Bremer, K., Friis, E. M., and Bremer, B. 2004. Molecular phylogenetic dating of asterid flowering plants shows Early Cretaceous diversification.

 

Supplementary information to be posted on suitable website [belonging to journal and/or www.systbot.uu.se]

 

Input file for r8s analysis with semi-parametric rate smoothing (penalized likelihood with smoothing factor 3; Sanderson 2002a, b) of a 111-taxon asterid tree from Bremer et al. (2002) with maximum likelihood branch lengths from PAUP* (Swofford 2001) applying the GTR+Г (shape parameter 0.5) model and empirical base frequencies.

 

#nexus

 

begin trees;

tree Asterids6sequences = (((Cornus:0.033344,Grubbia:0.036720)HironoiaFossil:0.002779,Loasa:0.050486):0.007297,((((((((Actinidia:0.027475,Roridula:0.064030)SaurauiaFossil:0.008572,(Clethra:0.021295,Cyrilla:0.046044):0.003872):0.005097,((Camellia:0.021850,Schima:0.016938):0.010644,((Halesia:0.013596,Styrax:0.032164):0.019832,Symplocos:0.047587):0.001631):0.001024):0.000972,((Pentaphylax:0.025918,Ternstroemia:0.015396)EuryaFossil:0.007122,Sladenia:0.037020):0.002730):0.000212,((Barringtonia:0.055177,Diospyros:0.032376):0.002849,(Manilkara:0.034126,((Myrsine:0.031627,Primula:0.056810):0.024355,Theophrasta:0.056845):0.037045):0.002338):0.000843):0.000435,(Fouquieria:0.027071,Polemonium:0.081346):0.005239):0.007882,((Impatiens:0.083922,(Pelliciera:0.040265,Tetramerista:0.025141):0.012394):0.003428,Marcgravia:0.020516):0.048613):0.019181,((((((Brunia:0.053312,(Columellia:0.047898,Desfontainia:0.033550):0.029574):0.001410,((((((Acicarpha:0.011488,Boopis:0.015587):0.013311,Helianthus:0.045257):0.006027,Scaevola:0.093022):0.025051,Menyanthes:0.022324):0.006260,((Alseuosmia:0.041692,Phelline:0.021791):0.001769,Argophyllum:0.037024):0.002591):0.005052,(Pentaphragma:0.076646,(Roussea:0.059265,Stylidium:0.142503):0.003237):0.001489):0.020634):0.001803,((Eremosyne:0.128158,Escallonia:0.042197):0.006358,(Polyosma:0.041906,Tribeles:0.054876):0.000821):0.004491):0.000519,(((Paracryphia:0.019133,Quintinia:0.023970):0.002678,(((Diervilla:0.015704,((Dipsacus:0.035314,Valeriana:0.086088):0.007744,(Linnaea:0.013926,Morina:0.021660):0.000750):0.017155):0.006656,Lonicera:0.028906):0.020884,Viburnum:0.024812):0.006809):0.001038,((((Apium:0.067128,Pittosporum:0.039950):0.003543,Aralia:0.029296)AraliaFossil:0.006883,Griselinia:0.014517):0.002293,(Aralidium:0.009240,(Melanophylla:0.009026,Torricellia:0.014151):0.001714):0.014724):0.017736):0.000982):0.009105,(Cardiopteris:0.080762,((Helwingia:0.036317,Phyllonoma:0.060317):0.006752,Ilex:0.029581)IlexFossil:0.019998):0.005551):0.004191,((Apodytes:0.038237,(Aucuba:0.045675,Oncotheca:0.046818):0.002054):0.000261,((((Borago:0.113830,Vahlia:0.050253):0.002874,((Plocosperma:0.069702,(((((((((((Acanthus:0.065707,Avicennia:0.045134):0.013275,Schlegelia:0.013921):0.000932,(Sesamum:0.020531,Stilbe:0.026057):0.001350):0.000321,(Jacaranda:0.011320,(Lamium:0.071306,Verbena:0.046395):0.003311):0.001207):0.001310,Proboscidea:0.017023):0.000401,(((Cyclocheilon:0.052841,Lindenbergia:0.041852):0.015915,Paulownia:0.015526):0.001561,Phryma:0.038506):0.003228):0.003303,((Androya:0.014876,Myoporum:0.020026):0.011113,(Buddleja:0.012592,(Scrophularia:0.024050,Selago:0.058011):0.002857):0.010787):0.004125):0.001720,(Antirrhinum:0.041777,(Globularia:0.040728,Plantago:0.105433):0.011348):0.010454):0.002046,(Peltanthera:0.014593,Streptocarpus:0.076524):0.004741):0.015247,(Polypremum:0.034510,Tetrachondra:0.027710):0.028594):0.003733,Olea:0.026828):0.009032):0.014183,((((Grevea:0.021931,Montinia:0.026439):0.013159,Kaliphora:0.039820):0.046619,Sphenoclea:0.075440):0.007293,(Ipomoea:0.111866,Nicotiana:0.060155):0.012334):0.005862):0.001160):0.002214,(((Alstonia:0.034547,Gentiana:0.126012):0.007100,(Gelsemium:0.039903,Logania:0.061122):0.002067):0.011619,Luculia:0.042946):0.030885):0.019158,(Cassinopsis:0.019714,(Icacina:0.017279,Pyrenacantha:0.067494):0.052918):0.002524)IcacinicaryaFossil:0.000806):0.006868):0.008989):0.003421)Asterids;

