Otto, S. P. & Whitton, J. Polyploid incidence and evolution. Annu. Rev. Genet. 34, 401–437 (2000).
Wood, T. E. et al. The frequency of polyploid speciation in vascular plants. Proc. Natl Acad. Sci. USA 106, 13875–13879 (2009).
Stebbins, G. L. Variation and Evolution in Plants (Columbia Univ. Press, 1950).
Levin, D. A. Polyploidy and novelty in flowering plants. Am. Nat. 122, 1–25 (1983).
Tank, D. C. et al. Nested radiations and the pulse of angiosperm diversification: increased diversification rates often follow whole genome duplications. New Phytol. 207, 454–467 (2015).
Landis, J. B. et al. Impact of whole-genome duplication events on diversification rates in angiosperms. Am. J. Bot. 105, 348–363 (2018).
Smith, S. A. et al. Disparity, diversity and duplications in the Caryophyllales. New Phytol. 217, 836–854 (2017).
Walden, N. et al. Nested whole-genome duplications coincide with diversification and high morphological disparity in Brassicaceae. Nat. Commun. 11, 3795 (2020).
Soltis, P. S. & Soltis, D. E. Ancient WGD events as drivers of key innovations in angiosperms. Curr. Opin. Genet. Dev. 30, 159–165 (2016).
Guo, J. et al. Phylotranscriptomics in Cucurbitaceae reveal multiple whole-genome duplications and key morphological and molecular innovations. Mol. Plant 13, 1117–1133 (2020).
Sheehan, H. et al. Evolution of L-DOPA 4,5-dioxygenase activity allows for recurrent specialization to betalain pigmentation in Caryophyllales. New Phytol. 227, 914–929 (2020).
Stroud, J. T. & Losos, J. B. Ecological opportunity and adaptive radiation. Annu. Rev. Ecol. Evol. Syst. 47, 507–532 (2016).
Parins-Fukuchi, C., Stull, G. W. & Smith, S. A. Phylogenomic conflict coincides with rapid morphological innovation. Proc. Natl Acad. Sci. USA 118, e2023058118 (2021).
Cantino, P. D. et al. Towards a phylogenetic nomenclature of Tracheophyta. Taxon 56, E1–E44 (2007).
Doyle, J. A. Phylogenetic analyses and morphological innovations in land plants. Annu. Plant Rev. 45, 1–50 (2013).
DiMichele, W. A., Pfefferkorn, H. W. & Gastaldo, R. A. Response of Late Carboniferous and early Permian plant communities to climate change. Annu. Rev. Earth Planet. Sci. 29, 461–487 (2001).
Behrensmeyer, A. K. et al. Terrestrial Ecosystems Through Time: Evolutionary Paleoecology of Terrestrial Plants and Animals (Univ. Chicago Press, 1992).
Crane, P. R. Phylogenetic analysis of seed plants and the origin of angiosperms. Ann. Mo. Bot. Gard. 72, 716–793 (1985).
Taylor, E. L., Taylor, T. N. & Krings, M. Paleobotany: The Biology and Evolution of Fossil Plants (Academic Press, 2009).
Nagalingum, N. S. et al. Recent synchronous radiation of a living fossil. Science 334, 796–799 (2011).
Leslie, A. B. et al. Hemisphere-scale differences in conifer evolutionary dynamics. Proc. Natl Acad. Sci. USA 109, 16217–16221 (2012).
Li, Z. et al. Early genome duplications in conifers and other seed plants. Sci. Adv. 1, e1501084 (2015).
Guan, R. et al. Draft genome of the living fossil Ginkgo biloba. GigaScience 5, 49 (2016).
Farhat, P. et al. Polyploidy in the conifer genus Juniperus: an unexpectedly high rate. Front. Plant Sci. 10, 676 (2019).
Ickert-Bond, S. M. et al. Polyploidy in gymnosperms—insights into the genomic and evolutionary consequences of polyploidy in Ephedra. Mol. Phylogenet. Evol. 147, 106786 (2020).
Khoshoo, T. N. Polyploidy in gymnosperms. Evolution 13, 24–39 (1959).
Lewis, W. H. Polyploidy—Biological Relevance (Plenum Press, 1980).
Yang, Y. et al. Improved transcriptome sampling pinpoints 26 ancient and more recent polyploidy events in Caryophyllales, including two allopolyploidy events. New Phytol. 217, 855–870 (2018).
