supplemental information for€¦ · mimulus guttatus tamarix chinensis vaccinium corymbosum...
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Supplemental Information for
Phylogenomic insights into deep phylogeny of angiosperms based on
broad nuclear gene sampling
Lingxiao Yang, Danyan Su, Xin Chang, Charles S. P. Foster, Linhua Sun,
Chien-Hsun Huang, Xiaofan Zhou, Liping Zeng, Hong Ma, Bojian Zhong*
*Corresponding author: E-mail: [email protected]
This PDF file includes:
Tables S1 to S3
Figures S1 to S13
Detailed analyses for divergence time estimation
Phylogenetic and age justifications for fossil calibrations
References
Table S1. Transcriptome features of Hedyosmum orientale Characteristics Number of reads 29,907,986 Number of contigs 26027 Percent GC 45.48% Contig N50 1311 Medium contig length 723 Average contig length 980 Length range of contigs 297-12774
Table S2. Taxa included in this study
Species name Family Order Groups Source Arabidopsis thaliana Brassicaceae Brassicales Rosids Phytozome Arabidopsis lyrata Brassicaceae Brassicales Rosids Phytozome Capsella rubella Brassicaceae Brassicales Rosids Phytozome
Brassica rapa Brassicaceae Brassicales Rosids Phytozome Eutrema salsugineum Brassicaceae Brassicales Rosids Phytozome
Cleome serrulata Cleomaceae Brassicales Rosids Huang et al. 2016a Carica papaya Caricaceae Brassicales Rosids Phytozome
Theobroma cacao Malvaceae Malvales Rosids Phytozome Gossypium raimondii Malvaceae Malvales Rosids Phytozome
Citrus sinensis Rutaceae Sapindales Rosids Phytozome Citrus clementina Rutaceae Sapindales Rosids Phytozome Cedrela sinensis Meliaceae Sapindales Rosids NCBI
Dimocarpus longan Sapindaceae Sapindales Rosids NCBI Stachyurus yunnanensis Stachyuraceae Crossosomatales Rosids NCBI
Elaeocarpus glabripetalus Elaeocarpaceae Oxalidales Rosids NCBI Oxalis corniculata Oxalidaceae Oxalidales Rosids NCBI Manihot esculenta Euphorbiaceae Malpighiales Rosids Phytozome Ricinus communis Euphorbiaceae Malpighiales Rosids Phytozome Rafflesia cantleyi Rafflesiaceae Malpighiales Rosids NCBI
Linum usitatissimum Linaceae Malpighiales Rosids Phytozome Populus trichocarpa Salicaceae Malpighiales Rosids Phytozome Euonymus carnosus Celastraceae Celastrales Rosids NCBI
Tripterygium wilfordii Celastraceae Celastrales Rosids NCBI
Boehmeria nivea Urticaceae Rosales Rosids NCBI Hippophae rhamnoides Elaeagnaceae Rosales Rosids NCBI
Glycine max Fabaceae Fabales Rosids Phytozome Phaseolus vulgaris Fabaceae Fabales Rosids Phytozome
Cyclobalanopsis glauca Fagaceae Fagales Rosids NCBI Corylus avellana Betulaceae Fagales Rosids NCBI
Juglans regia Juglandaceae Fagales Rosids NCBI Myrica rubra Myricaceae Fagales Rosids NCBI
Eucalyptus grandis Myrtaceae Myrtales Rosids Phytozome Paeonia lactiflora Paeoniaceae Saxifragales Rosids Zeng et al. 2017
Cercidiphyllum japonicum Cercidiphyllaceae Saxifragales Rosids Zeng et al. 2017 Distylium buxifolium Hamamelidaceae Saxifragales Rosids NCBI
Santalum album Santalaceae Santalales Rosids Zeng et al. 2017 Viscum ovalifolium Viscaceae Santalales Rosids Zeng et al. 2017
Aextoxicon punctatum Aextoxicaceae Berberidopsidales Rosids Zeng et al. 2017 Berberidopsis beckleri Berberidopsidaceae Berberidopsidales Rosids The 1KP Project
Parthenocissus tricuspidata Vitaceae Vitales Rosids Zeng et al. 2017 Cayratia japonica Vitaceae Vitales Rosids Zeng et al. 2017 Cissus microcarpa Vitaceae Vitales Rosids NCBI Ampelopsis cordata Vitaceae Vitales Rosids NCBI
Leea guineensis Vitaceae Vitales Rosids NCBI Vitis vinifera Vitaceae Vitales Rosids Phytozome
Mimulus guttatus Phrymaceae Lamiales Asterids Phytozome Mentha canadensis Lamiaceae Lamiales Asterids NCBI
Olea europaea Oleaceae Lamiales Asterids NCBI Avicennia marina Acanthaceae Lamiales Asterids NCBI
Orobanche aegyptiaca Orobanchaceae Lamiales Asterids NCBI Phyla dulcis Verbenaceae Lamiales Asterids NCBI
Bothriospermum chinense Boraginaceae Boraginales Asterids NCBI Trigonotis peduncularis Boraginaceae Boraginales Asterids NCBI Solanum lycopersicum Solanaceae Solanales Asterids Phytozome
Cuscuta reflexa Convolvulaceae Solanales Asterids NCBI Vinca major Apocynaceae Gentianales Asterids NCBI
Gardenia jasminoides Rubiaceae Gentianales Asterids Zeng et al. 2017 Ilex chinensis Aquifoliaceae Aquifoliales Asterids Zeng et al. 2017
Aucuba japonica Garryaceae Garryales Asterids NCBI Apium graveolens Apiaceae Apiales Asterids NCBI
Ligusticum striatum Apiaceae Apiales Asterids Zeng et al. 2017 Hedera nepalensis Araliaceae Apiales Asterids NCBI Dipsacus laciniatus Caprifoliaceae Dipsacales Asterids NCBI Lonicera japonica Caprifoliaceae Dipsacales Asterids NCBI
Valeriana officinalis Caprifoliaceae Dipsacales Asterids NCBI Lactuca sativa Asteraceae Asterales Asterids NCBI Sonchus asper Asteraceae Asterales Asterids Huang et al. 2016b
Cirsium vulgare Asteraceae Asterales Asterids Huang et al. 2016b Pilosella caespitosa Asteraceae Asterales Asterids Zeng et al. 2017 Cichorium intybus Asteraceae Asterales Asterids Huang et al. 2016b
Tagetes erecta Asteraceae Asterales Asterids Zhang et.al, unpublished Dahlia pinnata Asteraceae Asterales Asterids Zeng et al. 2017
Artemisia annua Asteraceae Asterales Asterids NCBI Hydrangea macrophylla Hydrangeaceae Cornales Asterids NCBI
Philadelphus incanus Hydrangeaceae Cornales Asterids NCBI
Cornus wilsoniana Cornaceae Cornales Asterids NCBI Vaccinium corymbosum Ericaceae Ericales Asterids NCBI
Actinidia arguta Actinidiaceae Ericales Asterids NCBI Camellia japonica Theaceae Ericales Asterids NCBI Dionaea muscipula Droseraceae Caryophyllales uncertain NCBI
Phytolacca americana Phytolaccaceae Caryophyllales uncertain Zeng et al. 2017 Mirabilis jalapa Nymphaeaceae Caryophyllales uncertain Zeng et al. 2017
Tamarix chinensis Tamaricaceae Caryophyllales uncertain Zeng et al. 2017 Polygonum runcinatum Polygonaceae Caryophyllales uncertain NCBI
Stellaria media Caryophyllaceae Caryophyllales uncertain Zeng et al. 2017 Opuntia dillenii Cactaceae Caryophyllales uncertain Zeng et al. 2017
Alternanthera philoxeroides Amaranthaceae Caryophyllales uncertain Zeng et al. 2017 Delosperma cooperi Aizoaceae Caryophyllales uncertain Zeng et al. 2017
Dillenia indica Dilleniaceae Dilleniaceae uncertain Zeng et al. 2017 Dillenia turbinata Dilleniaceae Dilleniaceae uncertain Zeng et al. 2017 Gunnera manicata Gunneraceae Gunnerales core eudicots Zeng et al. 2017
Buxus sinica Buxaceae Buxales basal eudicots Zeng et al. 2014 Platanus × acerifolia Platanaceae Proteales basal eudicots Zeng et al. 2014
Nelumbo nucifera Nelumbonaceae Proteales basal eudicots NCBI Meliosma parviflora Sabiaceae Sabiaceae basal eudicots Zeng et al. 2017 Aquilegia coerulea Ranunculaceae Ranunculales basal eudicots Phytozome Nandina domestica Berberidaceae Ranunculales basal eudicots NCBI
Eschscholzia californica Papaveraceae Ranunculales basal eudicots NCBI Ceratophyllum demersum Ceratophyllaceae Ceratophyllales Ceratophyllales Zeng et al. 2014 Ceratophyllum oryzetorum Ceratophyllaceae Ceratophyllales Ceratophyllales NCBI
Hedyosmum orientale Chloranthaceae Chloranthales Chloranthales This study
Chloranthus japonicus Chloranthaceae Chloranthales Chloranthales NCBI Sarcandra glabra Chloranthaceae Chloranthales Chloranthales NCBI
Ascarina rubricaulis Chloranthaceae Chloranthales Chloranthales The 1KP Project Cinnamomum camphora Lauraceae Laurales Magnoliids NCBI
Litsea cubeba Lauraceae Laurales Magnoliids NCBI Persea borbonia Lauraceae Laurales Magnoliids The 1KP Project
Gyrocarpus americanus Hernandiaceae Laurales Magnoliids The 1KP Project Peumus boldus Monimiaceae Laurales Magnoliids The 1KP Project
Gomortega keule Gomortegaceae Laurales Magnoliids The 1KP Project Laurelia sempervirens Atherospermataceae Laurales Magnoliids The 1KP Project Chimonanthus praecox Calycanthaceae Laurales Magnoliids NCBI
Magnolia denudata Magnoliaceae Magnoliales Magnoliids NCBI Liriodendron chinense × tulipifera Magnoliaceae Magnoliales Magnoliids NCBI
Eupomatia bennettii Eupomatiaceae Magnoliales Magnoliids The 1KP Project Annona muricata Annonaceae Magnoliales Magnoliids The 1KP Project
Myristica fragrans Myristicaceae Magnoliales Magnoliids The 1KP Project Houttuynia cordata Saururaceae Piperales Magnoliids NCBI
Piper nigrum Piperaceae Piperales Magnoliids NCBI Saruma henryi Aristolochiaceae Piperales Magnoliids The 1KP Project
Aristolochia tagala Aristolochiaceae Piperales Magnoliids NCBI Canella winterana Canellaceae Canellales Magnoliids The 1KP Project
Drimys winteri Winteraceae Canellales Magnoliids The 1KP Project Sorghum bicolor Poaceae Poales Monocots Phytozome
Zea mays Poaceae Poales Monocots Phytozome Setaria italica Poaceae Poales Monocots Phytozome
Panicum virgatum Poaceae Poales Monocots Phytozome
Oryza sativa Poaceae Poales Monocots Phytozome Brachypodium distachyon Poaceae Poales Monocots Phytozome
Acorus calamus Acoraceae Acorales Monocots NCBI Acorus americanus Acoraceae Acorales Monocots The 1KP Project
Alisma plantago-aquatica Alismataceae Alismatales Monocots NCBI Pinellia ternata Araceae Alismatales Monocots NCBI
Spirodela polyrhiza Araceae Alismatales Monocots Phytozome Trachycarpus fortunei Arecaceae Arecales Monocots NCBI
Sabal bermudana Arecaceae Arecales Monocots The 1KP Project Yucca filamentosa Asparagaceae Asparagales Monocots NCBI
Asparagus officinalis Asparagaceae Asparagales Monocots NCBI Iris japonica Iridaceae Asparagales Monocots NCBI
Dioscorea opposita Dioscoreaceae Dioscoreales Monocots NCBI Dioscorea villosa Dioscoreaceae Dioscoreales Monocots The 1KP Project
Lilium brownii Liliaceae Liliales Monocots NCBI Smilax bona-nox Smilacaceae Liliales Monocots The 1KP Project
Colchicum autumnale Colchicaceae Liliales Monocots The 1KP Project Pandanus utilis Pandanaceae Pandanales Monocots NCBI Canna indica Cannaceae Zingiberales Monocots NCBI
Musa acuminata Musaceae Zingiberales Monocots Phytozome Illicium henryi Schisandraceae Austrobaileyales Basal angiosperm NCBI
Cabomba caroliniana Cabombaceae Nymphaeales Basal angiosperm NCBI Nuphar advena Nymphaeaceae Nymphaeales Basal angiosperm NCBI
Amborella trichopoda Amborellaceae Amborellales Basal angiosperm Phytozome Ginkgo biloba Ginkgoaceae Ginkgoales Gymnosperms Phytozome Pinus taeda Pinaceae Pinales Gymnosperms NCBI
Table S3. Estimated ages of major angiosperm clades.
Clade Strategy A Strategy B Strategy C The subset (64 taxa)
Mean age (95% HPD) (Ma) Mean age (95% HPD) (Ma) Mean age (95% HPD) (Ma) Mean age (95% HPD) (Ma)
Angiosperms 240.2 (255.08 - 222.2) 237.02 (252.45 - 216.94) 239.53 (258.44 - 216.67) 232.95 (254.31 - 205.97)
Mesangiospermae 178.82 (192.16 - 166.44) 180.21 (194.01 - 167.12) 181.70 (196.02 - 168.25) -
Magnoliids 159.16 (170.73 - 147.14) 158.94 (171.58 - 146.92) 159.95 (172.51 - 147.21) 151.02 (171.12 - 131.11)
Monocots 160.52 (174.64 - 145.71) 162.85 (176.7 - 148.67) 163.76 (178.16 - 149.15) -
Eudicots 129.17 (131.06 - 127.79) 129.16 (131 - 127.78) 129.15 (130.89 - 127.64) 128.36 (129.66 - 126.72)
Eudicots - Ceratophyllales 151.81 (163.89 - 140.63) 151.51 (164.03 - 140.24) 152.52 (165.42 - 140.89) -
Core eudicots 121.07 (123.78 - 118.48) 121.07 (123.62 - 118.26) 121.14 (123.76 - 118.6) 120.83 (123.97 - 126.72)
Berberidopsidales - rest
eudicots
119.40 (122.05 - 116.59) 119.39 (122.14 - 116.62) 119.45 (122.08 - 116.68) 118.31 (121.85 - 114.86)
Caryophyllales - Asterids 115.44 (118.61 - 112.3) 115.44 (118.56 - 112.31) 115.47 (118.54 - 112.32) 113.07 (117.3 - 108.71)
Asterids 110.30 (114.29 - 106.23) 110.32 (114.28 - 106.36) 110.24 (114.23 - 106.05) 107.30 (112.12 - 102.19)
Santalales - Superrosids 116.56 (119.50 - 113.58) 116.55 (119.42 - 113.6) 116.61 (119.51 - 113.68) 114.95 (118.58 - 110.93)
Vitales - (Rosids +
Saxifragales)
114.56 (117.56 - 111.24) 114.57 (117.68 - 111.55) 114.64 (117.71 - 111.55) 112.65 (116.54 - 108.17)
Rosids - Saxifragales 112.51 (115.83 - 109.16) 112.52 (115.75 - 109.36) 112.59 (115.81 - 109.28) 109.89 (114.26 - 105.22)
Rosids 108.04 (111.61 - 104.35) 108.07 (111.77 - 104.5) 108.18 (111.81 - 104.59) 104.68 (109.85 - 99.54)
Two gene trees were inferred for each OG.
