The DOI matches its Crossref record; 122 of the 124 references it cites were found in a registry or an index.
Phylotranscriptomic analysis of the origin and early diversification of land plants
Open accessAbstract
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.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
In the citing paper
“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
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
Basic local alignment search tool
Altschul, S. F., Gish, W., Miller, W., Myers, E. W., & Lipman, D. J. (1990) · Journal of Molecular Biology · doi:10.1006/jmbi.1990.9999 · Cited by 98,669
RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models
Stamatakis, A. (2006) · Bioinformatics · doi:10.1093/bioinformatics/btl446 · Cited by 15,582
Algorithm AS 136: A K-Means Clustering Algorithm
Hartigan, J. A., & Wong, M. A. (1979) · Applied Statistics · doi:10.2307/2346830 · Cited by 14,523
The Angiosperm Phylogeny Group (2016) · Botanical Journal of the Linnean Society · doi:10.1111/boj.12385 · Cited by 9,583
The rapid generation of mutation data matrices from protein sequences
Jones, D. T., Taylor, W. R., & Thornton, J. M. (1992) · Computer applications in the biosciences · doi:10.1093/bioinformatics/8.3.275 · Cited by 7,003
Accelerated Profile HMM Searches
Eddy, S. R. (2011) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1002195 · Cited by 6,975
OrthoMCL: Identification of Ortholog Groups for Eukaryotic Genomes
Li, L., Stoeckert, C. J., & Roos, D. S. (2003) · Genome Research · doi:10.1101/gr.1224503 · Cited by 5,707
TNT, a free program for phylogenetic analysis
Goloboff, P. A., Farris, J. S., & Nixon, K. C. (2008) · Cladistics · doi:10.1111/j.1096-0031.2008.00217.x · Cited by 5,352
THE ANGIOSPERM PHYLOGENY GROUP (2009) · Botanical Journal of the Linnean Society · doi:10.1111/j.1095-8339.2009.00996.x · Cited by 4,911
Apg (2009) · Botanical Journal of the Linnean Society · Cited by 3,627
Research works printed but not linked: 4
- M Melkonian, B Surek, Phylogeny of the Chlorophyta—Congruence between ultrastructural and molecular evidence. Bulletin De La Societe Zoologique De France-Evolution Et Zoologie 120, 191–208 (1995).
- RE Timme, CF Delwiche, Phylogenomic reconstruction of the Charophytes: A multilocus approach to resolving the phylogeny of plants’ closest relatives. J Phycol 47, 16 (2011).
- JD Pickett-Heaps, The evoltuion of mitotic apparatus—An attempt at comparative ultrastructural cytology in dividing plant cells. Cytobios 1, 257–280 (1969).
- WR Philipson, A new approach to the origins of vascular plants. Botanische Jahrbucher 113, 443–460 (1991).
Cited by
Sorted by citations
Items 501–600 of 1,000
The Evolution of Sexual Fluids in Gymnosperms From Pollination Drops to Nectar
von Aderkas, P., Prior, N., & Little, S. A. (2018) · Frontiers in Plant Science · doi:10.3389/fpls.2018.01844 · Cited by 34
“This is due, in part to the prevalence of sexual fluids among the majority of modern gymnosperm groups and thus the ancestral condition of having a pollination drop would be similar among all major lineages given alternative topologies (i.e., Zhong et al., 2011; Xi et al., 2013; Ruhfel et al., 2014; Wickett et al., 20…”
BackgroundSunscreen mucilage: a photoprotective adaptation found in terrestrial green algae (Zygnematophyceae)
Busch, A., & Hess, S. (2021) · European Journal of Phycology · doi:10.1080/09670262.2021.1898677 · Cited by 34
Unlocking the Hidden Genetic Diversity of Varicosaviruses, the Neglected Plant Rhabdoviruses
Bejerman, N., Dietzgen, R. G., & Debat, H. (2022) · Pathogens · doi:10.3390/pathogens11101127 · Cited by 34
“Japanese umbrella pine (Sciadopitys verticillata) Gymnosperm/ Sciadopityaceae Sciadopitys virus 1_Can/ SciV1_Can PRJEB4921/ [51] RNA1/14.”
BackgroundSpecies Tree Estimation Using ASTRAL: How Many Genes Are Enough?
Shekhar, S., Roch, S., & Mirarab, S. (2017) · IEEE Transactions on Computational Biology and Bioinformatics · doi:10.1109/tcbb.2017.2757930 · Cited by 34
“, [20], [32], [33], [34], [35], [36], [37], [38], [39], [40], [41]).”
