Rampant gene loss in the underground orchid Rhizanthella gardneri highlights evolutionary constraints on plastid genomes.

abstract：:Knowledge of mutation rates is crucial for calibrating population genetics models of demographic history in units of years. However, mutation rates remain challenging to estimate because of the need to identify extremely rare events. We estimated the nuclear mutation rate in wolves by identifying de novo mutations in ...

journal_title：Molecular biology and evolution

authors： Koch E,Schweizer RM,Schweizer TM,Stahler DR,Smith DW,Wayne RK,Novembre J

更新日期：2019-07-12 00:00:00

abstract：:The shikimate dehydrogenases (SDH) represent a widely distributed enzyme family with an essential role in secondary metabolism. This superfamily had been previously subdivided into 4 enzyme groups (AroE, YdiB, SdhL, and RifI), which show clear biochemical and functional differences ranging from amino acid biosynthesis...

journal_title：Molecular biology and evolution

authors： Singh S,Stavrinides J,Christendat D,Guttman DS

更新日期：2008-10-01 00:00:00

abstract：:We investigate the effect of purifying selection at multiple sites on both the shape of the genealogy and the distribution of mutations on the tree. We find that the primary effect of purifying selection on a genealogy is to shift the distribution of mutations on the tree, whereas the shape of the tree remains largely...

journal_title：Molecular biology and evolution

authors： Williamson S,Orive ME

更新日期：2002-08-01 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：:Most "tests of neutrality" assess whether particular data sets depart from the predictions of a standard neutral model with no recombination. For Drosophila, where nuclear polymorphism data routinely show evidence of genetic exchange, the assumption of no recombination is often unrealistic. In addition, while conserva...

journal_title：Molecular biology and evolution

authors： Przeworski M,Wall JD,Andolfatto P

更新日期：2001-03-01 00:00:00

abstract：:We report the complete sequence of a paralogous copy of elongation factor-1 alpha (EF-1 alpha) in the honeybee, Apis mellifera (Hymenoptera: Apidae). This copy differs from a previously described copy in the positions of five introns and in 25% of the nucleotide sites in the coding regions. The existence of two paralo...

journal_title：Molecular biology and evolution

authors： Danforth BN,Ji S

更新日期：1998-03-01 00:00:00

abstract：:Liver and intestinal flukes of the family Fasciolidae cause zoonotic food-borne infections that impact both agriculture and human health throughout the world. Their evolutionary history and the genetic basis underlying their phenotypic and ecological diversity are not well understood. To close that knowledge gap, we c...

journal_title：Molecular biology and evolution

authors： Choi YJ,Fontenla S,Fischer PU,Le TH,Costábile A,Blair D,Brindley PJ,Tort JF,Cabada MM,Mitreva M

更新日期：2020-01-01 00:00:00

abstract：:The human major histocompatibility complex (Mhc) is a chromosomal segment approximately 4 million bp long that contains > or = 84 genes. Some of these genes code for the class I and class II molecules, while the remaining genes code for complement components, cytochrome P450, tumor necrosis factor, and many other, unr...

journal_title：Molecular biology and evolution

authors： Klein J,O'hUigin C,Figueroa F,Mayer WE,Klein D

更新日期：1993-01-01 00:00:00

abstract：:Despite the importance of plant-plant interactions on plant community dynamics and crop yield, our understanding of the adaptive genetics underlying these interactions is still limited and deserves to be investigated in the context of complex and diffuse interactions occurring in plant assemblages. Here, based on 145 ...

journal_title：Molecular biology and evolution

authors： Frachon L,Mayjonade B,Bartoli C,Hautekèete NC,Roux F

更新日期：2019-07-01 00:00:00

abstract：:Immunoglobulin diversity is generated primarily by the heavy- and light-chain variable-region gene families. To understand the pattern of long-term evolution of the heavy-chain variable-region (VH) gene family, which is composed of a large number of member genes, the evolutionary relationships of representative VH gen...

journal_title：Molecular biology and evolution

authors： Ota T,Nei M

更新日期：1994-05-01 00:00:00

abstract：:Many intron positions are conserved in varying subsets of eukaryotic genomes and, consequently, comprise a potentially informative class of phylogenetic characters. Roy and Gilbert developed a method of phylogenetic reconstruction using the patterns of intron presence-absence in eukaryotic genes and, applying this met...

journal_title：Molecular biology and evolution

authors： Zheng J,Rogozin IB,Koonin EV,Przytycka TM

更新日期：2007-11-01 00:00:00

abstract：:Numerous studies have used indices of genetic distance between species to reconstruct evolutionary relationships and to estimate divergence time. However, the empirical relationship between molecular-based indices of genetic divergence and divergence time based on the fossil record is poorly known. To date, the result...