Jiao, Y. et al. Ancestral polyploidy in seed plants and angiosperms. Nature 473, 97–100 (2011).
Roodt, D. et al. Evidence for an ancient whole-genome duplication in the cycad lineage. PLoS ONE 12, e0184454 (2017).
Ruprecht, C. et al. Revisiting ancestral polyploidy in plants. Sci. Adv. 3, e1603195 (2017).
Leebens-Mack, J. H. et al. One thousand plant transcriptomes and the phylogenomics of green plants. Nature 574, 679–685 (2019).
Scott, A. D., Stenz, N. W. M., Ingvarsson, P. K. & Baum, D. A. Whole-genome duplication in coast redwood (Sequoia sempervirens) and its implications for explaining the rarity of polyploidy in conifers. New Phytol. 211, 186–193 (2016).
Rabosky, D. L. Automatic detection of key innovations, rate shifts and diversity‐dependence on phylogenetic trees. PLoS ONE 9, e89543 (2014).
Ohno, S. Evolution by Gene Duplication (Springer Verlag, 1970).
Rensing, S. A. Gene duplication as a driver of plant morphogenetic evolution. Curr. Opin. Plant Biol. 14, 43–48 (2014).
Marques, D. A., Meier, J. I. & Seehausen, O. A combinatorial view on speciation and adaptive radiation. Trends Ecol. Evol. 34, 531–544 (2019).
de la Torre, A. R., Li, Z., van de Peer, Y. & Ingvarsson, P. K. Contrasting rates of molecular evolution and patterns of selection among gymnosperms and flowering plants. Mol. Biol. Evol. 34, 1363–1377 (2017).
Ran, J.-H., Shen, T.-T., Wang, M.-M. & Wang, X.-Q. Phylogenomics resolves the deep phylogeny of seed plants and indicates partial convergent or homoplastic evolution between Gnetales and angiosperms. Proc. R. Soc. B 285, 20181012 (2018).
Oliver, J. C. Microevolutionary processes generate phylogenomic discordance at ancient divergences. Evolution 67, 1823–1839 (2013).
Farjon, A. A Natural History of Conifers (Timber Press, 2008).
Pellicer, J., Hidalgo, O., Dodsworth, S. & Leitch, I. J. Genome size diversity and its impact on land plants. Genes 9, 88 (2018).
Otto, S. P. The evolutionary consequences of polyploidy. Cell 131, 452–462 (2007).
Louca, S. & Pennell, M. W. Extant timetrees are consistent with a myriad of diversification histories. Nature 580, 502–505 (2020).
Bond, W. J. The tortoise and the hare: ecology of angiosperm dominance and gymnosperm persistence. Biol. J. Linn. Soc. 36, 227–249 (1989).
Lupia, R., Ligard, S. & Crane, P. R. Comparing palynological abundance and diversity: implications for biotic replacement during the Cretaceous angiosperm radiation. Paleobiology 25, 305–340 (1999).
Zachos, J., Pagani, M., Sloan, L., Thomas, E. & Billups, K. Trends, rhythms and aberrations in global climate 65 Ma to present. Science 292, 686–693 (2001).
Wing, S. L. & Boucher, L. D. Ecological aspects of the Cretaceous flowering plant radiation. Annu Rev. Earth Planet. Sci. 26, 379–421 (1998).
Tiffney, B. H. Seed size, dispersal syndromes and the rise of the angiosperms: evidence and hypothesis. Ann. Mo. Bot. Gard. 71, 551–576 (1984).
Rice, A. et al. The chromosome counts database (CCDB)—a community resource of plant chromosome numbers. New Phytol. 206, 19–26 (2015).
Pellicer, J. & Leitch, I. J. The plant DNA C-values database (release 7.1): an updated online repository of plant genome size data for comparative studies. New Phytol. 226, 301–305 (2020).
Biffin, E. et al. Leaf evolution in Southern Hemisphere conifers tracks the angiosperm ecological radiation. Proc. R. Soc. B 279, 341–348 (2012).
Brodribb, T. J., McAdam, S. A., Jordan, G. J. & Martins, S. C. Conifer species adapt to low-rainfall climates by following one of two divergent pathways. Proc. Natl Acad. Sci. USA 111, 14489–14493 (2014).
English, J. M. & Johnson, S. T. The Laramide orogeny: what were the driving forces? Int. Geol. Rev. 46, 833–838 (2004).
