Abstract:
:Here, we address a much-debated topic: is there or is there not an organismal tree of gamma-proteobacteria that can be unambiguously inferred from a core of shared genes? We apply several recently developed analytical methods to this problem, for the first time. Our heat map analyses of P values and of bootstrap bipartitions show the presence of conflicting phylogenetic signals among these core genes. Our synthesis reconstruction suggests that at least 10% of these genes have been laterally transferred during the divergence of the gamma-proteobacteria, and that for most of the rest, there is too little phylogenetic signal to permit firm conclusions about the mode of inheritance. Although there is clearly a central tendency in this data set (it is far from random), lateral gene transfers cannot be ruled out. Instead of an organismal tree, we propose that these core genes could be used to define a more subtle and partially reticulated pattern of relationships.
journal_name
Mol Biol Evoljournal_title
Molecular biology and evolutionauthors
Susko E,Leigh J,Doolittle WF,Bapteste Edoi
10.1093/molbev/msj113subject
Has Abstractpub_date
2006-05-01 00:00:00pages
1019-30issue
5eissn
0737-4038issn
1537-1719pii
msj113journal_volume
23pub_type
杂志文章abstract::We report the complete sequence of a paralogous copy of elongation factor-1 alpha (EF-1 alpha) in the honeybee, Apis mellifera (Hymenoptera: Apidae). This copy differs from a previously described copy in the positions of five introns and in 25% of the nucleotide sites in the coding regions. The existence of two paralo...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a025920
更新日期:1998-03-01 00:00:00
abstract::That natural selection affects molecular evolution at synonymous sites in protein-coding sequences is well established and is thought to predominantly reflect selection for translational efficiency/accuracy mediated through codon bias. However, a recently developed maximum likelihood framework, when applied to 18 codi...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msm196
更新日期:2007-12-01 00:00:00
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journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/mst206
更新日期:2014-02-01 00:00:00
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journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msu326
更新日期:2015-03-01 00:00:00
abstract::Protein tyrosine phosphorylation is a key regulatory modification in metazoans, and the corresponding kinase enzymes have diversified dramatically. This diversification is correlated with a genome-wide reduction in protein tyrosine content, and it was recently suggested that this reduction was driven by selection to a...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msu284
更新日期:2015-01-01 00:00:00
abstract::To test whether gaps resulting from sequence alignment contain phylogenetic signal concordant with those of base substitutions, we analyzed the occurrence of indel mutations upon a well-resolved, substitution-based tree for three nuclear genes in bumble bees (Bombus, Apidae: Bombini). The regions analyzed were exon an...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msg007
更新日期:2003-01-01 00:00:00
abstract::Polyploidization events have occurred during the evolution of many fungi, plant, and animal species and are thought to contribute to speciation and tumorigenesis, however little is known about how ploidy level contributes to adaptation at the molecular level. Here we integrate whole genome sequencing, RNA expression a...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msx205
更新日期:2017-10-01 00:00:00
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journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a025902
更新日期:1998-12-01 00:00:00
abstract::Dinoflagellate chloroplast genes are unique in that each gene is on a separate minicircular chromosome. To understand the origin and evolution of this exceptional genomic organization we completely sequenced chloroplast psbA and 23S rRNA gene minicircles from four dinoflagellates: three closely related Heterocapsa spe...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a004104
更新日期:2002-04-01 00:00:00
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journal_title:Molecular biology and evolution
pub_type: 杂志文章
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更新日期:2018-05-01 00:00:00
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journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msw293
更新日期:2017-04-01 00:00:00
abstract::The nucleotide sequences of the 5'-flanking regions of the duplicated Amy genes in eight sibling species belonging to the melanogaster species subgroup are analyzed. In Drosophila melanogaster, a region of about 450 bp immediately upstream of the translation initiation site of the two paralogous genes (the proximal an...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a025617
更新日期:1996-04-01 00:00:00