journal_title：Molecular biology and evolution

authors： Wayne RK,Van Valkenburgh B,O'Brien SJ

更新日期：1991-05-01 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：: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 describe here a case of homologous introns containing homologous open reading frames (ORFs) that are inserted at the same site in the large subunit (LSU) rRNA gene of different organelles in distantly related organisms. We show that the chloroplast LSU rRNA gene of the green alga Chlamydomonas pallidostigmatica con...

journal_title：Molecular biology and evolution

authors： Turmel M,Côté V,Otis C,Mercier JP,Gray MW,Lonergan KM,Lemieux C

更新日期：1995-07-01 00:00:00

abstract：:Clines in chromosomal inversion polymorphisms-presumably driven by climatic gradients-are common but there is surprisingly little evidence for selection acting on them. Here we address this long-standing issue in Drosophila melanogaster by using diagnostic single nucleotide polymorphism (SNP) markers to estimate inver...

journal_title：Molecular biology and evolution

authors： Kapun M,Fabian DK,Goudet J,Flatt T

更新日期：2016-05-01 00:00:00

abstract：:In the age of whole-genome population genetics, so-called genomic scan studies often conclude with a long list of putatively selected loci. These lists are then further scrutinized to annotate these regions by gene function, corresponding biological processes, expression levels, or gene networks. Such annotations are ...

journal_title：Molecular biology and evolution

authors： Pavlidis P,Jensen JD,Stephan W,Stamatakis A

更新日期：2012-10-01 00:00:00

abstract：:The T1 family of retrotransposable elements is interspersed and moderately repeated in five member species of the Anopheles gambiae sibling-species complex and has diverged little since the radiation of the complex. T1 includes two closely related but independent subfamilies, defined by the presence or absence of link...

journal_title：Molecular biology and evolution

authors： Besansky NJ

更新日期：1990-05-01 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：:Operons coding for the enzyme arsenite oxidase have been detected in the genomes from Archaea and Bacteria by Blast searches using the amino acid sequences of the respective enzyme characterized in two different beta-proteobacteria as templates. Sequence analyses show that in all these species, arsenite oxidase is tra...

journal_title：Molecular biology and evolution

authors： Lebrun E,Brugna M,Baymann F,Muller D,Lièvremont D,Lett MC,Nitschke W

更新日期：2003-05-01 00:00:00

abstract：:Measuring natural selection on genomic elements involved in the cis-regulation of gene expression--such as transcriptional enhancers and promoters--is critical for understanding the evolution of genomes, yet it remains a major challenge. Many studies have attempted to detect positive or negative selection in these non...

journal_title：Molecular biology and evolution

authors： Smith JD,McManus KF,Fraser HB

更新日期：2013-11-01 00:00:00

abstract：:Spatial distribution and clustering of repetitive elements are extensively studied during the last years, as well as their colocalization with other genomic components. Here we investigate the large-scale features of Alu and LINE1 spatial arrangement in the human genome by studying the size distribution of interrepeat...

journal_title：Molecular biology and evolution

authors： Sellis D,Provata A,Almirantis Y

更新日期：2007-11-01 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：: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：:MrBayes, using Metropolis-coupled Markov chain Monte Carlo (MCMCMC or (MC)(3)), is a popular program for Bayesian inference. As a leading method of using DNA data to infer phylogeny, the (MC)(3) Bayesian algorithm and its improved and parallel versions are now not fast enough for biologists to analyze massive real-wor...

journal_title：Molecular biology and evolution

authors： Bao J,Xia H,Zhou J,Liu X,Wang G

更新日期：2013-06-01 00:00:00

abstract：:Untangling the root of the evolutionary tree of placental mammals has been nearly an impossible task. The good news is that only three possibilities are seriously considered. The bad news is that all three possibilities are seriously considered. Paleontologists favor a root anchored by Xenarthra (e.g., sloths and ante...

journal_title：Molecular biology and evolution

authors： Teeling EC,Hedges SB

更新日期：2013-09-01 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：:Barley (Hordeum vulgare) is a major crop, grown worldwide and in a wide range of climatic conditions. Despite its importance as a crop species, little is known about the population genetics of barley and the effects of bottlenecks, adaptation, and gene flow on genetic diversity within and between landrace populations....

journal_title：Molecular biology and evolution

authors： Leino MW,Hagenblad J

更新日期：2010-04-01 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：:Genetic studies of Tibetans, an ethnic group with a long-lasting presence on the Tibetan Plateau which is known as the highest plateau in the world, may offer a unique opportunity to understand the biological adaptations of human beings to high-altitude environments. We conducted a genome-wide study of 1,000,000 genet...

journal_title：Molecular biology and evolution

authors： Xu S,Li S,Yang Y,Tan J,Lou H,Jin W,Yang L,Pan X,Wang J,Shen Y,Wu B,Wang H,Jin L

更新日期：2011-02-01 00:00:00