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Relative rates of nucleotide substitution at the rbc l locus of...

SummaryWe subjected 35 rbcL nucleotide sequences from monocotyledonous taxa to maximum likelihood relative rate tests and estimated relative differences in rates of nucleotide substitution between...

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Molecular Clocks and Nucleotide Substitution Rates in Higher Plants

AbstractIn the early 1960s, researchers noticed that the number of differences between amino acid sequences varied roughly linearly with the time of divergence between the species from which the amino...

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Evolution of genes and taxa: a primer

AbstractThe rapidly growing fields of molecular evolution and systematics have much to offer to molecular biology, but like any field have their own repertoire of terms and concepts. Homology, for...

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Evolution of genes and taxa: a primer

AbstractThe rapidly growing fields of molecular evolution and systematics have much to offer to molecular biology, but like any field have their own repertoire of terms and concepts. Homology, for...

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Plant Molecular Evolution

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Neutral and Nonneutral Mitochondrial Genetic Variation in Deep-Sea Clams from...

Abstract. Nucleotide sequences at two mitochondrial genes from 57 individuals representing eight species of deep-sea clams (Vesicomyidae) were examined for variation consistent with the neutral model...

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The Interaction of Protein Structure, Selection, and Recombination on the...

Abstract. Fimbrial adhesins allow bacteria to interact with and attach to their environment. The bacteria possibly benefit from these interactions, but all external structures including adhesins also...

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A Survey of the Molecular Evolutionary Dynamics of Twenty-Five Multigene...

Abstract. We surveyed the molecular evolutionary characteristics of 25 plant gene families, with the goal of better understanding general processes in plant gene family evolution. The survey was based...

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Transcription-related mutations and GC content drive variation in nucleotide...

AbstractBackgroundThere has been remarkably little study of nucleotide substitution rate variation among plant nuclear genes, in part because orthology is difficult to establish. Orthology is even more...

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A comparative computational analysis of nonautonomous Helitron elements...

AbstractBackgroundHelitrons are DNA transposable elements that are proposed to replicate via a rolling circle mechanism. Non-autonomous helitron elements have captured gene fragments from many genes in...

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The Contribution of Transposable Elements to Expressed Coding Sequence in...

AbstractThe goal of this study was to assess the extent to which transposable elements (TEs) have contributed to protein-coding regions in Arabidopsis thaliana. To do this, we first characterized the...

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The evolution of transposable elements in natural populations of...

AbstractBackgroundTransposable Elements (TEs) make up the majority of plant genomes, and thus understanding TE evolutionary dynamics is key to understanding plant genome evolution. Plant reproductive...

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Using Nextgen Sequencing to Investigate Genome Size Variation and...

AbstractTransposable element (TE) content explains a large part of Eukaryotic genome size variation. TE content is determined by transposition, removal and host responses, but the efficiency of these...

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Evolution of Escherichia coli rifampicin resistance in an antibiotic-free...

AbstractBackgroundBeneficial mutations play an essential role in bacterial adaptation, yet little is known about their fitness effects across genetic backgrounds and environments. One prominent example...

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The Reproducibility of Adaptation in the Light of Experimental Evolution with...

AbstractA key question in evolutionary biology is the reproducibility of adaptation. This question can now be quantitatively analyzed using experimental evolution coupled to whole genome sequencing...

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The phenotypic signature of adaptation to thermal stress in Escherichia coli

AbstractBackgroundIn the short-term, organisms acclimate to stress through phenotypic plasticity, but in the longer term they adapt to stress genetically. The mutations that accrue during adaptation...

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Considerations and complications of mapping small RNA high-throughput data to...

AbstractBackgroundHigh-throughput sequencing (HTS) has revolutionized the way in which epigenetic research is conducted. When coupled with fully-sequenced genomes, millions of small RNA (sRNA) reads...

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Evolutionary Genomics and the Domestication of Grapes

AbstractWe summarize aspects of the domestication of grapevines (Vitis vinifera ssp. sativa) from its wild ancestor (Vitis vinifera ssp. sylvestris) by focusing on the first three stages of the...

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Maize transposable elements contribute to long non-coding RNAs that are...

AbstractBackgroundSeveral studies have mined short-read RNA sequencing datasets to identify long non-coding RNAs (lncRNAs), and others have focused on the function of individual lncRNAs in abiotic...

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Genomic evidence for recurrent genetic admixture during the domestication of...

AbstractBackgroundOlive tree (Olea europaea L. subsp. europaea, Oleaceae) has been the most emblematic perennial crop for Mediterranean countries since its domestication around 6000 years ago in the...

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