Evolution of nucleic acids coding for ribonucleases: the mRNA sequence of mouse pancreatic ribonuclease.

abstract：:Taxonomic congruence and total evidence are competing paradigms in phylogenetic inference. Taxonomic congruence focuses on deriving a consensus from the results obtained from separately analyzed data sets, whereas total evidence uses character congruence in the search for the best-fitting hypothesis for all of the ava...

journal_title：Molecular biology and evolution

authors： Eernisse DJ,Kluge AG

更新日期：1993-11-01 00:00:00

abstract：:We compared sex chromosomal and autosomal regions of similar GC contents and found that the human Y chromosome contains nine times as many full-length (FL) ancestral LINE-1 (L1) elements per megabase as do autosomes and that the X chromosome contains three times as many. In addition, both sex chromosomes contain a ca....

journal_title：Molecular biology and evolution

authors： Boissinot S,Entezam A,Furano AV

更新日期：2001-06-01 00:00:00

abstract：:The serial coalescent extends traditional coalescent theory to include genealogies in which not all individuals were sampled at the same time. Inference in this framework is powerful because population size and evolutionary rate may be estimated independently. However, when the sequences in question are affected by se...

journal_title：Molecular biology and evolution

authors： O'Fallon BD

更新日期：2011-11-01 00:00:00

abstract：:Horizontal gene transfer (HGT) has been described as a common mechanism of transferring genetic material between prokaryotes, whereas genetic transfers from eukaryotes to prokaryotes have been rarely documented. Here we report a rare case of HGT in which plant expansin genes that code for plant cell-wall loosening pro...

journal_title：Molecular biology and evolution

authors： Nikolaidis N,Doran N,Cosgrove DJ

更新日期：2014-02-01 00:00:00

abstract：:The diversity and evolution of bitter taste perception in mammals is not well understood. Recent discoveries of bitter taste receptor (T2R) genes provide an opportunity for a genetic approach to this question. We here report the identification of 10 and 30 putative T2R genes from the draft human and mouse genome seque...

journal_title：Molecular biology and evolution

authors： Shi P,Zhang J,Yang H,Zhang YP

更新日期：2003-05-01 00:00:00

abstract：:We report a major update of the MAFFT multiple sequence alignment program. This version has several new features, including options for adding unaligned sequences into an existing alignment, adjustment of direction in nucleotide alignment, constrained alignment and parallel processing, which were implemented after the...

journal_title：Molecular biology and evolution

authors： Katoh K,Standley DM

更新日期：2013-04-01 00:00:00

abstract：:Genome and transcript sequences are composed of long strings of nucleotide monomers (A, C, G, and T/U) that require different quantities of nitrogen atoms for biosynthesis. Here, it is shown that the strength of selection acting on transcript nitrogen content is influenced by the amount of nitrogen plants require to c...

journal_title：Molecular biology and evolution

authors： Kelly S

更新日期：2018-07-01 00:00:00

abstract：:ModelTest-NG is a reimplementation from scratch of jModelTest and ProtTest, two popular tools for selecting the best-fit nucleotide and amino acid substitution models, respectively. ModelTest-NG is one to two orders of magnitude faster than jModelTest and ProtTest but equally accurate and introduces several new featur...

journal_title：Molecular biology and evolution

authors： Darriba D,Posada D,Kozlov AM,Stamatakis A,Morel B,Flouri T

更新日期：2020-01-01 00:00:00

abstract：:Among mammals, several lineages have independently adapted to a subterranean niche and possess similar phenotypic traits for burrowing (e.g., cylindrical bodies, short limbs, and absent pinnae). Previous research on mole-rats has revealed molecular adaptations for coping with reduced oxygen, elevated carbon dioxide, a...

journal_title：Molecular biology and evolution

authors： Davies KTJ,Bennett NC,Faulkes CG,Rossiter SJ

更新日期：2018-10-01 00:00:00

abstract：:We determine the phylogenetic backbone of the East Asian mtDNA tree by using published complete mtDNA sequences and assessing both coding and control region variation in 69 Han individuals from southern China. This approach assists in the interpretation of published mtDNA data on East Asians based on either control re...

