Functional evolution of the yeast protein interaction network.

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：: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：:A central goal in biology is to determine the ways in which evolution repeats itself. One of the most remarkable examples in nature of convergent evolutionary novelty is animal venom. Across diverse animal phyla, various specialized organs and anatomical structures have evolved from disparate developmental tissues to ...

journal_title：Molecular biology and evolution

authors： Zancolli G,Casewell NR

更新日期：2020-10-01 00:00:00

abstract：:Interspecific hybridization is one of the major factors leading to phylogenetic incongruence among loci, but the knowledge is still limited about the potential of each locus to introgress between species. By directly sequencing three DNA regions: chloroplast DNAs (matK gene and trnL-F noncoding region), the nuclear ri...

journal_title：Molecular biology and evolution

authors： Okuyama Y,Fujii N,Wakabayashi M,Kawakita A,Ito M,Watanabe M,Murakami N,Kato M

更新日期：2005-02-01 00:00:00

abstract：:Estimation of evolutionary distances from coding sequences must take into account protein-level selection to avoid relative underestimation of longer evolutionary distances. Current modeling of selection via site-to-site rate heterogeneity generally neglects another aspect of selection, namely position-specific amino ...

journal_title：Molecular biology and evolution

authors： Halpern AL,Bruno WJ

更新日期：1998-07-01 00:00:00

abstract：:Silks are strong protein fibers produced by a broad array of spiders and insects. The vast majority of known silks are large, repetitive proteins assembled into extended beta-sheet structures. Honeybees, however, have found a radically different evolutionary solution to the need for a building material. The 4 fibrous ...

journal_title：Molecular biology and evolution

authors： Sutherland TD,Weisman S,Trueman HE,Sriskantha A,Trueman JW,Haritos VS

更新日期：2007-11-01 00:00:00

abstract：:To explain why informational genes (i.e., those involved in transcription, translation, and related processes) are less likely than housekeeping genes to be horizontally transferred, Jain and coworkers proposed the complexity hypothesis. The underlying idea is that informational genes belong to large, complex systems ...

journal_title：Molecular biology and evolution

authors： Aris-Brosou S

更新日期：2005-02-01 00:00:00

abstract：:The detection of selection, both positive and negative, acting on a DNA sequence or class of nucleotide sites requires comparison with a reference sequence that is unaffected by selection. In Drosophila, recent findings of widespread selective constraint, as well as adaptive evolution, in both coding and noncoding reg...

journal_title：Molecular biology and evolution

authors： Parsch J,Novozhilov S,Saminadin-Peter SS,Wong KM,Andolfatto P

更新日期：2010-06-01 00:00:00

abstract：:Sherpa population is an ethnic group living in south mountainside of Himalayas for hundreds of years. They are famous as extraordinary mountaineers and guides, considered as a good example for successful adaptation to low oxygen environment in Tibetan highlands. Mitochondrial DNA (mtDNA) variations might be important ...

journal_title：Molecular biology and evolution

authors： Kang L,Zheng HX,Chen F,Yan S,Liu K,Qin Z,Liu L,Zhao Z,Li L,Wang X,He Y,Jin L

更新日期：2013-12-01 00:00:00

abstract：:Recent results from large-scale genomic projects suggest that allele frequencies, which are highly relevant for medical purposes, differ considerably across different populations. The need for a detailed catalog of local variability motivated the whole-exome sequencing of 267 unrelated individuals, representative of t...

journal_title：Molecular biology and evolution

authors： Dopazo J,Amadoz A,Bleda M,Garcia-Alonso L,Alemán A,García-García F,Rodriguez JA,Daub JT,Muntané G,Rueda A,Vela-Boza A,López-Domingo FJ,Florido JP,Arce P,Ruiz-Ferrer M,Méndez-Vidal C,Arnold TE,Spleiss O,Alvarez-Tejado

更新日期：2016-05-01 00:00:00

abstract：:Naked lobose amoebae (gymnamoebae) are among the most abundant group of protists present in all aquatic and terrestrial biotopes. Yet, because of lack of informative morphological characters, the origin and evolutionary history of gymnamoebae are poorly known. The first molecular studies revealed multiple origins for ...

journal_title：Molecular biology and evolution

authors： Bolivar I,Fahrni JF,Smirnov A,Pawlowski J

更新日期：2001-12-01 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：:Maximum likelihood codon substitution models have proven useful for studying when and how protein function evolves, but they have recently been criticized on a number of fronts. The strengths and weaknesses of such methods must therefore be identified and improved upon. Here, using simulations, we show that the Clade ...

journal_title：Molecular biology and evolution

authors： Weadick CJ,Chang BS

更新日期：2012-05-01 00:00:00

abstract：:Next-generation sequencing opened up new possibilities in phylogenetics; however, choosing an appropriate method of sample preparation remains challenging. Here, we demonstrate that restriction-site-associated DNA sequencing (RAD-seq) generates useful data for phylogenomics. Analysis of our RAD library using current b...