Condamine, F. L., Silvestro, D., Koppelhus, E. B. & Antonelli, A. The rise of angiosperms pushed conifers to decline during global cooling. Proc. Natl Acad. Sci. USA 117, 28867–28875 (2020).
Fragnière, Y., Bétrisey, S., Cardinaux, L., Stoffel, M. & Kozlowski, G. Fighting their last stand? A global analysis of the distribution and conservation status of gymnosperms. J. Biogeogr. 42, 809–820 (2015).
Forest, F. et al. Gymnosperms on the EDGE. Sci. Rep. 8, 6053 (2018).
Rundel, P. W. A Neogene heritage: conifer distributions and endemism in Mediterranean-climate ecosystems. Front. Ecol. Evol. 7, 364 (2019).
Jin, W.-T. et al. Phylogenomic and ecological analyses reveal the spatiotemporal evolution of global pines. Proc. Natl Acad. Sci. USA 118, e2022302118 (2021).
Zwaenepoel, A. & van de Peer, Y. Inference of ancient whole-genome duplications and the evolution of gene duplication and loss rates. Mol. Biol. Evol. 36, 1384–1404 (2019).
Goodstein, D. M. et al. Phytozome: a comparative platform for green plant genomics. Nucleic Acids Res. 40, 1178–1186 (2012).
Mendes, F. K. & Hahn, M. W. Gene tree discordance causes apparent substitution rate variation. Syst. Biol. 65, 711–721 (2016).
Walker, J. F., Walker-Hale, N., Vargas, O. M., Larson, D. A. & Stull, G. W. Characterizing gene tree conflict in plastome-inferred phylogenies. PeerJ 7, e7747 (2019).
Zhong, B., Yonezawa, T., Zhong, Y. & Hasegawa, M. The position of Gnetales among seed plants: overcoming pitfalls of chloroplast phylogenomics. Mol. Biol. Evol. 27, 2855–2863 (2010).
Grabherr, M. G. et al. Full-length transcriptome assembly from RNA-seq data without a reference genome. Nat. Biotechnol. 29, 644–652 (2011).
Li, R. et al. De novo assembly of human genomes with massively parallel short read sequencing. Genome Res. 20, 265–272 (2010).
Haas, B. J. et al. De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis. Nat. Protoc. 8, 1494–1512 (2013).
Fu, L., Niu, B., Zhu, Z., Wu, S. & Li, W. CD-HIT: accelerated for clustering the next-generation sequencing data. Bioinformatics 28, 3150–3152 (2012).
Doyle, J. J. & Doyle, J. L. A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem. Bull. 19, 11–15 (1987).
Jin, J.-J. et al. GetOrganelle: a fast and versatile toolkit for accurate de novo assembly of organelle genomes. Genome Biol. 21, 241 (2020).
Bankevich, A. et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J. Comput. Biol. 19, 455–477 (2012).
Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357–359 (2012).
Qu, X. J., Moore, M. J., Li, D. Z. & Yi, T. S. PGA: a software package for rapid, accurate and flexible batch annotation of plastomes. Plant Methods 15, 50 (2019).
Walker, J. F. et al. From cacti to carnivores: improved phylotranscriptomic sampling and hierarchical homology inference provide further insights into the evolution of Caryophyllales. Am. J. Bot. 105, 446–462 (2018).
Altschul, S. F. et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25, 3389–3402 (1997).
Yang, Y. & Smith, S. A. Orthology inference in non-model organisms using transcriptomes and low-coverage genomes: improving accuracy and matrix occupancy for phylogenomics. Mol. Biol. Evol. 31, 3081–3092 (2014).
Brown, J. W., Walker, J. F. & Smith, S. A. Phyx: phylogenetic tools for unix. Bioinformatics 33, 1886–1888 (2017).
Stamatakis, A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30, 1312–1313 (2014).
Zhang, C. et al. ASTRAL-III: polynomial time species tree reconstruction from partially resolved gene trees. BMC Bioinformatics 19, 153 (2018).
Junier, T. & Zdobnov, E. M. The Newick utilities: high-throughput phylogenetic tree processing in the UNIX shell. Bioinformatics 26, 1669–1670 (2010).
Nguyen, L.-T., Schmidt, H. A., von Haeseler, A. & Minh, B. Q. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum likelihood phylogenies. Mol. Biol. Evol. 32, 268–274 (2015).
