The following is a lightly annotated selection of Rothfels lab publications; for a full list of Carl’s publications, see his Google Scholar profile (selected earlier publications are also available on his subpage).
Li, F.-W., Brouwer, P., Carretero-Paulet, L., Cheng, S., Vries, J., Delaux, P.-M., Eily, A., Koppers, N., Kuo, L.-Y., Li, Z., Simenc, M., Small, I., Wafula, E.K., Angarita, S., Barker, M.S., Bäutigam, A., dePamphilis, C., Gould, S., Hosmani, P.S., Huang, Y.-M., Huettel, B., Kato, Y., Liu, X., Maere, S., McDowell, R., Mueller, L.A., Nierop, K.G.J., Rensing, S.A., Robison, T., Rothfels, C.J., Sigel, E.M., Song, Y., Timilsena, P.R., Van de Peer, Y., Wang, H., Wilhelmsson, P.K.I., Wolf, P.G., Xu, X., Der, J.P., Schluepmann, H., Wong, G.K.-S., and Pryer, K.M. 2018. Fern genomes elucidate land plant evolution and cyanobacterial symbioses. Nature Plants. 1-16.
WOOOOO!! At long last, fern genome sequences! Two of them, even (Azolla and Salvinia). Cover article! Special congratulations to former Rothfels Labmate Fay-Wei Li for making this happen. And I’m not the only one who’s excited–so is Discover Magazine, Cosmos, Earth.com, Cornell Chronicle, BTI press release, inverse.com, and Nature Plants News & Views.
Extant Isoëtes–diminuitive rush-like plants–are continuing a process of evolutionary simplification from their tree-like ancestors. For methods nerds, this paper shows some cool ways to test for directional selection in morphological traits and to use reversible-jump MCMC to present model-averaged results, effectively taking uncertainty in the underlying evolutionary model into account.
A delightfully convoluted example of how the rules of nomenclature can result in unexpected … uh.. results.
(Honorary RLab member) Jeff Benca blazes into fame!
Dauphin, B., J.R. Grant, D.R. Farrar, and C.J. Rothfels. 2018. Rapid allopolyploid radiation of moonwort ferns (Botrychium; Ophioglossaceae) revealed by PacBio sequencing of homologous and homeologous nuclear regions. Molecular Phylogenetics and Evolution. 120: 342–353.
Ben brings the PURC down on Botrychium–a recent rapid allopolyploid radiation.
Chen, C.-W.*, C.J. Rothfels*, A.M.A. Mustapeng, M. Gubilil, D.N. Karger, M. Kessler, and Y.-M. Huang. 2018. End of an enigma: Aenigmopteris belongs in Tectaria (Tectariaceae: Polypodiopsida). Journal of Plant Research.
The title sums it up nicely, I think. This was a fun project, stemming from fieldwork in Borneo.
Freyman, W.A. and S. Höhna. 2017. Cladogenetic and anagenetic models of chromosome number evolution: A Bayesian model averaging approach. Systematic Biology.
Will’s an honorary Rothfels lab member and besides, this paper is awesome.
Zúñiga, J.D., M.R. Gostel, D.G. Mulcahy, K. Barker, A. Hill, M. Sedaghatpour, S.Q. Vo, V.A. Funk, J.A. Coddington. 2017. Data release: DNA barcodes of plant species collected for the Global Genome Initiative for Gardens Program, National Museum of Natural History, Smithsonian Institution. PhytoKeys 88: 119–122.
Maryam’s first paper!!!
Chery, J.G., Sass, C. and C.D.Specht. 2017. Development of single copy nuclear markers for species-level phylogenetics: Case study with Paullinieae (Sapindaceae). Applications in Plant Sciences 5(9): 1700051
Efforts towards the Paullinia phylogeny!
Rothfels, C.J., F-W. Li, and K.M. Pryer. 2017. Next-generation polyploid phylogenetics: Rapid resolution of hybrid polyploid complexes using PacBio single-molecule sequencing. New Phytologist. 213(1): 413–429. doi:10.1111/nph.14111
The long-awaited (by us) paper describing a method to quickly and economically generate information-rich sequence data for polyploids (it works well on non-polyploids, too), including the ability to sequence all copies (alleles, homeologs, paralogs, etc) present in each individual sample. Included is a description of the wet lab workflow, and a bioinformatic pipline–PURC, the Pipeline for Untangling Reticulate Complexes–for inferring the true biological sequences from the raw sequencing reads. We hope that this method will greatly facilitate the phylogenetic study of polyploid complexes, where research has historically be inhibited by the horrors of cloning.
Coate, J.E., M.J. Song, A. Bombarely, and J.J. Doyle. 2016. Expression‐level support for gene dosage sensitivity in three Glycine subgenus Glycine polyploids and their diploid progenitors. New Phytologist. 212(4): 1083–1093.
What a keener! See also this.
Hsu, P.Y., L. Calviello, H.-Y.L. Wu, F.-W. Li, C.J. Rothfels, U. Ohler, and P.N. Benfey. 2016. Super-resolution ribosome profiling reveals unannotated translation events in Arabidopsis. PNAS. 113(35).
And now for something completely different… It was an honor to be included in this project and, frankly, ribsome profiling is amazing.
