*The extended mix
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).
2023
Martínez-Gómez, J., Song, M.J., Tribble, C.M., Kopperud, B.T., Freyman, W.A., Höhna, S., Specht, C.D., and Rothfels, C.J. 2023. Commonly used Bayesian diversification methods lead to biologically meaningful differences in branch-specific rates on empirical phylogenies. Evolution Letters
You may have heard of the BAMM controversy, but does it matter? (Spoiler, yes! But depends).
Song, M.J., Rothfels, C.J., Schuettpelz, E., Nitta, J., Huiet, L., Li, F.W., and Wefferling, K.M. 2023. Resolving deep relationships and revealing ancient whole-genome duplications in Pteridaceae using transcriptomic data. American Fern Journal
Mick and Keir powerhouse pub! Phylogenomics and moderate-data analyses, the perilous waters of whole-genome duplication inference, Pteridaceae–full of goodies!
May, M.R. and Rothfels, C.J. 2023. Diversification models conflate likelihood and prior, and cannot be compared using conventional model-comparison tools. Systematic Biology.
This paper is just so good (no thanks to me). Basically, we can’t do model selection on tree models (such as birth-death models, etc), even though our results may be extremely sensitive to those models. If you do divergence-time estimation or diversification-rate inference, please read this paper.
Escudero, M., Maguilla, E., Márquez-Corro, J.I., Martín-Bravo, S., Mayrose, I., Shafir, A., Tan, L., Tribble, C., and Zenil-Ferguson, R. 2023. Using ChromEvol to Determine the Mode of Chromosomal Evolution. In Plant Cytogenetics and Cytogenomics: Methods and Protocols
Freyman, W.A., Johnson, M.G., and Rothfels, C.J. 2023. homologizer: Phylogenetic phasing of gene copies into polyploid subgenomes. Methods in Ecology and Evolution
homologize all the gene copies! (I.e., how to infer multi-locus phylogenies for polyploids and other cases of the “multiple copy problem”.)
Clark, J.L., Fierro-Minda, A., Exe, N., Johnson, M., Tribble, C.M., and Jost, L. 2023. Bomarea pastazensis (Alstroemeriaceae), an exceptionally small new species from the eastern Andean slopes of Ecuador. PhytoKeys
:star-eyes emoticon:
Schafran, P., Li, F.W., and Rothfels, C.J. 2023. PURC Provides Improved Sequence Inference for Polyploid Phylogenetics and Other Manifestations of the Multiple-Copy Problem. In Polyploidy: Methods and Protocols
… much improved, thanks to Peter Schafran (this is PURC II–you can get it here).
Tribble, C.M., May, M.R., Jackson-Gain, A., Zenil-Ferguson, R., Specht, C.D., and Rothfels, C.J. 2023. Unearthing modes of climatic adaptation in underground storage organs across Liliales. Systematic Biology
Dr. Tribble showing how’s it’s done! Want to account for the developmental origins of your focal traits, incorporate and compare complex models of trait evolution, or test for correlations among continous and discrete characters? Check it out! (Also, the lilies are pretty cool..)
2022
Ekrt, L., Košnar, J., Rothfels, C.J., Hanušová, K., Hornych, O. and Urfus, T. 2022. Cytogenetic, geographical, spore type and plastid haplotype data reveal cryptic patterns of species diversity in the cosmopolitan Cystopteris fragilis complex (Polypodiopsida: Cystopteridaceae). Botanical Journal of the Linnean Society
Mehlferber, E.C., Song, M.J., Pelaez, J.N., Jaenisch, J., Coate, J.E., Koskella, B., and Rothfels, C.J. 2022. Polyploidy and microbiome associations mediate similar responses to pathogens in Arabidopsis. Current Biology
Mick “Is Chill” Song just casually publishing a super cool Current Biology paper! You know, no biggie.
Ekwealor, J.T., Benjamin, S.D., Jomsky, J.Z., Bowker, M.A., Stark, L.R., McLetchie, D.N., Mishler, B.D., and Fisher, K.M. 2022. Genotypic confirmation of a biased phenotypic sex ratio in a dryland moss using restriction fragment length polymorphisms. Applications in Plant Sciences
2021
Chery, J. G., R. A. E. Glos, and C. T. Anderson, 2021. Do woody vines use gelatinous fibers to climb?. New Phytologist.
