Patterns of mutation and selection at synonymous sites in Drosophila.

abstract：:Nei and Gojobori (1986) developed a simple method to estimate the numbers of synonymous (ds) and nonsynonymous (dN) substitutions per site. In the present paper, we have developed a method for computing variances and covariances of ds's and dN's and of the proportions of synonymous (ps) and nonsynonymous (pN) differen...

journal_title：Molecular biology and evolution

authors： Ota T,Nei M

更新日期：1994-07-01 00:00:00

abstract：:Cyanobacteria contain up to three highly divergent glyceraldehyde-3-phosphate dehydrogenase (GAPDH) genes: gap1, gap2, and gap3. Genes gap1 and gap2 are closely related at the sequence level to the nuclear genes encoding cytosolic and chloroplast GAPDH of higher plants and have recently been shown to play distinct key...

journal_title：Molecular biology and evolution

authors： Figge RM,Schubert M,Brinkmann H,Cerff R

更新日期：1999-04-01 00:00:00

abstract：:The nuclear large subunit (LSU) rRNA gene is a rich source of phylogenetic characters because of its large size, mosaic of slowly and rapidly evolving regions, and complex secondary structure variation. Nevertheless, many studies have indicated that inconsistency, bias, and gene-specific error (e.g., within-individual...

journal_title：Molecular biology and evolution

authors： Omilian AR,Taylor DJ

更新日期：2001-12-01 00:00:00

abstract：:Sex-biased gene expression is becoming an increasingly important way to study sexual selection at the molecular genetic level. However, little is known about the timing, persistence, and continuity of gene expression required in the creation of distinct male and female phenotypes, and even less about how sex-specific ...

journal_title：Molecular biology and evolution

authors： Mank JE,Nam K,Brunström B,Ellegren H

更新日期：2010-07-01 00:00:00

abstract：:Proteomic analyses of the nucleolus have revealed almost 700 functionally diverse proteins implicated in ribosome biogenesis, nucleolar assembly, and regulation of vital cellular processes. However, this nucleolar inventory has not unveiled a specific consensus motif necessary for nucleolar binding. The ribosomal prot...

journal_title：Molecular biology and evolution

authors： Kundu-Michalik S,Bisotti MA,Lipsius E,Bauche A,Kruppa A,Klokow T,Kammler G,Kruppa J

更新日期：2008-03-01 00:00:00

abstract：:Hybridization between different species plays an important role in plant genome evolution, as well as is a widely used approach for crop improvement. McClintock has predicted that plant wide hybridization constitutes a "genomic shock" whereby cryptic transposable elements may be activated. However, direct experimental...

journal_title：Molecular biology and evolution

authors： Shan X,Liu Z,Dong Z,Wang Y,Chen Y,Lin X,Long L,Han F,Dong Y,Liu B

更新日期：2005-04-01 00:00:00

abstract：:Evolution at silent sites is often used to estimate the pace of selectively neutral processes or to infer differences in divergence times of genes. However, silent sites are subject to selection in favor of preferred codons, and the strength of such selection varies dramatically across genes. Here, we use the relation...

journal_title：Molecular biology and evolution

authors： Hirsh AE,Fraser HB,Wall DP

更新日期：2005-01-01 00:00:00

abstract：:The human Y chromosome consists of ampliconic genes, which are located in palindromes and undergo frequent gene conversion, and single-copy genes including the primary sex-determining locus, SRY. Here, we demonstrate that SRY is duplicated in a large palindrome in the European rabbit (Oryctolagus cuniculus). Furthermo...

journal_title：Molecular biology and evolution

authors： Geraldes A,Rambo T,Wing RA,Ferrand N,Nachman MW

更新日期：2010-11-01 00:00:00

abstract：:Polyploidization events have occurred during the evolution of many fungi, plant, and animal species and are thought to contribute to speciation and tumorigenesis, however little is known about how ploidy level contributes to adaptation at the molecular level. Here we integrate whole genome sequencing, RNA expression a...

journal_title：Molecular biology and evolution

authors： Scott AL,Richmond PA,Dowell RD,Selmecki AM

更新日期：2017-10-01 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 examine rate heterogeneity among evolutionary lineages of the grass family at two plasmid loci, ndhF and rbcL, and we introduce a method to determine whether patterns of rate heterogeneity are correlated between loci. We show both that rates of synonymous evolution are heterogeneous among grass lineages and that ar...

journal_title：Molecular biology and evolution

authors： Gaut BS,Clark LG,Wendel JF,Muse SV

更新日期：1997-07-01 00:00:00

abstract：:The variation of amino acid substitution rates in proteins depends on several variables. Among these, the protein's expression level, functional category, essentiality, or metabolic costs of its amino acid residues may play an important role. However, the relative importance of each variable has not yet been evaluated...

journal_title：Molecular biology and evolution

authors： Rocha EP,Danchin A

更新日期：2004-01-01 00:00:00

abstract：:With growing amounts of genome data and constant improvement of models of molecular evolution, phylogenetic reconstruction became more reliable. However, our knowledge of the real process of molecular evolution is still limited. When enough large-sized data sets are analyzed, any subtle biases in statistical models ca...

journal_title：Molecular biology and evolution

authors： Kitazoe Y,Kishino H,Okabayashi T,Watabe T,Nakajima N,Okuhara Y,Kurihara Y

更新日期：2005-03-01 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：: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：: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 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：:The spacer between the 16S and 23S rRNA genes of the chloroplast DNA has been implicated as an origin of replication in several species of plants. In the evening primrose, Oenothera, this site was found to vary greatly in size, with plastid genomes (plastomes) being readily distinguished. To determine whether plastome...

