Luke J Harmon

Summary

Affiliation: University of Idaho
Country: USA

Publications

  1. pmc Phylotastic! Making tree-of-life knowledge accessible, reusable and convenient
    Arlin Stoltzfus
    Institute for Bioscience and Biotechnology Research, Biosystems and Biomaterials Division, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA
    BMC Bioinformatics 14:158. 2013
  2. pmc An inordinate fondness for eukaryotic diversity
    Luke J Harmon
    Department of Biological Sciences, University of Idaho, Moscow, Idaho, USA
    PLoS Biol 10:e1001382. 2012
  3. pmc Did genome duplication drive the origin of teleosts? A comparative study of diversification in ray-finned fishes
    Francesco Santini
    Department of Ecology and Evolutionary Biology, University of California at Los Angeles, 651 Charles Young Dr, South, Los Angeles, CA 90095, USA
    BMC Evol Biol 9:194. 2009
  4. ncbi request reprint GEIGER: investigating evolutionary radiations
    Luke J Harmon
    Department of Biological Sciences, University of Idaho, Moscow, ID 83844, USA
    Bioinformatics 24:129-31. 2008
  5. doi request reprint Early bursts of body size and shape evolution are rare in comparative data
    Luke J Harmon
    Department of Biological Sciences, University of Idaho, Moscow, Idaho 83844, USA
    Evolution 64:2385-96. 2010
  6. ncbi request reprint Poor statistical performance of the Mantel test in phylogenetic comparative analyses
    Luke J Harmon
    Department of Biological Sciences, University of Idaho, Moscow, Idaho 83844, USA
    Evolution 64:2173-8. 2010
  7. ncbi request reprint The role of geography and ecological opportunity in the diversification of day geckos (Phelsuma)
    Luke J Harmon
    Department of Biological Sciences, University of Idaho, Moscow, Idaho 83844 3051, USA
    Syst Biol 57:562-73. 2008
  8. doi request reprint Evolutionary diversification in stickleback affects ecosystem functioning
    Luke J Harmon
    Department of Biological Sciences, University of Idaho, Moscow, Idaho 83844 3051, USA
    Nature 458:1167-70. 2009
  9. pmc Ecological and evolutionary effects of stickleback on community structure
    Simone Des Roches
    Department of Biological Sciences, University of Idaho, Moscow, Idaho, United States of America
    PLoS ONE 8:e59644. 2013
  10. doi request reprint An integrative view of phylogenetic comparative methods: connections to population genetics, community ecology, and paleobiology
    Matthew W Pennell
    Department of Biological Sciences and Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, Idaho, USA
    Ann N Y Acad Sci 1289:90-105. 2013