May, M. R., Contreras, D. L., Sundue, M. A., Nagalingum, N. S., Looy, C. V., and C. J. Rothfels, 2021. Inferring the Total-Evidence Timescale of Marattialean Fern Evolution in the Face of Model Sensitivity. Systematic Biology.
Beware the uniform tree model!
Ekwealor J. T. B., T. A. Clark, O. Dautermann, A. Russell, S. Ebrahimi, L. R. Stark, K. K. Niyogi, and B. D. Mishler, 2021. Natural ultraviolet radiation exposure alters photosynthetic biology and improves recovery from desiccation in a desert moss. Journal of Experimental Botany.
Tribble, C. M., W. A. Freyman, J. Y. Lim, M. J. Landis, J. Barido-Sottani, B. T. Kopperud, S. Höhna, and M. R. May, 2021. RevGadgets: an R Package for visualizing Bayesian phylogenetic analyses from RevBayes. bioRxiv.
RevBayes and pretty figures: what’s not to like?
Tribble, C. M., J. Martínez‐Gómez, C. C Howard, J. Males, V. Sosa, E. B. Sessa, N. Cellinese, and C. D. Specht, 2021. Get the shovel: morphological and evolutionary complexities of belowground organs in geophytes. AJB, 108(3), pp.372-387.
Howard, C. C., C. M. Tribble, J Martínez‐Gómez, E. B. Sessa, C. D. Specht, and N. Cellinese., 2021. 1, 2, 3, GO! Venture beyond gene ontologies in plant evolutionary research. AJB, 108(3): 361–365
Tribble, C. M., J. Martínez-Gómez, F. Alzate-Guarin, C. J. Rothfels, and C. D. Specht, 2021. Comparative transcriptomics of a monocotyledonous geophyte reveals shared molecular mechanisms of underground storage organ formation. Evol. Dev, 23:155–173.
Rothfels, C. J., 2021. Polyploid phylogenetics. New Phytologist. 230(1), 66–72.
I wrote a review! It was unexpectedly scary: Do I have anything interesting to say? Read it and let me know 😉 [Actually, please do–negative feedback would be helpful as always, and I think I can handle it.] Also: infer all the polyploids!
2020
Lichter‐Marck, I. H., W. A. Freyman, C. M. Siniscalchi, J. R. Mandel, A. Castro‐Castro, G. Johnson, and B. G. Baldwin, 2020. Phylogenomics of Perityleae (Compositae) provides new insights into morphological and chromosomal evolution of the rock daisies. JSE.
Silva A. T., B. Gao, K. M. Fisher, B. D. Mishler, J. T. B. Ekwealor, L. R. Stark, X. Li, D. Zhang, M. A. Bowker, J. C. Brinda, K. K. Coe, and M. J. Oliver, 2020. To dry perchance to live: insights from the genome of the desiccation-tolerant biocrust moss Syntrichia caninervis.. The Plant Journal.
Ekwealor J. T. B. and K. Fisher, 2020. Life under quartz: Hypolithic mosses in the Mojave Desert. PLOS ONE.
Chery, J. G., da Cunha Neto, I. L., Pace, M. R., Acevedo-Rodríguez, P., Specht, C. D., and C. J. Rothfels, 2020. Wood anatomy of the neotropical liana lineage Paullinia L. (Sapindaceae). IAWA Journal, 41(3), 278-300.
For which Joyce was awarded the IB Bailey Award!!
Chery, J.G., M.R. Pace, P. Acevedo-Rodríguez, C.D. Specht, and C.J. Rothfels. 2020. Modifications during early plant development promote the evolution of nature’s most complex woods. Current Biology 30:237–244.
Joyce, knocking it out of the park with a cover article in Current Biology! This study, uniting comparative phylogenetics and classical anatomy to understand the evolution of the development of the complex wood forms that allow lianas to climb, was described by one of the reviewers as a “future textbook example.”
