Estimation of evolutionary distances under stationary and nonstationary models of nucleotide substitution.

Abstract:

:Estimation of evolutionary distances has always been a major issue in the study of molecular evolution because evolutionary distances are required for estimating the rate of evolution in a gene, the divergence dates between genes or organisms, and the relationships among genes or organisms. Other closely related issues are the estimation of the pattern of nucleotide substitution, the estimation of the degree of rate variation among sites in a DNA sequence, and statistical testing of the molecular clock hypothesis. Mathematical treatments of these problems are considerably simplified by the assumption of a stationary process in which the nucleotide compositions of the sequences under study have remained approximately constant over time, and there now exist fairly extensive studies of stationary models of nucleotide substitution, although some problems remain to be solved. Nonstationary models are much more complex, but significant progress has been recently made by the development of the paralinear and LogDet distances. This paper reviews recent studies on the above issues and reports results on correcting the estimation bias of evolutionary distances, the estimation of the pattern of nucleotide substitution, and the estimation of rate variation among the sites in a sequence.

authors

Gu X,Li WH

doi

10.1073/pnas.95.11.5899

subject

Has Abstract

pub_date

1998-05-26 00:00:00

pages

5899-905

issue

11

eissn

0027-8424

issn

1091-6490

journal_volume

95

pub_type

杂志文章
  • Internal fluid pressure influences muscle contractile force.

    abstract::Fluid fills intracellular, extracellular, and capillary spaces within muscle. During normal physiological activity, intramuscular fluid pressures develop as muscle exerts a portion of its developed force internally. These pressures, typically ranging between 10 and 250 mmHg, are rarely considered in mechanical models ...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1914433117

    authors: Sleboda DA,Roberts TJ

    更新日期:2020-01-21 00:00:00

  • Thermodynamic aspects of the linkage between binding of chloride and oxygen to human hemoglobin.

    abstract::Oxygen isotherms of human hemoglobin measured in distilled water and in solutions of sodium chloride in the concentration range from 0.02 to 3.0 M indicate that the oxygen affinity decreases up to about 1 M salt and then begins to increase. The isotherms obtained in the range from 0.02 to 0.6 M sodium chloride, at 37 ...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.74.10.4135

    authors: Haire RN,Hedlund BE

    更新日期:1977-10-01 00:00:00

  • Monkeypox virus evades antiviral CD4+ and CD8+ T cell responses by suppressing cognate T cell activation.

    abstract::Monkeypox virus (MPV) is a virulent human pathogen that has gained increased attention because of its potential use as a bioterrorism agent and inadvertent introduction into North America in 2003. The US outbreak also provided an important opportunity to study MPV-specific T cell immunity. Although MPV-specific CD4(+)...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.0800589105

    authors: Hammarlund E,Dasgupta A,Pinilla C,Norori P,Früh K,Slifka MK

    更新日期:2008-09-23 00:00:00

  • Nigrostriatal alpha-synucleinopathy induced by viral vector-mediated overexpression of human alpha-synuclein: a new primate model of Parkinson's disease.

    abstract::We used a high-titer recombinant adeno-associated virus (rAAV) vector to express WT or mutant human alpha-synuclein in the substantia nigra of adult marmosets. The alpha-synuclein protein was expressed in 90-95% of all nigral dopamine neurons and distributed by anterograde transport throughout their axonal and dendrit...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.0536383100

    authors: Kirik D,Annett LE,Burger C,Muzyczka N,Mandel RJ,Björklund A

    更新日期:2003-03-04 00:00:00

  • Ultrasensitive detection of malignant melanoma using PET molecular imaging probes.

    abstract::Malignant melanoma has one of the highest mortality rates of any cancer because of its aggressive nature and high metastatic potential. Clinical staging of the disease at the time of diagnosis is very important for the prognosis and outcome of melanoma treatment. In this study, we designed and synthesized the 18F-labe...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1922313117

    authors: Pyo A,Kim DY,Kim H,Lim D,Kwon SY,Kang SR,Kim HS,Bom HS,Min JJ

    更新日期:2020-06-09 00:00:00

  • AID-induced decrease in topoisomerase 1 induces DNA structural alteration and DNA cleavage for class switch recombination.

    abstract::To initiate class switch recombination (CSR) activation-induced cytidine deaminase (AID) induces staggered nick cleavage in the S region, which lies 5' to each Ig constant region gene and is rich in palindromic sequences. Topoisomerase 1 (Top1) controls the supercoiling of DNA by nicking, rotating, and religating one ...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.0911879106

    authors: Kobayashi M,Aida M,Nagaoka H,Begum NA,Kitawaki Y,Nakata M,Stanlie A,Doi T,Kato L,Okazaki IM,Shinkura R,Muramatsu M,Kinoshita K,Honjo T

