James Dietrich Boyko - Curriculum Vitae

Current Appointment: The Michigan Institute for Data Science, University of Michigan
Web page: https://www.jamesboyko.com
Github: jboyko
Email: jboyko@umich.edu

Academic Background

Schmidt Futures AI in Science Post-doctoral fellow, University of Michigan (January 2023 - Present)
Research Project: Deep-neural networks as a framework for understanding major evolutionary transitions in animal body form
Mentors: Dr. Dan Rabosky and Dr. Yuanfang Guan

Post-doctoral research associate, University of Tennessee, Knoxville (October 2022 - January 2023)
Research Project: Assessing ascertainment bias in diversification rate estimates
Mentor: Dr. Brian O’Meara

Ph.D., University of Arkansas, Biological Sciences (August 2017 - August 2022)
Dissertation: Hiding in plain sight: accounting for rate heterogeneity in trait evolution models.
Mentor: Dr. Jeremy M. Beaulieu

M.Sc., University of Toronto, Department of Ecology and Evolutionary Biology (August 2015 - July 2017)
Thesis: The Effect of Congeners on Trait Evolution and Sexual Dimorphism in Lesser Antillean Anolis Lizards.
Mentor: Dr. Luke D. Mahler

B.A., University of Toronto, Biology and History (September 2010 - June 2015)
Research Project: Meta-analysis of phylogenetic community assembly.
Mentor: Dr. Benjamin Gilbert

Publications

Boyko, J. D., and B. C. O’Meara. 2023. dentist: Computing uncertainty by sampling points around maximum likelihood estimates. bioRxiv 2023.01.10.523430. In review.

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

Boyko J.D., Beaulieu J.M, Hagen E.R., and Vasconcelos T.N.C. 2023. Long-term responses of life-history strategies to climatic variability in flowering plants. New Phytologist (special issue). In reivew.

Boyko, J.D. and Beaulieu, J.M. 2022. Reducing the biases in false correlations between discrete characters. Systematic Biology. Accepted.

Mortimer S.M., Boyko J.D., Beaulieu J.M., Tank D.C. 2022. Synthesizing Existing Phylogenetic Data to Advance Phylogenetic Research in Orobanchaceae. Systematic Botany. 47, 533-544.

Vasconcelos T.N.C., Boyko J.D., Beaulieu J.M. 2021. Linking mode of seed dispersal and climatic niche evolution in flowering plants. Journal of Biogeography.

Boyko, J. D. & Beaulieu, J. M. 2021. Generalized hidden Markov models for phylogenetic comparative datasets. Methods Ecology and Evolution, 12, 468–478.

Nakov, T., Boyko, J.D., Alverson, A.J. and Beaulieu, J.M., 2017. Models with unequal transition rates favor marine origins of Cyanobacteria and photosynthetic eukaryotes. PNAS, 114(50), pp. E10606-E10607.

Software contributions:

corHMM - Correlated Hidden Markov Models for comparative biology

dentist - Computing uncertainty by sampling points around maximum likelihood estimates

hiSSE - Hidden State Dependent Speciation Extinction models

OUwie - Estimates and compares rate differences of continuous character evolution under Brownian motion and a new set of Ornstein-Uhlenbeck (OU) models

Honors, Awards, and Funding

2023: $250 USD - UMPDA Professional Development Award

2022: $750 USD – Journal of Biogeography Innovation award

2021: $1000 USD – Outstanding graduate student research award

2019: $500 USD - American Society of Naturalists Travel Grant

2017 to 2021: $80,000 USD - Distinguished Doctoral Fellowship

2017: $750 USD - SGS Conference Grant

2016: $400 USD - Phylogenetic Symposium Travel Grant

Presentations

Boyko, J.D., Beaulieu, J.M. (2022) Reducing the biases in false correlations between discrete characters. (Evolution: Poster presentation - International Conference).

Boyko, J.D., Beaulieu, J.M. (2019) Quantifying the limits of our knowledge in phylogenetic comparative studies. (Quantitative Genetics Workshop: Oral presentation - International Workshop).

Boyko, J.D., Nakov, T., Alverson, A.J. and Beaulieu, J.M. (2019) Quantifying the limits of our knowledge in phylogenetic comparative studies. (Botany: Oral presentation – International Conference)

Boyko, J.D., Nakov, T., Alverson, A.J. and Beaulieu, J.M. (2018) Testing the signal of marine versus freshwater origins of photosynthetic eukaryotes. (Botany: Oral presentation – International Conference)

Boyko, J.D., Mahler, D. L. (2017) Testing for character displacement in Lesser Antillean anoles. (Atwood Colloquium: Oral presentation – Institutional Conference)

Boyko, J.D., Mahler, D. L. (2016) Character displacement in Lesser Antillean Anolis lizards. (Evolution: Oral presentation – International Conference)

Boyko, J.D., Mahler, D. L. (2016) Testing for repeated character displacement in Anolis lizards. (OE3C: Oral presentation – Provincial Conference)

Volunteering and Outreach

2018 to 2021: Vice president of the University of Arkansas Wildlife Society

2018 to 2021: Member of the Association for Women in Science (AWIS)

2018 to 2020: Watershed Conservation Resource Center

2018, 2019: Bearcat Hollow Maintenance

2017: Atwood Colloquium Volunteer Coordinator (University of Toronto)

2016: Atwood Colloquium Volunteer (University of Toronto)

Teaching Exerpience

2017 to 2020 Teaching Assistant: BIOL3023 (Evolutionary Biology) - University of Arkansas

2016 to 2017 Teaching Assistant: EEB365 (Macroevolution) - University of Toronto

2016 to 2017 Teaching Assistant: EEB225 (Biostatistics for Biologists) - University of Toronto

2015 to 2016 Teaching Assistant: BIO220 (From Genomes to Ecosystems in a Changing World) - University of Toronto

2015 to 2016 Teaching Assistant: BIO120 (Adaptation and Biodiversity) - University of Toronto

References

Dr. Jeremy M. Beaulieu – University of Arkansas

Dr. Brian C. O’Meara – University of Tennessee