2019
Bell, D., Q. Lin, W.K. Gerelle, S. Joya, Y. Chang, Z.N. Taylor, C.J. Rothfels, A. Larsson, J.C. Villarreal, F.‐W. Li, L. Pokorny, P. Szövényi, B. Crandall‐Stotler, L. DeGironimo, S.K. Floyd, D.J. Beerling, M.K. Deyholos, M. von Konrat, S. Ellis, A.J. Shaw, T. Chen, G.K‐S. Wong, D.W. Stevenson, J.D. Palmer, and S.W. Graham. 2019. Organellomic data sets confirm a cryptic consensus on (unrooted) land‐plant relationships and provide new insights into bryophyte molecular evolution. American Journal of Botany.
Congratulations to David Bell and Sean Graham for this cool study showing that much of the uncertainty in the relationships among the main land plant lineages (mosses, liverworts, hornworts, and vascular plants) is due to uncertainty in the position of the root of the phylogeny, and that there’s a pretty strong consensus as to the (unrooted) relationships among these lineages.
One Thousand Plant Transcriptomes Initiative (many many authors, including C.J. Rothfels and F.-W. Li). 2019. One thousand plant transcriptomes and the phylogenomics of green plants. Nature 574:679–685.
Nine years in the making, the 1KP capstone paper is out!
Chery, J.G., P. Acevedo-Rodríguez, C.J. Rothfels, and C.D. Specht. 2019. Phylogeny of Paullinia L. (Paullinieae: Sapindaceae), a diverse genus of lianas with dynamic fruit evolution. Mol Phylo Evol.
Sweet microfluidic primer-design pipeline Paullinia phylogeny action from Dr. Chery. Featuring both guaraná AND a cool fruit evolution story.
Xu, K. W., L. Zhang, C.J. Rothfels, A.R. Smith, R. Viane, D.H. Lorence, K.R. Wood, C.-W. Chen, R. Knapp, L. Zhou, N.T. Lu, X.-M. Zhou, H.-J. Wei, F. Qiang, S.F. Chen, D. Cicuzza, X.-F. Gao, W.B. Liao, and L.-B. Zhang. 2019. A global plastid phylogeny of the fern genus Asplenium (Aspleniaceae). Cladistics 19:716–50.
A powerhouse sampling of ferns’ largest genus! Guess how many of the species with multiple accessions included are resolved as monophyletic?
Kao, T.T., K.M. Pryer, F.D. Freund, M.D. Windham, and C.J. Rothfels. 2019. Low-copy nuclear sequence data confirm complex patterns of farina evolution in notholaenid ferns (Pteridaceae). Molecular Phylogenetics and Evolution 138: 139–155.
A return to my first (fern) love, Notholaena and friends. Thanks Tzu-Tong for taking us the next step!
2018
Hanušová, K., M. Certner, T. Urfus, P. Koutecký, J. Košnar, C.J. Rothfels, V. Jarolímová, J. Ptacek and L. Ekrt. 2018. Widespread co-occurrence of multiple ploidy levels in fragile ferns (Cystopteris fragilis complex; Cystopteridaceae) probably stems from similar ecology of cytotypes, their efficient dispersal and inter-ploidy hybridization. Annals of Botany.
In which the flow cytometry wizards determine the cytotypes of 5518 (5518!!) Cystopteris plants. This is a crazy cytogeography tour de force with lots of insights into the dynamics of polyploidy.
Li, F.-W., P. Brouwer, L. Carretero-Paulet, S. Cheng, J. Vries, P.-M. Delaux, A. Eily, N. Koppers, L.-Y. Kuo, Z. Li, M. Simenc, I. Small, E.K. Wafula, S. Angarita, M.S. Barker, A. Bäutigam, C. dePamphilis, S. Gould, P.S. Hosmani, Y.-M. Huang, B. Huettel, Y. Kato, X. Liu, S. Maere, R. McDowell, L.A. Mueller, K.G.J. Nierop, S.A. Rensing, T. Robison, C.J. Rothfels, E.M.Sigel, Y. Song, P.R. Timilsena, Y. Van de Peer, H. Wang, P.K.I. Wilhelmsson, P.G. Wolf, X. Xu, J.P. Der, H. Schluepmann, G.K.-S. Wong and K.M. Pryer. 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.
2017
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.
2016
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.
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.
2015
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.
Mayrose, I., 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.