Antony M Dean

Summary

Affiliation: University of Minnesota
Country: USA

Publications

  1. pmc Pervasive cryptic epistasis in molecular evolution
    Mark Lunzer
    Biotechnology Institute, University of Minnesota, St Paul, Minnesota, USA
    PLoS Genet 6:e1001162. 2010
  2. pmc Mechanistic approaches to the study of evolution: the functional synthesis
    Antony M Dean
    University of Minnesota, St Paul, Minnesota 55108, USA
    Nat Rev Genet 8:675-88. 2007
  3. ncbi request reprint Direct demonstration of an adaptive constraint
    Stephen P Miller
    Biotechnology Institute, University of Minnesota, St Paul, MN 55108, USA
    Science 314:458-61. 2006
  4. ncbi request reprint The biochemical architecture of an ancient adaptive landscape
    Mark Lunzer
    Biotechnology Institute, Evolution and Behavior, University of Minnesota, St Paul, MN 55108, USA
    Science 310:499-501. 2005
  5. ncbi request reprint The selective cause of an ancient adaptation
    Guoping Zhu
    Biotechnology Institute, University of Minnesota, St Paul, MN 55108, USA
    Science 307:1279-82. 2005
  6. ncbi request reprint Selection in a cyclical environment: possible impact of phenotypic lag on Darwinian fitness
    Amy M Suiter
    Biotechnology Institute, University of Minnesota, 1987 Upper Buford Circle, St Paul, MN 55108, USA
    J Mol Evol 61:153-70. 2005
  7. ncbi request reprint The argRB of Escherichia coli is rare in isolates obtained from natural sources
    Lauren M F Merlo
    University of Minnesota, Department of Ecology, Evolution, and Behavior, Saint Paul, MN, USA
    Gene 376:240-7. 2006
  8. pmc An empirical test of the concomitantly variable codon hypothesis
    Lauren M F Merlo
    Department of Ecology, Evolution, and Behavior, University of Minnesota, 100 Ecology Building, 1987 Upper Buford Circle, Saint Paul, MN 55108, USA
    Proc Natl Acad Sci U S A 104:10938-43. 2007
  9. pmc Evolutionary genomics of ecological specialization
    Shaobin Zhong
    Biotechnology Institute, University of Minnesota, St Paul, MN 55108, USA
    Proc Natl Acad Sci U S A 101:11719-24. 2004
  10. pmc Bounded population sizes, fluctuating selection and the tempo and mode of coexistence
    Xiao Yi
    Department of Ecology, Evolution, and Behavior, University of Minnesota, St Paul, MN 55108
    Proc Natl Acad Sci U S A 110:16945-50. 2013

