Abstract:
:TT virus (TTV) has a remarkable genetic heterogeneity. To study TTV evolution, phylogenetic analyses were performed on 739 DNA sequences mapping in the N22 region of ORF1. Analysis of neighbor-joining consensus trees shows significant differences between DNA and protein phylogeny. Median joining networks phylogenetic clustering indicates that DNA sequence analysis is biased by homoplasy (i.e., genetic variability not originated by descent), indicative of either hypermutation or recombination. Statistical analysis shows that the significant excess of homoplasy is due to frequent recombination among closely related strains. Recombination events imply that the transmission of TTV is not clonal and provide the necessary basis to explain (i) the high degree of genetic divergence between TTV isolates, (ii) the lack of population structure on a world scale, and (iii) the number of highly divergent strains that seems typical of this virus. We show that recombination phenomena can be detected by phylogenetic analyses in very short sequences when a sufficiently large data set is available.
journal_name
J Mol Evoljournal_title
Journal of molecular evolutionauthors
Manni F,Rotola A,Caselli E,Bertorelle G,Di Luca Ddoi
10.1007/s00239-002-2352-ykeywords:
subject
Has Abstractpub_date
2002-11-01 00:00:00pages
563-72issue
5eissn
0022-2844issn
1432-1432journal_volume
55pub_type
杂志文章abstract::Nuclear DNA contents were estimated by microdensitometry in five species of Akodon rodents: Arodon molinae, A. dolores, A. mollis, A. azarae, Bolomys obscurus) and in three chromosomal varieties of A. molinae (2n = 42; 2n = 43, 2n = 22). The data obtained showed that the species with the highest DNA content was B. obs...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/BF02101640
更新日期:1983-01-01 00:00:00
abstract::The periodic protein collagen is of special interest for the study of the relationship which exists between the structure of a protein and that of its mRNA, because oligopeptides containing glycine, proline (hydroxyproline) and alanine occur with great frequency in it. Collagen is particularly rich in these amino acid...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/BF01739101
更新日期:1976-08-03 00:00:00
abstract::We examined the cis- vs. trans-splicing status of the mitochondrial group II intron nad1i728 in 439 species (427 genera) of land plants, using both Southern hybridization results (for 416 species) and intron sequence data from the literature. A total of 164 species (157 genera), all angiosperms, was found to have a tr...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/s00239-004-2606-y
更新日期:2004-07-01 00:00:00
abstract::Two families of high-cysteine chorion proteins in Bombyx mori are encoded in 15 tandemly arranged nonidentical gene pairs. It is assumed that this locus arose by duplication with subsequent sequence divergence. We have compared DNA sequences from two such neighboring pairs of genes in an attempt to understand the mann...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/BF02104732
更新日期:1984-01-01 00:00:00
abstract::The DNA sequences of three members of the Alu family of repeated sequences located 5' to the chimpanzee alpha 2 gene have been determined. The base sequences of the three corresponding human Alu family repeats have been previously determined, permitting the comparison of identical Alu family members in human and chimp...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/BF02115687
更新日期:1985-01-01 00:00:00
abstract::The possibility of surface catalysed condensation of unsubstituted amino acids on kaolinite in aqueous systems at elevated temperatures was investigated; no evidence of clay catalysed polycondensation has been found. The thermodynamic feasibility of the hypothetical lysine/dilysine condensation reaction in the tempera...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/BF01733261
更新日期:1978-12-29 00:00:00
abstract::The diversity of functional genes and the related processes are important issues for conservation biology. This is especially relevant for populations that have suffered from demographic reduction as a consequence of the processes of postglacial colonization. In this perspective, the aims of the present study are (1) ...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/s00239-011-9456-1
更新日期:2011-08-01 00:00:00
abstract::The gene (fus) coding for elongation factor G (EF-G) of the extremely thermophilic eubacterium Thermotoga maritima was identified and sequenced. The EF-G coding sequence (2046 bp) was found to lie in an operon-like structure between the ribosomal protein S7 gene (rpsG) and the elongation factor Tu (EF-Tu) gene (tuf). ...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/BF02193628
更新日期:1991-08-01 00:00:00
abstract::In mammals, chicken-type (c-type) lysozymes are part of the innate immune system, killing bacteria by degrading peptidoglycan in their cell walls. Many of the studies on the evolution of c-type lysozymes have focused on its new digestive function, including the duplicated stomach lysozymes in ruminants. Similarly, in ...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/s00239-019-09910-7
更新日期:2019-12-01 00:00:00
abstract::Annotated, complete DNA sequences are available for 213 mitochondrial genomes from 132 species. These provide an extensive sample of evolutionary adjustment of codon usage and meaning spanning the history of this organelle. Because most known coding changes are mitochondrial, such data bear on the general mechanism of...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/s002390010220
更新日期:2001-10-01 00:00:00
abstract::The local stability of unbranched biosynthetic pathways is examined by mathematical analysis and computer simulation using a novel nonlinear formalism that appears to accurately describe biochemical systems. Four factors affecting the stability are examined: strength of feedback inhibition, equalization of the values...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/BF01741242
更新日期:1975-08-05 00:00:00
abstract::The nearly neutral theory attributes most nucleotide substitution and polymorphism to genetic drift acting on weakly selected mutants, and assumes that the selection coefficients for these mutants are drawn from a continuous distribution. This means that parameter estimation can require numerical integration, and this...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/s00239-008-9146-9
更新日期:2008-10-01 00:00:00
abstract::This paper constructs a temporal scale for bacterial evolution by tying ecological events that took place at known times in the geological past to specific branch points in the genealogical tree relating the 16S ribosomal RNAs of eubacteria, mitochondria, and chloroplasts. One thus obtains a relationship between time ...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/BF02111283
