Comparative Transcriptomics Analyses across Species, Organs, and Developmental Stages Reveal Functionally Constrained lncRNAs.

abstract：:As human populations dispersed throughout the world, they were subjected to new selective forces, which must have led to local adaptation via natural selection and hence altered patterns of genetic variation. Yet, there are very few examples known in which such local selection has clearly influenced human genetic vari...

journal_title：Molecular biology and evolution

authors： Kayser M,Brauer S,Stoneking M

更新日期：2003-06-01 00:00:00

abstract：:A long-standing enigma concerns the geographic and ecological origins of the intensively studied vinegar fly, Drosophila melanogaster. This globally distributed human commensal is thought to originate from sub-Saharan Africa, yet until recently, it had never been reported from undisturbed wilderness environments that ...

journal_title：Molecular biology and evolution

authors： Sprengelmeyer QD,Mansourian S,Lange JD,Matute DR,Cooper BS,Jirle EV,Stensmyr MC,Pool JE

更新日期：2020-03-01 00:00:00

abstract：:With growing amounts of genome data and constant improvement of models of molecular evolution, phylogenetic reconstruction became more reliable. However, our knowledge of the real process of molecular evolution is still limited. When enough large-sized data sets are analyzed, any subtle biases in statistical models ca...

journal_title：Molecular biology and evolution

authors： Kitazoe Y,Kishino H,Okabayashi T,Watabe T,Nakajima N,Okuhara Y,Kurihara Y

更新日期：2005-03-01 00:00:00

abstract：:Amino acids interact with each other, especially with neighboring amino acids, to generate protein structures. We studied the pattern of association and repulsion of amino acids based on 24,748 protein-coding genes from human, 11,321 from mouse, and 15,028 from Escherichia coli, and documented the pattern of neighbor ...

journal_title：Molecular biology and evolution

authors： Xia X,Xie Z

更新日期：2002-01-01 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：:The use of parameter-rich substitution models in molecular phylogenetics has been criticized on the basis that these models can cause a reduction both in accuracy and in the ability to discriminate among competing topologies. We have explored the relationship between nucleotide substitution model complexity and nonpar...

journal_title：Molecular biology and evolution

authors： Buckley TR,Cunningham CW

更新日期：2002-04-01 00:00:00

abstract：:Frequent positive selection is a hallmark of genes involved in the adaptive immune system of vertebrates, but the incidence of positive selection for genes underlying innate immunity in vertebrates has not been well studied. The toll-like receptors (TLRs) of the innate immune system represent the first line of defense...

journal_title：Molecular biology and evolution

authors： Wlasiuk G,Nachman MW

更新日期：2010-09-01 00:00:00

abstract：:Positive selection sites (PSSs), a class of amino acid sites with an excess of nonsynonymous to synonymous substitutions, are indicators of adaptive molecular evolution and have been detected in many protein families involved in a diversity of biological processes by statistical approaches. However, few studies are co...

journal_title：Molecular biology and evolution

authors： Zhu L,Peigneur S,Gao B,Zhang S,Tytgat J,Zhu S

更新日期：2016-08-01 00:00:00

abstract：:Direct sequencing of the mitochondrial displacement loop (D-loop) of shrews (genus Sorex) for the region between the tRNA(Pro) and the conserved sequence block-F revealed variable numbers of 79-bp tandem repeats. These repeats were found in all 19 individuals sequenced, representing three subspecies and one closely re...

journal_title：Molecular biology and evolution

authors： Stewart DT,Baker AJ

更新日期：1994-01-01 00:00:00

abstract：:The number of subunits of RNA polymerases (RNAPs) increases during evolution from 5 in eubacteria to 12 in archaea. In eukaryotes, which have at least three RNAPs, the number of subunits has expanded from 12 in RNA polymerase II (RNAPII) to 14 in RNA polymerase I (RNAPI) and to 17 in RNA polymerase III (RNAPIII). It w...

journal_title：Molecular biology and evolution

authors： Carter R,Drouin G

更新日期：2010-05-01 00:00:00

abstract：:Malaria is a deadly disease that causes nearly one million deaths each year. To develop methods to control and eradicate malaria, it is important to understand the genetic basis of Plasmodium falciparum adaptations to antimalarial treatments and the human immune system while taking into account its demographic history...

journal_title：Molecular biology and evolution

authors： Chang HH,Park DJ,Galinsky KJ,Schaffner SF,Ndiaye D,Ndir O,Mboup S,Wiegand RC,Volkman SK,Sabeti PC,Wirth DF,Neafsey DE,Hartl DL

更新日期：2012-11-01 00:00:00

abstract：:Several authors have postulated that genetic divergence between populations could result in genomic incompatibilities that would cause an increase in transposition in their hybrids, producing secondary effects such as sterility and therefore starting a speciation process. It has been demonstrated that transposition la...

journal_title：Molecular biology and evolution

authors： Labrador M,Farré M,Utzet F,Fontdevila A

更新日期：1999-07-01 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：:We have followed, in glucose-limited chemostats, the evolution of natural isolates of Escherichia coli possessing maximal growth rates of 0.48-1.43 doublings/h. Under these conditions a rapid-growth phenotype similar to that of standard laboratory wild-type strains was selected so that after 280 generations all of the...

journal_title：Molecular biology and evolution

authors： Mikkola R,Kurland CG

更新日期：1992-05-01 00:00:00

abstract：:Negative genetic regulators of phenotypic heterogeneity, or phenotypic capacitors/stabilizers, elevate population-average fitness by limiting deviation from the optimal phenotype and increase the efficacy of natural selection by enhancing the phenotypic differences among genotypes. Stabilizers can presumably be switch...