Collaborators

Detail Information

Publications21

  1. pmc Pervasive cryptic epistasis in molecular evolution
    Mark Lunzer
    Biotechnology Institute, University of Minnesota, St Paul, Minnesota, USA
    PLoS Genet 6:e1001162. 2010
    ..This demonstrates that epistatic interactions can occur between distant (>20Å) sites. Phylogenetic analysis shows that incompatible mutations were fixed in different lineages...
  2. pmc Mechanistic approaches to the study of evolution: the functional synthesis
    Antony M Dean
    University of Minnesota, St Paul, Minnesota 55108, USA
    Nat Rev Genet 8:675-88. 2007
    ..Here we describe this emerging approach, highlight important new insights that it has made possible, and suggest future directions for the field...
  3. ncbi request reprint Direct demonstration of an adaptive constraint
    Stephen P Miller
    Biotechnology Institute, University of Minnesota, St Paul, MN 55108, USA
    Science 314:458-61. 2006
    ..Our results show that selective mechanisms and evolutionary constraints are to be understood in terms of underlying adaptive landscapes...
  4. ncbi request reprint The biochemical architecture of an ancient adaptive landscape
    Mark Lunzer
    Biotechnology Institute, Evolution and Behavior, University of Minnesota, St Paul, MN 55108, USA
    Science 310:499-501. 2005
    ..The genotype-phenotype-fitness map shows that NAD use is a global optimum...
  5. ncbi request reprint The selective cause of an ancient adaptation
    Guoping Zhu
    Biotechnology Institute, University of Minnesota, St Paul, MN 55108, USA
    Science 307:1279-82. 2005
    ..Those with only an NAD-dependent IDH never have isocitrate lyase. Hence, the NADP dependence of prokaryotic IDH is an ancient adaptation to anabolic demand for reduced NADP during growth on acetate...
  6. ncbi request reprint Selection in a cyclical environment: possible impact of phenotypic lag on Darwinian fitness
    Amy M Suiter
    Biotechnology Institute, University of Minnesota, 1987 Upper Buford Circle, St Paul, MN 55108, USA
    J Mol Evol 61:153-70. 2005
    ..This suggests that phenotypic lag, wherein cellular physiology changes more slowly than the environment, may be influencing the outcome of competition in this experimental system...
  7. ncbi request reprint The argRB of Escherichia coli is rare in isolates obtained from natural sources
    Lauren M F Merlo
    University of Minnesota, Department of Ecology, Evolution, and Behavior, Saint Paul, MN, USA
    Gene 376:240-7. 2006
    ..Moreover, sequence analysis of 85 strains shows no evidence of selection at the arginine repressor locus. This illustrates that analysis of sequence data is insufficient to detect selection of uncommon alleles in rare environments...
  8. pmc An empirical test of the concomitantly variable codon hypothesis
    Lauren M F Merlo
    Department of Ecology, Evolution, and Behavior, University of Minnesota, 100 Ecology Building, 1987 Upper Buford Circle, Saint Paul, MN 55108, USA
    Proc Natl Acad Sci U S A 104:10938-43. 2007
    ..The evolution of covarions undermines a key assumption in phylogenetics and calls into question our ability to disentangle ancient relationships among major taxonomic groups...
  9. pmc Evolutionary genomics of ecological specialization
    Shaobin Zhong
    Biotechnology Institute, University of Minnesota, St Paul, MN 55108, USA
    Proc Natl Acad Sci U S A 101:11719-24. 2004
    ..Other mutations that repeatedly appear in replicate experiments are adaptations to the chemostat environment and are not specific to one or the other sugar...
  10. pmc Bounded population sizes, fluctuating selection and the tempo and mode of coexistence
    Xiao Yi
    Department of Ecology, Evolution, and Behavior, University of Minnesota, St Paul, MN 55108
    Proc Natl Acad Sci U S A 110:16945-50. 2013
    ..Simulations show the likelihood of coexistence increases with environmental uncertainty. The capacity of temporally variable environments to maintain biological diversity is far broader than generally envisaged. ..
  11. pmc Enzyme kinetics, substitutable resources and competition: from biochemistry to frequency-dependent selection in lac
    Mark Lunzer
    Biotechnology Institute, University of Minnesota, St Paul, Minnesota 55108, USA
    Genetics 162:485-99. 2002
    ..A comparison of predictions, based on first principles, with experimental outcomes reveals an additional, unanticipated source of weak selection...
  12. pmc Protecting haploid polymorphisms in temporally variable environments
    Antony M Dean
    BioTechnology Institute and Department of Ecology Evolution and Behavior, University of Minnesota, St Paul, Minnesota 55108 6106, USA
    Genetics 169:1147-56. 2005
    ..In temporally variable environments, frequency-dependent changes in generation times tend to counteract these invasions. Such changes can prevent fixation and protect polymorphisms...
  13. ncbi request reprint The pattern of amino acid replacements in alpha/beta-barrels
    Antony M Dean
    The Biological Process Technology Institute, University of Minnesota, St Paul, 55108, USA
    Mol Biol Evol 19:1846-64. 2002
    ..A statistical analysis shows that, in all cases, much of the remaining unexplained variation is not attributable to chance and that other, as yet unidentified, causal relations must exist...
  14. pmc Fitness consequences of a regulatory polymorphism in a seasonal environment
    Amy M Suiter
    Biotechnology Institute, University of Minnesota, 1479 Gortner Avenue, St Paul, MN 55108, USA
    Proc Natl Acad Sci U S A 100:12782-6. 2003
    ..In environments that cycle between high and low arginine, short seasons favor the K12 allele, whereas long seasons favor the B allele. Unexpectedly then, deregulated expression is adaptive in some seasonal habitats...
  15. ncbi request reprint Evolution of a transition state: role of lys100 in the active site of isocitrate dehydrogenase
    Stephen P Miller
    Biotechnology Institute, The University of Minnesota, 1479 Gortner Avenue, St Paul, MN 55108 USA
    Chembiochem 15:1145-53. 2014
    ..Partial activation of lysine mutants by K(+) and NH4 (+) represents a throwback to the primordial state of the first promiscuous substrate family member. ..
  16. pmc Rapid identification and mapping of insertion sequences in Escherichia coli genomes using vectorette PCR
    Shaobin Zhong
    Biotechnology Institute, University of Minnesota, 1479 Gortner Ave, St, Paul, MN 55108, USA
    BMC Microbiol 4:26. 2004
    ..Here, we use vectorette PCR to identify and map the genomic positions of the eight insertion sequences (IS1, 2, 3, 4, 5, 30, 150, and 186) found in E. coli strain CGSC6300, a close relative of MG1655 whose genome has been sequenced...
  17. pmc Evolution of specialists in an experimental microcosm
    Daniel E Dykhuizen
    Department of Ecology and Evolution, SUNY, Stony Brook, New York 11794, USA
    Genetics 167:2015-26. 2004
    ..Our results suggest that, once stabilized, ecological specialization prevented selective sweeps through the entire population, thereby promoting the maintenance of linked neutral polymorphisms...
  18. pmc The cost of expression of Escherichia coli lac operon proteins is in the process, not in the products
    Daniel M Stoebel
    Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York 11794, USA
    Genetics 178:1653-60. 2008
    ..Our results identify the basis of a single selective pressure likely acting across the entire E. coli transcriptome...
  19. ncbi request reprint Local migration promotes competitive restraint in a host-pathogen 'tragedy of the commons'
    Benjamin Kerr
    Department of Biology, University of Washington, Box 351800, Seattle, Washington 98195 1800, USA
    Nature 442:75-8. 2006
    ..Thus, migration pattern alone can determine whether a de novo tragedy of the commons is resolved in favour of restraint...
  20. pmc Evolving protein functional diversity in new genes of Drosophila
    Jianming Zhang
    Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637, USA
    Proc Natl Acad Sci U S A 101:16246-50. 2004
    ..These data suggest that protein functional diversity can expand rapidly under the joint forces of exon shuffling, gene duplication, and natural selection...
  21. ncbi request reprint The mitochondrial citrate transport protein: probing the secondary structure of transmembrane domain III, identification of residues that likely comprise a portion of the citrate transport pathway, and development of a model for the putative TMDIII-TMDIII
    Chunlong Ma
    Department of Biochemistry and Molecular Biology, Finch University of Health Sciences The Chicago Medical School, North Chicago, Illinois 60064, USA
    J Biol Chem 279:1533-40. 2004
    ....