1

23

45

6

Xanthorrhoeoideae

Asphodeloideae

Hemerocallidoideae

Acorus_2Acorus_1

TriglochinAponogeton

Butomus SagittariaAlisma

GymnostachysOrontium

ArisaemaSpathiphyllum

Mon_delJaponolirionAcanthochlamys

TalbotiaVelloziaPandanus

CyclanthusCroomia

Stemona TaccaTrichopus

NartheciumAletris Wurmbea_1

Wurmbea_2CampynemaZigadenus

Trillium EriocaulonTypha

Tillandsia_2Tillandsia_1

Flagellaria Elegia_2Baloskion

Elegia_1Bambusa_1Bambusa_2Kingia

Dasypogon_2Dasypogon_1

MauritiaCalamus

Nypa

PtychospermaCocos

OncospermaRoystoneaRaveneaBorassusLivistona

PhilydrumHydrothrix

MonochoriaEichhornia Anigozanthos

Hanguana_2Hanguana_1Strelitzia

RavenalaPhenakospermum

Heliconia MusaMusella

Ensete_1Ensete_2

CalatheaThaumatococcus

Canna

MarantaMarantochloa

Tapeinochilos

HedychiumGlobba

RiedeliaAlpinia

SiphonochilosDimerocostus

Costus

Clivia_1

Dendrobium

CypripediumSpiranthes

EpipactisBlandfordia_1Bor_sp9696Borya

Milligania Hypoxis

Dor_exc9818Tecophilaea

CyanastrumArthropodium

Iris_1Pat_occ9809

Iris_2 IxiolirionDie_rob9810

XeronemaClivia_2

TulbaghiaAgapanthus

Lom_con9817Lom_mul9815

Lom_gla9857Lom_gla9846Art_9826

Asparagus_1Asparagus_2

Joinvillea

Polygonatum_2DanaeComospermum

DasylirionPolygonatum_1Scilla_2 BowieaHyacinthus

Scilla_1Chlorophytum_1

Chlorophytum_2Anthericum

Hosta100 Chlorogalum

CamassiaYuccaAgave_2Agave_1 Eremurus

Tra_div9706Trachyandra

Bul_gla9825Haworthia

Knipho�aKni_uva9827

100

Xan_aus9833Xan_min9837Xan_mal9807Xan_acau9671Xan_mac9823Xan_pla9935Xan_dru9712Xan_pla_9683Xan_pre9707Xan_dru9997Xan_bre10012Xan_acan10027 Tricoryne

Tri_anc9824CorynothecaCor_mic9791

JohnsoniaCaesia

PasitheaGeitonoplesium

Pho_ten100

100Agrostocrinum

HensmaniaThelionemaThe_cae9819

Rhuacophila100 Sty_gla9702

StypandraDia_rev9699Dia_con9811Dia_cae9814

100

100

100

100

100

100

100

100

100

100

100

100

100

100

100

100

100100 100

100

100100

100100

100

100

100

100

100

100100

100

100

100

100

100

100100

100100100

100

100

100

100

100

100

100

100

99

99

99

99

99

9954

87

83

3147

4555

94

4339

8243 75

5033

9646

85

98

59

6992 48

27

97 5189

8086

86

4451

79

99 59

9287

5191

5163

5592

94

95

79

91

49

9797

89

34

95 80

8252

66

477477

8571

9372

6391

33

95

98

94

53

9642

4142

9994 69

53

0.07

Figure S2. Maximum likelihood phylogeny (best tree) of monocots including Xanthorrhoeaceae (bottom of page, with subfamilies labelled). The tree was derived using RAxML from combined sequences of ndhF and trnL-trnF (cpDNA), showing branch lengths proportional to substitutions per site. The tree is rooted using Acorus, which is the sister group to the rest of monocots. Xanthorrhoeaceae is at bottom of tree, with subfamilies labelled. Branch lengths are proportional to substitutions per site. Labels on branches indicate bootstrap support (some values below 50 have been omitted to minimise clutter near tips). Circled numbers indicate calibration points explained in the text.

