Evolutionary relationships of apusomonads inferred from taxon-rich analyses of 6 nuclear encoded genes.

abstract：:Genes encoding DNA replication proteins have been frequently exchanged between cells and mobile elements, such as viruses or plasmids. This raises potential problems to reconstruct their history. Here, we combine phylogenetic and genomic context analyses to study the evolution of the replicative minichromosome mainten...

journal_title：Molecular biology and evolution

authors： Krupovic M,Gribaldo S,Bamford DH,Forterre P

更新日期：2010-12-01 00:00:00

abstract：:Effective population size is fundamental in population genetics and characterizes genetic diversity. To infer past population dynamics from molecular sequence data, coalescent-based models have been developed for Bayesian nonparametric estimation of effective population size over time. Among the most successful is a G...

journal_title：Molecular biology and evolution

authors： Gill MS,Lemey P,Faria NR,Rambaut A,Shapiro B,Suchard MA

更新日期：2013-03-01 00:00:00

abstract：:Selection on phenotypes may cause genetic change. To understand the relationship between phenotype and gene expression from an evolutionary viewpoint, it is important to study the concordance between gene expression and profiles of phenotypes. In this study, we use a novel method of clustering to identify genes whose ...

journal_title：Molecular biology and evolution

authors： Qu Y,Xu S

更新日期：2006-08-01 00:00:00

abstract：:Unlike mammals, fish are able to regenerate axons in their central nervous system. This difference has been partly attributed to the loss/acquisition of inhibitory proteins during evolution. Nogo-A--the longest isoform of the reticulon4 (rtn4) gene product--is commonly found in mammalian myelin where it acts as a pote...

journal_title：Molecular biology and evolution

authors： Shypitsyna A,Málaga-Trillo E,Reuter A,Stuermer CA

更新日期：2011-04-01 00:00:00

abstract：:Alcohol dehydrogenase genes were amplified by PCR, cloned, and sequenced from 11 putative nonhybrid species of the angiosperm genus Paeonia. Sequences of five exons and six intron regions of the Adh gene were used to reconstruct the phylogeny of these species. Two paralogous genes, Adh1A, and Adh2, were found; an addi...

journal_title：Molecular biology and evolution

authors： Sang T,Donoghue MJ,Zhang D

更新日期：1997-10-01 00:00:00

abstract：:Purifying selection can substantially alter patterns of molecular evolution. Its main effect is to reduce overall levels of genetic variation, leading to a reduced effective population size. However, it also distorts genealogies relative to neutral expectations. A structured coalescent method has been used to describe...

journal_title：Molecular biology and evolution

authors： Nicolaisen LE,Desai MM

更新日期：2012-11-01 00:00:00

abstract：:It is widely accepted that evolutionary changes in conserved developmental signaling pathways play an important role in morphological evolution. However, few in silico studies were interested in tracking such changes in a signaling pathway. The Ectodysplasin (EDA) pathway provides an opportunity to fill this gap becau...

journal_title：Molecular biology and evolution

authors： Pantalacci S,Chaumot A,Benoît G,Sadier A,Delsuc F,Douzery EJ,Laudet V

更新日期：2008-05-01 00:00:00

abstract：:We have used analysis of variance to partition the variation in synonymous and amino acid substitution rates between three effects (gene, lineage, and a gene-by-lineage interaction) in mammalian nuclear and mitochondrial genes. We find that gene effects are stronger for amino acid substitution rates than for synonymou...

journal_title：Molecular biology and evolution

authors： Smith NG,Eyre-Walker A

更新日期：2003-01-01 00:00:00

abstract：:Most of the well-characterized mitochondrial genomes from diverse green algal lineages are circular mapping DNA molecules; however, Chlamydomonas reinhardtii has a linear 15.8 kb unit mitochondrial genome with 580 or 581 bp inverted repeat ends. In mitochondrial-enriched fractions prepared from Polytomella parva (=P. ...

journal_title：Molecular biology and evolution

authors： Fan J,Lee RW

更新日期：2002-07-01 00:00:00

abstract：:Bacterial plasmids substantially contribute to the rapid spread of antibiotic resistance, which is a crisis in healthcare today. Coevolution of plasmids and their hosts promotes this spread of resistance by ameliorating the cost of plasmid carriage. However, our knowledge of plasmid-bacteria coevolution is solely base...

journal_title：Molecular biology and evolution

authors： Stalder T,Cornwell B,Lacroix J,Kohler B,Dixon S,Yano H,Kerr B,Forney LJ,Top EM

更新日期：2020-06-01 00:00:00

abstract：:A labeled gene tree topology that is more probable than the labeled gene tree topology matching a species tree is called "anomalous." Species trees that can generate such anomalous gene trees are said to be in the "anomaly zone." Here, probabilities of "unranked" and "ranked" gene tree topologies under the multispecie...

journal_title：Molecular biology and evolution

authors： Kim A,Rosenberg NA,Degnan JH

更新日期：2020-05-01 00:00:00

abstract：:The heat shock protein (Hsp) sequences, because of their ubiquity and high degree of conservation, provide useful models for phylogenetic analysis. In this paper I have carried out a global alignment of all available sequences (a total of 31) for the 90-kD heat shock protein (Hsp90) family. The minimum amino acid iden...

journal_title：Molecular biology and evolution

authors： Gupta RS

更新日期：1995-11-01 00:00:00

abstract：:It is known that the effective population size (Ne) and the mutation rate (u) vary across the genome. Here, we show that ignoring this heterogeneity may lead to biased estimates of past demography. To solve the problem, we develop new methods for jointly inferring past changes in population size and detecting variatio...

