A phylogenetic mixture model for the evolution of gene expression.

abstract：:A phylogenetic analysis of sex-chromosomal zinc-finger genes (Zfx and Zfy) indicates that the genes have not evolved completely independently since their initial separation. The sequence similarities suggest gene conversion in the last exon between the duplicated Y-chromosomal genes Zfy-1 and Zfy-2 in the mouse. There...

journal_title：Molecular biology and evolution

authors： Pamilo P,Bianchi NO

更新日期：1993-03-01 00:00:00

abstract：:Understanding genome and chromosome evolution is important for understanding genetic inheritance and evolution. Universal events comprising DNA replication, transcription, repair, mobile genetic element transposition, chromosome rearrangements, mitosis, and meiosis underlie inheritance and variation of living organism...

journal_title：Molecular biology and evolution

authors： Li X,Zhu C,Lin Z,Wu Y,Zhang D,Bai G,Song W,Ma J,Muehlbauer GJ,Scanlon MJ,Zhang M,Yu J

更新日期：2011-06-01 00:00:00

abstract：:Purifying selection can substantially alter patterns of molecular evolution. Its main effect is to reduce overall levels of genetic variation, leading to a reduced effective population size. However, it also distorts genealogies relative to neutral expectations. A structured coalescent method has been used to describe...

journal_title：Molecular biology and evolution

authors： Nicolaisen LE,Desai MM

更新日期：2012-11-01 00:00:00

abstract：:Multiple sequence alignment (MSA) is the heart of comparative sequence analysis. Recent studies demonstrate that MSA algorithms can produce different outcomes when analyzing genomes, including phylogenetic tree inference and the detection of adaptive evolution. These studies also suggest that the difference between MS...

journal_title：Molecular biology and evolution

authors： Blackburne BP,Whelan S

更新日期：2013-03-01 00:00:00

abstract：:Transfer RNA (tRNA) is essential for the translation of genetic information into proteins, and understanding its molecular evolution is important if we are to understand the genetic code. In general, long variable-arm (V-arm) structures form in tRNA(Leu), tRNA(Ser), and bacterial and organellar tRNA(Tyr). However, as ...

journal_title：Molecular biology and evolution

authors： Hamashima K,Tomita M,Kanai A

更新日期：2016-02-01 00:00:00

abstract：:Chaperone-mediated autophagy (CMA) is a major pathway of lysosomal proteolysis recognized as a key player of the control of numerous cellular functions, and whose defects have been associated with several human pathologies. To date, this cellular function is presumed to be restricted to mammals and birds, due to the a...

journal_title：Molecular biology and evolution

authors： Lescat L,Véron V,Mourot B,Péron S,Chenais N,Dias K,Riera-Heredia N,Beaumatin F,Pinel K,Priault M,Panserat S,Salin B,Guiguen Y,Bobe J,Herpin A,Seiliez I

更新日期：2020-10-01 00:00:00

abstract：:The origin and maintenance of sex remains one of the most debated topics in evolutionary biology. Investigations of the molecular genetic consequences of asexuality, such as direct estimation of mutation and recombination rates in asexual lineages, are critical for explaining the prevalence of sex in nature. In this s...

journal_title：Molecular biology and evolution

authors： Xu S,Omilian AR,Cristescu ME

更新日期：2011-01-01 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：:Mouse has emerged as the most common model organism in biomedicine. Here, we analyzed the tolerance to the loss-of-function (LoF) of selenoprotein genes, estimated from mouse knockouts and the frequency of LoF variants in humans. We found not only a general correspondence in tolerance (e.g., GPX1, GPX2) and intoleranc...

journal_title：Molecular biology and evolution

authors： Santesmasses D,Mariotti M,Gladyshev VN

更新日期：2020-02-01 00:00:00

abstract：:Computational tools with a balanced sensitivity and specificity in identification of candidate cancer drivers are highly desired. In this study, we propose a new statistical test, namely the dJ/dS ratio test, to compute the relative mutation rate of exon/intron junction sites (dJ) to synonymous sites (dS); observation...