Hemerocallidoideae

Xanthorrhoeoideae

Asphodeloideae

Time before present (Ma)

Figure S3. Uncorrelated lognormal clock (UCLN) chronogram of monocots including Xanthorrhoeaceae (bottom of page, subfamilies labelled) and derived from combined partitioned ndhF and trnL-trnF (chloroplast DNA) sequences using BEAST with a Yule tree model. Numbers on branches are are posterior probabilities and blue node bars are 95% BCIs of node height posterior estimates. The scale indicates time before present (Ma).

X. lat 9835 copy 2

X. acau 9671 copy1

X. gla 9821 clone 6

X. aus 9860 a1

X. gra 10024 clone 22

X. acau 9671 copy 2

X. pla 9935 clone 1

X. tho 9784 clone 3

X. aus 9833

X. cae 9802 copy 2

X. sem 9800

X. cae 9802 copy 1

X. arb 9808 clone 4

X. arb 9808 clone 5

X. bre 10012 clone 5

X. dru 9712

X. med 9812 clone 1

X. res 9828 copy 1

X. res 9828 copy 2

X. con 9838 a1

X. con 9845 clone 5

X. ful 00323 clone 5

X. nan 9687 copy 1

X. bru 9813 copy 2

X. pre 9707

X. tho 9874 clone 2

X. joh 10238 clone 17

X. mal 9807 copy 2

X. joh 10173

X. ful 9831 copy 1

X. aca 10027 c8

X. bru 9710 clone 22

X. aca 10027 c1a

X. gla 9680 clone 3

X. lat 9834

X. pre 9701 clone 29

X. dru 9714 clone 4

X. nan 9687 copy 2

X. qua 9668

X. pum 10250 copy 1

X. min 9837 copy 1

X. min 9837 copy 2

X. mac 310

X. mac 9823

X. gra 9829 copy 1

Pho ten c3

Cor mic 9791 d

Cor mic 9791

Pho ten c2

Bul gla 9825 c2Bul gla 9825 c5

Bul gla 9825 d

Tra div 9706

Kni uva 9827

Art. sp. 9826

Xanthorrhoeoideae

Asphodeloideae

Hem

erocallidoideae

Figure S4. Maximum likelihood phylogeny of Xanthorrhoeaceae, derived using RAxML from sequences of rpb2 (nDNA), showing branch lengthsproportional to substitutions per site. The tree is rooted using Arthropodium (Art. sp. 9826) from the sister group, Asparagaceae. Clade labels with bars indicate subfamilies. Labels on branches indicate bootstrap support (most values within Xanthorrhoea have been omitted to minimiseclutter.

Lom con 9817

Lom mul 9815

Xanthorrhoeoideae

Asphodeloideae

Hem

erocallidoideae

X. dru 9712

X. pla 9683

X. pla 9335

X. pre 9707

Agrostocrinum

X. acan 10027

X. dru 9997

X. bre 10012

X. mal 9807

X. acau 9671

X. aus 9833

X. min 9837

X. mac 9823

Tra div 9706

Trachyandra

Eremurus

Knipho�a

Kni uva 9827

Bul gla 9825

Haworthia

Stypandra

Sty gla 9702

Rhuacophila

Thelionema

The cae 9819

Dia cae 9814

Dia con 9811

Dia rev 9699

Pho ten

Pasithea

Corynotheca

Cor mic 9791

Caesia

Johnsonia

Geitonoplesium

Hem litt

Lom gla 9846

Lom gla 9857

Figure S5. Maximum likelihood phylogeny of Xanthorrhoeaceae, derived using RAxML from combined partitioned ndhF and trnL-trnF (chloroplast DNA) sequences, showing branch lengths proportional to substitutions per site. The tree is rooted using Lomandra species from the sister group, Asparagaceae. Clade labels with bars indicate subfamilies. Labels on branches show bootstrap support (mostvalues within Xanthorrhoea have been omitted to reduce clutter.