journal_title：Molecular biology and evolution

authors： Kivisild T,Tolk HV,Parik J,Wang Y,Papiha SS,Bandelt HJ,Villems R

更新日期：2002-10-01 00:00:00

abstract：:Mitochondrial protein translation requires interactions between transfer RNAs encoded by the mitochondrial genome (mt-tRNAs) and mitochondrial aminoacyl tRNA synthetase proteins (mt-aaRS) encoded by the nuclear genome. It has been argued that animal mt-tRNAs have higher deleterious substitution rates relative to their...

journal_title：Molecular biology and evolution

authors： Adrion JR,White PS,Montooth KL

更新日期：2016-01-01 00:00:00

abstract：:Analysis of evolution of paralogous genes in a genome is central to our understanding of genome evolution. Comparison of closely related bacterial genomes, which has provided clues as to how genome sequences evolve under natural conditions, would help in such an analysis. With species Staphylococcus aureus, whole-geno...

journal_title：Molecular biology and evolution

authors： Tsuru T,Kawai M,Mizutani-Ui Y,Uchiyama I,Kobayashi I

更新日期：2006-06-01 00:00:00

abstract：:Analyses of the genomes of three prokaryotes, Escherichia coli, Bacillus subtilis, and Haemophilus influenzae, revealed a new type of genomic compartmentalization of base frequencies. There was a departure from intrastrand equifrequency between A and T or between C and G, showing that the substitution patterns of the ...

journal_title：Molecular biology and evolution

authors： Lobry JR

更新日期：1996-05-01 00:00:00

abstract：:The adaptive significance of enzyme variation has been of central interest in population genetics. Yet, how natural selection operates on enzymes in the larger context of biochemical pathways has not been broadly explored. A basic expectation is that natural selection on metabolic phenotypes will target enzymes that c...

journal_title：Molecular biology and evolution

authors： Flowers JM,Sezgin E,Kumagai S,Duvernell DD,Matzkin LM,Schmidt PS,Eanes WF

更新日期：2007-06-01 00:00:00

abstract：:Snake venom gene evolution has been studied intensively over the past several decades, yet most previous studies have lacked the context of complete snake genomes and the full context of gene expression across diverse snake tissues. We took a novel approach to studying snake venom evolution by leveraging the complete ...

journal_title：Molecular biology and evolution

authors： Reyes-Velasco J,Card DC,Andrew AL,Shaney KJ,Adams RH,Schield DR,Casewell NR,Mackessy SP,Castoe TA

更新日期：2015-01-01 00:00:00

abstract：:Until recently, evolutionary questions surrounding the nature of the genetic code have been mostly limited to the realm of conjecture, modeling, and simulation due to the difficulty of altering this fundamental property of living organisms. Concerted genome and protein engineering efforts now make it possible to exper...

journal_title：Molecular biology and evolution

authors： Hammerling MJ,Gollihar J,Mortensen C,Alnahhas RN,Ellington AD,Barrick JE

更新日期：2016-08-01 00:00:00

abstract：:Amastin is a transmembrane glycoprotein found on the cell surfaces of trypanosomatid parasites. Encoded by a large, diverse gene family, amastin was initially described from the intracellular, amastigote stage of Trypanosoma cruzi and Leishmania donovani. Genome sequences have subsequently shown that the amastin reper...

journal_title：Molecular biology and evolution

authors： Jackson AP

更新日期：2010-01-01 00:00:00

abstract：:A fundamental goal in evolutionary biology is to identify the molecular changes responsible for adaptive evolution. In this study, we describe a genetic analysis to determine whether the molecular changes contributing to adaptive flower color divergence in Mimulus aurantiacus affect gene expression or enzymatic activi...

journal_title：Molecular biology and evolution

authors： Streisfeld MA,Rausher MD

更新日期：2009-02-01 00:00:00

abstract：:Endogenous retroviruses provide molecular fossils for studying the ancient evolutionary history of retroviruses. Here, we report our independent discovery and analysis of endogenous lentiviral insertions (Mustelidae endogenous lentivirus [MELV]) within the genomes of weasel family (Mustelidae). Genome-scale screening ...

journal_title：Molecular biology and evolution

authors： Han GZ,Worobey M

更新日期：2012-10-01 00:00:00

abstract：:How gene function evolves is a central question of evolutionary biology. It can be investigated by comparing functional genomics results between species and between genes. Most comparative studies of functional genomics have used pairwise comparisons. Yet it has been shown that this can provide biased results, since g...

