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Phylotranscriptomic analysis of the origin and early diversification of land plants
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Significance: Early branching events in the diversification of land plants and closely related algal lineages remain fundamental and unresolved questions in plant evolutionary biology. Accurate reconstructions of these relationships are critical for testing hypotheses of character evolution: for example, the origins of the embryo, vascular tissue, seeds, and flowers. We investigated relationships among streptophyte algae and land plants using the largest set of nuclear genes that has been applied to this problem to date. Hypothesized relationships were rigorously tested through a series of analyses to assess systematic errors in phylogenetic inference caused by sampling artifacts and model misspecification. Results support some generally accepted phylogenetic hypotheses, while rejecting others. This work provides a new framework for studies of land plant evolution.
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“In addition to our analyses, all the supermatrices have also been previously extensively analyzed using either RAxML or ExaML (e.g., Jarvis et al. 2014; Misof et al. 2014; Wickett et al. 2014).”
From Evaluating fast maximum likelihood-based phylogenetic programs using empirical phylogenomic data sets (2018) · cites this paper as Wickett et al. 2014
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R2R3-MYBGene Evolution in Plants, Incorporating Ferns into the Story
Hernández-Hernández, B., Tapia‐López, R., Ambrose, B. A., & Vasco, A. (2020) · International Journal of Plant Sciences · doi:10.1086/710579 · Cited by 13
Berruezo, F., de Souza, F. S. J., Picca, P. I., Nemirovsky, S. I., Tosar, L. M., Rivero, M., Mentaberry, A. N., & Zelada, A. M. (2017) · PLoS ONE · doi:10.1371/journal.pone.0177573 · Cited by 13
Reappraising the origin of mycorrhizas
Rimington, W. R., Pressel, S., Field, K. J., Strullu‐Derrien, C., Duckett, J. G., & Bidartondo, M. I. (2016) · doi:10.1002/9781118951446.ch2 · Cited by 13
Han, Y., & Molloy, E. K. (2023) · Genome Research · doi:10.1101/gr.277629.122 · Cited by 13
Towards a comprehensive barcoding and phylogenomic reference for the European arctic–alpine flora
Lavergne, S., Pouchon, C., Roquet, C., Alberti, A., Boleda, M., Perrier, C., Renaud, J., Boyer, F., Bzeznik, B., Rome, M., et al. (2025) · Botany Letters · doi:10.1080/23818107.2025.2549565 · Cited by 12
“…inventory and sampling, the systematic sequencing of field or museum specimens, combined with the ever-increasing power of algorithms of phylogenomics, now allows inferring largely inclusive trees of life for thousands of species and hundreds of genes (Wickett et al. 2014; Li et al. 2019).”
Sadamitsu, A., Inoue, Y., Sakakibara, K., Tsubota, H., Yamaguchi, T., Deguchi, H., Nishiyama, T., & Shimamura, M. (2021) · Plant Molecular Biology · doi:10.1007/s11103-021-01214-z · Cited by 13
“We selected 16 accessions of bryophytes for the present analysis, of which 14 were mosses as ingroups, and one liverwort and one hornwort as outgroups based on the result by recent phylogenomic studies (Wickett et al. 2014; Puttick et al. 2018; Sousa et al. 2019).”
MethodZhang, C., Jiao, C., Sun, X., & Li, X. (2023) · International Journal of Molecular Sciences · doi:10.3390/ijms24032566 · Cited by 12
Self-citationKawaguchi, Y. W., Tsuchikane, Y., Tanaka, K., Taji, T., Suzuki, Y., Toyoda, A., Itô, M., Watano, Y., Nishiyama, T., Sekimoto, H., et al. (2023) · Genome Biology and Evolution · doi:10.1093/gbe/evad115 · Cited by 12
Oligogalactolipid production during cold challenge is conserved in early diverging lineages
Barnes, A. C., Myers, J. L., Surber, S. M., Liang, Z., Mower, J. P., Schnable, J. C., & Roston, R. (2023) · Journal of Experimental Botany · doi:10.1093/jxb/erad241 · Cited by 12
Biosynthesis, functional perspectives, and agricultural applications of strigolactones
Samynathan, R., Venkidasamy, B., Shariati, M. A., Muthuramalingam, P., & Thiruvengadam, M. (2023) · Revista Brasileira de Botânica · doi:10.1007/s40415-023-00958-w · Cited by 12
“A more recent model of the evolution of land plants indicates that hornworts are the latest divergent group of land plants and that a clade of liverworts and mosses is sister to vascular plants (Wickett et al. 2014).”
