supplemental information for€¦ · mimulus guttatus tamarix chinensis vaccinium corymbosum...

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

mailto:[email protected]

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


Trigonotis peduncularis

Cuscuta reflexa

Cabomba caroliniana


Euonymus carnosus

Musa acuminata

Dimocarpus longan

Dipsacus laciniatus


Yucca filamentosa


Houttuynia cordata

Distylium buxifolium

Lilium brownii


Lactuca sativa


Mentha canadensis

Nandina domestica

Panicum virgatum

Ligusticum striatum

Oxalis corniculata

Tamarix chinensis

Boehmeria nivea

Lonicera japonica


Aristolochia tagala

Cissus microcarpa

Opuntia dillenii

Aquilegia coerulea



Rafflesia cantleyi

Dillenia turbinata

Eucalyptus grandis


Meliosma parviflora



Gunnera manicata


Dahlia pinnata

Smilax bona-nox

Avicennia marina


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


Gardenia jasminoides

Pandanus utilis

Ilex chinensis

Olea europaea

Saruma henryi


Linum usitatissimum

Dillenia indica


Hedyosmum orientale

Cirsium vulgare

Myristica fragrans

Ricinus communis

Juglans regia

Iris japonica

Sonchus asper

Setaria italica

Mimulus guttatus

Cichorium intybus

Pinellia ternata

Acorus americanus



Dionaea muscipula

Sorghum bicolor




Amborella tricopoda

Annona muricata

Oryza sativa

Tagetes erecta

Illicium henryi

Colchicum autumnale

Dioscorea opposita


Spirodela polyrhiza

Cedrela sinensis

Cinnamomum camphora

Peumus boldus


Arabidopsis lyrata

Stellaria media

Mirabilis jalapa


Citrus clementina

Aucuba japonica

Ginkgo biloba


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


Viscum ovalifolium

Capsella rubella


Bothriospermum chinense

Cornus wilsoniana

Dioscorea villosa

Cleome serrulata

Cayratia japonica

Santalum album


Manihot esculenta

Populus trichocarpa

Hippophae rhamnoidesPhaseolus vulgaris

Actinidia arguta


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

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

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


Dimocarpus longanCedrela sinensis

Citrus clementinaCitrus sinensis


Boehmeria nivea

Paeonia lactiflora

Eucalyptus grandis

Myrica rubraJuglans regia

Corylus avellanaCyclobalanopsis glauca

Phaseolus vulgarisGlycine max


Cercidiphyllum japonicumDistylium buxifolium

Leea guineensis

Ampelopsis cordata

Cissus microcarpaCayratia japonica


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


Lactuca sativa

Valeriana officinalisLonicera japonica

Dipsacus laciniatus


Cirsium vulgare

Sonchus asper


Artemisia annua

Dahlia pinnataTagetes erecta

Cichorium intybus

Dionaea muscipula

Camellia japonica



Actinidia arguta

Cornus wilsoniana


Dillenia indica

Delosperma cooperiPhytolacca americanaMirabilis jalapa

Tamarix chinensisPolygonum runcinatum

Stellaria media

Opuntia dillenii

Hedyosmum orientale

Ceratophyllum oryzetorumCeratophyllum demersum


Nandina domesticaAquilegia coerulea

Meliosma parviflora

Nelumbo nuciferaPlatanus × acerifolia

Buxus sinicaGunnera manicata

Dillenia turbinata

Peumus boldusGyrocarpus americanus

Persea borbonia

Litsea cubebaCinnamomum camphora


Sarcandra glabraChloranthus japonicus

Annona muricataEupomatia bennettii

Liriodendron chinense × tulipiferaMagnolia denudata


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


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


Cissus microcarpa

Yucca filamentosa

Phaseolus vulgaris

Canella winterana

Stellaria media

Dionaea muscipula

Nuphar advena


Musa acuminata

Manihot esculenta

Paeonia lactiflora

Pinus taeda

Phyla dulcis

Dillenia indica

Spirodela polyrhiza

Corylus avellana

Vitis vinifera

Dimocarpus longan



Gomortega keule

Annona muricata

Aristolochia tagala

Mirabilis jalapa

Olea europaea

Persea borbonia

Sorghum bicolor

Pandanus utilis


