Cited by 1,252Protist diversity and phylogenyPlant Diversity and EvolutionGenomics and Phylogenetic Studies

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 access

Wickett, Norman J., Mirarab, Siavash, Nguyen, Nam, Warnow, Tandy, Carpenter, Eric, Matasci, Naim, Ayyampalayam, Saravanaraj, Barker, Michael S., Burleigh, J. Gordon, Gitzendanner, Matthew A., Ruhfel, Brad R., Wafula, Eric, Der, Joshua P., Graham, Sean W., Mathews, Sarah, Melkonian, Michael, Soltis, Douglas E., Soltis, Pamela S., Miles, Nicholas W., Rothfels, Carl J., Pokorny, Lisa, Shaw, A. Jonathan, DeGironimo, Lisa, Stevenson, Dennis W., Surek, Barbara, Villarreal, Juan Carlos, Roure, Béatrice, Philippe, Hervé, dePamphilis, Claude W., Chen, Tao, Deyholos, Michael K., Baucom, Regina S., Kutchan, Toni M., Augustin, Megan M., Wang, Jun, Zhang, Yong, Tian, Zhijian, Yan, Zhixiang, Wu, Xiaolei, Sun, Xiao, Wong, Gane Ka-Shu, Leebens-Mack, James·2014·Proceedings of the National Academy of Sciences

DOI 10.1073/pnas.1323926111PMC PMC4234587

Open this paper in CoChat — free account

Abstract

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.

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

Crossref · 10.1073/pnas.1323926111

Cites

122 of 122 references verified0 citation errors · 0 not checkable

Statistics

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?

