The Evolution of Gene Expression Underlying Vision Loss in Cave Animals.

abstract：:It is well known that knocking out a gene in an organism often causes no phenotypic effect. One possible explanation is the existence of duplicate genes; that is, the effect of knocking out a gene is compensated by a duplicate copy. Another explanation is the existence of alternative pathways. In terms of metabolic pr...

journal_title：Molecular biology and evolution

authors： Hanada K,Sawada Y,Kuromori T,Klausnitzer R,Saito K,Toyoda T,Shinozaki K,Li WH,Hirai MY

更新日期：2011-01-01 00:00:00

abstract：:In this article, we address the issue of estimating the phylogenetic tree based on sequence data across a set of genes. Recognizing that the individual gene trees may not all share the same evolutionary history due to lateral gene transfer or differences in rates of evolution for instance, we develop a robust algorith...

journal_title：Molecular biology and evolution

authors： Xu X,Dunn KA,Field C

更新日期：2015-08-01 00:00:00

abstract：:The mitoribosome, as known from studies in model organisms, deviates considerably from its ancestor, the bacterial ribosome. Deviations include substantial reduction of the mitochondrial ribosomal RNA (mt-rRNA) structure and acquisition of numerous mitochondrion-specific (M) mitoribosomal proteins (mtRPs). A broadly a...

journal_title：Molecular biology and evolution

authors： Valach M,Alcazar JAG,Sarrasin M,Lang BF,Gray MW,Burger G

更新日期：2020-09-04 00:00:00

abstract：:During the course of a random sequencing project of the genome of the dimorphic yeast Yarrowia lipolytica, we have identified sequences that were repeated in the genome and that matched the reverse transcriptase (RT) sequence of non-long terminal repeat (non-LTR) retrotransposons. Extension of sequencing on each side ...

journal_title：Molecular biology and evolution

authors： Casaregola S,Neuvéglise C,Bon E,Gaillardin C

更新日期：2002-05-01 00:00:00

abstract：:In phylogenetic inference, an evolutionary model describes the substitution processes along each edge of a phylogenetic tree. Misspecification of the model has important implications for the analysis of phylogenetic data. Conventionally, however, the selection of a suitable evolutionary model is based on heuristics or...

journal_title：Molecular biology and evolution

authors： Kedzierska AM,Drton M,Guigó R,Casanellas M

更新日期：2012-03-01 00:00:00

abstract：:Understanding how pathogens acquire resistance to drugs is important for the design of treatment strategies, particularly for rapidly evolving viruses such as HIV-1. Drug treatment can exert strong selective pressures and sites within targeted genes that confer resistance frequently evolve far more rapidly than the ne...

journal_title：Molecular biology and evolution

authors： Seoighe C,Ketwaroo F,Pillay V,Scheffler K,Wood N,Duffet R,Zvelebil M,Martinson N,McIntyre J,Morris L,Hide W

更新日期：2007-04-01 00:00:00

abstract：:Diverging from the classic paradigm of random gene order in eukaryotes, gene proximity can be leveraged to systematically identify functionally related gene neighborhoods in eukaryotes, utilizing techniques pioneered in bacteria. Current methods of identifying gene neighborhoods typically rely on sequence similarity t...

journal_title：Molecular biology and evolution

authors： Foflonker F,Blaby-Haas CE

更新日期：2021-01-23 00:00:00

abstract：:The genomes of many vertebrates show a characteristic heterogeneous distribution of GC content, the so-called GC isochore structure. The origin of isochores has been explained via the mechanism of GC-biased gene conversion (gBGC). However, although the isochore structure is declining in many mammalian genomes, the het...

journal_title：Molecular biology and evolution

authors： Mugal CF,Arndt PF,Ellegren H

更新日期：2013-07-01 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：:The Environment for Tree Exploration (ETE) is a computational framework that simplifies the reconstruction, analysis, and visualization of phylogenetic trees and multiple sequence alignments. Here, we present ETE v3, featuring numerous improvements in the underlying library of methods, and providing a novel set of sta...