BackgroundSelf-citationMecchia, M. A., Rövekamp, M., Giraldo‐Fonseca, A., Meier, D., Gadient, P., Vogler, H., Limacher, D., Bowman, J. L., & Grossniklaus, U. (2022) · Development · doi:10.1242/dev.200580 · Cited by 33
Progress in systematics and biogeography of Orchidaceae
WANG, Y., Wang, H., Ye, C., Wang, Z., Ma, C.-B., Lin, D.-L., & Jin, X. (2024) · Acta Botanica Yunnanica · doi:10.1016/j.pld.2024.05.002 · Cited by 33
Linear Plasmids and the Rate of Sequence Evolution in Plant Mitochondrial Genomes
Warren, J. M., Simmons, M. P., Wu, Z., & Sloan, D. B. (2016) · Genome Biology and Evolution · doi:10.1093/gbe/evw003 · Cited by 33
The Early Cretaceous Apple Bay flora of Vancouver Island: a hotspot of fossil bryophyte diversity
Tomescu, A. M. F. (2016) · Botany · doi:10.1139/cjb-2016-0054 · Cited by 33
“The deep geologic age of bryophytes (Edwards et al. 1995; Wellman et al. 2003), which are widely accepted today as being at least as old as vascular plants (Graham 1993; Kenrick and Crane 1997; Wickett et al. 2014), argues against the former and in support of the latter.”
BackgroundEvidence for an ancient whole genome duplication in the cycad lineage
Roodt, D., Lohaus, R., Sterck, L., Swanepoel, R. L., de Peer, Y. V., & Mizrachi, E. (2017) · PLoS ONE · doi:10.1371/journal.pone.0184454 · Cited by 34
A Comprehensive Assessment of the Fossil Record of Liverworts in Amber
Heinrichs, J., Feldberg, K., Bechteler, J., Regalado, L., Renner, M. A. M., Schäfer‐Verwimp, A., Gröhn, C., Müller, P., Schneider, H., & Krings, M. (2018) · Elsevier eBooks · doi:10.1016/b978-0-12-813012-4.00012-7 · Cited by 33
Yang, X., Zhou, T., Su, X., Wang, G., Zhang, X., Guo, Q., & Cao, F. (2020) · Journal of Forestry Research · doi:10.1007/s11676-019-01088-4 · Cited by 33
Phylogenomics indicates the “living fossil” Isoetes diversified in the Cenozoic
Wood, D. P., Besnard, G., Beerling, D. J., Osborne, C. P., & Christin, P. (2020) · PLoS ONE · doi:10.1371/journal.pone.0227525 · Cited by 33
“Nuclear markers can be more useful for molecular dating if they show less variation in rates among branches [24] as suggested from large scale embryophyte phylotranscriptomics [72, 73].”
Evolutionary Origins of Drought Tolerance in Spermatophytes
Bowles, A. M. C., Paps, J., & Bechtold, U. (2021) · Frontiers in Plant Science · doi:10.3389/fpls.2021.655924 · Cited by 33
“All extant land plants descend from a single common ancestor (Wickett et al., 2014; de Vries and Archibald, 2018) and have since diversified into almost 400,000 species that have shaped modern ecosystems (Kenrick and Crane, 1997; Willis, 2017).”
BackgroundStepwise changes in flavonoids in spores/pollen contributed to terrestrial adaptation of plants
Xue, J., Qiu, S., Jia, X., Shen, S., Shen, C.-W., Wang, S., Xu, P., Tong, Q., Lou, Y., Yang, N., et al. (2023) · PLANT PHYSIOLOGY · doi:10.1093/plphys/kiad313 · Cited by 33
Shape analysis of moss (Bryophyta) sporophytes: Insights into land plant evolution
Rose, J. P., Kriebel, R., & Sytsma, K. J. (2016) · American Journal of Botany · doi:10.3732/ajb.1500394 · Cited by 32
Phylogenetic and functional signals in gymnosperm ovular secretions
Nepi, M., Little, S. A., Guarnieri, M., Nocentini, D., Prior, N., Gill, J. E., TOMLINSON, P. B., Ickert‐Bond, S. M., Pirone, C., Pacini, E., et al. (2017) · Annals of Botany · doi:10.1093/aob/mcx103 · Cited by 32
“Empididae have also been reported in fly pollination of a number of angiosperms (reviewed in Woodcock et al. , 2014).”
