Active Research Evolutionary genomics of Drosophila Genetic diversity of P. falciparum Evolution of hybrid incompatibilities Evolution of gene expression Natural selection and protein evolution   Past Research Evolution of novel gene functions Bioinformatics Selective sweep C-value paradox Transposable element mariner Structure and sequence of the Drosophila genome Genome structure and evolution in D. virilis Cosuppression of transposable elements Molecular evolution in enteric bacteria Gregor Mendel

Molecular evolution in enteric bacteria Our laboratory pioneered the use of Escherichia coli and Salmonella enterica as experimental organisms in molecular population genetics and evolution. We began with chemostat studies of the fitness of organisms containing naturally occurring electrophoretic enzyme variants. The most important finding was that many alleles could be shown to affect fitness, but usually only under particular growth conditions (such as using the substrate of the enzyme as the sole source of carbon and energy) or particular genetic backgrounds. This led to the hypothesis of potential for selection, wherein alleles that are neutral or nearly neutral under one set of conditions can be subjected to selection under other conditions. Studies of enteric bacteria soon expanded toward more general features of microbial molecular evolution as well as studies of the distribution and abundance of transposable insertion sequences among natural isolates. We discovered that plausible models of transposition and self-regulation of transposition could account for the distribution of copy numbers of insertion sequences observed among natural isolates. An unexpected correlation in the presence of unrelated insertion sequences was traced to their joint horizontal transmission by plasmids. Plasmids themselves were shown to be mosaics of diverse types of sequences, and shown to undergo transmission between species in the absence of obvious selective agents. Sequences of genes from enteric bacteria were also used to make inferences about rates of recombination and intensities of selection affecting codon usage.   PDF Townsend, J. P., K. M. Nielsen, D. S. Fisher, and D. L. Hartl, 2003 Horizontal acquisition of divergent chromosomal DNA in bacteria: effects of mutator phenotypes. Genetics 164: 13-21.       Hartl, D. L., E. F. Boyd, C. D. Bustamante and S. A. Sawyer, 2000 The glean machine: What can we learn from DNA sequence polymorphisms? pp. 37-49 in Sandor Suhai (editor) Genomics and Proteomics, Plenum Press, New York.     PDF Boyd, E. F. and D. L. Hartl, 1997 Recent horizontal transmission of plasmids between natural populations of Escherichia coli and Salmonella enterica. J. Bacteriol. 179: 1622-1627.       Boyd, E. F., C. W. Hill, S. Rich, and D. L. Hartl, 1996 Mosaic structure of plasmids from natural populations of Escherichia coli. Genetics 143: 1091-1100.       Hartl, D. L., E. N. Moriyama, and S. A. Sawyer, 1994 Selection intensity for codon bias. Genetics 138: 227-234.       Lawrence, J. G., H. Ochman and D. L. Hartl, 1991 Molecular and evolutionary relationships among enteric bacteria. J. Gen. Microbiol. 137: 1911-1921.     PDF DuBose, R. F. and D. L. Hartl, 1989 An experimental approach to testing modular evolution: Directed replacement of a helices in a bacterial protein. Proc. Natl. Acad. Sci. USA 86: 9966-9970.     PDF DuBose, R. F., D. E. Dykhuizen and D. L. Hartl, 1988 Genetic exchange among natural isolates of bacteria: Recombination within the phoA gene of Escherichia coli. Proc. Natl. Acad. Sci. USA 85: 7036-7040.       Dean, A. M., D. E. Dykhuizen and D. L. Hartl, 1988 Fitness effects of amino-acid replacements in the beta-galactosidase of Escherichia coli. Mol. Biol. Evol. 5: 469-485.       Sawyer, S. A., D. E. Dykhuizen, R. F. DuBose, L. Green, T. Mutangadura-Mhlanga, D. F. Wolczyk and D. L. Hartl, 1987 Distribution and abundance of insertion sequences among natural isolates of Escherichia coli. Genetics 115: 51-63.     PDF Hartl, D. L., D. E. Dykhuizen and A. M. Dean, 1985 Limits of adaptation: The evolution of selective neutrality. Genetics 111: 655-674.       Hartl, D. L. and D. E. Dykhuizen, 1984 The population genetics of Escherichia coli. Ann. Rev. Genet. 18: 31-68.     PDF Hartl, D. L. and D. E. Dykhuizen, 1981 Potential for selection among nearly neutral allozymes of 6-phosphogluconate dehydrogenase in Escherichia coli. Proc. Natl. Acad. Sci. USA 78: 6344-6348.