Contact Information:

Kathleen Pryer
Department of Biology
Duke University
Durham, NC 27707-0338
Telephone: 919-660-7380
    • Fay-Wei

Fay-Wei Li 李飛葦, Postdoctoral Researcher


Google Scholar

Rm 326 Biological Sciences

Department of Biology, Duke University
Box 90338. Durham NC 27708



Ph.D. Department of Biology, Duke University (2010-2015)

B.S. Department of Life Science, National Taiwan University (2005-2009)


Neochrome evolution

The major goal of my dissertation research is to investigate the origin and evolution of neochrome—a chimeric photoreceptor that likely triggered the the modern radiation of ferns. Because neochrome is a chimera of phytochrome and phototropin genes, to investigate its origin I have reconstructed the first comprehensive phylogenies of phytochrome and phototropin. Using this phylogenetic framework, I was able to trace the origin of fern neochrome to hornworts (a bryophyte lineage). In hornworts, I discovered novel neochrome gene and I demonstrated that ferns acquired neochrome from hornworts via horizontal gene transfer (Li et al, 2014 PNAS). Currently, I'm further delving into the tempo and mode of neochrome evolution in ferns, and examining how that pertains to fern diversification. 

Horizontal gene transfer among ferns

I recently discovered that neochrome has been horizontally transferred among ferns in a seemingly high frequency (Li et al, 2014 PNAS). I aim to further use the 1KP transcriptomes to ask if neochrome is an exception, or HGT is rather common among fern genes. I will develop a phylogeny-based bioinformatics pipeline to identify incidences of HGT. Each reported HGT will be confirmed using genomic PCR and cloning. 

Fern genomics

Ferns is the only lineage of land plants that lacks reference genome. I'm currently involved in getting preliminary shotgun sequencing on selected fern species; these data will give us a first look at the fern genome space and structure. Kathleen and I also initiated a crowdfunding campaign to sequence the genome of Azolla, a little fern that has enormous green potential. I built two websites, one for crowdfunding and the other for the genome project. We raised $7,160 pledges from 123 backers. I am also in charge of the project twitter account @AzollaGenome. We together participated Reddit Science AMA, answering over a hundred questions with 6,349 upvotes. Our project has received several media coverage, including The Economist, The Washington Post, USA TodayThe Globe and Mail, Contra Costa TimesThe News & Observer, and Scientific American.    

Boechera Microsatellite Database

The Boechera Systematics Group, led by Michael D. Windham, has generated a wealth of microsatellite data for Boechera species (Brassicaceae). Total of 4,000 individual specimens— including >80 types—have been genotyped for 15 microsatellite loci. This data will be the basis for future taxonomical revision of the group, and has great potential to address various evolutionary and ecological questions. I am developing an integrated Boechera Database that researchers can easily access and analyze the metadata. I built a prototype at This user-friendly database portal currently runs several algorithms for data retrieval, microsatellite-based species identification, and can automatically deduce the genomic make-up of hybrid individuals.I will continue to integrate species descriptions, images, interactive keys, and metadata regarding ploidy, reproductive mode and geographic distribution into the database.


As first/co-first author:

Li, F.-W., M. Melkonian, C.J. Rothfels, J.C. Villareal, D. Stevenson, S.W. Graham, G.K.-S. Wong, K.M. Pryer, S. Mathews. Phytochrome diversity in green plants and the origin of canonical plant phytochromes. Nature Communications 6: 7852. Reprint PDF
Li, F.-W., C.J. Rothfels, M. Melkonian, J.C. Villarreal, D.W. Stevenson, S.W. Graham, G.K.-S. Wong, S. Mathews, and K.M. Pryer. The origin and evolution of phototropins in plants. Frontiers in Plant Science: in press.

Li, F.-W., K.M. Pryer. 2014. Crowdfunding the Azolla fern genome project: a grassroots approach. GigaScience, 3: 16. Reprint PDF

     Media coverage: GigaScience Editor's pick

Li, F.W., J.C. Villarreal, S. Kelly, C.J. Rothfels, M. Melkonian, E. Frangedakis, M. Ruhsam, E. M. Sigel, J.P. Der, J. Pittermann, D.O. Burge, L. Pokorny, A. Larsson, T. Chen, S. Weststrand, P. Thomas, E. Carpenter, Y. Zhang, Z. Tian, L. Chen, Z. Yan, Y. Zhu, X. Sun, J. Wang, D.W. Stevenson, B.J. Crandall-Stotler, A.J. Shaw, M.K. Deyholos, D.E. Soltis, S.W. Graham, M.D. Windham, J.A. Langdale, G.K.S. Wong, S. Mathews & K.M. Pryer. Horizontal transfer of an adaptive chimeric photoreceptor from bryophytes to ferns. Proceedings of the National Academy of Sciences USA, 111: 6672-6677. Reprint PDF