Plant Evolution: Phylogenetic Relationships between the Earliest Land Plants
Rensing, S. A. (2018) · Current Biology · doi:10.1016/j.cub.2018.01.034 · Cited by 32
“When considering site heterogeneity, the two most abundant positions of the hornworts reflect either the now more traditional view [15] of hornworts sister to tracheophytes (‘Hornwort– Tracheophyta’, Figure 1B; this topology is also supported when considering across-branch heterogeneity), or the position suggested in…”
BackgroundResultChallenges of comprehensive taxon sampling in comparative biology: Wrestling with rosids
Folk, R. A., Sun, M., Soltis, P. S., Smith, S. A., Soltis, P. S., & Guralnick, R. (2018) · American Journal of Botany · doi:10.1002/ajb2.1059 · Cited by 32
“…relationships in the angiosperms (Chase et al., 1993; Qiu et al., 1999; Soltis et al., 1999, 2011) with large-scale sequencing projects (e.g., 1KP, Matasci et al., 2014) resulting in robust backbone resolution (Wickett et al., 2014) and community consensus taxonomic products (APG IV, 2016).”
BackgroundSelf-citationPhyloToL: A Taxon/Gene-Rich Phylogenomic Pipeline to Explore Genome Evolution of Diverse Eukaryotes
Cerón-Romero, M. A., Maurer-Alcalá, X., Grattepanche, J., Yan, Y., Fonseca, M. M., & Katz, L. A. (2019) · Molecular biology and evolution · doi:10.1093/molbev/msz103 · Cited by 43
“Large-scale phylogenomic analyses allow for the exploration of deep evolutionary relationships (e.g., dos Reis et al. 2012; Wickett et al. 2014; Katz and Grant 2015; Hug et al. 2016), but such analyses require data-intensive computing”
BackgroundGao, B., Chen, M., Li, X., & Zhang, J. (2019) · Communications Biology · doi:10.1038/s42003-019-0469-4 · Cited by 32
Evolutionary Aspects of TRPMLs and TPCs
Jaślan, D., Böck, J., Krogsaeter, E., & Grimm, C. M. (2020) · International Journal of Molecular Sciences · doi:10.3390/ijms21114181 · Cited by 34
“All plants harbor at least one TPC gene, already present in the genome of charophytic algae around 793 million years ago [82,90,91].”
BackgroundBellini, E., Betti, C., & di Toppi, L. S. (2021) · Plants · doi:10.3390/plants10040770 · Cited by 32
“As charophytes are a sister group of all land plants [36,37], they can provide important “primeval” information, which is fundamental for reconstructing several biological functions from an evolutionary point of view [33,38,39].”
BackgroundwQFM: highly accurate genome-scale species tree estimation from weighted quartets
Mahbub, M., Wahab, Z., Reaz, R., Rahman, M. S., & Bayzid, M. S. (2021) · Bioinformatics · doi:10.1093/bioinformatics/btab428 · Cited by 35
Cui, X.-Y., Meng, F., Pan, X., Qiu, X.-Y., Zhang, S.-X., Li, C.-L., & Lu, S.-F. (2022) · Horticulture Research · doi:10.1093/hr/uhac005 · Cited by 32
“This result is in agreement with results from a phylotranscriptomic analysis of 92 streptophytes and land plants [28], an angiosperm phylogeny of 26 species [29], a phylogenomic analysis of the stout camphor tree [30], and a phylogenomic analysis of one thousand plant transcriptomes [31].”
