Molecular evolution and population genetics of duplicated accessory gland protein genes in Drosophila.

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：:Gene unscrambling in spirotrichous ciliates involves massive genome-wide DNA deletion and rearrangement events during development. During each sexual cycle, the somatic nucleus (macronucleus) regenerates from the germ line nucleus (micronucleus). Development of the polyploid somatic genome requires programmed DNA dele...

journal_title：Molecular biology and evolution

authors： Wong LC,Landweber LF

更新日期：2006-04-01 00:00:00

abstract：:Statistical methods for computing the standard errors of the branching points of an evolutionary tree are developed. These methods are for the unweighted pair-group method-determined (UPGMA) trees reconstructed from molecular data such as amino acid sequences, nucleotide sequences, restriction-sites data, and electrop...

journal_title：Molecular biology and evolution

authors： Nei M,Stephens JC,Saitou N

更新日期：1985-01-01 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：:Debate on the adaptive origins of primates has long focused on the functional ecology of the primate visual system. For example, it is hypothesized that variable expression of short- (SWS1) and middle-to-long-wavelength sensitive (M/LWS) opsins, which confer color vision, can be used to infer ancestral activity patter...

journal_title：Molecular biology and evolution

authors： Melin AD,Wells K,Moritz GL,Kistler L,Orkin JD,Timm RM,Bernard H,Lakim MB,Perry GH,Kawamura S,Dominy NJ

更新日期：2016-04-01 00:00:00

abstract：:Large-scale variation in chromosome size was analyzed in 35 natural isolates of Escherichia coli by physical mapping with a restriction enzyme whose sites are restricted to rDNA operons. Although the genetic maps and chromosome lengths of the laboratory strains E. coli K12 and Salmonella enterica sv. Typhimurium LT2 a...

journal_title：Molecular biology and evolution

authors： Bergthorsson U,Ochman H

更新日期：1998-01-01 00:00:00

abstract：:Sequencing multiple copies of the ITS1 region revealed the coexistence of two or more haplotypes within the genome of Chorthippus parallelus. Using a PCR-RFLP approach, the ITS1 numbers and frequencies of haplotypes present in each of 40 individuals were investigated, revealing a consistent lack of homogeneity. For ea...

journal_title：Molecular biology and evolution

authors： Parkin EJ,Butlin RK

更新日期：2004-08-01 00:00:00

abstract：:Several authors reported lower frequencies of protein sequence convergence between more distantly related evolutionary lineages and attributed this trend to epistasis, which renders the acceptable amino acids at a site more different and convergence less likely in more divergent lineages. A recent primate study, howev...

journal_title：Molecular biology and evolution

authors： Zou Z,Zhang J

更新日期：2017-07-01 00:00:00

abstract：:Length variation due to tandem repeats is now recognized as a common feature of animal mitochondrial DNA; however, the evolutionary dynamics of repeated sequences are not well understood. Using phylogenetic analysis, predictions of three models of repeat evolution were tested for arrays of 260-bp repeats in the cyprin...

journal_title：Molecular biology and evolution

authors： Broughton RE,Dowling TE

更新日期：1997-12-01 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：:The occurrence of a fish-specific genome duplication (FSGD) in the lineage leading to teleost fishes is widely accepted, but the consequences of this event remain elusive. Teleosts, and the cichlid fishes from the species flocks in the East African Great Lakes in particular, evolved a unique complexity and diversity o...

journal_title：Molecular biology and evolution

authors： Braasch I,Salzburger W,Meyer A

更新日期：2006-06-01 00:00:00

abstract：:Genetic variation in contemporary South Asian populations follows a northwest to southeast decreasing cline of shared West Eurasian ancestry. A growing body of ancient DNA evidence is being used to build increasingly more realistic models of demographic changes in the last few thousand years. Through high-quality mode...

journal_title：Molecular biology and evolution

authors： Yelmen B,Mondal M,Marnetto D,Pathak AK,Montinaro F,Gallego Romero I,Kivisild T,Metspalu M,Pagani L

更新日期：2019-08-01 00:00:00

abstract：:Whether coding or regulatory sequence change is more important to the evolution of phenotypic novelty is one of biology's major unresolved questions. The field of evo-devo has shown that in early development changes to regulatory regions are the dominant mode of genetic change, but whether this extends to the evolutio...

journal_title：Molecular biology and evolution

authors： Jasper WC,Linksvayer TA,Atallah J,Friedman D,Chiu JC,Johnson BR

更新日期：2015-02-01 00:00:00

abstract：:Identifying the genomic basis underlying local adaptation is paramount to evolutionary biology, and bears many applications in the fields of conservation biology, crop, and animal breeding, as well as personalized medicine. Although many approaches have been developed to detect signatures of positive selection within ...

journal_title：Molecular biology and evolution

authors： Librado P,Orlando L

更新日期：2018-06-01 00:00:00

abstract：:Evolution of sequences mostly involves independent changes at different sites. However, substitutions at neighboring sites may co-occur as multinucleotide replacement events (MNRs). Here, we compare noncoding sequences of several species of primates, and of three species of Drosophila fruit flies, in a phylogenetic an...

journal_title：Molecular biology and evolution

authors： Terekhanova NV,Bazykin GA,Neverov A,Kondrashov AS,Seplyarskiy VB

更新日期：2013-06-01 00:00:00

abstract：:Inference of intraspecific population divergence patterns typically requires genetic data for molecular markers with relatively high mutation rates. Microsatellites, or short tandem repeat (STR) polymorphisms, have proven informative in many such investigations. These markers are characterized, however, by high levels...