Saruma henryi

Dioscorea villosa

Colchicum autumnale



Zea mays

Acorus calamus


Cleome serrulata



Acorus americanus

Mimulus guttatus


Theobroma cacao

Euonymus carnosus

Litsea cubeba

Myristica fragrans

Cinnamomum camphora

Dahlia pinnata

Avicennia marina


Cuscuta reflexa


Aucuba japonica

Piper nigrum

Panicum virgatum



Apium graveolens

Arabidopsis lyrata

Artemisia annua

Nandina domestica

Ginkgo biloba

Dioscorea opposita

Ilex chinensis


Eucalyptus grandis


Sarcandra glabra


Juglans regia

Glycine max


Citrus clementina

Peumus boldus



Buxus sinica

Camellia japonica

Santalum album

Oryza sativa

Cornus wilsoniana

Brassica rapa


Rafflesia cantleyi

Gossypium raimondii


Meliosma parviflora

Linum usitatissimum

Delosperma cooperi

Canna indica

Citrus sinensis

Viscum ovalifolium

Sabal bermudana


Dillenia turbinata


Cayratia japonica

Tagetes erecta

Tamarix chinensis

Ampelopsis cordata

Drimys winteri


Ricinus communis

Carica papaya


Actinidia arguta

Gunnera manicata

Aquilegia coerulea

Populus trichocarpa


Setaria italica



Cabomba caroliniana


Hedera nepalensis

Lilium brownii

Lonicera japonica

Dipsacus laciniatus

Myrica rubra

Cichorium intybus


Smilax bona-nox

Eupomatia bennettii

Vinca major

Illicium henryi


Pinellia ternata

Magnolia denudata

Cedrela sinensis

Sonchus asper


Oxalis corniculata

Capsella rubellaEutrema salsugineum

Opuntia dillenii





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


Apium graveolens

Dipsacus laciniatus


Leea guineensis

Citrus sinensis



Spirodela polyrhiza

Ginkgo biloba

Eucalyptus grandis

Nelumbo nucifera

Canna indica

Delosperma cooperi


Cirsium vulgare



Myrica rubra

Ampelopsis cordata

Dioscorea villosa

Illicium henryi

Amborella tricopoda

Theobroma cacao

Stellaria media

Houttuynia cordata


Dahlia pinnataArtemisia annua

Meliosma parviflora

Cichorium intybus

Annona muricata


Yucca filamentosa

Colchicum autumnale


Cleome serrulata

Rafflesia cantleyi

Lonicera japonica

Gunnera manicata

Lilium brownii


Cissus microcarpa


Setaria italica


Aristolochia tagalaSaruma henryi

Sabal bermudana

Mimulus guttatus

Opuntia dillenii


Actinidia arguta

Canella winterana


Iris japonica

Dillenia indica

Olea europaea

Manihot esculenta



Smilax bona-nox

Tagetes erecta

Tamarix chinensis


Dillenia turbinata

Mirabilis jalapa

Magnolia denudata

Corylus avellana


Santalum album

Drimys winteri


Panicum virgatum

Piper nigrum

Pinus taeda

Dionaea muscipula

Eupomatia bennettii

Litsea cubeba

Eutrema salsugineum


Pandanus utilis


Linum usitatissimum

Sorghum bicolor


Vitis vinifera

Boehmeria nivea

Brassica rapa

Peumus boldus

Acorus calamus

Gossypium raimondii

Paeonia lactiflora

Pinellia ternata

Phaseolus vulgaris

Sarcandra glabra





Aquilegia coerulea

Mentha canadensis

Dimocarpus longan

Nandina domestica

Oxalis corniculata


Euonymus carnosus

Ilex chinensis

Capsella rubella

Hedyosmum orientale



Persea borbonia

Dioscorea opposita


Arabidopsis lyrata



Aucuba japonica

Hedera nepalensis


Viscum ovalifolium

Sonchus asper

Cuscuta reflexa

Nuphar advenaCabomba caroliniana

Oryza sativa

Cornus wilsoniana

Musa acuminata

Ligusticum striatum


Glycine max

Vinca major

Cedrela sinensis

Juglans regia

Ricinus communisPopulus trichocarpa

Citrus clementina

Carica papaya

Gomortega keule


Buxus sinica


Zea mays

Myristica fragrans

Phyla dulcis

Acorus americanus

Cayratia japonica


[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




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


Ricinus communis


Tamarix chinensis

Musa acuminata


Nuphar advena

Dionaea muscipula

Drimys winteri

Arabidopsis lyrata

Boehmeria nivea

Pinellia ternata

Dahlia pinnata

Pandanus utilis


Sorghum bicolor


Eucalyptus grandis

Illicium henryi

