Kyle T. David
Postdoctoral Scholar in the Rokas Lab at Vanderbilt University

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Research Interests

  • Macroevolution

    The rapid acceleration of both computer processing power and DNA sequencing technology have resulted in a proliferation of large-scale phylogenomic datasets. I seek to harness these data to discover evolutionary patterns and processes by exploring relationships between genotype, phenotype, and environment across the tree of life.

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    Latitudinal Gradients

    Despite being a computational biologist at heart, I have also been fortunate enough to conduct field research around the globe, from the Galápagos Islands to the Antarctic Circle. I am interested in exploring how biological phenomena such as speciation, extinction, and genome duplication are distributed across earth and how they contribute to the vast disparities between latitudes we observe today.

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    Bioinformatics of Non-models

    DNA sequencing is becoming cheaper and easier to use than ever before. In spite of this, most research efforts are concentrated to just a small number of model organisms. I am interested in computational methods which seek to understand non-model genomes, as well as employ phylogenetic comparative methods to assess how overreliance on model organisms biases our understanding of evolution and biodiversity.

Publications

David, K.T., Halanych, K.M. (2023). Unsupervised Deep Learning Can Identify Protein Functional Groups from Unaligned Sequences. Genome Biology and Evolution, evad084.

David, K.T. (2022). Global gradients in the distribution of animal polyploids. Proceedings of the National Academy of Sciences, 38(12), 5806-5818.

Tassia, M. G., David, K.T., Townsend, J.P., & Halanych, K.M. (2021). TIAMMAt: Leveraging biodiversity to revise protein domain models, evidence from innate immunity. Molecular Biology and Evolution, 48(5), 991-1000.

David, K. T. & Halanych, K. M. (2021). Spatial proximity between polyploids across South American frog genera. Journal of Biogeography, 48(5), 991-1000. [Editors' Choice]

Zhang, Y., Yap, K. N., David, K. T., & Swanson, D. L. (2021). The high-energy aerial insectivore lifestyle of swallows does not produce clear thermogenic side effects. Ornithology, 138(3), ukab022.

Li, Y.*, David, K. T.*, Shen, X. X., Steenwyk, J. L., Halanych, K. M., Rokas, A. (2020). Feature frequency profile-based phylogenies are inaccurate. Proceedings of the National Academy of Sciences, 117(50), 31580-31581.

David, K. T., Halanych, K. M., Oaks, J. R., (2020). Patterns of gene evolution following duplications and speciations in vertebrates. PeerJ, 8, e8813.

Li, Y., Tassia, M. G., Waits, D. S., Bogantes, V. E., David, K. T., Halanych, K. M. (2019). Genomic adaptations to chemosymbiosis in the deep-sea seep-dwelling tubeworm Lamellibrachia luymesi. BMC Biology, 17(1), 91.

David, K. T., Wilson, A. E., Halanych, K. M. (2019). Sequencing disparity in the genomic era. Molecular Biology and Evolution, 36(8), 1624-1627. [Featured Cover Article]

David, K. T. & Halanych, K. M. (2017). Mitochondrial genome of Dinophilus gyrociliatus (Annelida: Dinophilidae). Mitochondrial DNA Part B, 2(2), 831-832.

McMahan, C. D., Ginger, L., Cage, M., David, K. T., Chakrabarty, P., Johnston, M., & Matamoros, W. A. (2017). Pleistocene to holocene expansion of the black-belt cichlid in Central America, Vieja maculicauda (Teleostei: Cichlidae). PloS one, 12(5), e0178439.

David, K. T., Tanabe, P., Fieber, L. A. (2016). Resource availability drives mating role selection in a simultaneous hermaphrodite Aplysia californica. The Biological Bulletin, 231(3), 199-206.

*these authors contributed equally to the work

Curriculum Vitae