Brandon Gaut - Academia.edu (original) (raw)
Papers by Brandon Gaut
Plant Species Biology, 1996
... Page 2. Brandon S. Gaut probably due to a founder effect (Hey and Kliman, 19931. ... At prese... more ... Page 2. Brandon S. Gaut probably due to a founder effect (Hey and Kliman, 19931. ... At present, studies of nucleotide polymorphism in single copy nuclear genes have been published from four plant species: maize (Zea mays ssp. ...
Annual Review of Ecology, Evolution, and Systematics, 2011
... The Patterns and Causes of Variation in Plant Nucleotide Substitution Rates Brandon Gaut,1 Li... more ... The Patterns and Causes of Variation in Plant Nucleotide Substitution Rates Brandon Gaut,1 Liang Yang,1 Shohei Takuno,1 and Luis E. Eguiarte2 ... 252 Gaut et al. Changes may still occur before final publication online and in print Page 9. ... 6 7 8 9 10 Zea mays chromosomes a b ...
Genetics, 2002
Plant defense genes are subject to nonneutral evolutionary dynamics. Here we investigate the evol... more Plant defense genes are subject to nonneutral evolutionary dynamics. Here we investigate the evolutionary dynamics of the duplicated defense genes hm1 and hm2 in maize and its wild ancestor Zea mays ssp. parviglumis. Both genes have been shown to confer resistance to the fungal pathogen Cochliobolus carbonum race 1, but the effectiveness of resistance differs between loci. The genes also display different population histories. The hm1 locus has the highest nucleotide diversity of any gene yet sampled in the wild ancestor of maize, and it contains a large number of indel polymorphisms. There is no evidence, however, that high diversity in hm1 is a product of nonneutral evolution. In contrast, hm2 has very low nucleotide diversity in the wild ancestor of maize. The distribution of hm2 polymorphic sites is consistent with nonneutral evolution, as indicated by Tajima's D and other neutrality tests. In addition, one hm2 haplotype is more frequent than expected under the equilibrium n...
Molecular biology and evolution, 1994
Likelihood-ratio statistics are proposed to test for heterogeneity in nucleotide substitution rat... more Likelihood-ratio statistics are proposed to test for heterogeneity in nucleotide substitution rate among regions of a DNA sequence. The tests examine three-sequence phylogenies, and two specific tests are proposed: a test to detect rate heterogeneity among genic regions within a sequence, over all evolutionary lineages; and a test to detect rate heterogeneity among regions in a specific evolutionary lineage. Simulations examine the ability of tests to detect a single region that varies in nucleotide substitution rate relative to the remainder of the sequence. A 50-bp region with a fivefold substitution-rate increase can be detected > or = 90% of the time when it is found in all three lineages of the phylogeny, and a 50-bp region of fivefold rate increase can be detected with approximately 70% power when it is found in only one evolutionary lineage. Simulation also examines the effect of transition- and transversion-rate differences. The tests are applied to published DNA sequence...
Genetics, 1993
We investigated nucleotide polymorphism in the Adh1 locus of pearl millet (Pennisetum glaucum) (P... more We investigated nucleotide polymorphism in the Adh1 locus of pearl millet (Pennisetum glaucum) (Poaceae) by determining the DNA sequence of 20 alleles from 10 individuals. The individuals were sampled from throughout pearl millet's indigenous range and represent both wild and cultivated accessions. Our results indicated that there is little nucleotide polymorphism in the Adh1 locus. Estimates of per site nucleotide polymorphism did not differ significantly between cultivated and wild millet accessions. We compared nucleotide polymorphism in pearl millet Adh1 with nucleotide polymorphism in maize (Zea mays) Adh1 and conclude that the maize Adh1 sample is more polymorphic. Increased polymorphism in maize Adh1 may be attributable, in part, to faster substitution rates in the maize lineage. Analysis suggests that substitution rates in the maize Adh1 lineage are approximately 1.7 times faster than substitution rates in the millet Adh1 lineage.
