MICHELLE E. AFKHAMI Cox Science Center University of Miami [email protected] 1301 Memorial Dr. Department of Biology [email protected] Coral Gables, FL 33146 michelleafkhami.wordpress.com

Professional Appointments

Assistant Professor of Ecology Jan 2016 – Current University of Miami, Coral Gables, FL

National Science Foundation Postdoctoral Fellow, Plant Genome Initiative Sept 2014 – Dec 2015 Univ. of Toronto, Toronto, ON and Michigan State Univ., East Lansing, MI Supervisors: John Stinchcombe, Maren Friesen, Yair Shachar Hill

Ecology and Evolutionary Biology Departmental Research Fellow Nov 2013 – Aug 2014 University of Toronto, Toronto, ON Supervisor: John Stinchcombe

Education

Ph.D. – Population Biology Mar 2013 University of California, Davis, CA. (GPA: 4.0/4.0) Committee: Sharon Strauss (advisor), Kevin Rice, Jennifer Rudgers, John Stachowicz

M.A. – Ecology and Evolutionary Biology (thesis-based) Jan 2008 Rice University, Houston, TX. (GPA: 4.0/4.0) Committee: Jennifer Rudgers (advisor), Kenneth Whitney, Julian N. Holland

B.S. – Ecology and Evolutionary Biology May 2006 Rice University, Houston, TX. (GPA: 3.973/4.0, Magna Cum Laude, Phi Beta Kappa) Honors Thesis Advisors: Joan Strassmann, David Queller

Grants, Fellowships, and Awards Total Awarded ≈ $1,000,000

2018 – University of Miami College of Arts and Sciences Award for Recognition of Scholarly Achievement 2018 – Provost Research Award ($17,000) 2018 – Microbial Effects on Everglades Tree Islands Grant, South Florida Water Management District. ($90,000) 2017 – ULINK Fellows Award, Interdisciplinary Research Funding. (co-PI) 2017 – Interactive Effects of Hurricanes & Habitat Fragmentation on Ecological Interactions ($6,376) 2017 – Hurricane Preparedness and Recovery of Living Plant Collections ($10,000, co-PI) 2016 – Provost Research Award ($17,000) 2014 – National Science Foundation Postdoctoral Fellowship, Plant Genome Initiative ($216,000) 2014 – NSERC Banting Postdoctoral Fellowship ($140,000, Declined) 2013 – Ecology and Evol. Biology Departmental Postdoctoral Fellowship, University of Toronto ($80,000) 2013 – National Science Foundation Postdoctoral Fellowship, Plant Genome Init. ($207,000, Declined) 2012 – Mrs. George F. Jewett, Jr. Scholar, Achievement Rewards for College Scientists Award ($10,000) 2012 – Dean’s Mentorship Award, College of Biological Sciences ($5,000) 2012 – Hardman Foundation Award ($2,100) 2012 – Max Planck Institute Integral Projection Modeling Course Scholarship 2011 – ARCS Scholar, Achievement Rewards for College Scientists Award ($10,000) 2011 – Hardman Foundation Award ($2,500) 2011 – Center for Population Biology Travel Grant ($500) 2010 – National Science Foundation Doctoral Dissertation Improvement Grant ($14,991) 2010 – Center for Population Biology Research Grant ($2,100) 2010 – Center for Population Biology Travel Grant ($800) 2009 – Mildred E. Mathias Graduate Student Research Grant ($1,729) 2009 – Center for Population Biology Research Grant ($1,500) 2008 – Center for Population Biology Research Grant ($1,700) 2008 – Golden Key International Honour Society

2007 – National Science Foundation Graduate Student Fellowship ($121,500) 2007 – UC Davis Graduate Student Match Fellowship ($40,500) 2007 – Bodega Marine Laboratory Travel Grant Award ($975) 2006 – Houston Livestock Show and Rodeo Endowed Fellowship ($35,033)

2006 – The Julian Huxley Best Thesis Award, Dept. of Ecology and Evol. Biology, Rice University ($100)

Publications *undergraduate mentee, **graduate mentee, ***postdoctoral mentee

David, A.S.***, K.B. Thapa Magar*, & M.E. Afkhami (2018) Microbial Mitigation-Exacerbation Continuum: A novel framework for microbiome effects on hosts in the face of stress. Ecology. 99: 517-523.