Nandina domestica

Myrica rubra

Cuscuta reflexa


Setaria italica

Acorus calamus

Santalum album

Glycine max

Cichorium intybus

Dillenia turbinata

Dioscorea villosa

Camellia japonica


Cinnamomum camphora

Peumus boldus


Cayratia japonica

Dioscorea opposita


Phyla dulcis

Paeonia lactiflora

Platanus acerifolia

Actinidia arguta


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


Rafflesia cantleyi

Tagetes erecta

Oxalis corniculata

Dillenia indica

Hedyosmum orientale

Hedera nepalensis

Euonymus carnosus

Annona muricata

Vinca major

Persea borbonia

Citrus sinensis




Ilex chinensis

Carica papaya

Lactuca sativa

Stellaria media





Sonchus asper

Piper nigrumAristolochia tagala

Magnolia denudata

Panicum virgatum

Iris japonica

Avicennia marina

Canella winterana

Mimulus guttatus


Cirsium vulgare


Ginkgo biloba


Eupomatia bennettii



Acorus americanus


Litsea cubeba

Eutrema salsugineum

Viscum ovalifolium

Pinus taeda

Theobroma cacao


Ligusticum striatum

Cissus microcarpa

Mentha canadensis

Dipsacus laciniatus



Manihot esculenta

Ampelopsis cordata

Houttuynia cordata


Spirodela polyrhiza

Mirabilis jalapa

Aquilegia coerulea


Yucca filamentosa



Buxus sinica


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

1/100

1/100

1/100

1/100

1/100

1/100

1/100

1/100

1/100

1/100

1/100

1/100

1/3

1/100

1/100

0.99/99

1/100

1/100

1/100

1/99

1/100

1/100

1/100 1/100

1/100

0.86/37

0.8/87

1/100

1/100

1/87

1/100

1/100

1/100

1/100

1/100

1/100

1/100

1/100

1/97

1/100

1/100

1/100

11/00

0.9/96

1/36

11/00

1/100

1/100

1/0

1/100

0.45/6

1/100

1/100

1/100

0.95/1

11/00

1/100

1/60

1/100

1/100

1/100

1/100

1/100

1/100

1/100

1/100

1/100

1/100

1/100

1/85

1/100

1/100

1/100

1/100

0.86/19

1/100

1/100

1/100

1/100

1/100

1/100

1/100

1/100

1/93

1/100

1/100

1/100

1/100

1/100

0.98/45

1/100

1/100

1/100

1/26

1/100

1/100

1/100

1/76

1/99

1/100

1/100

1/100

1/94

1/100

1/100

1/100

1/0

1/100

1/73

1/100

1/100

1/100

1/100

1/100

1/100

0.91/25

1/27

1/100

0.83/87

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

1/99

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).

●

●●

●

●

●●

●●

●

●

● ●●

●●

●

●

●●

●●

●

●

●

●

●●

● ●●

●

●●

●

● ●

●

● ●●

●●

●

●● ●●

●●

●

●●●

●●

●●●

●

●

●●

●●

● ●●

●

● ●

●

●●

●

●

●

●

●

●

●●

●

●

●●

●

●

●

●●

●

●

●

●

●●●

●

●

●●●

●● ●

●

●●

●

●

●

●

●

●

●

●

●

●●

●

●●●

●●

●

●

●

●

●●●

●

●

●

●

●

●●

●●●

●

●

●

●

●

●

●

● ●●

●●

●

●

●●

●

●

● ●

●

●

●

●

●

●

●●●

●●

●

●

●

●

●

● ●

●

●

●

●●

●

● ●●●●

●

●

●

●

●

●

●● ●

●

●●

●

●●

●

●●

●

●

●

●

●

●●

●●

●●

●

●

● ●

●

●

●

●●●

●

●

●

●

●

●

●

●

●

●

●

●

●

●

●● ●

●

●

●

●● ●●●

●

● ●●

●

●

●

●

●●

●

● ●

●●●

●

●● ●

●

●●

● ●●

●

●

●

●

●● ●

●

●

●●●

●

●●●● ●●●

●

●

400 300 200 100 0

0.0

0.1

0.2

0.3

0.4

0.5

0.6

a

Millions of years age (Ma)

substitu

tions/s

ite/1

0 years

6

●

●●

●

●

● ●

●●

●

●● ●

●●

●●●

●

●

●●

●

●

●

●

● ●●●

●

●

● ●

●● ●

●

●●●

●

●●

●●

●

●●●● ●

●● ●

●

●●●

●●

●

●●

●

●

●●

●

●●

●

●●●

●

●

●

●

●

●●●

●

●●

●

●

●

●●

● ●●

●●

●●●

●

●

●

●●● ●

●

●●

●

●

●

●

●

●

●

●

●

●●

●

●●●

●●

●

●

●

●

●●

●

●

●

●

●

●

●

●

●●●

●●

●

●●

●

●

●

●●

●●

●

●

●●

●

●●

●

●

●

●

●

●

●

●●●

●●

●

●

●

●●

●●

●●

●

●●

●

● ●●●●

●

●

●●

●

●

●● ●

●

●●

●

●●

●● ●

●

●

●

●

●

●

●●●

● ●

●●

●

●

●

●

●

●●●

●

●

●

●

●

●

●

●●

●

●

●

●

●

●●

●

●

●

●

●

●●

●●●●

●●

●

●

●

●

● ●

●●

●

●

●●● ●

● ●

●

●●

●

●●

●●● ●

●

●●●

●

● ●●

●

● ●●● ●●●●

●

400 300 200 100 0

0.0

0.5

1.0

1.5

2.0

2.5

3.0

Millions of years age (Ma)