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

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
An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG IV
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
An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG III
THE ANGIOSPERM PHYLOGENY GROUP (2009) · Botanical Journal of the Linnean Society · doi:10.1111/j.1095-8339.2009.00996.x · Cited by 4,911
An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants : APG III
Apg (2009) · Botanical Journal of the Linnean Society · Cited by 3,627
Gene Trees in Species Trees
Maddison, W. P. (1997) · Systematic Biology · doi:10.1093/sysbio/46.3.523 · Cited by 3,039
An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG II
THE ANGIOSPERM PHYLOGENY GROUP* (2003) · Botanical Journal of the Linnean Society · doi:10.1046/j.1095-8339.2003.t01-1-00158.x · Cited by 3,030
De novo assembly of human genomes with massively parallel short read sequencing
Li, R., Zhu, H., Ruan, J., Qian, W., Fang, X., Shi, Z., Li, Y., Li, S., Shan, G., Kristiansen, K., et al. (2010) · Genome Research · doi:10.1101/gr.097261.109 · Cited by 2,926 · cited 1×
“RNA-Seq reads were assembled using SOAPdenovo v1 (111).”
MethodSelf-citation
GeneWise and genomewise
Birney, E., Clamp, M., & Durbin, R. (2004) · Genome Research · doi:10.1101/gr.1865504 · Cited by 2,542
Gene tree discordance, phylogenetic inference and the multispecies coalescent
Degnan, J. H., & Rosenberg, N. A. (2009) · Trends in Ecology & Evolution · doi:10.1016/j.tree.2009.01.009 · Cited by 1,978
A Bayesian Mixture Model for Across-Site Heterogeneities in the Amino-Acid Replacement Process
Lartillot, N., & Philippe, H. (2004) · Molecular Biology and Evolution · doi:10.1093/molbev/msh112 · Cited by 1,516
Self-citation
The origin and early evolution of plants on land
Kenrick, P., & Crane, P. R. (1997) · Nature · doi:10.1038/37918 · Cited by 1,466
An Ordinal Classification for the Families of Flowering Plants
(1998) · Annals of the Missouri Botanical Garden · doi:10.2307/2992015 · Cited by 1,465
Multiple Alignment of DNA Sequences with MAFFT
Katoh, K., Asimenos, G., & Toh, H. (2009) · Methods in molecular biology · doi:10.1007/978-1-59745-251-9_3 · Cited by 1,436
ASTRAL: genome-scale coalescent-based species tree estimation
Mirarab, S., Reaz, R., Bayzid, M. S., Zimmermann, T., Swenson, M. S., & Warnow, T. J. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btu462 · Cited by 1,323
Self-citation
PhyloBayes 3: a Bayesian software package for phylogenetic reconstruction and molecular dating
Lartillot, N., Lepage, T., & Blanquart, S. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp368 · Cited by 1,297
Angiosperm phylogeny inferred from 18S rDNA, rbcL, and atpB sequences
Soltis, P. S. (2000) · Botanical Journal of the Linnean Society · doi:10.1006/bojl.2000.0380 · Cited by 1,239
Self-citation
Analysis of 81 genes from 64 plastid genomes resolves relationships in angiosperms and identifies genome-scale evolutionary patterns
Jansen, R. K., Cai, Z., Raubeson, L. A., Daniell, H., dePamphilis, C. W., Leebens‐Mack, J., Müller, K., Guisinger, M. M., Haberle, R. C., Hansen, A. K., et al. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0709121104 · Cited by 1,226
Self-citation
PhyloBayes MPI: Phylogenetic reconstruction with infinite mixtures of profiles in a parallel environment
Lartillot, N., Rodrigue, N., Stubbs, D., & Richer, J. (2013) · Systematic Biology · doi:10.1093/sysbio/syt022 · Cited by 871 · cited 2×
“The extensively trimmed amino acid and nucleotide supermatrices were analyzed with the site-heterogeneous CAT+Gamma model using PhyloBayes MPI (118).”
Method
The earliest angiosperms: evidence from mitochondrial, plastid and nuclear genomes
Qiu, Y., Lee, J.-H., Bernasconi‐Quadroni, F., Soltis, P. S., Soltis, P. S., Zanis, M. J., Zimmer, E. A., Chen, Z., Savolainen, V., & Chase, M. W. (1999) · Nature · doi:10.1038/46536 · Cited by 842
Self-citation
Angiosperm phylogeny inferred from multiple genes as a tool for comparative biology
Soltis, P. S., Soltis, D. E., & Chase, M. W. (1999) · Nature · doi:10.1038/46528 · Cited by 790
Self-citation
Green algae and the origin of land plants.
Lewis, L., & McCourt, R. (2004) · American-Eurasian journal of botany · doi:10.3732/ajb.91.10.1535 · Cited by 751
Phylogenetic analysis of 83 plastid genes further resolves the early diversification of eudicots
