Cytonuclear Coevolution following Homoploid Hybrid Speciation in Aegilops tauschii.

abstract：:Long INterspersed Elements-1 (L1s) constitute >17% of the human genome and still actively transpose in it. Characterizing L1 transposition across the genome is critical for understanding genome evolution and somatic mutations. However, to date, L1 insertion and fixation patterns have not been studied comprehensively. ...

journal_title：Molecular biology and evolution

authors： Chen D,Cremona MA,Qi Z,Mitra RD,Chiaromonte F,Makova KD

更新日期：2020-12-16 00:00:00

abstract：:Large phylogenomics data sets require fast tree inference methods, especially for maximum-likelihood (ML) phylogenies. Fast programs exist, but due to inherent heuristics to find optimal trees, it is not clear whether the best tree is found. Thus, there is need for additional approaches that employ different search st...

journal_title：Molecular biology and evolution

authors： Nguyen LT,Schmidt HA,von Haeseler A,Minh BQ

更新日期：2015-01-01 00:00:00

abstract：:Comparing newly obtained and previously known nucleotide and amino-acid sequences underpins modern biological research. BLAST is a well-established tool for such comparisons but is challenging to use on new data sets. We combined a user-centric design philosophy with sustainable software development approaches to crea...

journal_title：Molecular biology and evolution

authors： Priyam A,Woodcroft BJ,Rai V,Moghul I,Munagala A,Ter F,Chowdhary H,Pieniak I,Maynard LJ,Gibbins MA,Moon H,Davis-Richardson A,Uludag M,Watson-Haigh NS,Challis R,Nakamura H,Favreau E,Gómez EA,Pluskal T,Leonard G,Rump

更新日期：2019-12-01 00:00:00

abstract：:Partial 18S rRNA sequence of the nemertine Cerebratulus lacteus was obtained and compared with those of coelomate metazoans and acoelomate platyhelminths to test whether nemertines share a most recent common ancestor with the platyhelminths, as traditionally has been implied, or whether nemertines lie within a protost...

journal_title：Molecular biology and evolution

authors： Turbeville JM,Field KG,Raff RA

更新日期：1992-03-01 00:00:00

abstract：:The Malagasy have been shown to be a genetically admixed population combining parental lineages with African and South East Asian ancestry. In the present paper, we fit the Malagasy admixture history in a highly resolved phylogeographic framework by typing a large set of mitochondrial DNA and Y DNA markers in unrelate...

journal_title：Molecular biology and evolution

authors： Tofanelli S,Bertoncini S,Castrì L,Luiselli D,Calafell F,Donati G,Paoli G

更新日期：2009-09-01 00:00:00

abstract：:A highly abundant satellite DNA comprising 17% of the Tribolium castaneum (Insecta, Coleoptera) genome was cloned and sequenced. The satellite monomer is 360 bp long, has a high A+T content of 73%, and lacks significant internal substructures. The sequence variability is 3.6%, essentially due to random distribution of...

journal_title：Molecular biology and evolution

authors： Ugarković D,Podnar M,Plohl M

更新日期：1996-10-01 00:00:00

abstract：:The marine cyanobacterium Prochlorococcus MED4 has the smallest sequenced genome of any photosynthetic organism. Prochlorococcus MED4 shares many genomic characteristics with chloroplasts and bacterial endosymbionts, including a reduced coding capacity, missing DNA repair genes, a minimal transcriptional regulatory ne...

journal_title：Molecular biology and evolution

authors： Hu J,Blanchard JL

更新日期：2009-01-01 00:00:00

abstract：:Positive Darwinian selection promotes fixations of advantageous mutations during gene evolution and is probably responsible for most adaptations. Detecting positive selection at the DNA sequence level is of substantial interest because such information provides significant insights into possible functional alterations...

journal_title：Molecular biology and evolution

authors： Zhang J

更新日期：2004-07-01 00:00:00

abstract：:Polytoma obtusum and Polytoma uvella are members of a clade of nonphotosynthetic chlorophyte algae closely related to Chlamydomonas humicola and other photosynthetic members of the Chlamydomonadaceae. Descended from a nonphotosynthetic mutant, these obligate heterotrophs retain a plastid (leucoplast) with a functional...

journal_title：Molecular biology and evolution

authors： Vernon D,Gutell RR,Cannone JJ,Rumpf RW,Birky CW Jr

更新日期：2001-09-01 00:00:00

abstract：:Bivalves have evolved a range of complex shell forming mechanisms that are reflected by their incredible diversity in shell mineralogy and microstructures. A suite of proteins exported to the shell matrix space plays a significant role in controlling these features, in addition to underpinning some of the physical pro...

journal_title：Molecular biology and evolution

authors： Arivalagan J,Yarra T,Marie B,Sleight VA,Duvernois-Berthet E,Clark MS,Marie A,Berland S

更新日期：2017-01-01 00:00:00

abstract：:Cyclooxygenase (COX) produces prostaglandins in animals via the oxidation and reduction of arachidonic acid. Different types and numbers of COX genes have been found in corals, sea squirts, fishes, and tetrapods, but no study has used a comparative phylogenetic approach to investigate the evolutionary history of this ...

journal_title：Molecular biology and evolution

authors： Havird JC,Miyamoto MM,Choe KP,Evans DH

更新日期：2008-11-01 00:00:00

abstract：:Here, we present a study of the molecular evolution of the pheromone receptor genes (pre-1 and pre-2) in Neurospora taxa with different mating systems. We focus on comparisons between heterothallic and homothallic taxa, reproducing sexually by outcrossing and by intrahaploid selfing, respectively. Our general aim was ...

