Michael J. Song

Education

PhD, Integrative Biology, UC Berkeley, 2021.
BA, Molecular Biology and Biochemistry, Reed College, 2015.

Professional Appointments

Peer-reviewed Journal Publications

  1. Song, M.J., Li, F.W., Freund, F., Tribble, C.M., Toffelmier, E., Miller, C., Shaffer, H.B., Rothfels, C.J., (accepted for 2025) "The nitrogen-fixing fern Azolla has a complex microbiome characterized by varying degrees of cophylogenetic signal," American Journal of Botany. Preprint: doi:10.1101/2024.05.20.592813
  2. González-Ramírez, I., Escalona, M., Miller, C., Chumchim, N., Marimuthu, M.P.A., Nguyen, O., Song, M.J., Mishler, B.D. (2024), "A genome assembly for the California Floristic Province paleoendemic liverwort Calasterella californica," Journal of Heredity, esae065. doi:10.1093/jhered/esae065
  3. Song, M., Pirro, S., Lahmeyer, S., Kyle, K.#, and White, M.# (2024), "The complete chloroplast sequence of the invasive feathered mosquito fern and a draft genome of its endosymbiont reveals that rates of genome erosion vary across the genus" American Fern Journal, in press.
  4. Martinez-Gomez, J.*, Song, M.J.*, Tribble, C.M.*, Kopperud, B.T., Freyman, W.A., Hohna, S., Specht, C.D., Rothfels, C.J. (2024), "Commonly used Bayesian diversification methods lead to biologically meaningful differences in branch-specific rates on empirical phylogenies." Evolution Letters qrad044. doi:10.1093/evlett/qrad044
  5. Song, M.J., Rothfels, C.J., Schuettpelz, E., Nitta, J., Huiet, L., Li, F.W., Wefferling, K.M. (2023), "Resolving Deep Relationships and Revealing Ancient Whole-Genome Duplications in Pteridaceae using Transcriptomic Data." American Fern Journal, 113(3):191-210. doi:10.1640/0002-8444-113.3.191
  6. Song, M.J., Huynh, M.#, Lahmeyer, S., Sedaghatpour, M. (2023), "A New Record of the invasive Azolla pinnata subsp. pinnata R. Br. (Salviniaceae) in California." American Fern Journal, 113(1):56-57. doi:10.1640/0002-8444-113.1.56
  7. Mehlferber, E.C.*, Song, M.J.*, Pelaez, J.N., Jaenisch, J., Coate, J.E., Koskella, B., Rothfels, C.J. (2022), "Polyploidy and microbiome associations mediate similar responses to pathogens in Arabidopsis." Current Biology, 32(12): 2719-2729.e5. doi:10.1016/j.cub.2022.05.015
  8. Bai, J.#, Song, M.J., Gao, J., Li, G. (2022), "Whole Genome Duplication and Dispersed Duplication Characterize The Evolution of The Plant Pinoid Gene Family Across Plant Species." Gene, Volume 829 Article 146494. doi:10.1016/j.gene.2022.146494
  9. Song, M.J.*, Potter, B.*, Doyle, J.J., Coate, J.E. (2020), “Gene Balance Predicts Transcriptional Responses Immediately Following Ploidy Change In Arabidopsis thaliana.” The Plant Cell, 32(5): 1434–1448. doi:10.1105/tpc.19.00832
  10. Frankel-Bricker, J.*, Song, M.J.*, Benner, M.J., Schaack, S. (2019), “Variation in the microbiome of Daphnia magna across genotypes and temperatures.” Microbial Ecology, 79: 731–742. doi:10.1007/s00248-019-01412-9
  11. Song, M.J., Schaack, S. (2018), “Evolutionary Conflict Between Mobile DNA and Their Host Genome.” American Naturalist, 192(2): 263-273. doi:10.1086/698482
  12. Song, M.J.*, Kuo, L*., Huiet, L., Pryer, K.M., Rothfels, C.J., Li, F. (2018), “A novel chloroplast gene reported for flagellate plants.” American Journal of Botany, 105(1): 117–121.
    13. doi:10.1002/ajb2.1010
  13. Adrion, J.R.*, Song, M.J.*, Schrider, D.R., Hahn, M.W., and Schaack, S. (2017), “Genome-wide estimates of transposable element insertion and deletion rates in Drosophila melanogaster.” Genome Biology and Evolution, 9(5): 1329–1340. doi:10.1093/gbe/evx050
  14. Coate, J.E., Song, M.J., Bombarely, A. and Doyle, J.J. (2016), "Expression-level support for gene dosage sensitivity in three Glycine subgenus Glycine polyploids and their diploid progenitors." New Phytologist, 212: 1083–1093. doi:10.1111/nph.14090
*contributed equally #former undergraduate student