X. dru 9712

X. pla 9683

X. pla 9335

X. pre 9707

Agrostocrinum

X. acan 10027

X. dru 9997

X. bre 10012

X. mal 9807

X. acau 9671

X. aus 9833

X. min 9837

X. mac 9823

Tra div 9706

Trachyandra

Eremurus

Knipho�a

Kni uva 9827

Bul gla 9825

Haworthia

Stypandra

Sty gla 9702

Rhuacophila

Thelionema

The cae 9819

Dia cae 9814

Dia con 9811

Dia rev 9699

Pho ten

Pasithea

Corynotheca

Cor mic 9791

Caesia

Johnsonia

Geitonoplesium

Hem litt

Estimated age (Ma)

80 70 0104060 50 30 20

XanthorrhoeoideaeA

sphodeloideaeH

emerocallidoideae

Figure S6. UCLN chronogram of Xanthorrhoeaceae derived from combined ndhF and trnL-trnF using BEAST with a Yule tree model. Branches are colored by median clock rates: red = fastest, blue = slowest, orange and green = intermediate. Clade labels with bars indicate subfamilies. The scale indicates time before present (Ma).

XanthorrhoeoideaeA

sphodeloideae

Hem

erocallidoideae

Estimated age (Ma)

?

?

X. lat 9835 copy 2X. acau 9671 copy1X. gla 9821 clone 6X. aus 9860 a1

X. gra 10024 clone 22

X. acau 9671 copy 2X. pla 9935 clone 1X. tho 9784 clone 3X. aus 9833X. cae 9802 copy 2

X. cae 9802 copy 1

X. arb 9808 clone 4X. arb 9808 clone 5

X. bre 10012 clone 5X. dru 9712X. med 9812 clone 2X. res 9828 copy 1X. res 9828 copy 2X. con 9838 a1X. con 9845 clone 5X. ful 00323 clone 5X. nan 9687 copy 1X. bru 9813 copy 2X. pre 9707X. tho 9874 clone 2X. joh 10238 clone 17X. mal 9807 copy 2X. joh 10173X. ful 9831 copy 1X. aca 10027 c8X. bru 9710 clone 22X. aca 10027 c1aX. gla 9680 clone 3X. lat 9834X. pre 9701 clone 29X. dru 9714 clone 4X. nan 9687 copy 2X. qua 9668X. pum 10250 copy 1X. min 9837 copy 1X. min 9837 copy 2X. mac 310X. mac 9823X. gra 9829 copy 1

Pho ten c3Cor mic 9791 dCor mic 9791Pho ten c2Bul gla 9825 c2Bul gla 9825 c5Bul gla 9825 dTra div 9706Kni uva 9827

X. sem 9800

Figure S7. RLC chronogram of Xanthorrhoeaceae derived from sequences of rpb2 (nuclear DNA) using BEAST with Yule tree model. Branches are colored by inferred local clock rates in the exons partition: red = fast, blue = slow. Pointers show the two inferred rate shifts: one downwards in the MRCA of Xanthorrhoeoideae (�lled pointer), followed by a second shift (open pointers), which was either a further downward shift in the stem of the large upper clade or a small upward shift in the stem of the X. macronema + X. gracilis clade. Clade labels with bars indicate subfamilies. The scale indicates time before present (Ma).

Estimated age (Ma)