journal_title：Molecular biology and evolution

authors： Begum T,Robinson-Rechavi M

更新日期：2020-11-10 00:00:00

abstract：:Debate on the adaptive origins of primates has long focused on the functional ecology of the primate visual system. For example, it is hypothesized that variable expression of short- (SWS1) and middle-to-long-wavelength sensitive (M/LWS) opsins, which confer color vision, can be used to infer ancestral activity patter...

journal_title：Molecular biology and evolution

authors： Melin AD,Wells K,Moritz GL,Kistler L,Orkin JD,Timm RM,Bernard H,Lakim MB,Perry GH,Kawamura S,Dominy NJ

更新日期：2016-04-01 00:00:00

abstract：:Alu is a predominant short interspersed element (SINE) family in the human genome and consists of two monomer units connected by an A-rich linker. At present, dimeric Alu elements are active in humans, but Alu monomers are present as fossilized sequences. A comparative genome analysis of human and chimpanzee genomes r...

journal_title：Molecular biology and evolution

authors： Kojima KK

更新日期：2011-01-01 00:00:00

abstract：:Empirical codon models (ECMs) estimated from a large number of globular protein families outperformed mechanistic codon models in their description of the general process of protein evolution. Among other factors, ECMs implicitly model the influence of amino acid properties and multiple nucleotide substitutions (MNS)....

journal_title：Molecular biology and evolution

authors： De Maio N,Holmes I,Schlötterer C,Kosiol C

更新日期：2013-03-01 00:00:00

abstract：:Cells react to oxidative stress conditions by launching a defense response through the induction of nuclear gene expression. The advent of microarray technologies allowed monitoring of oxidative stress-dependent changes of transcript levels at a comprehensive and genome-wide scale, resulting in a series of inventories...

journal_title：Molecular biology and evolution

authors： Vandenbroucke K,Robbens S,Vandepoele K,Inzé D,Van de Peer Y,Van Breusegem F

更新日期：2008-03-01 00:00:00

abstract：:Some genes have repeatedly been found to control diverse adaptations in a wide variety of organisms. Such gene reuse reveals not only the diversity of phenotypes these unique genes control but also the composition of developmental gene networks and the genetic routes available to and taken by organisms during adaptati...

journal_title：Molecular biology and evolution

authors： VanKuren NW,Massardo D,Nallu S,Kronforst MR

更新日期：2019-12-01 00:00:00

abstract：:A large majority of bacterial genomes show strand asymmetry, such that G and T preferentially accumulate on the leading strand. The mechanisms are unknown, but cytosine deaminations are thought to play an important role. Here, we have examined DNA strand asymmetry in three strains of the aphid endosymbiont Buchnera ap...

journal_title：Molecular biology and evolution

authors： Klasson L,Andersson SG

更新日期：2006-05-01 00:00:00

abstract：:The genotypic signature of spatially varying selection is ubiquitous across the Drosophila melanogaster genome. Spatially structured adaptive phenotypic differences are also commonly found, particularly along New World and Australian latitudinal gradients. However, investigation of gene expression variation in one or ...

journal_title：Molecular biology and evolution

authors： Levine MT,Eckert ML,Begun DJ

更新日期：2011-01-01 00:00:00

abstract：:The relative evolutionary rates at individual sites in proteins are informative measures of conservation or adaptation. Often used as evolutionarily aware conservation scores, relative rates reveal key functional or strongly selected residues. Estimating rates in a phylogenetic context requires specifying a protein su...

journal_title：Molecular biology and evolution

authors： Spielman SJ,Kosakovsky Pond SL

更新日期：2018-09-01 00:00:00

abstract：:Comparisons between human and rodent DNA sequences are widely used for the identification of regulatory regions (phylogenetic footprinting), and the importance of such intergenomic comparisons for promoter annotation is expanding. The efficacy of such comparisons for the identification of functional regulatory element...

journal_title：Molecular biology and evolution

authors： Dermitzakis ET,Clark AG

更新日期：2002-07-01 00:00:00

abstract：:Reconstruction of ancestral DNA and amino acid sequences is an important means of inferring information about past evolutionary events. Such reconstructions suggest changes in molecular function and evolutionary processes over the course of evolution and are used to infer adaptation and convergence. Maximum likelihood...

journal_title：Molecular biology and evolution

authors： Krishnan NM,Seligmann H,Stewart CB,De Koning AP,Pollock DD

更新日期：2004-10-01 00:00:00