Lindsey, C. R., Knoll, A. H., Herron, M. D., & Rosenzweig, F. (2024) · BMC Biology · doi:10.1186/s12915-024-01878-1 · Cited by 12
Evolutionary assembly of the plant terrestrialization toolkit from protein domains
Ashok, A. D., de Vries, S., Darienko, T., Irisarri, I., & de Vries, J. (2024) · Proceedings of the Royal Society B Biological Sciences · doi:10.1098/rspb.2024.0985 · Cited by 12
“Therein, Zygnematophyceae are the closest algal relatives to land plants [17– 19].”
BackgroundThe Genomes of Charophyte Green Algae
Delwiche, C. (2016) · Advances in botanical research · doi:10.1016/bs.abr.2016.02.002 · Cited by 13
The present and future for population genetics, species boundaries, biogeography and conservation
Fay, M. F., Gargiulo, R., & Viruel, J. (2019) · Botanical Journal of the Linnean Society · doi:10.1093/botlinnean/boz076 · Cited by 12
Diversity, development and evolution of archegonia in land plants
Sokoloff, D. D., & Remizowa, M. V. (2020) · Botanical Journal of the Linnean Society · doi:10.1093/botlinnean/boaa077 · Cited by 12
Advances in understanding of mycorrhizal-like associations in bryophytes
Pressel, S., Bidartondo, M. I., Field, K. J., & Duckett, J. G. (2021) · Bryophyte Diversity and Evolution · doi:10.11646/bde.43.1.20 · Cited by 12
“…challenged the general consensus of liverworts as sister to all other embryophytes and hornworts sister to the vascular plants (Qiu et al. 2006) and found strong support for the monophyly of liverworts and mosses (Setaphyta) (e.g. Wickett et al. 2014, Puttick et al. 2018, Sousa et al. 2018, 2020).”
BackgroundTriplet MaxCut: a new toolkit for rooted supertree
Sevillya, G., Frenkel, Z., & Snir, S. (2016) · Methods in Ecology and Evolution · doi:10.1111/2041-210x.12606 · Cited by 12
“2004; Snir &Rao 2010 and was used inmany other studies to analyse real biological data (see, e.g. Beck et al. 2006; Zhaxybayeva et al. 2006; Bansal et al. 2011; Nyakatura & Bininda-Emonds 2012; Holland, Jarvis & Sumner 2013; Sigwart & Lindberg 2015; Wickett et al. 2014).”
MethodLife's a beach – the colonization of the terrestrial environment
Plackett, A. R. G., & Coates, J. C. (2016) · New Phytologist · doi:10.1111/nph.14295 · Cited by 12
Flores, J. R., Suárez, G. M., & Hyvönen, J. (2019) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2019.106662 · Cited by 12
Alonso, M., Villarreal, J. C., McFarland, K. D., & Goffinet, B. (2020) · Frontiers in Plant Science · doi:10.3389/fpls.2020.00495 · Cited by 12
“Sequences reads were mapped to the nuclear transcriptome of N. aenigmaticus (SRA: ERS368224) (Wickett et al., 2014) using the software package BWA version 0.7.17 (Li and Durbin, 2009) and the SAMtools suite (Li, 2011) to convert the output of BWA to BAM format as required for Stacks (Rochette and Catchen, 2017).”