bioRxiv pre-prints

  1. Song, M.J.*, Li. F.W.*, Freund, F., Escalona, M., Toffelmier, E., Miller, C., Shaffer, H.B., Nguyen, O., Marimuthu, M.P.A, Chumchim, N., Tribble, C., Fairbairn, C.W., Seligmann, W., Rothfels, C.J., “The genome assembly of the duckweed fern, Azolla caroliniana,” in review at The Journal of Heredity. doi:10.1101/2024.10.22.619683v1
*contributed equally

Conference Papers

  1. Song, M.J. (2018), "On the Possibilities of Plant Knowledges." Future (Im)Perfect - UC Berkeley Comparative Literature Conference 2018.
  2. Song, M.J. (2020), "Support Our Tropes: Liberal Tropes in Faith Hill and Baratynsky." AATSEEL 2020.

Grants and Awards

  1. Skyline College Presidential Improvement Fund Award: "Earth Day Every Day" (2024) - $7500
  2. Skyline College Short-Term Faculty Professional Development Grant (2024) - $3000
  3. Skyline College Zero Text Book Cost Early Adopter Course Project Grant (2023) - $5000
  4. IB Dissertation Completion Award (2021) - $2500
  5. UC Berkeley Teaching Effectiveness Award (2021) - $500
  6. UC Berkeley Outstanding GSI Award (2021) - No money :P
  7. Graduate Remote Instruction Innovation Fellows Program (2020) - $2,000
  8. Conference Travel Grants Award, UC Berkeley (2018) - $900
  9. Graduate Division Summer Grant, UC Berkeley (2018) - $3,500
  10. American Society of Plant Taxonomists W. Hardy Eshbaugh Graduate Student Research Grant Award (2018) – $1,000
  11. Honorable Mention–National Science Foundation Graduate Research Fellowship Program (2018)
  12. Lawrence R. Heckard Endowment Fund of the Jepson Herbarium (2017) – $1,532
  13. Graduate Assembly Travel Award, UC Berkeley (2017) - $300
  14. Barbara Joe Hoshizaki Memorial Scholarship, Organization for Tropical Studies (2017) – $500
  15. Huayu Enrichment Scholarship, Ministry of Education, Taiwan (2016) – $4,000
  16. Stafford Research Fellowship for post-bac studies, Reed College (2015) – $5,500
  17. Plant Biology Summer Research Fellowship, Cornell University (2014) – $4,000
  18. Reed College Summer Undergraduate Research Fellowship (2013) – $5,500
  19. Betty C. Liu Summer Research Fellowship, Reed College (2012) – $5,500