S. Palakurty*, J.R. Stinchcombe, & M.E. Afkhami. (2018) Cooperation and Coexpression: How coexpression networks shift in response to multiple mutualists. Molecular Ecology. Special Issue on “The Host- Associated Microbiome: Pattern, Process, and Function” 27:1860-1873. doi.org/10.1111/mec.14550

Batstone, R. T.**, K. A. Carscadden**, M. E. Afkhami, & M. E. Frederickson. (2018) Using niche breadth theory to explain generalization in mutualisms. Ecology. 99: 1039-1050. doi.org/10.1002/ecy.2188

Afkhami, M.E., D.L. Mahler, J.H. Burns, M.G. Weber, M.F., Wojciechowski, J. Sprent & S.Y. Strauss. (2018) Symbioses with nitrogen-fixing bacteria: Nodulation and phylogenetic data across legume genera. Ecology. 99: 502.

Hernandez, D.**, K. Kiesewetter**, S. Palakurty*, J. Stinchcombe, and M.E. Afkhami. (2018) Synergism and symbiosis: Unpacking complex species interactions using transcriptomic approaches. The Model Legume Medicago truncatula. Ed. F.J. de Bruijn. Wiley Publishers. Accepted.

Afkhami, M.E. & J.R. Stinchcombe. (2016) Multiple mutualist effects on genomewide expression in the tripartite association between Medicago truncatula, nitrogen-fixing bacteria, and mycorrhizal fungi. Molecular Ecology. 25: 4946-4962.

Afkhami, M.E., & S.Y. Strauss. (2016) Native fungal endophytes suppress an exotic dominant and increase plant diversity over small and large spatial scales. Ecology. 97: 1159-1169.

E. Jones, M.E. Afkhami, E. Akcay, J.L. Bronstein, R. Bshary, M.E. Frederickson, K.D. Heath, J. Hoeksema, J. Ness, S. Pankey, S.S. Porter, J.L. Sachs, K. Scharnagl, & M.L. Friesen. (2015) Cheaters must prosper: reconciling theoretical and empirical perspectives on cheating in mutualism. Ecology Letters. 18:1270–84.(43 citations)

Afkhami, M.E., P.J. McIntyre, & S.Y. Strauss. (2014) Mutualist-mediated effects on species’ range limits across large geographic scales. Ecology Letters. 17: 1265-1273. (Recommended by Faculty 1000, 64 citations)

Charlton, N.D., K.D. Craven, M.E. Afkhami, B.A. Hall*, S.R. Ghimire, & C.A. Young. (2014) Interspecific hybridization and bioactive alkaloid variation increases diversity in endophytic Epichloë species of Bromus laevipes. FEMS Microbiology Ecology. 90: 276-289. (25 citations)

Afkhami, M.E., J.A. Rudgers, & J.J. Stachowicz. (2014) Multiple Mutualist Effects: Conflict and synergy in multispecies mutualisms. Ecology. 95: 833-844. (35 citations)

Gorischek, A.M.*, M.E. Afkhami, E.K. Seifert, & J.A. Rudgers. (2013) Fungal symbionts as manipulators of reproductive biology. The American Naturalist. 181: 562-570.

**Covered by Science News: Pennisi, E. (March 2013) Fungus get off my lawn.

Afkhami, M. E. (2012) Fungal endophyte-grass symbioses are rare in the California floristic province and other regions with Mediterranean-influenced climates. Fungal Ecology special issue. 5: 345-352.