Freund, F.D. 2016. Characterizing quantitative variation in the glossopodia of three western North American Isoëtes species. American Fern Journal. 106(2): 87–115.
Forrest’s first paper! And a sweet one, at that.
Li, F-W., L-Y. Kuo, K.M. Pryer, and C.J. Rothfels. 2016. Genes translocated into the plastid inverted repeat show decelerated substitution rates and elevated GC content. Genome Biology and Evolution. 8(8): 2452–2458.
Fay-Wei’s on fire!
Zhang, L., E. Schuettpelz, C.J. Rothfels, X.-M. Zhou, X.-F. Gao, and L.-B. Zhang. 2016. Circumscription and phylogeny of the fern family Tectariaceae based on plastid and nuclear markers, with the description of two new genera: Draconopteris and Malaifilix (Tectariaceae). Taxon. 65(4): 723–738.
Rothfels, C.J., and S.P. Otto. 2016. Polyploid speciation. In R. M. Kliman (Ed.), Encyclopedia of Evolutionary Biology (pp. 317–326). Oxford: Academic Press. http://doi.org/10.1016/B978-0-12-800049-6.00073-1
I’m secretly (or not so secretly) quite proud of this article with Sally Otto, synthesizing what we know about the role of polyploidy in speciation. Email me for a copy if you’re interested.
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(1): 24–31.
Pteridophyte Phylogeny Group (PPG1). 2016. A community‐derived classification for extant lycophytes and ferns. Journal of Systematics and Evolution. 54(6): 563–603.
In which 95 pteridologists got together to propose a classification for ferns and lycophytes. RIP Woodsiaceae sensu lato.
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, J.P. Der. 2015. An exploration of fern genome space. Genome Biology and Evolution. 7(9): 2533–2544.
Delaux, P.-M, G.V. Radhakrishnan, D. Jayaraman, J. Cheema, M. Malbreil, J.D. Volkening, H. Sekimoto, T. Nishiyama, M. Melkonian, L. Pokorny, C.J. Rothfels, H.W. Sederoff, D.W. Stevenson, B. Surek, Y. Zhang, M.R. Sussman, C. Dunand, R.J. Morris, C. Roux, G.K.-S. Wong, G.E.D. Oldroyd, J.-M. Ané. 2015. Algal ancestor of land plants was preadapted for symbiosis. PNAS. 12(43): 13390–13395.
Rothfels, C.J, F.-W. Li, E.M. Sigel, L. Huiet, A. Larsson, D.O. Burge, M. Ruhsam, M. Deyholos, D.E. Soltis, C.N. Stewart, S.W. Shaw, L. Pokorny, T. Chen, C. dePamphilis, L. DeGironimo, T. Chen, X. Wei, X. Sun, P. Korall, D.W. Stevenson, S.W. Graham, G.K-S. Wong, K.M. Pryer. The evolutionary history of ferns inferred from 25 single-copy nuclear genes. American Journal of Botany. 102(7): 1089–1107. Highlighted article.
Another foray in the “moderate data” crusade, and the first broad multi-locus nuclear phylogeny of ferns! Fortunately, it appears that the plastid wasn’t lying to us.
Zhou, X.-M., C.J. Rothfels, L. Zhang, Z.-R. He, T. Le Péchon, H. He, N.T. Lu, R. Knapp, D. Lorence, X.-J. He, X.-F. Gao, and L.-B. Zhang. 2015. A large-scale phylogeny of the lycophyte genus Selaginella (Selaginellaceae: Lycopodiopsida) based on plastid and nuclear loci. Cladistics. 32: 360–389.
Zhang, L., C.J. Rothfels, A. Ebihara, E. Schuettpelz, T.L. Péchon, P. Kamau, H. He, X-M. Zhou, J. Prado, A. Field, G. Yatskievych, X-F. Gao, L-B. Zhang. 2015. A global plastid phylogeny of the brake fern genus Pteris (Pteridaceae) and related genera in the Pteridoideae. Cladistics. 31: 406–423.
Rothfels, C.J, A.K. Johnson*, P.H. Hovenkamp, D.L. Swofford, H.C. Roskam, C.R. Fraser-Jenkins, M.D. Windham, K.M. Pryer. 2015. Natural hybridization between genera that diverged from each other approximately 60 million years ago. American Naturalist 185(3): 433–442. *Undergraduate mentee. Press.
Still rather blown away by this result. Also, somewhat overshadowed by the result itself is what I think is a very nice “sequential empirical Bayesian divergence dating” method for time-calibrating phylogenies of groups without fossils.
Itay, M., S. Zhan, C.J. Rothfels, N. Arrigo, M. Barker, L. Rieseberg, S. Otto. 2015. Methods for studying polyploid diversification and the dead end hypothesis: A reply to Soltis et al. (2014). New Phytologist. doi: 10.1111/nph.13192
“… we believe that model-based methodology applied over many character state transitions … is the best currently available approach for studying the effects on diversification of traits, like polyploidy, both in terms of its power and its relative insensitivity to biases … Like most mutations, our evaluation of the evidence to date is that polyploidization is typically deleterious … That most mutations are harmful does not preclude the occasional adaptive mutation, whether caused by a change in nucleotide or a change in ploidy level; indeed, evolution depends on such changes.”
For selected earlier publications see Carl’s subpage.