journal_title：Molecular biology and evolution

authors： Sears BB,Stoike LL,Chiu WL

更新日期：1996-07-01 00:00:00

abstract：:The third chromosome of Drosophila pseudoobscura is polymorphic for numerous gene arrangements that form classical clines in North America. The polytene salivary chromosomes isolated from natural populations revealed changes in gene order that allowed the different gene arrangements to be linked together by paracentri...

journal_title：Molecular biology and evolution

authors： Wallace AG,Detweiler D,Schaeffer SW

更新日期：2011-08-01 00:00:00

abstract：:Inaccurate inference of positional homologies in multiple sequence alignments and systematic errors introduced by alignment heuristics obfuscate phylogenetic inference. Alignment masking, the elimination of phylogenetically uninformative or misleading sites from an alignment before phylogenetic analysis, is a common p...

journal_title：Molecular biology and evolution

authors： Rajan V

更新日期：2013-03-01 00:00:00

abstract：:Heterotachy is a general term to describe positions that evolve at different rates in different lineages. Heterotachy also can generally be viewed as multivariate rates-across-sites variation, which can be described as randomly drawing rates (or branch lengths) from a multivariate distribution for each branch at each ...

journal_title：Molecular biology and evolution

authors： Wu J,Susko E

更新日期：2011-05-01 00:00:00

abstract：:The evolutionary expansion of CAG repeats in human triplet expansion disease genes is intriguing because of their deleterious phenotype. In the past, this expansion has been suggested to reflect a broad genomewide expansion of repeats, which would imply that mutational and evolutionary processes acting on repeats diff...

journal_title：Molecular biology and evolution

authors： Hancock JM,Worthey EA,Santibáñez-Koref MF

更新日期：2001-06-01 00:00:00

abstract：:The grass family (Poaceae), the fourth largest family of flowering plants, encompasses the most economically important cereal, forage, and energy crops, and exhibits a unique gametophytic self-incompatibility (SI) mechanism that is controlled by at least two multiallelic and independent loci, S and Z. Despite intense ...

journal_title：Molecular biology and evolution

authors： Manzanares C,Barth S,Thorogood D,Byrne SL,Yates S,Czaban A,Asp T,Yang B,Studer B

更新日期：2016-04-01 00:00:00

abstract：:Here, we address a much-debated topic: is there or is there not an organismal tree of gamma-proteobacteria that can be unambiguously inferred from a core of shared genes? We apply several recently developed analytical methods to this problem, for the first time. Our heat map analyses of P values and of bootstrap bipar...

journal_title：Molecular biology and evolution

authors： Susko E,Leigh J,Doolittle WF,Bapteste E

更新日期：2006-05-01 00:00:00

abstract：:Identifying mechanisms that underlie variation in adult survivorship provide insight into the evolution of life history strategies and phenotypic variation in longevity. There is accumulating evidence that shortening telomeres, the protective caps at the ends of chromosomes, play an important role in individual variat...

journal_title：Molecular biology and evolution

authors： Haussmann MF,Mauck RA

更新日期：2008-01-01 00:00:00

abstract：:MicroRNA (miRNA) sponges are vital components of posttranscriptional gene regulation. Yet, only a limited number of miRNA sponges have been identified. Here, we show that the recently evolved noncoding tumor suppressor transcript, antisense RNA to TP73 gene (TP73-AS1), functions as a natural sponge of human-specific m...

journal_title：Molecular biology and evolution

authors： Hu H,Liu JM,Hu Z,Jiang X,Yang X,Li J,Zhang Y,Yu H,Khaitovich P

更新日期：2018-05-01 00:00:00

abstract：:Hybridization in plants may result in hybrid speciation or introgression and, thus, is now widely understood to be an important mechanism of species diversity on an evolutionary timescale. Hybridization is particularly common in ferns, as is polyploidy, which often results from hybrid crosses. Nevertheless, hybrid spe...

journal_title：Molecular biology and evolution

authors： Wang J,Dong S,Yang L,Harris A,Schneider H,Kang M

更新日期：2020-09-01 00:00:00

abstract：:Transposable elements (TEs) make up around 10%-15% of the Drosophila melanogaster genome, but its sibling species Drosophila simulans carries only one third as many such repeat sequences. We do not, however, have an overall view of copy numbers of the various classes of TEs (long terminal repeat [LTR] retrotransposons...

journal_title：Molecular biology and evolution

authors： Vieira C,Lepetit D,Dumont S,Biémont C

更新日期：1999-09-01 00:00:00

abstract：:Sequencing multiple copies of the ITS1 region revealed the coexistence of two or more haplotypes within the genome of Chorthippus parallelus. Using a PCR-RFLP approach, the ITS1 numbers and frequencies of haplotypes present in each of 40 individuals were investigated, revealing a consistent lack of homogeneity. For ea...

journal_title：Molecular biology and evolution

authors： Parkin EJ,Butlin RK

更新日期：2004-08-01 00:00:00

abstract：:Negative genetic regulators of phenotypic heterogeneity, or phenotypic capacitors/stabilizers, elevate population-average fitness by limiting deviation from the optimal phenotype and increase the efficacy of natural selection by enhancing the phenotypic differences among genotypes. Stabilizers can presumably be switch...

journal_title：Molecular biology and evolution

authors： Mo N,Zhang X,Shi W,Yu G,Chen X,Yang JR

更新日期：2020-12-23 00:00:00