Afkhami, M. E. & J. A Rudgers. (2009) Endophyte-mediated resistance to herbivores depends on herbivore identity in the wild grass, Festuca subverticillata. Environmental Entomology. 38: 1086-1095. (33 citations)

Rudgers, J.A., M. E. Afkhami, M. A. Rúa, A. J. Davitt, S. Hammer, & V. M. Huguet. (2009) A fungus among us: broad patterns of endophyte distribution in the grasses. Ecology. 90: 1531-1539. (74 citations)

Afkhami, M. E. & J. A. Rudgers. (2008) Symbiosis Lost: Imperfect vertical transmission of fungal endophytes in grasses. The American Naturalist. 172: 405-416. (102 citations)

Afkhami, M. E. & J. E. Strassmann. (2007) Adult Yellow-crowned Night-herons face in opposite directions at the nest. The Wilson Journal of Ornithology. 119:747–749.

In Review, In Revision, Completed Manuscripts, and In Prep

David, A.S.***, P.F. Quintana-Ascencio, E.S. Menges, K.B. Thapa-Magar, M.E. Afkhamiϕ & C.A. Searcyϕ (Submitted) Soil microbes are key players for plant population persistence. Nature Ecology and Evolution. ϕ indicated co-senior authors

Garoutte A.ϕ, M.E. Afkhamiϕ, K. Childs, J.R. Stinchcombe, & M. Friesen. (In Review) Moving GWAS forward: Methodological considerations for using incomplete data in diverse natural populations. PlosOne. ϕ indicated co-first authors

Zanne, A.E., K. Abarenkov, M.E. Afkhami, et al. (In Review) Fungal functional ecology: Bringing a trait-based approach to plant-associated fungi. Ecology Letters.

Z. Fu, X. Zhang, L. Xu, M.E. Afkhami, L. Huang, J. Zhang, B. Zhang. (Completed Manuscript) Investigation on combined abiotic and biotic factors on influencing Plant – leaf litter – soil interactions along an elevational gradient. Target Journal: Science of the Total Environment.

David, A.S.***, S.Y. Strauss, C.A. Searcy ϕ, & M.E. Afkhami ϕ (In Prep) Mutualist-driven population persistence across plant species range. Target Journal: American Naturalist. ϕ indicated co-senior authors

ϕ ϕ David, A.D.***, E.S. Menges, K.B. Thapa-Magar, C.A. Searcy & M.E. Afkhami . (In Prep) Microbes benefit plant habitat specialists more than non-specialists. Target Journal: Journal of Ecology. ϕ indicated co-senior authors

Afkhami, M.E., M. Friesen & J.R. Stinchcombe. (In Prep) Party Crashers? Third-party mutualist required for fitness alignment of legume-rhizobia mutualism. Target Journal: Evolution.

Select Presentations (Total = 52, Invited talks in BOLD)

2019 – Virginia Polytechnic Institute, Blackburg, VA (upcoming) 2018 – “Ecology & evolution of antagonistic & mutualistic interactions” International CRC Symposium, Germany (upcoming) 2018 – International Microbial Genomes Conference, Lake Arrowhead, California (upcoming) 2018 – Ecological Society of America. New Orleans, LA (upcoming) 2018 – University of Florida’s Tropical Research and Education Center 2018 – Computer Science Department, University of Miami 2018 – Plant Biologists of South Florida, Key Largo 2018 – Gifford Arboretum Public Lecture Series 2017 – Max Planck Institute Workshop of Mutualism and Economics Plenary Speaker. Germany 2017 – Organized Session: Scaling up Mutualisms. Ecological Society of America. Portland, OR 2017 – Gordon Conference on Microbial Population Biology, Andover, NH 2017 – University of Central Florida, Orlando, FL 2017 – Archbold Biological Research Station’s Distinguished Scientist Series, Venus, FL 2016 – Florida International University, Miami, FL 2016 – University of Miami, Miami, FL 2016 – National Center for Ecological Analysis and Synthesis, Santa Barbara, CA 2016 – Ecological Society of America. Fort Lauderdale, FL.

