Life History of the Oldest Lentivirus: Characterization of ELVgv Integrations in the Dermopteran Genome.

abstract：:Large phylogenomics data sets require fast tree inference methods, especially for maximum-likelihood (ML) phylogenies. Fast programs exist, but due to inherent heuristics to find optimal trees, it is not clear whether the best tree is found. Thus, there is need for additional approaches that employ different search st...

journal_title：Molecular biology and evolution

authors： Nguyen LT,Schmidt HA,von Haeseler A,Minh BQ

更新日期：2015-01-01 00:00:00

abstract：:Substitution rates at the three codon positions (r1, r2, and r3) of mammalian mitochondrial genes are in the order of r3 > r1 > r2, and the rate heterogeneity at the three positions, as measured by the shape parameter of the gamma distribution (alpha 1, alpha 2, and alpha 3), is in the order of alpha 3 > alpha 1 > alp...

journal_title：Molecular biology and evolution

authors： Xia X

更新日期：1998-03-01 00:00:00

abstract：:Parasites sometimes expand their host range by acquiring a new host species. After a host change event, the selective regime acting on a given parasite gene may change as a result of host-specific adaptive alterations of protein functionality or host-specific immune-mediated selection. We present a codon-based model t...

journal_title：Molecular biology and evolution

authors： Forsberg R,Christiansen FB

更新日期：2003-08-01 00:00:00

abstract：:Geraniaceae plastid genomes (plastomes) have experienced a remarkable number of genomic changes. The plastomes of Erodium texanum, Geranium palmatum, and Monsonia speciosa were sequenced and compared with other rosids and the previously published Pelargonium hortorum plastome. Geraniaceae plastomes were found to be hi...

journal_title：Molecular biology and evolution

authors： Guisinger MM,Kuehl JV,Boore JL,Jansen RK

更新日期：2011-01-01 00:00:00

abstract：:Variola virus is at risk of re-emergence either through accidental release, bioterrorism, or synthetic biology. The use of phylogenetics and phylogeography to support epidemic field response is expected to grow as sequencing technology becomes miniaturized, cheap, and ubiquitous. In this study, we aimed to explore the...

journal_title：Molecular biology and evolution

authors： Adam DC,Scotch M,MacIntyre CR

更新日期：2018-11-01 00:00:00

abstract：:The relative efficiencies of the maximum parsimony (MP) and distance-matrix methods in obtaining the correct tree (topology) were studied by using computer simulation. The distance-matrix methods examined are the neighbor-joining, distance-Wagner, Tateno et al. modified Farris, Faith, and Li methods. In the computer s...

journal_title：Molecular biology and evolution

authors： Sourdis J,Nei M

更新日期：1988-05-01 00:00:00

abstract：:The cost of reproduction is a pivotal trade-off with various biological processes during the evolution of organisms. However, the genes and molecular mechanisms underlying the evolution of balancing reproductive capacity and its cost are still largely unknown. Here, we present a comprehensive study on the evolution, e...

journal_title：Molecular biology and evolution

authors： Zhan Z,Ding Y,Zhao R,Zhang Y,Yu H,Zhou Q,Yang S,Xiang H,Wang W

更新日期：2012-05-01 00:00:00

abstract：:The internal consistency of the PAM matrix model of protein evolution is here investigated. The 1 PAM matrix has been constructed from amino acid replacements observed in closely related sequences. Such replacements are of two types, those that do not require an intermediate amino acid replacement and those that do. T...

journal_title：Molecular biology and evolution

authors： Wilbur WJ

更新日期：1985-09-01 00:00:00

abstract：:The level of DNA polymorphism in the ancestral species at the time of speciation can be estimated using DNA sequences from many loci sampled from 2 or more extant species. The comparison between ancestral and extant polymorphism can be informative about the population genetics of speciation. In this study, we collecte...

journal_title：Molecular biology and evolution

authors： Zhou R,Zeng K,Wu W,Chen X,Yang Z,Shi S,Wu CI

更新日期：2007-12-01 00:00:00

abstract：:Mitochondrial ribosomes (mitoribosomes) are essential components of all mitochondria that synthesize proteins encoded by the mitochondrial genome. Unlike other ribosomes, mitoribosomes are highly variable across species. The basis for this diversity is not known. Here, we examine the composition and evolutionary histo...