journal_title：Molecular biology and evolution

authors： Mo N,Zhang X,Shi W,Yu G,Chen X,Yang JR

更新日期：2020-12-23 00:00:00

abstract：:Whole genome duplications (WGDs) have been hypothesized to be responsible for major transitions in evolution. However, the effects of WGD and subsequent gene loss on cellular behavior and metabolism are still poorly understood. Here we develop a genome scale evolutionary model to study the dynamics of gene loss and me...

journal_title：Molecular biology and evolution

authors： van Hoek MJ,Hogeweg P

更新日期：2009-11-01 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：:Past analyses of the genome of the yeast Saccharomyces cerevisiae have revealed substantial regional variation in G+C content. Important questions remain, though, as to the origin, nature, significance, and generality of this variation. We conducted an extensive analysis of the yeast genome to try to answer these ques...

journal_title：Molecular biology and evolution

authors： Bradnam KR,Seoighe C,Sharp PM,Wolfe KH

更新日期：1999-05-01 00:00:00

abstract：:The MIKC MADS-box gene family has been shaped by extensive gene duplications giving rise to subfamilies of genes with distinct functions and expression patterns. However, within these subfamilies the functional assignment is not that clear-cut, and considerable functional redundancy exists. One way to investigate the ...

journal_title：Molecular biology and evolution

authors： De Bodt S,Theissen G,Van de Peer Y

更新日期：2006-06-01 00:00:00

abstract：:The noncoding-DNA content of organelle and nuclear genomes can vary immensely. Both adaptive and nonadaptive explanations for this variation have been proposed. This study addresses a nonadaptive explanation called the mutational-hazard hypothesis and applies it to the mitochondrial, plastid, and nuclear genomes of th...

journal_title：Molecular biology and evolution

authors： Smith DR,Lee RW

更新日期：2010-10-01 00:00:00

abstract：:The plant pathogen Phytophthora infestans emerged in Europe in 1845, triggering the Irish potato famine and massive European potato crop losses that continued until effective fungicides were widely employed in the 20th century. Today the pathogen is ubiquitous, with more aggressive and virulent strains surfacing in re...

journal_title：Molecular biology and evolution

authors： Martin MD,Ho SY,Wales N,Ristaino JB,Gilbert MT

更新日期：2014-06-01 00:00:00

abstract：:The ancestral homeland of Australian dingoes and Pacific dogs is proposed to be in South China. However, the location and timing of their dispersal and relationship to dog domestication is unclear. Here, we sequenced 7,000- to 2,000-year-old complete mitochondrial DNA (mtDNA) genomes of 27 ancient canids (one gray wol...

journal_title：Molecular biology and evolution

authors： Zhang M,Sun G,Ren L,Yuan H,Dong G,Zhang L,Liu F,Cao P,Ko AM,Yang MA,Hu S,Wang GD,Fu Q

更新日期：2020-05-01 00:00:00

abstract：:Gene duplication is a major driving force in genome evolution. Here, we explore the nature and origin of the POT1 gene duplication in Arabidopsis thaliana. Protection of Telomeres (POT1) is a conserved multifunctional protein that modulates telomerase activity and its engagement with telomeres. Arabidopsis thaliana en...

journal_title：Molecular biology and evolution

authors： Beilstein MA,Renfrew KB,Song X,Shakirov EV,Zanis MJ,Shippen DE

更新日期：2015-05-01 00:00:00

abstract：:Unraveling how regulatory divergence contributes to species differences and adaptation requires identifying functional variants from among millions of genetic differences. Analysis of allelic imbalance (AI) reveals functional genetic differences in cis regulation and has demonstrated differences in cis regulation with...

journal_title：Molecular biology and evolution

authors： Graze RM,Novelo LL,Amin V,Fear JM,Casella G,Nuzhdin SV,McIntyre LM

更新日期：2012-06-01 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：:Phenotypic evolution may occur either through alterations to the structure of protein-coding genes or their expression. Evidence for which of these two mechanisms more commonly contribute to the evolution of a phenotype can be garnered from examples of parallel and convergent evolution. The visual system of East Afric...

journal_title：Molecular biology and evolution

authors： O'Quin KE,Hofmann CM,Hofmann HA,Carleton KL

更新日期：2010-12-01 00:00:00

abstract：:We carried out an in silico analysis of the complete genome sequences of 14 species, including eukaryotes, prokaryotes, and archaea, to investigate the proportion of amplified fragment length polymorphism bands that are homoplasious for the different species, as well as the distribution of fragment lengths. We investi...

journal_title：Molecular biology and evolution

authors： Caballero A,Quesada H

更新日期：2010-05-01 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：:Numerous studies have used indices of genetic distance between species to reconstruct evolutionary relationships and to estimate divergence time. However, the empirical relationship between molecular-based indices of genetic divergence and divergence time based on the fossil record is poorly known. To date, the result...

journal_title：Molecular biology and evolution

authors： Wayne RK,Van Valkenburgh B,O'Brien SJ

更新日期：1991-05-01 00:00:00

abstract：:The cellobiose catabolic system of Escherichia coli K12 is being used to study the role of cryptic genes in evolution of new functions. Escherichia coli does not use beta-glucoside sugars; however, mutations in several loci can activate the cryptic bgl operon and permit growth on the beta-glucoside sugars arbutin and ...

journal_title：Molecular biology and evolution

authors： Kricker M,Hall BG

更新日期：1984-02-01 00:00:00