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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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Homology-aware Phylogenomics at Gigabase Scales
Sanderson, M. J., Nicolae, M., & McMahon, M. M. (2016) · Systematic Biology · doi:10.1093/sysbio/syw104 · Cited by 38
“Construction of a phylogenetic tree from even a single (Felsenstein 2004), yet trees are now being inferred from entire transcriptomes (Wickett et al. 2014) or genomes (Neafsey et al. 2015) at a scale up to a million times larger than this—across taxa as diverse in scope as land plants (Wickett et…”
BackgroundThe Origin of Land Plants: A Phylogenomic Perspective
Zhong, B., Sun, L., & Penny, D. (2015) · Evolutionary Bioinformatics · doi:10.4137/ebo.s29089 · Cited by 37
Spores of relictual bryophytes: Diverse adaptations to life on land
Brown, R. C., Lemmon, B. E., Shimamura, M., Villarreal, J. C., & RENZAGLIA, K. S. (2015) · Review of Palaeobotany and Palynology · doi:10.1016/j.revpalbo.2015.01.004 · Cited by 37
Self-citationSmith, S. A., & Pease, J. B. (2016) · Briefings in Bioinformatics · doi:10.1093/bib/bbw034 · Cited by 39
Root apical meristem diversity in extant lycophytes and implications for root origins
Fujinami, R., Yamada, T., Nakajima, A., Takagi, S., Idogawa, A., Kawakami, E., Tsutsumi, M., & Imaichi, R. (2017) · New Phytologist · doi:10.1111/nph.14630 · Cited by 37
Tangled history of a multigene family: The evolution of ISOPENTENYLTRANSFERASE genes
Nishii, K., Wright, F., Chen, Y., & Möller, M. (2018) · PLoS ONE · doi:10.1371/journal.pone.0201198 · Cited by 34
“There is some controversy surrounding the paraphyly of bryophytes, with the latest work suggesting various scenarios [65, 66].”
Koch, N. M., & Gauthier, J. A. (2018) · PLoS ONE · doi:10.1371/journal.pone.0202729 · Cited by 38
MABERLY, S. C., & Gontero, B. (2018) · Advances in photosynthesis and respiration · doi:10.1007/978-3-319-93594-2_11 · Cited by 38
Dowdy, N. J., Keating, S. E., Lemmon, A. R., Lemmon, E. M., Conner, W. E., Chialvo, C. H. S., Weller, S. J., Simmons, R. B., Sisson, M. S., & Zaspel, J. M. (2020) · Systematic Entomology · doi:10.1111/syen.12433 · Cited by 36
“Many phylogenomic studies of animals utilize transcriptomic datasets (Hittinger et al., 2010; Hedin et al., 2012; Kawahara & Breinholt, 2014; Wickett et al., 2014; Garrison et al., 2016; Bazinet et al., 2017) or hybrid enrichment (Hodges et al.”
BackgroundKyozuka, J., Nomura, T., & Shimamura, M. (2021) · Current Opinion in Plant Biology · doi:10.1016/j.pbi.2021.102154 · Cited by 37
Li, Y., Luo, L., Liu, Y., He, Q., Yu, N., Gaowa, N., Yi, Z., Wang, J., Han, W. J., Peng, T., et al. (2024) · Journal of Systematics and Evolution · doi:10.1111/jse.13063 · Cited by 36
“Nonetheless monophyly is now widely accepted (Wickett et al., 2014; Puttick et al., 2018; de Sousa et al., 2019; Bell et al., 2020; Donoghue et al., 2021).”
Self-citationDelimiting Coalescence Genes (C-Genes) in Phylogenomic Data Sets
Springer, M. S., & Gatesy, J. (2018) · Genes · doi:10.3390/genes9030123 · Cited by 36
Testo, W., Field, A. R., & Barrington, D. S. (2018) · Journal of Biogeography · doi:10.1111/jbi.13373 · Cited by 36
“…previously reported within the Lycopodiaceae (Field et al., 2016) and within other major lineages, and the relationships among major land plant lineages were consistent with those recovered in recent large-scale analyses (Magall on, Hilu, & Quandt, 2013; Testo & Sundue, 2016; Wickett et al., 2014).”