Moore, M. J., Soltis, P. S., Bell, C. D., Burleigh, J. G., & Soltis, P. S. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0907801107 · Cited by 747
Self-citation
Angiosperm phylogeny: 17 genes, 640 taxa
Soltis, P. S., Smith, S. A., Cellinese, N., Wurdack, K. J., Tank, D. C., Brockington, S. F., Refulio, N., Walker, J. B., Moore, M. J., Carlsward, B. S., et al. (2011) · American Journal of Botany · doi:10.3732/ajb.1000404 · Cited by 706
Self-citation
Using plastid genome-scale data to resolve enigmatic relationships among basal angiosperms
Moore, M. J., Bell, C. D., Soltis, P. S., & Soltis, P. S. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0708072104 · Cited by 702
Self-citation
The deepest divergences in land plants inferred from phylogenomic evidence
Qiu, Y., Li, L., Wang, B., Chen, Z., Knoop, V., Groth‐Malonek, M., Dombrovska, O., Lee, J.-H., Kent, L., Rest, J. S., et al. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0603335103 · Cited by 652
The origin and early diversification of land plants: a cladistic study
(1998) · Choice Reviews Online · doi:10.5860/choice.35-3849 · Cited by 647
Horsetails and ferns are a monophyletic group and the closest living relatives to seed plants
Pryer, K. M., Schneider, H., Smith, A. Р., Cranfill, R., Wolf, P. G., Hunt, J. S., & Sipes, S. D. (2001) · Nature · doi:10.1038/35054555 · Cited by 641
Phylogeny and evolution of ferns (monilophytes) with a focus on the early leptosporangiate divergences
Pryer, K. M., Schuettpelz, E., Wolf, P. G., Schneider, H., Smith, A. Р., & Cranfill, R. (2004) · American Journal of Botany · doi:10.3732/ajb.91.10.1582 · Cited by 621
Fragments of the earliest land plants
Wellman, C. H., Osterloff, P. L., & Mohiuddin, U. (2003) · Nature · doi:10.1038/nature01884 · Cited by 612
Data access for the 1,000 Plants (1KP) project
Matasci, N., Hung, L., Yan, Z., Carpenter, E. J., Wickett, N. J., Mirarab, S., Nguyen, N., Warnow, T. J., Ayyampalayam, S., Barker, M. S., et al. (2014) · GigaScience · doi:10.1186/2047-217x-3-17 · Cited by 585
Self-citation
The Closest Living Relatives of Land Plants
Karol, K. G., McCourt, R. M., Cimino, M. T., & Delwiche, C. F. (2001) · Science · doi:10.1126/science.1065156 · Cited by 561
From algae to angiosperms–inferring the phylogeny of green plants (Viridiplantae) from 360 plastid genomes
Ruhfel, B. R., Gitzendanner, M. A., Soltis, P. S., Soltis, P. S., & Burleigh, J. G. (2014) · BMC Evolutionary Biology · doi:10.1186/1471-2148-14-23 · Cited by 560
Self-citation
Phylogeny of seed plants based on all three genomic compartments: Extant gymnosperms are monophyletic and Gnetales' closest relatives are conifers
Bowe, L. M., Coat, G., & dePamphilis, C. W. (2000) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.97.8.4092 · Cited by 476
Self-citation
The Root of Angiosperm Phylogeny Inferred from Duplicate Phytochrome Genes
Mathews, S., & Donoghue, M. J. (1999) · Science · doi:10.1126/science.286.5441.947 · Cited by 441
Self-citation
Early Middle Ordovician evidence for land plants in Argentina (eastern Gondwana)
Rubinstein, C. V., Gerrienne, P., de la Puente, G. S., Astini, R. A., & Steemans, P. (2010) · New Phytologist · doi:10.1111/j.1469-8137.2010.03433.x · Cited by 366
Impact of missing data on phylogenies inferred from empirical phylogenomic data sets
Roure, B., Baurain, D., & Philippe, H. (2013) · Molecular Biology and Evolution · doi:10.1093/molbev/mss208 · Cited by 365
Self-citation
First plants cooled the Ordovician
Lenton, T. M., Crouch, M., Johnson, M., Pires, N., & Dolan, L. (2012) · Nature Geoscience · doi:10.1038/ngeo1390 · Cited by 358
SATé-II: Very Fast and Accurate Simultaneous Estimation of Multiple Sequence Alignments and Phylogenetic Trees
Liu, K., Warnow, T. J., Holder, M. T., Nelesen, S. M., Yu, J., Stamatakis, A., & Linder, C. R. (2011) · Systematic Biology · doi:10.1093/sysbio/syr095 · Cited by 344
Self-citation
The gain of three mitochondrial introns identifies liverworts as the earliest land plants
Qiu, Y., Cho, Y., Cox, J. C., & Palmer, J. D. (1998) · Nature · doi:10.1038/29286 · Cited by 336
Origin of land plants: Do conjugating green algae hold the key?
Wodniok, S., Brinkmann, H., Glöckner, G., Heidel, A. J., Philippe, H., Melkonian, M., & Becker, B. (2011) · BMC Evolutionary Biology · doi:10.1186/1471-2148-11-104 · Cited by 333
Self-citation
Identification of shared single copy nuclear genes in Arabidopsis, Populus, Vitis and Oryzaand their phylogenetic utility across various taxonomic levels