One gene tree was built using RAxML with
GTR+G model and 100 bootstrap replicates
(referred to herein as ML gene tree). For the
other gene tree, we pruned the reference tree
to meet species in the alignment and estimated
branch lengths of the constrained topology by
RAxML under GTR+G model (referred to
herein as constrained gene tree).
If the ratio of the terminal branch length on the
ML gene tree (or constrained gene tree) to the
terminal branch length on the reference tree is
greater than or equal to 5 times.
If the Pearson correlation coefficient between
branch lengths on the constrained gene tree
and branch lengths on the reference tree is
considered as outlier among 2435 OGs.
2435 orthologous
Groups (OGs)
Individual gene trees
Remove putatively spurious
or paralogous sequences
Remove putatively
non-orthologous groups
Alignments and trimmingNumber of taxa
< 107 species
Gene Length
< 600 nucleotides
Removal of genes if
1696 orthologous
Groups (OGs)
Fig. S1. The workflow of paralogue-filtering strategy.
0.1
Lactuca sativa
Theobroma cacao
Drimys winteri
Lilium brownii
Phyla dulcis
Litsea cubeba
Phaseolus vulgaris
Apium graveolens
Persea borbonia
Cabomba caroliniana
Boehmeria nivea
Oxalis corniculata
Actinidia arguta
Aextoxicon punctatum
Illicium henryi
Cinnamomum camphora
Corylus avellana
Magnolia denudata
Philadelphus incanus
Sarcandra glabra
Dahlia pinnata
Opuntia dillenii
Arabidopsis thaliana
Liriodendron chinense × tulipifera
Brachypodium distachyon
Citrus clementina
Chloranthus japonicus
Gardenia jasminoidesAucuba japonica
Vinca major
Rafflesia cantleyi
Dillenia turbinata
Meliosma parviflora
Gyrocarpus americanus
Yucca filamentosa
Acorus americanus
Cissus microcarpa
Cirsium vulgare
Citrus sinensis
Delosperma cooperi
Eutrema salsugineum
Saruma henryi
Ascarina rubricaulis
Buxus sinica
Olea europaea
Leea guineensis
Hippophae rhamnoides
Dimocarpus longan
Cuscuta reflexa
Cedrela sinensis
Paeonia lactiflora
Cichorium intybus
Ligusticum striatum
Zea mays
Valeriana officinalis
Cyclobalanopsis glauca
Nuphar advena
Acorus calamus
Eschscholzia californica
Ginkgo biloba
Houttuynia cordata
Berberidopsis beckleri
Cornus wilsoniana
Brassica rapa
Juglans regia
Euonymus carnosus
Smilax bona-noxColchicum autumnale
Lonicera japonica
Hedyosmum orientale
Artemisia annua
Ceratophyllum demersum
Orobanche aegyptiaca
Dipsacus laciniatus
Mimulus guttatus
Tamarix chinensis
Vaccinium corymbosum
Gunnera manicata
Canna indica
Alisma plantago-aquatica
Peumus boldus
Musa acuminata
Vitis vinifera
Sonchus asper
Pinellia ternata
Santalum album
Eupomatia bennettii
Myrica rubra
Mirabilis jalapa
Myristica fragrans
Ilex chinensis
Stachyurus yunnanensis
Tripterygium wilfordii
Arabidopsis lyrata
Platanus × acerifolia
Sorghum bicolor
Dioscorea opposita
Iris japonica
Ricinus communis
Carica papaya
Avicennia marina
Hedera nepalensis
Nelumbo nucifera
Gomortega keule
Setaria italica
Camellia japonica
Elaeocarpus glabripetalus
Cleome serrulata
Cayratia japonica
Solanum lycopersicum
Tagetes erecta
Pandanus utilis
Piper nigrum
Spirodela polyrhiza
Nandina domestica
Hydrangea macrophylla
Populus trichocarpa
Aquilegia coerulea
Asparagus officinalis
Manihot esculenta
Trachycarpus fortunei
Mentha canadensis
Chimonanthus praecox
Stellaria media
Oryza sativa
Sabal bermudana
Ceratophyllum oryzetorum
Ampelopsis cordata
Amborella trichopoda
Parthenocissus tricuspidata
Pilosella caespitosa
Dionaea muscipula
Gossypium raimondii
Glycine max
Eucalyptus grandis
Capsella rubella
Aristolochia tagala
Viscum ovalifolium
Alternanthera philoxeroides
Panicum virgatum
Phytolacca americana
Laurelia sempervirens
Pinus taeda
Cercidiphyllum japonicumDistylium buxifolium
Trigonotis peduncularisBothriospermum chinense
Polygonum runcinatum
Annona muricata
Canella winterana
Linum usitatissimum
Dioscorea villosa
Dillenia indica
Figure S2 The concatenation-based species tree of 1594-genes data with summary of gene tree concordance and conflict. The pie charts at each node present the
proportion of gene tree concordance and conflict. Pie chart color coding: blue—the fraction of gene trees that are concordant with the species tree; green—fraction
of gene trees supporting the second most common topology; red—fraction of gene trees supporting all other alternative conflicting partitions; gray—fraction of
gene trees with <50% bootstrap support at that node. The branch lengths in coalescent units were estimated by ASTRAL.
4.0
Artemisia annua
Buxus sinica
Citrus sinensis
Brachypodium distachyon
Trigonotis peduncularis
Cuscuta reflexa
Cabomba caroliniana
Ascarina rubricaulis
Euonymus carnosus
Musa acuminata
Dimocarpus longan
Dipsacus laciniatus
Orobanche aegyptiaca
Yucca filamentosa
Chimonanthus praecox
Houttuynia cordata
Distylium buxifolium
Lilium brownii
Eschscholzia californica
Lactuca sativa
Phytolacca americana
Mentha canadensis
Nandina domestica
Panicum virgatum
Ligusticum striatum
Oxalis corniculata
Tamarix chinensis
Boehmeria nivea
Lonicera japonica
Gyrocarpus americanus
Aristolochia tagala
Cissus microcarpa
Opuntia dillenii
Aquilegia coerulea
Berberidopsis beckleri
Parthenocissus tricuspidata
Rafflesia cantleyi
Dillenia turbinata
Eucalyptus grandis
Polygonum runcinatum
Meliosma parviflora
Aextoxicon punctatum
Elaeocarpus glabripetalus
Gunnera manicata
Ceratophyllum oryzetorum
Dahlia pinnata
Smilax bona-nox
Avicennia marina
Valeriana officinalis
Sarcandra glabra
Persea borbonia
Corylus avellana
Pinus taeda
Eutrema salsugineum
Litsea cubeba
Theobroma cacao
Leea guineensis
Phyla dulcis
Vinca major
Zea mays
Nuphar advena
Ampelopsis cordata
Nelumbo nucifera
Carica papaya
Myrica rubra
Vaccinium corymbosum
Gardenia jasminoides
Pandanus utilis
Ilex chinensis
Olea europaea
Saruma henryi
Philadelphus incanus
Linum usitatissimum
Dillenia indica
Cyclobalanopsis glauca
Hedyosmum orientale
Cirsium vulgare
Myristica fragrans
Ricinus communis
Juglans regia
Iris japonica
Sonchus asper
Setaria italica
Mimulus guttatus
Cichorium intybus
Pinellia ternata
Acorus americanus
Laurelia sempervirens
Tripterygium wilfordii
Dionaea muscipula
Sorghum bicolor
Pilosella caespitosa
Ceratophyllum demersum
Chloranthus japonicus
Amborella tricopoda
Annona muricata
Oryza sativa
Tagetes erecta
Illicium henryi
Colchicum autumnale
Dioscorea opposita
Solanum lycopersicum
Spirodela polyrhiza
Cedrela sinensis
Cinnamomum camphora
Peumus boldus
Trachycarpus fortunei
Arabidopsis lyrata
Stellaria media
Mirabilis jalapa
Stachyurus yunnanensis
Citrus clementina
Aucuba japonica
Ginkgo biloba
Arabidopsis thaliana
Hedera nepalensis
Canna indica
Glycine max
Piper nigrum
Apium graveolens
Camellia japonica
Drimys winteri
Vitis vinifera
Liriodendron chinense×tulipifera
Sabal bermudana
Cercidiphyllum japonicum
Paeonia lactiflora
Delosperma cooperi
Asparagus officinalis
Viscum ovalifolium
Capsella rubella
Alternanthera philoxeroides
Bothriospermum chinense
Cornus wilsoniana
Dioscorea villosa
Cleome serrulata
Cayratia japonica
Santalum album
Hydrangea macrophylla
Manihot esculenta
Populus trichocarpa
Hippophae rhamnoidesPhaseolus vulgaris
Actinidia arguta
Alisma plantago-aquatica
Magnolia denudata
Brassica rapa
Gossypium raimondii
Canella winterana
Platanus×acerifolia
Eupomatia bennettii
Acorus calamus
Gomortega keule
[q1=0.55;q2=0.23;q3=0.22]
[q1=0.38;q2=0.32;q3=0.29]
[q1=0.9;q2=0.05;q3=0.05]
[q1=0.97;q2=0.01;q3=0.02]
[q1=0.94;q2=0.04;q3=0.02]
[q1=0.61;q2=0.22;q3=0.17]
[q1=0.95;q2=0.02;q3=0.03]
[q1=0.65;q2=0.18;q3=0.16]
[q1=0.68;q2=0.14;q3=0.17]
[q1=0.79;q2=0.12;q3=0.09]
[q1=0.93;q2=0.04;q3=0.02]
[q1=0.88;q2=0.05;q3=0.07]
[q1=0.47;q2=0.39;q3=0.14]
[q1=0.4;q2=0.31;q3=0.28]
[q1=0.44;q2=0.31;q3=0.25]
[q1=0.44;q2=0.31;q3=0.24]
[q1=1;q2=0;q3=0]
[q1=0.4;q2=0.3;q3=0.29]
[q1=0.96;q2=0.01;q3=0.02]
[q1=0.98;q2=0.01;q3=0.01]
[q1=0.87;q2=0.06;q3=0.07]
[q1=0.94;q2=0.03;q3=0.04]
[q1=0.54;q2=0.26;q3=0.2]
[q1=0.37;q2=0.26;q3=0.37]
[q1=0.41;q2=0.33;q3=0.27]
[q1=0.97;q2=0.01;q3=0.02]
[q1=0.38;q2=0.37;q3=0.26]
[q1=0.88;q2=0.05;q3=0.07]
[q1=0.94;q2=0.02;q3=0.04]
[q1=0.74;q2=0.12;q3=0.14]
[q1=0.94;q2=0.03;q3=0.03]
[q1=0.54;q2=0.22;q3=0.23]
[q1=1;q2=0;q3=0]
[q1=0.34;q2=0.34;q3=0.32]
[q1=0.41;q2=0.32;q3=0.26]
[q1=0.7;q2=0.14;q3=0.15]
[q1=0.76;q2=0.18;q3=0.06]
[q1=1;q2=0;q3=0]
[q1=0.96;q2=0.03;q3=0.01]
[q1=0.95;q2=0.03;q3=0.02]
[q1=0.47;q2=0.25;q3=0.28]
[q1=0.47;q2=0.24;q3=0.28]
[q1=0.96;q2=0.02;q3=0.02]
[q1=0.92;q2=0.04;q3=0.04]
[q1=0.65;q2=0.18;q3=0.17]
[q1=0.44;q2=0.42;
q3=0.13]
[q1=0.88;q2=0.07;q3=0.06]
[q1=0.78;q2=0.11;q3=0.11]
[q1=0.56;q2=0.23;q3=0.21]
[q1=0.86;q2=0.07;q3=0.07]
[q1=0.73;q2=0.12;q3=0.16]
[q1=0.98;q2=0.01;q3=0.01]
[q1=0.95;q2=0.03;q3=0.02]
[q1=0.52;q2=0.28;q3=0.2]
[q1=1;q2=0;q3=0]
[q1=0.62;q2=0.18;q3=0.2]
[q1=0.92;q2=0.04;q3=0.04]
[q1=0.93;q2=0.04;q3=0.04]
[q1=0.87;q2=0.07;q3=0.06]
[q1=1;q2=0;q3=0]
[q1=0.48;q2=0.26;q3=0.25]
[q1=0.9;q2=0.03;q3=0.06]
[q1=0.41;q2=0.25;q3=0.34]
[q1=0.5;q2=0.21;q3=0.29]
[q1=0.52;q2=0.31;q3=0.18]
[q1=0.98;q2=0.01;q3=0.01]
[q1=0.97;q2=0.01;q3=0.02]
[q1=0.38;q2=0.27;q3=0.35]
[q1=0.92;q2=0.04;q3=0.04]
[q1=0.97;q2=0.02;q3=0.02]
[q1=0.9;q2=0.05;q3=0.04]
[q1=0.54;q2=0.22;q3=0.24]
[q1=0.92;q2=0.03;q3=0.05]
[q1=0.68;q2=0.26;q3=0.06]
[q1=0.73;q2=0.14;q3=0.13]
[q1=0.41;q2=0.35;q3=0.24]
[q1=0.37;q2=0.32;q3=0.31]
[q1=0.4;q2=0.22;q3=0.37]
[q1=0.72;q2=0.19;q3=0.09]
[q1=0.65;q2=0.19;q3=0.15]
[q1=0.46;q2=0.32;q3=0.22]
[q1=0.84;q2=0.06;q3=0.11]
[q1=0.92;q2=0.04;q3=0.04]
[q1=1;q2=0;q3=0]
[q1=1;q2=0;q3=0]
[q1=0.46;q2=0.4;q3=0.14]
[q1=0.97;q2=0.02;q3=0.01]
[q1=0.43;q2=0.28;q3=0.28][q1=0.92;q2=0.04;q3=0.04]
[q1=0.37;q2=0.36;q3=0.27]
[q1=0.44;q2=0.29;q3=0.26]
[q1=1;q2=0;q3=0]
[q1=0.72;q2=0.1;q3=0.18]
[q1=0.83;q2=0.07;q3=0.1]
[q1=0.4;q2=0.25;q3=0.35]
[q1=0.87;q2=0.07;q3=0.06]
[q1=0.94;q2=0.03;q3=0.03]
[q1=0.57;q2=0.18;q3=0.25]
[q1=0.48;q2=0.27;q3=0.26]
[q1=0.92;q2=0.04;q3=0.04]
[q1=0.71;q2=0.12;q3=0.17]
[q1=0.84;q2=0.07;q3=0.09]
[q1=0.97;q2=0.01;q3=0.02]
[q1=0.5;q2=0.29;q3=0.21]
[q1=0.96;q2=0.02;q3=0.02]
[q1=0.94;q2=0.03;q3=0.03]
[q1=0.79;q2=0.12;q3=0.09]
[q1=0.92;q2=0.05;q3=0.04]
[q1=0.94;
q2=0.03;
q3=0.04]
[q1=0.6;q2=0.21;q3=0.19]
[q1=0.95;q2=0.03;q3=0.03]
[q1=0.69;q2=0.17;q3=0.14]
[q1=0.97;q2=0.01;q3=0.01]
[q1=0.76;q2=0.14;q3=0.11]
[q1=0.88;q2=0.04;q3=0.08]
[q1=0.55;q2=0.14;q3=0.31]
[q1=0.72;q2=0.13;q3=0.14]
[q1=0.96;q2=0.02;q3=0.02]
[q1=0.57;q2=0.21;q3=0.23]
[q1=0.86;q2=0.11;q3=0.04]
[q1=0.46;q2=0.31;q3=0.23]
[q1=0.95;q2=0.03;q3=0.02]
[q1=0.88;q2=0.08;q3=0.04]
[q1=0.42;q2=0.28;q3=0.3]
[q1=0.94;q2=0.03;q3=0.03]
[q1=0.38;q2=0.28;q3=0.33]
[q1=0.97;q2=0.02;q3=0.01]
[q1=0.44;q2=0.28;q3=0.27]
[q1=0.96;q2=0.02;q3=0.02]
[q1=0.99;q2=0;q3=0]
[q1=0.36;q2=0.32;q3=0.32]
[q1=0.38;q2=0.34;q3=0.28]
[q1=0.35;q2=0.31;q3=0.34]
[q1=0.97;q2=0.02;q3=0.01]
[q1=0.95;q2=0.02;q3=0.03]
[q1=0.54;q2=0.2;q3=0.26]
[q1=0.73;q2=0.14;q3=0.13]
[q1=0.62;q2=0.26;q3=0.12]
[q1=0.95;q2=0.02;q3=0.03]
[q1=0.54;q2=0.29;q3=0.17]
[q1=0.37;q2=0.29;q3=0.34]
[q1=0.99;q2=0;q3=0.01]
[q1=0.53;q2=0.31;q3=0.17]
[q1=0.75;q2=0.12;q3=0.13]
[q1=1;q2=0;q3=0]
[q1=0.67;q2=0.14;q3=0.19]
[q1=0.85;q2=0.08;q3=0.07]
[q1=0.81;q2=0.1;q3=0.09]
[q1=0.97;q2=0.02;q3=0.01]
[q1=0.8;q2=0.14;q3=0.06]
[q1=0.82;q2=0.12;q3=0.06]
Platanus
Figure S3 The quartet score for the coalescent-based species tree of 1594 genes. ‘q1’, ‘q2’, ‘q3’ show quartet support for the topology of current species tree, the first alternative, and the second alternative, respectively.