journal_title：Molecular biology and evolution

authors： Chen H,Xing K,He X

更新日期：2015-08-01 00:00:00

abstract：:Ecological diversity in fungi is largely defined by metabolic traits, including the ability to produce secondary or "specialized" metabolites (SMs) that mediate interactions with other organisms. Fungal SM pathways are frequently encoded in biosynthetic gene clusters (BGCs), which facilitate the identification and cha...

journal_title：Molecular biology and evolution

authors： Gluck-Thaler E,Haridas S,Binder M,Grigoriev IV,Crous PW,Spatafora JW,Bushley K,Slot JC

更新日期：2020-10-01 00:00:00

abstract：:At present there is tremendous interest in characterizing the magnitude and distribution of linkage disequilibrium (LD) throughout the human genome, which will provide the necessary foundation for genome-wide LD analyses and facilitate detailed evolutionary studies. To this end, a human high-density single-nucleotide ...

journal_title：Molecular biology and evolution

authors： Akey JM,Zhang K,Xiong M,Jin L

更新日期：2003-02-01 00:00:00

abstract：:Naked lobose amoebae (gymnamoebae) are among the most abundant group of protists present in all aquatic and terrestrial biotopes. Yet, because of lack of informative morphological characters, the origin and evolutionary history of gymnamoebae are poorly known. The first molecular studies revealed multiple origins for ...

journal_title：Molecular biology and evolution

authors： Bolivar I,Fahrni JF,Smirnov A,Pawlowski J

更新日期：2001-12-01 00:00:00

abstract：:Multiple haplotypes from each of three nuclear loci were isolated and sequenced from geographic populations of the American oyster, Crassostrea virginica. In tests of alternative phylogeographic hypotheses for this species, nuclear gene genealogies constructed for these haplotypes were compared to one another, to a mi...

journal_title：Molecular biology and evolution

authors： Hare MP,Avise JC

更新日期：1998-02-01 00:00:00

abstract：:The little fire ant, Wasmannia auropunctata, displays a peculiar breeding system polymorphism. Classical haplo-diploid sexual reproduction between reproductive individuals occurs in some populations, whereas, in others, queens and males reproduce clonally. Workers are produced sexually and are sterile in both clonal a...

journal_title：Molecular biology and evolution

authors： Rey O,Loiseau A,Facon B,Foucaud J,Orivel J,Cornuet JM,Robert S,Dobigny G,Delabie JH,Mariano Cdos S,Estoup A

更新日期：2011-09-01 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：:Cytochrome c oxidase (COX) consists of 13 subunits, 3 encoded in the mitochondrial genome and 10 in the nucleus. Little is known of the role of the nuclear-encoded subunits, some of which exhibit tissue-specific isoforms. Subunit VIa is unique in having tissue-specific isoforms in all mammalian species examined. We ex...

journal_title：Molecular biology and evolution

authors： Schmidt TR,Jaradat SA,Goodman M,Lomax MI,Grossman LI

更新日期：1997-06-01 00:00:00

abstract：:tRNAs are important players in the protein synthesis machinery, where they act as adapter molecules for translating the mRNA codons into the corresponding amino acid sequence. In a series of highly conserved maturation steps, the primary transcripts are converted into mature tRNAs. In the amoebozoan Acanthamoeba caste...

journal_title：Molecular biology and evolution

authors： Erber L,Betat H,Mörl M

更新日期：2020-10-23 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：:Models of codon evolution have attracted particular interest because of their unique capabilities to detect selection forces and their high fit when applied to sequence evolution. We described here a novel approach for modeling codon evolution, which is based on Kronecker product of matrices. The 61 × 61 codon substit...

