Rate acceleration and long-branch attraction in a conserved gene of cryptic daphniid (Crustacea) species.

abstract：:Model-based analyses of natural selection often categorize sites into a relatively small number of site classes. Forcing each site to belong to one of these classes places unrealistic constraints on the distribution of selection parameters, which can result in misleading inference due to model misspecification. We pre...

journal_title：Molecular biology and evolution

authors： Murrell B,Moola S,Mabona A,Weighill T,Sheward D,Kosakovsky Pond SL,Scheffler K

更新日期：2013-05-01 00:00:00

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：:MrBayes, using Metropolis-coupled Markov chain Monte Carlo (MCMCMC or (MC)(3)), is a popular program for Bayesian inference. As a leading method of using DNA data to infer phylogeny, the (MC)(3) Bayesian algorithm and its improved and parallel versions are now not fast enough for biologists to analyze massive real-wor...

journal_title：Molecular biology and evolution

authors： Bao J,Xia H,Zhou J,Liu X,Wang G

更新日期：2013-06-01 00:00:00

abstract：:Homeobox genes encode transcription factors involved in many aspects of developmental processes. The homeodomain-leucine zipper (HD-Zip) genes, which are characterized by the presence of both a homeodomain and a leucine zipper motif, form a clade within the homeobox superfamily and were previously reported only from v...

journal_title：Molecular biology and evolution

authors： Sakakibara K,Nishiyama T,Kato M,Hasebe M

更新日期：2001-04-01 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：:Estimation of population parameters for the common ancestors of humans and the great apes is important in understanding our evolutionary history. In particular, inference of population size for the human-chimpanzee common ancestor may shed light on the process by which the 2 species separated and on whether the human ...

journal_title：Molecular biology and evolution

authors： Burgess R,Yang Z

更新日期：2008-09-01 00:00:00

abstract：:Until recently, phylogenetic analyses have been routinely based on homologous sequences of a single gene. Given the vast number of gene sequences now available, phylogenetic studies are now based on the analysis of multiple genes. Thus, it has become necessary to devise statistical methods to combine multiple molecula...

journal_title：Molecular biology and evolution

authors： Pupko T,Huchon D,Cao Y,Okada N,Hasegawa M

更新日期：2002-12-01 00:00:00

abstract：:The cosmopolitan dinoflagellate genus Alexandrium, and especially the A. tamarense species complex, contain both toxic and nontoxic strains. An understanding of their evolution and paleogeography is a necessary precursor to unraveling the development and spread of toxic forms. The inclusion of more strains into the ex...

journal_title：Molecular biology and evolution

authors： John U,Fensome RA,Medlin LK

更新日期：2003-07-01 00:00:00

abstract：:In termites, as in many social insects, some individuals specialize in colony defense, developing diverse weaponry. As workers of the termite Neocapritermes taracua (Termitidae: Termitinae) age, their efficiency to perform general tasks decreases, while they accumulate defensive secretions and increase their readiness...

journal_title：Molecular biology and evolution

authors： Bourguignon T,Šobotník J,Brabcová J,Sillam-Dussès D,Buček A,Krasulová J,Vytisková B,Demianová Z,Mareš M,Roisin Y,Vogel H

更新日期：2016-03-01 00:00:00

abstract：:Noncoding DNA sequences, which play various roles in gene expression and regulation, are under evolutionary pressure. Gene regulation requires specific protein-DNA binding events, and our previous studies showed that both DNA sequence and shape readout are employed by transcription factors (TFs) to achieve DNA binding...

journal_title：Molecular biology and evolution

authors： Wang X,Zhou T,Wunderlich Z,Maurano MT,DePace AH,Nuzhdin SV,Rohs R

更新日期：2018-08-01 00:00:00

abstract：:Finding correct species relationships using phylogeny reconstruction based on molecular data is dependent on several empirical and technical factors. These include the choice of DNA sequence from which phylogeny is to be inferred, the establishment of character homology within a sequence alignment, and the phylogeny a...