ResultYang, T., Liao, X., Yang, L., Liu, Y., Mu, W., Liu, X., Liu, X., Strube, M. L., Zhong, B., & Liu, H. (2022) · Frontiers in Plant Science · doi:10.3389/fpls.2022.808156 · Cited by 40
Fang, L., Leliaert, F., Novis, P. M., Zhang, Z., Zhu, H., Liu, G., Penny, D., & Zhong, B. (2018) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2018.06.006 · Cited by 31
Reticulate evolution: Detection and utility in the phylogenomics era
Bjornson, S., Verbruggen, H., Upham, N. S., & Steenwyk, J. L. (2024) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2024.108197 · Cited by 36
The rise of polyploids during environmental upheaval
Chen, H., Almeida‐Silva, F., Logghe, G., Maere, S., Bonte, D., & de Peer, Y. V. (2026) · Cell · doi:10.1016/j.cell.2026.04.008 · Cited by 34
Crown Group Lejeuneaceae and Pleurocarpous Mosses in Early Eocene (Ypresian) Indian Amber
Heinrichs, J., Scheben, A., Bechteler, J., Lee, G. E., Schäfer‐Verwimp, A., Hedenäs, L., Singh, H., Pócs, T., Nascimbene, P. C., Peralta, D. F., et al. (2016) · PLoS ONE · doi:10.1371/journal.pone.0156301 · Cited by 31
Simmons, M. P. (2016) · Journal of Systematics and Evolution · doi:10.1111/jse.12233 · Cited by 30
Sexual reproduction and sex determination in green algae
Sekimoto, H. (2017) · Journal of Plant Research · doi:10.1007/s10265-017-0908-6 · Cited by 31
Shao, C.-C., Shen, T., Jin, W., Mao, H.-J., Ran, J., & Wang, X. (2019) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2019.106610 · Cited by 33
Transcriptome‐based target‐enrichment baits for stony corals (Cnidaria: Anthozoa: Scleractinia)
Quek, Z. B. R., Jain, S. S., Neo, M. L., Rouse, G. W., & Huang, D. (2020) · Molecular Ecology Resources · doi:10.1111/1755-0998.13150 · Cited by 30
“Since the advent of DNA sequencing, molecular data have been imperative for phylogenetic reconstructions across the tree of life (Laumer et al., 2019; Pizarro et al., 2018; Wickett et al., 2014), and scleractinian corals are no exception.”
BackgroundThree-dimensional growth: a developmental innovation that facilitated plant terrestrialization
Moody, L. A. (2020) · Journal of Plant Research · doi:10.1007/s10265-020-01173-4 · Cited by 31
Islam, M., Sarker, K., Das, T., Reaz, R., & Bayzid, M. S. (2020) · BMC Genomics · doi:10.1186/s12864-020-6519-y · Cited by 31
“Therefore, both orthologs and paralogs are not being included in many studies such as 1KP project [59], where many genes were discarded that evolved with duplications and losses.”
BackgroundExploring the phylogeny of the marattialean ferns
Lehtonen, S., Poczai, P., Sablok, G., Hyvönen, J., Karger, D. N., & Flores, J. R. (2020) · Cladistics · doi:10.1111/cla.12419 · Cited by 32
“…et al., 2015; Qi et al., 2018; Shen et al., 2018) generally support a sister relationship between the marattialean and leptosporangiate ferns (but see Wickett et al., 2014, and One Thousand Plant Transcriptomes Initiative,*Corresponding author: E-mail address: samile@utu.fi © 2020 The Authors.”
BackgroundPfeifer, L., Utermöhlen, J., Happ, K., Permann, C., Holzinger, A., von Schwartzenberg, K., & Classen, B. (2021) · The Plant Journal · doi:10.1111/tpj.15577 · Cited by 30
“However, recent phylogenomic analyses revealed that land plants evolved from streptophyte algae most closely related to extant Zygnematophyceae (Leebens-Mack et al., 2019; Ruhfel et al., 2014; Timme et al., 2012; Wickett et al., 2014; Wodniok et al., 2011).”
An overview of bioinformatics, genomics, and transcriptomics resources for bryophytes
Fernández‐Pozo, N., Haas, F. B., Gould, S. B., & Rensing, S. A. (2022) · Journal of Experimental Botany · doi:10.1093/jxb/erac052 · Cited by 31
Evolution of chlorophyll degradation is associated with plant transition to land
Schumacher, I., Menghini, D., Ovinnikov, S., Hauenstein, M., Fankhauser, N., Zipfel, C., Hörtensteiner, S., & Aubry, S. (2021) · The Plant Journal · doi:10.1111/tpj.15645 · Cited by 31
“Embryo-phytes are thought to be derived from a single clade within streptophytes and diverged some 450 – 500 million years ago (Wickett et al., 2014; de Vries and Archibald, 2018).”
Fisher, T. J., Flores‐Sandoval, E., Alvarez, J. P., & Bowman, J. L. (2023) · New Phytologist · doi:10.1111/nph.18854 · Cited by 26
Beilby, M. J. (2016) · Frontiers in Plant Science · doi:10.3389/fpls.2016.01052 · Cited by 31
“Wickett et al. (2014) provide strong support for Zygnematophyceae to be the sister-group to land plants.”
