80 | Nature | Vol 577 | 2 January 2020
Article
To minimize the potential shortcomings of sparse taxon sampling^6 ,
we also inferred an angiosperm species tree using sequences from
44 genomes and 71 transcriptomes, including representatives of the
ANA-grade, eudicots, magnoliids, monocots and a gymnosperm out-
group (Gnetum montanum, G. biloba, P. abies and P. taeda) (Methods).
For further phylogenetic inference of these 115 species, we selected,Type I
10%^46 Type III
28%^135
Type II 294
62%Type I
14%^26Type II(^108) 57%
Type III 56
29%
Type I 24
11%
Type II 116
54%
Type III 74
35%
Eudicots (E)
Monocots (M)
Amborellales (A)
Nymphaeales (N)
Gymnosperms (G)
Type I Type IIE
M
N
A
G
Bootstrap (BS) BS
Ginkgo biloba Picea abies Pinus taeda
Type IIIE
M
N
A
G
BS
a
b
c
F
At least 4 trees: BS ≥ 80
Low support
At least 4 trees: BS ≥ 70
Fossil calibration point
Summarized BS values from 5 coalescent trees
At least 3 trees: BS ≥ 80
Outgroup Total treesTrees Type I Type II Type III
Ginkgo biloba2,169 46 811
Picea abies1,535
Pinus taeda1,515
BS > 80%
6
7
e
777777777777777777777777777777777777777777777777777
1
2 3
4 5
(^89)
(^1011)
(^1213)
14
15 17 16
(^1819)
20
7
6
310 194 662 294 314 241 135
233 139 26 407 302 108 183 129 56
220 131 24 381 285 116 190 138 74
BS>50%BS>80%TreesBS>50%BS>80%TreesBS>50%BS>80%
d
(^12)
4 3
6 5
(^78)
10 9
(^1112)
1413
(^1516)
(^1718)
(^1920)
375 350 325 300 275 250 225 200 175 150 125 100 75 50 25 0
Stellaria media
Picea abies
Phytolacca americana
Fragaria vesca
Platanus acerifolia
Cornus wilsoniana
Phalaenopsis aphrodite
Sonchus asper
Amborella trichopoda
Vinca major
Medicago truncatula
Euryale ferox
Vitis vinifera
Sesamum indicum
Apium graveolens
Morus notabilis
Gnetum montanum
Prunus persica
Nuphar lutea
Hydrangea macrophylla
Piper nigrum
Hieracium umbellatum
Musa acuminata
Capsella rubella
Oryza sativa
Pinellia ternate
Phaseolus vulgaris
Pandanus utilis
Alternanthera philoxeroides
Cucumis sativus
Phyla dulcis
Asparagus officinalis
Illicium henryi
Aristolochia tagala
Lilium brownii
Victoria cruziana
Yucca filamentosa
Acorus calamus
Buxus sinica
Philadelphus incanus
Nymphaea ‘Woods blue goddess’
Arabidopsis thaliana
Nymphaea rubra
Manihot esculenta
Chenopodium quinoa
Nymphaea gigantea ‘Hybrid I’
Cinnamomum camphora
Nymphaea tetragona
Citrus clementina
Capsicum annuum
Citrullus lanatus
Spirodela polyrhiza
Nymphaea gigantea ‘Albert de Lestang’
Nymphaea Nymphaea ‘Midnight’‘Thong Garnjana’
Eucalyptus grandis
Litsea cubeba
Solanum lycopersicum
Trachycarpus fortunei
Glycine max
Mirabilis jalapa
Tamarix chinensis
Lactuca sativa
Theobroma cacao
Dioscorea opposita
Pinus taeda
Delosperma cooperi
Nelumbo nucifera
Brasenia schreberi
Beta vulgaris
Aucuba japonica
Gunnera manicata
Liriodendron chinense
Brachypodium distachyon
Nymphaea colorata
Sorghum bicolor
Nymphaea Nymphaea ‘Paramee’‘Choolarp’
Aquilegia coerulea
Zostera marina
Camellia japonica
Nymphaea prolifera
Cabomba caroliniana
Thellungiella halophilaGossypium arboreum
Lonicera japonica
Nymphaea mexicana
Cirsium vulgare
Nuphar advena
Opuntia dillenii
Cichorium intybus
Dahlia pinnata
Meliosma parviflora
Hedera nepalensis
Ricinus communis
Olea europaea
Tagetes erecta
Arabidopsis lyrata
Ligusticum striatum
Nymphaea potamophila
Nymphaeales
Chimonanthus praecox
Dipsacus laciniatus
Populus trichocarpa
Ginkgo biloba
Phalaenopsis equestris
Houttuynia cordata
Ananas comosus
Mimulus guttatusMentha canadensis
Daucus carota
Nymphaea caerulea
Nandina domesticaEschscholzia californica
Canna indica
Polygonum runcinatum
Austrobaileyales
Nymphaeales
Amborellales F11
F4
F3
F2
F1
F18
F17
F16
F15
F14
F13
F12
F10
F5
F6
F7
F8
F9
F19
F20
F21
Carboniferous Permian Triassic Jurassic Cretaceous Palaeogene Neogene
Time (Ma)
Gymnosperms
Monocots
ANA-grade angiosperms
Magnoliids
Eudicots
Caryophyllales
Asterids
Gunnerales
Piperales
Magnoliales
Laurales
Commelinids
Asparagales
Liliales
DioscorealesPandanales
Alismatales
Austrobaileyales
Amborellales
Acorales
Eudicot
Early-diverging
lineages
Vitales
Fig. 1 | Phylogenomic relationships of angiosperms. a, Three different
evolutionary relationships among major clades of angiosperms. b, Number of
LCN gene trees with different bootstrap support (BS) values based on
nucleotide sequences from six eudicots, six monocots, N. colorata, Amborella
and three different gymnosperms. c, Comparison of gene trees supporting the
three evolutionary relationships using each gymnosperm in turn as the
outgroup. The percentage was calculated by dividing the number of type I, II or
III trees (BS > 80%) by the total number of trees. d, Summary phylogeny and
timescale of 115 plant species. Blue bars at nodes represent 95% credibility
intervals of the estimated dates. e, The f lowers of the 20 sampled water lilies in
Nymphaeales used in d.