A method for determining the position and size of optimal sequence regions for phylogenetic analysis.


:The availability of fast and accurate sequencing procedures along with the use of PCR has led to a proliferation of studies of variability at the molecular level in populations. Nevertheless, it is often impractical to examine long genomic stretches and a large number of individuals at the same time. In order to optimize this kind of study, we suggest a heuristic procedure for detection of the shortest region whose informational content can be considered sufficient for significant phylogenetic reconstruction. The method is based on the comparison of the pairwise genetic distances obtained from a set of sequences of reference to those obtained for different windows of variable size and position by means of a simple index. We also present an approach for testing whether the informative content in the stretches selected in this way is significantly different from the corresponding content shown by the larger genomic regions used as reference. Application of this test to the analysis of the VP1 protein gene of foot-and-mouth-disease type C virus allowed us to define optimal stretches whose informative content is not significantly different from that displayed by the complete VP1 sequence. We showed that the predictions made for type C sequences are valid for type O sequences, indicating that the results of the procedure are consistent.


J Mol Evol


Martin MJ,González-Candelas F,Sobrino F,Dopazo J




Has Abstract


1995-12-01 00:00:00












  • Molecular characterization of the Rh-like locus and gene transcripts from the rhesus monkey (Macaca mulatta).

    abstract::The human Rh blood group locus consists of two structurally related genes (D and CcEe) in Rh-positive haplotypes but a single gene (CcEe) in Rh-negative haplotypes. The genome of rhesus monkeys (Macaca mulatta), while not expressing any of the human Rh D, C, c, E, or e specificities, carries a Rh-like locus strongly r...

    journal_title:Journal of molecular evolution

    pub_type: 杂志文章


    authors: Mouro I,Le Van Kim C,Cherif-Zahar B,Salvignol I,Blancher A,Cartron JP,Colin Y

    更新日期:1994-02-01 00:00:00

  • The compositional properties of human genes.

    abstract::The present work represents the first attempt to study in greater detail previously proposed compositional correlations in genomes, based on a body of additional data relating to gene localizations as well as to extended flanking sequences extracted from gene banks. We have investigated the correlations that exist bet...

    journal_title:Journal of molecular evolution

    pub_type: 杂志文章


    authors: Aïssani B,D'Onofrio G,Mouchiroud D,Gardiner K,Gautier C,Bernardi G

    更新日期:1991-06-01 00:00:00

  • Intron dynamics and the evolution of integrin beta-subunit genes: maintenance of an ancestral gene structure in the coral, Acropora millepora.

    abstract::We have determined the genomic structure of an integrin beta-subunit gene from the coral, Acropora millepora. The coding region of the gene contains 26 introns, spaced relatively uniformly, and this is significantly more than have been found in any integrin beta-subunit genes from higher animals. Twenty-five of the 26...

    journal_title:Journal of molecular evolution

    pub_type: 杂志文章


    authors: Schmitt DM,Brower DL

    更新日期:2001-12-01 00:00:00

  • Phylogeny of protozoa deduced from 5S rRNA sequences.

    abstract::The nucleotide sequences of 5S rRNAs from three protozoa, Bresslaua vorax, Euplotes woodruffi and Chlamydomonas sp. have been determined and aligned together with the sequences of 12 protozoa species including unicellular green algae already reported by the authors and others. Using this alignment, a phylogenic tree o...

    journal_title:Journal of molecular evolution

    pub_type: 杂志文章


    authors: Kumazaki T,Hori H,Osawa S

    更新日期:1983-01-01 00:00:00

  • Molecular clock calibrations and metazoan divergence dates.

    abstract::It has recently been argued that living metazoans diverged over 800 million years ago, based on evidence from 22 nuclear genes for such a deep divergence between vertebrates and arthropods (Gu 1998). Two "internal" calibration points were used. However, only one fossil divergence date (the mammal-bird split) was direc...

    journal_title:Journal of molecular evolution

    pub_type: 杂志文章


    authors: Lee MS

    更新日期:1999-09-01 00:00:00

  • The functional gene diversity in natural populations over postglacial areas: the shaping mechanisms behind genetic composition of longnose dace (Rhinichthys cataractae) in northeastern North America.