journal_title：Molecular biology and evolution

authors： Nygren K,Strandberg R,Gioti A,Karlsson M,Johannesson H

更新日期：2012-12-01 00:00:00

abstract：:We determine the phylogenetic backbone of the East Asian mtDNA tree by using published complete mtDNA sequences and assessing both coding and control region variation in 69 Han individuals from southern China. This approach assists in the interpretation of published mtDNA data on East Asians based on either control re...

journal_title：Molecular biology and evolution

authors： Kivisild T,Tolk HV,Parik J,Wang Y,Papiha SS,Bandelt HJ,Villems R

更新日期：2002-10-01 00:00:00

abstract：:The environment has profound effects on the expression of many traits and reaction norms describe the expression dynamics of a trait across a broad range of environmental conditions. Here, we analyze gene expression in Drosophila melanogaster across four different developmental temperatures (13-29 °C). Gene expression...

journal_title：Molecular biology and evolution

authors： Chen J,Nolte V,Schlötterer C

更新日期：2015-09-01 00:00:00

abstract：:The complete nucleotide sequence of the mt (mitochondrial) and cp (chloroplast) genomes of the unicellular green alga Ostreococcus tauri has been determined. The mt genome assembles as a circle of 44,237 bp and contains 65 genes. With an overall average length of only 42 bp for the intergenic regions, this is the most...

journal_title：Molecular biology and evolution

authors： Robbens S,Derelle E,Ferraz C,Wuyts J,Moreau H,Van de Peer Y

更新日期：2007-04-01 00:00:00

abstract：:Good phylogenetic trees are required to test hypotheses about evolutionary processes. We report four new avian mitochondrial genomes, which together with an improved method of phylogenetic analysis for vertebrate mt genomes give results for three questions in avian evolution. The new mt genomes are: magpie goose (Anse...

journal_title：Molecular biology and evolution

authors： Harrison GL,McLenachan PA,Phillips MJ,Slack KE,Cooper A,Penny D

更新日期：2004-06-01 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：: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：:How gene function evolves is a central question of evolutionary biology. It can be investigated by comparing functional genomics results between species and between genes. Most comparative studies of functional genomics have used pairwise comparisons. Yet it has been shown that this can provide biased results, since g...

journal_title：Molecular biology and evolution

authors： Begum T,Robinson-Rechavi M

更新日期：2020-11-10 00:00:00

abstract：:Purifying selection can substantially alter patterns of molecular evolution. Its main effect is to reduce overall levels of genetic variation, leading to a reduced effective population size. However, it also distorts genealogies relative to neutral expectations. A structured coalescent method has been used to describe...

journal_title：Molecular biology and evolution

authors： Nicolaisen LE,Desai MM

更新日期：2012-11-01 00:00:00

abstract：:The chemokine receptor CCR5 can serve as a coreceptor for M-tropic HIV-1 infection and both M-tropic and T-tropic SIV infection. We sequenced the entire CCR5 gene from 10 nonhuman primates: Pongo pygmaeus, Hylobates leucogenys, Trachypithecus francoisi, Trachypithecus phayrei, Pygathrix nemaeus, Rhinopithecus roxellan...

journal_title：Molecular biology and evolution

authors： Zhang YW,Ryder OA,Zhang YP

更新日期：1999-09-01 00:00:00

abstract：:Ribosomal DNA (rDNA) is one of the most conserved genes in eukaryotes. The multiples copies of rDNA in the genome evolve in a concerted manner, through unequal crossing over and/or gene conversion, two mechanisms related to homologous recombination. Recombination increases local GC content in several organisms through...

journal_title：Molecular biology and evolution

authors： Escobar JS,Glémin S,Galtier N

更新日期：2011-09-01 00:00:00

abstract：:Pax genes play key regulatory roles in embryonic and sensory organ development in metazoans but their evolution and ancestral functions remain widely unresolved. We have isolated a Pax gene from Placozoa, beside Porifera the only metazoan phylum that completely lacks nerve and sensory cells or organs. These simplest k...

journal_title：Molecular biology and evolution

authors： Hadrys T,DeSalle R,Sagasser S,Fischer N,Schierwater B

更新日期：2005-07-01 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：:CpG and TpA dinucleotides are underrepresented in the human genome. The CpG deficiency is due to the high mutation rate from C to T in methylated CpG's. The TpA suppression was thought to reflect a counterselection against TpA's destabilizing effect in RNA. Unexpectedly, the TpA and CpG deficiencies vary according to ...

journal_title：Molecular biology and evolution

authors： Duret L,Galtier N

更新日期：2000-11-01 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：:Herpesviruses have been infecting and codiverging with their vertebrate hosts for hundreds of millions of years. The primate simplex viruses exemplify this pattern of virus-host codivergence, at a minimum, as far back as the most recent common ancestor of New World monkeys, Old World monkeys, and apes. Humans are the ...

journal_title：Molecular biology and evolution

authors： Wertheim JO,Smith MD,Smith DM,Scheffler K,Kosakovsky Pond SL

更新日期：2014-09-01 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：:Models of codon evolution have attracted particular interest because of their unique capabilities to detect selection forces and their high fit when applied to sequence evolution. We described here a novel approach for modeling codon evolution, which is based on Kronecker product of matrices. The 61 × 61 codon substit...

journal_title：Molecular biology and evolution

authors： Zaheri M,Dib L,Salamin N

更新日期：2014-09-01 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