substitu

tions/s

ite/1

0 years

6

b

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


Gossypium raimondii

Populus trichocarpa

Tamarix chinensis

Dillenia indica

Pinus taeda

Piper nigrum

Actinidia arguta

Meliosma parviflora

Euonymus carnosus


Hedyosmum orientale


Gomortega keule



Leea guineensis

Cissus microcarpa

Santalum album

Buxus sinica

Hedera nepalensis

Dipsacus laciniatus

Theobroma cacao


Annona muricata




Cedrela sinensis

Corylus avellana

Manihot esculenta


Myrica rubra

Phyla dulcis

Myristica fragrans


Dillenia turbinata


Ampelopsis cordata

Sarcandra glabra

Eucalyptus grandis

Illicium henryi


Eupomatia bennettii


Vitis vinifera

Juglans regia

Peumus boldus


Dimocarpus longan

Camellia japonica

Citrus sinensis




Citrus clementina

Avicennia marina

Olea europaea

Cornus wilsoniana

Lonicera 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

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.


Annona muricata


Lilium brownii

Pinus taeda


Cichorium intybus

Apium graveolens

Panicum virgatum

Cayratia japonica



Arabidopsis lyrata

Glycine max


Sonchus asper

Manihot esculenta

Boehmeria nivea

Artemisia annua

Linum usitatissimum

Myristica fragrans

Phyla dulcis

Hedyosmum orientale

Nandina domestica

Phaseolus vulgaris



Aquilegia coerulea


Spirodela polyrhiza

Cleome serrulata


Stellaria media


Dioscorea opposita

Zea mays

Yucca filamentosa

Myrica rubra

Acorus americanus

Dionaea muscipula

Camellia japonica

Populus trichocarpa

Nuphar advena


Piper nigrum

Mimulus guttatus

Carica papaya

Brassica rapa


Peumus boldus

Sorghum bicolor


Canna indica


Cuscuta reflexa



Tamarix chinensis

Colchicum autumnale

Delosperma cooperi

Buxus sinica

Aucuba japonica

Ligusticum striatum

Canella winterana

Cornus wilsoniana



Aristolochia tagala

Capsella rubella

Lactuca sativa

Citrus clementina

Lonicera japonica


Leea guineensis


Sabal bermudana

Vitis vinifera

Theobroma cacao

Oxalis corniculata

Saruma henryi


Actinidia arguta

Dillenia indica


Dahlia pinnata

Gossypium raimondii

Mirabilis jalapa


Persea borbonia

Dillenia turbinata

Ginkgo biloba

Mentha canadensis

Ricinus communis


Euonymus carnosus

Dipsacus laciniatus

Musa acuminata

Cirsium vulgare

Smilax bona-nox

Avicennia marina

Gunnera manicata

Opuntia dillenii

Corylus avellana


Juglans regia

Acorus calamus

Magnolia denudata

Tagetes erecta


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


Cinnamomum camphora



Cissus microcarpa

Dioscorea villosa

Meliosma parviflora

Olea europaea

Vinca major

Ampelopsis cordata

Gomortega keule

Rafflesia cantleyi





Houttuynia cordata

Setaria italica

Santalum albumViscum ovalifolium



Citrus sinensis


Ilex chinensis

Paeonia lactiflora

Pandanus utilis

Litsea cubeba



Eucalyptus grandis

350 300 250 200 150 100 50 0 (Ma)370

350 300 250 200 150 100 50 0 (Ma)370


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. 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


