Abstract:
:Using gene genealogies constructed from gene sequence data, we show that both the mucosal and cutaneous papillomaviruses (PV)-supergroups A and B-appear to have been transmitted through susceptible populations faster than exponentially. The data and methods involved (1) examining the PV database for phylogenetic signal in an L1 open reading frame (ORF) fragment and an E1 ORF segment, (2) demonstrating that the same two fragments have evolved in a way consistent with a molecular clock, and (3) applying methods of phylogenetic tree analysis that test different scenarios for the dynamics of viral transmission within populations. The results indicate increases in PV populations of both supergroups A and B in the recent past. This form of the increases, which fit a null model of population growth with an exponent increasing in time, is compatible with the fact that human populations have grown at a faster than exponential rate, thus increasing the numbers of susceptible hosts for HPVs. There are, however, indications that the population of supergroup A has now stopped increasing in size.
journal_name
J Mol Evoljournal_title
Journal of molecular evolutionauthors
Ong CK,Nee S,Rambaut A,Bernard HU,Harvey PHdoi
10.1007/pl00006136subject
Has Abstractpub_date
1997-02-01 00:00:00pages
199-206issue
2eissn
0022-2844issn
1432-1432journal_volume
44pub_type
杂志文章abstract::We report the nucleotide sequence of the single muscle actin gene of the sea urchin Strongylocentrotus purpuratus. Comparison of the protein-coding sequence of this muscle actin gene (pSpG28) with that of two linked sea urchin cytoskeletal actin genes (pSpG17 and CyIIa) reveals a region of exceptional sequence conserv...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/BF02100039
更新日期:1987-01-01 00:00:00
abstract::Here we analyze the molecular evolution of the beta-esterase gene cluster in the Drosophila genus using the recently released genome sequences of 12 Drosophila species. Molecular evolution in this small cluster is noteworthy because it contains contrasting examples of the types and stages of loss of gene function. Spe...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/s00239-009-9236-3
更新日期:2009-07-01 00:00:00
abstract::The codon assignment of the quasi-universal genetic code can be assumed to have resulted from the evolutionary pressures that prevailed when the code was still evolving. Here, we review studies of the structure of the genetic code based on optimization models. We also review studies that, from the structure of the cod...
journal_title:Journal of molecular evolution
pub_type: 杂志文章,评审
doi:10.1007/s00239-009-9287-5
更新日期:2009-11-01 00:00:00
abstract::Microsporidia are unicellular eukaryotes living as obligate intracellular parasites. Lacking mitochondria, they were initially considered as having diverged before the endosymbiosis at the origin of mitochondria. That microsporidia were primitively amitochondriate was first questioned by the discovery of microsporidia...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/s00239-004-2673-0
更新日期:2004-12-01 00:00:00
abstract::The beta-globin gene cluster of Wistar rat was extensively cloned and the embryonic genes were mapped and sequenced. Four overlapping lambda Dash recombinant clones cover about 31 kb and contain four nonadult beta-globin genes, 5'-epsilon1-gamma1-gamma2-psigamma3-3'. The epsilon1 and gamma2 are active genes, since the...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/pl00006525
更新日期:1999-07-01 00:00:00
abstract::The neutral theory of molecular evolution states that most mutations are deleterious or neutral. It results that the evolutionary rate of a given position in an alignment is a function of the level of constraint acting on this position. Inferring evolutionary rates from a set of aligned sequences is hence a powerful m...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/s00239-008-9139-8
更新日期:2008-09-01 00:00:00
abstract::HMG boxes were initially identified as DNA-binding domains of the human RNA polymerase I (pol I) transcription factor hUBF and the animal high-mobility-group (HMG) protein family HMG1. Since then, numerous sequences of HMG-box-containing HMG proteins and other DNA-binding proteins from several species have become avai...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/BF02407357
更新日期:1993-08-01 00:00:00
abstract::We have studied the relative contribution of inversions, transpositions, deletions, and nucleotide substitutions to the evolution of Chlamydia trachomatis and Chlamydia pneumoniae. The minimal number of rearrangement events required for converting the gene order structure of one genome into that of the other was estim...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/s00239-001-0087-9