BackgroundXyloglucan evolution and the terrestrialization of green plants
Del‐Bem, L. (2018) · New Phytologist · doi:10.1111/nph.15191 · Cited by 30
The road to 10,000 plant genomes
Twyford, A. D. (2018) · Nature Plants · doi:10.1038/s41477-018-0165-2 · Cited by 30
Villarreal, J. C., Turmel, M., Bourgouin-Couture, M., Laroche, J., Allen, N. S., Li, F., Cheng, S., RENZAGLIA, K. S., & Lemieux, C. (2018) · PLoS ONE · doi:10.1371/journal.pone.0200491 · Cited by 30
Self-citationCompetition for epidermal space in the evolution of leaves with high physiological rates
Baresch, A., Crifò, C., & Boyce, C. K. (2018) · New Phytologist · doi:10.1111/nph.15476 · Cited by 30
Conidae phylogenomics and evolution
Abalde, S., Jimenez-Tenorio, M., Uribe, J. E., & Zardoya, R. (2019) · Zoologica Scripta · doi:10.1111/zsc.12329 · Cited by 30
“, 2018) or land plants (Wickett et al., 2014), among many others rapidly accumulating.”
BackgroundPandey, A., & Braun, E. L. (2020) · Biology · doi:10.3390/biology9040064 · Cited by 30
“, early land plant [5] or metazoan evolution [6,11] and efforts to identify to root of archaea [30] or eukaryotes [31]) and they are good candidates for this type of signal exploration.”
BackgroundA pseudomolecule‐scale genome assembly of the liverwort Marchantia polymorpha
Diop, S. I., Subotic, O., Giraldo‐Fonseca, A., Waller, M., Kirbis, A., Neubauer, A., Potente, G., Murray‐Watson, R. E., Bošković, F., Bont, Z., et al. (2019) · The Plant Journal · doi:10.1111/tpj.14602 · Cited by 30
“Phylogenomic data now indicate that liverworts and mosses are monophyletic, and that the tracheophytes (vascular plants) are sister to the clade of bryophytes including mosses, liverworts, and hornworts (Wickett et al., 2014; Cox, 2018; Puttick et al., 2018).”
BackgroundInsights into the ancestral flowers of Ranunculales
Carrive, L., Domenech, B., Sauquet, H., Jabbour, F., Damerval, C., & Nadot, S. (2020) · Botanical Journal of the Linnean Society · doi:10.1093/botlinnean/boaa031 · Cited by 30
The Molecular Phylogeny of Land Plants: Progress and Future Prospects
Liu, G., Lian, L., & Wang, W. (2022) · Diversity · doi:10.3390/d14100782 · Cited by 30
RENZAGLIA, K. S., Crandall‐Stotler, B., Pressel, S., Duckett, J. G., Schuette, S., & Strother, P. K. (2015) · Botanical Journal of the Linnean Society · doi:10.1111/boj.12343 · Cited by 30
“Even as recent studies (Cox et al., 2014; Wickett et al., 2014) have challenged both the paraphyly of the three bryophyte clades and the sister group relationship between liverworts and other embryophytes, the occurrence of permanent dyads in the clade that is sister to all other liverworts implies…”
ResultLobule shape evolution inRadula(Jungermanniopsida): one rate fits all?
Renner, M. A. M. (2015) · Botanical Journal of the Linnean Society · doi:10.1111/boj.12279 · Cited by 29
Future Perspectives and Challenges of Fungal Systematics in the Age of Big Data
Wang, Z., Nilsson, R. H., James, T. Y., Dai, Y., & Townsend, J. P. (2016) · Fungal biology · doi:10.1007/978-3-319-29137-6_3 · Cited by 29
Azolla: A Model System for Symbiotic Nitrogen Fixation and Evolutionary Developmental Biology
de Vries, S., & de Vries, J. (2018) · Springer eBooks · doi:10.1007/978-3-319-75103-0_2 · Cited by 30
NBS-LRR genes—Plant health sentinels: Structure, roles, evolution and biotechnological applications
Bezerra-Neto, J. P., de Araújo, F. C., Ferreira‐Neto, J. R. C., Silva, R. L. D. O., Borges, A. N. C., Matos, M. K. D. S., Silva, J. B., da Silva, M. D., Kido, É. A., & Benko‐Iseppon, A. M. (2019) · Elsevier eBooks · doi:10.1016/b978-0-12-816030-5.00004-5 · Cited by 29
Evolutionary History of the Marchantia polymorpha Complex
Linde, A., Sawangproh, W., Cronberg, N., Szövényi, P., & Lagercrantz, U. (2020) · Frontiers in Plant Science · doi:10.3389/fpls.2020.00829 · Cited by 29
“Marchantia polymorpha is one of the most studied species of liverworts but aspects of its phylogenetic relationships remain poorly resolved (Nishiyama et al., 2004; Qiu et al., 2006; Wickett et al., 2014), even after completion of whole-genome sequencing which was published in 2017 (Bowman et al.”
