Empirical assessment of RAD sequencing for interspecific phylogeny.

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：:Duplication, resulting in gene redundancy, is well known to be a driving force of evolutionary change. Gene families are therefore useful targets for approaching genome evolution. To address the gene death process, we examined the fate of the 10-member-large S288C DUP240 family in 15 Saccharomyces cerevisiae strains. ...

journal_title：Molecular biology and evolution

authors： Wirth B,Louis VL,Potier S,Souciet JL,Despons L

更新日期：2005-09-01 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：:The diversity and evolution of bitter taste perception in mammals is not well understood. Recent discoveries of bitter taste receptor (T2R) genes provide an opportunity for a genetic approach to this question. We here report the identification of 10 and 30 putative T2R genes from the draft human and mouse genome seque...

journal_title：Molecular biology and evolution

authors： Shi P,Zhang J,Yang H,Zhang YP

更新日期：2003-05-01 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：:Unraveling how regulatory divergence contributes to species differences and adaptation requires identifying functional variants from among millions of genetic differences. Analysis of allelic imbalance (AI) reveals functional genetic differences in cis regulation and has demonstrated differences in cis regulation with...

journal_title：Molecular biology and evolution

authors： Graze RM,Novelo LL,Amin V,Fear JM,Casella G,Nuzhdin SV,McIntyre LM

更新日期：2012-06-01 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：: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：:The noncoding-DNA content of organelle and nuclear genomes can vary immensely. Both adaptive and nonadaptive explanations for this variation have been proposed. This study addresses a nonadaptive explanation called the mutational-hazard hypothesis and applies it to the mitochondrial, plastid, and nuclear genomes of th...

journal_title：Molecular biology and evolution

authors： Smith DR,Lee RW

更新日期：2010-10-01 00:00:00

abstract：:The emergence of islands has been linked to spectacular radiations of diverse organisms. Although penguins spend much of their lives at sea, they rely on land for nesting, and a high proportion of extant species are endemic to geologically young islands. Islands may thus have been crucial to the evolutionary diversifi...

journal_title：Molecular biology and evolution

authors： Cole TL,Ksepka DT,Mitchell KJ,Tennyson AJD,Thomas DB,Pan H,Zhang G,Rawlence NJ,Wood JR,Bover P,Bouzat JL,Cooper A,Fiddaman SR,Hart T,Miller G,Ryan PG,Shepherd LD,Wilmshurst JM,Waters JM

更新日期：2019-04-01 00:00:00

abstract：:Discrepancies in phylogenetic trees of bacteria and archaea are often explained as lateral gene transfer events. However, such discrepancies may also be due to phylogenetic artifacts or orthology assignment problems. A first step that may help to resolve this dilemma is to estimate the extent of phylogenetic inconsist...

journal_title：Molecular biology and evolution

authors： Soria-Carrasco V,Castresana J

更新日期：2008-11-01 00:00:00

abstract：:Phenotypic evolution may occur either through alterations to the structure of protein-coding genes or their expression. Evidence for which of these two mechanisms more commonly contribute to the evolution of a phenotype can be garnered from examples of parallel and convergent evolution. The visual system of East Afric...

journal_title：Molecular biology and evolution

authors： O'Quin KE,Hofmann CM,Hofmann HA,Carleton KL

更新日期：2010-12-01 00:00:00

abstract：:Signaling peptides enable communication between cells, both within and between individuals, and are therefore key to the control of complex physiological and behavioral responses. Since their small sizes prevent direct transmission to secretory pathways, these peptides are often produced as part of a larger polyprotei...

journal_title：Molecular biology and evolution

authors： Rogers DW,McConnell E,Miller EL,Greig D

更新日期：2017-12-01 00:00:00

abstract：:The plant MADS-box regulatory gene family includes several loci that control different aspects of inflorescence and floral development. Orthologs to the Arabidopsis thaliana MADS-box floral meristem genes APETALA1 and CAULIFLOWER and the floral organ identity genes APETALA3 and PISTILLATA were isolated from the congen...

journal_title：Molecular biology and evolution

authors： Lawton-Rauh AL,Buckler ES 4th,Purugganan MD

更新日期：1999-08-01 00:00:00

abstract：:The variation of amino acid substitution rates in proteins depends on several variables. Among these, the protein's expression level, functional category, essentiality, or metabolic costs of its amino acid residues may play an important role. However, the relative importance of each variable has not yet been evaluated...

