Abstract：
:Langley and Fitch (1974, 1976) have shown that the pattern of nucleotide substitutions in proteins is inconsistent with a Poisson process with constant rate. From this they conclude that the rate is temporally heterogeneous. It is pointed out in this note that a process which is temporally homogeneous but not a Poisson process is compatible with the data if the coefficient of variation of the time between substitutions is around 1.63. Furthermore, theoretical analysis of samples from neutral phylogenies shows that these samples should not appear to be samples from a Poisson process, but should deviate from a Poisson process in the same direction, though perhaps not to the same extent, as do the data.
journal_name
J Mol Evoljournal_title
Journal of molecular evolutionauthors
Gillespie JH,Langley CHdoi
10.1007/BF01732751subject
Has Abstractpub_date
1979-06-08 00:00:00pages
27-34issue
1eissn
0022-2844issn
1432-1432journal_volume
13pub_type
杂志文章abstract：:Using all currently predicted coding regions in the honeybee genome, a novel form of synonymous codon bias is presented that affects the usage of particular codons dependent on the surrounding nucleotides in the coding region. Nucleotides at the third codon site are correlated, dependent on their weak (adenine [A] or ...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-006-0198-4
更新日期：2007-06-01 00:00:00
abstract：:Collagen is an important structural protein and the most abundant protein in mammals. In several research fields, structural analysis of collagens is performed. Fibrillar collagens almost entirely consist of continuous repeats of GXY, where G is glycine, X is often proline or alanine and Y is often hydroxyproline or a...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-018-9844-x
更新日期：2018-06-01 00:00:00
abstract：:Gene duplication by retrotransposition duplicates only the coding and untranslated regions of a gene and, thus, biases retroduplicated genes toward having different expression patterns from their parental genes. As such, genes duplicated by retrotransposition are more likely to develop novel expression domains. To exp...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-008-9098-0
更新日期：2008-05-01 00:00:00
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journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-004-2630-y
更新日期：2004-09-01 00:00:00
abstract：:Human endogenous retroviruses (HERVs) are the remnants of ancient germ cell infection by exogenous retroviruses and occupy up to 8% of the human genome. It has been suggested that HERV sequences have contributed to primate evolution by regulating the expression of cellular genes and mediating chromosome rearrangements...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-004-2656-1
更新日期：2004-11-01 00:00:00
abstract：:The evolutionary relationships among arthropod hemocyanins and insect hexamerins were investigated. A multiple sequence alignment of 12 hemocyanin and 31 hexamerin subunits was constructed and used for studying sequence conservation and protein phylogeny. Although hexamerins and hemocyanins belong to a highly divergen...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/pl00006366
更新日期：1998-07-01 00:00:00
abstract：:The mitochondrial genome of yeast (S. cerevisiae or S. carlsbergensis) appears to be formed by 60-70 genetic units, each one of which is formed by (1) a GC-rich sequence, possibly having a regulatory role; (2) a gene, and (3) an AT-rich spacer, which probably is not transcribed. Recombination in this genome appears to...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/BF01796120
更新日期：1976-12-31 00:00:00
abstract：:All modern mammals contain a distinctive, highly repeated (> or = 50,000 members) family of long interspersed repeated DNA called the L1 (LINE 1) family. While the modern L1 families were derived from a common ancestor that predated the mammalian radiation approximately 80 million years ago, most of the members of the...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/BF02407302
更新日期：1993-01-01 00:00:00
abstract：:The mammalian defensin molecule is a short, highly cationic peptide cytotoxic to both microbial and mammalian cells which is cleaved from a precursor including a signal peptide and a highly anionic propiece. A phylogenetic analysis of 28 complete sequences from five mammalian species (mouse, rat, guinea pig, rabbit, a...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/pl00006191
更新日期：1997-06-01 00:00:00
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journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-017-9815-7
更新日期：2017-12-01 00:00:00
abstract：:In this article, we investigated the structural and dynamical evolutionary behaviour of a set of ten thioredoxin proteins as formed by three extant forms and seven resurrected ones in laboratory. Starting from the crystallographic structures, we performed all-atom molecular dynamics simulations and compare the traject...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-019-09894-4
更新日期：2019-07-01 00:00:00
abstract：:Energised by the protonmotive force and with the intervention of inorganic catalysts, at base Life reacts hydrogen from a variety of sources with atmospheric carbon dioxide. It seems inescapable that life emerged to fulfil the same role (i.e., to hydrogenate CO(2)) on the early Earth, thus outcompeting the slow geoche...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-009-9289-3
更新日期：2009-11-01 00:00:00
abstract：:We have performed DNA-DNA hybridization experiments among several species of Drosophila using the evolutionarily conserved portion of the genome representing sequences coding for amino acids of proteins. This was done by using as tracer, radioactively labeled complementary DNA that was reverse transcribed from adult m...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/BF00182390
更新日期：1992-02-01 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：:Oligonucleotide cataloguing has been used to characterize a number of 5S RNA species from various Procaryotes. Such catalogs can be used to establish certain and detailed phylogenetic relationships among organisms. Confining attention at present to four Families of Procaryotes, theEnterobacteriaceae, theBacillaceae, t...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/BF01659163
更新日期：1972-06-01 00:00:00
abstract：:At least two polymorphic Alu insertions have been previously identified and characterized within the class I region of the major histocompatibility complex (MHC). We have identified another two new polymorphic Alu insertions, AluyHJ and AluyHF, located near HLA-J and HLA-F, respectively, within the a block of the MHC....