更新日期:1987-01-01 00:00:00
abstract::Computational and experimental attempts tried to characterize a universal core of genes representing the minimal set of functional needs for an organism. Based on the increasing number of available complete genomes, comparative genomics has concluded that the universal core contains < 50 genes. In contrast, experiment...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/s00239-005-0250-9
更新日期:2006-12-01 00:00:00
abstract::In the traditional concept for the origin of life as proposed by Oparin and Haldane in the 1920s, prebiotic reactants became slowly concentrated in the primordial oceans and life evolved slowly from a series of highly protracted chemical reactions during the first billion years of Earth's history. However, chemical e...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/BF02102187
更新日期:1991-01-01 00:00:00
abstract::It is generally considered that if an RNA World ever existed that it would be driven by an RNA capable of RNA replication. Whether such a catalytic RNA could emerge in an RNA World or not, there would need to be prior routes to increasing complexity in order to produce it. It is hypothesized here that increasing seque...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/s00239-018-9846-8
更新日期:2018-06-01 00:00:00
abstract::The first intron of the gene encoding one of the alcohol dehydrogenase isoenzymes (ADH-1) in Ceratitis capitata is highly polymorphic in size. Five size variants of this intron were isolated from different strains and populations and characterized. Restriction map and sequence analysis showed that the intron size poly...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/s00239-004-2596-9
更新日期:2004-06-01 00:00:00
abstract::Two catalytic functions were required, minimally, for the appearance of DNA in evolution: a ribonucleotide reductase (RNR) and a reverse transcriptase (RT). If one accepts the explanatory strength of the RNA world model, it is clear that DNA molecules arose in the RNA world at some stage during the early evolution of ...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/pl00006368
更新日期:1998-08-01 00:00:00
abstract::Lepidoptera (comprised of butterflies and moths) is one of the largest groups of insects, including more than 160,000 described species. Chemoreception plays important roles in the adaptation of these species to a wide range of niches, e.g., plant hosts, egg-laying sites, and mates. This study investigated the molecul...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/s00239-014-9633-0
更新日期:2014-08-01 00:00:00
abstract::Recent experience with molecular phylogeny has shown that all molecular markers have strengths and weaknesses. Nonetheless, despite several notable discrepancies with phylogenies obtained from protein data, the merits of the small subunit ribosomal RNA (SSU rRNA) as a molecular phylogenetic marker remain indisputable....
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/s002390010120
更新日期:2000-12-01 00:00:00
abstract::The slow-evolving mitochondrial DNAs of plants have potentially conserved information on the phylogenetic branching of the earliest land plants. We present the nad2 gene structures in hornworts and liverworts and in the presumptive earliest-branching vascular land plant clade, the Lycopodiopsida. Taken together with t...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/s00239-002-2324-2
更新日期:2002-09-01 00:00:00
abstract::One crucial event during evolution to multicellularity was the development of either direct cell-cell contact or indirect interaction via extracellular matrix (ECM) molecules. The identification of those polypeptides provides conclusive data on the phylogenetic relationship of metazoan phyla and helps us to understand...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/s002390010230
更新日期:2001-10-01 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::A reaction which oligomerizes nucleotides under possible prebiotic conditions has been characterized. Nucleoside monophosphate in the presence of cyanamide at acid pH condenses to form dithymideine pyrophosphate and phosphodiester bonded compounds. Imidazole compounds and activated precursors such as nucleoside tripho...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/BF01732356
更新日期:1975-11-04 00:00:00
abstract::Many proteins exhibit sequence periodicity, often correlated with a visible structural periodicity. The statistical significance of such periodicity can be assessed by means of a chi-squared-based test, with significance thresholds being calculated from shuffled sequences. Comparison of the complete proteomes of 45 sp...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/s00239-004-0189-2
更新日期:2005-04-01 00:00:00
abstract::Two competing effects at two vastly different scales may explain collagen's current translation length. The necessity to have long molecules for maintaining mechanical integrity at the organism and supraorganism scales may be limited by the need to have small molecules capable of robust self-assembly at the nanoscale....
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/s00239-008-9111-7
更新日期:2008-06-01 00:00:00
abstract::The trnT-trnF region is located in the large single-copy region of the chloroplast genome. It consists of the trnL intron, a group I intron, and the trnT-trnL and trnL-trnF intergenic spacers. We analyzed the evolution of the region in the three genera of the gymnosperm lineage Gnetales (Gnetum, Welwitschia, and Ephed...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/s00239-004-0240-3
更新日期:2005-10-01 00:00:00
abstract::Explicit evaluation of the accuracy and power of maximum likelihood and Bayesian methods for detecting site-specific positive Darwinian selection presents a challenge because selective consequences of single amino acid changes are generally unknown. We exploited extensive molecular and functional characterization of a...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/s00239-008-9172-7
更新日期:2008-11-01 00:00:00
abstract::Twenty-seven protein sequence elements, six to nine amino acids long, were extracted from 15 phylogenetically diverse complete prokaryotic proteomes. The elements are present in all of these proteomes, with at least one copy each (omnipresent elements), and have presumably been conserved since the last universal commo...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/s00239-007-9032-x
更新日期:2007-12-01 00:00:00
abstract::Members of the serpin (serine protease inhibitor) superfamily of genes are well represented in both human and murine genomes. In many cases it is possible to identify a definite ortholog on the basis of sequence similarity and by examining the surrounding genes at syntenic loci. We have recently examined the murine se...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/s00239-004-2640-9
更新日期:2004-10-01 00:00:00