A Working Model of the Deep Relationships of Diverse Modern Human Genetic Lineages Outside of Africa.

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：:The little fire ant, Wasmannia auropunctata, displays a peculiar breeding system polymorphism. Classical haplo-diploid sexual reproduction between reproductive individuals occurs in some populations, whereas, in others, queens and males reproduce clonally. Workers are produced sexually and are sterile in both clonal a...

journal_title：Molecular biology and evolution

authors： Rey O,Loiseau A,Facon B,Foucaud J,Orivel J,Cornuet JM,Robert S,Dobigny G,Delabie JH,Mariano Cdos S,Estoup A

更新日期：2011-09-01 00:00:00

abstract：:Inaccurate inference of positional homologies in multiple sequence alignments and systematic errors introduced by alignment heuristics obfuscate phylogenetic inference. Alignment masking, the elimination of phylogenetically uninformative or misleading sites from an alignment before phylogenetic analysis, is a common p...

journal_title：Molecular biology and evolution

authors： Rajan V

更新日期：2013-03-01 00:00:00

abstract：:Environmental or genomic changes during evolution can relax negative selection pressure on specific loci, permitting high frequency polymorphisms at previously conserved sites. Here, we jointly analyze population genomic and comparative genomic data to search for functional processes showing relaxed negative selection...

journal_title：Molecular biology and evolution

authors： Somel M,Wilson Sayres MA,Jordan G,Huerta-Sanchez E,Fumagalli M,Ferrer-Admetlla A,Nielsen R

更新日期：2013-08-01 00:00:00

abstract：:Although whole-organism aspects of life-history physiology are well studied and molecular information (e.g., transcript abundance) on life-history variation is accumulating rapidly, much less information is available on the biochemical (enzymological) basis of life-history adaptation. The present study investigated th...

journal_title：Molecular biology and evolution

authors： Schilder RJ,Zera AJ,Black C,Hoidal M,Wehrkamp C

更新日期：2011-12-01 00:00:00

abstract：:Assessing the influence of three-dimensional protein structure on sequence evolution is a difficult task, mainly because of the assumption of independence between sites required by probabilistic phylogenetic methods. Recently, models that include an explicit treatment of protein structure and site interdependencies ha...

journal_title：Molecular biology and evolution

authors： Kleinman CL,Rodrigue N,Lartillot N,Philippe H

更新日期：2010-07-01 00:00:00

abstract：:Whole-genome duplications (WGDs) have contributed to gene-repertoire enrichment in many eukaryotic lineages. However, most duplicated genes are eventually lost and it is still unclear why some duplicated genes are evolutionary successful whereas others quickly turn to pseudogenes. Here, we show that dosage constraints...

journal_title：Molecular biology and evolution

authors： Gout JF,Lynch M

更新日期：2015-08-01 00:00:00

abstract：:Discrepancies in phylogenetic trees of bacteria and archaea are often explained as lateral gene transfer events. However, such discrepancies may also be due to phylogenetic artifacts or orthology assignment problems. A first step that may help to resolve this dilemma is to estimate the extent of phylogenetic inconsist...

journal_title：Molecular biology and evolution

authors： Soria-Carrasco V,Castresana J

更新日期：2008-11-01 00:00:00

abstract：:Snake venom gene evolution has been studied intensively over the past several decades, yet most previous studies have lacked the context of complete snake genomes and the full context of gene expression across diverse snake tissues. We took a novel approach to studying snake venom evolution by leveraging the complete ...

journal_title：Molecular biology and evolution

authors： Reyes-Velasco J,Card DC,Andrew AL,Shaney KJ,Adams RH,Schield DR,Casewell NR,Mackessy SP,Castoe TA

更新日期：2015-01-01 00:00:00

abstract：:The selective pressure at the protein level is usually measured by the nonsynonymous/synonymous rate ratio (omega = dN/dS), with omega < 1, omega = 1, and omega > 1 indicating purifying (or negative) selection, neutral evolution, and diversifying (or positive) selection, respectively. The omega ratio is commonly calcu...

journal_title：Molecular biology and evolution

authors： Anisimova M,Bielawski JP,Yang Z

更新日期：2001-08-01 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：:As the relic of the ancient Champa Kingdom, the Cham people represent the major Austronesian speakers in Mainland Southeast Asia (MSEA) and their origin is evidently associated with the Austronesian diffusion in MSEA. Hitherto, hypotheses stemming mainly from linguistic and cultural viewpoints on the origin of the Cha...

journal_title：Molecular biology and evolution

authors： Peng MS,Quang HH,Dang KP,Trieu AV,Wang HW,Yao YG,Kong QP,Zhang YP

更新日期：2010-10-01 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：:The Mlc1 gene of Drosophila melanogaster encodes two MLC1 isoforms via developmentally regulated alternative pre-mRNA splicing. In larval muscle and tubular and abdominal muscles of adults, all of the six exons are included in the spliced mRNA, whereas, in the fibrillar indirect flight muscle of adult, exon 5 is exclu...

journal_title：Molecular biology and evolution

authors： Leicht BG,Lyckegaard EM,Benedict CM,Clark AG

更新日期：1993-07-01 00:00:00

abstract：:The authors of a recent manuscript in "Nature" claim to have discovered "universal trends" of amino acid gain and loss in protein evolution. Here, we show that this universal trend can be simply explained by a bias that is unavoidable with the 3-taxon trees used in the original analysis. We demonstrate that a rigorous...