PLOS Computational Biology, 2006
Not Available Bibtex entry for this abstract Preferred format for this abstract (see Preferences)... more Not Available Bibtex entry for this abstract Preferred format for this abstract (see Preferences) Find Similar Abstracts: Use: Authors Title Return: Query Results Return items starting with number Query Form Database: Astronomy Physics arXiv e-prints
Genetics, 2002
We investigate the interplay between genetic diversity and recombination in maize (Zea mays ssp. ... more We investigate the interplay between genetic diversity and recombination in maize (Zea mays ssp. mays). Genetic diversity was measured in three types of markers: single-nucleotide polymorphisms, indels, and microsatellites. All three were examined in a sample of previously published DNA sequences from 21 loci on maize chromosome 1. Small indels (1-5 bp) were numerous and far more common than large indels. Furthermore, large indels (>100 bp) were infrequent in the population sample, suggesting they are slightly deleterious. The 21 loci also contained 47 microsatellites, of which 33 were polymorphic. Diversity in SNPs, indels, and microsatellites was compared to two measures of recombination: C (=4Nc) estimated from DNA sequence data and R based on a quantitative recombination nodule map of maize synaptonemal complex 1. SNP diversity was correlated with C (r = 0.65; P = 0.007) but not with R (r = -0.10; P = 0.69). Given the lack of correlation between R and SNP diversity, the corre...
Genetics, 1996
Understanding which genes contribute to evolutionary change and the nature of the alterations in ... more Understanding which genes contribute to evolutionary change and the nature of the alterations in them are fundamental challenges in evolution. We analyzed regulatory and enzymatic genes in the maize anthocyanin pathway as related to the evolution of anthocyanin-pigmented kernels in maize from colorless kernels of its progenitor, teosinte. Genetic tests indicate that teosinte possesses functional alleles at all enzymatic loci. At two regulatory loci, most teosintes possess alleles that encode functional proteins, but ones that are not expressed during kernel development and not capable of activating anthocyanin biosynthesis there. We investigated nucleotide polymorphism at one of the regulatory loci, cl. Several observations suggest that cl has not evolved in a strictly neutral manner, including an exceptionally low level of polymorphism and a biased representation of haplotypes in maize. Curiously, sequence data show that most of our teosinte samples possess a promoter element neces...
Coding sequences from maize, rice, tobacco, and liverwort chloroplasts are aligned and subjected ... more Coding sequences from maize, rice, tobacco, and liverwort chloroplasts are aligned and subjected to relative rate tests. Results of rate tests suggest that coding sequences from maize and rice are evolving with homogeneous rates of nucleotide substitution while coding sequences from the grass lineages (i.e., maize and rice) are evolving at a faster rate than coding sequences from the tobacco chloroplast. Rate tests also suggest that particular loci evolve at significantly faster rates in grass chloroplast genomes than the tobacco chloroplast genome. These loci encode proteins important to RNA polymerase, the H(+)-ATPase complex, and the ribosomal proteins. Much of the variation at these loci can be attributed to differences in nonsynonymous substitution rates. Taken together, these studies suggest that the chloroplast DNA molecular clock varies both between evolutionary lineages and between protein coding loci.
Coding sequences from maize, rice, tobacco, and liverwort chloroplasts are aligned and subjected ... more Coding sequences from maize, rice, tobacco, and liverwort chloroplasts are aligned and subjected to relative rate tests. Results of rate tests suggest that coding sequences from maize and rice are evolving with homogeneous rates of nucleotide substitution while coding sequences from the grass lineages (i.e., maize and rice) are evolving at a faster rate than coding sequences from the tobacco chloroplast. Rate tests also suggest that particular loci evolve at significantly faster rates in grass chloroplast genomes than the tobacco chloroplast genome. These loci encode proteins important to RNA polymerase, the H(+)-ATPase complex, and the ribosomal proteins. Much of the variation at these loci can be attributed to differences in nonsynonymous substitution rates. Taken together, these studies suggest that the chloroplast DNA molecular clock varies both between evolutionary lineages and between protein coding loci.
... Manolo Gouy, Universite Lyon, France Dan Graur, University of Houston, USA Matthew Hahn, Indi... more ... Manolo Gouy, Universite Lyon, France Dan Graur, University of Houston, USA Matthew Hahn, Indiana University, USA Jody Hey, Rutgers ... Matisoo-Smith, University of Otago, New Zealand John H. McDonald, University of Delaware, USA James McInerney, National University of ...
