Fig. 1: Tree reconstruction of Asparagales.
a The species tree of Asparagales with each genus represented by one species. The species tree was inferred using ASTRAL with 857 nuclear genes from 501 samples (Supplementary Fig. 1). Subsequently, one species was selected for each genus from the ASTRAL tree. Pie charts represent gene trees for concordant bipartitions (blue), the most frequent alternative topology (green), remaining alternatives (red), and those uninformative for nodes (BS ≤ 50%) inferred from PhyParts. The numbers next to the branches represent the Quartet Sampling scores (QC, QD, and QI). Pie charts and numbers are displayed only for nodes included in PhyloNet analyses. (1) Polygonatum cyrtonema Hua, (2) Barnardia japonica (Thunb.) Schult. & Schult.f., (3) Muscari botryoides (L.) Mill., (4) Zephyranthes candida (Lindl.) Herb., (5) Allium cepa L., (6) Allium tuberosum Rottler ex Spreng., (7) Lycoris radiata (L’Hér.) Herb., (8) Hemerocallis fulva (L.) L., (9) Kniphofia uvaria (L.) Oken, (10) Crocus tommasinianus Herb., (11) Iris domestica (L.) Goldblatt & Mabb, (12) Cyanastrum cordifolium Oliv., (13) Ixiolirion tataricum (Pall.) Schult. & Schult.f., (14) Borya sp., (15) Cymbidium kanran Makino, (16) Bletilla striata (Thunb.) Rchb.f., (17) Paphiopedilum malipoense S. C. Chen & Z. H. Tsi., (18) Changnienia amoena S.S.Chien, (19) Pleione formosana Hayata, (20) Gastrochilus japonicus (Makino) Schltr. Photos were taken by Michael L. Moody, Ya-Dong Zhou, Zhong Zhang, Ye-Chun Xu, Xiao-Xiao Wang, Xue-Jia Zhang, Jia-Le Wang, Xiang-Yu Wang, and Ling-Yun Chen. b Topological comparison of trees inferred from different datasets or methods. Red lines indicate inconsistent relationships. APweb = Angiosperm Phylogeny Website. c The maximum posterior probability species network of Asparagales inferred with PhyloNet. The numbers next to the dashed lines indicate inheritance probabilities (γ). Source data underlying this figure is provided as Source Data file.