Brandon S. Gaut

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As population structure can result in spurious associations, it has constrained the use of association studies in human and plant genetics. Association mapping, however, holds great promise if true signals of functional association can be separated from the vast number of false signals generated by population structure. We have developed a unified(More)
A number of studies have noted that nucleotide substitution rates at the chloroplast-encoded rbcL locus violate the molecular clock principle. Substitution rate variation at this plastid gene is particularly pronounced between palms and grasses; for example, a previous study estimated that substitution rates in rbcL sequences are approximately 5-fold faster(More)
Retrotransposons, transposable elements related to animal retroviruses, are found in all eukaryotes investigated and make up the majority of many plant genomes. Their ubiquity points to their importance, especially in their contribution to the large-scale structure of complex genomes. The nature and frequency of retro-element appearance, activation and(More)
We measured sequence diversity in 21 loci distributed along chromosome 1 of maize (Zea mays ssp. mays L.). For each locus, we sequenced a common sample of 25 individuals representing 16 exotic landraces and nine U.S. inbred lines. The data indicated that maize has an average of one single nucleotide polymorphism (SNP) every 104 bp between two randomly(More)
It has long been suspected that maize is the product of an historical tetraploid event. Several observations support this possibility, including the fact that the maize genome contains duplicated chromosomal segments with colinear gene arrangements. Some of the genes from these duplicated segments have been sequenced. In this study, we examine the pattern(More)
Domestication promotes rapid phenotypic evolution through artificial selection. We investigated the genetic history by which the wild grass teosinte (Zea mays ssp. parviglumis) was domesticated into modern maize (Z. mays ssp. mays). Analysis of single-nucleotide polymorphisms in 774 genes indicates that 2 to 4% of these genes experienced artificial(More)
A model of DNA sequence evolution applicable to coding regions is presented. This represents the first evolutionary model that accounts for dependencies among nucleotides within a codon. The model uses the codon, as opposed to the nucleotide, as the unit of evolution, and is parameterized in terms of synonymous and nonsynonymous nucleotide substitution(More)
We report the 207-Mb genome sequence of the North American Arabidopsis lyrata strain MN47 based on 8.3× dideoxy sequence coverage. We predict 32,670 genes in this outcrossing species compared to the 27,025 genes in the selfing species Arabidopsis thaliana. The much smaller 125-Mb genome of A. thaliana, which diverged from A. lyrata 10 million years ago,(More)
The domestication of maize (Zea mays ssp. mays) from its wild ancestor (Zea mays ssp. parviglumis) led to a loss of genetic diversity both through a population bottleneck and through directional selection at agronomically important genes. In order to discriminate between those effects and to investigate the nature of the domestication bottleneck, we(More)