Presentations

Conference Talks and Invited Lectures as main presenter
  1. "Initial Insights from the California Conservation Genomics Project: what can we do with all these data?" Colloquium in Biology, San Francisco State University, 2024
  2. "Cheilanthoid Ferns and Desiccation Tolerance," North American Rock Garden Society Western Chapter Study Weekend 2024
  3. "Problems, Pitfalls, and Potenial of Organizing During the Covid Pandemic," Society for the Study of Social Problems 2022
  4. "The ecology and evolution of polyploid niches: investigating the interaction of ploidy, microbiome, and pathogen," Botany 2021
  5. "PhD Finishing Talk: The ecology and evolution of polyploid niches," Botany Lunch, University and Jepson Herbaria, UC Berkeley 2020
  6. "Quantifying transcriptome size variation and dosage responses immediately following ploidy change in Arabidopsis thaliana" Botany 2018.
  7. "Soybean from a land down under: testing the dosage balance hypothesis in Glycine subgen. Glycine," Botany Lunch, University and Jepson Herbaria, UC Berkeley, 2018.
  8. "Polyploidy: an evolutionary dead-end? Again?" Reed College invited lecture, 2017.
  9. "Learning From Linnaeus: rethinking scientific language in the age of Trump," Botany Lunch, University and Jepson Herbaria, UC Berkeley, 2017.
  10. “The Nature of Transposable Element Movement,” Evolution 2013.
Selected Conference Posters
  1. "Varying degrees of codiversification characterize the Azolla holobiont" Evolution 2023.
  2. "Commonly used Bayesian diversification-rate models produce biologically meaningful differences on empirical phylogenies" Evolution 2023.
  3. "Diversification rates across lineages: how does biological meaning differ across model-based approaches?" Botany 2019.
  4. "Difficulties in the Inference of Ancient Whole-Genome Duplications" Botany 2018.
  5. "Comparing gene repertoires in annual and perennial soybean (Glycine)" Evolution 2017.
  6. “Cross-species and cross-ploidy level transcriptomic data support important roles for selection on gene dosage in shaping gene networks?” Botany 2015.
  7. “Polyploidy and transcriptome size: Does genome doubling cause transcriptome doubling?” Plant Biology 2014.
  8. “Does genome doubling cause transcriptome doubling?” Botany 2014.
  9. “Quantifying whole transcriptome size variation across species, tissues and ploidy levels in Glycine,” SMBE 2014.
  10. “Transposable element rates in Drosophila melanogaster,” SMBE 2013.
Guest Lectures
  1. "Metagenomics and Evolution," Biology 352 (Bioinformatics), Reed College, Fall 2023.
  2. "Gene Duplication," IB 160 (Evolution), UC Berkeley, Fall 2020.
  3. "Leptosporangiate Ferns," IB 168LF (Vascular Plant Systematics), UC Berkeley, Spring 2019.
  4. "Current Topics in Microbiome Research," Biology 352 (Bioinformatics), Reed College, Fall 2018.
  5. "Polyploidy and Diversification," Biology 363 (Genes, Genetics, and Genomes), Reed College, Spring 2018.

Teaching

Certifications:
  1. University of California Certificate in Teaching and Learning in Higher Education
Instructor of Record:
  1. BIO 215, Organismal Biology, Skyline College, San Mateo County Community College District, Fall 2022, Spring 2023, Fall 2023, Spring 2024, Fall 2024
  2. BIO 101, Our Biological World, Skyline College, San Mateo County Community College District, Fall 2022, Spring 2023, Fall 2023, Spring 2024
  3. BIO 141, Principles of Cell and Molecular Biology, California State University East Bay, Spring 2022
  4. BIO 131, Principles of Organismal Biology: Evolution & Ecology, Diablo Valley College, Contra Costa Community College District, Spring 2022
Seminar Organizer:
  1. IB 290-365 Graduate Botany Seminar, UC Berkeley, Spring 2019.
Graduate Student Instructor:
  1. IB 160, Evolution Discussion, UC Berkeley, Fall 2018, Fall 2020
  2. IB 102LF, California Plant Life Lab, UC Berkeley, Spring 2018
  3. IB 168L, Vascular Plant Systematics Lab, UC Berkeley, Spring 2017, Spring 2021
  4. Bio 1B, Introductory Biology Lab, UC Berkeley, Fall 2016 2017 2019, Spring 2019
  5. IB 169, Evolutionary Medicine Discussion, UC Berkeley, Spring 2020
Undergraduate Thesis Students:
  1. Jonathan Qu, UC Berkeley 2019
Science Outreach
  1. Presenter at Science Slam, Black Pine Circle School, February 2019.
  2. Workshop Organiser at Expanding Your Horizons in Math and Science Conference at Skyline College, March 2023.

Languages

Service

Professional Societies