    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


    authors: Girard P,Angers B

    更新日期:2011-08-01 00:00:00

  • Pathways of Genetic Code Evolution in Ancient and Modern Organisms.

    abstract::There have been two distinct phases of evolution of the genetic code: an ancient phase--prior to the divergence of the three domains of life, during which the standard genetic code was established--and a modern phase, in which many alternative codes have arisen in specific groups of genomes that differ only slightly f...

    journal_title:Journal of molecular evolution

    pub_type: 杂志文章,评审


    authors: Sengupta S,Higgs PG

    更新日期:2015-06-01 00:00:00

  • The paradox of MHC-DRB exon/intron evolution: alpha-helix and beta-sheet encoding regions diverge while hypervariable intronic simple repeats coevolve with beta-sheet codons.

    abstract::Twenty-one different caprine and 13 ovine MHC-DRB exon 2 sequences were determined including part of the adjacent introns containing simple repetitive (gt)n(ga)m elements. The positions for highly polymorphic DRB amino acids vary slightly among ungulates and other mammals. From man and mouse to ungulates the basic (gt...

    journal_title:Journal of molecular evolution

    pub_type: 杂志文章


    authors: Schwaiger FW,Weyers E,Epplen C,Brün J,Ruff G,Crawford A,Epplen JT

    更新日期:1993-09-01 00:00:00

  • Characterization of mitochondrial small-subunit ribosomal RNAs from holoparasitic plants.

    abstract::Mitochondrial small-subunit (19S) rDNA sequences were obtained from 10 angiosperms to further characterize sequence divergence levels and structural variation in this molecule. These sequences were derived from seven holoparasitic (nonphotosynthetic) angiosperms as well as three photosynthetic plants. 19S rRNA is comp...

    journal_title:Journal of molecular evolution

    pub_type: 杂志文章


    authors: Duff RJ,Nickrent DL

    更新日期:1997-12-01 00:00:00

  • Fungal origin by horizontal transfer of a plant mitochondrial group I intron in the chimeric CoxI gene of Peperomia.

    abstract::We present phylogenetic evidence that a group I intron in an angiosperm mitochondrial gene arose recently by horizontal transfer from a fungal donor species. A 1,716-bp fragment of the mitochondrial coxI gene from the angiosperm Peperomia polybotrya was amplified via the polymerase chain reaction and sequenced. Compar...

    journal_title:Journal of molecular evolution

    pub_type: 杂志文章


    authors: Vaughn JC,Mason MT,Sper-Whitis GL,Kuhlman P,Palmer JD

    更新日期:1995-11-01 00:00:00

  • Detecting site-specific biochemical constraints through substitution mapping.

    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


    authors: Dutheil J

    更新日期:2008-09-01 00:00:00

  • Two paralogous genes encoding small subunits of ADP-glucose pyrophosphorylase in maize, Bt2 and L2, replace the single alternatively spliced gene found in other cereal species.

    abstract::Two types of gene encoding small subunits (SSU) of ADP-glucose pyrophosphorylase, a starch-biosynthetic enzyme, have been found in cereals and other grasses. One of these genes encodes two SSU proteins. These are targeted to different subcellular compartments and expressed in different organs of the plant: the endospe...

    journal_title:Journal of molecular evolution

    pub_type: 杂志文章


    authors: Rösti S,Denyer K

    更新日期:2007-09-01 00:00:00

  • Ubiquitin genes as a paradigm of concerted evolution of tandem repeats.

    abstract::Ubiquitin is remarkable for its ubiquitous distribution and its extreme protein sequence conservation. Ubiquitin genes comprise direct repeats of the ubiquitin coding unit with no spacers. The nucleotide sequences of several ubiquitin repeats from each of humans, chicken, Xenopus, Drosophila, barley, and yeast have re...