MethodInfluentialSelf-citationSexton, J. P., & Lomas, M. W. (2018) · Elsevier eBooks · doi:10.1016/b978-0-12-811405-6.00004-9 · Cited by 13
A roadmap to developing unified streptophyte algal model systems
Carrillo‐Carrasco, V. P., Hernández‐García, J., Girou, C., Grubor, I., Keller, J., Lim, E., Schmidt, V., Sørensen, I., Vosolsobě, S., Buschmann, H., et al. (2025) · Current Biology · doi:10.1016/j.cub.2025.05.023 · Cited by 11
“The chlorophyte green alga Chlamydomonas reinhardtii is a spectacular model system, but the lineage it belongs to, the chlor-ophytes, diverged from the streptophyte lineage about a billion years ago 8,9,13,15,23,24 .”
InfluentialShan, B., Mo, J., Yang, J., Qin, X., & Yu, H. (2024) · Plant Science · doi:10.1016/j.plantsci.2024.111989 · Cited by 11
Modeling compositional heterogeneity resolves deep phylogeny of flowering plants
Wang, Y., Li, Y., Wang, S., Tihelka, E., Engel, M. S., & Cai, C. (2024) · Acta Botanica Yunnanica · doi:10.1016/j.pld.2024.07.007 · Cited by 11
Singh, P., Kaufholdt, D., Awadalah, M., Hänsch, R., Beerhues, L., & Gaid, M. M. (2021) · Plant Physiology and Biochemistry · doi:10.1016/j.plaphy.2021.01.011 · Cited by 11
Growth control of Marchantia polymorpha gemmae using nonthermal plasma irradiation
Tsuboyama, S., Okumura, T., Attri, P., Koga, K., Shiratani, M., & Kuchitsu, K. (2024) · Scientific Reports · doi:10.1038/s41598-024-53104-1 · Cited by 11
“M. polymorpha is a basal land plant 19–22 and has recently gained attention as a new model plant among plant molecular biologists.”
BackgroundZhang, L., Wu, W., Yan, H., & Ge, X. (2015) · Evolutionary Bioinformatics · doi:10.4137/ebo.s22448 · Cited by 11
Hao, M.-S., & Rasmusson, A. G. (2016) · Physiologia Plantarum · doi:10.1111/ppl.12453 · Cited by 11
Yerramsetty, P., Stata, M., Siford, R., Sage, T. L., Sage, R. F., Wong, G. K., Albert, V. A., & Berry, J. O. (2016) · BMC Evolutionary Biology · doi:10.1186/s12862-016-0713-1 · Cited by 11
“RLSB-like transcript sequences were identified in eight Charophyte algae, from the Zygnematophyceae (recognized as the closest extant lineage to the land plants, [24–27]), Charales, and Klebsormidiales (the most distant relative of the Embryophyta in which an ortholog was found) (Figs.”
Self-citationInferring rooted species trees from unrooted gene trees using approximate Bayesian computation
Alanzi, A. R. A., & Degnan, J. H. (2017) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2017.07.017 · Cited by 11
“Simmons and Gatesy (2015) prefer the summary coalescent analysis of Wickett et al. (2014), which used the unrooted method ASTRAL (Mirarab et al., 2014) and found support for the Amborella-only outgroup hypothesis.”
Method
Metadata
- Authors
- Wickett, N. J., Mirarab, S., Nguyen, N., Warnow, T., Carpenter, E., Matasci, N., Ayyampalayam, S., Barker, M. S., Burleigh, J. G., Gitzendanner, M. A., Ruhfel, B. R., Wafula, E., Der, J. P., Graham, S. W., Mathews, S., Melkonian, M., Soltis, D. E., Soltis, P. S., Miles, N. W., Rothfels, C. J., Pokorny, L., Shaw, A. J., DeGironimo, L., Stevenson, D. W., Surek, B., Villarreal, J. C., Roure, B., Philippe, H., dePamphilis, C. W., Chen, T., Deyholos, M. K., Baucom, R. S., Kutchan, T. M., Augustin, M. M., Wang, J., Zhang, Y., Tian, Z., Yan, Z., Wu, X., Sun, X., Wong, G. K.-S., & Leebens-Mack, J.
