Megan Ruffley
National Science Foundation Postdoctoral Fellow
Carnegie Institution for Science, Stanford University
260 Panama St, Stanford, CA 94305
MeganRRuffley@gmail.com
Research Overview
Bioinformatics and computational biology Ph.D. with a focus in evolutionary plant biology, genomics, computer science and statistics. Experience implementing and developing bioinformatic software for biological data, including whole-genome sequence, phylogenetic, phenotypic, climatic, and geographic data. Field work experience in collection based research and common garden or greenhouse/growth chamber experiments. Research in population and quantitative genetics, genotype-phenotype mapping, and genomic adaptation. Collaborative, driven worker with excellent written and verbal communication skills.
Profession Preparation
Postdoctoral Researcher, Carnegie Institution for Science, Stanford, CA 2020-2024
PhD, Bioinformatics and Computational Biology, University of Idaho, ID. 2015-2020
BS, Botany, Minor Bioinformatics, Miami University, OH. 2011-2015
Appointments
National Science Foundation Plant Genome Research Project Postdoctoral Fellow 2021-2024
Postdoctoral Researcher, Carnegie Institution for Science, Stanford, CA 2020-2021
Graduate Teaching Assistant, Biology Department, University of Idaho, ID 2019-2020
Graduate Research Fellow, Bioinformatics and Comp. Biology, University of Idaho, ID 2015-2019
Publications full publication history
Ruffley M , Leventhal L, Hateley S, Rhee SY, Exposito-Alonso M. (2023) Conflicts in natural selection constrain adaptation to climate change in Arabidopsis thaliana. Manuscript available upon request.
Gillespie L, Ruffley M, Exposito-Alonso M. (2023) An image is worth a thousand species: mapping plant biodiversity with citizen science, remote sensing, and deep learning. BioRxiv doi: https://doi.org/10.1101/2022.08.16.504150
Exposito-Alonso M, … Ruffley M*, et al.* (2022) Genetic diversity loss in the Anthropocene. Science 377 (6613), 1431-1435.
*equal contribution
Ruffley M, Smith ML, Espindola AE, Turck DF, Mitchell N, Carstens BC, Sullivan J, Tank DC. (2022) Genomic evidence of an ancient inland temperate rainforest in the Pacific Northwest of North America. Molecular Ecology 31 (10), 2985-3001.
Lagerstrom KM, Vance S, Cornwell BH, Ruffley M, Bellagio T, Exposito-Alonso M, Palumbi SR, Hadly EA. (2022) From coral reefs to Joshua trees: What ecological interactions teach us about the adaptive capacity of biodiversity in the Anthropocene. Philosophical Transactions of the Royal Society B. 377 (1875) 20210389.
Overcast I*, Ruffley M*, Rosindell J, Hickerson M, Harmon L, Rominger A. et al. (2021) A unified model of species abundance, genetic diversity, and functional diversity reveals the mechanisms structuring ecological communities. Molecular Ecology Resources. 21 (8) 2782-2800.
*equal contribution
Ruffley M, Peterson K, Week B, Tank DC, Harmon LJ. (2019) Identifying Models of Trait-Mediated Community Assembly Using Random Forests and Approximate Bayesian Computation. Ecology & Evolution. 9 (23), 13218-13230
Sullivan J, Smith ML, Espindola AE, Ruffley M, Rankin A, Tank DC, Carstens BC. (2019) Integrating life history traits into predictive phylogeography. Molecular Ecology. 28 (8), 2062-2073.
Ruffley M, Smith ML, Espíndola A, Carstens BC, Sullivan J, Tank DC. (2018). Combining allele frequency and tree-based approaches improves phylogeographic inference from natural history collections. Molecular Ecology. 27 (4), 1012-1024.
Smith ML, Ruffley M, Espíndola A, Tank DC, Sullivan J, Carstens BC. (2017) Demographic model selection using random forests and the site frequency spectrum. Molecular Ecology. 26 (17), 4562-4573.
Espíndola A, Ruffley M, Smith ML, Tank DC, Carstens BC, Sullivan J. (2016) Identifying cryptic diversity with predictive phylogeography. Proceedings of the Royal Society B: Biological Sciences, 283, 20161529.
Awards and Grants
National Science Foundation Postdoctoral Fellowship, Plant Genome Research Project. 2021-2024
Bioinformatics and Computational Biology Fellowship, University of Idaho 2018-2019
Paul Joyce Research Fellowship, University of Idaho 2019
IBEST Director’s Research Fellowship, University of Idaho 2015-2018
National Science Foundation Graduate Research Fellowship Program, Honorable Mention 2017
Graduate Student Research Award, Society for Systematic Biologists 2017
Synergistic Activities
Outreach
Public Lecture given at the California Academy of Sciences; San Francisco, CA 2022
“Plant Evolution: A Journey Through Time”
Carnegie Institute Postdoc Association Representative 2021-2023
Advocate for fair pay and benefits for all postdocs
Instructor for Plant regenerative growth; Middle school level 2-week program 2021
“Plant Regeneration Station” focused on stimulating growth in veggies found at home
Randall Women in Science (RWiS) Seminar Series, student representative 2018-2020
https://www.uidaho.edu/sci/biology/news/seminars/randall-seminar
RWiS: Inclusion, Diversity, and Equality Alliance, graduate student board member 2018-2020
Host workshops for managing work-life balance, job applications, negotiations
“Science After Hours” presenter, Palouse Clearwater Environmental Institute 2018
Phylogeography of Pacific Northwest Plants
Nez Perce Tribe’s 7th Annual STEM Fair presenter for Junior High and High School Students 2016
Teaching
Teaching Assistant for Plant Ecology and Evolution in Arid Climates; Bio 200 level course 2022
Instructor Moises Exposito-Alonso, Stanford University, Stanford, CA
Teaching Assistant for Ecology and Population Biology; Bio 200 level course 2020
Instructor Dr. Scott Nuismer, University of Idaho, Moscow, ID
Teaching Assistant for Principles of Phylogenetics; Bio 400/500 level course 2019
Instructor Dr. Jack Sullivan, University of Idaho, Moscow, ID
Co-Instructor of Comparative Phylogeography and Community Ecology Workshop 2019
University of Oslo and ForBio, Drøbak, Norway.
CAMI workshop website: https://compphylo.github.io/Oslo2019/CAMI_files/CAMI.html
Co-Instructor;Website Developer, Predictive Phylogeography and Random Forest Workshop 2018
Society for Systematic Biologists meeting. Columbus, OH
Website and materials: https://predictivephylogeography-ssb2018.github.io
Teaching Assistant for Advanced Field Botany; Bio 500 level course 2017, 2018
Instructor Dr. David C. Tank, University of Idaho, McCall Outdoor Science School, ID
Mentorship
Postdoctoral Mentor: 2 Graduate Students, 1 Research Assistant, 2 Undergraduates
Graduate Student Mentor: 4 Graduate Students, 1 Undergraduate
Public Software
Community Assembly Model Inference (CAMI); R package. https://github.com/ruffleymr/CAMI
Documentation: ruffleymr.github.io/CAMI/CAMI_Installation.html
Massive Eco-Evolutionary Synthesis Simulation (MESS). https://github.com/messDiv/MESS
Documentation: pymess.readthedocs.io/en/latest/installation.html
Reviewer
The American Naturalist, Systematic Biology, Molecular Ecology, Molecular Ecology Resources, Evolutionary Ecology.