Duarte, J. M., Wall, P. K., Edger, P. P., Landherr, L. L., Mā, H., Pires, P. K., Leebens‐Mack, J., & dePamphilis, C. W. (2010) · BMC Evolutionary Biology · doi:10.1186/1471-2148-10-61 · Cited by 321
Self-citation
Phylogenetic analyses of Vitis (Vitaceae) based on complete chloroplast genome sequences: effects of taxon sampling and phylogenetic methods on resolving relationships among rosids
Jansen, R. K., Kaittanis, C., Saski, C. A., Lee, S. B., Tomkins, J. P., Alverson, A. J., & Daniell, H. (2006) · BMC Evolutionary Biology · doi:10.1186/1471-2148-6-32 · Cited by 297
Molecular phylogeny of extant gymnosperms and seed plant evolution: analysis of nuclear 18S rRNA sequences
Chaw, S., Zharkikh, A., Sung, H.-M., Lau, T. C., & Li, W. (1997) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a025702 · Cited by 291
Origin and Radiation of the Earliest Vascular Land Plants
Steemans, P., Hérissé, A. L., Melvin, J., Miller, M. A., Paris, F., Verniers, J., & Wellman, C. H. (2009) · Science · doi:10.1126/science.1169659 · Cited by 273
Identifying the Basal Angiosperm Node in Chloroplast Genome Phylogenies: Sampling One's Way \nOut of the Felsenstein Zone
Leebens‐Mack, J., Raubeson, L. A., Cui, L., Kuehl, J. V., Fourcade, M. H., Chumley, T. W., Boore, J. L., Jansen, R. K., & dePamphilis, C. W. (2005) · eScholarship (California Digital Library) · Cited by 271
Self-citation
Broad Phylogenomic Sampling and the Sister Lineage of Land Plants
Timme, R., Bachvaroff, T. R., & Delwiche, C. F. (2012) · PLoS ONE · doi:10.1371/journal.pone.0029696 · Cited by 263
Mitochondrial DNA suggests at least 11 origins of parasitism in angiosperms and reveals genomic chimerism in parasitic plants
Barkman, T. J., McNeal, J. R., Lim, S.-H., Coat, G., Croom, H. B., Young, N. D., & dePamphilis, C. W. (2007) · BMC Evolutionary Biology · doi:10.1186/1471-2148-7-248 · Cited by 253
Self-citation
Major transitions in the evolution of early land plants: a bryological perspective
Ligrone, R., Duckett, J. G., & RENZAGLIA, K. S. (2012) · Annals of Botany · doi:10.1093/aob/mcs017 · Cited by 246
Multigene Phylogeny of Land Plants with Special Reference to Bryophytes and the Earliest Land Plants
Nickrent, D. L., Parkinson, C. L., Palmer, J. D., & Duff, R. J. (2000) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a026290 · Cited by 244
Vegetative and reproductive innovations of early land plants: implications for a unified phylogeny
RENZAGLIA, K. S., Duff, R. J., Nickrent, D. L., & Garbary, D. J. (2000) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2000.0615 · Cited by 243
Multigene analyses identify the three earliest lineages of extant flowering plants
Parkinson, C. L., Adams, K. L., & Palmer, J. D. (1999) · Current Biology · doi:10.1016/s0960-9822(00)80119-0 · Cited by 240
Phylogenetic Analysis of Green Plant rbcL Sequences
Manhart, J. R. (1994) · Molecular Phylogenetics and Evolution · doi:10.1006/mpev.1994.1014 · Cited by 228
Bryophyte diversity and evolution: Windows into the early evolution of land plants
Shaw, A. J., Szövényi, P., & Shaw, B. (2011) · American Journal of Botany · doi:10.3732/ajb.1000316 · Cited by 228
Self-citation
TRANSITION TO A LAND FLORA: PHYLOGENETIC RELATIONSHIPS OF THE GREEN ALGAE AND BRYOPHYTES
Mishler, B. D., & Churchill, S. P. (1985) · Cladistics · doi:10.1111/j.1096-0031.1985.tb00431.x · Cited by 228
Multigene Phylogeny of the Green Lineage Reveals the Origin and Diversification of Land Plants
Finet, C., Timme, R., Delwiche, C. F., & Marlétaz, F. (2010) · Current Biology · doi:10.1016/j.cub.2010.11.035 · Cited by 228
Evaluating Methods for Isolating Total RNA and Predicting the Success of Sequencing Phylogenetically Diverse Plant Transcriptomes
Johnson, M. T. J., Carpenter, E. J., Tian, Z., Bruskiewich, R., Burris, J. N., Carrigan, C. T., Chase, M. W., Clarke, N. D., Covshoff, S., dePamphilis, C. W., et al. (2012) · PLoS ONE · doi:10.1371/journal.pone.0050226 · Cited by 218
Self-citation
Angiosperm phylogeny inferred from sequences of four mitochondrial genes
Qiu, Y.-L., Li, L., Wang, B., Xue, J.-Y., Hendry, T., Li, R., Brown, J. W., Liu, Y., Hudson, G. T., & Chen, Z.-D. (2010) · Journal of Systematics and Evolution · doi:10.1111/j.1759-6831.2010.00097.x · Cited by 218
Phylogenetic signal in nucleotide data from seed plants: implications for resolving the seed plant tree of life
Burleigh, J. G., & Mathews, S. (2004) · American Journal of Botany · doi:10.3732/ajb.91.10.1599 · Cited by 211
Self-citation
