Complete mtDNA sequence of the North American freshwater mussel, Lampsilis ornata (Unionidae): an examination of the evolution and phylogenetic utility of mitochondrial genome organization in Bivalvia (Mollusca).

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：:Animal venoms have evolved many times. Venomous species are especially common in three of the four main groups of arthropods (Chelicerata, Myriapoda, and Hexapoda), which together represent tens of thousands of species of venomous spiders, scorpions, centipedes, and hymenopterans. Surprisingly, despite their great div...

journal_title：Molecular biology and evolution

authors： von Reumont BM,Blanke A,Richter S,Alvarez F,Bleidorn C,Jenner RA

更新日期：2014-01-01 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：:There are many examples of groups (such as birds, bees, mammals, multicellular animals, and flowering plants) that have undergone a rapid radiation. In such cases, where there is a combination of short internal and long external branches, correctly estimating and rooting phylogenetic trees is known to be a difficult p...

journal_title：Molecular biology and evolution

authors： Shavit L,Penny D,Hendy MD,Holland BR

更新日期：2007-11-01 00:00:00

abstract：:Dormancy has evolved in all major metazoan lineages. It is critical for survival when environmental stresses are not conducive to growth, maturation, or reproduction. Embryonic diapause is a form of dormancy where development is reversibly delayed and metabolism is depressed. We report the diapause transcriptome of th...

journal_title：Molecular biology and evolution

authors： Thompson AW,Ortí G

更新日期：2016-09-01 00:00:00

abstract：:Molecular evolutionary rates within two protistan and three metazoan taxa were estimated using divergence times derived from fossil records. The results indicate that the small-subunit rRNA sequences within Dasycladales (Chlorophyta) and Bacillariophyceae evolved at a rate approximately two to three times faster than ...

journal_title：Molecular biology and evolution

authors： Sorhannus U

更新日期：1996-09-01 00:00:00

abstract：:The diploid D-genome lineage of the Triticum/Aegilops complex has an evolutionary history involving genomic contributions from ancient A- and B/S-genome species. We explored here the possible cytonuclear evolutionary responses to this history of hybridization. Phylogenetic analysis of chloroplast DNAs indicates that t...

journal_title：Molecular biology and evolution

authors： Li C,Sun X,Conover JL,Zhang Z,Wang J,Wang X,Deng X,Wang H,Liu B,Wendel JF,Gong L

更新日期：2019-02-01 00:00:00

abstract：:The internal consistency of the PAM matrix model of protein evolution is here investigated. The 1 PAM matrix has been constructed from amino acid replacements observed in closely related sequences. Such replacements are of two types, those that do not require an intermediate amino acid replacement and those that do. T...

journal_title：Molecular biology and evolution

authors： Wilbur WJ

更新日期：1985-09-01 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：:R2 non-long terminal repeat retrotransposable elements insert specifically into the 28S rRNA genes of a wide range of animals. These elements maintain long-term stable relationships with the host genome. By scoring the variation present at the 5' ends of individual R2 copies, lines of Drosophila simulans have been ide...

journal_title：Molecular biology and evolution

authors： Zhang X,Zhou J,Eickbush TH

更新日期：2008-01-01 00:00:00

abstract：:Molecular clocks are routinely tested for linearity using a relative rate test and routinely calibrated against the geological time scale using a single or average paleontologically determined time of divergence between living taxa. The relative rate test is a test of parallel rate equality, not a test of rate constan...

journal_title：Molecular biology and evolution

authors： Gingerich PD

更新日期：1986-05-01 00:00:00

abstract：:Modifications to transcriptional regulators play a major role in adaptation. Here, we compared the effects of multiple beneficial mutations within and between Escherichia coli rpoB, the gene encoding the RNA polymerase β subunit, and rho, which encodes a transcriptional terminator. These two genes have harbored adapti...

journal_title：Molecular biology and evolution

authors： González-González A,Hug SM,Rodríguez-Verdugo A,Patel JS,Gaut BS

更新日期：2017-11-01 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：:Polyploidization events have occurred during the evolution of many fungi, plant, and animal species and are thought to contribute to speciation and tumorigenesis, however little is known about how ploidy level contributes to adaptation at the molecular level. Here we integrate whole genome sequencing, RNA expression a...

journal_title：Molecular biology and evolution

authors： Scott AL,Richmond PA,Dowell RD,Selmecki AM

更新日期：2017-10-01 00:00:00

abstract：:Flowering time is one of the key determinants of crop adaptation to local environments during domestication. However, the genetic basis underlying flowering time is yet to be elucidated in most cereals. Although staple cereals, such as rice, maize, wheat, barley, and sorghum, have spread and adapted to a wide range of...