journal_title：Molecular biology and evolution

authors： Petrov AS,Wood EC,Bernier CR,Norris AM,Brown A,Amunts A

更新日期：2019-02-01 00:00:00

abstract：:Dormancy has evolved in all major metazoan lineages. It is critical for survival when environmental stresses are not conducive to growth, maturation, or reproduction. Embryonic diapause is a form of dormancy where development is reversibly delayed and metabolism is depressed. We report the diapause transcriptome of th...

journal_title：Molecular biology and evolution

authors： Thompson AW,Ortí G

更新日期：2016-09-01 00:00:00

abstract：:Estimation of evolutionary distances from coding sequences must take into account protein-level selection to avoid relative underestimation of longer evolutionary distances. Current modeling of selection via site-to-site rate heterogeneity generally neglects another aspect of selection, namely position-specific amino ...

journal_title：Molecular biology and evolution

authors： Halpern AL,Bruno WJ

更新日期：1998-07-01 00:00:00

abstract：:In numerous species, individual dispersal is restricted in space so that "continuous" populations evolve under isolation by distance. A method based on individual genotypes assuming a lattice population model was recently developed to estimate the product Dsigma2, where D is the population density and sigma2 is the av...

journal_title：Molecular biology and evolution

authors： Leblois R,Estoup A,Rousset F

更新日期：2003-04-01 00:00:00

abstract：:Homologues of glucosephosphate isomerase (GPI, EC 5.3.1.9) were purified to homogeneity and kinetically characterized from Mytilus edulis and Isognomon alatus, two bivalve molluscs experiencing contrasting thermal environments. The enzyme isolated from I. alatus functions at warmer temperatures (25-35 C) than GPI from...

journal_title：Molecular biology and evolution

authors： Hall JG

更新日期：1985-05-01 00:00:00

abstract：:Indirect tests have detected recombination in mitochondrial DNA (mtDNA) from many animal lineages, including mammals. However, it is possible that features of the molecular evolutionary process without recombination could be incorrectly inferred by indirect tests as being due to recombination. We have identified one s...

journal_title：Molecular biology and evolution

authors： Sun S,Evans BJ,Golding GB

更新日期：2011-09-01 00:00:00

abstract：:The genomes of many vertebrates show a characteristic heterogeneous distribution of GC content, the so-called GC isochore structure. The origin of isochores has been explained via the mechanism of GC-biased gene conversion (gBGC). However, although the isochore structure is declining in many mammalian genomes, the het...

journal_title：Molecular biology and evolution

authors： Mugal CF,Arndt PF,Ellegren H

更新日期：2013-07-01 00:00:00

abstract：:The activation peptide of mammalian trypsinogens contains a highly conserved tetra-aspartate sequence (D19-D20-D21-D22) preceding the K23-I24 scissile peptide bond, which is hydrolyzed as the first step in the activation process. Here, we examined the evolution and function of trypsinogen activation peptides through i...

journal_title：Molecular biology and evolution

authors： Chen JM,Kukor Z,Le Maréchal C,Tóth M,Tsakiris L,Raguénès O,Férec C,Sahin-Tóth M

更新日期：2003-11-01 00:00:00

abstract：:Evolution of sequences mostly involves independent changes at different sites. However, substitutions at neighboring sites may co-occur as multinucleotide replacement events (MNRs). Here, we compare noncoding sequences of several species of primates, and of three species of Drosophila fruit flies, in a phylogenetic an...

journal_title：Molecular biology and evolution

authors： Terekhanova NV,Bazykin GA,Neverov A,Kondrashov AS,Seplyarskiy VB

更新日期：2013-06-01 00:00:00

abstract：:Dinoflagellates are algae of tremendous importance to ecosystems and to public health. The cell biology and genome organization of dinoflagellate species is highly unusual. For example, the plastid genomes of peridinin-containing dinoflagellates encode only a minimal number of genes arranged on small elements termed "...

journal_title：Molecular biology and evolution

authors： Dorrell RG,Klinger CM,Newby RJ,Butterfield ER,Richardson E,Dacks JB,Howe CJ,Nisbet ER,Bowler C

更新日期：2017-02-01 00:00:00

abstract：:Long noncoding RNAs (lncRNAs) do not code for proteins but function as RNAs. Because the functions of an RNA rely on either its sequence or secondary structure, lncRNAs should be folded at least as strongly as messenger RNAs (mRNAs), which serve as messengers for translation and are generally thought to lack secondary...