journal_title：Molecular biology and evolution

authors： Goldstein RA,Pollock DD

更新日期：2006-07-01 00:00:00

abstract：:This paper discusses the optimization principle in phylogenetic analysis, in the case of distance data. We argue that the use of this principle cannot be called into question, except for computing time reasons. We show that the minimum-evolution criterion is not perfectly suited for distance data estimated from sequen...

journal_title：Molecular biology and evolution

authors： Gascuel O

更新日期：2000-03-01 00:00:00

abstract：:The mammalian family Talpidae (moles, shrew moles, desmans) is characterized by diverse ecomorphologies associated with terrestrial, semi-aquatic, semi-fossorial, fossorial, and aquatic-fossorial lifestyles. Prominent specializations involved with these different lifestyles, and the transitions between them, pose outs...

journal_title：Molecular biology and evolution

authors： He K,Shinohara A,Helgen KM,Springer MS,Jiang XL,Campbell KL

更新日期：2017-01-01 00:00:00

abstract：:Long noncoding RNAs (lncRNAs) do not code for proteins but function as RNAs. Because the functions of an RNA rely on either its sequence or secondary structure, lncRNAs should be folded at least as strongly as messenger RNAs (mRNAs), which serve as messengers for translation and are generally thought to lack secondary...

journal_title：Molecular biology and evolution

authors： Yang JR,Zhang J

更新日期：2015-04-01 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：: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：:Proteomic analyses of the nucleolus have revealed almost 700 functionally diverse proteins implicated in ribosome biogenesis, nucleolar assembly, and regulation of vital cellular processes. However, this nucleolar inventory has not unveiled a specific consensus motif necessary for nucleolar binding. The ribosomal prot...

journal_title：Molecular biology and evolution

authors： Kundu-Michalik S,Bisotti MA,Lipsius E,Bauche A,Kruppa A,Klokow T,Kammler G,Kruppa J

更新日期：2008-03-01 00:00:00

abstract：:A correspondence analysis of codon usage in Xenopus laevis revealed that the first axis is strongly correlated with the base composition at third codon positions. The second axis discriminates between putatively highly expressed genes and the other coding sequences, with expression levels being confirmed by the analys...

journal_title：Molecular biology and evolution

authors： Musto H,Cruveiller S,D'Onofrio G,Romero H,Bernardi G

更新日期：2001-09-01 00:00:00

abstract：:Amino acid substitution matrices describe the rates by which amino acids are replaced during evolution. In contrast to nucleotide or codon models, amino acid substitution matrices are in general parameterless and empirically estimated, probably because there is no obvious parametrization for amino acid substitutions. ...

journal_title：Molecular biology and evolution

authors： Zoller S,Schneider A

更新日期：2013-02-01 00:00:00

abstract：:Inferring past population dynamics over time from heterochronous molecular sequence data is often achieved using the Bayesian Skygrid model, a non-parametric coalescent model that estimates the effective population size over time. Available in BEAST, a cross-platform program for Bayesian analysis of molecular sequence...

journal_title：Molecular biology and evolution

authors： Hill V,Baele G

更新日期：2019-07-31 00:00:00

abstract：:The emergence of islands has been linked to spectacular radiations of diverse organisms. Although penguins spend much of their lives at sea, they rely on land for nesting, and a high proportion of extant species are endemic to geologically young islands. Islands may thus have been crucial to the evolutionary diversifi...

journal_title：Molecular biology and evolution

authors： Cole TL,Ksepka DT,Mitchell KJ,Tennyson AJD,Thomas DB,Pan H,Zhang G,Rawlence NJ,Wood JR,Bover P,Bouzat JL,Cooper A,Fiddaman SR,Hart T,Miller G,Ryan PG,Shepherd LD,Wilmshurst JM,Waters JM

更新日期：2019-04-01 00:00:00

abstract：:Disease response genes (DRGs) diverge under recurrent positive selection as a result of a molecular arms race between hosts and pathogens. Most of these studies were conducted in animals, and few defense genes have been shown to evolve adaptively in plants. To test for adaptation in the molecules mediating disease res...

journal_title：Molecular biology and evolution

authors： Zamora A,Sun Q,Hamblin MT,Aquadro CF,Kresovich S

更新日期：2009-09-01 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：: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：:Horizontal gene transfer (HGT) has been described as a common mechanism of transferring genetic material between prokaryotes, whereas genetic transfers from eukaryotes to prokaryotes have been rarely documented. Here we report a rare case of HGT in which plant expansin genes that code for plant cell-wall loosening pro...

journal_title：Molecular biology and evolution

authors： Nikolaidis N,Doran N,Cosgrove DJ

更新日期：2014-02-01 00:00:00

abstract：:IQ-TREE (http://www.iqtree.org, last accessed February 6, 2020) is a user-friendly and widely used software package for phylogenetic inference using maximum likelihood. Since the release of version 1 in 2014, we have continuously expanded IQ-TREE to integrate a plethora of new models of sequence evolution and efficien...

journal_title：Molecular biology and evolution

authors： Minh BQ,Schmidt HA,Chernomor O,Schrempf D,Woodhams MD,von Haeseler A,Lanfear R

更新日期：2020-05-01 00:00:00