    更新日期:2009-12-29 00:00:00

  • Molecular basis for heterosis for myelin basic protein content in mice.

    abstract::Poly(A)+ mRNA was isolated from the brains of C57BL/6J (B6), DBA/2J (D2), and F1 hybrid mice (B6 X D2) of 16-17 days of age. The yield of polysomal RNA, both poly(A)+ and poly(A)-, from the three strains of mice was comparable. When translated in vitro in a reticulocyte lysate system, the mRNA preparations had the sam...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.83.5.1532

    authors: Miskimins R,Ebato H,Seyfried TN,Yu RK

    更新日期:1986-03-01 00:00:00

  • Two precursors of melanin-concentrating hormone: DNA sequence analysis and in situ immunochemical localization.

    abstract::Two precursors to Chinook salmon (Oncorhynchus tshawytscha) melanin-concentrating hormone, an important factor in teleosts involved in the control of skin pigmentation and stress responsiveness, have been identified from DNA sequence analysis. Both precursors encode proteins of 132 amino acids and they share 107/132 a...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.86.11.4292

    authors: Minth CD,Qiu H,Akil H,Watson SJ,Dixon JE

    更新日期:1989-06-01 00:00:00

  • Purification and identification of pituitary cytotropic factor.

    abstract::It has been shown that the pituitary contains a cytotropic factor (CTF) that stimulates the secretion of catecholamines by dopaminergic neurons of the hypothalamus. In the present study, CTF was purified from rat pituitaries and found by means of mass spectrometric analysis to be adenosine. This finding was corroborat...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.92.12.5351

    authors: Porter JC,Ijames CF,Wang TC,Markey SP

    更新日期:1995-06-06 00:00:00

  • Four small Drosophila heat shock proteins are related to each other and to mammalian alpha-crystallin.

    abstract::The primary base sequence of the protein coding regions of the four small heat shock genes of Drosophila melanogaster present at cytological locus 67B has been determined. A single open reading frame large enough to encode a small heat shock protein is found for each gene. The molecular weights of the predicted protei...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.79.7.2360

    authors: Ingolia TD,Craig EA

    更新日期:1982-04-01 00:00:00

  • Why fisheries collapse and what to do about it.

    abstract::With the collapse of fisheries in many parts of the world causing widespread economic harm, attention is focused on a possible cause and remedy of fishery collapse. Economic theory for managing a renewable resource, such as a fishery, leads to an ecologically unstable equilibrium as difficult to maintain as balancing ...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.93.10.5078

    authors: Roughgarden J,Smith F

    更新日期:1996-05-14 00:00:00

  • Pathogenic adaptation of Escherichia coli by natural variation of the FimH adhesin.

    abstract::Conventional wisdom regarding mechanisms of bacterial pathogenesis holds that pathogens arise by external acquisition of distinct virulence factors, whereas determinants shared by pathogens and commensals are considered to be functionally equivalent and have been ignored as genes that could become adapted specifically...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.95.15.8922

    authors: Sokurenko EV,Chesnokova V,Dykhuizen DE,Ofek I,Wu XR,Krogfelt KA,Struve C,Schembri MA,Hasty DL

    更新日期:1998-07-21 00:00:00

  • Oligomerization of opioid receptors with beta 2-adrenergic receptors: a role in trafficking and mitogen-activated protein kinase activation.

    abstract::G-protein-coupled receptors (GPCRs) have recently joined the list of cell surface receptors that dimerize. Dimerization has been shown to alter the ligand-binding, signaling, and trafficking properties of these receptors. Recent studies have shown that GPCRs heterodimerize with closely related members, resulting in th...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.011384898

    authors: Jordan BA,Trapaidze N,Gomes I,Nivarthi R,Devi LA

    更新日期:2001-01-02 00:00:00

  • Remodeling of synaptic architecture during hippocampal "kindling".

    abstract::The "kindling" phenomenon is associated with long-lasting facilitation of synaptic transmission. A possible mechanism of such facilitation could involve changes in the number of synaptic contacts. However, previous attempts to demonstrate a synaptic morphological alteration that could account for the long-term effects...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.85.9.3260

    authors: Geinisman Y,Morrell F,deToledo-Morrell L

    更新日期:1988-05-01 00:00:00

  • p47 licenses activation of the immune deficiency pathway in the tick Ixodes scapularis.