BackgroundAlnC: An extensive database of long non-coding RNAs in angiosperms
Singh, A. B., Vivek, T., & Kumar, S. (2021) · PLoS ONE · doi:10.1371/journal.pone.0247215 · Cited by 29
“First, we excluded potential coding transcripts from the assembled transcripts set for that species (translated proteins of matched orthogroups derived from annotated plant genomes) [24].”
BackgroundZhang, L., Morales‐Briones, D. F., Li, Y., Zhang, G., Zhang, T., Huang, C., Guo, P., Zhang, K., Wang, Y., Wang, H., et al. (2023) · New Phytologist · doi:10.1111/nph.19175 · Cited by 29
Three rings for the evolution of plastid shape: a tale of land plant FtsZ
Grosche, C., & Rensing, S. (2017) · Protoplasma · doi:10.1007/s00709-017-1096-x · Cited by 28
Gene Duplication Leads to Altered Membrane Topology of a Cytochrome P450 Enzyme in Seed Plants
Renault, H., Marothy, M. D., Jonasson, G., Lara, P., Nelson, D. R., Nilsson, I., André, F., von HEIJNE, G., & Werck‐Reichhart, D. (2017) · Molecular Biology and Evolution · doi:10.1093/molbev/msx160 · Cited by 29
“…homologs were found in all investigated taxa of land plants, no related sequences were detected by BLAST in green algae, including Klebsormidiales and Zygnematales (supplementary tables S1–S3, Supplementary Material online), the sister group to land plants (Wickett et al. 2014; Chang et al. 2016).”
BackgroundFunctional genomic perspectives on plant terrestrialization
Kunz, C. F., Goldbecker, E. S., & de Vries, J. (2025) · Trends in Genetics · doi:10.1016/j.tig.2025.02.006 · Cited by 32
Phylogenomic approaches to deciphering the tree of life
Wen, J., Liu, J., Ge, S., Xiang, Q., & Zimmer, E. A. (2015) · Journal of Systematics and Evolution · doi:10.1111/jse.12175 · Cited by 28
Eliáš, M., Klimeš, V., Derelle, R., Vargová, R., & Tachezy, J. (2016) · Biology Direct · doi:10.1186/s13062-016-0107-8 · Cited by 27
“onekp/; [94]), but no RABL2 ortholog could be found in any of them (except one case of apparent rotifer contamination in the transcriptome of the moss Schwetschkeopsis”
BackgroundInfluentialCharacter evolution and missing (morphological) data across Asteridae
Stull, G. W., Schori, M., Soltis, P. S., & Soltis, P. S. (2018) · American Journal of Botany · doi:10.1002/ajb2.1050 · Cited by 28
Self-citationKondou, Y., Miyagi, Y., Morito, T., Fujihira, K., Miyauchi, W., Moriyama, A., Terasawa, T., Ishida, S., Iwabuchi, K., Kubo, H., et al. (2019) · Planta · doi:10.1007/s00425-019-03090-w · Cited by 28
Foster, C. S. P., & Ho, S. Y. W. (2017) · Genome Biology and Evolution · doi:10.1093/gbe/evx198 · Cited by 28
Zygnematophyceae: from living algae collections to the establishment of future models
Zhou, H., & von Schwartzenberg, K. (2020) · Journal of Experimental Botany · doi:10.1093/jxb/eraa091 · Cited by 28
Is Over-parameterization a Problem for Profile Mixture Models?
Baños, H., Susko, E., & Roger, A. J. (2023) · Systematic Biology · doi:10.1093/sysbio/syad063 · Cited by 33
Ghosh, T. K., Kaneko, M., Akter, K., Murai, S., Komatsu, K., Ishizaki, K., Yamato, K. T., Kohchi, T., & Takezawa, D. (2015) · Physiologia Plantarum · doi:10.1111/ppl.12385 · Cited by 28
The phycocyanobilin chromophore of streptophyte algal phytochromes is synthesized by HY2
Rockwell, N. C., Martin, S. S., Li, F., Mathews, S., & Lagarias, J. C. (2017) · New Phytologist · doi:10.1111/nph.14422 · Cited by 30
“Consistent with this hypothesis, the genome of the streptophyte alga Klebsormidium flaccidum contains HY2 but lacks PcyA (Hori et al., 2014).”