journal_title：Molecular biology and evolution

authors： Huerta-Cepas J,Serra F,Bork P

更新日期：2016-06-01 00:00:00

abstract：:Simple models of molecular evolution assume that sequences evolve by a Poisson process in which nucleotide or amino acid substitutions occur as rare independent events. In these models, the expected ratio of the variance to the mean of substitution counts equals 1, and substitution processes with a ratio greater than ...

journal_title：Molecular biology and evolution

authors： Bedford T,Hartl DL

更新日期：2008-08-01 00:00:00

abstract：:The functionality of long noncoding RNAs (lncRNAs) is disputed. In general, lncRNAs are under weak selective pressures, suggesting that the majority of lncRNAs may be nonfunctional. However, although some surveys showed negligible phenotypic effects upon lncRNA perturbation, key biological roles were demonstrated for ...

journal_title：Molecular biology and evolution

authors： Darbellay F,Necsulea A

更新日期：2020-01-01 00:00:00

abstract：:Mouse has emerged as the most common model organism in biomedicine. Here, we analyzed the tolerance to the loss-of-function (LoF) of selenoprotein genes, estimated from mouse knockouts and the frequency of LoF variants in humans. We found not only a general correspondence in tolerance (e.g., GPX1, GPX2) and intoleranc...

journal_title：Molecular biology and evolution

authors： Santesmasses D,Mariotti M,Gladyshev VN

更新日期：2020-02-01 00:00:00

abstract：:Despite the general assumption that site-specific mutation rates are independent of the local sequence context, a growing body of evidence suggests otherwise. To further examine context-dependent patterns of mutation, we amassed 5,645 spontaneous mutations in wild- type (WT) and mismatch-repair deficient (MMR(-)) muta...

journal_title：Molecular biology and evolution

authors： Sung W,Ackerman MS,Gout JF,Miller SF,Williams E,Foster PL,Lynch M

更新日期：2015-07-01 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：:Here, we sequenced the 5,419,609 bp circular genome of an Enterobacter aerogenes clinical isolate that killed a patient and was resistant to almost all current antibiotics (except gentamicin) commonly used to treat Enterobacterial infections, including colistin. Genomic and phylogenetic analyses explain the discrepanc...

journal_title：Molecular biology and evolution

authors： Diene SM,Merhej V,Henry M,El Filali A,Roux V,Robert C,Azza S,Gavory F,Barbe V,La Scola B,Raoult D,Rolain JM

更新日期：2013-02-01 00:00:00

abstract：:Microbial species play important roles in different environments and the production of high-quality genomes from metagenome data sets represents a major obstacle to understanding their ecological and evolutionary dynamics. Metagenome-Assembled Genomes Orchestra (MAGO) is a computational framework that integrates and s...

journal_title：Molecular biology and evolution

authors： Murovec B,Deutsch L,Stres B

更新日期：2020-02-01 00:00:00

abstract：:Here we use phylogenomics with expressed sequence tag (EST) data from the ecologically important coccolithophore-forming alga Emiliania huxleyi and the plastid-lacking cryptophyte Goniomonas cf. pacifica to establish their phylogenetic positions in the eukaryotic tree. Haptophytes and cryptophytes are members of the p...

journal_title：Molecular biology and evolution

authors： Hackett JD,Yoon HS,Li S,Reyes-Prieto A,Rümmele SE,Bhattacharya D

更新日期：2007-08-01 00:00:00

abstract：:We investigate the effect of purifying selection at multiple sites on both the shape of the genealogy and the distribution of mutations on the tree. We find that the primary effect of purifying selection on a genealogy is to shift the distribution of mutations on the tree, whereas the shape of the tree remains largely...

journal_title：Molecular biology and evolution

authors： Williamson S,Orive ME

更新日期：2002-08-01 00:00:00

abstract：:Genealogical trees have been constructed using mitochondrial ND5 gene sequences of 78 Damaster (s. str.) specimens from all over the Japanese Islands. Eight lineages (called races in this paper) have been recognized. The races are tightly linked to geography with sharp distribution boundaries between them. The races a...

