Publications

in review/in Press

Li, F.-W., and A. Harkess. A guide to sequence your favorite plant genomes. Applications in Plant Sciences [special issue “Methods for Exploring the Plant Tree of Life”] in review. 

Song, M., L.-Y. Kuo, L. Huiet, K.M. Pryer, C.J. Rothfels, F.-W. Li. A novel chloroplast gene reported for flagellate plants. American Journal of Botany. in review.

Schilling, M.P., Z. Gompert, F.-W. Li, M.D. Windham, P.G. Wolf. Admixture, evolution, and variation in reproductive isolation in the Boechera puberula clade. BMC Evolutionary Biology in review.  

Dijkhuizen, L., P. Brouwer, H. Bolhuis, G.-J. Reichart, N. Koppers, B. Huettel, A. Bolger, F.-W. Li, S. Cheng, X. Liu, G.K.-S. Wong, K.M. Pryer, A. Weber, A. Bräutigam, H. Schluepmann. Is there foul play in the leaf pocket? The metagenome of floating fern Azolla reveals endophytes that do not fix N2 but may denitrify. New Phytologist. in press.

2017

Li, F.-W., J.C. Villarreal, P. Szovenyi. 2017. Hornworts, an overlooked window into carbon-concentrating mechanism. Trends in Plant Science 22: 275-277. Reprint PDF

Li, F.-W., C.A. Rushworth, J.B. Beck, M.D. Windham. 2017. Boechera Microsatellite Website: an online portal for species identification and hybrid relationship resolution. Database 1: baw169. Reprint PDF
Source code, Website

Rockwell, N.C., S.S. Martin, F.-W. Li, S. Mathews, J.C. Lagarias. 2017. The phycocyanobilin chromophore of streptophyte algal phytochromes is synthesized by HY2. New Phytologist 214: 1145-1157. Reprint PDF

Rothfels, C.J., K.M. Pryer, F.-W. Li. 2017. Next-generation polyploid phylogenetics: Rapid resolution of hybrid polyploid complexes using PacBio single-molecule sequencing. New Phytologist 213: 413-429. Reprint PDF
*I am the major developer of the PURC pipeline. Source code 

2016

Li, F.-W., L.-Y. Kuo, K.M. Pryer, C.J. Rothfels. 2016. Genes translocated into the plastid inverted repeat show a marked deceleration in substitution rates and an elevated GC content. Genome Biology and Evolution 8: 2452-2458. Reprint PDF

Li, F.-W., L.Y. Kuo, Y.H. Chang, T.C. Hsu, H.C. Hung, W.L. Chiou, C.J. Rothfels, Y.M. Huang. 2016. Asplenium pifongiae (Aspleniaceae: Polypodiales), a new species from Taiwan. Systematic Botany 41: 24-31. Reprint PDF

Hsu, P.Y., L. Calviello, H.-.Y. L. Wu*, F.-W. Li*, C.J. Rothfels, U. Ohler, P.N. Benfey. 2016. Super-resolution ribosome profiling reveals unannotated translation events in ArabidopsisProceedings of the National Academy of Sciences USA 113: E7126-E7135. Reprint PDF
     *Equally contributed 

Jia, Q., G. Li, T.G. Köllner, J. Fu, X. Chen, W. Xiong, B.J. Crandall-Stotler, J.L. Bowman, D.J. Weston, Y. Zhang, L. Chen, Y. Xie, F.-W. Li, C.J. Rothfels, A. Larsson, S.W. Graham, D.W. Stevenson, G.K.-S. Wong, J. Gershenzon, F. Chen. 2016. Microbial-type terpene synthase genes occur widely in nonseed land plants, but not in seed plants. Proceedings of the National Academy of Sciences USA 113: 12328-12333. Reprint PDF

Stevenson, S.R., Y. Kamisugi, J. Schmutz, J.W. Jenkins, J. Grimwood, W. Muchero, G.A. Tuskan, S.A. Rensing, D. Lang, R. Reski, C. Trinh, M. Melkonian, C.J. Rothfels, F.-W. Li, A. Larsson, G.K.S. Wong, T. Edwards, A.C. Cuming. 2016. Genetic analysis of Physcomitrella patens identifies ABSCISIC ACID NON-RESPONSIVE (ANR): a regulator of ABA responses unique to basal land plants, required for desiccation tolerance. Plant Cell 28 1310–1327. Reprint PDF

Pryer, K.M., L. Huiet, F.-W. Li, C.J. Rothfels, E. Schuettpelz. 2016. Maidenhair ferns, Adiantum, are indeed monophyletic, and sister to to the shoestring ferns, vittaroids (Pteridaceae). Systematic Botany 41: 14-23. Reprint PDF

The Pteridophyte Phylogeny Group. 2016. A community-derived classification for extant lycophytes and ferns. Journal of Systematics and Evolution 54: 563-603. Reprint PDF

2015

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. 2015. Phytochrome diversity in green plants and the origin of canonical plant phytochromes. Nature Communications 6: 7852. Reprint PDF
     Featured inDuke Today, Science Daily, Phys.org, Faculty of 1000

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. 2015. The origin and evolution of phototropins in plants. Frontiers in Plant Science: 6: 637. Reprint PDF

Li, F.-W., S. Mathews. 2015. Evolutionary aspects of plant photoreceptors [invited review]. Journal of Plant Research 129: 115-122. Reprint PDF

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. 2015. Searching for diamonds in the apomictic rough: A case study involving Boechera lignifera (Brassicaceae). Systematic Botany 40: 1031-1044. Reprint PDF

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. 2015. An exploration into fern genome space. Genome Biology and Evolution 7: 2533-2544. Reprint PDF

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. 2015. The evolutionary history of ferns inferred from 25 single-copy nuclear genes. American Journal of Botany 102: 1089-1107. Reprint PDF

2014

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. 2014. Horizontal transfer of an adaptive chimeric photoreceptor from bryophytes to ferns. Proceedings of the National Academy of Sciences USA, 111: 6672-6677. Reprint PDF
     Featured in: New York Times, The Economist, National Geographic, Scientific American, AeonFaculty of 1000, Current Biology, Nature Reviews Genetics

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

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

2009-2013

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

Li, F.-W., K.M. Pryer, M.D. Windham. 2012. Gaga, a new genus segregated from Cheilanthes (Pteridaceae). Systematic Botany 37: 845-860. Reprint PDF
     Featured in: New York TimesRolling Stone, National GeographicHuffington Post, Wired, The Guardian

Li, F.-W., L.Y. Kuo, C.J. Rothfels, A. Ebihara, W.L. Chiou, M.D. Windham, K.M. Pryer. 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., F.-W. Li*, W.L. Chiou, C.N. Wang. 2011. The first insight into fern matK phylogeny. Molecular Phylogenetics and Evolution 59: 556-566. Reprint PDF
     *Equally contributed 

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

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