journal_title：Molecular biology and evolution

authors： Zeng K,Jackson BC,Barton HJ

更新日期：2019-02-01 00:00:00

abstract：:Quercus petraea and Quercus robur are two closely related oak species that frequently hybridize. We sequenced 70 clones containing the 5.8S and ITS2 regions of ribosomal DNA (rDNA) from these two species and did not detect a species-specific difference. Surprisingly, three divergent (up to 12.6%) rDNA families were id...

journal_title：Molecular biology and evolution

authors： Muir G,Fleming CC,Schlötterer C

更新日期：2001-02-01 00:00:00

abstract：:The human Y chromosome consists of ampliconic genes, which are located in palindromes and undergo frequent gene conversion, and single-copy genes including the primary sex-determining locus, SRY. Here, we demonstrate that SRY is duplicated in a large palindrome in the European rabbit (Oryctolagus cuniculus). Furthermo...

journal_title：Molecular biology and evolution

authors： Geraldes A,Rambo T,Wing RA,Ferrand N,Nachman MW

更新日期：2010-11-01 00:00:00

abstract：:Heterotachy is a general term to describe positions that evolve at different rates in different lineages. Heterotachy also can generally be viewed as multivariate rates-across-sites variation, which can be described as randomly drawing rates (or branch lengths) from a multivariate distribution for each branch at each ...

journal_title：Molecular biology and evolution

authors： Wu J,Susko E

更新日期：2011-05-01 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：:The retroid family consists of all genetic elements that encode a potential reverse transcriptase (RT). Members of this family include a diversity of eukaryotic genetic elements (viruses, transposable elements, organelle introns, and plasmids) and the retrons of prokaryotes. Some retroid elements have, in addition to ...

journal_title：Molecular biology and evolution

authors： McClure MA

更新日期：1991-11-01 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：:A simple model for the evolution of the rate of molecular evolution is presented. With a Bayesian approach, this model can serve as the basis for estimating dates of important evolutionary events even in the absence of the assumption of constant rates among evolutionary lineages. The method can be used in conjunction ...

journal_title：Molecular biology and evolution

authors： Thorne JL,Kishino H,Painter IS

更新日期：1998-12-01 00:00:00

abstract：:The third chromosome of Drosophila pseudoobscura is polymorphic for numerous gene arrangements that form classical clines in North America. The polytene salivary chromosomes isolated from natural populations revealed changes in gene order that allowed the different gene arrangements to be linked together by paracentri...

journal_title：Molecular biology and evolution

authors： Wallace AG,Detweiler D,Schaeffer SW

更新日期：2011-08-01 00:00:00

abstract：:In a striking contrast, matK is one of the most rapidly evolving plastid genes and also one of the few plastid genes to be retained in all nonphotosynthetic plants examined to date. DNA sequences of this region were obtained from photosynthetic and nonphotosynthetic plants of Orobanchaceae and their relatives. The res...

journal_title：Molecular biology and evolution

authors： Young ND,dePamphilis CW

更新日期：2000-12-01 00:00:00

abstract：:The phylogenetic position of the Pedetidae, represented by a single species Pedetes capensis, is controversial, reflecting in part the retention of both Hystricomorphous and Sciurognathous characteristics in this rodent. In an attempt to clarify the species evolutionary relationships, mtDNA gene sequences from 10 rode...

journal_title：Molecular biology and evolution

authors： Matthee CA,Robinson TJ

更新日期：1997-01-01 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：:C repeats constitute the predominant family of short interspersed repeats (SINEs) in the rabbit genome. Determination of the nucleotide sequence 5' to rabbit zeta-globin genes reveals clusters of C repeats, and analysis of these and other sequenced regions of rabbit chromosomes shows that the C repeats have a strong t...

journal_title：Molecular biology and evolution

authors： Krane DE,Clark AG,Cheng JF,Hardison RC

更新日期：1991-01-01 00:00:00

abstract：:This study describes the distribution of hobo-hybridizing sequences in the genus Drosophila. Southern blot analysis of 134 species revealed that hobo sequences are limited to the melanogaster and montium subgroups of the melanogaster-species group. Of the hobo-bearing species, only D. melanogaster and two of its sibli...

journal_title：Molecular biology and evolution

authors： Daniels SB,Chovnick A,Boussy IA

更新日期：1990-11-01 00:00:00

abstract：:We report the genomic organization and deduced protein sequence of a cephalochordate member of the Otx homeobox gene family (AmphiOtx) and show its probable single-copy state in the genome. We also present molecular phylogenetic analysis indicating that there was single ancestral Otx gene in the first chordates which ...

journal_title：Molecular biology and evolution

authors： Williams NA,Holland PW

更新日期：1998-05-01 00:00:00

abstract：:Random genetic drift, or stochastic change in gene frequency, is a fundamental evolutionary force that is usually defined within the ideal Wright-Fisher (WF) population. However, as the theory is increasingly applied to populations that deviate strongly from the ideal model, a paradox of random drift has emerged. When...

journal_title：Molecular biology and evolution

authors： Chen Y,Tong D,Wu CI

更新日期：2017-08-01 00:00:00

abstract：:This review explores features of the origin and evolution of colicins in Escherichia coli. First, the evolutionary relationships of 16 colicin and colicin-related proteins are inferred from amino acid and DNA sequence comparisons. These comparisons are employed to detail the evolutionary mechanisms involved in the ori...

journal_title：Molecular biology and evolution

authors： Riley MA

更新日期：1993-11-01 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