indecisive
53% reject one hypothesis
29%
reject four hypotheses
3%
reject two hypotheses
12%
reject three hypotheses
3%
Fig. S4 Results from phylogenetic signal analyses by using AU test. These
results show that insufficient phylogenetic signals are prevalent in 1594-gene
data.
4.0
1/100
1/100
1/100
1/100
1/100
1/99
1/100
1/100
1/100
1/100
1/100
1/100
1/97
1/100
1/100
1/100
1/100
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1/100
1/100
1/100
1/100
1/100
1/100
1/100
1/100
1/100
1/100
1/100
1/100
0.76/92
1/100
1/100
1/100
1/100
1/100
1/100
1/100
1/100
1/100
1/100
1/49
1/100
1/100
1/100
0.99/55
0.47/38
1/100
1/100
0.99/85
1/100
1/100
1/100
0.62/80
1/100
1/100
1/100
1/100
1/100
0.82/27
0.68/51
1/100
0.56/74
1/100
0.71/19
1/100
1/100
1/100
0.72/3
0.97/13
1/100
1/100
0.82/271/89
1/100
1/100
1/100
1/100
1/100
1/100
1/100
1/100
1/100
1/100
1/100
1/100
1/100
1/100
1/100
1/100
1/100
1/100
1/89
1/100
1/100
1/100
1/100
1/100
1/100
1/100
1/100
1/100
1/100
1/100
1/100
1/100
1/100
1/100
1/100
1/100
1/100
1/100
1/100
1/100
1/96
1/100
1/100
1/100
1/100
1/100
1/100
0.99/97
1/100
1/100
1/100
1/99
1/100
1/100
1/96
1/100
1/100
1/100
1/100
1/100
1/100
1/100
1/100
0.89/80
1/100
1/100
1/100
1/100
1/100
1/100
1/100
1/100
1/100
1/100
1/99
0.41/12
Arabidopsis thalianaArabidopsis lyrata
Brassica rapaCapsella rubella
Eutrema salsugineumCleome serrulata
Gossypium raimondii
Phyla dulcis
Carica papayaTheobroma cacao
Euonymus carnosus
Populus trichocarpaLinum usitatissimum
Rafflesia cantleyi
Ricinus communisManihot esculenta
Oxalis corniculataElaeocarpus glabripetalus
Stachyurus yunnanensis
Dimocarpus longanCedrela sinensis
Citrus clementinaCitrus sinensis
Tripterygium wilfordii
Boehmeria nivea
Paeonia lactiflora
Eucalyptus grandis
Myrica rubraJuglans regia
Corylus avellanaCyclobalanopsis glauca
Phaseolus vulgarisGlycine max
Hippophae rhamnoides
Cercidiphyllum japonicumDistylium buxifolium
Leea guineensis
Ampelopsis cordata
Cissus microcarpaCayratia japonica
Parthenocissus tricuspidata
Berberidopsis beckleriAextoxicon punctatum
Viscum ovalifoliumSantalum album
Vitis vinifera
Olea europaea
Mentha canadensisMimulus guttatus
Hedera nepalensis
Bothriospermum chinenseTrigonotis peduncularis
Solanum lycopersicumCuscuta reflexa
Ligusticum striatumApium graveolens
Aucuba japonicaIlex chinensis
Gardenia jasminoidesVinca major
Avicennia marina
Orobanche aegyptiaca
Lactuca sativa
Valeriana officinalisLonicera japonica
Dipsacus laciniatus
Vaccinium corymbosum
Cirsium vulgare
Sonchus asper
Hydrangea macrophylla
Artemisia annua
Dahlia pinnataTagetes erecta
Cichorium intybus
Dionaea muscipula
Camellia japonica
Pilosella caespitosa
Philadelphus incanus
Actinidia arguta
Cornus wilsoniana
Alternanthera philoxeroides
Dillenia indica
Delosperma cooperiPhytolacca americanaMirabilis jalapa
Tamarix chinensisPolygonum runcinatum
Stellaria media
Opuntia dillenii
Hedyosmum orientale
Ceratophyllum oryzetorumCeratophyllum demersum
Eschscholzia californica
Nandina domesticaAquilegia coerulea
Meliosma parviflora
Nelumbo nuciferaPlatanus × acerifolia
Buxus sinicaGunnera manicata
Dillenia turbinata
Peumus boldusGyrocarpus americanus
Persea borbonia
Litsea cubebaCinnamomum camphora
Ascarina rubricaulis
Sarcandra glabraChloranthus japonicus
Annona muricataEupomatia bennettii
Liriodendron chinense × tulipiferaMagnolia denudata
Chimonanthus praecox
Laurelia sempervirensGomortega keule
Sorghum bicolor
Drimys winteriCanella winterana
Aristolochia tagalaSaruma henryi
Piper nigrumHouttuynia cordata
Myristica fragrans
Asparagus officinalisYucca filamentosa
Sabal bermudanaTrachycarpus fortunei
Spirodela polyrhizaPinellia ternata
Alisma plantago-aquatica
Acorus americanusAcorus calamus
Brachypodium distachyonOryza sativa
Panicum virgatumSetaria italica
Zea mays
Lilium brownii
Dioscorea opposita
Iris japonica
Dioscorea villosaPandanus utilis
Colchicum autumnale
Smilax bona-nox
Musa acuminataCanna indica
Pinus taedaGinkgo biloba
Amborella tricopoda
Nuphar advenaCabomba caroliniana
Illicium henryi
Fig. S5 The coalescent-based species tree was inferred by ASTRAL using 756 genes. Numbers associated with nodes are support values obtained by the posterior probability (PP on the left) and the multilocus bootstrapping (BS on the right).
4.0
Nelumbo nucifera
Ligusticum striatum
Mentha canadensis
Iris japonica
Amborella tricopoda
Alisma plantago-aquatica
Cissus microcarpa
Yucca filamentosa
Phaseolus vulgaris
Canella winterana
Stellaria media
Dionaea muscipula
Nuphar advena
Solanum lycopersicum
Musa acuminata
Manihot esculenta
Paeonia lactiflora
Pinus taeda
Phyla dulcis
Dillenia indica
Spirodela polyrhiza
Corylus avellana
Vitis vinifera
Dimocarpus longan
Tripterygium wilfordii
Brachypodium distachyon
Gomortega keule
Annona muricata
Aristolochia tagala
Mirabilis jalapa
Olea europaea
Persea borbonia
Sorghum bicolor
Pandanus utilis
Parthenocissus tricuspidata
Saruma henryi
Dioscorea villosa
Colchicum autumnale
Ascarina rubricaulis
Valeriana officinalis
Zea mays
Acorus calamus
Berberidopsis beckleri
Cleome serrulata
Cercidiphyllum japonicum
Trachycarpus fortunei
Acorus americanus
Mimulus guttatus
Hippophae rhamnoides
Theobroma cacao
Euonymus carnosus
Litsea cubeba
Myristica fragrans
Cinnamomum camphora
Dahlia pinnata
Avicennia marina
Ceratophyllum demersum
Cuscuta reflexa
Laurelia sempervirens
Aucuba japonica
Piper nigrum
Panicum virgatum
Cyclobalanopsis glauca
Liriodendron chinense×tulipifera
Apium graveolens
Arabidopsis lyrata
Artemisia annua
Nandina domestica
Ginkgo biloba
Dioscorea opposita
Ilex chinensis
Gardenia jasminoides
Eucalyptus grandis
Orobanche aegyptiaca
Sarcandra glabra
Elaeocarpus glabripetalus
Juglans regia
Glycine max
Gyrocarpus americanus
Citrus clementina
Peumus boldus
Philadelphus incanus
Chloranthus japonicus
Buxus sinica
Camellia japonica
Santalum album
Oryza sativa
Cornus wilsoniana
Brassica rapa
Asparagus officinalis
Rafflesia cantleyi
Gossypium raimondii
Aextoxicon punctatum
Meliosma parviflora
Linum usitatissimum
Delosperma cooperi
Canna indica
Citrus sinensis
Viscum ovalifolium
Sabal bermudana
Arabidopsis thaliana
Dillenia turbinata
Ceratophyllum oryzetorum
Cayratia japonica
Tagetes erecta
Tamarix chinensis
Ampelopsis cordata
Drimys winteri
Polygonum runcinatum
Ricinus communis
Carica papaya
Bothriospermum chinense
Actinidia arguta
Gunnera manicata
Aquilegia coerulea
Populus trichocarpa
Platanus×acerifolia
Setaria italica
Stachyurus yunnanensis
Vaccinium corymbosum
Cabomba caroliniana
Hydrangea macrophylla
Hedera nepalensis
Lilium brownii
Lonicera japonica
Dipsacus laciniatus
Myrica rubra
Cichorium intybus
Chimonanthus praecox
Smilax bona-nox
Eupomatia bennettii
Vinca major
Illicium henryi
Trigonotis peduncularis
Pinellia ternata
Magnolia denudata
Cedrela sinensis
Sonchus asper
Alternanthera philoxeroides
Oxalis corniculata
Capsella rubellaEutrema salsugineum
Opuntia dillenii
Phytolacca americana
Eschscholzia californica
Distylium buxifolium
Pilosella caespitosa
Lactuca sativa
Houttuynia cordata
Hedyosmum orientale
Cirsium vulgare
Boehmeria nivea
Leea guineensis
[q1=0.65;q2=0.19;q3=0.16]
[q1=0.42;q2=0.35;
q3=0.23]
[q1=0.96;q2=0.03;q3=0.01]
[q1=0.73;q2=0.13;q3=0.14]
[q1=0.93;q2=0.02;q3=0.05]
[q1=0.88;q2=0.07;q3=0.05]
[q1=0.39;q2=0.29;q3=0.32]
[q1=0.71;q2=0.1;q3=0.19]
[q1=0.96;q2=0.02;q3=0.02]
[q1=0.89;q2=0.05;q3=0.06]
[q1=0.98;q2=0.01;q3=0.01]
[q1=0.88;q2=0.04;q3=0.08]
[q1=0.86;q2=0.11;q3=0.03]
[q1=0.35;q2=0.32;q3=0.33]
[q1=0.54;q2=0.29;
q3=0.17]
[q1=0.47;q2=0.3;q3=0.23]
[q1=0.45;q2=0.29;q3=0.26]
[q1=0.56;q2=0.2;q3=0.23]
[q1=0.97;q2=0.02;q3=0.01]
[q1=0.37;q2=0.31;q3=0.31]
[q1=0.37;q2=0.36;q3=0.27]
[q1=0.94;q2=0.03;q3=0.04]
[q1=0.89;q2=0.07;q3=0.04]
[q1=0.52;q2=0.21;q3=0.27]
[q1=0.59;q2=0.21;q3=0.2]
[q1=0.95;q2=0.03;q3=0.02]
[q1=0.4;q2=0.26;q3=0.35]
[q1=0.96;q2=0.01;q3=0.03]
[q1=0.51;q2=0.29;q3=0.2]
[q1=1;q2=0;q3=0]
[q1=0.96;q2=0.03;q3=0.02]
[q1=0.43;q2=0.17;q3=0.4]
[q1=1;q2=0;q3=0]
[q1=0.98;q2=0.01;q3=0.01]
[q1=0.98;q2=0.01;q3=0.01]
[q1=0.94;q2=0.02;q3=0.03]
[q1=0.98;q2=0.01;q3=0]
[q1=0.83;q2=0.1;q3=0.07]
[q1=0.55;q2=0.13;q3=0.32]
[q1=0.55;q2=0.22;q3=0.24]
[q1=0.96;q2=0.02;q3=0.03]
[q1=0.94;q2=0.02;q3=0.04]
[q1=0.75;q2=0.12;q3=0.13]
[q1=0.44;q2=0.25;q3=0.31]
[q1=0.88;q2=0.04;q3=0.08]
[q1=0.65;q2=0.19;q3=0.16]
[q1=0.69;q2=0.17;q3=0.14]
[q1=0.69;q2=0.15;q3=0.16]
[q1=0.82;q2=0.09;q3=0.09]
[q1=0.43;q2=0.43;
q3=0.14]
[q1=1;q2=0;q3=0]
[q1=0.42;q2=0.21;q3=0.37]
[q1=0.88;q2=0.06;q3=0.06]
[q1=0.49;q2=0.29;q3=0.22]
[q1=0.93;q2=0.02;q3=0.05]
[q1=0.46;q2=0.41;q3=0.13]
[q1=0.46;q2=0.33;q3=0.21]
[q1=0.75;q2=0.12;q3=0.13]
[q1=0.97;q2=0.02;q3=0.02]
[q1=0.57;q2=0.19;q3=0.24]
[q1=0.67;q2=0.16;q3=0.18]
[q1=0.72;q2=0.11;q3=0.17]
[q1=0.73;q2=0.11;q3=0.15]
[q1=0.73;q2=0.21;q3=0.06]
[q1=0.45;q2=0.27;q3=0.28]
[q1=0.91;q2=0.04;q3=0.04]
[q1=0.95;q2=0.01;q3=0.03]
[q1=0.48;q2=0.27;q3=0.25]
[q1=0.94;q2=0.03;q3=0.03]
[q1=0.42;q2=0.3;q3=0.29]
[q1=0.92;q2=0.04;q3=0.04]
[q1=0.99;q2=0.01;q3=0]
[q1=0.39;q2=0.22;q3=0.39]
[q1=0.97;q2=0.01;q3=0.02]
[q1=0.63;q2=0.17;q3=0.19]
[q1=0.44;q2=0.3;q3=0.27]