更新日期:2002-07-01 00:00:00
abstract::While studies of the evolutionary histories of protein families are commonplace, little is known on noncoding RNAs beyond microRNAs and some snoRNAs. Here we investigate in detail the evolutionary history of the nine spliceosomal snRNA families (U1, U2, U4, U5, U6, U11, U12, U4atac, and U6atac) across the completely o...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/s00239-008-9149-6
更新日期:2008-12-01 00:00:00
abstract::Orphan genes, lacking detectable homologs in outgroup species, typically represent 10-30% of eukaryotic genomes. Efforts to find the source of these young genes indicate that de novo emergence from non-coding DNA may in part explain their prevalence. Here, we investigate the roots of orphan gene emergence in the Droso...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/s00239-020-09939-z
更新日期:2020-05-01 00:00:00
abstract::This paper presents an essentially new method used to construct phylogenetic trees from related amino acid sequences. The method is based on a new distance measure which describes sequence relationships by means of typical steric and physicochemical properties of the amino acids and is advantageous in some essential p...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/BF00160324
更新日期:1995-10-01 00:00:00
abstract::The circadian clock regulates a multitude of plant developmental and metabolic processes. In crop species, it contributes significantly to plant performance and productivity and to the adaptation and geographical range over which crops can be grown. To understand the clock in barley and how it relates to the component...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/s00239-015-9665-0
更新日期:2015-02-01 00:00:00
abstract::The accuracies and efficiencies of three different methods of making phylogenetic trees from gene frequency data were examined by using computer simulation. The methods examined are UPGMA, Farris' (1972) method, and Tateno et al.'s (1982) modified Farris method. In the computer simulation eight species (or populations...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/BF02300753
更新日期:1983-01-01 00:00:00
abstract::Autosomal chorion genes s18, s15, and s19 are shown to diverge at extremely rapid rates in closely related taxa of Hawaiian Drosophila. Their nucleotide divergence rates are at least as fast as those of intergenic regions that are known to evolve more extensively between distantly related species. Their amino acid div...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/BF02106055
更新日期:1990-11-01 00:00:00
abstract::The activated dimonophosphate of 3'-deoxyadenosine (cordycepin) undergoes oligomerization to produce a new family of pyrophosphate-linked oligomers in which the average repeating unit involves a nine-atom structural group. The presence of a poly(U) template increases the relative yields of higher oligomers, although t...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/BF02101146
更新日期:1987-01-01 00:00:00
abstract::Cosmochemical considerations suggest various potential sources for the accumulation of organic matter on Mars. However the Viking Molecular Analysis did not indicate any indigenous organic compounds on the surface of Mars. Their disappearance from the top layer is most likely caused by the combined action of the high ...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/BF01732374
更新日期:1979-12-01 00:00:00
abstract::We have further characterized the Asian genotypes (Types 2 and 7) and subtypes of JC virus (JCV). Urine samples from 224 individuals with Han and Mongolian populations were collected in five regions in eastern China: Kunming, Chengdu, Shenyang, Chifeng, and Manzhouli. Also, 99 urine samples were collected from coastal...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/s00239-003-2579-2
更新日期:2004-05-01 00:00:00
abstract::Multiple genes of the hoatzin encoding stomach lysozyme c and closely related members of this calcium-binding lysozyme c group were cloned from a genomic DNA library and sequenced. There are a minimum of five genes represented among these sequences that encode two distinct groups of protein sequences. One group of thr...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/BF02338801
更新日期:1996-06-01 00:00:00
abstract::Statistical and biochemical studies of the genetic code have found evidence of nonrandom patterns in the distribution of codon assignments. It has, for example, been shown that the code minimizes the effects of point mutation or mistranslation: erroneous codons are either synonymous or code for an amino acid with chem...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/pl00006381
