A novel abundant family of retroposed elements (DAS-SINEs) in the nine-banded armadillo (Dasypus novemcinctus).

abstract：:Phenotypic convergence is an exciting outcome of adaptive evolution, occurring when different species find similar solutions to the same problem. Unraveling the molecular basis of convergence provides a way to link genotype to adaptive phenotypes, but can also shed light on the extent to which molecular evolution is r...

journal_title：Molecular biology and evolution

authors： Mendes FK,Hahn Y,Hahn MW

更新日期：2016-12-01 00:00:00

abstract：:Sequences of 1,862 chromosomally encoded Escherichia coli K12 proteins were examined to identify genes likely to have arisen by duplication of genes in an ancestral chromosome. The criteria for sequence relatedness were an alignment of at least 100 amino acid residues and a PAM distance (number of accepted point mutat...

journal_title：Molecular biology and evolution

authors： Labedan B,Riley M

更新日期：1995-11-01 00:00:00

abstract：:The question of multiple sequence alignment quality has received much attention from developers of alignment methods. Less forthcoming, however, are practical measures for addressing alignment quality issues in real life settings. Here, we present a simple methodology to help identify and quantify the uncertainties in...

journal_title：Molecular biology and evolution

authors： Landan G,Graur D

更新日期：2007-06-01 00:00:00

abstract：:We compared sex chromosomal and autosomal regions of similar GC contents and found that the human Y chromosome contains nine times as many full-length (FL) ancestral LINE-1 (L1) elements per megabase as do autosomes and that the X chromosome contains three times as many. In addition, both sex chromosomes contain a ca....

journal_title：Molecular biology and evolution

authors： Boissinot S,Entezam A,Furano AV

更新日期：2001-06-01 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

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：:Enzyme function is strongly affected by temperature, and orthologs from species adapted to different thermal environments often show temperature compensation in kinetic properties. Antarctic notothenioid fishes live in a habitat of constant, extreme cold (-1.86 +/- 2 degrees C), and orthologs of the enzyme A4-lactate ...

journal_title：Molecular biology and evolution

authors： Fields PA,Houseman DE

更新日期：2004-12-01 00:00:00

abstract：:The SLiM forward genetic simulation framework has proved to be a powerful and flexible tool for population genetic modeling. However, as a complex piece of software with many features that allow simulating a diverse assortment of evolutionary models, its initial learning curve can be difficult. Here we provide a step-...

journal_title：Molecular biology and evolution

authors： Haller BC,Messer PW

更新日期：2019-05-01 00:00:00

abstract：:A major topic of interest in human prehistory is how the large-scale genetic structure of modern populations outside of Africa was established. Demographic models have been developed that capture the relationships among small numbers of populations or within particular geographical regions, but constructing a phylogen...

journal_title：Molecular biology and evolution

authors： Lipson M,Reich D

更新日期：2017-04-01 00:00:00

abstract：:Coevolutionary conflict among imprinted genes that influence traits such as offspring growth may arise when maternal and paternal genomes have different evolutionary optima. This conflict is expected in outcrossing taxa with multiple paternity, but not self-fertilizing taxa. MEDEA (MEA) is an imprinted plant gene that...

journal_title：Molecular biology and evolution

authors： Miyake T,Takebayashi N,Wolf DE

更新日期：2009-04-01 00:00:00

abstract：:In primates, the craniofacial skeleton and the dentition are marked by high levels of interspecific variation. Despite this, there are few comparative species studies conducted at the molecular level to investigate this functional diversity. We have determined nucleotide sequences of MSX1 and PAX9, two developmental g...

journal_title：Molecular biology and evolution

authors： Perry GH,Verrelli BC,Stone AC

更新日期：2006-03-01 00:00:00

abstract：:Dinoflagellates are algae of tremendous importance to ecosystems and to public health. The cell biology and genome organization of dinoflagellate species is highly unusual. For example, the plastid genomes of peridinin-containing dinoflagellates encode only a minimal number of genes arranged on small elements termed "...

journal_title：Molecular biology and evolution

authors： Dorrell RG,Klinger CM,Newby RJ,Butterfield ER,Richardson E,Dacks JB,Howe CJ,Nisbet ER,Bowler C

更新日期：2017-02-01 00:00:00

abstract：:Microarray platforms are used increasingly to make comparative inferences through genome-wide surveys of gene expression. Although recent studies focus on describing the evidence for natural selection using estimates of the within- and between-taxa mutational variances, these methods do not explicitly or flexibly acco...

journal_title：Molecular biology and evolution

authors： Eng KH,Bravo HC,Keleş S

更新日期：2009-10-01 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：:Ecological diversity in fungi is largely defined by metabolic traits, including the ability to produce secondary or "specialized" metabolites (SMs) that mediate interactions with other organisms. Fungal SM pathways are frequently encoded in biosynthetic gene clusters (BGCs), which facilitate the identification and cha...

journal_title：Molecular biology and evolution

authors： Gluck-Thaler E,Haridas S,Binder M,Grigoriev IV,Crous PW,Spatafora JW,Bushley K,Slot JC

更新日期：2020-10-01 00:00:00

abstract：:Despite its poorly adapted codon usage, HIV-1 replicates and is expressed extremely well in human host cells. HIV-1 has recently been shown to package non-lysyl transfer RNAs (tRNAs) in addition to the tRNA(Lys) needed for priming reverse transcription and integration of the HIV-1 genome. By comparing the codon usage ...

journal_title：Molecular biology and evolution

authors： van Weringh A,Ragonnet-Cronin M,Pranckeviciene E,Pavon-Eternod M,Kleiman L,Xia X

