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Reading the entrails of chickens: molecular timescales of evolution and the illusion of precision.
For almost a decade now, a team of molecular evolutionists has produced a plethora of seemingly precise molecular clock estimates for divergence events ranging from the speciation of cats and dogs toExpand
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Finding the missing honey bee genes: lessons learned from a genome upgrade
BackgroundThe first generation of genome sequence assemblies and annotations have had a significant impact upon our understanding of the biology of the sequenced species, the phylogeneticExpand
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On the Immortality of Television Sets: “Function” in the Human Genome According to the Evolution-Free Gospel of ENCODE
A recent slew of ENCyclopedia Of DNA Elements (ENCODE) Consortium publications, specifically the article signed by all Consortium members, put forward the idea that more than 80% of the human genomeExpand
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Minimal conditions for exonization of intronic sequences: 5' splice site formation in alu exons.
Alu exonization, which is an evolutionary pathway that creates primate-specific transcriptomic diversity, is a powerful tool for studying alternative-splicing regulation. Through bioinformaticExpand
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Incongruent expression profiles between human and mouse orthologous genes suggest widespread neutral evolution of transcription control.
Rapid rates of evolution can signify either a lack of selective constraint and the consequent accumulation of neutral alleles, or positive Darwinian selection driving the fixation of advantageousExpand
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A potentially novel overlapping gene in the genomes of Israeli acute paralysis virus and its relatives
The Israeli acute paralysis virus (IAPV) is a honeybee-infecting virus that was found to be associated with colony collapse disorder. The IAPV genome contains two genes encoding a structural and aExpand
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An Evolutionary Classification of Genomic Function
The pronouncements of the ENCODE Project Consortium regarding “junk DNA” exposed the need for an evolutionary classification of genomic elements according to their selected-effect function. In theExpand
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Same-strand overlapping genes in bacteria: compositional determinants of phase bias
BackgroundSame-strand overlapping genes may occur in frameshifts of one (phase 1) or two nucleotides (phase 2). In previous studies of bacterial genomes, long phase-1 overlaps were found to be moreExpand
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Estimates of Positive Darwinian Selection Are Inflated by Errors in Sequencing, Annotation, and Alignment
Published estimates of the proportion of positively selected genes (PSGs) in human vary over three orders of magnitude. In mammals, estimates of the proportion of PSGs cover an even wider range ofExpand
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