[q1=0.93;q2=0.05;q3=0.02]
[q1=0.62;q2=0.22;q3=0.16]
[q1=0.41;q2=0.29;q3=0.3]
[q1=0.96;q2=0.02;
q3=0.02]
[q1=1;q2=0;q3=0]
[q1=0.93;q2=0.03;
q3=0.04]
[q1=0.86;q2=0.07;q3=0.07]
[q1=0.92;q2=0.04;q3=0.04]
[q1=0.87;q2=0.06;q3=0.07]
[q1=0.99;q2=0.01;q3=0.01]
[q1=0.96;q2=0.02;q3=0.02]
[q1=0.92;q2=0.03;q3=0.06]
[q1=0.77;q2=0.13;q3=0.09]
[q1=0.48;q2=0.22;q3=0.3]
[q1=1;q2=0;q3=0]
[q1=0.55;q2=0.29;q3=0.16]
[q1=0.45;q2=0.26;q3=0.28]
[q1=0.71;q2=0.13;q3=0.17]
[q1=0.98;q2=0.01;q3=0.01]
[q1=0.62;q2=0.28;q3=0.1]
[q1=0.94;q2=0.03;q3=0.03]
[q1=1;q2=0;q3=0]
[q1=0.78;q2=0.12;
q3=0.1]
[q1=0.95;q2=0.02;q3=0.03]
[q1=0.97;q2=0.01;q3=0.02]
[q1=0.66;q2=0.17;q3=0.17]
[q1=0.51;q2=0.29;q3=0.2]
[q1=0.92;q2=0.05;q3=0.04]
[q1=0.95;q2=0.02;q3=0.02]
[q1=0.34;q2=0.32;q3=0.34]
[q1=0.74;q2=0.14;q3=0.12]
[q1=0.87;q2=0.07;q3=0.06]
[q1=0.7;q2=0.13;q3=0.17]
[q1=0.98;q2=0.01;q3=0.01]
[q1=0.39;q2=0.32;q3=0.29]
[q1=0.42;q2=0.29;q3=0.29]
[q1=0.92;q2=0.05;q3=0.04]
[q1=0.73;q2=0.2;q3=0.07]
[q1=0.36;q2=0.29;q3=0.35]
[q1=0.38;q2=0.35;q3=0.27]
[q1=0.93;q2=0.03;q3=0.04]
[q1=0.85;q2=0.07;q3=0.07]
[q1=0.39;q2=0.27;q3=0.34]
[q1=0.53;q2=0.2;q3=0.27]
[q1=1;q2=0;q3=0]
[q1=0.57;q2=0.2;q3=0.23]
[q1=0.37;q2=0.36;q3=0.27]
[q1=0.79;q2=0.15;q3=0.06]
[q1=0.83;q2=0.06;q3=0.11]
[q1=0.47;q2=0.39;q3=0.15]
[q1=0.96;q2=0.02;
q3=0.02]
[q1=0.43;q2=0.33;q3=0.24]
[q1=0.55;q2=0.28;q3=0.17]
[q1=0.81;q2=0.13;q3=0.06]
[q1=0.44;q2=0.25;q3=0.31]
[q1=0.57;q2=0.21;q3=0.22]
[q1=0.47;q2=0.26;q3=0.28]
[q1=0.87;q2=0.04;q3=0.09]
[q1=0.98;q2=0.01;q3=0.01]
[q1=0.93;q2=0.04;q3=0.02]
[q1=0.89;q2=0.06;q3=0.05]
[q1=0.76;q2=0.12;q3=0.12]
[q1=1;q2=0;q3=0]
[q1=0.79;q2=0.11;q3=0.11]
[q1=0.91;q2=0.03;q3=0.06]
[q1=0.42;q2=0.32;q3=0.25]
[q1=0.93;q2=0.04;
q3=0.03]
[q1=0.35;q2=0.32;q3=0.33]
[q1=0.37;q2=0.29;q3=0.34]
[q1=0.96;q2=0.02;q3=0.02]
[q1=0.95;q2=0.03;q3=0.03]
[q1=1;q2=0;q3=0]
[q1=0.72;q2=0.2;q3=0.08]
[q1=0.93;q2=0.03;q3=0.04]
[q1=0.84;q2=0.07;q3=0.09]
Figure S6 The quartet score for the coalescent-based species tree of 756 genes. ‘q1’, ‘q2’, ‘q3’ show quartet support for the topology of current species tree, the first alternative, and the second alternative, respectively.
4.0
Cinnamomum camphora
Avicennia marina
Camellia japonica
Lactuca sativa
Brachypodium distachyon
Apium graveolens
Dipsacus laciniatus
Eschscholzia californica
Leea guineensis
Citrus sinensis
Elaeocarpus glabripetalus
Vaccinium corymbosum
Spirodela polyrhiza
Ginkgo biloba
Eucalyptus grandis
Nelumbo nucifera
Canna indica
Delosperma cooperi
Chloranthus japonicus
Cirsium vulgare
Berberidopsis beckleri
Platanus×acerifolia
Myrica rubra
Ampelopsis cordata
Dioscorea villosa
Illicium henryi
Amborella tricopoda
Theobroma cacao
Stellaria media
Houttuynia cordata
Asparagus officinalis
Dahlia pinnataArtemisia annua
Meliosma parviflora
Cichorium intybus
Annona muricata
Bothriospermum chinense
Yucca filamentosa
Colchicum autumnale
Trachycarpus fortunei
Cleome serrulata
Rafflesia cantleyi
Lonicera japonica
Gunnera manicata
Lilium brownii
Phytolacca americana
Cissus microcarpa
Tripterygium wilfordii
Setaria italica
Parthenocissus tricuspidata
Aristolochia tagalaSaruma henryi
Sabal bermudana
Mimulus guttatus
Opuntia dillenii
Liriodendron chinense×tulipifera
Actinidia arguta
Canella winterana
Alternanthera philoxeroides
Iris japonica
Dillenia indica
Olea europaea
Manihot esculenta
Orobanche aegyptiaca
Gyrocarpus americanus
Smilax bona-nox
Tagetes erecta
Tamarix chinensis
Philadelphus incanus
Dillenia turbinata
Mirabilis jalapa
Magnolia denudata
Corylus avellana
Aextoxicon punctatum
Santalum album
Drimys winteri
Hippophae rhamnoides
Panicum virgatum
Piper nigrum
Pinus taeda
Dionaea muscipula
Eupomatia bennettii
Litsea cubeba
Eutrema salsugineum
Ceratophyllum demersum
Pandanus utilis
Arabidopsis thaliana
Linum usitatissimum
Sorghum bicolor
Valeriana officinalis
Vitis vinifera
Boehmeria nivea
Brassica rapa
Peumus boldus
Acorus calamus
Gossypium raimondii
Paeonia lactiflora
Pinellia ternata
Phaseolus vulgaris
Sarcandra glabra
Alisma plantago-aquatica
Stachyurus yunnanensis
Ascarina rubricaulis
Chimonanthus praecox
Aquilegia coerulea
Mentha canadensis
Dimocarpus longan
Nandina domestica
Oxalis corniculata
Cercidiphyllum japonicum
Euonymus carnosus
Ilex chinensis
Capsella rubella
Hedyosmum orientale
Laurelia sempervirens
Distylium buxifolium
Persea borbonia
Dioscorea opposita
Cyclobalanopsis glauca
Arabidopsis lyrata
Polygonum runcinatum
Pilosella caespitosa
Aucuba japonica
Hedera nepalensis
Trigonotis peduncularis
Viscum ovalifolium
Sonchus asper
Cuscuta reflexa
Nuphar advenaCabomba caroliniana
Oryza sativa
Cornus wilsoniana
Musa acuminata
Ligusticum striatum
Hydrangea macrophylla
Glycine max
Vinca major
Cedrela sinensis
Juglans regia
Ricinus communisPopulus trichocarpa
Citrus clementina
Carica papaya
Gomortega keule
Solanum lycopersicum
Buxus sinica
Gardenia jasminoides
Zea mays
Myristica fragrans
Phyla dulcis
Acorus americanus
Cayratia japonica
Ceratophyllum oryzetorum
[q1=0.74;q2=0.14;q3=0.12]
[q1=0.88;q2=0.03;q3=0.08]
[q1=0.71;q2=0.21;q3=0.08]
[q1=0.99;q2=0.01;q3=0]
[q1=0.97;q2=0.01;
q3=0.02]
[q1=0.96;q2=0.03;q3=0.01]
[q1=0.91;q2=0.05;q3=0.04]
[q1=0.47;q2=0.39;q3=0.14]
[q1=0.93;q2=0.03;q3=0.04]
[q1=0.79;q2=0.1;q3=0.11]
[q1=1;q2=0;q3=0]
[q1=0.91;q2=0.02;q3=0.08]
[q1=0.76;q2=0.16;q3=0.08]
[q1=0.83;q2=0.06;q3=0.11]
[q1=0.55;q2=0.19;q3=0.26]
[q1=0.59;q2=0.18;q3=0.23]
[q1=0.72;q2=0.14;q3=0.14]
[q1=0.39;q2=0.33;q3=0.28]
[q1=0.73;q2=0.13;
q3=0.13]
[q1=0.36;q2=0.3;q3=0.34]
[q1=0.41;q2=0.28;q3=0.31]
[q1=0.42;q2=0.31;q3=0.26]
[q1=0.94;q2=0.02;q3=0.05]
[q1=0.49;q2=0.3;q3=0.21]
[q1=0.94;q2=0.02;q3=0.04]
[q1=1;q2=0;q3=0]
[q1=0.96;q2=0.03;q3=0]
[q1=0.94;q2=0.02;q3=0.03]
[q1=0.85;q2=0.08;q3=0.08]
[q1=0.92;q2=0.04;q3=0.04]
[q1=0.61;q2=0.2;q3=0.19]
[q1=0.38;q2=0.3;q3=0.32]
[q1=0.68;q2=0.16;q3=0.16]
[q1=0.48;q2=0.26;q3=0.25]
[q1=0.55;q2=0.24;q3=0.21]
[q1=0.42;q2=0.35;q3=0.23]
[q1=0.52;
q2=0.31;
q3=0.17]
[q1=0.67;q2=0.26;q3=0.07]
[q1=0.4;q2=0.36;q3=0.24]
[q1=0.91;
q2=0.04;
q3=0.05]
[q1=0.93;q2=0.03;q3=0.05]
[q1=0.65;q2=0.19;q3=0.16]
[q1=0.88;q2=0.07;q3=0.05]
[q1=0.37;q2=0.33;q3=0.3]
[q1=0.46;q2=0.13;q3=0.41]
[q1=0.42;q2=0.29;q3=0.29]
[q1=0.98;q2=0.02;q3=0]
[q1=0.84;q2=0.07;q3=0.09]
[q1=0.39;q2=0.33;q3=0.28]
[q1=0.97;q2=0.01;q3=0.02]
[q1=0.69;q2=0.15;q3=0.16]
[q1=0.49;q2=0.23;q3=0.28]
[q1=0.92;q2=0.03;q3=0.05]
[q1=0.49;q2=0.2;q3=0.32]
[q1=0.38;q2=0.32;q3=0.3]
[q1=0.95;q2=0.01;q3=0.04]
[q1=0.92;q2=0.04;q3=0.04]
[q1=0.92;q2=0.03;q3=0.06]
[q1=0.41;q2=0.19;q3=0.4]
[q1=0.53;q2=0.28;q3=0.18]
[q1=0.72;q2=0.11;q3=0.18]
[q1=0.45;q2=0.33;q3=0.23]
[q1=0.89;q2=0.06;q3=0.05]
[q1=0.95;q2=0.03;q3=0.02]
[q1=0.89;q2=0.06;q3=0.06]
[q1=0.41;q2=0.28;q3=0.31]
[q1=0.72;q2=0.12;q3=0.16][q1=0.72;q2=0.21;q3=0.07]
[q1=0.52;q2=0.33;q3=0.16]
[q1=0.5;q2=0.25;q3=0.25]
[q1=0.94;q2=0.03;q3=0.03]
[q1=0.91;q2=0.06;q3=0.03]
[q1=0.45;q2=0.32;q3=0.23]
[q1=1;q2=0;q3=0]
[q1=0.36;q2=0.33;q3=0.32]
[q1=0.91;q2=0.05;
q3=0.04]
[q1=0.87;q2=0.05;q3=0.08]
[q1=0.89;q2=0.09;q3=0.02]
[q1=0.69;q2=0.16;q3=0.14]
[q1=0.64;q2=0.18;q3=0.18]
[q1=0.98;q2=0.01;q3=0.01]
[q1=0.64;q2=0.15;q3=0.21]
[q1=0.93;q2=0.03;q3=0.04]
[q1=0.91;q2=0.05;q3=0.04]
[q1=0.93;q2=0.04;q3=0.02]
[q1=0.98;q2=0.01;q3=0.01]
[q1=0.51;q2=0.27;q3=0.22]
[q1=0.98;q2=0.02;q3=0.01]
[q1=0.44;q2=0.29;q3=0.27]
[q1=0.45;q2=0.27;q3=0.28]
[q1=1;q2=0;q3=0]
[q1=0.38;q2=0.28;q3=0.35]
[q1=0.75;q2=0.11;q3=0.14][q1=0.92;q2=0.02;q3=0.06]
[q1=0.45;q2=0.22;q3=0.34]
[q1=0.7;q2=0.13;q3=0.17]
[q1=0.82;q2=0.13;q3=0.06]
[q1=0.91;q2=0.05;q3=0.04]
[q1=0.51;q2=0.2;q3=0.29]
[q1=0.85;q2=0.09;q3=0.06]
[q1=0.41;
q2=0.31;
q3=0.29]
[q1=0.49;q2=0.28;q3=0.23]
[q1=0.87;q2=0.07;q3=0.06]
[q1=0.67;q2=0.17;q3=0.16]
[q1=0.53;q2=0.19;q3=0.28]
[q1=0.98;q2=0;q3=0.02]
[q1=0.42;q2=0.23;q3=0.35]
[q1=0.91;q2=0.05;q3=0.05]
[q1=0.57;q2=0.26;q3=0.17]
[q1=0.99;q2=0.01;q3=0]
[q1=1;q2=0;q3=0]
[q1=0.79;q2=0.14;q3=0.06]
[q1=0.97;q2=0.01;q3=0.02]
[q1=0.69;q2=0.13;q3=0.18]
[q1=0.96;q2=0.02;q3=0.01]
[q1=0.49;q2=0.21;q3=0.31]
[q1=0.41;q2=0.33;q3=0.26]
[q1=0.94;q2=0.04;q3=0.02]
[q1=0.69;q2=0.1;q3=0.21]
[q1=0.93;q2=0.04;
q3=0.03]
[q1=0.94;q2=0.02;q3=0.04]
[q1=0.44;q2=0.31;q3=0.24]
[q1=0.41;q2=0.35;q3=0.25]
[q1=0.66;q2=0.16;q3=0.18]
[q1=0.97;q2=0.01;
q3=0.01]
[q1=0.71;q2=0.15;q3=0.14]
[q1=0.44;q2=0.25;q3=0.31]
[q1=0.54;q2=0.14;q3=0.31]
[q1=0.95;q2=0.03;q3=0.02]
[q1=0.47;q2=0.14;q3=0.39]
[q1=0.94;q2=0.03;q3=0.03]
[q1=0.39;q2=0.28;q3=0.33]
[q1=1;q2=0;q3=0]
[q1=0.83;q2=0.1;q3=0.08]
[q1=0.91;q2=0.03;q3=0.06]
[q1=0.98;q2=0.01;q3=0.01]
[q1=0.83;q2=0.09;q3=0.08]
[q1=1;q2=0;q3=0]
[q1=0.95;q2=0.01;q3=0.04]
[q1=0.59;q2=0.28;q3=0.13]
[q1=0.61;q2=0.28;q3=0.11]
[q1=0.96;q2=0.02;q3=0.02]
[q1=0.68;q2=0.16;q3=0.16]
[q1=1;q2=0;q3=0]
[q1=0.95;q2=0.03;q3=0.02]
[q1=0.87;q2=0.02;q3=0.11]
[q1=0.79;q2=0.1;q3=0.1]
[q1=0.99;q2=0.01;q3=0]
[q1=0.86;q2=0.05;q3=0.09]
[q1=0.89;q2=0.07;q3=0.04]
[q1=0.47;q2=0.29;q3=0.25]
Figure S7 The quartet score for the coalescent-based species tree of 296genes. ‘q1’, ‘q2’, ‘q3’ show quartet support for the topology of current species tree, the first alternative, and the second alternative, respectively.