    journal_title:Journal of molecular evolution

    pub_type: 杂志文章


    authors: Sharp PM,Li WH

    更新日期:1987-01-01 00:00:00

  • Molecular evolution at the self-incompatibility locus of Physalis longifolia (Solanaceae).

    abstract::The simple codominant expression of the alleles at the self-incompatibility locus ( S) of Solanaceae and their extraordinary spectrum of sequence diversity present an ideal case for understanding the molecular forces that shape the sequence polymorphism of genes involved in recognition reactions. Here, with unpreceden...

    journal_title:Journal of molecular evolution

    pub_type: 杂志文章


    authors: Lu Y

    更新日期:2002-06-01 00:00:00

  • Evolution of Single-Domain Globins in Hydrothermal Vent Scale-Worms.

    abstract::Hypoxia at deep-sea hydrothermal vents represents one of the most basic challenges for metazoans, which then requires specific adaptations to acquire oxygen to meet their metabolic needs. Hydrothermal vent scale-worms (Polychaeta; Polynoidae) express large amounts of extracellular single- and multi-domain hemoglobins,...

    journal_title:Journal of molecular evolution

    pub_type: 杂志文章


    authors: Projecto-Garcia J,Le Port AS,Govindji T,Jollivet D,Schaeffer SW,Hourdez S

    更新日期:2017-12-01 00:00:00

  • Phylogenetic depth of Thermotoga maritima inferred from analysis of the fus gene: amino acid sequence of elongation factor G and organization of the Thermotoga str operon.

    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


    authors: Tiboni O,Cantoni R,Creti R,Cammarano P,Sanangelantoni AM

    更新日期:1991-08-01 00:00:00

  • Evolutionary sequence divergence within repeated DNA families of higher plant genomes. II. Analysis of thermal denaturation.

    abstract::An assay based on derivative analysis of thermal denaturation (melting) behavior of reassociated DNA was developed in an attempt to characterize the sequence relationships in repeated DNA families according to the homogeneous or heterogeneous models of Bendich and Anderson (1977). The validity of the technique was con...

    journal_title:Journal of molecular evolution

    pub_type: 杂志文章


    authors: Preisler RS,Thompson WF

    更新日期:1981-01-01 00:00:00

  • Horizontal gene transfer of "prototype" Nramp in bacteria.

    abstract::Eukaryotic Nramp genes encode divalent metal ion permeases important for nutrition and resistance to microbial infection. Bacterial homologs encode proton-dependent transporters of manganese (MntH), and other divalent metal ions. Bacterial MntH were classified in three homology groups (A, B, C) and MntH C further subd...

    journal_title:Journal of molecular evolution

    pub_type: 杂志文章


    authors: Richer E,Courville P,Bergevin I,Cellier MF

    更新日期:2003-10-01 00:00:00

  • Accuracy of estimated phylogenetic trees from molecular data. II. Gene frequency data.

    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


    authors: Nei M,Tajima F,Tateno Y

    更新日期:1983-01-01 00:00:00

  • Structural constraints in expansion segments from a midge 26S rDNA.

    abstract::DNA sequences representing approximately 40% of the large-subunit rRNA gene from the lower dipteran Chironomus thummi were analyzed. Once aligned with their Drosophila counterparts, sequence and base content comparisons were carried out. Sequence identity was found to be high overall, except for six regions that displ...

    journal_title:Journal of molecular evolution

    pub_type: 杂志文章


    authors: Gorab E,Garcia de Lacoba M,Botella LM

    更新日期:1995-12-01 00:00:00

  • Enzyme-coding genes as molecular clocks: the molecular evolution of animal alpha-amylases.

