Toward assigning helical regions in alignments of ribosomal RNA and testing the appropriateness of evolutionary models.

abstract：:Group I introns are mobile RNA enzymes (ribozymes) that encode conserved primary and secondary structures required for autocatalysis. The group I intron that interrupts the tRNA-Leu gene in cyanobacteria and plastids is remarkable because it is the oldest known intervening sequence and may have been present in the com...

journal_title：Journal of molecular evolution

authors： Simon D,Fewer D,Friedl T,Bhattacharya D

更新日期：2003-12-01 00:00:00

abstract：:Introns are generally believed to evolve too rapidly and too erratically to be of much use in phylogenetic reconstructions. Few phylogenetically informative intron sequences are available, however, to ascertain the validity of this supposition. In the present study the supposition was tested on the example of the mamm...

journal_title：Journal of molecular evolution

authors： Kupfermann H,Satta Y,Takahata N,Tichy H,Klein J

更新日期：1999-06-01 00:00:00

abstract：:Since the genetic code first was determined, many have claimed that it is organized adaptively, so as to assign similar codons to similar amino acids. This claim has proved difficult to establish due to the absence of relevant comparative data on alternative primordial codes and of objective measures of amino acid exc...

journal_title：Journal of molecular evolution

authors： Stoltzfus A,Yampolsky LY

更新日期：2007-10-01 00:00:00

abstract：:Computer analyses of various genome sequences revealed the existence of certain periodical patterns of adenine-adenine dinucleotides (ApA). For each genome sequence of 13 eubacteria, 3 archaebacteria, 10 eukaryotes, 60 mitochondria, and 9 chloroplasts, we counted frequencies of ApA dinucleotides at each downstream pos...

journal_title：Journal of molecular evolution

authors： Tomita M,Wada M,Kawashima Y

更新日期：1999-08-01 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

authors： Jin RZ,Tang JC,Lin EC

更新日期：1983-01-01 00:00:00

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

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

更新日期：1995-11-01 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

authors： Del Galdo S,Alba J,Amadei A,D'Abramo M

更新日期：2019-07-01 00:00:00

abstract：:In this study, the molecular population genetics of the orangutan's alpha-2 globin (HBA2) gene were investigated in order to test for the action of natural selection. Haplotypes from 28 orangutan chromosomes were collected from a 1.46-kilobase region of the alpha-2 globin locus. While many aspects of the data were con...

journal_title：Journal of molecular evolution

authors： Steiper ME,Wolfe ND,Karesh WB,Kilbourn AM,Bosi EJ,Ruvolo M

更新日期：2005-03-01 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

authors： Dalevi DA,Eriksen N,Eriksson K,Andersson SG

更新日期：2002-07-01 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

authors： Welch JJ,Eyre-Walker A,Waxman D

更新日期：2008-10-01 00:00:00

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

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

更新日期：1991-06-01 00:00:00

abstract：:A comparison of mitochondrial DNA sequences was undertaken for two genes among orangutans from Borneo and Sumatra. The distribution of haplotypes among 42 individuals for NADH dehydrogenease subunit 3 and 39 individuals for cytochrome B was used to infer population structure. The haplotypes among all Bornean orangutan...

journal_title：Journal of molecular evolution

authors： Muir CC,Galdikas BM,Beckenbach AT

更新日期：2000-11-01 00:00:00

abstract：:Four cloned unique sequences from the human Y chromosome, two of which are found only on the Y chromosome and two of which are on both the X and Y chromosomes, were hybridized to restriction enzyme-treated DNA samples of a male and a female chimpanzee (Pan troglodytes), gorilla (Gorilla gorilla), and pig-tailed macaqu...

journal_title：Journal of molecular evolution

authors： Erickson RP

更新日期：1987-01-01 00:00:00

abstract：:We recently sequenced the genome of the first subterrestrial metazoan, the nematode Halicephalobus mephisto. A central finding was a dramatic expansion of genes encoding avrRpt2 induced gene (AIG1), and 70 kDa heat shock (Hsp70) domains. While the role of Hsp70 in thermotolerance is well established, the contribution ...

journal_title：Journal of molecular evolution

authors： Guerin MN,Weinstein DJ,Bracht JR

更新日期：2019-12-01 00:00:00

abstract：:Ornithine decarboxylase (ODC) is the first enzyme in the polyamine biosynthetic pathway. We have studied the evolutionary history of the mammalian ODC mRNA, focusing on the rate of accumulation of sequence divergence within specific subregions of the molecule. The phylogenetic relationships among the mRNAs from severa...