4.0
Corylus avellanaCyclobalanopsis glauca
Vitis vinifera
Trigonotis peduncularis
Philadelphus incanus
Alisma plantago-aquatica
Artemisia annua
Apium graveolens
Populus trichocarpa
Meliosma parviflora
Aucuba japonica
Delosperma cooperi
Myristica fragrans
Liriodendron chinense tulipifera
Brassica rapa
Smilax bona-nox
Sabal bermudana
Linum usitatissimum
Dimocarpus longan
Juglans regia
Gossypium raimondii
Gardenia jasminoides
Ricinus communis
Ascarina rubricaulis
Tamarix chinensis
Musa acuminata
Parthenocissus tricuspidata
Nuphar advena
Dionaea muscipula
Drimys winteri
Arabidopsis lyrata
Boehmeria nivea
Pinellia ternata
Dahlia pinnata
Pandanus utilis
Chimonanthus praecox
Sorghum bicolor
Distylium buxifolium
Eucalyptus grandis
Illicium henryi
Nandina domestica
Myrica rubra
Cuscuta reflexa
Ceratophyllum oryzetorum
Setaria italica
Acorus calamus
Santalum album
Glycine max
Cichorium intybus
Dillenia turbinata
Dioscorea villosa
Camellia japonica
Eschscholzia californica
Cinnamomum camphora
Peumus boldus
Phytolacca americana
Cayratia japonica
Dioscorea opposita
Polygonum runcinatum
Phyla dulcis
Paeonia lactiflora
Platanus acerifolia
Actinidia arguta
Ceratophyllum demersum
Lilium brownii
Colchicum autumnale
Cedrela sinensis
Citrus clementina
Zea mays
Sarcandra glabra
Lonicera japonica
Saruma henryi
Canna indica
Phaseolus vulgaris
Gunnera manicata
Amborella tricopoda
Leea guineensis
Opuntia dillenii
Brachypodium distachyon
Rafflesia cantleyi
Tagetes erecta
Oxalis corniculata
Dillenia indica
Hedyosmum orientale
Hedera nepalensis
Euonymus carnosus
Annona muricata
Vinca major
Persea borbonia
Citrus sinensis
Aextoxicon punctatum
Tripterygium wilfordii
Arabidopsis thaliana
Ilex chinensis
Carica papaya
Lactuca sativa
Stellaria media
Gyrocarpus americanus
Solanum lycopersicum
Stachyurus yunnanensis
Laurelia sempervirens
Sonchus asper
Piper nigrumAristolochia tagala
Magnolia denudata
Panicum virgatum
Iris japonica
Avicennia marina
Canella winterana
Mimulus guttatus
Asparagus officinalis
Cirsium vulgare
Elaeocarpus glabripetalus
Ginkgo biloba
Hydrangea macrophylla
Eupomatia bennettii
Cercidiphyllum japonicum
Valeriana officinalis
Acorus americanus
Chloranthus japonicus
Litsea cubeba
Eutrema salsugineum
Viscum ovalifolium
Pinus taeda
Theobroma cacao
Hippophae rhamnoides
Ligusticum striatum
Cissus microcarpa
Mentha canadensis
Dipsacus laciniatus
Vaccinium corymbosum
Bothriospermum chinense
Manihot esculenta
Ampelopsis cordata
Houttuynia cordata
Trachycarpus fortunei
Spirodela polyrhiza
Mirabilis jalapa
Aquilegia coerulea
Alternanthera philoxeroides
Yucca filamentosa
Berberidopsis beckleri
Orobanche aegyptiaca
Buxus sinica
Pilosella caespitosa
Olea europaea
Oryza sativa
Capsella rubella
Cornus wilsoniana
Cleome serrulata
Nelumbo nucifera
Gomortega keule
Cabomba caroliniana
1/100
1/100
1/100
1/97
1/100
1/100
0.94/46
1/100
1/100
0.83/66
1/100
1/100
1/100
1/91
1/100
0.99/5
1/100
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0.86/37
0.8/87
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0.9/96
1/36
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1/0
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0.45/6
1/100
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0.95/1
11/00
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0.86/19
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1/93
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0.98/45
1/100
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1/26
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1/76
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1/94
1/100
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1/0
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1/73
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0.91/25
1/27
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0.83/87
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100
Figure S8 The coalescent-based species tree was inferred by ASTRAL using 838 genes. Numbers associated with nodes are support values obtained by the posterior probability (PP on the left) and the multilocus bootstrapping (BS on the right).
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Fig.S9 Branch-specific substitution rates plotted against the midpoint ages of these branches, for (a) first and second codon positions, and (b) third codon positions. Both
the rates and ages were estimated using Strategy A in MCMCTree.
Ricinus communis
Aucuba japonica
Orobanche aegyptiaca
Gossypium raimondii
Populus trichocarpa
Tamarix chinensis
Dillenia indica
Pinus taeda
Piper nigrum
Actinidia arguta
Meliosma parviflora
Euonymus carnosus
Chimonanthus praecox
Hedyosmum orientale
Laurelia sempervirens
Gomortega keule
Gardenia jasminoides
Vaccinium corymbosum
Leea guineensis
Cissus microcarpa
Santalum album
Buxus sinica
Hedera nepalensis
Dipsacus laciniatus
Theobroma cacao
Amborella trichopoda
Annona muricata
Distylium buxifolium
Stachyurus yunnanensis
Ascarina rubricaulis
Cedrela sinensis
Corylus avellana
Manihot esculenta
Platanus × acerifolia
Myrica rubra
Phyla dulcis
Myristica fragrans
Gyrocarpus americanus
Dillenia turbinata
Cyclobalanopsis glauca
Ampelopsis cordata
Sarcandra glabra
Eucalyptus grandis
Illicium henryi
Cercidiphyllum japonicum
Eupomatia bennettii
Parthenocissus tricuspidata
Vitis vinifera
Juglans regia
Peumus boldus
Aextoxicon punctatum
Dimocarpus longan
Camellia japonica
Citrus sinensis
Hydrangea macrophylla
Berberidopsis beckleri
Elaeocarpus glabripetalus
Citrus clementina
Avicennia marina
Olea europaea
Cornus wilsoniana
Lonicera japonica
Tripterygium wilfordii
Philadelphus incanus
350 300 250 200 150 100 50 0 (Ma)370
350 300 250 200 150 100 50 0 (Ma)370
Carboniferous Permian CenozoicCretaceousJurassicTriassic
1
3
18
36
6
7
15
16
17
22
21
25
24
30
31
32
34
35
Angiosperms
Eudicots
Magnoliids
Fig. S10 Chronogram depicting the angiosperm evolutionary timescale, as estimated using Bayesian analysis of 296 genes from 64 taxa (remove all current or ancestrally herbaceous taxa), with 18 fossil calibrations and an uncorrelated
relaxed clock, in MCMCTREE. Fossil constraints are shown with red dots, and the details of fossils were available in the supplementary materials. Horizontal bars represent 95% credibility intervals.
Arabidopsis thaliana
Annona muricata
Trachycarpus fortunei
Lilium brownii
Pinus taeda
Platanus × acerifolia
Cichorium intybus
Apium graveolens
Panicum virgatum
Cayratia japonica
Berberidopsis beckleri
Polygonum runcinatum
Arabidopsis lyrata
Glycine max
Elaeocarpus glabripetalus
Sonchus asper
Manihot esculenta
Boehmeria nivea
Artemisia annua
Linum usitatissimum
Myristica fragrans
Phyla dulcis
Hedyosmum orientale
Nandina domestica
Phaseolus vulgaris
Hippophae rhamnoides
Alisma plantago-aquatica
Aquilegia coerulea
Trigonotis peduncularis
Spirodela polyrhiza
Cleome serrulata
Ceratophyllum demersum
Stellaria media
Phytolacca americana
Dioscorea opposita
Zea mays
Yucca filamentosa
Myrica rubra
Acorus americanus
Dionaea muscipula
Camellia japonica
Populus trichocarpa
Nuphar advena
Eschscholzia californica
Piper nigrum
Mimulus guttatus
Carica papaya
Brassica rapa
Hydrangea macrophylla
Peumus boldus
Sorghum bicolor
Chloranthus japonicus
Canna indica
Laurelia sempervirens
Cuscuta reflexa
Alternanthera philoxeroides
Chimonanthus praecox
Tamarix chinensis
Colchicum autumnale
Delosperma cooperi
Buxus sinica
Aucuba japonica
Ligusticum striatum
Canella winterana
Cornus wilsoniana
Cyclobalanopsis glauca
Gardenia jasminoides
Aristolochia tagala
Capsella rubella
Lactuca sativa
Citrus clementina
Lonicera japonica
Solanum lycopersicum
Leea guineensis
Philadelphus incanus
Sabal bermudana
Vitis vinifera
Theobroma cacao
Oxalis corniculata
Saruma henryi
Ascarina rubricaulis
Actinidia arguta
Dillenia indica
Brachypodium distachyon
Dahlia pinnata
Gossypium raimondii
Mirabilis jalapa
Orobanche aegyptiaca
Persea borbonia
Dillenia turbinata
Ginkgo biloba
Mentha canadensis
Ricinus communis
Aextoxicon punctatum
Euonymus carnosus
Dipsacus laciniatus
Musa acuminata
Cirsium vulgare
Smilax bona-nox
Avicennia marina
Gunnera manicata
Opuntia dillenii
Corylus avellana
Distylium buxifolium
Juglans regia
Acorus calamus
Magnolia denudata
Tagetes erecta
Ceratophyllum oryzetorum
Eutrema salsugineum
Nelumbo nucifera
Dimocarpus longan
Iris japonica
Eupomatia bennettii
Hedera nepalensis
Cedrela sinensis
Illicium henryi
Pinellia ternata
Cabomba caroliniana
Sarcandra glabra
Oryza sativa
Drimys winteri
Valeriana officinalis
Cinnamomum camphora
Parthenocissus tricuspidata
Bothriospermum chinense
Cissus microcarpa
Dioscorea villosa
Meliosma parviflora
Olea europaea
Vinca major
Ampelopsis cordata
Gomortega keule
Rafflesia cantleyi
Asparagus officinalis
Pilosella caespitosa
Cercidiphyllum japonicum
Amborella trichopoda
Houttuynia cordata
Setaria italica
Santalum albumViscum ovalifolium
Gyrocarpus americanus
Stachyurus yunnanensis
Citrus sinensis
Liriodendron chinense × tulipifera
Ilex chinensis
Paeonia lactiflora
Pandanus utilis
Litsea cubeba
Tripterygium wilfordii
Vaccinium corymbosum
Eucalyptus grandis
350 300 250 200 150 100 50 0 (Ma)370
350 300 250 200 150 100 50 0 (Ma)370
Carboniferous Permian CenozoicCretaceousJurassicTriassic
1
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Angiosperms
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Monocots
Mesangiospermae
Fig. S11 Chronogram depicting the angiosperm evolutionary timescale, as estimated using Bayesian analysis of 296 genes from 153 taxa, with 35 fossil calibrations (strategy B: reduce three calibration nodes: Node 5, Node 6 and Node 7) and
an uncorrelated relaxed clock, in MCMCTREE. Fossil constraints are shown with red dots, and the details of fossils were available in the supplementary materials. Horizontal bars represent 95% credibility intervals.
