Extended Data Fig. 9: Phylogenetic relationships of seed plants based on parsimony, maximum likelihood and Bayesian analyses of a dataset for living and fossil seed plants.

See Supplementary Data 1 for the dataset. All trees are rooted with Elkinsia. As with all previous analyses of seed plant relationships^5,9,10,30 support for most nodes is not strong. a, Strict consensus of 10 most parsimonious trees (221 steps. Consistency index (CI) = 0.5385; retention index (RI) = 0.7198) from an unconstrained parsimony analysis. Numbers at nodes above the lines are bootstrap values greater than 50%. b–d, Phylogenetic analyses with relationships among extant taxa constrained to be compatible to a molecular-backbone tree in which extant Gnetales and Pinaceae are sister taxa (GNE-PINE tree) (Supplementary Information). b, Strict consensus of the 45 most-parsimonious trees (236 steps, CI = 0.5042, RI = 0.6786) from a constrained parsimony analysis. Numbers at nodes above the lines are bootstrap values greater than 50%. c, Maximum likelihood tree inferred from a constrained analysis. Numbers at nodes above the lines are bootstrap values. d, The 50% majority-rule consensus from a constrained Bayesian analysis (Supplementary Data 2) with posterior probabilities indicated by numbers at the nodes. BEG is the abbreviation for the Bennettitales–Erdtmanithecales–Gnetales group³⁰. See Supplementary Information for details of characters, taxa, additional information, analyses and discussion.