2015 – Cornell University. Ithaca, NY 2015 – University of Rochester. Rochester, NY 2015 – Gordon Conference on Ecological and Evolutionary Genomics. Biddeford, MN 2015 – Ecological Society of America. Baltimore, MD 2015 – Michigan State University. East Lansing, MI 2015 – Yale University. New Haven, CT 2015 – University of Kentucky. Lexington, KY 2015 – Iowa State University. Ames, IA 2015 – Purdue University. West Lafayette, IN 2015 – University of Tennessee. Knoxville, KY 2015 – Utah State University. Logan, UT 2015 – University of Oklahoma. Norman, OK 2015 – University of California LA. Los Angeles, CA 2015 – University of Miami. Miami, FL 2014 – Dartmouth University. Hanover, NH 2014 – Oregon State University. Corvallis, OR 2014 – University of Wisconsin, Madison. Madison, WI 2014 – York University. Ontario, Canada 2014 – National Science Foundation Plant Genomics Meeting. Arlington, VA 2014 – University of Toronto, St. George. Ontario, Canada. 2014 – Ecological Society of America. Sacramento, CA 2014 – Canadian Society for Ecology and Evolution’s Genomes to Biomes. Quebec, Canada 2014 – University of Toronto, Mississauga. Ontario, Canada 2013 – Center for Population Biology, University of California, Davis. Davis, CA 2013 – Dept. of Plant Pathology, University of California, Davis. Davis, CA 2012 – Symbiosis Meeting. Yosemite National Park, CA 2012 – Mathias Symposium. Bodega Bay, CA 2012 – Ecological Society of America. Portland, OR 2012 – International Symposium on the Molecular Breeding of Forage and Turf. Salt Lake, UT (coauthor) 2011 – Ecological Society of America. Austin, TX 2010 – Ecological Society of America. Pittsburgh, PA 2010 – International Symposium on Fungal Endophyte of Grasses (ISFEG) – Mycological Society of America (MSA) Joint Meeting. Lexington, KY. (oral and several poster presentations) 2009 – Ecological Society of America. Albuquerque, NM 2007 – Gordon Conference on plant-herbivore interactions. Ventura, CA 2007 – Ecological Society of America – Society for Ecological Restoration Conference. San Jose, CA 2007 – Rice University. Houston, TX 2006 – Syracuse University. Syracuse, NY

Teaching and Mentoring

Current Large Courses – Ecology (BIL 330; Fall) Ecological Lab (BIL 331; Fall) HHMI Evolution and Biodiversity Laboratory (BIL 162, Spring)

Current Graduate Student Dissertation Committee Service (12 total): Brianna Almedia Edward James (Wilson lab) Catherine Bravo (Feeley lab) Kasey Kiesewetter Stephanie Clements (Searcy lab) Alex Kula (van Dyken lab) Belén Fadrique (Feeley lab) Caitlin Mothes (Searcy lab) Damian Hernandez Blessing Mutiti Hunter Howell (Searcy lab) Andrew Reeve (Whitlock lab)

Graduate Students Mentees – Brianna Almeida (PhD; 2017-current) Awarded: University Fellowship Award, $120,000

Awarded: McKnight Doctoral Fellowship Award, $51,000 Awarded: McKnight Doctoral Fellowship Award UM Supplement

Damian Hernandez (PhD; 2017-current) Awarded: Maytag Fellowship Award, $165,000 Awarded: Best Presentation Award at UM-Fairchild Tropical Botanical Gardens Symposium, $100

Kasey Kiesewetter (PhD; 2016-current) Awarded: National Science Foundation, Graduate Student Research Fellowship, $138,000 Awarded: Lisa D. Anness Fellowship in Tropical Plant Biology, $27,000 Awarded: Dean’s Summer Research Fellowship, $5000 Awarded: Envoy Research Award, $400

Blessing Mutiti (PhD; 2017-current) Awarded: Lisa D. Anness Fellowship in Tropical Plant Biology, $27,000

Postdoctoral and Visiting Scientist Mentees – Aaron David (Postdoctoral Researcher; 2016-2018) Awarded: Forest Fungal Ecology Research Award, Mycological Society of America, $5000

Khum Thapa Magar (post-baccalaureate, 2016-2017) – Started PhD at Colorado State University in fall 2017.

