abstract：:While studies of the evolutionary histories of protein families are commonplace, little is known on noncoding RNAs beyond microRNAs and some snoRNAs. Here we investigate in detail the evolutionary history of the nine spliceosomal snRNA families (U1, U2, U4, U5, U6, U11, U12, U4atac, and U6atac) across the completely o...

journal_title：Journal of molecular evolution

authors： Marz M,Kirsten T,Stadler PF

更新日期：2008-12-01 00:00:00

abstract：:We have performed a genome-wide analysis of the mimp family of miniature inverted-repeat transposable elements, taking advantage of the recent release of the F. oxysporum genome sequence. Using different approaches, we detected 103 mimp elements, corresponding to 75 nonredundant copies, half of which are located on a ...

journal_title：Journal of molecular evolution

authors： Bergemann M,Lespinet O,M'Barek SB,Daboussi MJ,Dufresne M

更新日期：2008-12-01 00:00:00

abstract：:Simple sequence repeats (SSRs) in DNA sequences are tandem iterations of a single nucleotide or a short oligonucleotide. SSRs are subject to slipped-strand mutations and a common source of phase variation in bacteria and antigenic variation in pathogens. Significantly long SSRs are generally rare in prokaryotic genome...

journal_title：Journal of molecular evolution

authors： Guo X,Mrázek J

更新日期：2008-11-01 00:00:00

abstract：:Gamete-recognition proteins have been shown to evolve by positive selection in diverse organism groups, such as marine invertebrates and mammals, although underlying evolutionary mechanisms driving this rapid divergence are poorly understood. However, several hypotheses have been put forward to explain the observed pa...

journal_title：Journal of molecular evolution

authors： Berlin S,Qu L,Ellegren H

更新日期：2008-11-01 00:00:00

abstract：:Explicit evaluation of the accuracy and power of maximum likelihood and Bayesian methods for detecting site-specific positive Darwinian selection presents a challenge because selective consequences of single amino acid changes are generally unknown. We exploited extensive molecular and functional characterization of a...

journal_title：Journal of molecular evolution

authors： Cavatorta JR,Savage AE,Yeam I,Gray SM,Jahn MM

更新日期：2008-11-01 00:00:00

abstract：:The nearly neutral theory attributes most nucleotide substitution and polymorphism to genetic drift acting on weakly selected mutants, and assumes that the selection coefficients for these mutants are drawn from a continuous distribution. This means that parameter estimation can require numerical integration, and this...

journal_title：Journal of molecular evolution

authors： Welch JJ,Eyre-Walker A,Waxman D

更新日期：2008-10-01 00:00:00

abstract：:The neutral theory of molecular evolution states that most mutations are deleterious or neutral. It results that the evolutionary rate of a given position in an alignment is a function of the level of constraint acting on this position. Inferring evolutionary rates from a set of aligned sequences is hence a powerful m...

journal_title：Journal of molecular evolution

authors： Dutheil J

更新日期：2008-09-01 00:00:00

abstract：:It has been argued that the common ancestor of about 75% of all dicots possessed an S-RNase-based gametophytic self-incompatibility (GSI) system. S-RNase genes should thus be found in most plant families showing GSI. The S-RNase gene (or a duplicate) may also acquire a new function and thus genes belonging to the S-RN...

journal_title：Journal of molecular evolution

authors： Vieira J,Fonseca NA,Vieira CP

更新日期：2008-08-01 00:00:00

abstract：:It has been argued that downstream enzymes in metabolic pathways are expected to be subject to reduced selective constraint, while upstream enzymes, particularly those at pathway branch points, are expected to exhibit more frequent adaptive substitution than downstream enzymes. We examined whether these expectations a...

journal_title：Journal of molecular evolution

authors： Rausher MD,Lu Y,Meyer K

更新日期：2008-08-01 00:00:00

abstract：:Pax genes encode transcription factors critical for metazoan development. Large-scale gene duplication with subsequent gene losses during vertebrate evolution has resulted in two human genes for each of the Pax1/9, Pax3/7, and Pax4/6 subfamilies and three for the Pax2/5/8 subfamily, compared to one each in the cephalo...

journal_title：Journal of molecular evolution

authors： Short S,Holland LZ

更新日期：2008-06-01 00:00:00

abstract：:Two competing effects at two vastly different scales may explain collagen's current translation length. The necessity to have long molecules for maintaining mechanical integrity at the organism and supraorganism scales may be limited by the need to have small molecules capable of robust self-assembly at the nanoscale....