Coalescent versus Concatenation Methods and the Placement of Amborella as Sister to Water Lilies
Xi, Z., Liu, L., Rest, J. S., & Davis, C. “. (2014) · Systematic Biology · doi:10.1093/sysbio/syu055 · Cited by 208
The Chloroplast Genome Sequence of Chara vulgaris Sheds New Light into the Closest Green Algal Relatives of Land Plants
Turmel, M., Otis, C., & Lemieux, C. (2006) · Molecular Biology and Evolution · doi:10.1093/molbev/msk018 · Cited by 206
Calculating Bootstrap Probabilities of Phylogeny Using Multilocus Sequence Data
Seo, T. (2008) · Molecular Biology and Evolution · doi:10.1093/molbev/msn043 · Cited by 204
Conflicting Phylogenies for Early Land Plants are Caused by Composition Biases among Synonymous Substitutions
Cox, C. J., Li, B., Foster, P. G., Embley, T. M., & Civáň, P. (2014) · Systematic Biology · doi:10.1093/sysbio/syt109 · Cited by 197
A Nonflowering Land Plant Phylogeny Inferred from Nucleotide Sequences of Seven Chloroplast, Mitochondrial, and Nuclear Genes
Qiu, Y., Li, L., Wang, B., Chen, Z., Dombrovska, O., Lee, J.-H., Kent, L., Li, R., Jobson, R. W., Hendry, T. A., et al. (2007) · International Journal of Plant Sciences · doi:10.1086/513474 · Cited by 190
Origins and diversity of eukaryotic CO2-concentrating mechanisms: lessons for the future
Meyer, M. T., & Griffiths, H. (2013) · Journal of Experimental Botany · doi:10.1093/jxb/ers390 · Cited by 175
Phylogeny of early land plants: insights from genes and genomes
Qiu, Y., & Palmer, J. D. (1999) · Trends in Plant Science · doi:10.1016/s1360-1385(98)01361-2 · Cited by 168
SUMMARY OF GREEN PLANT PHYLOGENY AND CLASSIFICATION
Bremer, K. (1985) · Cladistics · doi:10.1111/j.1096-0031.1985.tb00434.x · Cited by 158
Mitochondrial Phylogenomics of Early Land Plants: Mitigating the Effects of Saturation, Compositional Heterogeneity, and Codon-Usage Bias
Liu, Y., Cox, C. J., Wang, W., & Goffinet, B. (2014) · Systematic Biology · doi:10.1093/sysbio/syu049 · Cited by 151
Plant cytokinesis: fission by fusion
Jürgens, G. (2005) · Trends in Cell Biology · doi:10.1016/j.tcb.2005.03.005 · Cited by 149
A Functional Phylogenomic View of the Seed Plants
Lee, E. K., Cibrián‐Jaramillo, A., Kolokotronis, S., Katari, M. S., Stamatakis, A., Ott, M., Chiu, J. C., Little, D. P., Stevenson, D. W., McCombie, W. R., et al. (2011) · PLoS Genetics · doi:10.1371/journal.pgen.1002411 · Cited by 146
Self-citation
Long branch attraction, taxon sampling, and the earliest angiosperms: Amborella or monocots?
Stefanović, S., Rice, D. W., & Palmer, J. D. (2004) · BMC Evolutionary Biology · doi:10.1186/1471-2148-4-35 · Cited by 145
The gain of two chloroplast tRNA introns marks the green algal ancestors of land plants
Manhart, J. R., & Palmer, J. D. (1990) · Nature · doi:10.1038/345268a0 · Cited by 143
Identifying the rooted species tree from the distribution of unrooted gene trees under the coalescent
Allman, E. S., Degnan, J. H., & Rhodes, J. A. (2010) · Journal of Mathematical Biology · doi:10.1007/s00285-010-0355-7 · Cited by 139
Chloroplast Phylogeny Indicates that Bryophytes Are Monophyletic
Nishiyama, T., Wolf, P. G., Kugita, M., Sinclair, R. B., Sugita, M., Sugiura, C., Wakasugi, T., Yamada, K., Yoshinaga, K., Yamaguchi, K., et al. (2004) · Molecular Biology and Evolution · doi:10.1093/molbev/msh203 · Cited by 138
A clade uniting the green algae Mesostigma viride and Chlorokybus atmophyticus represents the deepest branch of the Streptophyta in chloroplast genome-based phylogenies
Lemieux, C., Otis, C., & Turmel, M. (2007) · BMC Biology · doi:10.1186/1741-7007-5-2 · Cited by 136
Genome-Scale Phylogenetics: Inferring the Plant Tree of Life from 18,896 Gene Trees
Burleigh, J. G., Bansal, M. S., Eulenstein, O., Hartmann, S. A., Wehe, A., & Vision, T. (2010) · Systematic Biology · doi:10.1093/sysbio/syq072 · Cited by 134
Self-citation
Phylogenetic relationships among seed plants: Persistent questions and the limits of molecular data
Mathews, S. (2008) · American Journal of Botany · doi:10.3732/ajb.0800178 · Cited by 134
Self-citation
Origin of land plants revisited in the light of sequence contamination and missing data
Laurin-Lemay, S., Brinkmann, H., & Philippe, H. (2012) · Current Biology · doi:10.1016/j.cub.2012.06.013 · Cited by 132
Self-citation
Complete plastome sequences of Equisetum arvense and Isoetes flaccida: implications for phylogeny and plastid genome evolution of early land plant lineages