更新日期:1998-09-01 00:00:00
abstract::Protamine P1 genes have been sequenced by PCR amplification and direct DNA sequencing from 9 primates representing 5 major families, Cebidae (new world monkeys), Cercopithecidae (old world monkeys), Hylobatidae (gibbons), Pongidae (gorilla, orangutan, and chimpanzee), and Hominidae (human). In this recently diverged g...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/BF00178872
更新日期:1993-10-01 00:00:00
abstract::Soluble lead salts and a number of lead-containing minerals catalyze the formation of oligonucleotides from nucleoside 5'-phosphorimidazolides. The effectiveness of lead compounds correlates strongly with their solubility. Under optimal conditions we were able to obtain 18% of pentamer and higher oligomers from ImpA. ...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/BF01732030
更新日期:1979-04-12 00:00:00
abstract::The organization of histone gene clusters of the duck Cairina moschata was studied in the DNA inserts of two recombinant phage that overlap and feature identical histone gene arrangements but differ in sequence details and in the extent of repetition of an AT-rich motif in one of the nontranscribed spacer regions. The...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/BF02102477
更新日期:1989-03-01 00:00:00
abstract::Pituitary prolactin, like growth hormone (GH) and several other protein hormones, shows an episodic pattern of molecular evolution in which sustained bursts of rapid change contrast with long periods of slow evolution. A period of rapid change occurred in the evolution of prolactin in primates, leading to marked seque...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/s00239-004-0239-9
更新日期:2005-05-01 00:00:00
abstract::Previous studies have shown that pituitary growth hormone displays an episodic pattern of evolution, with a slow underlying evolutionary rate and occasional sustained bursts of rapid change. The present study establishes that pituitary prolactin shows a similar pattern. During much of tetrapod evolution the sequence o...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/s002390010049
更新日期:2000-05-01 00:00:00
abstract::Recombination has been suggested to be an important factor for the genetic variation of bacterial genes, but few studies have dealt with intragenic recombination between the same or closely related species of cyanobacteria. Here we provide strong evidence for recombination in the microcystin synthetase (mcy) gene clus...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/s00239-004-2583-1
更新日期:2004-06-01 00:00:00
abstract::The helix-turn-helix domain-containing family of transcriptional regulators is of ancient origin and has been incorporated into numerous disparate biological processes. As a consequence, the forces shaping its early evolution have been difficult to reconstruct. Herein, we analyze this large and diverse family with a c...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/pl00006552
更新日期:1999-09-01 00:00:00
abstract::We have implemented a routine procedure for screening protein sequences for evidence of intragenic duplications. We tested 163 protein sequences representing 116 superfamilies of unrelated proteins. Twenty superfamilies contain proteins with internal gene duplications. The intragenic duplications detected can be divid...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/BF01734217
更新日期:1978-02-21 00:00:00
abstract::A 2550-bp portion of the mitochondrial genome of a Demosponge, genus Tetilla, was amplified from whole genomic DNA extract and sequenced. The sequence was found to code for the 3' end of the 16S rRNA gene, cytochrome c oxidase subunit II, a lysine tRNA, ATPase subunit 8, and a 5' portion of ATPase subunit 6. The Porif...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/pl00006497
更新日期:1999-05-01 00:00:00
abstract::Antibody binding site are formed by six hypervariable regions or complementarity determining regions (CDRs). The CDRs, three from the heavy chain and three from the light chain, are known as hypervariable segments and provide a surface complementary to that of the epitope. In recent work it was found that the amino ac...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/BF00175497
更新日期:1994-01-01 00:00:00
abstract::L1 elements are retrotransposons that have been replicating and evolving in mammalian genomes since before the mammalian radiation. Rattus norvegicus shares the young L1mlvi2 clade only with its sister taxon, Rattus cf moluccarius. Here we compared the L1mlvi2 clade in these recently diverged species and found that it...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/pl00006246
更新日期:1997-10-01 00:00:00