Hedera nepalensis

Gomortega keule

Persea borbonia

Mirabilis jalapa

Capsella rubella


Litsea cubeba


Canella winterana

Gossypium raimondii

Sarcandra glabra



Oxalis corniculata

Panicum virgatum

Eucalyptus grandis


Musa acuminata

Sorghum bicolor

Viscum ovalifolium


Avicennia marina

Buxus sinica

Artemisia annua

Lonicera japonica

Dimocarpus longan

Carica papaya


Leea guineensis

Phyla dulcis

Paeonia lactiflora


Acorus calamus

Lilium brownii

Santalum album


Actinidia arguta



Smilax bona-nox

Piper nigrum

Cirsium vulgare

Ligusticum striatum





Manihot esculenta

Lactuca sativa


Boehmeria nivea

Tamarix chinensis

Delosperma cooperi

Gunnera manicata


Cabomba caroliniana

Cedrela sinensis

Dioscorea villosa

Mentha canadensis

Aucuba japonica

Meliosma parviflora

Cuscuta reflexa

Euonymus carnosus

Eupomatia bennettii


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


Annona muricata

Yucca filamentosa

Stellaria media

Oryza sativa


Linum usitatissimum

Acorus americanus

Pinellia ternata


Cissus microcarpa

Vinca major

Theobroma cacao



Sonchus asper

Citrus sinensis

Dipsacus laciniatus

Ilex chinensis



Peumus boldus

Juglans regia

Ginkgo biloba

Populus trichocarpa

Pinus taeda

Pandanus utilis


Ampelopsis cordata

Eutrema salsugineum


Zea mays



Sabal bermudanaBrachypodium distachyon

Citrus clementina

Dioscorea opposita

Dillenia turbinata

Cayratia japonica

Dahlia pinnata


Rafflesia cantleyi

Cleome serrulata


Cinnamomum camphora

Aristolochia tagala


Camellia japonica

Glycine max

Vitis vinifera

Ricinus communis

Canna indica

Myrica rubra

Corylus avellana


Myristica fragrans

Drimys winteri

Colchicum autumnale


Phaseolus vulgaris

Nuphar advena

Mimulus guttatus

Houttuynia cordata

Cornus wilsoniana

Aquilegia coerulea



Illicium henryi


Iris japonica

350 300 250 200 150 100 50 0 (Ma)370

350 300 250 200 150 100 50 0 (Ma)370


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

0.00

0.01

0.02

0.03

Node 1D

ensi

ty

100 200 300

0.00

0.02

0.04

Node 2

50 150 250

0.00

0.005

0.01

0.015

Node 3

100 200 300

0.000

0.01

0.02

Node 4

100 200 300

0.00

0.01

0.02

Node 5

100 200 300

0.0000.005

0.010

0.015

Node 6

50 150 250

0.0000.004

0.008

0.012

Node 7

50 150 250

0.00

0.01

0.02

Node 8

50 150 250

0.00

0.01

0.02

Node 9

50 150 250

0.00

0.01

0.02

0.03

Node 10

0 100 200 300

0.00

0.02

0.04

Node 11

50 150 250

0.00

0.02

0.04

0.06

Node 12

50 150 250

0.00

0.02

0.04

Node 13

50 150 250

0.000

0.01

0.02

Node 14

50 150 250

0.00

0.01

0.02

0.03

Node 15

50 150 250

0.000

0.010

0.020

Node 16

115 125 135

0.0

0.2

0.4

Node 17

105 115 125

0.00

0.04

0.08Node 18

135 100 120 140

0.00

0.04

0.08Node 19

90 110 130

0.00

0.10

0.20

Node 20

0 40 80 120

0.0000.005

0.0100.015

Node 21

60 100 140

0.00

0.04

0.08

Node 22

70 90 110 130

0.00

0.01

0.02

0.03

Node 23

70 90 110 130

0.00

0.01

0.02

0.03

Node 24

40 80 120

0.00

0.02

0.04

0.06

Node 25

60 100 140

0.0000.0050.0100.015

Node 26

0 50 100

0.000

0.005

0.010

0.015Node 27

150 0 50 100 150

0.00

0.01

0.02

Node 28

40 80 120

0.00

0.02

0.04

0.06Node 29

60 100 140

0.00

0.02

0.04

Node 30

60 100 140

0.00

0.02

0.04

Node 31

40 80 120

0.00

0.01

0.02

0.03

Node 32

0 50 100 150

0.0000.004

0.0080.012

Node 33

40 80 120

0.00

0.01

0.02

Node 34

60 100 140

0.00

0.02

0.04

Node 35

80 100 120 140

0.00

0.02

0.04

Node 36

0 50 100 150

0.00

0.01

0.02

0.03

Node 37 Node 38

300 320 340 360

0.00

0.01

0.02

0.03

Den

sity

Den

sity

Den

sity

Den

sity

Den

sity

Den

sity

Den

sity

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).



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


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.



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.




1990).




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




Node 6 | Austrobaileyales – Mesangiospermae | 125 Ma – 247.2 Ma.




1990).





this group. Tricolpate pollen grain is the earliest unequivocal evidence of this group.

Minimum age. 125 Ma




Node 7 | CG Mesangiospermae | 125 Ma – 247.2 Ma.




1990).





Mesangiospermae. Tricolpate pollen grain is the earliest unequivocal evidence of

Mesangiospermae.

Minimum age. 125 Ma




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


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.



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



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 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.



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


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 .



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).



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).



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


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).



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


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.



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.



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.



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


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.



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


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.



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


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.



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


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).



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.



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


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.



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.



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


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).



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.



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.



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


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.



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).



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


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.




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.




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.



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.



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).

References

Berry EW. 1930. Revision of the Lower Eocene Wilcox Flora of the southeastern

states with descriptions of new species, chiefly from Tennessee and Kentucky.

U.S. Geol. Surv. Prof. Paper. 156:1-196.