journal_title：Molecular biology and evolution

authors： Su ZH,Tominaga O,Okamoto M,Osawa S

更新日期：1998-08-01 00:00:00

abstract：:It is well known that molecular data "saturates" with increasing sequence divergence (thereby losing phylogenetic information) and that in addition the accumulation of misleading information due to chance similarities or to systematic bias may accompany saturation as well. Exploratory data analysis methods that can qu...

journal_title：Molecular biology and evolution

authors： White WT,Hills SF,Gaddam R,Holland BR,Penny D

更新日期：2007-09-01 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 presence of four nuclear paralogs of a 380-bp segment of cytochrome b in callitrichine primates (marmosets and tamarins). The mitochondrial cytochrome b sequence and each nuclear paralog were obtained from several species, allowing multiple comparisons of rates and patterns of substitution both between m...

journal_title：Molecular biology and evolution

authors： Mundy NI,Pissinatti A,Woodruff DS

更新日期：2000-07-01 00:00:00

abstract：:Some genes have repeatedly been found to control diverse adaptations in a wide variety of organisms. Such gene reuse reveals not only the diversity of phenotypes these unique genes control but also the composition of developmental gene networks and the genetic routes available to and taken by organisms during adaptati...

journal_title：Molecular biology and evolution

authors： VanKuren NW,Massardo D,Nallu S,Kronforst MR

更新日期：2019-12-01 00:00:00

abstract：:Many methods exist for detecting introgression between nonsister species, but the most commonly used require either a single sequence from four or more taxa or multiple sequences from each of three taxa. Here, we present a test for introgression that uses only a single sequence from three taxa. This test, denoted D3, ...

journal_title：Molecular biology and evolution

authors： Hahn MW,Hibbins MS

更新日期：2019-12-01 00:00:00

abstract：:R2 non-long terminal repeat retrotransposable elements insert specifically into the 28S rRNA genes of a wide range of animals. These elements maintain long-term stable relationships with the host genome. By scoring the variation present at the 5' ends of individual R2 copies, lines of Drosophila simulans have been ide...

journal_title：Molecular biology and evolution

authors： Zhang X,Zhou J,Eickbush TH

更新日期：2008-01-01 00:00:00

abstract：:The question of multiple sequence alignment quality has received much attention from developers of alignment methods. Less forthcoming, however, are practical measures for addressing alignment quality issues in real life settings. Here, we present a simple methodology to help identify and quantify the uncertainties in...

journal_title：Molecular biology and evolution

authors： Landan G,Graur D

更新日期：2007-06-01 00:00:00

abstract：:The evolutionary expansion of CAG repeats in human triplet expansion disease genes is intriguing because of their deleterious phenotype. In the past, this expansion has been suggested to reflect a broad genomewide expansion of repeats, which would imply that mutational and evolutionary processes acting on repeats diff...

journal_title：Molecular biology and evolution

authors： Hancock JM,Worthey EA,Santibáñez-Koref MF

更新日期：2001-06-01 00:00:00

abstract：:Natural selection is expected to act strongly on immune system genes as hosts adapt to novel, diverse, and coevolving pathogens. Population genetic studies of host defense genes with parallel functions in model organisms have revealed distinct evolutionary histories among the different components-receptors, adaptors, ...

journal_title：Molecular biology and evolution

authors： Fornarino S,Laval G,Barreiro LB,Manry J,Vasseur E,Quintana-Murci L

更新日期：2011-11-01 00:00:00

abstract：:A large majority of bacterial genomes show strand asymmetry, such that G and T preferentially accumulate on the leading strand. The mechanisms are unknown, but cytosine deaminations are thought to play an important role. Here, we have examined DNA strand asymmetry in three strains of the aphid endosymbiont Buchnera ap...

journal_title：Molecular biology and evolution

authors： Klasson L,Andersson SG

更新日期：2006-05-01 00:00:00