The Effect of Nonreversibility on Inferring Rooted Phylogenies.

abstract：:During the adaptation of an organism to a parasitic lifestyle, various gene functions may be rendered superfluous due to the fact that the host may supply these needs. As a consequence, obligate symbiotic bacterial pathogens tend to undergo reductive genomic evolution through gene death (nonfunctionalization or pseudo...

journal_title：Molecular biology and evolution

authors： Dagan T,Blekhman R,Graur D

更新日期：2006-02-01 00:00:00

abstract：:Analysis of evolution of paralogous genes in a genome is central to our understanding of genome evolution. Comparison of closely related bacterial genomes, which has provided clues as to how genome sequences evolve under natural conditions, would help in such an analysis. With species Staphylococcus aureus, whole-geno...

journal_title：Molecular biology and evolution

authors： Tsuru T,Kawai M,Mizutani-Ui Y,Uchiyama I,Kobayashi I

更新日期：2006-06-01 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：:Adaptation of a complex trait often requires the accumulation of many modifications to finely tune its underpinning molecular components to novel environmental requirements. The investigation of cis-acting regulatory modifications can be used to pinpoint molecular systems partaking in such complex adaptations. Here, w...

journal_title：Molecular biology and evolution

authors： He F,Arce AL,Schmitz G,Koornneef M,Novikova P,Beyer A,de Meaux J

更新日期：2016-08-01 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：:Hybrid males resulting from crosses between closely related species of Drosophila are sterile. The F1 hybrid sterility phenotype is mainly due to defects occurring during late stages of development that relate to sperm individualization, and so genes controlling sperm development may have been subjected to selective d...

journal_title：Molecular biology and evolution

authors： Civetta A,Rajakumar SA,Brouwers B,Bacik JP

更新日期：2006-03-01 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：:In this article, we address the issue of estimating the phylogenetic tree based on sequence data across a set of genes. Recognizing that the individual gene trees may not all share the same evolutionary history due to lateral gene transfer or differences in rates of evolution for instance, we develop a robust algorith...

journal_title：Molecular biology and evolution

authors： Xu X,Dunn KA,Field C

更新日期：2015-08-01 00:00:00

abstract：:It has recently been observed by Ho et al. (Ho SYW, Phillips MJ, Cooper A, Drummond AJ. 2005. Time dependency of molecular rate estimates and systematic overestimation of recent divergence times. Mol Biol Evol. 22(7):1561-1568) that apparent rates of molecular evolution increase when measured over short timespans. I i...

journal_title：Molecular biology and evolution

authors： Woodhams M

更新日期：2006-12-01 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：:Examination of the genomic sequence of the telomere region makes it possible to understand the evolution of the structure of chromosomal ends. We compared the genomic sequences of 14 chromosomal ends of rice, Oryza sativa, L., on the basis of the variation in TTTAGGG repeats. In the proximal telomere repeats, nucleoti...

journal_title：Molecular biology and evolution

authors： Mizuno H,Wu J,Katayose Y,Kanamori H,Sasaki T,Matsumoto T

更新日期：2008-01-01 00:00:00

abstract：:The evolutionary origin of eukaryotes is a question of great interest for which many different hypotheses have been proposed. These hypotheses predict distinct patterns of evolutionary relationships for individual genes of the ancestral eukaryotic genome. The availability of numerous completely sequenced genomes cover...

journal_title：Molecular biology and evolution

authors： Rochette NC,Brochier-Armanet C,Gouy M

更新日期：2014-04-01 00:00:00

abstract：:In contrast to prokaryotes, eukaryotic cells are characterized by a complex set of internal membrane-bound compartments. A subset of these, and the protein machineries that move material between them, define the membrane-trafficking system (MTS), the emergence of which represents a landmark in eukaryotic evolution. Un...

journal_title：Molecular biology and evolution

authors： Klinger CM,Spang A,Dacks JB,Ettema TJ

更新日期：2016-06-01 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：:Gene conversion is considered to play important roles in the formation of genomic makeup such as homogenization of multigene families and diversification of alleles. We devised two statistical tests on quartets for detecting gene conversion events. Each "quartet" consists of two pairs of orthologous sequences supposed...

journal_title：Molecular biology and evolution

authors： Ezawa K,OOta S,Saitou N,SMBE Tri-National Young Investigators.