Karol, K., Arumuganathan, K., Boore, J., Duffy, A., de Everett, K., Hall, J. D., Hansen, S., Kuehl, J., Mandoli, D., Mishler, B., et al. (2010) · BMC Evolutionary Biology · doi:10.1186/1471-2148-10-321 · Cited by 130
The phylogeny of land plants: A cladistic analysis based on male gametogenesis
Garbary, D. J., RENZAGLIA, K. S., & Duckett, J. G. (1994) · Plant Systematics and Evolution · doi:10.1007/bf00937730 · Cited by 129
The first complete chloroplast genome sequence of a lycophyte, Huperzia lucidula (Lycopodiaceae).
Wolf, P., Karol, K., Mandoli, D., Kuehl, J., Arumuganathan, K., Ellis, M., Mishler, B., Kelch, D., Olmstead, R., & Boore, J. (2005) · Gene · doi:10.1016/j.gene.2005.01.018 · Cited by 120
The Gametophyte Generation of Some Early Devonian Land Plants
Remy, W., Gensel, P. G., & Hass, H. (1993) · International Journal of Plant Sciences · doi:10.1086/297089 · Cited by 118
Origin of land plants using the multispecies coalescent model
Zhong, B., Liu, L., Yan, Z., & Penny, D. (2013) · Trends in Plant Science · doi:10.1016/j.tplants.2013.04.009 · Cited by 118
Self-citation
Systematic Error in Seed Plant Phylogenomics
Zhong, B., Deusch, O., Goremykin, V. V., Penny, D., Biggs, P. J., Atherton, R. A., Nikiforova, S. V., & Lockhart, P. J. (2011) · Genome Biology and Evolution · doi:10.1093/gbe/evr105 · Cited by 118
Ancestors of Trans-Splicing Mitochondrial Introns Support Serial Sister Group Relationships of Hornworts and Mosses with Vascular Plants
Groth‐Malonek, M. (2004) · Molecular Biology and Evolution · doi:10.1093/molbev/msh259 · Cited by 116
Inferring the higher‐order phylogeny of mosses (Bryophyta) and relatives using a large, multigene plastid data set
Chang, Y., & Graham, S. W. (2011) · American Journal of Botany · doi:10.3732/ajb.0900384 · Cited by 112
Self-citation
Complete plastid genomes from Ophioglossum californicum, Psilotum nudum, and Equisetum hyemale reveal an ancestral land plant genome structure and resolve the position of Equisetales among monilophytes
Grewe, F., Guo, W., Gubbels, E. A., Hansen, A. K., & Mower, J. P. (2013) · BMC Evolutionary Biology · doi:10.1186/1471-2148-13-8 · Cited by 107
Plastid genome sequencing, comparative genomics, and phylogenomics: Current status and prospects
Gao, L., Su, Y., & Wang, T. (2010) · Journal of Systematics and Evolution · doi:10.1111/j.1759-6831.2010.00071.x · Cited by 106
Inferring phylogenies with incomplete data sets: a 5-gene, 567-taxon analysis of angiosperms
Burleigh, J. G., Hilu, K. W., & Soltis, P. S. (2009) · BMC Evolutionary Biology · doi:10.1186/1471-2148-9-61 · Cited by 102
Self-citation
CELL DIVISION IN SPIROGYRA. II. CYTOKINESIS
Fowke, L. C., & Pickett‐Heaps, J. D. (1969) · Journal of Phycology · doi:10.1111/j.1529-8817.1969.tb02614.x · Cited by 97
EvoPipes.net: Bioinformatic Tools for Ecological and Evolutionary Genomics
Barker, M. S., Dlugosch, K. M., Dinh, L., Challa, R. S., Kane, N. C., King, M. G., & Rieseberg, L. H. (2010) · Evolutionary Bioinformatics · doi:10.4137/ebo.s5861 · Cited by 88
Self-citation
Anomalous Unrooted Gene Trees
Degnan, J. H. (2013) · Systematic Biology · doi:10.1093/sysbio/syt023 · Cited by 84
The Green Algal Ancestry of Land Plants as Revealed by the Chloroplast Genome
Turmel, M., Pombert, J.-F., Charlebois, P., Otis, C., & Lemieux, C. (2007) · INTERNATIONAL JOURNAL PLANT SCIENCES · doi:10.1086/513470 · Cited by 84
Difficult phylogenetic questions: more data, maybe; better methods, certainly
Philippe, H., & Roure, B. (2011) · BMC Biology · doi:10.1186/1741-7007-9-91 · Cited by 81
Self-citation
The position of gnetales among seed plants: overcoming pitfalls of chloroplast phylogenomics.
Zhong, B.-J., Yonezawa, T., Zhong, Y., & Hasegawa, M. (2010) · Molecular biology and evolution · doi:10.1093/molbev/msq170 · Cited by 79
The evolutionary root of flowering plants.
Goremykin, V., Nikiforova, S., Biggs, P., Zhong, B.-J., Delange, P., Martin, W., Woetzel, S., Atherton, R., Mclenachan, P., & Lockhart, P. (2013) · Systematic Biology · doi:10.1093/sysbio/sys070 · Cited by 76
SuperFine: Fast and Accurate Supertree Estimation
Swenson, M. S., Suri, R., Linder, C. R., & Warnow, T. J. (2011) · Systematic Biology · doi:10.1093/sysbio/syr092 · Cited by 76
Self-citation
Utility of a large, multigene plastid data set in inferring higher‐order relationships in ferns and relatives (monilophytes)
Rai, H. S., & Graham, S. W. (2010) · American Journal of Botany · doi:10.3732/ajb.0900305 · Cited by 74
Self-citation
Analyses of Charophyte Chloroplast Genomes Help Characterize the Ancestral Chloroplast Genome of Land Plants