80 70 0104060 50 30 20

X. lat 9835 copy 2

X. acau 9671 copy1

X. gla 9821 clone 6

X. aus 9860 a1

X. gra 10024 clone 22

X. acau 9671 copy 2

X. pla 9935 clone 1X. tho 9784 clone 3

X. aus 9833

X. cae 9802 copy 2

X. sem 9800

X. cae 9802 copy 1

X. arb 9808 clone 4

X. arb 9808 clone 5

X. bre 10012 clone 5

X. dru 9712

X. med 9812 clone 1X. res 9828 copy 1

X. res 9828 copy 2

X. con 9838 a1

X. con 9845 clone 5

X. ful 00323 clone 5

X. nan 9687 copy 1X. bru 9813 copy 2

X. pre 9707

X. tho 9874 clone 2

X. joh 10238 clone 17

X. mal 9807 copy 2

X. joh 10173

X. ful 9831 copy 1

X. aca 10027 c8

X. bru 9710 clone 22

X. aca 10027 c1a

X. gla 9680 clone 3X. lat 9834

X. pre 9701 clone 29

X. dru 9714 clone 4

X. nan 9687 copy 2

X. qua 9668

X. pum 10250 copy 1X. min 9837 copy 1

X. min 9837 copy 2

X. mac 310

X. mac 9823

X. gra 9829 copy 1

Pho ten c3

Cor mic 9791 d

Cor mic 9791Pho ten c2

Bul gla 9825 c2

Bul gla 9825 c5

Bul gla 9825 dTra div 9706

Kni uva 9827

XanthorrhoeoideaeA

sphodeloideaeH

emerocallidoideae

Figure S8. RLC chronogram of Xanthorrhoeaceae derived from sequences of rpb2 (nDNA) using BEAST with a Birth-death tree model. Unlike other analyses of either dataset using the RLC clock, this one inferred a young age for the Xanthorrhoea crown (5.0 Ma). However, the model combination including a Yule clock was very strongly preferred for this dataset in Bayes factor tests. Branches are colored by inferred local clock rates in the introns partition: red = fast, blue = slow. The pointer shows the single inferred rate shift (downwards), which occurred in the MRCA of Xanthorrhoea. Clade labels with bars indicate subfamilies. The scale indicates time before present (Ma).

X. lat 9835 copy 2

X. acau 9671 copy1

X. gla 9821 clone 6X. aus 9860 a1

X. gra 10024 clone 22

X. acau 9671 copy 2

X. pla 9935 clone 1X. tho 9784 clone 3

X. aus 9833

X. cae 9802 copy 2X. sem 9800X. cae 9802 copy 1

X. arb 9808 clone 4X. arb 9808 clone 5

X. bre 10012 clone 5

X. dru 9712

X. med 9812 clone 1X. res 9828 copy 1

X. res 9828 copy 2

X. con 9838 a1X. con 9845 clone 5

X. ful 00323 clone 5

X. nan 9687 copy 1X. bru 9813 copy 2

X. pre 9707

X. tho 9874 clone 2

X. joh 10238 clone 17

X. mal 9807 copy 2X. joh 10173

X. ful 9831 copy 1

X. aca 10027 c8

X. bru 9710 clone 22

X. aca 10027 c1a

X. gla 9680 clone 3X. lat 9834

X. pre 9701 clone 29X. dru 9714 clone 4

X. nan 9687 copy 2X. qua 9668

X. pum 10250 copy 1X. min 9837 copy 1

X. min 9837 copy 2

X. mac 310X. mac 9823

X. gra 9829 copy 1

Pho ten c3Cor mic 9791 dCor mic 9791Pho ten c2Bul gla 9825 c2Bul gla 9825 c5Bul gla 9825 dTra div 9706Kni uva 9827

Estimated age (Ma)

70 0104060 50 30 20

XanthorrhoeoideaeA

sphodeloideaeH

emerocallidoideae

Figure S9. RLC chronogram of Xanthorrhoeaceae derived from sequences of rpb2 (nDNA) using BEAST with a Birth-death tree model. Unlike other analyses of either dataset using the RLC clock, this one inferred a young age for the Xanthorrhoea crown (5.0 Ma). However, the model combination including a Yule clock was very strongly preferred for this dataset in Bayes factor tests. Branches are colored by inferred local clock rates in the exons partition: red = fast, blue = slow, i.e. in the exons, there is essentially no rate variation and the rate is much slower than in the introns. Clade labels with bars indicate subfamilies. The scale indicates time before present (Ma).

