Lab Publications

google scholar link

  • Maya-Lastra, C.A. and D. Eaton. (20xx) Genetic incompatibilities do not snowball in a demographic model of speciation. In Review.

  • McKenzie, P.F. and D. Eaton. (2020) The MultiSpecies Coalescent in Space and Time. In Press (Biorxiv: https://www.biorxiv.org/content/10.1101/2020.08.02.233395v1).

  • McKenzie, P.F. and D. Eaton. (2020) ipcoal: An interactive Python package for simulating and analyzing genealogies and sequences on a species tree or network. Bioinformatics.

  • Eaton, D.A.R and I. Overcast. (2020) ipyrad: interactive assembly and analysis of RAD-seq data. Bioinformatics.

  • Eaton, D.A.R. (2020) Toytree: A minimalist tree visualization and manipulation library for Python Methods in Ecology and Evolution. https://besjournals.onlinelibrary.wiley.com/doi/full/10.1111/2041-210X.13313

  • Landis, M.J, Eaton, D.A.R., Clement, W.L., Park, B., Spriggs, E.L., Sweeney, P., Edwards, E.J, and M.J. Donoghue (2019). Joint phylogenetic estimation of geographic movements and biome shifts during the global diversification of Viburnum. Systematic Biology.

  • Paetzold, C., Wood, K.R., Eaton, D.A.R., Wagner, W.L., and M. S. Appelhans. (2019) Phylogeny of Hawaiian Melicope (Rutaceae): RAD-Seq resolves species relationships and reveals ancient introgression. Frontiers in Plant Science 10, 1074. doi: 10.3389/fpls.2019.01074

  • Satler, J.D., Herre, A., Jander, C., Eaton, D.A.R., Machado, C.A., Heath, T.A., and J.D. Nason (2019). Inferring Processes of Coevolutionary Diversification in a Community of Panamanian Strangler Figs and Associated Pollinating Wasps Evolution.

  • Spriggs E.L., Schlutius, C.; Eaton, D.A.R., Park, B., Sweeney, P., Edwards, E., and M. Donoghue (2019). Differences in flowering time maintain species boundaries in a continental radiation of Viburnum. American Journal of Botany. https://doi.org/10.1002/ajb2.1292

  • Spriggs, E.L., Eaton, D.A.R., Sweeney, P., Schlutius, C., Edwards, E., and M.J. Donoghue (2019). Restriction-Site-Associated DNA Sequencing Reveals a Cryptic Viburnum Species on the North American Coastal Plain. Systematic Biology, syy084, https://doi.org/10.1093/sysbio/syy084.

  • Park, B., Sinnott-Armstrong, M., Schlutius, C., Penagos Zuluaga, J., Spriggs, E.L, Simpson, R., Benavides, E., Landis, M., Sweeney, P., Eaton, D.A.R., and M.J. Donoghue (2018). Sterile marginal flowers increase visitation and fruit set in the hobblebush (Viburnum lantanoides, Adoxaceae) at multiple spatial scales. Annals of Botany mcy117, https://doi.org/10.1093/aob/mcy117

  • Miller, J., Quinzin, M., Edwards, D., Eaton, D.A.R., Jensen, E., Russello, M., Gibbs, J., Tapia, W., Rueda, D., and A. Caccone (2018). Genome-wide assessment of diversity and divergence among extant Galápagos giant tortoise species. Journal of Heredity 109(6):611-619. https://doi.org/10.1093/jhered/esy031.

  • Federman, S., Donoghue, M.J., Daly, D., and D.A.R. Eaton (2018). Reconciling Species Diversity in a Tropical Plant Clade (Canarium, Burseraceae). PLoS ONE 13(6): e0198882. (Open access link) (reproducible code).

  • (All authors contributed equally) M.R. McKain, M.G. Johnson, S. Uribe‐Convers, D.A.R. Eaton and Y. Yang (2018). Practical considerations for plant phylogenomics. Applications in Plant Sciences 6: e1038 (Open Access Review Article).