abstract::Because they represent the earliest divergences of the Chlorophyta and include the smallest known eukaryotes (e.g., the coccoid Ostreococcus), the morphologically diverse unicellular green algae making up the Prasinophyceae are central to our understanding of the evolutionary patterns that accompanied the radiation of...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msn285
更新日期:2009-03-01 00:00:00
abstract::DNA cytosine methylation is central to many biological processes, including regulation of gene expression, cellular differentiation, and development. This DNA modification is conserved across animals, having been found in representatives of sponges, ctenophores, cnidarians, and bilaterians, and with very few known ins...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msaa214
更新日期:2021-01-23 00:00:00
abstract::We present QNet, a method for constructing split networks from weighted quartet trees. QNet can be viewed as a quartet analogue of the distance-based Neighbor-Net (NNet) method for network construction. Just as NNet, QNet works by agglomeratively computing a collection of circular weighted splits of the taxa set which...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msl180
更新日期:2007-02-01 00:00:00
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journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msm250
更新日期:2008-01-01 00:00:00
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journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msh194
更新日期:2004-09-01 00:00:00
abstract::Complex metazoan bodies require cell-to-cell communication for development, a process often mediated by signaling molecules binding to specific receptors. Relatively few signaling pathways have been recruited during evolution to build multicellular animals from unicellular zygotes. Of these few signaling pathways, one...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/mst222
更新日期:2014-02-01 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
pub_type: 杂志文章
doi:10.1093/molbev/msaa133
更新日期:2020-10-01 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
pub_type: 杂志文章
doi:10.1093/molbev/msp114
更新日期:2009-09-01 00:00:00
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journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msj070
更新日期:2006-03-01 00:00:00
abstract::A phylogenetic tree of a gene family of nicotinic acetylcholine receptor subunits was constructed using 84 nucleotide sequences of receptor subunits from 18 different species in order to elucidate the evolutionary origin of receptor subunits. The tree constructed showed that the common ancestor of all subunits may hav...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a025951
更新日期:1998-05-01 00:00:00
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journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a040111
更新日期:1994-03-01 00:00:00
abstract::When bacteria evolve resistance against a particular antibiotic, they may simultaneously gain increased sensitivity against a second one. Such collateral sensitivity may be exploited to develop novel, sustainable antibiotic treatment strategies aimed at containing the current, dramatic spread of drug resistance. To da...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msx158
更新日期:2017-09-01 00:00:00
abstract::Although there is substantial evidence that, in animals, male-inherited neutral DNA evolves at a higher rate than female-inherited DNA, the relative evolutionary rate of male- versus female-inherited DNA has not been investigated in plants. We compared the substitution rates at neutral sites of maternally and paternal...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a004151
更新日期:2002-06-01 00:00:00
abstract::The genomics era has expanded our knowledge about the diversity of the living world, yet harnessing high-throughput sequencing data to investigate alternative evolutionary trajectories, such as hybridization, is still challenging. Here we present sppIDer, a pipeline for the characterization of interspecies hybrids and...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msy166
更新日期:2018-11-01 00:00:00
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journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a040382
更新日期:1986-03-01 00:00:00
abstract::The elongation factor 1 alpha (EF-1 alpha) has become widely employed as a phylogenetic marker for studying eukaryotic evolution. However, a disturbing problem, the artifactual polyphyly of ciliates, is always observed. It has been suggested that the addition of new sequences will help to circumvent this problem. Thus...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a026105
更新日期:1999-02-01 00:00:00
abstract::Sequencing multiple copies of the ITS1 region revealed the coexistence of two or more haplotypes within the genome of Chorthippus parallelus. Using a PCR-RFLP approach, the ITS1 numbers and frequencies of haplotypes present in each of 40 individuals were investigated, revealing a consistent lack of homogeneity. For ea...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
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更新日期:2004-08-01 00:00:00
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journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msv045
更新日期:2015-06-01 00:00:00