    abstract::The E3 ubiquitin ligase X-linked inhibitor of apoptosis (XIAP) acts as a molecular rheostat for the immune deficiency (IMD) pathway of the tick Ixodes scapularis How XIAP activates the IMD pathway in response to microbial infection remains ill defined. Here, we identified the XIAP enzymatic substrate p47 as a positive...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1808905116

    authors: McClure Carroll EE,Wang X,Shaw DK,O'Neal AJ,Oliva Chávez AS,Brown LJ,Boradia VM,Hammond HL,Pedra JHF

    更新日期:2019-01-02 00:00:00

  • Inhibition of erythrocyte phosphate transport by high pressures.

    abstract::Pressures of 200-1000 atmospheres (20-100 MPa) are found to decrease significantly the amount of phosphate (H32PO4-2)transported into the rabbit erythrocyte under otherwise physiological conditions. Such compression does not cause irreversible morphological changes or result in membrane disruption. The findings are in...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.73.8.2767

    authors: Murphy RB,Libby WF

    更新日期:1976-08-01 00:00:00

  • Three-body interactions improve the prediction of rate and mechanism in protein folding models.

    abstract::Here we study the effects of many-body interactions on rate and mechanism in protein folding by using the results of molecular dynamics simulations on numerous coarse-grained Calpha-model single-domain proteins. After adding three-body interactions explicitly as a perturbation to a Gō-like Hamiltonian with native pair...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.0403486101

    authors: Ejtehadi MR,Avall SP,Plotkin SS

    更新日期:2004-10-19 00:00:00

  • Novel human DNA alkyltransferases obtained by random substitution and genetic selection in bacteria.

    abstract::DNA repair alkyltransferases protect organisms against the cytotoxic, mutagenic, and carcinogenic effects of alkylating agents by transferring alkyl adducts from DNA to an active cysteine on the protein, thereby restoring the native DNA structure. We used random sequence substitutions to gain structure-function inform...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.93.12.6124

    authors: Christians FC,Loeb LA

    更新日期:1996-06-11 00:00:00

  • Role of the hypothalamus in the control of atrial natriuretic peptide release.

    abstract::Stimulation of the region antero-ventral to the third cerebral ventricle (AV3V) by a cholinergic drug, carbachol, and lesions of the AV3V have been demonstrated in previous studies to either augment or decrease sodium excretion, respectively. Atrial natriuretic peptide (ANP) dramatically increases renal sodium excreti...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.86.23.9621

    authors: Baldissera S,Menani JW,dos Santos LF,Favaretto AL,Gutkowska J,Turrin MQ,McCann SM,Antunes-Rodrigues J

    更新日期:1989-12-01 00:00:00

  • Broad resistance to plant viruses in transgenic plants conferred by antisense inhibition of a host gene essential in S-adenosylmethionine-dependent transmethylation reactions.

    abstract::S-Adenosylhomocysteine hydrolase (SAHH) is a key enzyme in transmethylation reactions that use S-adenosylmethionine as the methyl donor. Because of the importance of SAHH in a number of S-adenosylmethionine-dependent transmethylation reactions, particularly the 5' capping of mRNA during viral replication, SAHH has bee...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.92.13.6117

    authors: Masuta C,Tanaka H,Uehara K,Kuwata S,Koiwai A,Noma M

    更新日期:1995-06-20 00:00:00

  • Pelizaeus-Merzbacher disease: a valine to phenylalanine point mutation in a putative extracellular loop of myelin proteolipid.

    abstract::In the central nervous system, myelin proteolipid protein isoforms (PLP and DM20) play an essential structural role in myelination. It has been shown in several species that myelination is impaired by molecular defects resulting from single base mutations in the PLP gene. We have used DNA amplification by polymerase c...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.88.17.7562

    authors: Pham-Dinh D,Popot JL,Boespflug-Tanguy O,Landrieu P,Deleuze JF,Boué J,Jollès P,Dautigny A

    更新日期:1991-09-01 00:00:00

  • Overreplication and recombination of DNA in higher eukaryotes: potential consequences and biological implications.

    abstract::We propose that a fundamental problem in the faithful replication of complex chromosomes of higher eukaryotes is the proper control of both the number and timing of the multiple initiations of replication on single chromosomes. When replication patterns are disrupted by any of a variety of agents, overreplication of D...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.83.7.2157

    authors: Schimke RT,Sherwood SW,Hill AB,Johnston RN

    更新日期:1986-04-01 00:00:00

  • Genomic analysis using a yeast artificial chromosome library with mouse DNA inserts.