  • Forsman Z.H., Knapp I.S.S., Tisthammer K., Eaton D.A.R., Belcaid M., Toonen R.J. (2017). Coral hybridization or phenotypic variation? Genomic data reveal gene flow between Porites lobata and P. compressa. Molecular Phylogenetics and Evolution 111: 132:148. (link)

  • Eaton, D.A.R., Spriggs, E.L., Park, B., & M.J. Donoghue (2017). Misconceptions of Missing data in RAD-seq phylogenetics with a Deep-scale Example from Flowering Plants. Systematic Biology 66(3): 399:412. (link); (reproducible code); (cover image)

  • Eaton, D.A.R., Hipp, A., Gonzalez-Rodriguez, A. & J. Cavender-Bares (2015). Historical introgression among the American live oaks and the comparative nature of tests for introgression. Evolution 69(10) 2587-2601. (link); (reproducible science)

  • Cavender-Bares, J., Gonzalez-Rodriguez, A., Eaton, D.A.R., Hipp, A., Buelke, A., & P. Manos (2015). Phylogeny and biogeography of the American live oaks (Quercus subsection Virentes): A genomic and population genetic approach. Molecular Ecology 24(14): 3668-3687.

  • Escudero, M., Eaton, D.A.R., Hahn, M. & A. Hipp (2014). Genotyping-by-sequencing as a tool for phylogenetic inference and testing ancestral hybridization: A case study in Carex (Cyperaceae). Molecular Phylogenetics and Evolution. 79: 359-367. DOI: 10.1016/j.ympev.2014.06.026. (Reproducible code)

  • Hipp, A., Eaton, D.A.R., Cavender-Bares, J., Fitzek, E., Nipper, R. and P.S. Manos (2014). A framework phylogeny of the American oak clade based on sequenced RAD data. PLoS ONE 9(4): e93975. DOI: 10.1371/journal.pone.0093975. (Open Access Link)

  • Eaton, D.A.R. (2014). PyRAD: assembly of de novo RADseq loci for phylogenetic analyses. Bioinformatics 30(13): 1844-1849. doi: 10.1093/bioinformatics/btu121. (preprint), (Reproducible science: Files, Notebook)

  • Eaton, D.A.R. and R.H. Ree (2013). Inferring phylogeny and introgression using genomic RADseq data: An example from flowering plants (Pedicularis: Orobanchaceae). Systematic Biology, 62: 689-706. (Open Access Link), (cover image)

  • Xueqin, W., Lei, Z., Eaton, D.A.R. & G. Zhenhua (2013). Identification of SNP markers for inferring phylogeny in temperate bamboos (Poaceae: Bambusoideae) using RAD tag sequencing. Molecular Ecology Resources, 13: 938-945.

  • Fournier-Level A., Wilczek, A.M., Cooper, M.D., Roe, J.L, Anderson, J.A., Eaton, D.A.R., Moyers, B.T., Petipas, R.H., Schaeffer, R.N., Pieper, B., Reymond, M., Koorneef, M., Welch, S.M., Remington, D.L. and J.S. Schmitt (2013). Paths to selection on life-history loci in different natural environments across the native range of Arabidopsis thaliana. Molecular Ecology, 22: 3552-3566.

  • Hipp, A.L, Manos, P.S., Cavender-Bares, J, Eaton, D.A.R., & R. Nipper (2013). Using phylogenomics to infer the evolutionary history of oaks. International Oak Journal, 24: 61-71.

  • Eaton, D.A.R., Fenster, C.B., Hereford, J., Huang, S-Q. and R.H. Ree (2012). Floral diversity and community structure in Pedicularis (Orobanchaceae). Ecology, 93: S182:S194. (Open Access Link)

In Prep

  • Eaton, D.A.R., Huang, S-Q. and R.H. Ree. Interspecific reproductive character displacement affects gene flow among intraspecific populations of a widespread alpine plant species. In Prep.

  • Eaton, D.A.R., Ree, R.H. and S-Q. Huang. Evolutionary constraint and pollen-pistil relationships above and below the species-level in Chinese Pedicularis. In Prep.