journal_title：Molecular biology and evolution

authors： Ramakrishnan U,Mountain JL

更新日期：2004-10-01 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：:Whole genome duplications (WGDs) have been hypothesized to be responsible for major transitions in evolution. However, the effects of WGD and subsequent gene loss on cellular behavior and metabolism are still poorly understood. Here we develop a genome scale evolutionary model to study the dynamics of gene loss and me...

journal_title：Molecular biology and evolution

authors： van Hoek MJ,Hogeweg P

更新日期：2009-11-01 00:00:00

abstract：:The use of parameter-rich substitution models in molecular phylogenetics has been criticized on the basis that these models can cause a reduction both in accuracy and in the ability to discriminate among competing topologies. We have explored the relationship between nucleotide substitution model complexity and nonpar...

journal_title：Molecular biology and evolution

authors： Buckley TR,Cunningham CW

更新日期：2002-04-01 00:00:00

abstract：:Detecting selection on codon usage (CU) is a difficult task, since CU can be shaped by both the mutational process and selective constraints operating at the DNA, RNA, and protein levels. Yang and Nielsen (2008) developed a test (which we call CUYN) for detecting selection on CU using two competing mutation-selection ...

journal_title：Molecular biology and evolution

authors： Laurin-Lemay S,Philippe H,Rodrigue N

更新日期：2018-06-01 00:00:00

abstract：:Hybridization in plants may result in hybrid speciation or introgression and, thus, is now widely understood to be an important mechanism of species diversity on an evolutionary timescale. Hybridization is particularly common in ferns, as is polyploidy, which often results from hybrid crosses. Nevertheless, hybrid spe...

journal_title：Molecular biology and evolution

authors： Wang J,Dong S,Yang L,Harris A,Schneider H,Kang M

更新日期：2020-09-01 00:00:00

abstract：:Chemosensory genes are frequently the target of positive selection and are often present in large gene families, but little is known about heterogeneity of selection in these cases and its relation to function. Here, we use the vomeronasal-1 receptor (V1R) repertoire of mouse lemurs (Microcebus spp.) as a model system...

journal_title：Molecular biology and evolution

authors： Hohenbrink P,Radespiel U,Mundy NI

更新日期：2012-12-01 00:00:00

abstract：:Herpes simplex virus types 1 and 2 (HSV-1 and HSV-2) are ubiquitous human pathogens. Both viruses evolved from simplex viruses infecting African primates and they are thus thought to have left Africa during early human migrations. We analyzed the population structure of HSV-1 and HSV-2 circulating strains. Results ind...

journal_title：Molecular biology and evolution

authors： Forni D,Pontremoli C,Clerici M,Pozzoli U,Cagliani R,Sironi M

更新日期：2020-05-01 00:00:00

abstract：:Baleen whales (suborder Mysticeti) comprise 11 extant species that are classified into four families. Although several phylogenetic hypotheses about these taxa have been proposed, their phylogenetic relationships remain confused. We addressed this problem using short interspersed repetitive element (SINE) insertion da...

journal_title：Molecular biology and evolution

authors： Nikaido M,Hamilton H,Makino H,Sasaki T,Takahashi K,Goto M,Kanda N,Pastene LA,Okada N,SMBE Tri-National Young Investigators.

更新日期：2006-05-01 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：:Identifying mechanisms that underlie variation in adult survivorship provide insight into the evolution of life history strategies and phenotypic variation in longevity. There is accumulating evidence that shortening telomeres, the protective caps at the ends of chromosomes, play an important role in individual variat...

journal_title：Molecular biology and evolution

authors： Haussmann MF,Mauck RA

更新日期：2008-01-01 00:00:00

abstract：:Positive selection sites (PSSs), a class of amino acid sites with an excess of nonsynonymous to synonymous substitutions, are indicators of adaptive molecular evolution and have been detected in many protein families involved in a diversity of biological processes by statistical approaches. However, few studies are co...

journal_title：Molecular biology and evolution

authors： Zhu L,Peigneur S,Gao B,Zhang S,Tytgat J,Zhu S

更新日期：2016-08-01 00:00:00

abstract：:Pathogen-mediated balancing selection is regarded as a key driver of host immunogenetic diversity. A hallmark for balancing selection in humans is the heterozygote advantage at genes of the human leukocyte antigen (HLA), resulting in improved HIV-1 control. However, the actual mechanism of the observed heterozygote ad...

journal_title：Molecular biology and evolution

authors： Arora J,Pierini F,McLaren PJ,Carrington M,Fellay J,Lenz TL

更新日期：2020-03-01 00:00:00

abstract：:Although endogenous retroviruses are common across vertebrate genomes, the koala retrovirus (KoRV) is the only retrovirus known to be currently invading the germ line of its host. KoRV is believed to have first infected koalas in northern Australia less than two centuries ago. We examined KoRV in 28 koala museum skins...

journal_title：Molecular biology and evolution

authors： Ávila-Arcos MC,Ho SY,Ishida Y,Nikolaidis N,Tsangaras K,Hönig K,Medina R,Rasmussen M,Fordyce SL,Calvignac-Spencer S,Willerslev E,Gilbert MT,Helgen KM,Roca AL,Greenwood AD

更新日期：2013-02-01 00:00:00

abstract：:We examined microsatellite variation in two diploid, outcrossing relatives of Arabidopsis thaliana, Arabis petraea and Arabis lyrata. The primer sequences were derived from A. thaliana. About 50% (14 loci) of the A. thaliana primers could successfully amplify microsatellites in the related species. Analysis of microsa...

journal_title：Molecular biology and evolution

authors： van Treuren R,Kuittinen H,Kärkkäinen K,Baena-Gonzalez E,Savolainen O

更新日期：1997-03-01 00:00:00