X. lat 9835 copy 2

X. acau 9671 copy1

X. gla 9821 clone 6

X. aus 9860 a1

X. gra 10024 clone 22

X. acau 9671 copy 2

X. pla 9935 clone 1

X. tho 9784 clone 3

X. aus 9833

X. cae 9802 copy 2X. sem 9800X. cae 9802 copy 1

X. arb 9808 clone 4X. arb 9808 clone 5

X. bre 10012 clone 5

X. dru 9712

X. med 9812 clone 1

X. res 9828 copy 1X. res 9828 copy 2

X. con 9838 a1

X. con 9845 clone 5X. ful 00323 clone 5

X. nan 9687 copy 1

X. bru 9813 copy 2

X. pre 9707

X. tho 9874 clone 2

X. joh 10238 clone 17

X. mal 9807 copy 2X. joh 10173

X. ful 9831 copy 1

X. aca 10027 c8

X. bru 9710 clone 22X. aca 10027 c1a

X. gla 9680 clone 3

X. lat 9834

X. pre 9701 clone 29X. dru 9714 clone 4

X. nan 9687 copy 2

X. qua 9668

X. pum 10250 copy 1

X. min 9837 copy 1

X. min 9837 copy 2

X. mac 310X. mac 9823

X. gra 9829 copy 1

Pho ten c3Cor mic 9791 dCor mic 9791Pho ten c2Bul gla 9825 c2

Bul gla 9825 c5Bul gla 9825 dTra div 9706Kni uva 9827

XanthorrhoeoideaeA

sphodeloideaeH

emerocallidoideae

Estimated age (Ma)

80 70 0104060 50 30 20

Fig S8 rpb2 introns UCLN Yule

Figure S10. UCLN chronogram of Xanthorrhoeaceae derived from sequences of rpb2 (nDNA) using BEAST with a Yule tree model. Branches are colored by median clock rates in the introns partition: red = fastest, blue = slowest, orange and green = intermediate. Clade labels with bars indicate subfamilies. The scale indicates time before present (Ma).

Rate

(site

-1 M

a-1 x

104 )

a) cpDNA UCLN Yule

d) cpDNA RLC Yule

b) rpb2 exons UCLN Yule

e) rpb2 exons RLC Yule

b) rpb2 introns UCLN Yule

f ) rpb2 introns RLC Yule

20

15

10

5

0

20

15

10

5

0

20

15

10

5

0

20

15

10

5

0

100

50

0

100

50

0

Monocots Xanthstem

Xanthcrown

Hem Asph(outgroups)

Xanthstem

Xanthcrown

Hem Asph(outgroups)

Xanthstem

Xanthcrown

Hem Asph(outgroups)

Xanthstem

Xanthcrown

Hem Asph(outgroups)

Xanthstem

Xanthcrown

Hem Asph(outgroups)

Xanthstem

Xanthcrown

Hem Asph(outgroups)

Figure S11. Estimates of DNA substitution rates in monocots, Xanthorrhoea and its two sister groups using BEAST for all three datasets (cpDNA-monocots, cpDNA-Xanthorrhoeaceae and rpb2-Xanthorrhoeaceae) under both alternative clock models (UCLN and RLC) and the Yule tree-growth model. For comparability of rates between the large (monocot) and small (Xanthorrhoeaceae) cpDNA datasets, neither was partitioned. It was not possible to estimate a rate using the RLC clock with the monocots-cpDNA dataset because none of the six analyses converged. Symbols represent means, and error bars the 95% CIs, of the “rate median” parameter values across all branches within the given taxon, as plotted on the annotated maximum clade credibility tree using FigTree v1.4.0 (Rambaut, 2012). This could not be done for the Xanthorrhoea stem, which is a single node. Taxon abbreviations: Xanth = Xanthorrhoea; Hem = Hemerocallidoideae; Asph = Asphodeloideae.

0 1 2 3 4 5 6 7 8 9

0 1 2 3 4 5 6

0 1 2 3 4 5

cpDNA

rpb2 exons

rpb2 introns

Prob

abili

ty

Number of rate shifts

0.6

0.4

0.2

0.0

0.6

0.4

0.2

0.0

0.6

0.4

0.2

0.0

0.8Prior 95% BCIPrior tailPosterior 95% BCIPosterior tail

Figure S12. Prior and posterior distributions of number of rate shifts inferred by RLC clock analyses using BEAST from cpDNA and rpb2 sequences. The lack of overlap by the 95% Bayesian credibility intervals (BCIs) indicates rejection of the prior hypothesis of no rate shifts under a strict clock. Additionally, Fisher exact tests indicate that each pair of prior and posterior distributions is signi�cantly di�erent (P = 0.0000).