journal_title：Molecular biology and evolution

authors： Cruaud A,Gautier M,Galan M,Foucaud J,Sauné L,Genson G,Dubois E,Nidelet S,Deuve T,Rasplus JY

更新日期：2014-05-01 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：: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：:Coevolutionary conflict among imprinted genes that influence traits such as offspring growth may arise when maternal and paternal genomes have different evolutionary optima. This conflict is expected in outcrossing taxa with multiple paternity, but not self-fertilizing taxa. MEDEA (MEA) is an imprinted plant gene that...

journal_title：Molecular biology and evolution

authors： Miyake T,Takebayashi N,Wolf DE

更新日期：2009-04-01 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：:Molecular systematists need increased access to nuclear genes. Highly conserved, low copy number protein-encoding nuclear genes have attractive features for phylogenetic inference but have heretofore been applied mostly to very ancient divergences. By virtue of their synonymous substitutions, such genes should contain...

journal_title：Molecular biology and evolution

authors： Cho S,Mitchell A,Regier JC,Mitter C,Poole RW,Friedlander TP,Zhao S

更新日期：1995-07-01 00:00:00

abstract：:Novel coronaviruses, including SARS-CoV-2, SARS, and MERS, often originate from recombination events. The mechanism of recombination in RNA viruses is template switching. Coronavirus transcription also involves template switching at specific regions, called transcriptional regulatory sequences (TRS). It is hypothesize...

journal_title：Molecular biology and evolution

authors： Yang Y,Yan W,Hall AB,Jiang X

更新日期：2020-11-04 00:00:00

abstract：:Geraniaceae plastid genomes (plastomes) have experienced a remarkable number of genomic changes. The plastomes of Erodium texanum, Geranium palmatum, and Monsonia speciosa were sequenced and compared with other rosids and the previously published Pelargonium hortorum plastome. Geraniaceae plastomes were found to be hi...

journal_title：Molecular biology and evolution

authors： Guisinger MM,Kuehl JV,Boore JL,Jansen RK

更新日期：2011-01-01 00:00:00

abstract：:Evolution of sequences mostly involves independent changes at different sites. However, substitutions at neighboring sites may co-occur as multinucleotide replacement events (MNRs). Here, we compare noncoding sequences of several species of primates, and of three species of Drosophila fruit flies, in a phylogenetic an...

journal_title：Molecular biology and evolution

authors： Terekhanova NV,Bazykin GA,Neverov A,Kondrashov AS,Seplyarskiy VB

更新日期：2013-06-01 00:00:00

abstract：:Sequences of 1,862 chromosomally encoded Escherichia coli K12 proteins were examined to identify genes likely to have arisen by duplication of genes in an ancestral chromosome. The criteria for sequence relatedness were an alignment of at least 100 amino acid residues and a PAM distance (number of accepted point mutat...

journal_title：Molecular biology and evolution

authors： Labedan B,Riley M

更新日期：1995-11-01 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：:Phylogenomic analyses have revealed several important metazoan clades, such as the Ecdysozoa and the Lophotrochozoa. However, the phylogenetic positions of a few taxa, such as ctenophores, chaetognaths, acoelomorphs, and Xenoturbella, remain contentious. Thus, the findings of qualitative markers or "rare genomic chang...

journal_title：Molecular biology and evolution

authors： de Mendoza A,Ruiz-Trillo I

更新日期：2011-11-01 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：:Amastin is a transmembrane glycoprotein found on the cell surfaces of trypanosomatid parasites. Encoded by a large, diverse gene family, amastin was initially described from the intracellular, amastigote stage of Trypanosoma cruzi and Leishmania donovani. Genome sequences have subsequently shown that the amastin reper...

journal_title：Molecular biology and evolution

authors： Jackson AP

更新日期：2010-01-01 00:00:00

abstract：:Length variation due to tandem repeats is now recognized as a common feature of animal mitochondrial DNA; however, the evolutionary dynamics of repeated sequences are not well understood. Using phylogenetic analysis, predictions of three models of repeat evolution were tested for arrays of 260-bp repeats in the cyprin...

journal_title：Molecular biology and evolution

authors： Broughton RE,Dowling TE

更新日期：1997-12-01 00:00:00

abstract：:The temporal change of phenotypes during the adaptive process remains largely unexplored, as do the genetic changes that affect these phenotypic changes. Here we focused on three mutations that rose to high frequency in the early stages of adaptation within 12 Escherichia coli populations subjected to thermal stress (...

journal_title：Molecular biology and evolution

authors： Rodríguez-Verdugo A,Tenaillon O,Gaut BS

更新日期：2016-01-01 00:00:00

abstract：:Influenza A viruses from wild aquatic birds, their natural reservoir species, are thought to have reached a form of stasis, characterized by low rates of evolutionary change. We tested this hypothesis by estimating rates of nucleotide substitution in a diverse array of avian influenza viruses (AIV) and allowing for ra...

journal_title：Molecular biology and evolution

authors： Chen R,Holmes EC

更新日期：2006-12-01 00:00:00