Becker HF. 1961. Oligocene plants from the upper Ruby River Basin, southwestern

Montana. Geol Soc Am Memoirs. 82: 1-127.

Bogner J, Johnson KR, Kvacek Z, Upchurch Jr. GR. 2007. New fossil leaves of

Araceae from the Late Cretaceous and Paleogene of western North America.

Zitteliana. A47:133-147.

Beilstein MA, Nagalingum NS, Clements MD, Manchester SR, Mathews S. 2010.

Dated molecular phylogenies indicate a Miocene origin for Arabidopsis thaliana.

Proc Natl Acad Sci USA. 107: 18724-18728.

Barreda VD, Palazzesi L, Katinas L, Crisci JV, Tellería MC, Bremer K, Passalia MG,

Bechis F, Corsolini R. 2012. An extinct Eocene taxon of the daisy family

(Asteraceae): evolutionary, ecological and biogeographical implications. Ann Bot.

109: 127-134.

Barba-Montoya J, Reis MD, Schneider H, Donoghue PCJ, Yang Z. 2018.

Constraining uncertainty in the timescale of angiosperm evolution and the

veracity of a cretaceous terrestrial revolution. New Phytol. 218:819-834.

Beaulieu JM, O'Meara BC, Crane P, Donoghue MJ. 2015. Heterogeneous rates of

molecular evolution and diversification could explain the Triassic age estimate

for angiosperms. Syst Biol. 64(5):869-78.

Brown JW, Smith SA. 2018. The Past Sure Is Tense: On interpreting phylogenetic

divergence time estimates. Syst Biol. 67(2):340-353.

Coiro M, Doyle JA, Hilton J. 2019. How deep is the conflict between molecular and

fossil evidence on the age of angiosperms? New Phytol. doi: 10.1111/nph.15708.

Chandler MEJ. 1964. The Lower Tertiary Floras of Southern England. Volume IV. A

Summary and Survey of findings in Light of Recent Botanical Observations.

London, UK: British Museum (Natural History).

Crane PR, Pedersen KR, Friis EM, Drinnan AN. 1993. Early Cretaceous (early to

middleAlbian) platanoid inflorescences associated with Sapindopsis leaves from

the Potomac Group of eastern North America. Syst Bot. 18: 328-344.

Crepet WL, Nixon KC, Gandolfo MA. 2005. An extinct calycanthoid taxon,

Jerseyanthus calycanthoides, from the Late Cretaceous of New Jersey. Am J Bot.

92:1475-85.

Cevallos-Ferriz SRS, Estrada-Ruiz E, Pérez-Hernández BR. 2008. Phytolaccaceae

infructescence from Cerro del Pueblo Formation, Upper Cretaceous (Late

Campanian), Coahuila, Mexico. Am J Bot. 95: 77-83.

Clarke JT, Warnock RCM, Donoghue PCJ. 2011. Establishing a time-scale for plant

evolution. New Phytol. 192(1):266-301.

Doyle J, Hotton C, Ward JV. 1990. Early Cretaceous tetrads, zonasulcate pollen, and

Winteraceae. I. Taxonomy, morphology and ultrastructure. Am J Bot. 77:

154-1557.

Drinnan AN, Crane PR, Friis EM, Pedersen KR. 1991. Angiosperm flowers and

tricolpate pollen of buxaceous affinity from the Potomac Group (mid-Cretaceous)

of eastern North America. Am J Bot. 3: 153-176.

Doyle JA. 1992. Revised palynological correlations of the lower Potomac Group

(USA) and the Cocobeach sequence of Gabon (Barremian-Aptian). Cretaceous

Res. 13: 337-349.

Dilcher DL, Sun G, Ji Q, Li H. 2006. An early infructescence Hyrcantha decussata

(comb. Nov.) from the Yixian Formation in northeastern China. Pro Natl Acad

Sci USA. 104(22):9370-4.

Doyle JA, Endress PK, Upchurch GR. 2008. Early Cretaceous monocots: a

phylogenetic evaluation. Acta Mus. Nat. Pragae, Ser. B, Hist. Nat. 64: 59-87.

Doyle JA, Endress PK. 2010. Integrating Early Cretaceous fossils into the phylogeny

of living angiosperms: Magnoliidae and eudicots. J Syst Evol. 48 (1): 1-35.

Doyle JA. 2015. Recognising angiosperm clades in the Early Cretaceous fossil record.

Hist Biol. 27(3-4): 414-429.

Eklund H, Doyle JA, Herendeen PS. 2004. Morphological phylogenetic analysis of

living and fossil Chloranthaceae. Int J Plant Sci. 165: 107-151.

Friis EM. 1988. Spirematospermum chandlerae sp. nov., an extinct species of

Zingiberacea from the North American Cretaceous. Tertiary Research. 9: 7-12.

