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：:Since the discovery of ING1 class II tumor suppressors in 1996, five different ING genes (ING1 to ING5) encoding proteins with highly conserved plant homeodomain (PHD) motifs and several splicing isoforms of the ING1 and ING2 gene have been identified. The ING family functions in DNA repair and apoptosis in response t...

journal_title：Molecular biology and evolution

authors： He GH,Helbing CC,Wagner MJ,Sensen CW,Riabowol K

更新日期：2005-01-01 00:00:00

abstract：:Evolution at silent sites is often used to estimate the pace of selectively neutral processes or to infer differences in divergence times of genes. However, silent sites are subject to selection in favor of preferred codons, and the strength of such selection varies dramatically across genes. Here, we use the relation...

journal_title：Molecular biology and evolution

authors： Hirsh AE,Fraser HB,Wall DP

更新日期：2005-01-01 00:00:00

abstract：:Pseudogenes are nonfunctional relics of formerly functional genes and are thought to evolve neutrally. In some pseudogenes, however, the molecular evolutionary patterns are atypical of neutrally evolving sequences, exhibiting sequence conservation, codon-usage bias, and other features associated with functional genes....

journal_title：Molecular biology and evolution

authors： Podlaha O,Zhang J

更新日期：2004-12-01 00:00:00

abstract：:Enzyme function is strongly affected by temperature, and orthologs from species adapted to different thermal environments often show temperature compensation in kinetic properties. Antarctic notothenioid fishes live in a habitat of constant, extreme cold (-1.86 +/- 2 degrees C), and orthologs of the enzyme A4-lactate ...

journal_title：Molecular biology and evolution

authors： Fields PA,Houseman DE

更新日期：2004-12-01 00:00:00

abstract：:Based on previous observations that newly inserted LINEs and SINEs have particularly long 3' A-tails, which shorten rapidly during evolutionary time, we have analyzed the rat and mouse genomes for evidence of recently inserted SINEs and LINEs. We find that the youngest predicted subfamilies of rodent identifier (ID) e...

journal_title：Molecular biology and evolution

authors： Odom GL,Robichaux JL,Deininger PL

更新日期：2004-11-01 00:00:00

abstract：:Reconstruction of ancestral DNA and amino acid sequences is an important means of inferring information about past evolutionary events. Such reconstructions suggest changes in molecular function and evolutionary processes over the course of evolution and are used to infer adaptation and convergence. Maximum likelihood...

journal_title：Molecular biology and evolution

authors： Krishnan NM,Seligmann H,Stewart CB,De Koning AP,Pollock DD

更新日期：2004-10-01 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：:The malaria parasite's chloroquine resistance transporter (CRT) is an integral membrane protein localized to the parasite's acidic digestive vacuole. The function of CRT is not known and the protein was originally described as a transporter simply because it possesses 10 transmembrane domains. In wild-type (chloroquin...

journal_title：Molecular biology and evolution

authors： Martin RE,Kirk K

更新日期：2004-10-01 00:00:00

abstract：:Several new families of DNA transposons were identified by computer-assisted searches in a wide range of animal species that includes nematodes, flat worms, mosquitoes, sea squirt, zebrafish, and humans. Many of these elements have coding capacity for transposases, which are related to each other and to those encoded ...

journal_title：Molecular biology and evolution

authors： Feschotte C

更新日期：2004-09-01 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：:To investigate the potential importance of gene duplication in D. melanogaster accessory gland protein (Acp) gene evolution we carried out a computational analysis comparing annotated D. melanogaster Acp genes to the entire D. melanogaster genome. We found that two known Acp genes are actually members of small multige...

journal_title：Molecular biology and evolution

authors： Holloway AK,Begun DJ

更新日期：2004-09-01 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：:Drosophila melanogaster is widely used as a model in DNA variation studies. Patterns of polymorphism have, however, been affected by the history of this species, which is thought to have recently spread out of Africa to the rest of the world. We analyzed DNA sequence variation in 11 populations, including four contine...

journal_title：Molecular biology and evolution

authors： Baudry E,Viginier B,Veuille M

更新日期：2004-08-01 00:00:00

abstract：:A sample of the second largest subunit of low-copy nuclear RNA polymerase II (rpb2) sequences from Malvaceae subfamily Malvoideae suggests that rpb2 has been duplicated early in the subfamily's history. Hibiscus and related taxa possess two rpb2 genes, both of which produce congruent phylogenetic patterns that are lar...

journal_title：Molecular biology and evolution

authors： Pfeil BE,Brubaker CL,Craven LA,Crisp MD

更新日期：2004-07-01 00:00:00

abstract：:Protein interactions are central to most biological processes. We investigated the dynamics of emergence of the protein interaction network of Saccharomyces cerevisiae by mapping origins of proteins on an evolutionary tree. We demonstrate that evolutionary periods are characterized by distinct connectivity levels of t...