journal_title：Molecular biology and evolution

authors： Rocha EP,Danchin A

更新日期：2004-01-01 00:00:00

abstract：:ModelTest-NG is a reimplementation from scratch of jModelTest and ProtTest, two popular tools for selecting the best-fit nucleotide and amino acid substitution models, respectively. ModelTest-NG is one to two orders of magnitude faster than jModelTest and ProtTest but equally accurate and introduces several new featur...

journal_title：Molecular biology and evolution

authors： Darriba D,Posada D,Kozlov AM,Stamatakis A,Morel B,Flouri T

更新日期：2020-01-01 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：:The ancestral homeland of Australian dingoes and Pacific dogs is proposed to be in South China. However, the location and timing of their dispersal and relationship to dog domestication is unclear. Here, we sequenced 7,000- to 2,000-year-old complete mitochondrial DNA (mtDNA) genomes of 27 ancient canids (one gray wol...

journal_title：Molecular biology and evolution

authors： Zhang M,Sun G,Ren L,Yuan H,Dong G,Zhang L,Liu F,Cao P,Ko AM,Yang MA,Hu S,Wang GD,Fu Q

更新日期：2020-05-01 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：:Simple models of molecular evolution assume that sequences evolve by a Poisson process in which nucleotide or amino acid substitutions occur as rare independent events. In these models, the expected ratio of the variance to the mean of substitution counts equals 1, and substitution processes with a ratio greater than ...

journal_title：Molecular biology and evolution

authors： Bedford T,Hartl DL

更新日期：2008-08-01 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：: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：:A novel algorithm, GS-Aligner, that uses bit-level operations was developed for aligning genomic sequences. GS-Aligner is efficient in terms of both time and space for aligning two very long genomic sequences and for identifying genomic rearrangements such as translocations and inversions. It is suitable for aligning ...

journal_title：Molecular biology and evolution

authors： Shih AC,Li WH

更新日期：2003-08-01 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：:Phylogenomic analyses have revealed several important metazoan clades, such as the Ecdysozoa and the Lophotrochozoa. However, the phylogenetic positions of a few taxa, such as ctenophores, chaetognaths, acoelomorphs, and Xenoturbella, remain contentious. Thus, the findings of qualitative markers or "rare genomic chang...

journal_title：Molecular biology and evolution

authors： de Mendoza A,Ruiz-Trillo I

更新日期：2011-11-01 00:00:00

abstract：:The shikimate dehydrogenases (SDH) represent a widely distributed enzyme family with an essential role in secondary metabolism. This superfamily had been previously subdivided into 4 enzyme groups (AroE, YdiB, SdhL, and RifI), which show clear biochemical and functional differences ranging from amino acid biosynthesis...

journal_title：Molecular biology and evolution

authors： Singh S,Stavrinides J,Christendat D,Guttman DS

更新日期：2008-10-01 00:00:00

abstract：:Statistical criteria have long been the standard for selecting the best model for phylogenetic reconstruction and downstream statistical inference. Although model selection is regarded as a fundamental step in phylogenetics, existing methods for this task consume computational resources for long processing time, they ...

journal_title：Molecular biology and evolution

authors： Abadi S,Avram O,Rosset S,Pupko T,Mayrose I

更新日期：2020-11-01 00:00:00

abstract：:While it is widely accepted that most animals (Metazoa) do not have endogenous cellulases, relying instead on intestinal symbionts for cellulose digestion, the glycosyl hydrolase family 9 (GHF9) cellulases found in the genomes of termites, abalone, and sea squirts could be an exception. Using information from expresse...

journal_title：Molecular biology and evolution

authors： Davison A,Blaxter M

更新日期：2005-05-01 00:00:00

abstract：:Epigenetic information, which can be passed on independently of the DNA sequence, is stored in part in the form of histone posttranslational modifications and specific histone variants. Although complexes necessary for deposition have been identified for canonical and variant histones, information regarding the chroma...

journal_title：Molecular biology and evolution

authors： Ashraf K,Nabeel-Shah S,Garg J,Saettone A,Derynck J,Gingras AC,Lambert JP,Pearlman RE,Fillingham J

更新日期：2019-05-01 00:00:00

abstract：:A correspondence analysis of codon usage in Xenopus laevis revealed that the first axis is strongly correlated with the base composition at third codon positions. The second axis discriminates between putatively highly expressed genes and the other coding sequences, with expression levels being confirmed by the analys...

journal_title：Molecular biology and evolution

authors： Musto H,Cruveiller S,D'Onofrio G,Romero H,Bernardi G

更新日期：2001-09-01 00:00:00