journal_title：Journal of molecular evolution

authors： Johannes GJ,Berger FG

更新日期：1993-06-01 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

authors： Calixto CP,Waugh R,Brown JW

更新日期：2015-02-01 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

authors： Schütze J,Skorokhod A,Müller IM,Müller WE

更新日期：2001-10-01 00:00:00

abstract：:Sequence data from regions of five vertebrate vitellogenin genes were used to examine the frequency, distribution, and mutability of the dinucleotide CpG, the preferred modification site for eukaryotic DNA methyltransferases. The observed level of the CpG dinucleotide in all five genes was markedly lower than that exp...

journal_title：Journal of molecular evolution

authors： Cooper DN,Gerber-Huber S,Nardelli D,Schubiger JL,Wahli W

更新日期：1987-01-01 00:00:00

abstract：:The incomplete correlation between the organismal complexities and the number of genes among eukaryotic organisms can be partially explained by multiple protein products of a gene created by alternative splicing. One type of alternative splicing involves alternative selection of mutually exclusive exons and creates pr...

journal_title：Journal of molecular evolution

authors： Chen YC,Lin WH,Tzeng DW,Chow WY

更新日期：2006-02-01 00:00:00

abstract：:Horizontal gene transfer (HGT) has a major impact on the evolution of prokaryotic genomes, as it allows genes evolved in different contexts to be combined in a single genome, greatly enhancing the ways evolving organisms can explore the gene content space and adapt to the environment. A systematic analysis of HGT in a...

journal_title：Journal of molecular evolution

authors： Paquola ACM,Asif H,Pereira CAB,Feltes BC,Bonatto D,Lima WC,Menck CFM

更新日期：2018-04-01 00:00:00

abstract：:The semen of many primate species coagulates into a mating plug believed to prevent the sperm of subsequent mating events from accessing the ova. The texture of the coagulum varies among species: from a semisoft mass in humans to a firm plug in chimpanzees. In humans, a component of the coagulum, semenogelin I, also i...

journal_title：Journal of molecular evolution

authors： Kingan SB,Tatar M,Rand DM

更新日期：2003-08-01 00:00:00

abstract：:The alpha-esterase cluster of D. melanogaster contains 11 esterase genes dispersed over 60 kb. Embedded in the cluster are two unrelated open reading frames that have sequence similarity with genes encoding ubiquitin-conjugating enzyme and tropomyosin. The esterase amino acid sequences show 37-66% identity with one an...

journal_title：Journal of molecular evolution

authors： Robin C,Russell RJ,Medveczky KM,Oakeshott JG

更新日期：1996-09-01 00:00:00

abstract：:Here we report DNA sequences from mitochondrial cytochrome b gene segments (1,005 base pairs per species) for the extinct woolly mammoth (Mammuthus primigenius) and Steller's sea cow (Hydrodamalis gigas) and the extant Asian elephant (Elephas maximus), the Western Indian manatee (Trichechus manatus), and the hyrax (Pr...

journal_title：Journal of molecular evolution

authors： Ozawa T,Hayashi S,Mikhelson VM

更新日期：1997-04-01 00:00:00

abstract：:Pax genes encode transcription factors critical for metazoan development. Large-scale gene duplication with subsequent gene losses during vertebrate evolution has resulted in two human genes for each of the Pax1/9, Pax3/7, and Pax4/6 subfamilies and three for the Pax2/5/8 subfamily, compared to one each in the cephalo...

journal_title：Journal of molecular evolution

authors： Short S,Holland LZ

更新日期：2008-06-01 00:00:00

abstract：:Available molecular and biochemical data offer conflicting evidence for the origin of the cyanelle of Cyanophora paradoxa. We show that the similarity of cyanelle and green chloroplast sequences is probably a result of these two lineages independently developing the same pattern of directional nucleotide change (subst...

journal_title：Journal of molecular evolution

authors： Lockhart PJ,Howe CJ,Bryant DA,Beanland TJ,Larkum AW

更新日期：1992-02-01 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

authors： Carbone A

更新日期：2006-12-01 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

authors： Tanabe Y,Kaya K,Watanabe MM

更新日期：2004-06-01 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

authors： Nei M,Tajima F,Tateno Y

更新日期：1983-01-01 00:00:00

abstract：:Segmental pattern in Drosophila melanogaster is set up via a set of cell-cell interactions mediated by the products of the segment polarity genes. Among these is the armadillo gene, whose product seems to be required for the reception of an intercellular signal encoded by the wingless gene. As part of our effort to re...

journal_title：Journal of molecular evolution

authors： Peifer M,Wieschaus E

更新日期：1993-03-01 00:00:00

abstract：:In the maximum likelihood (ML) method for estimating a molecular phylogenetic tree, the pattern of nucleotide substitutions for computing likelihood values is assumed to be simpler than that of the actual evolutionary process, simply because the process, considered to be quite devious, is unknown. The problem, however...

journal_title：Journal of molecular evolution

authors： Fukami-Kobayashi K,Tateno Y

更新日期：1991-01-01 00:00:00