Publications

17 peer-reviewed articles, 3 manuscripts under review, and 1 preprint. Titles link to the publisher where a DOI exists. The CV carries the complete record.

Published & accepted 17

2026
Automatic Discovery of Optimal Discrete Character Models
Boyko, J. D.

Systematic Biology, syag018.
2026
The Geometry of Macroevolution: Phenotypic Evolution on Non-Euclidean Manifolds
Boyko, J. D. and Rabosky, D. L.

The American Naturalist.
2026
Resolving competing evolutionary histories in joint ancestral state reconstruction
Boyko, J. D., Gontjes, K. J., Snitkin, E. S., and Smith, S. A.

Proceedings of the National Academy of Sciences, 123(15), e2528064123.
2025
SegmentR: Deep Learning for Automated Segmentation with an R Interface
Boyko, J. D.

Ecological Informatics, 103259.
2025
Phylogenetic Context of Antibiotic Resistance Provides Insights into the Dynamics of Resistance Emergence and Spread
Gontjes, K. J., Singh, A., Sansom, S. E., Boyko, J. D., Smith, S. A., Lautenbach, E., and Snitkin, E.

The Journal of Infectious Diseases, jiaf478.
2025
Punctuated Versus Gradual Shifts in the Multivariate Evolutionary Process: A Test With Paired Radiations of Scincid Lizards
Stepanova, N., Boyko, J. D., Lin, J., Davis Rabosky, A. R., and Rabosky, D. L.

Systematic Biology, 74(3), 483–498.
2025
mvh: An R Tool to Assemble and Organize Virtual Herbaria from Openly Available Specimen Images
Vasconcelos, T. and Boyko, J. D.

Applications in Plant Sciences, 13(2), e11631.
2025
Automated Extraction of Leaf Mass per Area from Digitized Herbarium Specimens
Vasconcelos, T., Weaver, W. N., Baumgartner, A., Bugnaski, Z., and Boyko, J. D.

New Phytologist.
2024
dentist: Quantifying Uncertainty by Sampling Points Around Maximum Likelihood Estimates
Boyko, J. D. and O'Meara, B. C.

Methods in Ecology and Evolution, 15(4), 628–638.
2024
Investigating Historical Drivers of Latitudinal Gradients in Polyploid Plant Biogeography: A Multiclade Perspective
Hagen, E. R., Vasconcelos, T., Boyko, J. D., and Beaulieu, J. M.

American Journal of Botany, e16356.
2023
The Evolutionary Responses of Life-History Strategies to Climatic Variability in Flowering Plants
Boyko, J. D., Hagen, E. R., Beaulieu, J. M., and Vasconcelos, T.

New Phytologist.
2023
A Novel Method for Jointly Modeling the Evolution of Discrete and Continuous Traits
Boyko, J. D., O'Meara, B. C., and Beaulieu, J. M.

Evolution.
2022
Reducing the Biases in False Correlations Between Discrete Characters
Boyko, J. D. and Beaulieu, J. M.

Systematic Biology.
2022
Synthesizing Existing Phylogenetic Data to Advance Phylogenetic Research in Orobanchaceae
Mortimer, S. M. E., Boyko, J. D., Beaulieu, J. M., and Tank, D. C.

Systematic Botany, 47, 533–544.
2021
Generalized Hidden Markov Models for Phylogenetic Comparative Datasets
Boyko, J. D. and Beaulieu, J. M.

Methods in Ecology and Evolution, 12(3), 468–478.
2021
Linking Mode of Seed Dispersal and Climatic Niche Evolution in Flowering Plants
Vasconcelos, T., Boyko, J. D., and Beaulieu, J. M.

Journal of Biogeography, 50, 43–56.
2017
Models with Unequal Transition Rates Favor Marine Origins of Cyanobacteria and Photosynthetic Eukaryotes
Nakov, T., Boyko, J. D., Alverson, A. J., and Beaulieu, J. M.

Proceedings of the National Academy of Sciences, 114, E10606–E10607.

Under review 3

2026
Multiple Trans-Marine Dispersals and Niche Conservatism Underlie the Pantropical Distribution of Eugeniinae (Myrtaceae)
Gaem, P. H., Boyko, J. D., Mazine, F. F., Valdemarin, K. S., Smith, S. A., and Vasconcelos, T.

Journal of Biogeography.
2026
The Hypercubic Mk Model in Reduced State Space for the Coupled, Reversible Coevolution of Multiple Binary Characters
Johnston, I., Diaz-Uriarte, R., and Boyko, J. D.

Systematic Biology.
2026
Evolutionary Correlation of Floral and Fruit Traits Reflects Trade-offs Between Pollination and Seed Dispersal in Melastomataceae
Rodrigues Ferreira de Melo, L., Marra, C. C. T., Boyko, J. D., Reginato, M., Morellato, L. P. C., Vasconcelos, T., and de Brito, V. L. G.

Perspectives in Plant Ecology, Evolution and Systematics.

Preprints 1

2023
An Interdisciplinary Outlook on Large Language Models for Scientific Research
Boyko, J. D., Cohen, J., Fox, N., Han Veiga, M., Li, J. I.-H., Liu, J., Modenesi, B., Rauch, A. H., Reid, K. N., Tribedi, S., Visheratina, A., and Xie, X.

arXiv, 2311.04929 [cs.CL].