Characterizing transcriptional regulatory sequences in coronaviruses and their role in recombination.

abstract：:Current data on green algal mitochondrial genomes suggest an unexpected dichotomy within the group with respect to genome structure, organization, and sequence affiliations. The present study suggests that there is a correlation between this dichotomy on one hand and the differences in the abundance, base composition,...

journal_title：Molecular biology and evolution

authors： Nedelcu AM,Lee RW

更新日期：1998-06-01 00:00:00

abstract：:Male sexual behavior in the fruit fly Drosophila melanogaster is regulated by fruitless (fru), a sex-determination gene specifying the synthesis of BTB-Zn finger proteins that likely function as male-specific transcriptional regulators. Expression of fru in the nervous system specifies male sexual behavior and the mus...

journal_title：Molecular biology and evolution

authors： Gailey DA,Billeter JC,Liu JH,Bauzon F,Allendorfer JB,Goodwin SF

更新日期：2006-03-01 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：: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：:Whether higher-order chromatin organization is related to genome stability over evolutionary time remains elusive. We find that regions of conserved gene order across the genus Drosophila are larger if they harbor genes bound by B-type lamin (Lam) and Suppressor of Under-Replication (SUUR), two proteins located at the...

journal_title：Molecular biology and evolution

authors： Ranz JM,Díaz-Castillo C,Petersen R

更新日期：2012-01-01 00:00:00

abstract：:Insertions and deletions (indels) in protein-coding genes are important sources of genetic variation. Their role in creating new proteins may be especially important after gene duplication. However, little is known about how indels affect the divergence of duplicate genes. We here study thousands of duplicate genes in...

journal_title：Molecular biology and evolution

authors： Guo B,Zou M,Wagner A

更新日期：2012-10-01 00:00:00

abstract：:A sample of the second largest subunit of low-copy nuclear RNA polymerase II (rpb2) sequences from Malvaceae subfamily Malvoideae suggests that rpb2 has been duplicated early in the subfamily's history. Hibiscus and related taxa possess two rpb2 genes, both of which produce congruent phylogenetic patterns that are lar...

journal_title：Molecular biology and evolution

authors： Pfeil BE,Brubaker CL,Craven LA,Crisp MD

更新日期：2004-07-01 00:00:00

abstract：:Transposable elements are widespread mobile DNA sequences able to integrate into new locations within genomes. Through transposition and recombination, they significantly contribute to genome plasticity and evolution. They can also regulate gene expression and provide regulatory and coding sequences (CDSs) for the evo...

journal_title：Molecular biology and evolution

authors： Böhne A,Zhou Q,Darras A,Schmidt C,Schartl M,Galiana-Arnoux D,Volff JN

更新日期：2012-02-01 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：:Plasticity and robustness of signaling pathways partly rely on genetic redundancy, although the precise mechanism that provides functional specificity to the different redundant elements in a given process is often unknown. In Arabidopsis, functional redundancy in gibberellin signaling has been largely attributed to t...

journal_title：Molecular biology and evolution

authors： Gallego-Bartolomé J,Minguet EG,Marín JA,Prat S,Blázquez MA,Alabadí D

更新日期：2010-06-01 00:00:00

abstract：:Methods such as maximum parsimony (MP) are frequently criticized as being statistically unsound and not being based on any "model." On the other hand, advocates of MP claim that maximum likelihood (ML) has some fundamental problems. Here, we explore the connection between the different versions of MP and ML methods, p...

journal_title：Molecular biology and evolution

authors： Steel M,Penny D

更新日期：2000-06-01 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：:Previous studies have shown that splicing efficiency, and thus maturation of pre-mRNA, depends on the correct folding of the RNA molecule into a secondary or higher order structure. When disrupted by a mutation, aberrant folding may result in a lower splicing efficiency. However, the structure can be restored by a sec...

journal_title：Molecular biology and evolution

authors： Piskol R,Stephan W

更新日期：2008-11-01 00:00:00

abstract：:In all anthropoid species, the coding region of the involucrin gene contains a segment of short tandem repeats that were added sequentially, beginning in a common anthropoid ancestor. The involucrin coding region of each of two platyrrhine species, the white-fronted capuchin (Cebus albifrons) and the cottontop tamarin...

journal_title：Molecular biology and evolution

authors： Phillips M,Rice RH,Djian P,Green H

更新日期：1991-09-01 00:00:00

abstract：:The increased interest in asexual organisms calls for in-depth studies of asexual complexes that actively give rise to new clones. We present an extensive molecular study of the Otiorhynchus scaber (Coleoptera, Curculionidae) weevil system. Three forms have traditionally been recognized: diploid sexuals, triploid, and...

journal_title：Molecular biology and evolution

authors： Stenberg P,Lundmark M,Knutelski S,Saura A

更新日期：2003-10-01 00:00:00

abstract：:We have followed, in glucose-limited chemostats, the evolution of natural isolates of Escherichia coli possessing maximal growth rates of 0.48-1.43 doublings/h. Under these conditions a rapid-growth phenotype similar to that of standard laboratory wild-type strains was selected so that after 280 generations all of the...

journal_title：Molecular biology and evolution

authors： Mikkola R,Kurland CG

更新日期：1992-05-01 00:00:00

abstract：:We present QNet, a method for constructing split networks from weighted quartet trees. QNet can be viewed as a quartet analogue of the distance-based Neighbor-Net (NNet) method for network construction. Just as NNet, QNet works by agglomeratively computing a collection of circular weighted splits of the taxa set which...

journal_title：Molecular biology and evolution

authors： Grünewald S,Forslund K,Dress A,Moulton V

更新日期：2007-02-01 00:00:00

abstract：:The complete mitochondrial DNA (mtDNA) control region was sequenced for 71 individuals from five species of the rodent genus Clethrionomys both to understand patterns of variation and to explore the existence of previously described domains and other elements. Among species, the control region ranged from 942 to 971 b...