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-002-2367-4
更新日期：2002-12-01 00:00:00
abstract：:Wild-type Escherichia coli utilizes glycerol aerobically through an inducible pathway mediated by an ATP-dependent kinase and a glycerol 3-phosphate dehydrogenase which is a flavoprotein. A mutant, strain ECL424, employing a novel pathway for glycerol utilization was isolated. The novel pathway is mediated by an NAD-l...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/BF02102318
更新日期：1983-01-01 00:00:00
abstract：:DEAD-box proteins are found in all domains of life and participate in almost all cellular processes that involve RNA. The presence of DEAD and Helicase_C conserved domains distinguish these proteins. DEAD-box proteins exhibit RNA-dependent ATPase activity in vitro, and several also show RNA helicase activity. In this ...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-011-9441-8
更新日期：2011-04-01 00:00:00
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
doi：10.1007/pl00006562
更新日期：1999-09-01 00:00:00
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
doi：10.1007/BF01732678
更新日期：1981-01-01 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：:Small heat shock proteins (sHSPs), as one subclass of molecular chaperones, are important for cells to protect proteins under stress conditions. Unlike the large HSPs (represented by Hsp60 and Hsp70), sHSPs are highly divergent in both primary sequences and oligomeric status, with their evolutionary relationships bein...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-005-0076-5
更新日期：2006-03-01 00:00:00
abstract：:It is known that globin genes contain three exons with the middle exon coding for a four-helical supersecondary structure responsible for heme binding. Since this portion of the globin peptide chain can be structurally superimposed onto the cytochrome c and cytochrome b5 chains (Argos and Rossmann 1979), it can be inf...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/BF01731583
更新日期：1980-12-01 00:00:00
abstract：:The transposable element mariner occurs widely in the melanogaster species group of Drosophila. However, in drosophilids outside of the melanogaster species group, sequences showing strong DNA hybridization with mariner are found only in the genus Zaprionus. The mariner sequence obtained from Zaprionus tuberculatus is...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/BF02102804
更新日期：1991-12-01 00:00:00
abstract：:We have sequenced the nuclear and mitochondrial small subunit rRNA genes (rns) and the mitochondrial genes coding for subunits 1 and 3 of the cytochrome oxidase (cox1 and cox3, respectively) of the chytridiomycete Allomyces macrogynus. Phylogenetic trees inferred from the derived COX1 and COX3 proteins and the nuclear...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/BF00175824
更新日期：1995-11-01 00:00:00
abstract：:Spermatogenesis is one of the most complex biological processes undergone by any organism, making it susceptible to perturbations that result in male sterility. Research has demonstrated that mutant phenotypes can be obtained from the disruption of epigenetic modifications, which are commonly microRNA guided. Employin...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-011-9478-8
更新日期：2011-12-01 00:00:00
abstract：:In this work detailed statistics on ancestral gene duplication and gene conservation in completely sequenced cellular genomes are presented. Analysis of open reading frame (ORF) products having simultaneous matches in several distinct organisms showed a significant correlation between duplication and conservation. Sys...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/pl00006580
更新日期：1999-11-01 00:00:00
abstract：:It has been argued that downstream enzymes in metabolic pathways are expected to be subject to reduced selective constraint, while upstream enzymes, particularly those at pathway branch points, are expected to exhibit more frequent adaptive substitution than downstream enzymes. We examined whether these expectations a...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-008-9105-5
更新日期：2008-08-01 00:00:00
abstract：:The finding that ribozymes can catalyze RNA chain elongation has led to the proposal that an early self-replicating system could have consisted of RNA alone. In such a chain elongation reaction, the Tetrahymena ribozyme was found to select 3',5'-linked substrates from a pool that contained a large molar excess of 2',5...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/BF02602919
更新日期：1989-12-01 00:00:00
abstract：:Mutational bias toward expansion or contraction of simple sequence repeats (SSRs) is referred to as directionality of SSR evolution. In this communication, we report the mutational bias exhibited by mononucleotide SSRs occurring in the non-coding regions of several prokaryotic genomes. Our investigations revealed that...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-012-9491-6
更新日期：2012-04-01 00:00:00
