Geographic variation and positive selection on M7 lysin, an acrosomal sperm protein in mussels (Mytilus spp.).

abstract：:Inferring past population dynamics over time from heterochronous molecular sequence data is often achieved using the Bayesian Skygrid model, a non-parametric coalescent model that estimates the effective population size over time. Available in BEAST, a cross-platform program for Bayesian analysis of molecular sequence...

journal_title：Molecular biology and evolution

authors： Hill V,Baele G

更新日期：2019-07-31 00:00:00

abstract：:The ribosome is responsible for protein synthesis in all living organisms. It is best known to exist around 3.5-3.7 Ga whereat life on Earth inhabited anoxic environment with abundant soluble irons. The RNAs and proteins are the two biopolymers that constitute the ribosome. However, both proteins and RNAs require meta...

journal_title：Molecular biology and evolution

authors： Lin SY,Wang YC,Hsiao C

更新日期：2019-05-01 00:00:00

abstract：:Several authors have postulated that genetic divergence between populations could result in genomic incompatibilities that would cause an increase in transposition in their hybrids, producing secondary effects such as sterility and therefore starting a speciation process. It has been demonstrated that transposition la...

journal_title：Molecular biology and evolution

authors： Labrador M,Farré M,Utzet F,Fontdevila A

更新日期：1999-07-01 00:00:00

abstract：:Maximum likelihood codon substitution models have proven useful for studying when and how protein function evolves, but they have recently been criticized on a number of fronts. The strengths and weaknesses of such methods must therefore be identified and improved upon. Here, using simulations, we show that the Clade ...

journal_title：Molecular biology and evolution

authors： Weadick CJ,Chang BS

更新日期：2012-05-01 00:00:00

abstract：:The apparent stasis in the evolution of avian chromosomes suggests that birds may have experienced relatively low rates of gene gain and loss in multigene families. To investigate this possibility and to explore the phenotypic consequences of variation in gene copy number, we examined evolutionary changes in the famil...

journal_title：Molecular biology and evolution

authors： Opazo JC,Hoffmann FG,Natarajan C,Witt CC,Berenbrink M,Storz JF

更新日期：2015-04-01 00:00:00

abstract：:The evolution of DNA base composition evolution is simplified to a six-parameter model when there are no strand biases for mutation and selection. We analyzed the dynamics of this model with special attention to the influence of a change in substitution rates. The G + C content of the DNA sequence tends to an equilibr...

journal_title：Molecular biology and evolution

authors： Lobry JR,Lobry C

更新日期：1999-06-01 00:00:00

abstract：:How is adaptability generated in a system composed of interacting cellular machineries, each with a separate and functionally critical job to perform? The machinery for organelle inheritance is precisely one such system, requiring coordination between robust and ancient cellular modules, including the cell cycle, cyto...

journal_title：Molecular biology and evolution

authors： Mast FD,Rachubinski RA,Dacks JB

更新日期：2012-03-01 00:00:00

abstract：:The authors of a recent manuscript in "Nature" claim to have discovered "universal trends" of amino acid gain and loss in protein evolution. Here, we show that this universal trend can be simply explained by a bias that is unavoidable with the 3-taxon trees used in the original analysis. We demonstrate that a rigorous...

journal_title：Molecular biology and evolution

authors： Goldstein RA,Pollock DD

更新日期：2006-07-01 00:00:00

abstract：:Directional evolution in microsatellites is the tendency for microsatellites either to increase or to decrease in size over time between populations. We analyzed 99 microsatellite loci in a sample of 193 maize plants representing the entire pre-Columbian range of this crop for evidence of directional evolution. We too...

journal_title：Molecular biology and evolution

authors： Vigouroux Y,Matsuoka Y,Doebley J

更新日期：2003-09-01 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：: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：: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：:The SLiM forward genetic simulation framework has proved to be a powerful and flexible tool for population genetic modeling. However, as a complex piece of software with many features that allow simulating a diverse assortment of evolutionary models, its initial learning curve can be difficult. Here we provide a step-...

journal_title：Molecular biology and evolution

authors： Haller BC,Messer PW

更新日期：2019-05-01 00:00:00

abstract：:Short interspersed repetitive elements (SINEs) have been shown to be excellent markers of molecular phylogeny, since the integration of a SINE at a particular position in a genome can be considered an unambiguous derived homologous character. In the present study, we isolated a new family of SINEs from cichlids in Lak...

journal_title：Molecular biology and evolution

authors： Takahashi K,Terai Y,Nishida M,Okada N

更新日期：1998-04-01 00:00:00

abstract：:Light-dependent and dark-operative protochlorophyllide oxidoreductases (LPORs and DPORs) are evolutionary and structurally distinct enzymes that are essential for the synthesis of (bacterio)chlorophyll, the primary pigment needed for both anoxygenic and oxygenic photosynthesis. In contrast to the long-held hypothesis ...

journal_title：Molecular biology and evolution

authors： Chernomor O,Peters L,Schneidewind J,Loeschcke A,Knieps-Grünhagen E,Schmitz F,von Lieres E,Kutta RJ,Svensson V,Jaeger KE,Drepper T,von Haeseler A,Krauss U

更新日期：2020-09-15 00:00:00

abstract：:The genomics era has expanded our knowledge about the diversity of the living world, yet harnessing high-throughput sequencing data to investigate alternative evolutionary trajectories, such as hybridization, is still challenging. Here we present sppIDer, a pipeline for the characterization of interspecies hybrids and...