更新日期：2006-05-01 00:00:00

abstract：:Molecular systematists need increased access to nuclear genes. Highly conserved, low copy number protein-encoding nuclear genes have attractive features for phylogenetic inference but have heretofore been applied mostly to very ancient divergences. By virtue of their synonymous substitutions, such genes should contain...

journal_title：Molecular biology and evolution

authors： Cho S,Mitchell A,Regier JC,Mitter C,Poole RW,Friedlander TP,Zhao S

更新日期：1995-07-01 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：: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：: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：:The AID/APOBEC family (comprising AID, APOBEC1, APOBEC2, and APOBEC3 subgroups) contains members that can deaminate cytidine in RNA and/or DNA and exhibit diverse physiological functions (AID and APOBEC3 deaminating DNA to trigger pathways in adaptive and innate immunity; APOBEC1 mediating apolipoprotein B RNA editing...

journal_title：Molecular biology and evolution

authors： Conticello SG,Thomas CJ,Petersen-Mahrt SK,Neuberger MS

更新日期：2005-02-01 00:00:00

abstract：:The ability to counter periods of low humidity is an important determinant of distribution range in Drosophila. Climate specialists with low physiological tolerance to desiccation stress are restricted to the tropics and may lack the ability to further increase resistance through evolution. Although the physiological ...

journal_title：Molecular biology and evolution

authors： Telonis-Scott M,Gane M,DeGaris S,Sgrò CM,Hoffmann AA

更新日期：2012-05-01 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：:The quantitative immunological technique of micro-complement fixation (MC'F) has been routinely used during the past decade to assess evolutionary relationships among living vertebrate species. The large data base that has been generated, along with the excellent correlations between immunologically measured genetic d...

journal_title：Molecular biology and evolution

authors： Maxson RD,Maxson LR

更新日期：1986-09-01 00:00:00

abstract：:The ribosome is responsible for protein synthesis in all living organisms. It is best known to exist around 3.5-3.7 Ga whereat life on Earth inhabited anoxic environment with abundant soluble irons. The RNAs and proteins are the two biopolymers that constitute the ribosome. However, both proteins and RNAs require meta...

journal_title：Molecular biology and evolution

authors： Lin SY,Wang YC,Hsiao C

更新日期：2019-05-01 00:00:00

abstract：:It is well known that knocking out a gene in an organism often causes no phenotypic effect. One possible explanation is the existence of duplicate genes; that is, the effect of knocking out a gene is compensated by a duplicate copy. Another explanation is the existence of alternative pathways. In terms of metabolic pr...

journal_title：Molecular biology and evolution

authors： Hanada K,Sawada Y,Kuromori T,Klausnitzer R,Saito K,Toyoda T,Shinozaki K,Li WH,Hirai MY

更新日期：2011-01-01 00:00:00

abstract：:Much like other indigenous domesticated animals, Tibetan chickens living at high altitudes (2,200-4,100 m) show specific physiological adaptations to the extreme environmental conditions of the Tibetan Plateau, but the genetic bases of these adaptations are not well characterized. Here, we assembled a de novo genome o...

journal_title：Molecular biology and evolution

authors： Wang MS,Li Y,Peng MS,Zhong L,Wang ZJ,Li QY,Tu XL,Dong Y,Zhu CL,Wang L,Yang MM,Wu SF,Miao YW,Liu JP,Irwin DM,Wang W,Wu DD,Zhang YP

更新日期：2015-07-01 00:00:00

abstract：:We investigate the effect of purifying selection at multiple sites on both the shape of the genealogy and the distribution of mutations on the tree. We find that the primary effect of purifying selection on a genealogy is to shift the distribution of mutations on the tree, whereas the shape of the tree remains largely...

journal_title：Molecular biology and evolution

authors： Williamson S,Orive ME

更新日期：2002-08-01 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：:Proteins present in the seminal fluid of Drosophila melanogaster (accessory gland proteins Acps) contribute to female postmating behavioral changes, sperm storage, sperm competition, and immunity. Consequently, male-female coevolution and host-pathogen interactions are thought to underlie the rapid, adaptive evolution...

journal_title：Molecular biology and evolution

authors： Wong A,Turchin MC,Wolfner MF,Aquadro CF

更新日期：2008-03-01 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