InfluentialSelf-citationWu, F., Tang, C., Guo, Y.-M., Bian, Z.-W., Fu, J., Lu, G., Qi, J., Pang, Y.-J., & Yang, Y. (2017) · Scientific Reports · doi:10.1038/s41598-017-04750-1 · Cited by 28
Hussain, T., Espley, R. V., Gertsch, J., Whare, T., Stehle, F., & Kayser, O. (2019) · Phytochemistry Reviews · doi:10.1007/s11101-019-09638-8 · Cited by 28
Major Changes in Plastid Protein Import and the Origin of the Chloroplastida
Knopp, M. R., Garg, S. G., Handrich, M. R., & Gould, S. B. (2020) · iScience · doi:10.1016/j.isci.2020.100896 · Cited by 28
Evolution of plant metabolism: the state-of-the-art
Fernie, A. R., de Vries, S., & de Vries, J. (2024) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2023.0347 · Cited by 30
“The different phylogenomic studies robustly recovering Zygnematophyceae as the sister group to land plants [41,43–46] are allowing us now to trace those characteristics that the conquerors of land already possessed.”
BackgroundMoody, L. A., Saidi, Y., Gibbs, D. J., Choudhary, A., Holloway, D., Vesty, E. F., Bansal, K. K., Bradshaw, S. J., & Coates, J. C. (2016) · New Phytologist · doi:10.1111/nph.13938 · Cited by 27
“Whether charophyte ARABIDILLO homologues (which our searches suggest exist; Timme & Delwiche, 2010; Hori et al., 2014; Matasci et al., 2014; Wickett et al., 2014) are part of this regulation is currently unknown.”
BackgroundPease, J. B., & Rosenzweig, B. K. (2015) · IEEE Transactions on Computational Biology and Bioinformatics · doi:10.1109/tcbb.2015.2509997 · Cited by 28
“rather than being aligned to single reference genome [11], [12].”
BackgroundPierangelini, M., Glaser, K., Mikhailyuk, T. I., Karsten, U., & Holzinger, A. (2018) · Microbial Ecology · doi:10.1007/s00248-018-1225-x · Cited by 27
INSTRAL: Discordance-Aware Phylogenetic Placement Using Quartet Scores
Rabiee, M., & Mirarab, S. (2019) · Systematic Biology · doi:10.1093/sysbio/syz045 · Cited by 31
Self-citationZhang, H.-R., Wei, R., Xiang, Q., & Zhang, X. (2020) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2020.106788 · Cited by 27
Sousa, F., Civáň, P., Brazão, J., Foster, P. G., & Cox, C. J. (2020) · PeerJ · doi:10.7717/peerj.8995 · Cited by 27
PlantTribes2: Tools for comparative gene family analysis in plant genomics
Wafula, E. K., Zhang, H., Kuster, G. V., Leebens‐Mack, J., Honaas, L. A., & dePamphilis, C. W. (2023) · Frontiers in Plant Science · doi:10.3389/fpls.2022.1011199 · Cited by 28
“, 2020), resolving species relationships (Timme et al., 2012; Rothfels et al., 2013; Wickett et al., 2014; Zeng et al., 2014; Yang et al., 2015a; Huang et al., 2016; Xiang et al., 2017; One Thousand Plant Transcriptomes Initiative, 2019; Hodel et al., 2022), accurate identification of orthologous and paralogous genes…”
BackgroundMethodSelf-citationUddenberg, D., Akhter, S., Ramachandran, P., Sundström, J. F., & Carlsbecker, A. (2015) · Frontiers in Plant Science · doi:10.3389/fpls.2015.00970 · Cited by 27
“The tree is based on the comprehensive studies of seed plant phylogeny by Wickett et al. (2014) and Ruhfel et al. (2014).”