Proceedings of the National Academy of Sciences, 2014
PLoS ONE, 2011
To characterize and dissect genetic variation for salinity tolerance, we assessed variation in sa... more To characterize and dissect genetic variation for salinity tolerance, we assessed variation in salinity tolerance during germination and seedling growth for a worldwide sample of Arabidopsis thaliana accessions. By combining QTL mapping, association mapping and expression data, we identified genomic regions involved in salinity response. Among the worldwide sample, we found germination ability within a moderately saline environment (150 mM NaCl) varied considerable, from >90% among the most tolerant lines to complete inability to germinate among the most susceptible. Our results also demonstrated wide variation in salinity tolerance within A. thaliana RIL populations and identified multiple genomic regions that contribute to this variation. These regions contain known candidate genes, but at least four of the regions contain loci not yet associated with salinity tolerance response phenotypes. Our observations suggest A. thaliana natural variation may be an underutilized resource for investigating salinity stress response.
Nature Genetics, 2014
A new study reports the genome of common bean (Phaseolus vulgaris) and genome-wide resequencing d... more A new study reports the genome of common bean (Phaseolus vulgaris) and genome-wide resequencing data from both wild and domesticated accessions. These data confirm that common bean was domesticated at least twice, in Mesoamerica and South America, and also provide a framework to identify genes that contributed to the phenotypic changes associated with domestication.
Plant Molecular Evolution, 2000
Evolutionary Biology, 1998
... 102 Brandon S. Gaut lR genes, on the other hand, evolve at roughly half the rate of mito-chon... more ... 102 Brandon S. Gaut lR genes, on the other hand, evolve at roughly half the rate of mito-chondrial genes at nonsynonymous ... appear to be general phenomena because relatively slow nonsynonymous rates were also noted in contrasts between monocots and dicots (Wolfe et al ...
Advances in Experimental Medicine and Biology, 2013
Annals of the Missouri Botanical …, 1993
PHYLOGENETIC W. Dennis Clark,2 Brandon S. Gaut,3 RFT А ТТПгЧГЧНТРЧ OF THF Melvin R. Duvall,3 and ... more PHYLOGENETIC W. Dennis Clark,2 Brandon S. Gaut,3 RFT А ТТПгЧГЧНТРЧ OF THF Melvin R. Duvall,3 and Michael T. Clegg3 BROMELIIFLORAE-COMMELINIFLORAE-ZINGIBERIFLORAE COMPLEX OF MONOCOTS BASED ON rbcL SEQUENCE COMPARISONS1 Abstract ...
Plant Species Biology, 1996
... Page 2. Brandon S. Gaut probably due to a founder effect (Hey and Kliman, 19931. ... At prese... more ... Page 2. Brandon S. Gaut probably due to a founder effect (Hey and Kliman, 19931. ... At present, studies of nucleotide polymorphism in single copy nuclear genes have been published from four plant species: maize (Zea mays ssp. ...
Annual Review of Ecology, Evolution, and Systematics, 2011
... The Patterns and Causes of Variation in Plant Nucleotide Substitution Rates Brandon Gaut,1 Li... more ... The Patterns and Causes of Variation in Plant Nucleotide Substitution Rates Brandon Gaut,1 Liang Yang,1 Shohei Takuno,1 and Luis E. Eguiarte2 ... 252 Gaut et al. Changes may still occur before final publication online and in print Page 9. ... 6 7 8 9 10 Zea mays chromosomes a b ...
Genetics, 2002
Plant defense genes are subject to nonneutral evolutionary dynamics. Here we investigate the evol... more Plant defense genes are subject to nonneutral evolutionary dynamics. Here we investigate the evolutionary dynamics of the duplicated defense genes hm1 and hm2 in maize and its wild ancestor Zea mays ssp. parviglumis. Both genes have been shown to confer resistance to the fungal pathogen Cochliobolus carbonum race 1, but the effectiveness of resistance differs between loci. The genes also display different population histories. The hm1 locus has the highest nucleotide diversity of any gene yet sampled in the wild ancestor of maize, and it contains a large number of indel polymorphisms. There is no evidence, however, that high diversity in hm1 is a product of nonneutral evolution. In contrast, hm2 has very low nucleotide diversity in the wild ancestor of maize. The distribution of hm2 polymorphic sites is consistent with nonneutral evolution, as indicated by Tajima's D and other neutrality tests. In addition, one hm2 haplotype is more frequent than expected under the equilibrium n...
