogenetic tree reconstruction methods assume that there is a single underlying tree topology for all sites along the sequence. The presence of mosaic sequences due to recombination violates this assumption and will cause phylogenetic methods to give misleading results due to the imposition of a single tree ...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a025722
更新日期:1997-11-01 00:00:00
abstract::The role of adaptation in the divergence of lineages has long been a central question in evolutionary biology, and as multilocus sequence data sets have become available for a wide range of taxa, empirical estimates of levels of adaptive molecular evolution are increasingly common. Estimates vary widely among taxa, wi...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msq270
更新日期:2011-05-01 00:00:00