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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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Taxonomic Concepts and Taxonomic Evolution in European Characeae
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Weeks, Z., Chaturvedi, G., Day, E., Kelly, S. L., & Moody, L. A. (2025) · Development · doi:10.1242/dev.204508 · Cited by 3
“As a result, the morphologies represented within the multicellular charophytes are typically filamentous (e.g. Chara braunii ) or disc-like (e.g. Coleochaete orbicularis ) (Kenrick and Crane, 1997; Wickett et al., 2014; Delwiche and Cooper, 2015; Harrison, 2017).”
Branch Length Transforms using Optimal Tree Metric Matching
Arasti, S., Tabaghi, P., Tabatabaee, Y., Mayer, A., & Mirarab, S. (2026) · Systematic Biology · doi:10.1093/sysbio/syag025 · Cited by 4
Self-citationChlorokybophyceae, Klebsormidiophyceae, Coleochaetophyceae
Cook, M., & Graham, L. (2016) · Springer eBooks · doi:10.1007/978-3-319-32669-6_36-1 · Cited by 6
Modern Approaches for Transcriptome Analyses in Plants
Riaño‐Pachón, D. M., Espitia-Navarro, H. F., Riascos, J. J., & Margarido, G. R. A. (2021) · Advances in experimental medicine and biology · doi:10.1007/978-3-030-80352-0_2 · Cited by 4
An evo-devo perspective on no Ordovician land plants
Strother, P. K. (2023) · Proceedings of the Estonian Academy of Sciences Geology · doi:10.3176/earth.2023.31 · Cited by 3
“…a consensus is now emerging on the Zygnematales as the most closely related group to the Embryophyta (Wodniok et al. 2011; Zhong et al. 2013; Wickett et al. 2014), although on the basis of classical morphological and developmental char - acters, the Coleochaetales possess synapomorphies…”
BackgroundAsymmetric Cluster-Based Measures for Comparative Phylogenetics
Wagle, S., Markin, A., Górecki, P., Anderson, T. K., & Eulenstein, O. (2024) · Journal of Computational Biology · doi:10.1089/cmb.2023.0338 · Cited by 3
Ambrose, B. A., & Stevenson, D. W. (2024) · Current Opinion in Plant Biology · doi:10.1016/j.pbi.2024.102563 · Cited by 3
Self-citationTerraces in species tree inference from gene trees
Habib, M., Roy, K., Hasan, S., Rahman, A. H., & Bayzid, M. S. (2024) · BMC Ecology and Evolution · doi:10.1186/s12862-024-02309-z · Cited by 3
“The mathematical characterizations of species tree ter-races and the new results on terraces in the gene tree-species tree context presented here are timely and important as large genome-scale phylogenomic studies with substantial amounts of missing data are becoming increasingly common [45, 46].”
BackgroundSaltational Episodes of Reticulate Evolution in the Drosophila saltans Species Group
Prediger, C., Ferreira, E. A., Zorzato, S. V., Hua‐Van, A., Klasson, L., Miller, W. J., Yassin, A., & Madi-Ravazzi, L. (2024) · Molecular Biology and Evolution · doi:10.1093/molbev/msae250 · Cited by 5
Neofunctionalization of VAMP7 opened up a plant-unique vacuolar transport pathway
Fujimoto, M., Shimizu, Y., Ito, Y., Ebine, K., Minamino, N., Kanazawa, T., Fukao, Y., Nakano, A., Uemura, T., & Ueda, T. (2025) · Current Biology · doi:10.1016/j.cub.2025.04.062 · Cited by 3
Genome Sequence of Castor Bean
Chan, A. P.-Y. (2018) · Compendium of plant genomes · doi:10.1007/978-3-319-97280-0_7 · Cited by 3
Zeb, U., Wang, X., Fiaz, S., Azizullah, A., Shah, A. A., Ali, S., Rahim, F., Ullah, H., Leghari, U. A., Wang, W., et al. (2022) · PLoS ONE · doi:10.1371/journal.pone.0262040 · Cited by 3
“The low degree of genomic divergence among Pinus species has been attributed to a large number of molecular evolution takeing place in related species [9].”
BackgroundRetractedFull Chromosomal Relationships Between Populations and the Origin of Humans
Dong, R., Pei, S., Guan, M., Yau, S.-C., Yin, C., He, R. L., & Yau, S. S. ‐. (2022) · Frontiers in Genetics · doi:10.3389/fgene.2021.828805 · Cited by 3
“to the conflict results mainly caused by different choices of genes, incomplete data and different data types (Wickett et al., 2014).”
BackgroundStatistical Consistency of Coalescent-Based Species Tree Methods Under Models of Missing Data
Nute, M., & Chou, J. (2017) · Lecture notes in computer science · doi:10.1007/978-3-319-67979-2_15 · Cited by 3
Correlation between plant physiology and CO2 removable
Leman, A. M., Shamsuri, M. M. S., Hariri, A., Kadir, A. B. A., Idris, A. F., & Afandi, A. (2017) · AIP conference proceedings · doi:10.1063/1.5002203 · Cited by 3
Ryo, M., Yamashino, T., Yamakawa, H., Fujita, Y., & Aoki, S. (2018) · Biochemical and Biophysical Research Communications · doi:10.1016/j.bbrc.2018.08.056 · Cited by 3
Phylogeny, Evolution, and Ecology of Sexual Systems Across the Land Plants
Case, A. L., & Jesson, L. K. (2018) · Springer eBooks · doi:10.1007/978-3-319-94139-4_2 · Cited by 3
Establishment of a Clonal Culture of Unicellular Conjugating Algae
Tsuchikane, Y., Hamaji, T., Ota, K., & Kato, S. (2018) · Journal of Visualized Experiments · doi:10.3791/57761-v · Cited by 3
Ligrone, R. (2019) · Springer eBooks · doi:10.1007/978-3-030-16057-9_11 · Cited by 3
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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