Molecular biology and evolution, 1994
Likelihood-ratio statistics are proposed to test for heterogeneity in nucleotide substitution rat... more Likelihood-ratio statistics are proposed to test for heterogeneity in nucleotide substitution rate among regions of a DNA sequence. The tests examine three-sequence phylogenies, and two specific tests are proposed: a test to detect rate heterogeneity among genic regions within a sequence, over all evolutionary lineages; and a test to detect rate heterogeneity among regions in a specific evolutionary lineage. Simulations examine the ability of tests to detect a single region that varies in nucleotide substitution rate relative to the remainder of the sequence. A 50-bp region with a fivefold substitution-rate increase can be detected > or = 90% of the time when it is found in all three lineages of the phylogeny, and a 50-bp region of fivefold rate increase can be detected with approximately 70% power when it is found in only one evolutionary lineage. Simulation also examines the effect of transition- and transversion-rate differences. The tests are applied to published DNA sequence...
Genetics, 1993
We investigated nucleotide polymorphism in the Adh1 locus of pearl millet (Pennisetum glaucum) (P... more We investigated nucleotide polymorphism in the Adh1 locus of pearl millet (Pennisetum glaucum) (Poaceae) by determining the DNA sequence of 20 alleles from 10 individuals. The individuals were sampled from throughout pearl millet's indigenous range and represent both wild and cultivated accessions. Our results indicated that there is little nucleotide polymorphism in the Adh1 locus. Estimates of per site nucleotide polymorphism did not differ significantly between cultivated and wild millet accessions. We compared nucleotide polymorphism in pearl millet Adh1 with nucleotide polymorphism in maize (Zea mays) Adh1 and conclude that the maize Adh1 sample is more polymorphic. Increased polymorphism in maize Adh1 may be attributable, in part, to faster substitution rates in the maize lineage. Analysis suggests that substitution rates in the maize Adh1 lineage are approximately 1.7 times faster than substitution rates in the millet Adh1 lineage.
PLOS Computational Biology, 2006
Not Available Bibtex entry for this abstract Preferred format for this abstract (see Preferences)... more Not Available Bibtex entry for this abstract Preferred format for this abstract (see Preferences) Find Similar Abstracts: Use: Authors Title Return: Query Results Return items starting with number Query Form Database: Astronomy Physics arXiv e-prints
Genetics, 2002
We investigate the interplay between genetic diversity and recombination in maize (Zea mays ssp. ... more We investigate the interplay between genetic diversity and recombination in maize (Zea mays ssp. mays). Genetic diversity was measured in three types of markers: single-nucleotide polymorphisms, indels, and microsatellites. All three were examined in a sample of previously published DNA sequences from 21 loci on maize chromosome 1. Small indels (1-5 bp) were numerous and far more common than large indels. Furthermore, large indels (>100 bp) were infrequent in the population sample, suggesting they are slightly deleterious. The 21 loci also contained 47 microsatellites, of which 33 were polymorphic. Diversity in SNPs, indels, and microsatellites was compared to two measures of recombination: C (=4Nc) estimated from DNA sequence data and R based on a quantitative recombination nodule map of maize synaptonemal complex 1. SNP diversity was correlated with C (r = 0.65; P = 0.007) but not with R (r = -0.10; P = 0.69). Given the lack of correlation between R and SNP diversity, the corre...
Genetics, 1996
Understanding which genes contribute to evolutionary change and the nature of the alterations in ... more Understanding which genes contribute to evolutionary change and the nature of the alterations in them are fundamental challenges in evolution. We analyzed regulatory and enzymatic genes in the maize anthocyanin pathway as related to the evolution of anthocyanin-pigmented kernels in maize from colorless kernels of its progenitor, teosinte. Genetic tests indicate that teosinte possesses functional alleles at all enzymatic loci. At two regulatory loci, most teosintes possess alleles that encode functional proteins, but ones that are not expressed during kernel development and not capable of activating anthocyanin biosynthesis there. We investigated nucleotide polymorphism at one of the regulatory loci, cl. Several observations suggest that cl has not evolved in a strictly neutral manner, including an exceptionally low level of polymorphism and a biased representation of haplotypes in maize. Curiously, sequence data show that most of our teosinte samples possess a promoter element neces...