Collaborators

Detail Information

Publications17

  1. pmc Phylotastic! Making tree-of-life knowledge accessible, reusable and convenient
    Arlin Stoltzfus
    Institute for Bioscience and Biotechnology Research, Biosystems and Biomaterials Division, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA
    BMC Bioinformatics 14:158. 2013
    ..Such a system could become a sustainable community resource if implemented as a distributed system of loosely coupled parts that interact through clearly defined interfaces...
  2. pmc An inordinate fondness for eukaryotic diversity
    Luke J Harmon
    Department of Biological Sciences, University of Idaho, Moscow, Idaho, USA
    PLoS Biol 10:e1001382. 2012
    ..This pattern suggests complex dynamics of speciation and extinction in the history of eukaryotes. Rabosky et al.'s paper represents the latest development in our efforts to understand the Earth's biodiversity at the broadest scales...
  3. pmc Did genome duplication drive the origin of teleosts? A comparative study of diversification in ray-finned fishes
    Francesco Santini
    Department of Ecology and Evolutionary Biology, University of California at Los Angeles, 651 Charles Young Dr, South, Los Angeles, CA 90095, USA
    BMC Evol Biol 9:194. 2009
    ..However, one critical assumption of this hypothesis, that diversification rates in teleosts increased soon after the acquisition of a duplicated genome, has never been tested...
  4. ncbi request reprint GEIGER: investigating evolutionary radiations
    Luke J Harmon
    Department of Biological Sciences, University of Idaho, Moscow, ID 83844, USA
    Bioinformatics 24:129-31. 2008
    ..GEIGER can carry out simulations, parameter estimation and statistical hypothesis testing. Additionally, GEIGER's simulation algorithms can be used to analyze the statistical power of comparative approaches...
  5. doi request reprint Early bursts of body size and shape evolution are rare in comparative data
    Luke J Harmon
    Department of Biological Sciences, University of Idaho, Moscow, Idaho 83844, USA
    Evolution 64:2385-96. 2010
    ..We suggest that the classical model of adaptive radiation, where morphological evolution is initially rapid and slows through time, may be rare in comparative data...
  6. ncbi request reprint Poor statistical performance of the Mantel test in phylogenetic comparative analyses
    Luke J Harmon
    Department of Biological Sciences, University of Idaho, Moscow, Idaho 83844, USA
    Evolution 64:2173-8. 2010
    ..We recommend that use of the Mantel test should be restricted to cases in which data can only be expressed as pairwise distances among taxa...
  7. ncbi request reprint The role of geography and ecological opportunity in the diversification of day geckos (Phelsuma)
    Luke J Harmon
    Department of Biological Sciences, University of Idaho, Moscow, Idaho 83844 3051, USA
    Syst Biol 57:562-73. 2008
    ..This negative relationship between rate of morphological evolution and island area suggests that ecological opportunity is an important factor in diversification of day gecko species...
  8. doi request reprint Evolutionary diversification in stickleback affects ecosystem functioning
    Luke J Harmon
    Department of Biological Sciences, University of Idaho, Moscow, Idaho 83844 3051, USA
    Nature 458:1167-70. 2009
    ..It is well known that ecological factors influence adaptive radiation. We demonstrate that adaptive radiation, even over short timescales, can have profound effects on ecosystems...
  9. pmc Ecological and evolutionary effects of stickleback on community structure
    Simone Des Roches
    Department of Biological Sciences, University of Idaho, Moscow, Idaho, United States of America
    PLoS ONE 8:e59644. 2013
    ..Our results stress the importance of concurrently evaluating both changes in density and phenotypic diversity on the structure and composition of communities...
  10. doi request reprint An integrative view of phylogenetic comparative methods: connections to population genetics, community ecology, and paleobiology
    Matthew W Pennell
    Department of Biological Sciences and Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, Idaho, USA
    Ann N Y Acad Sci 1289:90-105. 2013
    ..We argue that PCMs will continue to be a key set of tools in evolutionary biology, shedding new light on how evolutionary processes have shaped patterns of biodiversity through deep time...
  11. ncbi request reprint geiger v2.0: an expanded suite of methods for fitting macroevolutionary models to phylogenetic trees
    Matthew W Pennell
    Department of Biological Sciences and Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID 83844, Department of Paleobiology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20013, Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA, Department of Biological Sciences, Macquarie University, Sydney, NSW 2109, Australia and Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA
    Bioinformatics 30:2216-8. 2014
    ..r-project.org/web/packages/geiger/. All source code is also available on github http://github.com/mwpennell/geiger-v2. geiger v2.0 depends on the ape package...
  12. pmc Trees of unusual size: biased inference of early bursts from large molecular phylogenies
    Matthew W Pennell
    Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, Idaho, United States of America
    PLoS ONE 7:e43348. 2012
    ..We suggest that examining clades in isolation may result in spurious inferences that rates of diversification have changed through time...
  13. doi request reprint A novel comparative method for identifying shifts in the rate of character evolution on trees
    Jonathan M Eastman
    Department of Biological Sciences, Institute for Bioinformatics and Evolutionary Studies IBEST, University of Idaho, Moscow, Idaho 83843 3051, USA
    Evolution 65:3578-89. 2011
    ..auteur will facilitate identification of exceptional evolutionary dynamics, essential to the study of both adaptive radiation and stasis...
  14. ncbi request reprint Is there room for punctuated equilibrium in macroevolution?
    Matthew W Pennell
    Department of Biological Sciences and Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID 83844, USA Electronic address
    Trends Ecol Evol 29:23-32. 2014
    ....
  15. pmc The evolution of antibiotic susceptibility and resistance during the formation of Escherichia coli biofilms in the absence of antibiotics
    Jabus G Tyerman
    Department of Biological Sciences, University of Idaho, Campus Box 3051, Moscow, ID 83843, USA
    BMC Evol Biol 13:22. 2013
    ..Explanations for bacterial biofilm persistence during antibiotic treatment typically depend on non-genetic mechanisms, and rarely consider the contribution of evolutionary processes...
  16. doi request reprint Integrating fossils with molecular phylogenies improves inference of trait evolution
    Graham J Slater
    Department of Ecology and Evolutionary Biology, University of California, 610 Charles E Young Drive South, Los Angeles, California 90095 1606, USA
    Evolution 66:3931-44. 2012
    ..Our approach highlights the importance of considering fossil information when making macroevolutionary inference, and provides a way to integrate the kind of sparse fossil information that is available to most evolutionary biologists...
  17. doi request reprint "Same same but different": replicated ecological speciation at White Sands
    Erica Bree Rosenblum
    Department of Biological Sciences, University of Idaho, Moscow, ID 83844 3051, USA
    Evolution 65:946-60. 2011
    ..We suggest that evaluating cases from the natural world that are "same same but different" can reveal the mechanisms of ecological speciation...