Kailani Acosta (post-baccalaureate; 2017-2018) – Started PhD at Columbia University in fall 2018.

Catalina Aristizabal (Assoc. Prof., Miami Dade College, Summer 2018) – HHMI curricula development program

Undergraduate Students Mentees (>50 total) – Includes >30 women, 11 under-represented minority students, and 3 students with disabilities. *student went on to research job (Total = 18) ** student also went/will go on to grad school in ecology or related field (Total = 14)

University of Miami (13 students): Diego Aguirre Aguilar, Adriana Bevilacqua, Adriana Bolanos, Colleen Cook, Shivam Khosla, Ka Lam Nguyen, Jordan Oria, Sathvik Palakurty (First author paper in revision at Molecular Ecology), Jordan Reid, Mackenzie Smyth, Mackland Steele, Diego Torres, Tim Yassa

Miami Dade College (2 students) Dayana Gari (HHMI program), Leydiana Otano (MDC Bridge program)

University of Toronto (9 students): Gloria Cho** (NSERC Undergrad Research Support Award, ~$6,000), Najma Aryan**, Liliana Corak**, Michelle Kwan, Hasom Lee, Arleen Matinca, Fiona So, Mia Song**, Teresa Tufts

UC Davis (26 students): Sharleen Agvateesiri, Aaron Alokozai**, Mitchell Bamford**, Audrey Duong, Desalegn Ejigu*, Dai Fukumoto, Naisha Gaines*, Kyle Garrone (SUREE Intern), Lindsey Hack**, Sergei Horowitz, Michael Hower, Caprice Lee** (Center for Biophotonics Science & Tech Symposium’s Best Oral Presentation, 2011), Christopher Liao, Kristina Mardinian, Megan Mateo**, Kristin Matsumoto*, Melissa Moore**, Dayna Napolillo*, Scott Peacock, Achille Peiris, Tran Phan*, Grant Reed*, Nicholas Sou, Thuy Tran**, Kathryn Weldon, Travis Winter

Rice University (5 students): Olivia Bartlett**, Carina Baskett**, Alex Gorischek (Thesis published in American Naturalist), John Land*, William Valencia, (Paul Wheeler and Joy Gooch Research Award, $200)

Other Universities (3 Students): Aparajita Chandrasekar (U of Rochester), Kino Maravillas (Emory University), Brittany Stallworth** (Howard University, Evolution & Ecology Graduate Admissions Pathway)

Young Scholars High School Students: Nicholas Meyer, Jorge Vargas

Professional Service and Outreach

2018 – Evolutionary Demography Society Sixth Annual Meeting (Jan 10-12, 2019) Organizing Committee 2018 – Department of Biology Undergraduate Curriculum Committee 2018 – Loxahatchee Impoundment Landscape Assessment Coordination Committee 2018 – Gifford Arboretum Advisory Committee 2018 – Hurricane Preparedness and Recovery for Living Collections Workshop