journal_title：Molecular biology and evolution

authors： Langdon QK,Peris D,Kyle B,Hittinger CT

更新日期：2018-11-01 00:00:00

abstract：:The fossil record has long supported the view that most animal phyla originated during a brief period approximately 520 MYA known as the Cambrian explosion. However, molecular data analyses over the past 3 decades have found deeper divergences among animals (approximately 800 to 1,200 MYA), with and without the assump...

journal_title：Molecular biology and evolution

authors： Blair JE,Hedges SB

更新日期：2005-03-01 00:00:00

abstract：:Amino acids interact with each other, especially with neighboring amino acids, to generate protein structures. We studied the pattern of association and repulsion of amino acids based on 24,748 protein-coding genes from human, 11,321 from mouse, and 15,028 from Escherichia coli, and documented the pattern of neighbor ...

journal_title：Molecular biology and evolution

authors： Xia X,Xie Z

更新日期：2002-01-01 00:00:00

abstract：:Whole-genome duplications (WGDs) have contributed to gene-repertoire enrichment in many eukaryotic lineages. However, most duplicated genes are eventually lost and it is still unclear why some duplicated genes are evolutionary successful whereas others quickly turn to pseudogenes. Here, we show that dosage constraints...

journal_title：Molecular biology and evolution

authors： Gout JF,Lynch M

更新日期：2015-08-01 00:00:00

abstract：:Alternative splicing (AS) contributes to increased transcriptome and proteome diversity in various eukaryotic lineages. Previous studies showed low levels of conservation of alternatively spliced (cassette) exons within mammals and within dipterans. We report a strikingly different pattern in Caenorhabditis nematodes-...

journal_title：Molecular biology and evolution

authors： Irimia M,Rukov JL,Penny D,Garcia-Fernandez J,Vinther J,Roy SW

更新日期：2008-02-01 00:00:00

abstract：:DNA cytosine methylation is central to many biological processes, including regulation of gene expression, cellular differentiation, and development. This DNA modification is conserved across animals, having been found in representatives of sponges, ctenophores, cnidarians, and bilaterians, and with very few known ins...

journal_title：Molecular biology and evolution

authors： Kyger R,Luzuriaga-Neira A,Layman T,Milkewitz Sandberg TO,Singh D,Huchon D,Peri S,Atkinson SD,Bartholomew JL,Yi SV,Alvarez-Ponce D

更新日期：2021-01-23 00:00:00

abstract：:The orientation of closely linked genes in mammalian genomes is not random: there are more head-to-head (h2h) gene pairs than expected. To understand the origin of this enrichment in h2h gene pairs, we have analyzed the phylogenetic distribution of gene pairs separated by less than 600 bp of intergenic DNA (gene duos)...

journal_title：Molecular biology and evolution

authors： Franck E,Hulsen T,Huynen MA,de Jong WW,Lubsen NH,Madsen O

更新日期：2008-09-01 00:00:00

abstract：:Human DNA variation is currently a subject of intense research because of its importance for studying human origins, evolution, and demographic history and for association studies of complex diseases. A approximately 10-kb region on chromosome 1, which contains only four small exons (each <155 bp), was sequenced for 6...

journal_title：Molecular biology and evolution

authors： Yu N,Zhao Z,Fu YX,Sambuughin N,Ramsay M,Jenkins T,Leskinen E,Patthy L,Jorde LB,Kuromori T,Li WH

更新日期：2001-02-01 00:00:00

abstract：:Fish mitochondrial genome (mitogenome) data form a fundamental basis for revealing vertebrate evolution and hydrosphere ecology. Here, we report recent functional updates of MitoFish, which is a database of fish mitogenomes with a precise annotation pipeline MitoAnnotator. Most importantly, we describe implementation ...

journal_title：Molecular biology and evolution

authors： Sato Y,Miya M,Fukunaga T,Sado T,Iwasaki W

更新日期：2018-06-01 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：:In this study, we used an empirical example based on 100 mitochondrial genomes from higher teleost fishes to compare the accuracy of parsimony-based jackknife values with Bayesian support values. Phylogenetic analyses of 366 partitions, using differential taxon and character sampling from the entire data matrix of 100...

journal_title：Molecular biology and evolution

authors： Simmons MP,Pickett KM,Miya M

更新日期：2004-01-01 00:00:00

abstract：:Quercus petraea and Quercus robur are two closely related oak species that frequently hybridize. We sequenced 70 clones containing the 5.8S and ITS2 regions of ribosomal DNA (rDNA) from these two species and did not detect a species-specific difference. Surprisingly, three divergent (up to 12.6%) rDNA families were id...

journal_title：Molecular biology and evolution

authors： Muir G,Fleming CC,Schlötterer C

更新日期：2001-02-01 00:00:00

abstract：:The cadherin-catenin complex (CCC) mediates cell-cell adhesion in bilaterian animals by linking extracellular cadherin-based adhesions to the actin cytoskeleton. However, it is unknown whether the basic organization of the complex is conserved across all metazoans. We tested whether protein interactions and actin-bind...

journal_title：Molecular biology and evolution

authors： Clarke DN,Miller PW,Lowe CJ,Weis WI,Nelson WJ

更新日期：2016-08-01 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：:Gene duplication is a major driving force in genome evolution. Here, we explore the nature and origin of the POT1 gene duplication in Arabidopsis thaliana. Protection of Telomeres (POT1) is a conserved multifunctional protein that modulates telomerase activity and its engagement with telomeres. Arabidopsis thaliana en...

journal_title：Molecular biology and evolution

authors： Beilstein MA,Renfrew KB,Song X,Shakirov EV,Zanis MJ,Shippen DE

更新日期：2015-05-01 00:00:00