    abstract::A yeast artificial chromosome library with mouse genomic DNA inserts has been constructed. The library encompasses a 2.5-fold coverage of the mouse genome, with an average insert size of 250 kilobases. The screening strategy uses the polymerase chain reaction on pooled DNAs prepared from individually stored clones. Th...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.89.6.2456

    authors: Rossi JM,Burke DT,Leung JC,Koos DS,Chen H,Tilghman SM

    更新日期:1992-03-15 00:00:00

  • Partial purification and characterization of a membrane-derived factor regulating neurotransmitter phenotypic expression.

    abstract::Cell membrane contact induces the de novo expression of choline O-acetyltransferase (CAT; acetyl-CoA: choline O-acetyltransferase, EC 2.3.1.6) activity in cultures of virtually pure neonatal rat dissociated sympathetic neurons. To identify molecular mechanisms underlying membrane-associated CAT induction, the responsi...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.86.3.1080

    authors: Adler JE,Schleifer LS,Black IB

    更新日期:1989-02-01 00:00:00

  • Transition state for the NSD2-catalyzed methylation of histone H3 lysine 36.

    abstract::Nuclear receptor SET domain containing protein 2 (NSD2) catalyzes the methylation of histone H3 lysine 36 (H3K36). It is a determinant in Wolf-Hirschhorn syndrome and is overexpressed in human multiple myeloma. Despite the relevance of NSD2 to cancer, there are no potent, selective inhibitors of this enzyme reported. ...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1521036113

    authors: Poulin MB,Schneck JL,Matico RE,McDevitt PJ,Huddleston MJ,Hou W,Johnson NW,Thrall SH,Meek TD,Schramm VL

    更新日期:2016-02-02 00:00:00

  • Regulation of Cl- transport in T84 cell clones expressing a mutant regulatory subunit of cAMP-dependent protein kinase.

    abstract::Cl- channels in the apical membranes of salt-secreting epithelia are activated by both cAMP and Ca2+ second-messenger systems, and dysfunctions in their hormonal regulation have been demonstrated in patients with cystic fibrosis. We have transfected the epithelial cell line T84 with an expression vector containing a m...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.87.22.8975

    authors: Rogers KV,Goldman PS,Frizzell RA,McKnight GS

    更新日期:1990-11-01 00:00:00

  • The paradoxical lean phenotype of hypothyroid mice is marked by increased adaptive thermogenesis in the skeletal muscle.

    abstract::Obesity is a major health problem worldwide, given its growing incidence and its association with a variety of comorbidities. Weight gain results from an increase in energy intake without a concomitant increase in energy expenditure. To combat the obesity epidemic, many studies have focused on the pathways underlying ...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.2008919117

    authors: Kaspari RR,Reyna-Neyra A,Jung L,Torres-Manzo AP,Hirabara SM,Carrasco N

    更新日期:2020-09-08 00:00:00

  • Neuroanatomical correlates of encoding in episodic memory: levels of processing effect.

    abstract::Cognitive studies of memory processes demonstrate that memory for stimuli is a function of how they are encoded; stimuli processed semantically are better remembered than those processed in a perceptual or shallow fashion. This study investigates the neural correlates of this cognitive phenomenon. Twelve subjects perf...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.91.6.2008

    authors: Kapur S,Craik FI,Tulving E,Wilson AA,Houle S,Brown GM

    更新日期:1994-03-15 00:00:00

  • Lipopeptide nanoparticles for potent and selective siRNA delivery in rodents and nonhuman primates.

    abstract::siRNA therapeutics have promise for the treatment of a wide range of genetic disorders. Motivated by lipoproteins, we report lipopeptide nanoparticles as potent and selective siRNA carriers with a wide therapeutic index. Lead material cKK-E12 showed potent silencing effects in mice (ED50 ∼ 0.002 mg/kg), rats (ED50 < 0...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1322937111

    authors: Dong Y,Love KT,Dorkin JR,Sirirungruang S,Zhang Y,Chen D,Bogorad RL,Yin H,Chen Y,Vegas AJ,Alabi CA,Sahay G,Olejnik KT,Wang W,Schroeder A,Lytton-Jean AK,Siegwart DJ,Akinc A,Barnes C,Barros SA,Carioto M,Fitzgerald

    更新日期:2014-03-18 00:00:00

  • Impairments in verb morphology after brain injury: a connectionist model.

    abstract::The formation of the past tense of verbs in English has been the focus of the debate concerning connectionist vs. symbolic accounts of language. Brain-injured patients differ with respect to whether they are more impaired in generating irregular past tenses (TAKE-TOOK) or past tenses for nonce verbs (WUG-WUGGED). Such...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.96.13.7592

    authors: Joanisse MF,Seidenberg MS

    更新日期:1999-06-22 00:00:00