Civáň, P., Foster, P., Embley, M., Séneca, A., & Cox, C. (2014) · Genome Biology and Evolution · doi:10.1093/gbe/evu061 · Cited by 72
More letters of Charles Darwin : a record of his work in a series of hitherto unpublished letters
Darwin, C. R., Darwin, F., & Charles, S. S. A. (1903) · J. Murray eBooks · doi:10.5962/bhl.title.21196 · Cited by 72
Different gymnosperm outgroups have (mostly) congruent signal regarding the root of flowering plant phylogeny
Graham, S. W., & Iles, W. J. D. (2008) · American Journal of Botany · doi:10.3732/ajb.0800320 · Cited by 69
Self-citation
The Impact of Outgroup Choice and Missing Data on Major Seed Plant Phylogenetics Using Genome-Wide EST Data
de la Torre-Bárcena, J. E., Kolokotronis, S., Lee, E. K., Stevenson, D. W., Brenner, E. D., Katari, M. S., Coruzzi, G. M., & DeSalle, R. (2009) · PLoS ONE · doi:10.1371/journal.pone.0005764 · Cited by 65
Self-citation
The anthocerote chloroplast: a review
Vaughn, K. C., Ligrone, R., Owen, H. A., HASEGAWA, J., Campbell, E. O., RENZAGLIA, K. S., & Mónge-Nájera, J. (1992) · New Phytologist · doi:10.1111/j.1469-8137.1992.tb05653.x · Cited by 62
Phragmoplast of the green alga Spirogyra is functionally distinct from the higher plant phragmoplast.
Sawitzky, H., & Grolig, F. (1995) · The Journal of Cell Biology · doi:10.1083/jcb.130.6.1359 · Cited by 54
Evidence for the most basal split in land plants dividing bryophyte and tracheophyte lineages
Goremykin, V. V., & Hellwig, F. H. (2005) · Plant Systematics and Evolution · doi:10.1007/s00606-005-0337-1 · Cited by 52
Ribosomal RNA sequence comparisons demonstrate an evolutionary relationship betweenZygnematales and charophytes
Surek, B., Beemelmanns, U., Melkonian, M., & Bhattacharya, D. (1994) · Plant Systematics and Evolution · doi:10.1007/bf00984663 · Cited by 49
Self-citation
Higher plant origins and the phylogeny of green algae
Devereux, R., Loeblich, A. R., & Fox, G. E. (1990) · Journal of Molecular Evolution · doi:10.1007/bf02101788 · Cited by 45
Novel Parallelization Schemes for Large-Scale Likelihood-based Phylogenetic Inference
Stamatakis, A., & Aberer, A. J. (2013) · IEEE International Parallel and Distributed Processing Symposium (IPDPS) · doi:10.1109/ipdps.2013.70 · Cited by 42
Spindle function in the green alga Mougeotia: Absence of anaphase A correlates with postmitotic nuclear migration
Pickett‐Heaps, J. D., & Wetherbee, R. (1987) · Cell Motility and the Cytoskeleton · doi:10.1002/cm.970070109 · Cited by 32
Unusual position of the genus Spirotaenia (Zygnematophyceae) among streptophytes revealed by SSU rDNA and rbcL sequence comparisons
Gontcharov, A. A., & Melkonian, M. (2004) · Phycologia · doi:10.2216/i0031-8884-43-1-105.1 · Cited by 32
Self-citation
Ultrastructure of mitosis and cytokinesis inZygnema sp. (Zygnematales, Chlorophyta)
Bakker, M. E., & Lokhorst, G. M. (1987) · PROTOPLASMA · doi:10.1007/bf01281019 · Cited by 31
Towards an understanding of the differences between the blepharoplasts of mosses and liverworts, and comparisons with hornworts, biflagellate lycopods and charophytes: a numerical analysis
RENZAGLIA, K. S., & Duckett, J. G. (1991) · New Phytologist · doi:10.1111/j.1469-8137.1991.tb04900.x · Cited by 30
Using Phylogenomic Patterns and Gene Ontology to Identify Proteins of Importance in Plant Evolution
Cibrián‐Jaramillo, A., de la Torre-Bárcena, J. E., Lee, E. K., Katari, M. S., Little, D. P., Stevenson, D. W., Martienssen, R. A., Coruzzi, G. M., & DeSalle, R. (2010) · Genome Biology and Evolution · doi:10.1093/gbe/evq012 · Cited by 30
Self-citation
IMMUNOFLUORESCENT LOCALIZATION OF MICROTUBULES THROUGHOUT THE CELL CYCLE IN THE GREEN ALGA MOUGEOTIA (ZYGNEMATACEAE)
Galway, M. E., & Hardham, A. R. (1991) · American Journal of Botany · doi:10.1002/j.1537-2197.1991.tb15211.x · Cited by 29
Phragmoplast-mediated cytokinesis in Trentepohlia: results of TEM and immunofluorescence cytochemistry.
Chapman, R. L., Borkhsenious, O. N., Brown, R. C., Henk, M. C., & Waters, D. A. (2001) · INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY · doi:10.1099/00207713-51-3-759 · Cited by 25
More letters of Charles Darwin. A record of his work in a series of hitherto unpublished letters
Darwin, C. R., Darwin, F., & Charles, S. S. A. (1903) · J. Murray eBooks · doi:10.5962/bhl.title.1477 · Cited by 24
Cryptogamic Botany. Vol. II. Bryophytes and Pteridophytes
(1955) · AIBS Bulletin · doi:10.1093/aibsbulletin/5.2.15-a · Cited by 20