journal_title：Molecular biology and evolution

authors： Matson CW,Baker RJ

更新日期：2001-08-01 00:00:00

abstract：:A phylogenetic tree of a gene family of nicotinic acetylcholine receptor subunits was constructed using 84 nucleotide sequences of receptor subunits from 18 different species in order to elucidate the evolutionary origin of receptor subunits. The tree constructed showed that the common ancestor of all subunits may hav...

journal_title：Molecular biology and evolution

authors： Tsunoyama K,Gojobori T

更新日期：1998-05-01 00:00:00

abstract：:With the desire to model population genetic processes under increasingly realistic scenarios, forward genetic simulations have become a critical part of the toolbox of modern evolutionary biology. The SLiM forward genetic simulation framework is one of the most powerful and widely used tools in this area. However, its...

journal_title：Molecular biology and evolution

authors： Haller BC,Messer PW

更新日期：2019-03-01 00:00:00

abstract：:The genotypic signature of spatially varying selection is ubiquitous across the Drosophila melanogaster genome. Spatially structured adaptive phenotypic differences are also commonly found, particularly along New World and Australian latitudinal gradients. However, investigation of gene expression variation in one or ...

journal_title：Molecular biology and evolution

authors： Levine MT,Eckert ML,Begun DJ

更新日期：2011-01-01 00:00:00

abstract：:Noncoding DNA sequences, which play various roles in gene expression and regulation, are under evolutionary pressure. Gene regulation requires specific protein-DNA binding events, and our previous studies showed that both DNA sequence and shape readout are employed by transcription factors (TFs) to achieve DNA binding...

journal_title：Molecular biology and evolution

authors： Wang X,Zhou T,Wunderlich Z,Maurano MT,DePace AH,Nuzhdin SV,Rohs R

更新日期：2018-08-01 00:00:00

abstract：:The heat shock protein (Hsp) sequences, because of their ubiquity and high degree of conservation, provide useful models for phylogenetic analysis. In this paper I have carried out a global alignment of all available sequences (a total of 31) for the 90-kD heat shock protein (Hsp90) family. The minimum amino acid iden...

journal_title：Molecular biology and evolution

authors： Gupta RS

更新日期：1995-11-01 00:00:00

abstract：:We show how to make appropriate likelihood ratio tests for evolutionary tree models when parameters such as edge (internodes or branches) lengths have nonnegativity constraints. In such cases, under the null model of an edge length being zero, the marginal distribution of this parameter is proven to be a "half-normal"...

journal_title：Molecular biology and evolution

authors： Ota R,Waddell PJ,Hasegawa M,Shimodaira H,Kishino H

更新日期：2000-05-01 00:00:00

abstract：:The spread of farming out of the Balkans and into the rest of Europe followed two distinct routes: An initial expansion represented by the Impressa and Cardial traditions, which followed the Northern Mediterranean coastline; and another expansion represented by the LBK (Linearbandkeramik) tradition, which followed the...

journal_title：Molecular biology and evolution

authors： Olalde I,Schroeder H,Sandoval-Velasco M,Vinner L,Lobón I,Ramirez O,Civit S,García Borja P,Salazar-García DC,Talamo S,María Fullola J,Xavier Oms F,Pedro M,Martínez P,Sanz M,Daura J,Zilhão J,Marquès-Bonet T,Gilbert MT,

更新日期：2015-12-01 00:00:00

abstract：:The selective constraints influencing mRNA editing in plant organelles are largely unknown. To investigate these, we compared patterns of editing between monocot and dicot mitochondrial mRNA. On average, 24% of sites that are edited form C to U in one species have been substituted during evolution by a genomic T in th...

journal_title：Molecular biology and evolution

authors： Shields DC,Wolfe KH

更新日期：1997-03-01 00:00:00

abstract：:Many species, including humans, have dramatically expanded their range in the past, and such range expansions had certainly an impact on their genetic diversity. For example, mutations arising in populations at the edge of a range expansion can sometimes surf on the wave of advance and thus reach a larger spatial dist...

journal_title：Molecular biology and evolution

authors： Klopfstein S,Currat M,Excoffier L

更新日期：2006-03-01 00:00:00

abstract：:Why are certain bacterial genomes so small and compact? The adaptive genome streamlining hypothesis posits that selection acts to reduce genome size because of the metabolic burden of replicating DNA. To reveal the impact of genome streamlining on cellular traits, we reduced the Escherichia coli genome by up to 20% by...

journal_title：Molecular biology and evolution

authors： Karcagi I,Draskovits G,Umenhoffer K,Fekete G,Kovács K,Méhi O,Balikó G,Szappanos B,Györfy Z,Fehér T,Bogos B,Blattner FR,Pál C,Pósfai G,Papp B

更新日期：2016-05-01 00:00:00

abstract：:The ParaHox and Hox gene clusters control aspects of animal anterior-posterior development and are related as paralogous evolutionary sisters. Despite this relationship, it is not clear if the clusters operate in similar ways, with similar constraints. To compare clusters, we examined the transposable-element (TE) con...

journal_title：Molecular biology and evolution

authors： Osborne PW,Ferrier DE

更新日期：2010-02-01 00:00:00

abstract：:In the past 40 years, there has been increasing acceptance that variation in levels of gene expression represents a major source of evolutionary novelty. Gene expression divergence is therefore likely to be involved in the emergence of incipient species, namely, in a context of adaptive radiation. In the lake whitefis...

journal_title：Molecular biology and evolution

authors： Jeukens J,Bittner D,Knudsen R,Bernatchez L

更新日期：2009-01-01 00:00:00