更新日期：2011-06-01 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：:The mutation rate of an organism is influenced by the interaction of evolutionary forces such as natural selection and genetic drift. However, the mutation spectrum (i.e., the frequency distribution of different types of mutations) can be heavily influenced by DNA repair. Using mutation-accumulation lines of the extre...

journal_title：Molecular biology and evolution

authors： Long H,Miller SF,Williams E,Lynch M

更新日期：2018-10-01 00:00:00

abstract：:We report the presence of four nuclear paralogs of a 380-bp segment of cytochrome b in callitrichine primates (marmosets and tamarins). The mitochondrial cytochrome b sequence and each nuclear paralog were obtained from several species, allowing multiple comparisons of rates and patterns of substitution both between m...

journal_title：Molecular biology and evolution

authors： Mundy NI,Pissinatti A,Woodruff DS

更新日期：2000-07-01 00:00:00

abstract：:The 20 protein-coding amino acids are found in proteomes with different relative abundances. The most abundant amino acid, leucine, is nearly an order of magnitude more prevalent than the least abundant amino acid, cysteine. Amino acid metabolic costs differ similarly, constraining their incorporation into proteins. O...

journal_title：Molecular biology and evolution

authors： Krick T,Verstraete N,Alonso LG,Shub DA,Ferreiro DU,Shub M,Sánchez IE

更新日期：2014-11-01 00:00:00

abstract：:Phenotypes and behaviors respond to resource constraints via adaptation, but the influence of ecological limitations on the composition of eukaryotic genomes is still unclear. We trace connections between plant ecology and genomes through their elemental composition. Inorganic sources of nitrogen (N) are severely limi...

journal_title：Molecular biology and evolution

authors： Acquisti C,Elser JJ,Kumar S

更新日期：2009-05-01 00:00:00

abstract：:The plant pathogen Phytophthora infestans emerged in Europe in 1845, triggering the Irish potato famine and massive European potato crop losses that continued until effective fungicides were widely employed in the 20th century. Today the pathogen is ubiquitous, with more aggressive and virulent strains surfacing in re...

journal_title：Molecular biology and evolution

authors： Martin MD,Ho SY,Wales N,Ristaino JB,Gilbert MT

更新日期：2014-06-01 00:00:00

abstract：:Amino acid substitution matrices describe the rates by which amino acids are replaced during evolution. In contrast to nucleotide or codon models, amino acid substitution matrices are in general parameterless and empirically estimated, probably because there is no obvious parametrization for amino acid substitutions. ...

journal_title：Molecular biology and evolution

authors： Zoller S,Schneider A

更新日期：2013-02-01 00:00:00

abstract：:We compared the single-nucleotide polymorphisms (SNPs) in humans in 182 housekeeping and 148 tissue-specific genes. SNPs were divided into rare and common polymorphisms based on their frequencies. We found that housekeeping genes tend to be less polymorphic than tissue-specific genes for both rare and common SNPs. Usi...

journal_title：Molecular biology and evolution

authors： Zhang L,Li WH

更新日期：2005-12-01 00:00:00

abstract：:Because they represent the earliest divergences of the Chlorophyta and include the smallest known eukaryotes (e.g., the coccoid Ostreococcus), the morphologically diverse unicellular green algae making up the Prasinophyceae are central to our understanding of the evolutionary patterns that accompanied the radiation of...

journal_title：Molecular biology and evolution

authors： Turmel M,Gagnon MC,O'Kelly CJ,Otis C,Lemieux C

更新日期：2009-03-01 00:00:00

abstract：:Interbreeding between hatchery-reared and wild fish, through deliberate stocking or escapes from fish farms, can result in rapid phenotypic and gene expression changes in hybrids, but the underlying mechanisms are unknown. We assessed if one generation of captive breeding was sufficient to generate inter- and/or trans...

journal_title：Molecular biology and evolution

authors： Rodriguez Barreto D,Garcia de Leaniz C,Verspoor E,Sobolewska H,Coulson M,Consuegra S

更新日期：2019-10-01 00:00:00

abstract：:Here we use phylogenomics with expressed sequence tag (EST) data from the ecologically important coccolithophore-forming alga Emiliania huxleyi and the plastid-lacking cryptophyte Goniomonas cf. pacifica to establish their phylogenetic positions in the eukaryotic tree. Haptophytes and cryptophytes are members of the p...

journal_title：Molecular biology and evolution

authors： Hackett JD,Yoon HS,Li S,Reyes-Prieto A,Rümmele SE,Bhattacharya D

更新日期：2007-08-01 00:00:00

abstract：:Nei and Gojobori (1986) developed a simple method to estimate the numbers of synonymous (ds) and nonsynonymous (dN) substitutions per site. In the present paper, we have developed a method for computing variances and covariances of ds's and dN's and of the proportions of synonymous (ps) and nonsynonymous (pN) differen...

journal_title：Molecular biology and evolution

authors： Ota T,Nei M

更新日期：1994-07-01 00:00:00

abstract：:The similarity of certain reported angiosperm rDNA internal transcribed spacer (ITS) region sequences to those of green algae prompted our analysis of the deep-level phylogenetic signal in the highly conserved but short 5.8S and hypervariable ITS2 sequences. We found that 5.8S sequences yield phylogenetic trees simila...

journal_title：Molecular biology and evolution

authors： Hershkovitz MA,Lewis LA

更新日期：1996-11-01 00:00:00

abstract：:Most mitochondrial proteins are synthesized in the cytosol of eukaryotic cells as precursor proteins carrying N-terminal extensions called transit peptides or presequences, which mediate their specific transport into mitochondria. However, plant cells possess a second potential target organelle for such transit peptid...

journal_title：Molecular biology and evolution

authors： Staiger C,Hinneburg A,Klösgen RB

更新日期：2009-08-01 00:00:00