journal_title：Molecular biology and evolution

authors： Mugridge NB,Morrison DA,Jäkel T,Heckeroth AR,Tenter AM,Johnson AM

更新日期：2000-12-01 00:00:00

abstract：:The capacity to biomineralize is closely linked to the rapid expansion of animal life during the early Cambrian, with many skeletonized phyla first appearing in the fossil record at this time. The appearance of disparate molluscan forms during this period leaves open the possibility that shells evolved independently a...

journal_title：Molecular biology and evolution

authors： Jackson DJ,McDougall C,Woodcroft B,Moase P,Rose RA,Kube M,Reinhardt R,Rokhsar DS,Montagnani C,Joubert C,Piquemal D,Degnan BM

更新日期：2010-03-01 00:00:00

abstract：:In the past 40 years, there has been increasing acceptance that variation in levels of gene expression represents a major source of evolutionary novelty. Gene expression divergence is therefore likely to be involved in the emergence of incipient species, namely, in a context of adaptive radiation. In the lake whitefis...

journal_title：Molecular biology and evolution

authors： Jeukens J,Bittner D,Knudsen R,Bernatchez L

更新日期：2009-01-01 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：:The degree to which an amino acid site is free to vary is strongly dependent on its structural and functional importance. An amino acid that plays an essential role is unlikely to change over evolutionary time. Hence, the evolutionary rate at an amino acid site is indicative of how conserved this site is and, in turn,...

journal_title：Molecular biology and evolution

authors： Mayrose I,Graur D,Ben-Tal N,Pupko T

更新日期：2004-09-01 00:00:00

abstract：:The T1 family of retrotransposable elements is interspersed and moderately repeated in five member species of the Anopheles gambiae sibling-species complex and has diverged little since the radiation of the complex. T1 includes two closely related but independent subfamilies, defined by the presence or absence of link...

journal_title：Molecular biology and evolution

authors： Besansky NJ

更新日期：1990-05-01 00:00:00

abstract：:Serum response factor (SRF) and myocyte enhancer factor 2 (MEF2) represent two types of members of the MCM1, AGAMOUS, DEFICIENS, and SRF (MADS)-box transcription factor family present in animals and fungi. Each type has distinct biological functions, which are reflected by the distinct specificities of the proteins bo...

journal_title：Molecular biology and evolution

authors： Wu W,Huang X,Cheng J,Li Z,de Folter S,Huang Z,Jiang X,Pang H,Tao S

更新日期：2011-01-01 00:00:00

abstract：:Hantaviruses are considered one of the best examples of a long-term association between RNA viruses and their hosts. Based on the appearance of strong host specificity, it has been suggested that hantaviruses cospeciated with the rodents and insectivores they infect since these mammals last shared a common ancestor, a...

journal_title：Molecular biology and evolution

authors： Ramsden C,Holmes EC,Charleston MA

更新日期：2009-01-01 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：:Although whole-organism aspects of life-history physiology are well studied and molecular information (e.g., transcript abundance) on life-history variation is accumulating rapidly, much less information is available on the biochemical (enzymological) basis of life-history adaptation. The present study investigated th...

journal_title：Molecular biology and evolution

authors： Schilder RJ,Zera AJ,Black C,Hoidal M,Wehrkamp C

更新日期：2011-12-01 00:00:00

abstract：:The complete mitochondrial DNA (mtDNA) control region was sequenced for 71 individuals from five species of the rodent genus Clethrionomys both to understand patterns of variation and to explore the existence of previously described domains and other elements. Among species, the control region ranged from 942 to 971 b...

journal_title：Molecular biology and evolution

authors： Matson CW,Baker RJ

更新日期：2001-08-01 00:00:00

abstract：:Nonsense-mediated decay (NMD) pathways for detection and degradation of transcripts containing premature termination (stop) codons (PTCs) are ubiquitous among the eukaryotes. NMD uses the presence of a second signal downstream of a termination codon to distinguish a PTC from a true stop codon. In mammals and perhaps o...