Setaria italica
Tagetes erecta
Trigonotis peduncularis
Hedera nepalensis
Gomortega keule
Persea borbonia
Mirabilis jalapa
Capsella rubella
Philadelphus incanus
Litsea cubeba
Chloranthus japonicus
Canella winterana
Gossypium raimondii
Sarcandra glabra
Trachycarpus fortunei
Gyrocarpus americanus
Oxalis corniculata
Panicum virgatum
Eucalyptus grandis
Alisma plantago-aquatica
Musa acuminata
Sorghum bicolor
Viscum ovalifolium
Polygonum runcinatum
Avicennia marina
Buxus sinica
Artemisia annua
Lonicera japonica
Dimocarpus longan
Carica papaya
Berberidopsis beckleri
Leea guineensis
Phyla dulcis
Paeonia lactiflora
Tripterygium wilfordii
Acorus calamus
Lilium brownii
Santalum album
Aextoxicon punctatum
Actinidia arguta
Eschscholzia californica
Distylium buxifolium
Smilax bona-nox
Piper nigrum
Cirsium vulgare
Ligusticum striatum
Hydrangea macrophylla
Hippophae rhamnoides
Elaeocarpus glabripetalus
Orobanche aegyptiaca
Manihot esculenta
Lactuca sativa
Ascarina rubricaulis
Boehmeria nivea
Tamarix chinensis
Delosperma cooperi
Gunnera manicata
Phytolacca americana
Cabomba caroliniana
Cedrela sinensis
Dioscorea villosa
Mentha canadensis
Aucuba japonica
Meliosma parviflora
Cuscuta reflexa
Euonymus carnosus
Eupomatia bennettii
Valeriana officinalis
Brassica rapa
Nandina domestica
Opuntia dillenii
Hedyosmum orientale
Dionaea muscipula
Dillenia indica
Magnolia denudata
Arabidopsis lyrata
Olea europaea
Nelumbo nucifera
Spirodela polyrhiza
Apium graveolens
Saruma henryi
Cichorium intybus
Solanum lycopersicum
Annona muricata
Yucca filamentosa
Stellaria media
Oryza sativa
Parthenocissus tricuspidata
Linum usitatissimum
Acorus americanus
Pinellia ternata
Vaccinium corymbosum
Cissus microcarpa
Vinca major
Theobroma cacao
Cyclobalanopsis glauca
Platanus × acerifolia
Sonchus asper
Citrus sinensis
Dipsacus laciniatus
Ilex chinensis
Ceratophyllum demersum
Bothriospermum chinense
Peumus boldus
Juglans regia
Ginkgo biloba
Populus trichocarpa
Pinus taeda
Pandanus utilis
Laurelia sempervirens
Ampelopsis cordata
Eutrema salsugineum
Cercidiphyllum japonicum
Zea mays
Amborella trichopoda
Chimonanthus praecox
Sabal bermudanaBrachypodium distachyon
Citrus clementina
Dioscorea opposita
Dillenia turbinata
Cayratia japonica
Dahlia pinnata
Stachyurus yunnanensis
Rafflesia cantleyi
Cleome serrulata
Arabidopsis thaliana
Cinnamomum camphora
Aristolochia tagala
Ceratophyllum oryzetorum
Camellia japonica
Glycine max
Vitis vinifera
Ricinus communis
Canna indica
Myrica rubra
Corylus avellana
Pilosella caespitosa
Myristica fragrans
Drimys winteri
Colchicum autumnale
Gardenia jasminoides
Phaseolus vulgaris
Nuphar advena
Mimulus guttatus
Houttuynia cordata
Cornus wilsoniana
Aquilegia coerulea
Asparagus officinalis
Liriodendron chinense × tulipifera
Illicium henryi
Alternanthera philoxeroides
Iris japonica
350 300 250 200 150 100 50 0 (Ma)370
350 300 250 200 150 100 50 0 (Ma)370
Carboniferous Permian CenozoicCretaceousJurassicTriassic
1
2
3
4
89
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28 29
30
31
32
33
34
35
36
37
38
Angiosperms
Eudicots
Magnoliids
Monocots
Mesangiospermae
Fig. S12 Chronogram depicting the angiosperm evolutionary timescale, as estimated using Bayesian analysis of 296 genes from 153 taxa, with 35 fossil calibrations (strategy C: reduce three calibration nodes (Node 5, Node 6 and Node 7)
and decrease the minimum fossil constraint of crown angiosperms) and an uncorrelated relaxed clock, in MCMCTREE. Fossil constraints are shown with red dots, and the details of fossils were available in the supplementary materials.
Horizontal bars represent 95% credibility intervals.
300 340 380
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0.02
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0.02
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Node 6
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Node 7
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Fig. S13. Comparison of the age distributions on the 38 calibrated nodes for the specified priors (black line) and
effective priors (purple) using uniform prior distributions on the coalescent-based species tree.
Detailed analyses for divergence time estimation
The gap between molecular ages and the oldest fossil records of angiosperms
(Early Cretaceous) has triggered many researches in recent years. Fossil calibrations
provide the fundamental information for the estimates of absolute times and rates in
molecular clock dating analyses. The placement of the fossil on the tree is most
important to all strategies. The widely used crown-angiosperm constraints were
tricolpate pollen grains from the Barremian-Aptian boundary (~125 Ma), which was
unequivocally related to the eudicot clade (Magallón et al., 2015; Coiro et al. 2019).
These fossils may represent the limitations of the fossil record, but may also be
uninformative. Obviously, they are ‘too young’ for the crown node of angiosperms.
We employed three calibration strategies to test the influence of these fossils for the
gap between molecular age and fossil evidence of angiosperms. In strategy A (the
main analyses that are described in Results), all 38 fossil constraints were used to
calibrate the timetree. For strategy B, we removed three calibration nodes (Node 5,
Node 6 and Node 7). For strategy C, we further decreased the minimum fossil
constraint of crown angiosperms on the basis of strategy B. We ran the MCMCTree
analyses for both strategy B and strategy C and inferred highly congruent ages for
crown angiosperms (strategy B: 252.45 - 216.94 Ma, Supplementary fig.S11; strategy
C: 258.44 - 216.67 Ma, Supplementary fig.S12). Despite tricolpate pollen grains are
likely to provide limited information for this node, we chose to use these fossils to
calibrate the minimum constraint of angiosperms for replenishing fossil information
as much as possible. Comparing the molecular ages between strategy A and strategy
B, two different strategies both supported a pre-Cretaceous origin of angiosperms, but
more calibration points produced a narrower 95% credible interval width (strategy A:
255.08 - 222.2 Ma; strategy B: 252.45 - 216.94 Ma). Fewer calibration nodes tended
to increase the variance of age estimates remarkably (Salomo et al., 2017). We used
the results of strategy A as our main analyses.
Through a series of simulations, Beaulieu et al. (2015) demonstrated that the
potential biases caused by rate heterogeneity between herbaceous and woody species
tended to generate the older age estimates, especially there were large shifts in branch
rates among early-diverging lineages of angiosperms. However, Foster et al. (2017)
indicated that estimated divergence ages without herbaceous lineages were congruent
with other analyses. Salomo et al. (2017) also considered the rate heterogeneity, and
the results didn’t show great influence of rates on the crown node of angiosperms. We
evaluated the impacts of rate heterogeneity between herbaceous and woody species.
First, we checked shifts in branch rates in the results of our main MCMCTree analysis.
The branch rates from our main MCMCTree analyse were plotted against the
midpoint ages of branches by the R package NELSI v0.21 (Ho et al., 2015). The
rategrams for each locus (Supplementary fig. S9) didn’t show large shifts in the early
branches of angiosperms, implying that rate changes between early-diverging
angiosperm species had little fluctuation. Besides, in order to further eliminate the
impact of rate heterogeneity among these two different kinds of groups, we divided
153 species into woody perennials and herbaceous annuals, and reconstructed their
ancestral states by using the make.simmap function (R package Phytools v0.6-60,
Revell 2012). Then, all lineages that are currently and were ancestrally herbaceous
were removed, as faster rates might be expected in herbaceous annuals. We ran
MCMCTree analyses for the reduced dataset (64 taxa), and obtained the highly
similar ages of crown angiosperms with the main analyses (254.31 - 205.97 Ma,
Supplementary fig. S10) after removing all herbaceous annuals. The heterogeneous
rates across a phylogenetic tree have little effect for the age of crown angiosperms in
our data set.
In summary, our divergence time estimations are robust and support a
pre-Cretaceous origin of angiosperms. To explain the mystery of the gap between
molecular age and fossil evidence of angiosperms, we need to make future efforts not
only in developing new molecular methods, but also in making the fossil records more
abundant.
Phylogenetic and age justifications for fossil calibrations
We implemented three maximum age constraints:
(1) 365.629 Ma for Node 1 and Node 2, the soft maximum constraint which
follows Morris et al. (2018) is based on the first records of seeds in the form of
preovules that satisfy the criteria of the seed habit.
(2) 247.2 Ma for Node 3 ~ Node 16, the soft maximum constraint which follows
Morris et al. (2018) is based on sediments devoid of angiosperm-like pollen below
their first report in the Middle Triassic.
(3) 128.63 Ma for Node 17 ~ Node 38. The age constraint is based on the
maximum age of the oldest potential age of tricolpate pollen (the earliest
unequivocal angiosperm fossils,Hughes and McDougall 1990), from the middle
Atherfield Wealden Bed 35 of the Cowleaze Chine Member, Vectis Formation
(Hughes and McDougall 1990) which occurs within the M1n polarity chron in
the Late Barremian (Clarke et al. 2011 ). And the base of the M1n chron is
approximately correlated with the base of the Gerhardtia sartousi Biozone,
dated at 128.63 Ma (Morris et al. 2018).
Node 1 | CG Spermatophyta | 308.14 Ma – 365.629 Ma.
Fossil taxon and specimen. Cordaixylon iowensis [ OUPH 9616-9742 and UIC
12,233: Ohio University Paleobotanical Herbarium, Department of Botany, Ohio
University, Athens, Ohio ] from coal balls from the Laddsdale Coal, Lower Cherokee
Group, Desmoinesian (upper Moscovian – Kasimovian), Middle – Upper
Pennsylvanian (Carboniferous), near What Cheer, Iowa (Trivett 1992).
Phylogenetic justification. Clarke et al. (2011) confirm cordaitean coniferophytes as
the oldest records of the crown group of the Acrogymnospermae clade. Afterwards,
they rely on cordaitean taxa that are known from whole-plant reconstructions which
have informed cladistic analyses, the oldest of which is Cordaixylon iowensis from
the Laddsdale Coals (Cherokee Group, Desmoinesian) near What Cheer, Iowa
(Trivett 1992).
Minimum age. 308.14 Ma
Maximum age. 365.629 Ma
Age justification. Following Morris et al. (2018) and Barba-Montoya et al. (2018),
we use 308.14 Ma as the minimum constraint of Cordaixylon iowensis and 365.625
Ma as the maximum age of this node.
Node 2 | CG Gymnosperm | 308.14 Ma – 365.629 Ma.
Fossil taxon and specimen. Cordaixylon iowensis [ OUPH 9616-9742 and UIC
12,233: Ohio University Paleobotanical Herbarium, Department of Botany, Ohio
University, Athens, Ohio ] from coal balls from the Laddsdale Coal, Lower Cherokee
Group, Desmoinesian (upper Moscovian – Kasimovian), Middle – Upper
Pennsylvanian (Carboniferous), near What Cheer, Iowa (Trivett 1992).
Phylogenetic justification. Clarke et al. (2011) confirm cordaitean coniferophytes as
the oldest records of the crown group of the Acrogymnospermae clade. Afterwards,
they rely on cordaitean taxa that are known from whole-plant reconstructions which
have informed cladistic analyses, the oldest of which is Cordaixylon iowensis from
the Laddsdale Coals (Cherokee Group, Desmoinesian) near What Cheer, Iowa
(Trivett 1992).
Minimum age. 308.14 Ma
Maximum age. 365.629 Ma
Age justification. Following Morris et al. (2018) and Barba-Montoya et al. (2018),
we use 308.14 Ma as the minimum constraint of Cordaixylon iowensis and 365.625
Ma as the maximum age of this node.
Node 3 | CG Angiospermae | 125 Ma – 247.2 Ma.
Fossil taxon and specimen. Tricolpate pollen grain from sample BRN 126 of the
middle Atherfield Wealden Bed 35, corresponding to the mid- to late Barremian in the
Early Cretaceous succession in southern and eastern England (Hughes and McDougall
1990).
Phylogenetic justification. Magallón et al. (2015) identify that the oldest fossil
tricolpate pollen grains lack any distinctive features to link them to a particular living
group within eudicots and these grains should be used to calibrate the stem node of
eudicots. As there are no confirmed fossils which are order than them within
Angiospermae, Tricolpate pollen grain is regarded as the earliest unequivocal
evidence of angiosperms.
Minimum age. 125 Ma
Maximum age. 247.2 Ma
Age justification. Following Morris et al. (2018), we use 125 Ma as the minimum
constraint of tricolpate pollen grain and 247.2 Ma as the maximum age of this node.
Node 4 | SG Cabombaceae | 110.87 Ma – 247.2 Ma.
Fossil taxon and specimen. Pluricarpellatia peltata [ MB. Pb. 2000/80: Museum of
Natural History, Berlin,Germany], from the Crato Formation of Brazil (Mohr et al.
2008).
Phylogenetic justification. Taylor et al. (2008) identify Pluricarpellatia peltata is the
member of Cabomba.
Minimum age. 110.87 Ma
Maximum age. 247.2 Ma
Age justification. Following Barba-Montoya et al. (2018), we use 110.87 Ma as the
minimum constraint of Pluricarpellatia peltata.
Node 5 | Nymphaeales – [Austrobaileyales + Mesangiospermae] | 125 Ma – 247.2
Ma.
Fossil taxon and specimen. Tricolpate pollen grain from sample BRN 126 of the
middle Atherfield Wealden Bed 35, corresponding to the mid- to late Barremian in the
Early Cretaceous succession in southern and eastern England (Hughes and McDougall
1990).
Phylogenetic justification. Magallón et al. (2015) identify that the oldest fossil
tricolpate pollen grains lack any distinctive features to link them to a particular living
group within eudicots and these grains should be used to calibrate the stem node of
eudicots. However, there are no confirmed fossils which are order than them within
this group. Tricolpate pollen grain is the earliest unequivocal evidence of this group.
Minimum age. 125 Ma
Maximum age. 247.2 Ma
Age justification. Following Morris et al. (2018), we use 125 Ma as the minimum
constraint of tricolpate pollen grain and 247.2 Ma as the maximum age of this node.
Node 6 | Austrobaileyales – Mesangiospermae | 125 Ma – 247.2 Ma.
Fossil taxon and specimen. Tricolpate pollen grain from sample BRN 126 of the
middle Atherfield Wealden Bed 35, corresponding to the mid- to late Barremian in the
Early Cretaceous succession in southern and eastern England (Hughes and McDougall
1990).
Phylogenetic justification. Magallón et al. (2015) identify that the oldest fossil
tricolpate pollen grains lack any distinctive features to link them to a particular living
group within eudicots and these grains should be used to calibrate the stem node of
eudicots. However, there are no confirmed fossils which are order than them within
this group. Tricolpate pollen grain is the earliest unequivocal evidence of this group.
Minimum age. 125 Ma
Maximum age. 247.2 Ma
Age justification. Following Morris et al. (2018), we use 125 Ma as the minimum
constraint of tricolpate pollen grain and 247.2 Ma as the maximum age of this node.
Node 7 | CG Mesangiospermae | 125 Ma – 247.2 Ma.
Fossil taxon and specimen. Tricolpate pollen grain from sample BRN 126 of the
middle Atherfield Wealden Bed 35, corresponding to the mid- to late Barremian in the
Early Cretaceous succession in southern and eastern England (Hughes and McDougall
1990).