2018 – College of Art and Sciences Gifford Arboretum and Greenhouse Planning Committee 2018 – Board of Directors for Not-for-profit ResearchGuild 2017 – Organized Ecological Society of America Meeting Oral Presentation Session 2017 – Department of Biology External Seminar Series Organizer 2017 – Department of Biology Undergraduate Curriculum Committee 2017 – University of Miami Arboretum and BioReach Outreach Program Development 2017 – Office of Undergrad Research Newsletter Contribution 2017 – LILA (Loxahatchee Impoundment Landscape Assessment) 10-Year Planning for Everglades Committee 2017 – University of Miami Arboretum and BioReach Program Outreach Days (co-organization and execution) 2017 – Gifford Arboretum Advisory Committee 2017 – Gifford Arboretum Newsletter Article Contribution 2017 – HHMI Undergraduate Research Symposium Judge 2016 – Department of Biology External Seminar Series Organizer 2016 – Microscopy Experience Outreach Module for Fourth-Graders Co-organizer 2016 – National Science Foundation External Reviewer (May & Oct) 2016 – Fairchild Graduate Student Symposium Judge 2015 – Interviewed for an article on fungal endophytes in the popular magazine Organic Gardening. 2014 – Panelist for “Careers and Research in Ecology & Evolution” Undergraduate Weekend Workshop 2014 – Judge for Undergraduate Honors Thesis Research Award, University of Toronto 2014 – Judge for Braun/Bell Award for Best Poster/Talk at ESA Conference 2013 – IIASA Peccei and Mikhalevich Award Reviewer 2013 – Graduate School Question/Answer Panel for Undergraduates 2012 – Evolution and Ecology Faculty Search Graduate Student Panel Member 2012 – Center for Population Biology Postdoctoral Search Graduate Student Panel Member 2012 – Picnic Day Community Outreach Organizational Committee 2012 – Graduate Student Recruitment Field Trip to Quail Ridge Reserve Organizer 2012 – Evolution and Ecology Seminar Speaker Nominator/Host for Jennifer Rudgers 2011 – Population Biology Graduate Group Admissions Committee 2011 – Chancellor’s Ambassador for University of California, Davis 2011 – Center for Population Biology Workshop on Hierarchical Models Co-organizer 2011 – Graduate Student Recruitment Field Trip to Quail Ridge Reserve Co-Organizer 2011 – Kids into Discovering Science (KiDS) Field Trip (2011, 2012, 2013) 2010 – Evol. and Ecology Seminar Speaker Nominator/Host for Judith Bronstein 2009 – Symbiosis Discussion Group Co-organizer 2009 – Quail Ridge Reserve Advisory Committee (2009-2011) 2009 – Picnic Day Outreach: Native Plant Booth (2009, 2010, 2011, 2012)

Reviewer:  External reviewer for the National Science Foundation (Dimensions of Biodiversity, Population & Community Ecology, Geobiology and Low-Temperature Geochemistry Programs), Canada’s NSERC, Israeli Science Foundation, University of Miami Beyond the Book Grants, IIASA Peccei and Mikhalevich Award Reviewer  African J of Agriculture, American J of Botany, The American Naturalist (3), AOB Plants, Biological Invasions, Coral Reefs (2), Ecological Entomology, Ecological Research, Ecology (3), Evolution (2), Frontiers in Plant Sciences, Fungal Ecology (4), J of Ecology (2), J of Medicinal Plant Research, Molecular Ecology, Oecologica (4), Plant & Soil, Trends in Ecology & Evolution (2)

Professional Societies and Workshops

(A) Professional Societies and Organizations (within last 5 years):  American Association for the Advancement of Science (AAAS)  Canadian Society for Ecology & Evolution (CSEE)  Ecological Society of America (ESA)  Mycological Society of America (MSA)  Women In Tenure Track Years (WITTY)

(B) Working Groups:  National Center for Ecological Analysis and Synthesis (NCEAS) – National Science Foundation-supported working group on “Forming an integrated understanding of function across fungi” (2016-current)  Quantifying Niche Breadth Working Group (2015-current)  National Center for Ecological Analysis and Synthesis (NCEAS) – Working Group on Cheating in Mutualisms (2012-2015)

(C) Workshops: Software Carpentry Workshop (2014), Python Methods Workshop (2014), AMF Methods Workshop (2013), Max Planck Institute’s Integral Projection Modeling Course (2012), ESA’s Integral Projection Modeling Workshop (2012), Center for Population Biology Workshops on: Phylogenetics Methods (2013), Hierarchical Models (2011), R Tools (2008), and Coevolution (2008)