BackgroundMethodInfluentialCells, walls, and endless forms
Monniaux, M., & Hay, A. (2016) · Current Opinion in Plant Biology · doi:10.1016/j.pbi.2016.10.010 · Cited by 27
Yu, Y., Xiang, Q., Manos, P. S., Soltis, P. S., Soltis, P. S., Song, B., Cheng, S., Liu, X., & Wong, G. K. (2017) · PLoS ONE · doi:10.1371/journal.pone.0171361 · Cited by 29
Self-citationShaw, A. J., Schmutz, J., Devos, N., Shu, S., Carrell, A. A., & Weston, D. J. (2016) · Advances in botanical research · doi:10.1016/bs.abr.2016.01.003 · Cited by 27
Self-citationMolecular evolution of key metabolic genes during transitions to C4 and CAM photosynthesis
Goolsby, E. W., Moore, A. J., Hancock, L. P., de Vos, J. M., & Edwards, E. J. (2018) · American Journal of Botany · doi:10.1002/ajb2.1051 · Cited by 27
Systems Biology of Streptophyte Cell Evolution
Goldbecker, E. S., & de Vries, J. (2025) · Annual Review of Plant Biology · doi:10.1146/annurev-arplant-083123-060254 · Cited by 27
Anchoring quartet-based phylogenetic distances and applications to species tree reconstruction
Sayyari, E., & Mirarab, S. (2016) · BMC Genomics · doi:10.1186/s12864-016-3098-z · Cited by 26
Self-citationBiogeography and diversification rates in hornworts: The limitations of diversification modeling
Villarreal, J. C., Cusimano, N., & Renner, S. S. (2015) · Taxon · doi:10.12705/642.7 · Cited by 26
Self-citationDivergence and support among slightly suboptimal likelihood gene trees
Simmons, M. P., & Kessenich, J. (2019) · Cladistics · doi:10.1111/cla.12404 · Cited by 26
Althoff, F., & Zachgo, S. (2020) · International Journal of Molecular Sciences · doi:10.3390/ijms21155410 · Cited by 26
He, B., Zhao, Y., Su, C., Lin, G., Wang, Y., Li, L., Ma, J., Yang, Q., & Hao, J. (2023) · Systematic Entomology · doi:10.1111/syen.12592 · Cited by 28
“observed discordance, including the numerous conflicting topologies and the low recovery rate of deep nodes between concatenated gene trees and sliding-window gene trees (Jiao et al., 2020; Suh et al., 2015; Wickett et al., 2014).”
BackgroundThe fate of sex chromosomes during the evolution of monoicy from dioicy in liverworts
Singh, S., Davies, K. M., Chagné, D., & Bowman, J. L. (2023) · Current Biology · doi:10.1016/j.cub.2023.07.023 · Cited by 26
Biodiversity synthesis across the green branches of the tree of life
Allen, J. M., Folk, R. A., Soltis, P. S., Soltis, D. E., & Guralnick, R. (2018) · Nature Plants · doi:10.1038/s41477-018-0322-7 · Cited by 26
Self-citationHow land plant life cycles first evolved
Kenrick, P. (2017) · Science · doi:10.1126/science.aan2923 · Cited by 26
Introduction to the Special Issue on Bryophytes
Budke, J. M., Bernard, E. C., Gray, D. J., Huttunen, S., Piechulla, B., & Trigiano, R. N. (2018) · Critical Reviews in Plant Sciences · doi:10.1080/07352689.2018.1482396 · Cited by 26
“Recent phylogenetic analyses support two main evolutionary hypotheses (Nishiyama et al., 2004; Wickett et al. 2014; Cox, 2018; Puttick et al., 2018 in this Special Issue): (1) the liverworts and mosses are a monophyletic clade with the hornworts as an independent lineage and (2) all three bryophyte…”
BackgroundMendoza, C. G., Naumann, J., Samain, M., Goetghebeur, P., Smet, Y. D., & Wanke, S. (2015) · BMC Evolutionary Biology · doi:10.1186/s12862-015-0416-z · Cited by 25
“Among these two strategies, mining publicly available transcriptome resources for developing novel NSCG markers for non-model plant species is being increasingly applied [29, 38 – 41].”
BackgroundMultilocus Phylogenetics of New World Milkweed Vines (Apocynaceae, Asclepiadoideae, Gonolobinae)
McDonnell, A., Parks, M., & Fishbein, M. (2018) · Systematic Botany · doi:10.1600/036364418x697021 · Cited by 26
“…and are important for phylogeny reconstruction using the multispecies coalescent (Degnan and Rosenberg 2009), which has been widely used in recent years for the estimation of species trees from gene trees in many angiosperm lineages (Wickett et al. 2014; Xi et al. 2014; Stephens et al. 2015).”
BackgroundSousa, F., Civáň, P., Foster, P. G., & Cox, C. J. (2020) · Frontiers in Plant Science · doi:10.3389/fpls.2020.01062 · Cited by 26
“Relationships among the streptophyte algae have been determined with increasing congruence and statistical confidence, converging on a phylogeny that places the conjugating algae of the Zygnematophyceae as the sister-group of land plants (Wickett et al., 2014; Puttick et al., 2018).”
BackgroundKawai, J., Kanazawa, M., Suzuki, R., Kikuchi, N., Hayakawa, Y., & Sekimoto, H. (2021) · New Phytologist · doi:10.1111/nph.17763 · Cited by 25
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
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