journal_title：Molecular biology and evolution

authors： Zaheri M,Dib L,Salamin N

更新日期：2014-09-01 00:00:00

abstract：:The minimum-evolution (ME) method of phylogenetic inference is based on the assumption that the tree with the smallest sum of branch length estimates is most likely to be the true one. In the past this assumption has been used without mathematical proof. Here we present the theoretical basis of this method by showing ...

journal_title：Molecular biology and evolution

authors： Rzhetsky A,Nei M

更新日期：1993-09-01 00:00:00

abstract：:Cyanobacteria are among the most ancient organisms known to have circadian rhythms. The cpmA gene is involved in controlling the circadian output signal. We studied polymorphism and divergence of this gene in six populations of a stress-tolerant cyanobacterium, Chroococcidiopsis sp., sampled in extreme habitats across...

journal_title：Molecular biology and evolution

authors： Dvornyk V,Jahan AS

更新日期：2012-12-01 00:00:00

abstract：:Heterotachy occurs when the relative evolutionary rates among sites are not the same across lineages. Sequence alignments are likely to exhibit heterotachy with varying severity because the intensity of purifying selection and adaptive forces at a given amino acid or DNA sequence position is unlikely to be the same in...

journal_title：Molecular biology and evolution

authors： Gadagkar SR,Kumar S

更新日期：2005-11-01 00:00:00

abstract：:A labeled gene tree topology that is more probable than the labeled gene tree topology matching a species tree is called "anomalous." Species trees that can generate such anomalous gene trees are said to be in the "anomaly zone." Here, probabilities of "unranked" and "ranked" gene tree topologies under the multispecie...

journal_title：Molecular biology and evolution

authors： Kim A,Rosenberg NA,Degnan JH

更新日期：2020-05-01 00:00:00

abstract：:The Orthonectida is a small, poorly known phylum of parasites of marine invertebrates. Their phylogenetic placement is obscure; they have been considered to be multicellular protozoans, primitive animals at a "mesozoan" grade of organization, or secondarily simplified flatworm-like organisms. The best known species in...

journal_title：Molecular biology and evolution

authors： Hanelt B,Van Schyndel D,Adema CM,Lewis LA,Loker ES

更新日期：1996-11-01 00:00:00

abstract：:The evolution of mitochondria from ancestral bacteria required that new protein transport machinery be established. Recent controversy over the evolution of these new molecular machines hinges on the degree to which ancestral bacterial transporters contributed during the establishment of the new protein import pathway...

journal_title：Molecular biology and evolution

authors： Tong J,Dolezal P,Selkrig J,Crawford S,Simpson AG,Noinaj N,Buchanan SK,Gabriel K,Lithgow T

更新日期：2011-05-01 00:00:00

abstract：:In phylogenetic inference, an evolutionary model describes the substitution processes along each edge of a phylogenetic tree. Misspecification of the model has important implications for the analysis of phylogenetic data. Conventionally, however, the selection of a suitable evolutionary model is based on heuristics or...

journal_title：Molecular biology and evolution

authors： Kedzierska AM,Drton M,Guigó R,Casanellas M

更新日期：2012-03-01 00:00:00

abstract：:It has recently been observed by Ho et al. (Ho SYW, Phillips MJ, Cooper A, Drummond AJ. 2005. Time dependency of molecular rate estimates and systematic overestimation of recent divergence times. Mol Biol Evol. 22(7):1561-1568) that apparent rates of molecular evolution increase when measured over short timespans. I i...

journal_title：Molecular biology and evolution

authors： Woodhams M

更新日期：2006-12-01 00:00:00

abstract：:DNA supercoiling is the master function that interconnects chromosome structure and global gene transcription. This function has recently been shown to be under strong selection in Escherichia coli. During the evolution of 12 initially identical populations propagated in a defined environment for 20,000 generations, p...

journal_title：Molecular biology and evolution

authors： Crozat E,Winkworth C,Gaffé J,Hallin PF,Riley MA,Lenski RE,Schneider D

更新日期：2010-09-01 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