Chernomor, O., von Haeseler, A. & Minh, B. Q. Terrace aware data structure for phylogenomic inference from supermatrices. Syst. Biol. 65, 997–1008 (2016).
Smith, S. A., Moore, M. J., Brown, J. W. & Yang, Y. Analysis of phylogenomic datasets reveals conflict, concordance and gene duplications with examples from animals and plants. BMC Evol. Biol. 15, 150 (2015).
Walker, J. F. et al. Widespread paleopolyploidy, gene tree conflict and recalcitrant relationships among the carnivorous Caryophyllales. Am. J. Bot. 104, 858–867 (2017).
Smith, S. A. & Walker, J. F. PyPHLAWD: a python tool for phylogenetic dataset construction. Methods Ecol. Evol. 10, 104–108 (2019).
Katoh, K. & Standley, D. M. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol. Biol. Evol. 30, 772–780 (2013).
Lanfear, R., Frandsen, P. B., Wright, A. M., Senfeld, T. & Calcott, B. PartitionFinder 2: new methods for selecting partitioned models of evolution for molecular and morphological phylogenetic analyses. Mol. Biol. Evol. 34, 772–773 (2017).
Kozlov, A. M., Darriba, D., Flouri, T., Morel, B. & Stamatakis, A. RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference. Bioinformatics 35, 4453–4455 (2019).
Smith, S. A. & O’Meara, B. C. treePL: divergence time estimation using penalized likelihood for large phylogenies. Bioinformatics 28, 2689–2690 (2012).
Glick, L. & Mayrose, I. ChromEvol: assessing the pattern of chromosome number evolution and the inference of polyploidy along a phylogeny. Mol. Biol. Evol. 31, 1914–1922 (2014).
R Core Team R: A Language and Environment for Statistical Computing (R Foundation for Statistical Computing, 2020); https://www.R-project.org
Revell, L. J. Phytools: an R package for phylogenetic comparative biology (and other things). Methods Ecol. Evol. 3, 217–223 (2012).
Rabosky, D. L. et al. Rates of speciation and morphological evolution are correlated across the largest vertebrate radiation. Nat. Commun. 4, 1958 (2013).
Rabosky, D. L. et al. BAMM tools: an R package for the analysis of evolutionary dynamics on phylogenetic trees. Methods Ecol. Evol. 5, 701–707 (2014).
Zizka, A. et al. CoordinateCleaner: standardized cleaning of occurrence records from biological collection databases. Methods Ecol. Evol. 10, 744–751 (2019).
Hart, J. A. A cladistics analysis of conifers: preliminary results. J. Arnold Arbor. 68, 269–307 (1987).
Hilton, J. & Bateman, R. M. Pteridosperms are the backbone of seed-plant phylogeny. J. Torrey Bot. Soc. 133, 119–168 (2006).
Mao, K. et al. Distribution of living Cupressaceae reflects the breakup of Pangea. Proc. Natl Acad. Sci. USA 109, 7793–7798 (2012).
Escapa, I. H. & Catalano, S. A. Phylogenetic analysis of Araucariaceae: integrating molecules, morphology and fossils. Int. J. Plant Sci. 174, 1153–1170 (2013).
Coiro, M. & Pott, C. Eobowenia gen. nov. from the Early Cretaceous of Patagonia: indication for an early divergence of Bowenia? BMC Evol. Biol. 17, 97 (2017).
Herrera, F. et al. Cupressaceae conifers from the Early Cretaceous of Mongolia. Int. J. Plant Sci. 178, 19–41 (2017).
Herrera, F. et al. Reconstructing Krassilovia mongolica supports recognition of a new and unusual group of Mesozoic conifers. PLoS ONE 15, e0226779 (2020).
Gernandt, D. S. et al. Incorporating fossils into the Pinaceae tree of life. Am. J. Bot. 105, 1329–1344 (2018).
Andruchow-Colombo, A., Wilf, P. & Escapa, I. H. A South American fossil relative of Phyllocladus: Huncocladus laubenfelsii gen. et sp. nov. (Podocarpaceae) from the early Eocene of Laguna del Hunco, Patagonia, Argentina. Aust. Syst. Bot. 32, 290–309 (2019).
Nixon, K. C., Crepet, W. L., Stevenson, D. & Friis, E. M. A reevaluation of seed-plant phylogeny. Ann. Mo. Bot. Gard. 81, 484–533 (1994).