journal_title：Journal of molecular evolution

authors： Layton BE,D'Souza AJ,Dampier W,Zeiger A,Sabur A,Jean-Charles J

更新日期：2008-06-01 00:00:00

abstract：:Gene duplication by retrotransposition duplicates only the coding and untranslated regions of a gene and, thus, biases retroduplicated genes toward having different expression patterns from their parental genes. As such, genes duplicated by retrotransposition are more likely to develop novel expression domains. To exp...

journal_title：Journal of molecular evolution

authors： Penney J,Bossé J,Clark DV

更新日期：2008-05-01 00:00:00

abstract：:A problem with studying evolutionary dynamics of mitochondrial (mt) DNA is that classical population genetic techniques cannot identify selected substitutions because of genetic hitchhiking. We circumvented this problem by employing a candidate complex approach to study sequence variation in cytochrome c oxidase (COX)...

journal_title：Journal of molecular evolution

authors： Melvin RG,Katewa SD,Ballard JW

更新日期：2008-03-01 00:00:00

abstract：:The size and diversity of bacteriophage populations require methodologies to quantitatively study the landscape of phage differences. Statistical approaches are confronted with small genome sizes forbidding significant single-phage analysis, and comparative methods analyzing full phage genomes represent an alternative...

journal_title：Journal of molecular evolution

authors： Carbone A

更新日期：2008-03-01 00:00:00

abstract：:The evolution rates of mtDNA in early metazoans hold important implications for DNA barcoding. Here, we present a comprehensive analysis of intra- and interspecific COI variabilities in Porifera and Cnidaria (separately as Anthozoa, Hydrozoa, and Scyphozoa) using a data set of 619 sequences from 224 species. We found ...

journal_title：Journal of molecular evolution

authors： Huang D,Meier R,Todd PA,Chou LM

更新日期：2008-02-01 00:00:00

abstract：:Covarion processes allow changes in evolutionary rates at sites along the branches of a phylogenetic tree. Covarion-like evolution is increasingly recognized as an important mode of protein evolution. Several recent reports suggest that maximum likelihood estimation employing covarion models may support different opti...

journal_title：Journal of molecular evolution

authors： Wang HC,Susko E,Spencer M,Roger AJ

更新日期：2008-01-01 00:00:00

abstract：:Twenty-seven protein sequence elements, six to nine amino acids long, were extracted from 15 phylogenetically diverse complete prokaryotic proteomes. The elements are present in all of these proteomes, with at least one copy each (omnipresent elements), and have presumably been conserved since the last universal commo...

journal_title：Journal of molecular evolution

authors： Sobolevsky Y,Frenkel ZM,Trifonov EN

更新日期：2007-12-01 00:00:00

abstract：:Since the genetic code first was determined, many have claimed that it is organized adaptively, so as to assign similar codons to similar amino acids. This claim has proved difficult to establish due to the absence of relevant comparative data on alternative primordial codes and of objective measures of amino acid exc...

journal_title：Journal of molecular evolution

authors： Stoltzfus A,Yampolsky LY

更新日期：2007-10-01 00:00:00

abstract：:Two types of gene encoding small subunits (SSU) of ADP-glucose pyrophosphorylase, a starch-biosynthetic enzyme, have been found in cereals and other grasses. One of these genes encodes two SSU proteins. These are targeted to different subcellular compartments and expressed in different organs of the plant: the endospe...

journal_title：Journal of molecular evolution

authors： Rösti S,Denyer K

更新日期：2007-09-01 00:00:00

abstract：:One of the key problems in the study of ancient DNA is that of authenticating sequences obtained from PCR amplifications of highly degraded samples. Contamination of ancient samples and postmortem damage to endogenous DNA templates are the major obstacles facing researchers in this task. In particular, the authenticat...

journal_title：Journal of molecular evolution

authors： Helgason A,Pálsson S,Lalueza-Fox C,Ghosh S,Sigurdardóttir S,Baker A,Hrafnkelsson B,Arnadóttir L,Thorsteinsdóttir U,Stefánsson K

更新日期：2007-07-01 00:00:00

abstract：:Using all currently predicted coding regions in the honeybee genome, a novel form of synonymous codon bias is presented that affects the usage of particular codons dependent on the surrounding nucleotides in the coding region. Nucleotides at the third codon site are correlated, dependent on their weak (adenine [A] or ...