Friis EM, Eklund H, Pedersen KR., Crane PR. 1994a. Virginianthus calycanthoides

gen. et sp. nov.—A calycanthaceous flower from the Potomac Group (Early

Cretaceous) of eastern North America. Int J Plant Sci. 155: 772-785.

Friis EM, Pedersen KR, Crane PR. 1994b. Angiosperm floral structures from the

Early Cretaceous of Portugal. Plant Sys Evol. 8: 31-49.

Friis EM, Pedersen KR, Crane PR. 1999. Early angiosperm diversification: the

diversity of pollen associated with angiosperm reproductive structures in Early

Cretaceous floras from Portugal. Ann Mo Bot Gard. 86: 259-296.

Friis EM, Pedersen KR, Crane PR. 2004. Araceae from the Early Cretaceous of

Portugal: Evidence on the emergence of monocotyledons Else. Proc Natl Acad

Sci USA. 101(47): 16565-16570.

Friis EM, Crane PR, Pedersen KR. 2011. Early flowers and angiosperm evolution.

Cambridge, UK: Cambridge University Press.

Gandolfo MA, Nixon KC, Crepet WL. 1998a. Tylerianthus crossmanensis gen. et sp.

nov. (aff. Hydrangeaceae) from the Upper Cretaceous of New Jersey. Am J Bot.

85: 376-386.

Gandolfo MA, Nixon KC, Crepet WL. 1998b. A new fossil flower from the Turonian

of New Jersey: Dressiantha bicarpellata gen. et sp. nov. (Capparales). Am J Bot.

85: 964–974.

Hickey LJ, Doyle JA. 1977. Early Cretaceous evidence for angiosperm evolution. Bot

Rev. 43: 1-104.

Hughes NF, McDougall AB. 1990. Barremian-Aptian angiospermid pollen records

from southern England. Rev Palaeobot Palyno. 65: 145-151.

Herendeen PS, Crane PR. 1992. Early Caesalpinioid fruits from the Palaeogene of

southern England. In: Herendeen PS, Dilcher LD. Advances in Legume

Systematics Part 4. Kew, UK: Royal Botanic Gardens. p. 57-68.

Heimhofer U, Hochuli PA, Burla S, Weissert H. 2007. New records of Early

Cretaceous angiosperm pollen from Portuguese coastal deposits: Implications for

the timing of the early angiosperm radiation. Rev Palaeobot Palyno. 144: 39–76.

Herendeen PS, Friis EM, Pedersen KR, Crane PR. 2017. Palaeobotanical redux:

revisiting the age of the angiosperms. Nat Plants. 3:17015.

Ho SY, Duchêne S, Duchêne D. 2015. Simulating and detecting autocorrelation of

molecular evolutionary rates among lineages. Mol Ecol Resour. 15(4):688-96.

Iles WJD, Smith SY, Gandolfo MA, Graham SW. 2015. Monocot fossils suitable for

molecular dating analyses. Bot J Linn Soc. 178: 346-374.

Knobloch E, Mai DH. 1986. Monographie der Früchte und Samen in der Kreide von

Mitteleuropa. Rozpravy Útřdnío Útavu Geologickéo. 47: 1-219.

MacGinitie HD. 1969. The Eocene Green River flora of northwestern Colorado and

northeastern Utah. UC Publiations in Geological Sciences. 83: 1-140.

Mai D. 1970. Subtropische Elemente im Europäischer Tertiär I: Die Gattungen

Gironiera, Sarcococa, Illicium, Evodia, Ilex, Mastixia, Alangium, Symplocos

und Rehderodendron. Paläontologische Abhandlungen Abteilung B,

Paläobotanik. 3: 441-503.

Magallón-Puebla S, Herendeen PS, Endress PK. 1996. Allonia decandra: floral

remains of the tribe Hamamelideae (Hamamelidaceae) from Campanian strata of

southeastern USA. Plant Syst Evol. 202: 177-198.

Magallón S, Herendeen PS, Crane PR. 2001. Androdecidua endressii gen. et sp. nov.,

from the Late Cretaceous of Georgia (United States): further floral diversity in

Hamamelidoideae (Hamamelidaceae). Int J Plant Sci. 162: 963-983.

Mohr BAR, Bernardes-de-Oliveira MEC. 2004. Endressinia brasiliana, a

magnolialean angiosperm from the lower Cretaceous Crato Formation (Brazil).

Intl J Plant Sci. 165: 1121-1133.

Mohr BAR, Bernardes-de-Oliveira MEC, Taylor DW. 2008. Pluricarpellatia, a

nymphaealean angiosperm from the Lower Cretaceous of northern Gondwana

(Crato Formation, Brazil). Taxon. 57(4): 1147-1158.

Manchester SR, Kvaček Z. 2009. Fruits of Sloanea (Elaeocarpaceae) in the Paleogene

of North America and Greenland. Int J Plant Sci. 170: 941-950.