     Media coverage: New York TimesThe EconomistNational GeographicScientific AmericanFaculty of 1000Current BiologyNature Reviews Genetics

Li, F.W., Pryer, K.M., Windham, M.D. 2012. Gaga, a new genus segregated from Cheilanthes (Pteridaceae). Systematic Botany37: 845-860. Reprint PDF

     Media coverage: Rolling StoneWiredHuffington PostNational GeographicGuardianNew York Times

Li, F.W., Kuo, L.Y., Rothfels, C.J., Ebihara, A., Chiou, W.L., Windham, M.D., Pryer, K.M. 2011. rbcL and matK earn two thumbs up as the core DNA barcode for ferns. PLoS One 6: e26597. Reprint PDF

Li, F.W. 2011. Book review: Knapp, Ralf. 2011. Ferns and Fern Allies of Taiwan. Taxon 60: 1233-1234. Reprint PDF

Kuo*, L.Y., Li*, F.W., Chiou, W.L., Wang, C.N. 2011. The first insight into fern matK phylogeny. Molecular Phylogenetics and Evolution 59: 556-566. *Equally contributed Reprint PDF

Li*, F.W., Kuo*, L.Y., Huang, Y.M., Chiou, W.L., Wang, C.N. 2010. Tissue-Direct PCR, a rapid and extraction-free method for barcoding of ferns. Molecular Ecology Resources 10: 92-95. *Equally contributed Reprint PDF

Li, F.W., Tan, B.C., Buchbender, V., Moran, R.C., Rouhan, G., Wang, C.N., Quandt, D. 2009. Identifying a mysterious aquatic fern gametophyte. Plant Systematics and Evolution 281: 77-86. Reprint PDF

As co-author:

Windham, M.D., J.B. Beck, F.-W. Li, A. Allphin, J.G. Carman, C.A. Rushworth, E.M. Sigel, P.J. Alexander, C.D. Bailey, I.A. Al-Shehbaz. Searching for diamonds in the apomictic rough. I: Do rare sexual populations of Boechera lignifera (Brassicaceae) represent a distinct species? Systematic Botany (in review).
Wolf, P.G., E.B. Sessa, D.B. Marchant, F.-W. Li, C.J. Rothfels, E.M. Sigel, M.A. Gitzendanner, C.J. Visger, J.A. Banks, D.E. Soltis, P.S. Soltis, K.M. Pryer, and J.P. Der. An exploration into fern genome space. (in review).
Pryer, K.M., L. Huiet, F.-W. Li, C.J. Rothfels, E. Schuettpelz. Maidenhair ferns––Adiantum––are indeed monophyletic, and sister to to the shoestring ferns––vittaroids (Pteridaceae). (in review).
Rothfels C.J., F.-W. Li, E.M Sigel., L. Huiet, A. Larsson, D.O. Burge, M. Ruhsam, M. Deyholos, D. Soltis, N. Stewart, S. Shaw, L.M. Pokorny, T. Chen, C. dePamphilis, L. DeGironimo, D.W. Stevenson, S.W. Graham, G.K.-S. Wong, and K.M. Pryer. The evolutionary history of ferns inferred from 25 single-copy nuclear genes. American Journal of Botany 102: 1089-1107. Reprint PDF

Sessa, E.B., J.A. Banks, M.S. Barker, J.P. Der, A.M. Duffy, S.W. Graham, M. Hasebe, J. Langdale, F.-W. Li, D.B. Marchant, K.M. Pryer, C.J. Rothfels, S.J. Roux, M.L. Salmi, E.M. Sigel, D.E. Soltis, P.S. Soltis, D.W. Stevenson, P.G. Wolf. 2014. Between two fern genomes. GigaScience, 3:15. Reprint PDF

Zhang, W.Y., L.Y. Kuo, F.W. Li, C.N. Wang, W.L. Chiou. 2014. The hybrid origin of Adiantum meishanianum (Pteridaceae): a rare and endemic species in Taiwan. Systematic Botany, 39: 1034-1041. Reprint PDF

Rothfels, C.J., A. Larsson, F.W. Li, E.M. Sigel, L. Huiet, D.O. Burge, M. Ruhsam, S. Graham, D. Stevenson, G.K.S. Wong, P. Korall, K.M. Pryer. 2013. Transcriptome-mining for Fern Single-copy Nuclear Regions. PLoS One 8: e76957. Reprint PDF

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