Assessing horizontal transfer of nifHDK genes in eubacteria: nucleotide sequence of nifK from Frankia strain HFPCcI3.

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：:A major theoretical consequence of selection at a locus is the genetic hitchhiking of linked sites (selective sweep). The extent of hitchhiking around a gene is related to the strength of selection and the rate of recombination, with its impact diminishing with distance from the selected site. At the Rop-1 locus of th...

journal_title：Molecular biology and evolution

authors： Rose CJ,Chapman JR,Marshall SD,Lee SF,Batterham P,Ross HA,Newcomb RD

更新日期：2011-06-01 00:00:00

abstract：:Over time, natural selection molds every gene into a unique mosaic of sites evolving rapidly or resisting change-an "evolutionary fingerprint" of the gene. Aspects of this evolutionary fingerprint, such as the site-specific ratio of nonsynonymous to synonymous substitution rates (dN/dS), are commonly used to identify ...

journal_title：Molecular biology and evolution

authors： Pond SL,Scheffler K,Gravenor MB,Poon AF,Frost SD

更新日期：2010-03-01 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：: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：:Human c-Myb proto-oncogene is highly expressed in hematopoietic progenitors as well as leukemia and certain solid tumor. However, the regulatory mechanisms of its expression and biological functions remain largely unclear. Recently, c-Myb has been shown to be targeted by microRNA-150 (miR-150) which thereby controls B...

journal_title：Molecular biology and evolution

authors： Lin YC,Kuo MW,Yu J,Kuo HH,Lin RJ,Lo WL,Yu AL

更新日期：2008-10-01 00:00:00

abstract：:This paper discusses the optimization principle in phylogenetic analysis, in the case of distance data. We argue that the use of this principle cannot be called into question, except for computing time reasons. We show that the minimum-evolution criterion is not perfectly suited for distance data estimated from sequen...

journal_title：Molecular biology and evolution

authors： Gascuel O

更新日期：2000-03-01 00:00:00

abstract：:We report the results of a phylogenetic survey of the retrotransposon copia in the melanogaster subgroup of the Drosophila genus. The polymerase chain reaction was used to amplify the copia 5' long terminal repeat and the adjacent untranslated leader region from representative melanogaster subgroup species. Restrictio...

journal_title：Molecular biology and evolution

authors： Jordan IK,McDonald JF

更新日期：1998-09-01 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：:Remarkably little is known about the population-level processes leading up to the extinction of the neandertal. To examine this, we use mitochondrial DNA sequences from 13 neandertal individuals, including a novel sequence from northern Spain, to examine neandertal demographic history. Our analyses indicate that recen...

journal_title：Molecular biology and evolution

authors： Dalén L,Orlando L,Shapiro B,Brandström-Durling M,Quam R,Gilbert MT,Díez Fernández-Lomana JC,Willerslev E,Arsuaga JL,Götherström A

更新日期：2012-08-01 00:00:00

abstract：:The assumption of a molecular clock for dating events from sequence information is often frustrated by the presence of heterogeneity among evolutionary rates due, among other factors, to positively selected sites. In this work, our goal is to explore methods to estimate infection dates from sequence analysis. One such...

journal_title：Molecular biology and evolution

authors： Wróbel B,Torres-Puente M,Jiménez N,Bracho MA,García-Robles I,Moya A,González-Candelas F

更新日期：2006-06-01 00:00:00

abstract：:Horizontal gene transfer threatens the therapeutic success of antibiotics by facilitating the rapid dissemination of resistance alleles among bacterial species. The conjugative mobile element Tn916 provides an excellent context for examining the role of adaptive parasexuality as it carries the tetracycline-resistance ...

journal_title：Molecular biology and evolution

authors： Beabout K,Hammerstrom TG,Wang TT,Bhatty M,Christie PJ,Saxer G,Shamoo Y

更新日期：2015-10-01 00:00:00

abstract：:There is increasing evidence that dosage compensation is not a ubiquitous feature following sex chromosome evolution, especially not in organisms where females are the heterogametic sex, like in birds. Even when it occurs, compensation can be incomplete and limited to dosage-sensitive genes. However, previous work has...

journal_title：Molecular biology and evolution

authors： Uebbing S,Konzer A,Xu L,Backström N,Brunström B,Bergquist J,Ellegren H

更新日期：2015-10-01 00:00:00

abstract：:Hantaviruses are considered one of the best examples of a long-term association between RNA viruses and their hosts. Based on the appearance of strong host specificity, it has been suggested that hantaviruses cospeciated with the rodents and insectivores they infect since these mammals last shared a common ancestor, a...