Phylogenetic justification. Magallón et al. (2015) identify that the oldest fossil
tricolpate pollen grains lack any distinctive features to link them to a particular living
group within eudicots and these grains should be used to calibrate the stem node of
eudicots. However, there are no confirmed fossils which are order than them within
Mesangiospermae. Tricolpate pollen grain is the earliest unequivocal evidence of
Mesangiospermae.
Minimum age. 125 Ma
Maximum age. 247.2 Ma
Age justification. Following Morris et al. (2018), we use 125 Ma as the minimum
constraint of tricolpate pollen grain and 247.2 Ma as the maximum age of this node.
Node 8 | CG Monocots | 113 Ma – 247.2 Ma.
Fossil taxon and specimen. Liliacidites sp. A [palynological slide 71-8-1d], from the
Potomac Group, Albian Zone I (Early Cretaceous), at the Trent’s Reach Locality,
Virginia, USA (Hickey and Doyle 1977; Doyle et al. 2008).
Phylogenetic justification. By using a morphological data set of basal angiosperms
and assuming relationships among living taxa derived from morphological and
molecular data, Doyle et al. (2008) support a monocot affinity for Liliacidites. The
pollen assigned to Liliacidites can represent the stem of monocots (Doyle et al. 2008).
Morris et al. (2018) consider it as the oldest secure record of the monocot total group.
Minimum age. 113 Ma
Maximum age. 247.2 Ma
Age justification. Morris et al. (2018) use the Aptian-Albian boundary to calibrate
these earliest records of Liliacidites, according to the absence of further stratigraphic
constraint. Thus, we use 113 Ma to calibrate the minimum age of this node
(International Chronostratigraphic Chart, v.2019/05).
Node 9 | CG Alismatales | 96.24 Ma – 247.2 Ma.
Fossil taxon and specimen. Mayoa portugallica [S136663: Swedish Museum of
Natural History Palaeobotanical Collection], from the Torres Vedras flora of the
Figueira da Foz Formation (Friis et al. 2004).
Phylogenetic justification. Following Friis et al. (2004), Mayoa portugallica is
assigned to the tribe Spathiphylleae of the extant monocotyledonous family Araceae.
Similarly, Magallón et al. (2013) propose that these striate and inaperturate pollen
grains of Mayoa portugallica are similar in detail to those of Monsteroideae (Araceae),
such as Holochlamys and Spathiphyllum. We here use it to calibrate the crown group
of Alismatales.
Minimum age. 96.24 Ma
Maximum age. 247.2 Ma
Age justification. Barba-Montoya et al. (2018) consider that an unequivocal
minimum age is provided by the appearance of ostracod Fossocytheridea merlensis in
the overlying Canecas Formation, attributable to the base of the Middle Cenomanian,
which coincides with the base of the Conlinoveras gilberti Zone, dated to 96.24 Ma.
Node 10 | CG Araceae | 76.0 Ma – 247.2 Ma.
Fossil taxon and specimen. Lysichiton (Araciphyllites) austriacus [NHMW
1999B0057/0183: Natural History Museum, Vienna, Austria], from the Grünbach
Formation of Austria (Bogner et al. 2007).
Phylogenetic justification. Bogner et al. (2007) confirm that the fossil is a
representative member of the subfamily Orontioideae (family Araceae).
Minimum age. 76 Ma
Maximum age. 247.2 Ma
Age justification. Following Barba-Montoya et al. (2018), we use 76.0 Ma as the
minimum age of this node, corresponding to the UC15-UC16 boundary.
Node 11 | SG Musaceae | 74.6 Ma – 247.2 Ma.
Fossil taxon and specimen. Isolated seeds and groups of seeds assigned to
Spirematospermum chandlerae (Friis 1988), from the Neuse River locality, Black
Creek Formation, southwest of Goldsboro, Wayne County, North Carolina, USA.
Phylogenetic justification. Following Barba-Montoya et al. (2018), they use
Spirematospermum chandlerae to calibrate the stem node of Musaceae based on
previous studies. We use it to constraint the stem node of Musaceae.
Minimum age. 74.6 Ma
Maximum age. 247.2 Ma
Age justification. Following Barba-Montoya et al. (2018), we use 74.6 Ma as the
minimum age of this node, corresponding to the age of Black Creek Formation.
Node 12 | CG Poaceae | 66.0 Ma– 247.2 Ma .
Fossil taxon and specimen. Changii indicum [Holotype: slide 13160; Coordinates:
Q-14-3], from coprolites from Red clays, Lameta Formation, Pisdura East and Pisdura
South (Prasad et al. 2011).
Phylogenetic justification. Prasad et al. (2011) reveal that Changii indicum is most
likely a member of the Oryzeae. Iles et al. (2015) identify that it is suitable for dating
the stem node of Oryzeae or the crown node of Ehrhartoideae.
Minimum age. 66.0 Ma
Maximum age. 247.2 Ma
Age justification. Following Iles et al. (2015), we use the upper boundary of the
Maastrichtian as the minimum age of Changii indicum (International
Chronostratigraphic Chart, v.2019/05), according as it was recovered from dinosaur
coprolites in horizons containing dinosaur bones.
Node 13 | SG Winteraceae | 125 Ma – 247.2 Ma.
Fossil taxon and specimen. Dispersed pollen tetrads assigned to Walkeripollis
gabonensis described by Doyle et al. (1990) from sample 2963 (939-944 m) in the
N’Toum No. 1well, Gabon, from the upper part of Elf-Aquitaine palynozone C-VII.
Phylogenetic justification. Doyle and Endress (2010) use a morphological dataset for
living basal angiosperms to assess the most parsimonious positions of early
angiosperm fossils on cladograms of Recent plants. They confirm that Walkeripollis
gabonensis is sister to Winteraceae, which can be used to calibrate the Winteraceae
stem group.
Minimum age. 125 Ma
Maximum age. 247.2 Ma
Age justification. The more recent data (Doyle et al. 1990; Doyle 1992) suggest that
Walkeripollis gabonensis may be late Barremian. We here use 125 Ma as the
minimum constraint of Walkeripollis gabonensis, corresponding to the upper
boundary of the Barremian (International Chronostratigraphic Chart, v.2019/05).
Node 14 | CG Magnoliineae | 110.87 Ma – 247.2 Ma.
Fossil taxon and specimen. Endressinia brasiliana Mohr and Bernardes-de-Oliveira
(Mohr and Bernardes-de-Oliveira 2004) [MB. PB. 2001/1455; Museum of Natural
History, Institute of Paleontology, Berlin, Germany] consists of a branching axis with
attached simple, narrowly ovate leaves and several terminal small flowers, from the
Crato Formation, Brazil.
Phylogenetic justification. By summarizing the results of other studies, Massoni et
al. (2015) conclude that Endressinia brasiliana provides a safe minimum age for the
crown node of Magnoliineae .
Minimum age. 110.87 Ma
Maximum age. 247.2 Ma
Age justification. Massoni et al. (2015) propose a minimum age for Endressinia
brasiliana corresponding to the Aptian-Albian boundary, we here use 110.87 Ma as
the minimum constraint of this node (Morris et al. 2018).
Node 15 | CG Laurales | 107.59 Ma – 247.2 Ma.
Fossil taxon and specimen. Virginianthus calycanthoides Friis, Eklund, Pedersen
and Crane (Friis et al. 1994a) [PP43703], from the Albian of Puddledock, Virginia.
Phylogenetic justification. Friis et al. (1994a) support Virginianthus calycanthoides
as the stem lineage of Calycanthaceae, while Crepet et al. (2005) consider it as the
sister lineage of entire Laurales or core Laurales (entire Laurales except
Calycanthaceae). Although the most parsimonious position of Virginianthus
calycanthoides remains controversial, Massoni et al. (2015) believe Virginianthus
provides a minimum age for the crown node of Laurales following the result of Doyle
et al. (2008).
Minimum age. 107.59 Ma
Maximum age. 247.2 Ma
Age justification. Massoni et al. (2015) consider Virginianthus is of middle Albian
age and use the middle-late Albian boundary to calibrate the minimum age for
Virginianthus. We here use 107.59 Ma to constrain the minimum age of the
Laurales’s crown node.
Node 16 | CG core Laurales | 107.59 Ma – 247.2 Ma.
Fossil taxon and specimen. Cohongarootonia hispida von Balthazar, Crane,
Pedersen, and Friis (von Balthazar et al. 2011), from the Puddledock Flora.
Phylogenetic justification. Massoni et al. (2015) believe that Cohongarootonia
hispida provides a minimum age for the crown node of core Laurales (entire Laurales
excluding Calycanthaceae).
Minimum age. 107.59 Ma
Maximum age. 247.2 Ma
Age justification. Massoni et al. (2015) consider that Cohongarootonia hispida is of
middle Albian age, and they use the middle-late Albian boundary to calibrate the
minimum age for it. We here use 107.59 Ma to constrain the minimum age of the core
Laurales’s crown node.
Node 17 | SG Hedyosmum | 121 Ma – 247.2 Ma.
Fossil taxon and specimen. Trigonous flowers/fruits with attached Asteropollis
pollen from the Torres Vedras locality, Estremadura Region, Portugal (Friis et al.
1994b, 1999).
Phylogenetic justification. Based on substantial morphological and structural
similarities of the flowers and attached pollen with extant Hedyosmum (Friis et al.
1994b, 1999), and combining with the phylogenetic result of Eklund et al. (2004), it
can represent a crown group member or stem representative of Hedyosmum
(Magallón et al. 2015).
Minimum age. 121 Ma
Maximum age. 247.2 Ma
Age justification. The Torres Vedras locality is considered to correspond to the late
Barremian to early Aptian (Heimhofer et al. 2007). Magallón et al. (2015) use 120.7
Ma (the lower third part of the Aptian) as its minimum age. Hence, we use 121 Ma
(the lower third part of the Aptian) as its minimum age (International
Chronostratigraphic Chart, v.2019/05).
Node 18 | CG Eudicots | 119.6 Ma – 128.63 Ma.
Fossil taxon and specimen. Hyrcantha decussata [NJU-DES02-001: Geological
Institute, Chinese Academy of Sciences, Beijing], from the lower part of the Yixian
Formation, Jehol Group, Aptian (Early Cretaceous), from the Liaoning Province,
China (Dilcher et al. 2006).
Phylogenetic justification. Hyrcantha karatscheensis from western Kazakhstan and
the species Hyrcantha decussata have many fairly similar characteristics. Dilcher et al.
(2006) report that there is great similarity among Hyrcantha karatscheensis,
Hyrcantha decussata and Sinocarpus decussatus Leng et Friis. Moreover, these taxa
should be combined with the genus Hyrcantha. And Hyrcantha could be considered
as a stem lineage of Ranunculaceae (Wang et al.2016). Following Morris et al. (2018),
we here use Hyrcantha decussata to calibrate the stem node of Ranunanlales (crown
node of Eudicots).
Minimum age. 119.6 Ma
Maximum age. 128.63 Ma
Age justification. Morris et al. (2018) establish a minimum constraint of 119.6 Ma
based on the Jiufontang Formation.
Node 19 | CG Ranunanlales | 113 Ma – 128.63 Ma.
Fossil taxon and specimen. Teixeiraea lusitanica, spec. nov., von Balthazar,
Pedersen and Friis (von Balthazar et al. 2005) [S125001 (from sample vale de Agua 364)], from the Farmalicão locality of the Figueira da Foz Formation. Phylogenetic justification. Floral morphology and pollen structure of Teixeiraea
lusitanica suggest a closer relationship to Ranunculales (von Balthazar et al. 2005).
Magallón et al. (2015) consider it to be a stem lineage member of the least inclusive
clade which included all these extant families. Hence, we use it to constrain crown
node of Ranunculales.
Minimum age. 113 Ma
Maximum age. 128.63 Ma
Age justification. Friis et al. (2011) identify that Teixeiraea lusitanica was from the
late Aptian, and Magallón et al. (2015) use the upper boundary of the Aptian as the
minimum age. Following these analyses, we here use 113 Ma to calibrate the
minimum constraint of this node (International Chronostratigraphic Chart, v.2019/05).
Node 20 | CG Proteales | 107.59 Ma – 128.63 Ma.
Fossil taxon and specimen. Aquia brookensis [PP4295: Field Museum, Chicago IL,
USA] described by Crane et al. (1993) from the Potomac Formation at Bank, near
Brooke, Virginia, USA.
Phylogenetic justification. Doyle (2015) identifies Aquia (including Sapindopsis
variabilis, Platanocarpus brookensis, Aquia brookensis) as a stem group member of
the genus Platanus.
Minimum age. 107.59 Ma
Maximum age. 128.63 Ma
Age justification. From Barba-Montoya et al. (2018), they establish a minimum
constraint for Proteales corresponding to the middle-late Albian Boundary. Thus, we
here use 107.59 Ma as the minimum constraint of this node.
Node 21 | SG Buxales | 100.5 Ma – 128.63 Ma.
Fossil taxon and specimen. Spanomera marylandensis sp. nov. [PP42978: Field
Museum, Chicago IL, USA] (Drinnan et al. 1991), from Elk Neck beds, Potomac
Group, Mauldin Mountain, northeastern Maryland, USA.
Phylogenetic justification. Drinnan et al. (1991) identify Spanomera marylandensis
as a member of Spanomera, and morophological and structural features of Spanomera
suggest a relationship with Buxaceae. Doyle and Endress (2010) confirm that the best
position of Spanomera is sister to Buxaceae.
Minimum age. 100.5 Ma
Maximum age. 128.63 Ma
Age justification. Spanomera marylandensis sp. nov. was from the late Albian
Patapsco Formatio (Drinnan et al. 1991) and we use the upper limit of the Albian as
the minimum constraint of this node (International Chronostratigraphic Chart,
v.2019/05).
Node 22 | CG Dilleniales | 47.8 Ma – 128.63 Ma.
Fossil taxon and specimen. Seeds similar to Hibbertia and Tetracera (Chandler
1964), from the Early Eocene of England, UK.
Phylogenetic justification. The phylogenetic relationships of these seeds have been
clarified by Magallón et al. (2015), considering them as the crown node of
Dilleniaceae.
Minimum age. 47.8 Ma
Maximum age. 128.63 Ma
Age justification. Following Magallón et al. (2015), we use the upper boundary of
the Early Eocene (47.8 Ma) to constrain the minimum age of this node (International
Chronostratigraphic Chart, v.2019/05).
Node 23 | CG Caryophyllales | 72.1 Ma – 128.63 Ma.
Fossil taxon and specimen. Fossil infructescences and fruits assigned to
Coahuilacarpon phytolaccoides Cevallos-Ferriz, Estrada-Ruiz et Pérez-Hernández,
from the Cerro del Pueblo Formation, Coahuila, Mexico (Cevallos-Ferriz et al. 2008)
[Colecci�n Nacional de Paleontolog�a, Instituto de Geolog�a, Universidad Nacional
Aut�noma de M�xico, catalogue no. IGM-PB 1244].