journal_title：Journal of molecular evolution

authors： Cutler RW,Chantawannakul P

更新日期：2007-06-01 00:00:00

abstract：:As the origin(s) of life on Earth remains an open question, detailed characteristics about the "last universal ancestor" (LUA) continue to be obscured. Here we provide arguments that strengthen the bacterial-like nature of the LUA. Our view attempts to recreate the evolution of archaeal lipids, the major components of...

journal_title：Journal of molecular evolution

authors： Payandeh J,Pai EF

更新日期：2007-03-01 00:00:00

abstract：:Catalyzed by a family of enzymes called glycosyltransferases, glycosylation reactions are essential for the bioactivities of secondary metabolites such as antibiotics. Due to the special characters of antibiotic glycosyltransferases (AGts), antibiotics can function by attaching some unusual deoxy-sugars to their aglyc...

journal_title：Journal of molecular evolution

authors： Liang D,Qiao J

更新日期：2007-03-01 00:00:00

abstract：:Analysis of cDNAs from Macrovipera lebetina transmediterranea (Mlt) and Echis ocellatus (Eo) venom gland libraries encoding disintegrins argued strongly for a common ancestry of the messengers of short disintegrins and those for precursors of dimeric disintegrin chains. We now report the sequence analysis of disintegr...

journal_title：Journal of molecular evolution

authors： Bazaa A,Juárez P,Marrakchi N,Bel Lasfer Z,El Ayeb M,Harrison RA,Calvete JJ,Sanz L

更新日期：2007-02-01 00:00:00

abstract：:We analyzed precursor messenger RNAs (pre-mRNAs) of 12 eukaryotic species. In each species, three groups of highly expressed genes, ribosomal proteins, heat shock proteins, and amino-acyl tRNA synthetases, were compared with a control group (randomly selected genes). The purine-pyrimidine (R-Y) composition of pre-mRNA...

journal_title：Journal of molecular evolution

authors： Paz A,Mester D,Nevo E,Korol A

更新日期：2007-02-01 00:00:00

abstract：:Since their discovery in Metazoa, the three nuclear RNA polymerases (RNAPs) have been found in fungi, plants, and diverse protists. In all eukaryotes studied to date, RNAPs I, II, and III collectively transcribe all major RNAs made in the nucleus. We have found genes for the largest subunit (RPD1/RPE1) of a new DNA-de...

journal_title：Journal of molecular evolution

authors： Luo J,Hall BD

更新日期：2007-01-01 00:00:00

abstract：:The retrieval of Neanderthal (Homo neanderthalsensis) mitochondrial DNA is thought to be among the most significant ancient DNA contributions to date, allowing conflicting hypotheses on modern human (Homo sapiens) evolution to be tested directly. Recently, however, both the authenticity of the Neanderthal sequences an...

journal_title：Journal of molecular evolution

authors： Hebsgaard MB,Wiuf C,Gilbert MT,Glenner H,Willerslev E

更新日期：2007-01-01 00:00:00

abstract：:Ca(2+)/cation antiporter (CaCA) proteins are integral membrane proteins that transport Ca(2+) or other cations using the H(+) or Na(+) gradient generated by primary transporters. The CAX (for CAtion eXchanger) family is one of the five families that make up the CaCA superfamily. CAX genes have been found in bacteria, ...

journal_title：Journal of molecular evolution

authors： Shigaki T,Rees I,Nakhleh L,Hirschi KD

更新日期：2006-12-01 00:00:00

abstract：:Computational and experimental attempts tried to characterize a universal core of genes representing the minimal set of functional needs for an organism. Based on the increasing number of available complete genomes, comparative genomics has concluded that the universal core contains < 50 genes. In contrast, experiment...

journal_title：Journal of molecular evolution

authors： Carbone A

更新日期：2006-12-01 00:00:00

abstract：:Selection pressures on proteins are usually measured by comparing homologous nucleotide sequences (Zuckerkandl and Pauling 1965). Recently we introduced a novel method, termed volatility, to estimate selection pressures on proteins on the basis of their synonymous codon usage (Plotkin and Dushoff 2003; Plotkin et al. ...