- Affiliations
- Northwestern University (US)
- The University of Texas at Austin (US)
- University of Alberta (CA)
- University of Arizona (US)
- University of Georgia (US)
- Department of Biology and
- University of Florida (US)
- Eastern Kentucky University (US)
- Pennsylvania State University (US)
- Department of Botany and
- Harvard University (US)
- University of Cologne (DE)
- Florida Museum of Natural History (US)
- University of British Columbia (CA)
- Consejo Superior de Investigaciones Científicas (ES)
- Duke University (US)
- New York Botanical Garden (US)
- Ludwig-Maximilians-Universität München (DE)
- Université de Montréal (CA)
- Centre National de la Recherche Scientifique (FR)
- Chinese Academy of Sciences (CN)
- University of Michigan (US)
- Donald Danforth Plant Science Center (US)
- BGI Group (China) (CN)
- Department of Plant Biology, University of Georgia, Athens, GA 30602;
- ORCID
- Wickett, Norman J.
- Mirarab, Siavash
- Nguyen, Nam
- Warnow, Tandy
- Carpenter, Eric
- Matasci, Naim
- Barker, Michael S.
- Burleigh, J. Gordon
- Gitzendanner, Matthew A.
- Ruhfel, Brad R.
- Wafula, Eric
- Der, Joshua P.
- Graham, Sean W.
- Mathews, Sarah
- Melkonian, Michael
- Rothfels, Carl J.
- Pokorny, Lisa
- Shaw, A. Jonathan
- Stevenson, Dennis W.
- Villarreal, Juan Carlos
- Philippe, Hervé
- dePamphilis, Claude W.
- Chen, Tao
- Deyholos, Michael K.
- Baucom, Regina S.
- Kutchan, Toni M.
- Augustin, Megan M.
- Wang, Jun
- Zhang, Yong
- Yan, Zhixiang
- Wu, Xiaolei
- Sun, Xiao
- Wong, Gane Ka-Shu
- Venue
- Proceedings of the National Academy of Sciences
- Publisher
- National Academy of Sciences
- Published
- 2014-10-29
- Volume
- 111
- Issue
- 45
- Pages
- E4859-68
- ISSN
- 0027-8424 (ISSN-L)
- 1091-6490
- PMC
- PMC4234587
- OpenAlex
- W2013277649
- Cited by
- 1,252
- References
- 124
- Citations by year
- 2026: 33 · 2025: 56 · 2024: 92 · 2023: 73 · 2022: 98 · 2021: 144 · 2020: 125 · 2019: 139 · 2018: 168 · 2017: 124 · 2016: 116 · 2015: 81 · 2014: 2
- FWCI
- 44.12
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Proceedings of the National Academy of Sciences (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Kölner Universitäts PublikationsServer (Universität zu Köln) (publishedVersion)
- DIGITAL.CSIC (Spanish National Research Council (CSIC)) (acceptedVersion)
- Civil War Book Review (submittedVersion)
- HAL (submittedVersion)
- Funders
- National Institute on Drug Abuse (R01DA025197)
- Topics
- Life Sciences › Agricultural and Biological Sciences › Ecology, Evolution, Behavior and Systematics › Protist diversity and phylogeny
- Life Sciences › Agricultural and Biological Sciences › Ecology, Evolution, Behavior and Systematics › Plant Diversity and Evolution
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Keywords
- land plant origin, Zygnematophyceae, liverworts, bryophytes, plant phylogeny, nuclear gene phylogeny, phylogenetic robustness, coalescent phylogenetics, supertree, supermatrix
- MeSH terms
- Phylogeny, Sequence Alignment, DNA, Plant, Genome, Plant, Evolution, Molecular, Quantitative Trait, Heritable, Gene Expression Profiling, Streptophyta, Transcriptome
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