Coding sequences from maize, rice, tobacco, and liverwort chloroplasts are aligned and subjected ... more Coding sequences from maize, rice, tobacco, and liverwort chloroplasts are aligned and subjected to relative rate tests. Results of rate tests suggest that coding sequences from maize and rice are evolving with homogeneous rates of nucleotide substitution while coding sequences from the grass lineages (i.e., maize and rice) are evolving at a faster rate than coding sequences from the tobacco chloroplast. Rate tests also suggest that particular loci evolve at significantly faster rates in grass chloroplast genomes than the tobacco chloroplast genome. These loci encode proteins important to RNA polymerase, the H(+)-ATPase complex, and the ribosomal proteins. Much of the variation at these loci can be attributed to differences in nonsynonymous substitution rates. Taken together, these studies suggest that the chloroplast DNA molecular clock varies both between evolutionary lineages and between protein coding loci.
Coding sequences from maize, rice, tobacco, and liverwort chloroplasts are aligned and subjected ... more Coding sequences from maize, rice, tobacco, and liverwort chloroplasts are aligned and subjected to relative rate tests. Results of rate tests suggest that coding sequences from maize and rice are evolving with homogeneous rates of nucleotide substitution while coding sequences from the grass lineages (i.e., maize and rice) are evolving at a faster rate than coding sequences from the tobacco chloroplast. Rate tests also suggest that particular loci evolve at significantly faster rates in grass chloroplast genomes than the tobacco chloroplast genome. These loci encode proteins important to RNA polymerase, the H(+)-ATPase complex, and the ribosomal proteins. Much of the variation at these loci can be attributed to differences in nonsynonymous substitution rates. Taken together, these studies suggest that the chloroplast DNA molecular clock varies both between evolutionary lineages and between protein coding loci.
... Manolo Gouy, Universite Lyon, France Dan Graur, University of Houston, USA Matthew Hahn, Indi... more ... Manolo Gouy, Universite Lyon, France Dan Graur, University of Houston, USA Matthew Hahn, Indiana University, USA Jody Hey, Rutgers ... Matisoo-Smith, University of Otago, New Zealand John H. McDonald, University of Delaware, USA James McInerney, National University of ...
Proceedings of the National Academy of Sciences, 2014
PLoS ONE, 2011
To characterize and dissect genetic variation for salinity tolerance, we assessed variation in sa... more To characterize and dissect genetic variation for salinity tolerance, we assessed variation in salinity tolerance during germination and seedling growth for a worldwide sample of Arabidopsis thaliana accessions. By combining QTL mapping, association mapping and expression data, we identified genomic regions involved in salinity response. Among the worldwide sample, we found germination ability within a moderately saline environment (150 mM NaCl) varied considerable, from >90% among the most tolerant lines to complete inability to germinate among the most susceptible. Our results also demonstrated wide variation in salinity tolerance within A. thaliana RIL populations and identified multiple genomic regions that contribute to this variation. These regions contain known candidate genes, but at least four of the regions contain loci not yet associated with salinity tolerance response phenotypes. Our observations suggest A. thaliana natural variation may be an underutilized resource for investigating salinity stress response.
Nature Genetics, 2014
A new study reports the genome of common bean (Phaseolus vulgaris) and genome-wide resequencing d... more A new study reports the genome of common bean (Phaseolus vulgaris) and genome-wide resequencing data from both wild and domesticated accessions. These data confirm that common bean was domesticated at least twice, in Mesoamerica and South America, and also provide a framework to identify genes that contributed to the phenotypic changes associated with domestication.
Plant Molecular Evolution, 2000
Evolutionary Biology, 1998
... 102 Brandon S. Gaut lR genes, on the other hand, evolve at roughly half the rate of mito-chon... more ... 102 Brandon S. Gaut lR genes, on the other hand, evolve at roughly half the rate of mito-chondrial genes at nonsynonymous ... appear to be general phenomena because relatively slow nonsynonymous rates were also noted in contrasts between monocots and dicots (Wolfe et al ...
Advances in Experimental Medicine and Biology, 2013
Annals of the Missouri Botanical …, 1993
PHYLOGENETIC W. Dennis Clark,2 Brandon S. Gaut,3 RFT А ТТПгЧГЧНТРЧ OF THF Melvin R. Duvall,3 and ... more PHYLOGENETIC W. Dennis Clark,2 Brandon S. Gaut,3 RFT А ТТПгЧГЧНТРЧ OF THF Melvin R. Duvall,3 and Michael T. Clegg3 BROMELIIFLORAE-COMMELINIFLORAE-ZINGIBERIFLORAE COMPLEX OF MONOCOTS BASED ON rbcL SEQUENCE COMPARISONS1 Abstract ...