BackgroundResultEvolution and co-option of developmental regulatory networks in early land plants
Bowman, J. L., Briginshaw, L. N., & Florent, S. N. (2018) · Current topics in developmental biology/Current Topics in Developmental Biology · doi:10.1016/bs.ctdb.2018.10.001 · Cited by 34
Accelerated Estimation of Frequency Classes in Site-Heterogeneous Profile Mixture Models
Susko, E., Lincker, L., & Roger, A. J. (2018) · Molecular Biology and Evolution · doi:10.1093/molbev/msy026 · Cited by 29
Nightmare or delight: Taxonomic circumscription meets reticulate evolution in the phylogenomic era
Jin, Z., Hodel, R. G. J., Ma, D., Wang, H., Liu, G., Ren, C., Ge, B., Fan, Q., Jin, S.-H., Xu, C., et al. (2023) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2023.107914 · Cited by 36
Livshultz, T., Kaltenegger, E., Straub, S. C. K., Weitemier, K., Hirsch, E., Koval, K., Mema, L., & Liston, A. (2018) · New Phytologist · doi:10.1111/nph.15061 · Cited by 35
“The GenBank Nucleotide database (NCBI Resource Coordinators, 2017) and three transcriptome databases: 1KP (Johnson et al., 2012; Matasci et al., 2014; Wickett et al., 2014; Xie et al., 2014), Medicinal Plant Genomics Resource (G ongora-Castillo et al.”
A roadmap for global synthesis of the plant tree of life
Eiserhardt, W. L., Antonelli, A., Bennett, D. J., Botigué, L. R., Burleigh, J. G., Dodsworth, S., Enquist, B. J., Forest, F., Kim, J. T., Kozlov, A. M., et al. (2018) · American Journal of Botany · doi:10.1002/ajb2.1041 · Cited by 35
Self-citationRoth, S., Kilgore, M. B., Kutchan, T. M., & Müller, M. (2018) · ChemBioChem · doi:10.1002/cbic.201800291 · Cited by 35
Self-citationA transcriptome-based resolution for a key taxonomic controversy in Cupressaceae
Mao, K., Ruhsam, M., Ma, Y., Graham, S. W., Liu, J., Thomas, P., MILNE, R. I., & Hollingsworth, P. M. (2018) · Annals of Botany · doi:10.1093/aob/mcy152 · Cited by 35
Self-citationCoiro, M., Chomicki, G., & Doyle, J. A. (2018) · Paleobiology · doi:10.1017/pab.2018.23 · Cited by 36
“…Pinaceae (Bowe et al. 2000; Chaw et al. 2000; Gugerli et al. 2001; Qiu et al. 2007; Zhong et al. 2011), conifers other than Pinaceae (cupressophytes) (Nickrent et al. 2000; Rydin and Källersjö 2002), or conifers as a whole (Wickett et al. 2014), which we refer to collectively as “gneconifer” trees.”
BackgroundThode, V. A., Lohmann, L., & Sanmartín, I. (2020) · Journal of Systematics and Evolution · doi:10.1111/jse.12579 · Cited by 31
“Most studies using the CAT model have focused on animal nuclear or mitochondrial data (Lartillot et al., 2007, 2009; Delsuc et al., 2008; Dunn et al., 2008; Wickett et al., 2014; Li et al., 2015; Song et al., 2016).”
BackgroundMethodResultInfluentialThe Land–Sea Connection: Insights Into the Plant Lineage from a Green Algal Perspective
Bachy, C., Wittmers, F., Muschiol, J., Hamilton, M., Henrissat, B., & Worden, A. Z. (2022) · Annual Review of Plant Biology · doi:10.1146/annurev-arplant-071921-100530 · Cited by 37
Xue, J., Dong, S., Wang, M., Song, T., Zhou, G., Li, Z., de Peer, Y. V., Shao, Z., Wang, W., Chen, M., et al. (2020) · Journal of Systematics and Evolution · doi:10.1111/jse.12708 · Cited by 34
Self-citationLiu, X.-Q., Xia, X., Chen, L., & Wang, X. (2022) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2022.107606 · Cited by 36
Water lily research: Past, present, and future
Xiong, X., Zhang, J., Yang, Y. P., Chen, Y., Su, Q., Zhao, Y. Y., Wang, J., Xia, Z., Wang, L., Zhang, L., et al. (2023) · Tropical Plants · doi:10.48130/tp-2023-0001 · Cited by 34
Self-citationContrasting and conserved roles of NPR pathways in diverged land plant lineages
Jeon, H., Iwakawa, H., Naramoto, S., Herrfurth, C., Gutsche, N., Schlüter, T., Kyozuka, J., Miyauchi, S., Feußner, I., Zachgo, S., et al. (2024) · New Phytologist · doi:10.1111/nph.19981 · Cited by 34
Characteristics of guaiacyl-syringyl lignin in reaction wood in the gymnosperm Gnetum gnemon L.
Nawawi, D. S., Syafii, W., Akiyama, T., & Matsumoto, Y. (2016) · Holzforschung · doi:10.1515/hf-2015-0107 · Cited by 34
Labiak, P. H., & Karol, K. G. (2017) · American Journal of Botany · doi:10.3732/ajb.1700135 · Cited by 34
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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