journal_title：Molecular biology and evolution

authors： Liu H,Liu H,Zhou L,Zhang Z,Zhang X,Wang M,Li H,Lin Z

更新日期：2015-10-01 00:00:00

abstract：:The authors of a recent manuscript in "Nature" claim to have discovered "universal trends" of amino acid gain and loss in protein evolution. Here, we show that this universal trend can be simply explained by a bias that is unavoidable with the 3-taxon trees used in the original analysis. We demonstrate that a rigorous...

journal_title：Molecular biology and evolution

authors： Goldstein RA,Pollock DD

更新日期：2006-07-01 00:00:00

abstract：:Most "tests of neutrality" assess whether particular data sets depart from the predictions of a standard neutral model with no recombination. For Drosophila, where nuclear polymorphism data routinely show evidence of genetic exchange, the assumption of no recombination is often unrealistic. In addition, while conserva...

journal_title：Molecular biology and evolution

authors： Przeworski M,Wall JD,Andolfatto P

更新日期：2001-03-01 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：:The high frequency of alternative splicing among the serine/arginine-rich (SR) family of proteins in plants has been linked to important roles in gene regulation during development and in response to environmental stress. In this article, we have searched and manually annotated all the SR proteins in the genomes of ma...

journal_title：Molecular biology and evolution

authors： Rauch HB,Patrick TL,Klusman KM,Battistuzzi FU,Mei W,Brendel VP,Lal SK

更新日期：2014-03-01 00:00:00

abstract：:We report a major update of the MAFFT multiple sequence alignment program. This version has several new features, including options for adding unaligned sequences into an existing alignment, adjustment of direction in nucleotide alignment, constrained alignment and parallel processing, which were implemented after the...

journal_title：Molecular biology and evolution

authors： Katoh K,Standley DM

更新日期：2013-04-01 00:00:00

abstract：:Bacterial populations have been shown to accumulate deleterious mutations during spatial expansions that overall decrease their fitness and ability to grow. However, it is unclear if and how they can respond to selection in face of this mutation load. We examine here if artificial selection can counteract the negative...

journal_title：Molecular biology and evolution

authors： Bosshard L,Peischl S,Ackermann M,Excoffier L

更新日期：2019-10-01 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：:Gene orders have been shown to be generally unstable by comprehensive analyses in several complete genomes. In this study, we examined instability of genome structures within operons, where functionally related genes are clustered. We compared gene orders of known operons obtained from Escherichia coli and Bacillus su...

journal_title：Molecular biology and evolution

authors： Itoh T,Takemoto K,Mori H,Gojobori T

更新日期：1999-03-01 00:00:00

abstract：:Cancer progression is an evolutionary process. During this process, evolving cancer cell populations encounter restrictive ecological niches within the body, such as the primary tumor, circulatory system, and diverse metastatic sites. Efforts to prevent or delay cancer evolution-and progression-require a deep understa...

journal_title：Molecular biology and evolution

authors： Somarelli JA,Gardner H,Cannataro VL,Gunady EF,Boddy AM,Johnson NA,Fisk JN,Gaffney SG,Chuang JH,Li S,Ciccarelli FD,Panchenko AR,Megquier K,Kumar S,Dornburg A,DeGregori J,Townsend JP

更新日期：2020-02-01 00:00:00

abstract：:A novel family of non-long-terminal-repeat (non-LTR) retrotransposons, named MosquI, was discovered in the yellow fever mosquito, Aedes aegypti. There were approximately 14 copies of MosquI in the A. aegypti genome. Four of the five analyzed MosquI elements were truncated at the 5' ends while one of them, MosquI-Aa2, ...

journal_title：Molecular biology and evolution

authors： Tu Z,Hill JJ

更新日期：1999-12-01 00:00:00

abstract：:It is known that the effective population size (Ne) and the mutation rate (u) vary across the genome. Here, we show that ignoring this heterogeneity may lead to biased estimates of past demography. To solve the problem, we develop new methods for jointly inferring past changes in population size and detecting variatio...

journal_title：Molecular biology and evolution

authors： Zeng K,Jackson BC,Barton HJ

更新日期：2019-02-01 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

abstract：:From the stirodont Arbacia lixula we determined the sequence of 5,127 nucleotides of mitochondrial DNA (mtDNA) encompassing 18 tRNAs, two complete coding genes, parts of three other coding genes, and part of the 12S ribosomal RNA (rRNA). The sequence confirms that the organization of mtDNA is conserved within echinoid...

journal_title：Molecular biology and evolution

authors： De Giorgi C,Lanave C,Musci MD,Saccone C

更新日期：1991-07-01 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：:The cellobiose catabolic system of Escherichia coli K12 is being used to study the role of cryptic genes in evolution of new functions. Escherichia coli does not use beta-glucoside sugars; however, mutations in several loci can activate the cryptic bgl operon and permit growth on the beta-glucoside sugars arbutin and ...

journal_title：Molecular biology and evolution

authors： Kricker M,Hall BG

更新日期：1984-02-01 00:00:00