journal_title：Molecular biology and evolution

authors： Yang JR,Zhang J

更新日期：2015-04-01 00:00:00

abstract：:The nucleotide sequences of the 5'-flanking regions of the duplicated Amy genes in eight sibling species belonging to the melanogaster species subgroup are analyzed. In Drosophila melanogaster, a region of about 450 bp immediately upstream of the translation initiation site of the two paralogous genes (the proximal an...

journal_title：Molecular biology and evolution

authors： Okuyama E,Shibata H,Tachida H,Yamazaki T

更新日期：1996-04-01 00:00:00

abstract：:Colias eurytheme butterflies display extensive allozyme polymorphism in the enzyme phosphoglucose isomerase (PGI). Earlier studies on biochemical and fitness effects of these genotypes found evidence of strong natural selection maintaining this polymorphism in the wild. Here we analyze the molecular features of this p...

journal_title：Molecular biology and evolution

authors： Wheat CW,Watt WB,Pollock DD,Schulte PM

更新日期：2006-03-01 00:00:00

abstract：:The similarity of certain reported angiosperm rDNA internal transcribed spacer (ITS) region sequences to those of green algae prompted our analysis of the deep-level phylogenetic signal in the highly conserved but short 5.8S and hypervariable ITS2 sequences. We found that 5.8S sequences yield phylogenetic trees simila...

journal_title：Molecular biology and evolution

authors： Hershkovitz MA,Lewis LA

更新日期：1996-11-01 00:00:00

abstract：:Mitochondrial transcription factor B (mtTFB), an essential component in regulating the expression of mitochondrial DNA-encoded genes in both yeast and humans, is a dimethyladenosine methyltransferase (DMT) that has acquired a secondary role in mitochondrial transcription. So far, mtTFB has only been well studied in Op...

journal_title：Molecular biology and evolution

authors： Shutt TE,Gray MW

更新日期：2006-06-01 00:00:00

abstract：:Signaling peptides enable communication between cells, both within and between individuals, and are therefore key to the control of complex physiological and behavioral responses. Since their small sizes prevent direct transmission to secretory pathways, these peptides are often produced as part of a larger polyprotei...

journal_title：Molecular biology and evolution

authors： Rogers DW,McConnell E,Miller EL,Greig D

更新日期：2017-12-01 00:00:00

abstract：:The acquisition of photosynthesis by eukaryotic cells through enslavement of a cyanobacterium represents one of the most remarkable turning points in the history of life on Earth. In addition to endosymbiotic gene transfer, the acquisition of a protein import apparatus and the coordination of gene expression between h...

journal_title：Molecular biology and evolution

authors： Colleoni C,Linka M,Deschamps P,Handford MG,Dupree P,Weber AP,Ball SG

更新日期：2010-12-01 00:00:00

abstract：:To gain insight into the evolution of the methionine biosynthesis pathway, in vivo complementation tests were performed. The substrate specificity of three enzymes that intrinsically use different homoserine-esterified substrates and have different sulfur assimilation pathways was examined: two cystathionine gamma-syn...

journal_title：Molecular biology and evolution

authors： Hacham Y,Gophna U,Amir R

更新日期：2003-09-01 00:00:00

abstract：:The role of adaptation in the divergence of lineages has long been a central question in evolutionary biology, and as multilocus sequence data sets have become available for a wide range of taxa, empirical estimates of levels of adaptive molecular evolution are increasingly common. Estimates vary widely among taxa, wi...

journal_title：Molecular biology and evolution

authors： Strasburg JL,Kane NC,Raduski AR,Bonin A,Michelmore R,Rieseberg LH

更新日期：2011-05-01 00:00:00

abstract：:The DnaK-DnaJ-GrpE (KJE) chaperone system functions at the fulcrum of protein homeostasis in bacteria. It interacts both with nascent polypeptides and with proteins that have become unfolded, either funneling its clients toward the native state or ushering misfolded proteins into degradation. In line with its key role...

journal_title：Molecular biology and evolution

authors： Warnecke T

更新日期：2012-11-01 00:00:00

abstract：:Restriction site variations in nuclear ribosomal DNA (rDNA) spacers and mitochondrial DNA (mtDNA) were examined in several populations of mole rats with variable numbers of chromosomes, which represented the two superspecies Spalax leucodon (2n = 38, 54, or 62) and Spalax ehrenbergi (2n = 52, 54, 58, or 60). Sequence ...

journal_title：Molecular biology and evolution

authors： Suzuki H,Wakana S,Yonekawa H,Moriwaki K,Sakurai S,Nevo E

更新日期：1996-01-01 00:00:00