journal_title：Molecular biology and evolution

authors： Kunin V,Pereira-Leal JB,Ouzounis CA

更新日期：2004-07-01 00:00:00

abstract：:Positive Darwinian selection promotes fixations of advantageous mutations during gene evolution and is probably responsible for most adaptations. Detecting positive selection at the DNA sequence level is of substantial interest because such information provides significant insights into possible functional alterations...

journal_title：Molecular biology and evolution

authors： Zhang J

更新日期：2004-07-01 00:00:00

abstract：:Good phylogenetic trees are required to test hypotheses about evolutionary processes. We report four new avian mitochondrial genomes, which together with an improved method of phylogenetic analysis for vertebrate mt genomes give results for three questions in avian evolution. The new mt genomes are: magpie goose (Anse...

journal_title：Molecular biology and evolution

authors： Harrison GL,McLenachan PA,Phillips MJ,Slack KE,Cooper A,Penny D

更新日期：2004-06-01 00:00:00

abstract：:A common problem in molecular phylogenetics is choosing a model of DNA substitution that does a good job of explaining the DNA sequence alignment without introducing superfluous parameters. A number of methods have been used to choose among a small set of candidate substitution models, such as the likelihood ratio tes...

journal_title：Molecular biology and evolution

authors： Huelsenbeck JP,Larget B,Alfaro ME

更新日期：2004-06-01 00:00:00

abstract：:Alpha-defensins are a family of mammalian antimicrobial peptides that exhibit variable activity against a panel of microbes, including bacteria, fungi, and enveloped viruses. We have employed a maximum-likelihood approach to detect evidence of positive selection (adaptive evolution) in the evolution of these important...

journal_title：Molecular biology and evolution

authors： Lynn DJ,Lloyd AT,Fares MA,O'Farrelly C

更新日期：2004-05-01 00:00:00

abstract：:The mitochondrial genome has undergone radical changes in both the Chlorophyta and Streptophyta, yet little is known about the dynamics of mtDNA evolution in either of these lineages. In the Chlorophyta, which comprises four of the five recognized classes of green algae (Prasinophyceae, Trebouxiophyceae, Ulvophyceae, ...

journal_title：Molecular biology and evolution

authors： Pombert JF,Otis C,Lemieux C,Turmel M

更新日期：2004-05-01 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

abstract：:The human scavenger receptor class B type I (SR-BI and splice variant SR-BII) plays a central role in HDL cholesterol metabolism and represents a candidate gene for a number of related diseases. We examined the genetic diversity of its coding and flanking regions in a sample of 178 chromosomes from individuals of Euro...

journal_title：Molecular biology and evolution

authors： Le Jossec M,Wambach T,Labuda D,Sinnett D,Levy E

更新日期：2004-04-01 00:00:00

abstract：:The protein tyrosine phosphatase (PTP) family plays a central role in signal transduction pathways by controlling the phosphorylation state of serine, threonine, and tyrosine residues. PTPs can be divided into dual specificity phosphatases and the classical PTPs, which can comprise of one or two phosphatase domains. W...

journal_title：Molecular biology and evolution

authors： Pils B,Schultz J

更新日期：2004-04-01 00:00:00

abstract：:This study aims to unravel the biogeography of a model symbiont/host system by exploiting the prediction that a symbiont will leave a signature of infection on the host. Specifically, a global sample of 1,442 Drosophila simulans from 33 countries and 64 sampling localities was employed to infer the phylogeography of t...

journal_title：Molecular biology and evolution

authors： Ballard JW

更新日期：2004-03-01 00:00:00

abstract：:Due to its speed, the distance approach remains the best hope for building phylogenies on very large sets of taxa. Recently (R. Desper and O. Gascuel, J. Comp. Biol. 9:687-705, 2002), we introduced a new "balanced" minimum evolution (BME) principle, based on a branch length estimation scheme of Y. Pauplin (J. Mol. Evo...

journal_title：Molecular biology and evolution

authors： Desper R,Gascuel O

更新日期：2004-03-01 00:00:00

abstract：:We present Neighbor-Net, a distance based method for constructing phylogenetic networks that is based on the Neighbor-Joining (NJ) algorithm of Saitou and Nei. Neighbor-Net provides a snapshot of the data that can guide more detailed analysis. Unlike split decomposition, Neighbor-Net scales well and can quickly produc...