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).

Sorted by citations

An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG IV
The Angiosperm Phylogeny Group (2016) · Botanical Journal of the Linnean Society · doi:10.1111/boj.12385 · Cited by 9,583
“Zeng et al. (2014) and Wickett et al. (2014) both analysed low-copy nuclear genes (59 and 852 genes, respectively), but relatively few angiosperms (60 and 37, respectively, the latter focused on all green plants), and reached similar conclusions about relationships to those found in the majority of…”
ASTRAL-III: polynomial time species tree reconstruction from partially resolved gene trees
Zhang, C., Rabiee, M., Sayyari, E., & Mirarab, S. (2018) · BMC Bioinformatics · doi:10.1186/s12859-018-2129-y · Cited by 2,471
Self-citation
One thousand plant transcriptomes and the phylogenomics of green plants
Initiative, O. T. P. T. (2019) · Nature · doi:10.1038/s41586-019-1693-2 · Cited by 1,734
A community‐derived classification for extant lycophytes and ferns
I, P. (2016) · Journal of Systematics and Evolution · doi:10.1111/jse.12229 · Cited by 1,673
“Monophyletic (Pryer et al., 2001, 2004; Qiu et al., 2007; Schneider et al., 2009; Ruhfel et al., 2014; Wickett et al., 2014; Rothfels et al., 2015).”
BackgroundInfluential
Insights into Land Plant Evolution Garnered from the Marchantia polymorpha Genome
Bowman, J. L., Kohchi, T., Yamato, K. T., Jenkins, J. W., Shu, S., Ishizaki, K., Yamaoka, S., Nishihama, R., Nakamura, Y., Berger, F., et al. (2017) · Cell · doi:10.1016/j.cell.2017.09.030 · Cited by 1,201
“Bryophyte phylogenetic relationships remain enigmatic, 288 Cell 171, 287–304, October 5, 2017 with nearly every possible topology proposed (Nishiyama et al., 2004; Qiu et al., 2006; Wickett et al., 2014).”
Background

See all 1,252

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
DOI: 10.1073/pnas.1323926111
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

Phylotranscriptomic analysis of the origin and early diversification of land plants

Abstract

Overview

Integrity signals

Verification

Claims the paper makes

Claims other papers make about this one

Self-check

Citations

Cites

Cited by

Related

Metadata

Record

About these checks