    abstract::We constructed a cDNA library for the beetle, Tribolium castaneum. This library was screened using a cloned amylase gene from Drosophila melanogaster as a molecular probe. Beetle amylase cDNA clones were isolated from this bank, and the nucleotide sequence was obtained for a cDNA clone with a coding capacity for 228 a...

    journal_title:Journal of molecular evolution

    pub_type: 杂志文章


    authors: Hickey DA,Benkel BF,Boer PH,Genest Y,Abukashawa S,Ben-David G

    更新日期:1987-01-01 00:00:00

  • Nonuniform evolution of duplicated, developmentally controlled chorion genes in a silkmoth.

    abstract::We report the sequence of A/B.L1, a tightly linked pair of genes from the A and B chorion families in Bombyx mori. Comparison with the previously characterized A/B.L11 and A/B.L12 pairs from the same species reveals moderate sequence divergence, which is clearly nonuniform. Although the average divergence of A/B.L12 f...

    journal_title:Journal of molecular evolution

    pub_type: 杂志文章


    authors: Tsitilou SG,Kafatos FC

    更新日期:1989-11-01 00:00:00

  • Phylogenetic relationships of HMG box DNA-binding domains.

    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


    authors: Griess EA,Rensing SA,Grasser KD,Maier UG,Feix G

    更新日期:1993-08-01 00:00:00

  • The photolytic degradation and oxidation of organic compounds under simulated Martian conditions.

    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


    authors: Oró J,Holzer G

    更新日期:1979-12-01 00:00:00

  • Estimation of hominoid phylogeny from a DNA hybridization data set.

    abstract::Analysis of the expanded data set of Sibley and Ahlquist (1987) on primate phylogeny using a maximum likelihood mixed model analysis of variance method shows that there is significant evidence for resolving the Homo-Pan-Gorilla trifurcation in favor of a Homo-Pan clade. The resulting tree is close to that estimated by...

    journal_title:Journal of molecular evolution

    pub_type: 杂志文章


    authors: Felsenstein J

    更新日期:1987-01-01 00:00:00

  • Phylogenetic and biochemical studies reveal a potential evolutionary origin of small heat shock proteins of animals from bacterial class A.

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    journal_title:Journal of molecular evolution

    pub_type: 杂志文章


    authors: Fu X,Jiao W,Chang Z

    更新日期:2006-03-01 00:00:00

  • Analysis of directional mutation pressure and nucleotide content in mitochondrial cytochrome b genes.

    abstract::We present a new approach for analyzing directional mutation pressure and nucleotide content in protein-coding genes. Directional mutation pressure, the heterogenicity in the likelihood of different nucleotide substitutions, is used to explain the increasing or decreasing guanine-cytosine content (GC%) in DNA and is r...

    journal_title:Journal of molecular evolution

    pub_type: 杂志文章


    authors: Jermiin LS,Graur D,Lowe RM,Crozier RH

    更新日期:1994-08-01 00:00:00

  • DNA polymerase C of the thermophilic bacterium Thermus aquaticus: classification and phylogenetic analysis of the family C DNA polymerases.

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    journal_title:Journal of molecular evolution

    pub_type: 杂志文章


    authors: Huang YP,Ito J

    更新日期:1999-06-01 00:00:00

  • Reduced polymorphism in the chimpanzee semen coagulating protein, semenogelin I.

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    journal_title:Journal of molecular evolution

    pub_type: 杂志文章


    authors: Kingan SB,Tatar M,Rand DM

    更新日期:2003-08-01 00:00:00

  • The 3-Minihelix tRNA Evolution Theorem.

    abstract::Transfer RNA (tRNA) is the central intellectual property in the evolution of life on Earth. tRNA evolved from repeats and inverted repeats of known sequence. The anticodon and the T stem-loop-stems are homologs with significant conserved sequence identity. A number of models have been advanced to explain tRNA evolutio...

    journal_title:Journal of molecular evolution

    pub_type: 信件


    authors: Burton ZF

    更新日期:2020-04-01 00:00:00