journal_title：Journal of molecular evolution

authors： Plotkin JB,Dushoff J,Desai MM,Fraser HB

更新日期：2006-11-01 00:00:00

abstract：:Universal scale of the sequence conservation has been recently introduced based on omnipresence of the protein sequence motifs across species. A large spectrum of short sequences, up to eight residues has been found to reside in all or almost all prokaryotic organisms. By this discovery a principally novel quantitativ...

journal_title：Journal of molecular evolution

authors： Sobolevsky Y,Trifonov EN

更新日期：2006-11-01 00:00:00

abstract：:Leucine-rich repeat receptor-like kinases (LRR RLKs) comprise the largest group within the plant receptor-like kinase (RLK) superfamily, and the Arabidopsis genome alone contains over 200 LRR RLK genes. Although there is clear evidence for diverse roles played by individual LRR RLK genes in Arabidopsis growth and deve...

journal_title：Journal of molecular evolution

authors： Zhang XS,Choi JH,Heinz J,Chetty CS

更新日期：2006-11-01 00:00:00

abstract：:The genome organization of the Hardness locus in the tribe Triticeae constitutes an excellent model for studying the mechanisms of evolution that played a role in the preservation and potential functional innovations of duplicate genes. Here we applied the nonsynonymous-synonymous rate ratio (d ( N )/d ( S ) or omega)...

journal_title：Journal of molecular evolution

authors： Massa AN,Morris CF

更新日期：2006-10-01 00:00:00

abstract：:Many eubacteria contain an ATP-dependent protease complex, which is built by multiple copies of the HslV and HslU proteins and is therefore called HslVU. HslU proteins are AAA + ATPases, while HslV proteins are proteases that show highly significant similarity to beta subunits of proteasomes. Therefore, the HslVU comp...

journal_title：Journal of molecular evolution

authors： Ruiz-González MX,Marín I

更新日期：2006-10-01 00:00:00

abstract：:Single likelihood ancestor counting (SLAC), fixed effects likelihood (FEL), and several random effects likelihood (REL) methods were utilized to identify positively and negatively selected sites in sexually induced gene 1 (Sig1) of four different Thalassiosira species. The SLAC analysis did not find any sites affected...

journal_title：Journal of molecular evolution

authors： Sorhannus U,Kosakovsky Pond SL

更新日期：2006-08-01 00:00:00

abstract：:The gene content of a mitochondrial (mt) genome, i.e., 37 genes and a large noncoding region (LNR), is usually conserved in Metazoa. The arrangement of these genes and the LNR is generally conserved at low taxonomic levels but varies substantially at high levels. We report here a variation in mt gene content and gene ...

journal_title：Journal of molecular evolution

authors： Shao R,Barker SC,Mitani H,Takahashi M,Fukunaga M

更新日期：2006-08-01 00:00:00

abstract：:In the present study we focus on the nucleotide and the inferred amino acid variation occurring in humans and other primate species for mitochondrial NAD(+)-dependent succinic semialdehyde dehydrogenase, a gene recently supposed to contribute to cognitive performance in humans. We determined 2527 bp of coding, introni...

journal_title：Journal of molecular evolution

authors： Blasi P,Palmerio F,Aiello A,Rocchi M,Malaspina P,Novelletto A

更新日期：2006-07-01 00:00:00

abstract：:The Pten gene was initially identified in humans as a tumor suppressor. It has since been shown to play important roles in the control of cell size, cell motility, apoptosis, and organ size, and it has also been implicated in aging. Pten is highly conserved among organisms as diverse as nematodes, insects, and vertebr...

journal_title：Journal of molecular evolution

authors： Baudry E,Desmadril M,Werren JH

更新日期：2006-06-01 00:00:00

abstract：:Circadian clock genes are remarkably conserved between eucoelomates. Although Drosophila has one copy of each major component, vertebrates have two or (in the case of the Period genes) three paralogs (Per1-3). We investigated the possibility that the vertebrate Per genes arose through two genome duplications during th...

journal_title：Journal of molecular evolution

authors： von Schantz M,Jenkins A,Archer SN

更新日期：2006-06-01 00:00:00

abstract：:Heterokonts are evolutionarily important as the most nutritionally diverse eukaryote supergroup and the most species-rich branch of the eukaryotic kingdom Chromista. Ancestrally photosynthetic/phagotrophic algae (mixotrophs), they include several ecologically important purely heterotrophic lineages, all grossly unders...

journal_title：Journal of molecular evolution

authors： Cavalier-Smith T,Chao EE

更新日期：2006-04-01 00:00:00