journal_title：Molecular biology and evolution

authors： Bryant D,Moulton V

更新日期：2004-02-01 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：:In this study, we used an empirical example based on 100 mitochondrial genomes from higher teleost fishes to compare the accuracy of parsimony-based jackknife values with Bayesian support values. Phylogenetic analyses of 366 partitions, using differential taxon and character sampling from the entire data matrix of 100...

journal_title：Molecular biology and evolution

authors： Simmons MP,Pickett KM,Miya M

更新日期：2004-01-01 00:00:00

abstract：:Several recent analyses have used quartet-based methods to assess the congruence among phylogenies derived for large sets of genes from prokaryotic genomes. The principal conclusion from these studies is that lateral gene transfer (LGT) has blurred prokaryotic phylogenies to such a degree that the darwinian scheme of ...

journal_title：Molecular biology and evolution

authors： Daubin V,Ochman H

更新日期：2004-01-01 00:00:00

abstract：:We present a method for pairwise Assessment of Nonfunctionalization Times (pANT) in processed pseudogenes. Contrary to existing methods for estimating nonfunctionalization times, pANT utilizes previously calculated probabilities of nucleotide substitution as explicit rate measurements, rather than assume that the subs...

journal_title：Molecular biology and evolution

authors： Fleishman SJ,Dagan T,Graur D

更新日期：2003-11-01 00:00:00

abstract：:Molluscs in general, and bivalves in particular, exhibit an extraordinary degree of mitochondrial gene order variation when compared with other metazoans. Two factors inhibiting our understanding the evolution of gene rearrangement in bivalves are inadequate taxonomic sampling and failure to examine gene order in a ph...

journal_title：Molecular biology and evolution

authors： Serb JM,Lydeard C

更新日期：2003-11-01 00:00:00

abstract：:The activation peptide of mammalian trypsinogens contains a highly conserved tetra-aspartate sequence (D19-D20-D21-D22) preceding the K23-I24 scissile peptide bond, which is hydrolyzed as the first step in the activation process. Here, we examined the evolution and function of trypsinogen activation peptides through i...

journal_title：Molecular biology and evolution

authors： Chen JM,Kukor Z,Le Maréchal C,Tóth M,Tsakiris L,Raguénès O,Férec C,Sahin-Tóth M

更新日期：2003-11-01 00:00:00

abstract：:The increased interest in asexual organisms calls for in-depth studies of asexual complexes that actively give rise to new clones. We present an extensive molecular study of the Otiorhynchus scaber (Coleoptera, Curculionidae) weevil system. Three forms have traditionally been recognized: diploid sexuals, triploid, and...

journal_title：Molecular biology and evolution

authors： Stenberg P,Lundmark M,Knutelski S,Saura A

更新日期：2003-10-01 00:00:00

abstract：:We have evaluated the molecular evolution of the chemokine receptor CCR5 in primates. The chemokine receptor CCR5 serves as a major co-receptor for human immunodeficiency virus/simian immunodeficiency virus (HIV/SIV) infection. Knowledge of evolution of the CCR5 molecule and selection on the CCR5 gene may shed light o...

journal_title：Molecular biology and evolution

authors： Zhang YW,Ryder OA,Zhang YP

更新日期：2003-10-01 00:00:00

abstract：:To gain insight into the evolution of the methionine biosynthesis pathway, in vivo complementation tests were performed. The substrate specificity of three enzymes that intrinsically use different homoserine-esterified substrates and have different sulfur assimilation pathways was examined: two cystathionine gamma-syn...

journal_title：Molecular biology and evolution

authors： Hacham Y,Gophna U,Amir R

更新日期：2003-09-01 00:00:00

abstract：:Directional evolution in microsatellites is the tendency for microsatellites either to increase or to decrease in size over time between populations. We analyzed 99 microsatellite loci in a sample of 193 maize plants representing the entire pre-Columbian range of this crop for evidence of directional evolution. We too...

journal_title：Molecular biology and evolution

authors： Vigouroux Y,Matsuoka Y,Doebley J

更新日期：2003-09-01 00:00:00

abstract：:Parasites sometimes expand their host range by acquiring a new host species. After a host change event, the selective regime acting on a given parasite gene may change as a result of host-specific adaptive alterations of protein functionality or host-specific immune-mediated selection. We present a codon-based model t...

journal_title：Molecular biology and evolution

authors： Forsberg R,Christiansen FB

更新日期：2003-08-01 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：:There is increasing evidence that X chromosomes have an unusual complement of genes, especially genes that have sex-specific expression. However, whereas in worm and fly the X chromosome has a dearth of male-specific genes, in mice genes that are uniquely expressed in spermatogonia are especially abundant on the X chr...

journal_title：Molecular biology and evolution

authors： Lercher MJ,Urrutia AO,Hurst LD

更新日期：2003-07-01 00:00:00