journal_title：Molecular biology and evolution

authors： Scofield DG,Hong X,Lynch M

更新日期：2007-04-01 00:00:00

abstract：:The distribution of fitness effects of mutations is a factor of fundamental importance in evolutionary biology. We determined the distribution of fitness effects of 510 mutants that each carried between 1 and 10 mutations (synonymous and nonsynonymous) in the hisA gene, encoding an essential enzyme in the l-histidine ...

journal_title：Molecular biology and evolution

authors： Lundin E,Tang PC,Guy L,Näsvall J,Andersson DI

更新日期：2018-03-01 00:00:00

abstract：:Significance levels obtained from a chi 2 contingency test are suspect when sample sizes are small. Traditionally this has meant that data must be combined. However, such an approach may obscure heterogeneity and hence potentially reduce the power of the statistical test. In this paper, we present a Monte Carlo soluti...

journal_title：Molecular biology and evolution

authors： Roff DA,Bentzen P

更新日期：1989-09-01 00:00:00

abstract：:Reconstructing phylogenies from intraspecific data (such as human mitochondrial DNA variation) is often a challenging task because of large sample sizes and small genetic distances between individuals. The resulting multitude of plausible trees is best expressed by a network which displays alternative potential evolut...

journal_title：Molecular biology and evolution

authors： Bandelt HJ,Forster P,Röhl A

更新日期：1999-01-01 00:00:00

abstract：:Proteins evolve not only through point mutations but also by insertion and deletion events, which affect the length of the protein. It is well known that such indel events most frequently occur in surface-exposed loops. However, detailed analysis of indel events in distantly related and fast-evolving proteins is hampe...

journal_title：Molecular biology and evolution

authors： Light S,Sagit R,Sachenkova O,Ekman D,Elofsson A

更新日期：2013-12-01 00:00:00

abstract：:Why are certain bacterial genomes so small and compact? The adaptive genome streamlining hypothesis posits that selection acts to reduce genome size because of the metabolic burden of replicating DNA. To reveal the impact of genome streamlining on cellular traits, we reduced the Escherichia coli genome by up to 20% by...

journal_title：Molecular biology and evolution

authors： Karcagi I,Draskovits G,Umenhoffer K,Fekete G,Kovács K,Méhi O,Balikó G,Szappanos B,Györfy Z,Fehér T,Bogos B,Blattner FR,Pál C,Pósfai G,Papp B

更新日期：2016-05-01 00:00:00

abstract：:Here, we address a much-debated topic: is there or is there not an organismal tree of gamma-proteobacteria that can be unambiguously inferred from a core of shared genes? We apply several recently developed analytical methods to this problem, for the first time. Our heat map analyses of P values and of bootstrap bipar...

journal_title：Molecular biology and evolution

authors： Susko E,Leigh J,Doolittle WF,Bapteste E

更新日期：2006-05-01 00:00:00

abstract：:DNA cytosine methylation is central to many biological processes, including regulation of gene expression, cellular differentiation, and development. This DNA modification is conserved across animals, having been found in representatives of sponges, ctenophores, cnidarians, and bilaterians, and with very few known ins...

journal_title：Molecular biology and evolution

authors： Kyger R,Luzuriaga-Neira A,Layman T,Milkewitz Sandberg TO,Singh D,Huchon D,Peri S,Atkinson SD,Bartholomew JL,Yi SV,Alvarez-Ponce D

更新日期：2021-01-23 00:00:00

abstract：:Proof of authenticity is the greatest challenge in palaeogenetic research, and many safeguards have become standard routine in laboratories specialized on ancient DNA research. Here we describe an as-yet unknown source of artifacts that will require special attention in the future. We show that ancient DNA extracts on...

journal_title：Molecular biology and evolution

authors： Pusch CM,Bachmann L

更新日期：2004-05-01 00:00:00