Phylogenetic justification. Cevallos-Ferriz et al. (2008) report the fossil
Coahuilacarpon phytolaccoides has many similar morphological and anatomical
characters with those found in Caryophyllales, particularly in Phytolaccaceae.
Minimum age. 72.1 Ma
Maximum age. 128.63 Ma
Age justification. The plants represented by infructescences contained in the
sediments grew during the late Campanian based on its stratigraphic position and
sedimentary correlation (Cevallos-Ferriz et al. 2008). Thus, we use the upper
boundary of the Campanian as the minimum constraint of this node (International
Chronostratigraphic Chart, v.2019/05).
Node 24 | SG Hydrangeaceae | 89.8 Ma – 128.63 Ma.
Fossil taxon and specimen. Flowers assigned to Tylerianthus crossmanensis
Gandolfo, Nixon et Crepet, sp. nov. Generic, from Old Crossman Pit, Raritan
Formation, New Jersey, USA (Gandolfo et al. 1998a) [CUPC 1047].
Phylogenetic justification. Gandolfo et al. (1998a) compare the characters of these
flowers assigned to Tylerianthus crossmanensis with those of extant flowers (form
several families of the saxifragalean complex). They find that these flowers have a
close relationship with extant members of the Saxifragaceae and Hydrangeaceae.
Magallón et al. (2015) consider Tylerianthus crossmanensis to be related to
Hydrangeaceae and use it to calibrate the stem node of Hydrangeaceae.
Minimum age. 89.8 Ma
Maximum age. 128.63 Ma
Age justification. Gandolfo et al. (1998a) identify that Tylerianthus crossmanensis is
dated back to the Turonian on the basis of palynology. We here use the upper
boundary of the Turonian as the minimum age of this fossil (International
Chronostratigraphic Chart, v.2019/05).
Node 25 | CG Ericales | 89.8 Ma – 128.63 Ma.
Fossil taxon and specimen. Pentapetalum trifasciculandricus Martínez-Millán,
Crepet et Nixon gen.et sp.nov. (Martínez-Millán et al. 2009), from Old Crossoman
Clay Pit locality of Sayreville, New Jersey [Holotype: part CUPC579 and counterpart
CUPC591].
Phylogenetic justification. Martínez-Millán et al. (2009) compare Pentapetalum
trifasciculandricus with extant taxa by using traditional methods of identification and
support a relation with the Theaceae (Stewartia). However, the phylogenetic analyses
propose a different view and support another relationship to the
Ternstroemiaceae/Pentaphylacaceae. Magallón et al. (2015) follow the explicit
phylogenetic results that are consistent with other assignments, and use Pentapetalum
trifasciculandricus to calibrate the crown node of Ericales.
Minimum age. 89.8 Ma
Maximum age. 128.63 Ma
Age justification. Pentapetalum trifasciculandricus is dated back to the Turonian of
New Jersey in North America (Martínez-Millán et al. 2009). We here use the upper
boundary of the Turonian as the minimum age of this fossil (International
Chronostratigraphic Chart, v.2019/05).
Node 26 | SG Asteraceae | 47.5 Ma – 128.63 Ma.
Fossil taxon and specimen. Raiguenrayun cura Barreda, Katinas, Passalia &
Palazzesi sp. nov. (Barreda et al. 2012), from Río Pichileufú fossil-bearing strata,
Huitara Formation, Argentina [Specimen MLG 1156: ‘Museo del Lago Gutiérrez Dr.
Rosendo Pascual de Geología y Paleontología’ Villa Los Coihues, San Carlos de
Bariloche, Río Negro Province, Argentina].
Phylogenetic justification. The extinct taxa Raiguenrayun cura doesn’t match
exactly any living member of the family. This taxa is closely related to the root of
Asteraceae and is the oldest well-dated member of Asteraceae (Barreda et al. 2012).
Minimum age. 47.5 Ma
Maximum age. 128.63 Ma
Age justification. Wilf et al. (2005) constrain the age of Río Pichileufú fossil-bearing
strata about 47.46 ± 0.05 Ma based on radiometric data. Thus, we use 47.5 Ma as the
minimum age of this fossil.
Node 27 | SG Aquifoliaceae | 61.6 Ma – 128.63 Ma .
Fossil taxon and specimen. Seed assigned to Ilex hercynica Mai, from Gonna,
Germany (Mai 1970) [MAI, Nr. 6004: Zentralsammlung Zentrales Geologisches
Institut Berlin].
Phylogenetic justification. The seeds assigned to Ilex hercynica can be used as the
reliable fossils of Aquifoliaceae (Martínez-Millán et al. 2010). Magallón et al. (2015)
use it to calibrate the stem node of Aquifoliaceae.
Minimum age. 61.6 Ma
Maximum age. 128.63 Ma
Age justification. Martínez-Millán et al. (2010) consider the fossil Ilex hercynica as
the member of the Early Paleocene fossils. We use the upper boundary of the Early
Paleocene (Danian) to calibrate the minimum age of this node (International
Chronostratigraphic Chart, v.2019/05).
Node 28 | CG Solanales | 37.3 Ma – 128.63 Ma.
Fossil taxon and specimen. Solanites crassus [USNM-39949: Smithsonian
Institution National Museum of Natural History, Washington DC, USA], from Holly
Springs sand, Mill Creek, railroad cut north of Shandy, Hardeman County, Tenn
(Berry 1930).
Phylogenetic justification. Berry (1930) find that these flowers assigned to Solanites
crassus resemble those of several genera of the Solanaceae and they are clearly
referable to this family.
Minimum age. 37.3 Ma
Maximum age. 128.63 Ma
Age justification. From Barba-Montoya et al. (2018), they use 37.3 Ma to constrain
the minimum age of Solanites crassus based on the combined age model of
Vandenberghe et al. (2012).
Node 29 | SG Lamiaceae | 27.82 Ma – 128.63 Ma.
Fossil taxon and specimen. Fruits assigned to Ajuginucula smithii Reid et Chandler
and Melissa parva Reid et Chandler (Reid and Chandler 1926), from Bembridge,
England.
Phylogenetic justification. Martínez-Millán et al.. (2010) propose that the fruits from
the Bembridge flora in England are the oldest fossils of Lamiaceae. We here use them
to calibrate the node between Lamiaceae and Phrymaceae.
Minimum age. 27.82 Ma
Maximum age. 128.63 Ma
Age justification. Martínez-Millán et al.. (2010) identify these fossils from the
Early-Middle Oligocene. Thus, we use 27.82 Ma as the minimum constraint of this
node, corresponding to the upper boundary of Early Oligocene (International
Chronostratigraphic Chart, v.2019/05).
Node 30 | CG Vitaceae | 65.508 Ma – 128.63 Ma.
Fossil taxon and specimen. Fruits and seeds assigned to Indovitis chitaleyae
(Manchester et al. 2013) [UF19279-56220: Florida Museum of Natural History (UF)
Gainesville, Florida, USA], from serial sections and peels of chert from the Deccan
Intertrappean beds of central India.
Phylogenetic justification. Indovitis chitaleyae is conformed closely to extant Vitis in
a suite of characters and it is the oldest known fossil occurrence of Vitaceae
(Manchester et al. 2013).
Minimum age. 65.508 Ma
Maximum age. 128.63 Ma
Age justification. From Barba-Montoya et al. (2018), they consider that the minimum
age of Indovitis chitaleyae can be constrained by the minimum age of Deccan
volcanism, which is constrained to 65.535 Ma ± 0.027 Myr (Schoene et al. 2015),
thus, 65.508 Ma.
Node 31 | SG Hamamelidaceae | 83.6 Ma – 128.63 Ma.
Fossil taxon and specimen. Flowers assigned to Allonia decandra Magallón-Puebla,
Herendeen & Endress [PP44595: Paleobotanical Collections of the Field Museum,
Chicago], and to Androdecidua endressi Magallón, Herendeen & Crane, from the
Allon locality, Buffalo Creek Member, Gaillard Formation, Georgia, USA
(Magallón-Puebla et al. 1996; Magallón et al. 2001).
Phylogenetic justification. Magallón-Puebla et al. (1996) identify that Allonia is
closely related to the extant genus Maingaya based on morphological characters.
Magallón et al. (2001) suggest a relationship between Androdecidua and
Hamamelidaceae. Following Magallón et al. (2015), they consider these two genera as
the sister taxa to Hamamelis and use them to calibrate the crown node of
Hamamelidaceae. We here use these fossils to calibrate the node between
Hamamelidaceae and Cercidiphyllaceae.
Minimum age. 83.6 Ma
Maximum age. 128.63 Ma
Age justification. From Magallón et al. (2015), they use the upper boundary of the
Santonian to constraint the minimum age of this fossil, thus we use 83.6 Ma
corresponding to this boundary (International Chronostratigraphic Chart, v.2019/05).
Node 32 | SG Juglandaceae plus Myricaceae | 83.6 Ma – 128.63 Ma.
Fossil taxon and specimen. Three types of fossil flowers and fruits that are referred
to Caryanthus (Sims et al. 1999), from the upper Santonian (Upper Cretaceous)
Buffalo Creek Member of the Gaillard Formation in central Georgia, USA.
Phylogenetic justification. Sims et al. (1999) identify these types of fossil flowers
and fruits (from the Gaillard Formation in central Georgia, USA) are referred to
Caryanthus. Magallón et al. (2015) consider that Caryanthus is more closely related
to Rhoipteleaceae, Myricaceae and Juglandaceae, and they use these fossils to
calibrate the stem node of the clade including Juglandaceae and Myricaceae.
Minimum age. 83.6 Ma
Maximum age. 128.63 Ma
Age justification. These types of fossil flowers and fruits are identified from the
upper Santonian by Sims et al. (1999). We here use 83.6 Ma, corresponding to the
upper boundary of the Santonian, as the minimum age of this node (International
Chronostratigraphic Chart, v.2019/05).
Node 33 | SG Fabaceae | 56.0 Ma – 128.63 Ma.
Fossil taxon and specimen. Infructescence and fruits assigned to Leguminocarpon
gardneri (Herendeen and Crane 1992), from the Reading Formation, England.
Phylogenetic justification. Herendeen and Crane (1992) find some features observed
in Leguminocarpon gardneri are similar with those of different genera within
Caesalpinioiideae. Magallón et al. (2015) use it to calibrate the stem node of
Fabaceae.
Minimum age. 56.0 Ma
Maximum age. 128.63 Ma
Age justification. Herendeen and Crane (1992) confirm these infructescence and
fruits assigned to Leguminocarpon gardneri are dated back to the Paleocene. Hence,
we use 56.0 Ma to calibrate the minimum age of this node, corresponding to the
boundary of the Paleocene (International Chronostratigraphic Chart, v.2019/05).
Node 34 | CG Celastraceae | 37.8 Ma – 128.63 Ma.
Fossil taxon and specimen. Leaves of Celastrus from the Green River Flora, USA
(MacGinitie 1969).
Phylogenetic justification. Only leaf fossils have been reported in Celastraceae
(Taylor 1990). The phylogenetic relationships of these leaves have been discussed by
Magallón et al. (2015).
Minimum age. 37.8 Ma
Maximum age. 128.63 Ma
Age justification. MacGinitie (1969) identifies that these leaves assigned to Celastrus
are dated back to Middle Eocene. Hence, we use 37.8 Ma to calibrate the minimum
age of this node, corresponding to the boundary of the Middle Eocene (International
Chronostratigraphic Chart, v.2019/05).
Node 35 | SG Elaeocarpaceae | 61.6 Ma – 128.63 Ma.
Fossil taxon and specimen. Sloanea ungeri (Heer) Manch. & Z. Kva cek comb. n.
(Manchester and Kvaček 2009), from the Great Plains regions of North America, in
sediments from early Paleocene (Puercan) to late Paleocene (Tiffanian) of Wyoming
and Montana; and from the Early Eocene of the Wind River Formation.
Phylogenetic justification. Manchester and Kvaček (2009) confirm that fruits
assigned to Sloanea ungeri have a close relationship with those of extant Sloanea, in
terms of shape and number of values. We use these fossils to calibrate the node
between Elaeocarpaceae and Oxalidaceae.
Minimum age. 61.6 Ma
Maximum age. 128.63 Ma
Age justification. From Magallón et al. (2015), they use the upper boundary of the
Danian (Lower Paleocene) to constrain the minimum age of this fossil, then we use
61.6 Ma corresponding to this boundary (International Chronostratigraphic Chart,
v.2019/05).
Node 36 | CG Rutaceae | 66.0 Ma – 128.63 Ma.
Fossil taxon and specimen. Seeds assigned to Rutaspermum biornatum Knobloch &
Mai from Walbeck, Germany, corresponding to the Maastrichtian (Knobloch & Mai,
1986).
Phylogenetic justification. The phylogenetic relationships of these seeds have been
discussed by Magallón et al. (2015). They acknowledge that these seeds are the oldest
representatives of Rutaceae and use them to calibrate the crown node of Rutaceae.
Minimum age. 66.0 Ma
Maximum age. 128.63 Ma
Age justification. From Magallón et al. (2015), they use the upper boundary of the
Maastrichtian to constrain the minimum age of this fossil, then we use 66.0 Ma
corresponding to this boundary (International Chronostratigraphic Chart, v.2019/05).
Node 37 | SG Brassicales | 89.8 Ma – 128.63 Ma.
Fossil taxon and specimen. Flowers assigned to Dressiantha bicarpelata Gandolfo,
Nixon & Crepet (Gandolfo et al. 1998b), from the Old Crossman Clay Pit, Raritan
Formation, New Jersey, USA.
Phylogenetic justification. The fossil species has unique suite of characters that are
found in extant families of the Order Capparales. Hence, Dressiantha bicarpelata
constitutes the oldest fossil record for this order (Gandolfo et al. 1998b). Magallón et
al. (2015) consider it as a stem or crown member of Brassicales. We here use it to
calibrate the stem node of Brassicales.
Minimum age. 89.8 Ma
Maximum age. 128.63 Ma
Age justification. The fossils were collected from outcrops of the Raritan Formation
and the age of the formation was calculated as Turonian (Gandolfo et al. 1998b).
Therefore, we use the upper boundary of the Turonian as the minimum constraint of
this node.
Node 38 | CG Brassicaceae | 23.03 Ma – 128.63 Ma.
Fossil taxon and specimen. Fruits assigned to Thlaspi primaevum Becker (Becker
1961), from the Ruby River Basin, Montana, USA.
Phylogenetic justification. Becker (1961) assigned Thlaspi primaevum to the extant
genus Thlaspi (Brassicaceae), and Beilstein et al. (2010) further support this
justification.
Minimum age. 23.03 Ma
Maximum age. 128.63 Ma
Age justification. Thlaspi primaevum is an Oligocene fossil with angustiseptate
winged fruits from the Ruby Basin Flora of southwestern Montana (Becker 1961;
Beilstein et al. 2010). Thus, we use the upper boundary of the Oligocene as the
minimum constraint of this node (International Chronostratigraphic Chart, v.2019/05).
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