Martínez-Millán M, Crepet WL, Nixon KC. 2009. Pentapetalum trifasciculandricus

gen. et sp. nov., a thealean fossil flower from the Raritan Formation, New Jersey,

USA (Turonian, Late Cretaceous). Am J Bot. 96: 933-49.

Martínez-Millán M. 2010. Fossil record and age of the Asteridae. Bot Rev. 76:

83-135.

Manchester SR, Kapgate DK, Wen J. 2013. Oldest fruits of the grape family

(Vitaceae) from the Late Cretaceous Deccan Cherts of India. Am J Bot.

100(9):1849-1859.

Magallón S, Hilu KW, Quandt D. 2013. Land plant evolutionary timeline: gene

effects are secondary to fossil constraints in relaxed clock estimation of age and

substitution rates. Am J Bot. 100(3): 556-573.

Magallón S, Gómez-Acevedo S, Sánchez-Reyes LL, Hernández-Hernández T. 2015.

A metacalibrated time-tree documents the early rise of flowering plant

phylogenetic diversity. New Phytol. 207:437-453.

Massoni J, Doyle J, Sauquet H. 2015. Fossil calibration of Magnoliidae, an ancient

lineage of angiosperms. Palaeontol Electron. 2FC:1-25.

Morris JL, Puttick MN, Clark JW, Edwards D, Kenrick P, Pressel S, Wellman CH,

Yang Z, Schneider H, Donoghue PCJ. 2018. The timescale of early land plant

evolution. Pro Natl Acad Sci USA. 115:E2274-E2283.

Prasad V, Strömberg CAE, Leaché AD, Samant B, Patnaik R, Tang L, Mohabey DM,

Ge S, Sahni A. 2011. Late Cretaceous origin of the rice tribe provides evidence

for early diversification in Poaceae. Nat Commun. 2:480.

Reid E, Chandler M. 1926. Catalogue of Cainozoic Plants in the Department of

Geology. Vol. 1. The Brembridge Flora. London, UK: British Museum (Natural

History).

Revell LJ. 2012. phytools: An R package for phylogenetic comparative biology (and

other things). Methods Ecol. Evol. 3217-223.

Sims HJ, Herendeen PS, Lupia R, Christopher R, Crane PR. 1999. Fossil flowers with

Normapolles pollen from the Upper Cretaceous of southeastern North America.

Rev Palaeobot Palyno. 106: 131–151.

Schoene B, Samperton KM, Eddy MP., Keller G, Adatte T, Bowring SA, Khadri

SFR., Gertsch B. 2015. U-Pb geochronology of the Deccan Traps and relation to

the end-Cretaceous mass extinction. Science. 347:182-184.

Taylor DW. 1990. Paleobiogeographic relationships of angiosperms from the

Cretaceous and early Tertiary of the North American area. Bot Rev. 56: 279-417.

Trivett ML. 1992. Growt, architecture, structure, and relationships of Cordaixylon

iowensis nov comb(Cordaitales). Int J of Plant Sci. 153(2): 273-287.

Taylor DW, Brenner GJ, Basha SH. 2008. Scutifolium jordanicum gen. et sp nov

(Cabombaceae), an aquatic fossil plant from the Lower Cretaceous of Jordan,

and the relationships of related leaf fossils to living genera. Am J Bot. 95(3):

340-352.

von Balthazar M, Pedersen KR, Friis EM. 2005. Teixeiraea lusitanica, a new fossil

flower from the Early Cretaceous of Portugal with affinities to Ranunculales. Pl

Syst Evol. 255: 55-75.

von Balthazar M, Crane PR, Pedersen KR, Friis EM. 2011. New flowers of Laurales

from the Early Cretaceous (Early to Middle Albian) of eastern North America. In:

Wanntorp L, Ronse De Craene LP, editors. Flowers on the tree of life,

Cambridge Cambridge University Press. p. 49–87.

Vandenberghe N, Hilgen FJ, Speijer RP. 2012. The Paleogene Period. In: Gradstein

FM, Ogg JG, Schmitz M, Ogg G. The geologic timescale 2012. Ansterdam,

Elsevier. p. 855-921.

Wilf P, Johnson K, Cúneo N, Smith M, Singer B, Gandolfo M. 2005. Eocene plant

diversity at Laguna del Hunco and Río Pichileufú, Patagonia, Argentina. Am Nat.

165: 634-650.

Wang W, Dilcher DL, Sun G, Wang H, Chen Z. 2016. Accelerated evolution of early

angiosperms: Evidence from ranunculalean phylogeny by integrating living and

fossil data. J Syst Ecol. 54: 336-341.

supplemental information for€¦ · mimulus guttatus tamarix chinensis vaccinium corymbosum...

Documents