journal_title：Molecular biology and evolution

authors： Ramsden C,Holmes EC,Charleston MA

更新日期：2009-01-01 00:00:00

abstract：:Random genetic drift, or stochastic change in gene frequency, is a fundamental evolutionary force that is usually defined within the ideal Wright-Fisher (WF) population. However, as the theory is increasingly applied to populations that deviate strongly from the ideal model, a paradox of random drift has emerged. When...

journal_title：Molecular biology and evolution

authors： Chen Y,Tong D,Wu CI

更新日期：2017-08-01 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：: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：: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：:Lineage-specific gene duplications contribute to a large variation in specialized metabolites among different plant species. There is also considerable variability in the specialized metabolites within a single plant species. However, it is unclear whether copy number variations (CNVs) derived from gene duplication ev...

journal_title：Molecular biology and evolution

authors： Shirai K,Matsuda F,Nakabayashi R,Okamoto M,Tanaka M,Fujimoto A,Shimizu M,Shinozaki K,Seki M,Saito K,Hanada K

更新日期：2017-12-01 00:00:00

abstract：:Adaptive evolution at the molecular level can be studied by detecting convergent and parallel evolution at the amino acid sequence level. For a set of homologous protein sequences, the ancestral amino acids at all interior nodes of the phylogenetic tree of the proteins can be statistically inferred. The amino acid sit...

journal_title：Molecular biology and evolution

authors： Zhang J,Kumar S

更新日期：1997-05-01 00:00:00

abstract：:Single-stranded DNA(ssDNA) viral life cycles must balance double-stranded DNA (dsDNA) and ssDNA biosynthesis. Previously published in vitro results suggest that microvirus C and host cell SSB proteins play antagonistic roles to achieve this balance. To investigate this in vivo, microvirus DNA replication was character...

journal_title：Molecular biology and evolution

authors： Doore SM,Baird CD,2012 University of Arizona Virology Undergraduate Lab.,Roznowski AP,Fane BA

更新日期：2014-06-01 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：: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：:Parasitoid wasps use venom to manipulate the immunity and metabolism of their host insects in a variety of ways to provide resources for their offspring. Yet, how genes are recruited and evolve to perform venom functions remain open questions. A recently recognized source of eukaryotic genome innovation is lateral gen...

journal_title：Molecular biology and evolution

authors： Martinson EO,Martinson VG,Edwards R,Mrinalini,Werren JH

更新日期：2016-04-01 00:00:00

abstract：:We describe a stochastic birth-and-death model of evolution of horizontally transferred genes in microbial populations. The model is a generalization of the stochastic model described by Berg and Kurland and includes five parameters: the rate of mutational inactivation, selection coefficient, invasion rate (i.e., rate...

journal_title：Molecular biology and evolution

authors： Novozhilov AS,Karev GP,Koonin EV

更新日期：2005-08-01 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：:We have investigated intron evolution in the compact genomes of 2 closely related species of pufferfishes, Fugu rubripes and Tetraodon nigroviridis, that diverged about 32 million years ago (MYA). Analysis of 148,028 aligned intron positions in 13,547 gene pairs using human as an outgroup identified 57 and 24 intron l...

journal_title：Molecular biology and evolution

authors： Loh YH,Brenner S,Venkatesh B

更新日期：2008-03-01 00:00:00

abstract：:Crabs of the infra-order Brachyura are one of the most diverse groups of crustaceans with approximately 7,000 described species in 98 families, occurring in marine, freshwater, and terrestrial habitats. The relationships among the brachyuran families are poorly understood due to the high morphological complexity of th...

journal_title：Molecular biology and evolution

authors： Tsang LM,Schubart CD,Ahyong ST,Lai JC,Au EY,Chan TY,Ng PK,Chu KH

更新日期：2014-05-01 00:00:00

abstract：:Odorant receptors (ORs) are essential for plant-insect interactions. However, despite the global impacts of Lepidoptera (moths and butterflies) as major herbivores and pollinators, little functional data is available about Lepidoptera ORs involved in plant volatile detection. Here, we initially characterized the plant...

journal_title：Molecular biology and evolution

authors： Guo M,Du L,Chen Q,Feng Y,Zhang J,Zhang X,Tian K,Cao S,Huang T,Jacquin-Joly E,Wang G,Liu Y

更新日期：2020-11-24 00:00:00

abstract：:Recent studies of mitochondrial DNA (mtDNA) variation in mammals and Drosophila have shown an excess of amino acid variation within species (replacement polymorphism) relative to the number of silent and replacement differences fixed between species. To examine further this pattern of nonneutral mtDNA evolution, we pr...

journal_title：Molecular biology and evolution

authors： Rand DM,Kann LM

更新日期：1996-07-01 00:00:00