end;

 

begin rates;

 

blformat nsites=9914 lengths=persite;

 

collapse;

 

fixage taxon=Asterids age=128;

 

constrain taxon=HironoiaFossil minage=88;

constrain taxon=SaurauiaFossil minage=89;

constrain taxon=EuryaFossil minage=86;

constrain taxon=IcacinicaryaFossil minage=89;

constrain taxon=IlexFossil minage=70;

constrain taxon=AraliaFossil minage=70;

 

set seed=3 num_time_guesses=3 num_restarts=3 maxiter=3000 verbose=0 smoothing=3;

 

divtime method=PL algorithm=TN;

 

describe plot=phylogram;

 

showage;

 

end;

Bremer, K., Friis, E. M., and Bremer, B. 2004. Molecular phylogenetic dating of asterid flowering plants shows Early Cretaceous diversification.

 

Supplementary information to be posted on suitable website [belonging to journal and/or www.systbot.uu.se]

 

Stem node ages and crown node ages in my in boldface for major groups, orders, and some families of asterids obtained from semi-parametric rate smoothing (penalized likelihood with smoothing factor 3; Sanderson 2002a, b) of a 111-taxon asterid tree from Bremer et al. (2002) with maximum likelihood branch lengths from six molecular markers and calibration with six reference fossils, followed by

 

boot = confidence intervals obtained by bootstrap analysis of 100 replicates of the data matrix

topo = range of age estimates obtained with varying topologies*

samp = age estimates obtained after deletion of 22 of the 111 taxa

code = age estimates obtained with the three coding sequences only

nonc = age estimates obtained with the three non-coding sequences only

nprs = age estimates obtained with non-parametric rate smoothing

lfcl = age estimates obtained with the Langley-Fitch clock-based method

cali = range of age estimates obtained with calibration by one only of the six reference fossils

 

*by collapsing reference nodes 1, 3 and 6 (Figure 1) followed by alternative resolutions of the resulting trichotomy, and by forcing alternative interrelationships among the orders of core campanulids (Apiales, Dipsacales, Asterales) and among the orders of core lamiids (Gentianales, Solanales, Lamiales), respectively

 

 

Major groups, orders and families	stem age	boot	topo	samp	code	nonc	nprs	lfcl	cali	crown age	boot	topo	samp	code	nonc	nprs	lfcl	cali
asterids	-	-	-	-	-	-	-	-	-	128	-	128	128	128	128	128	128	96-156
Cornales	128	-	128	128	128	128	128	128	96-156	112	±5.1	112-114	115	112	112	114	96	90-136
Ericales	127	±1.8	127	126	127	127	126	127	96-154	114	±4.9	112-114	113	114	114	113	111	93-133
Pentaphylacaceae	107	±5.8	104-107	106	107	107	106	99	92-121	102	±2.9	99-101	101	102	101	101	95	90-113
Styracaceae	100	±4.4	96-99	99	99	99	99	81	87-112	55	±12.0	53-55	55	44	44	55	40	48-62
Tetrameristaceae	56	±8.2	55-56	47	55	56	61	64	46-66	41	±7.8	40	33	41	42	46	47	33-48
Theaceae	103	±1.2	99-103	103	102	102	102	84	90-116	68	±20.5	64-66	68	69	69	71	43	59-77
euasterids	127	±1.8	127	126	127	127	126	127	96-154	123	±0.3	123	122	123	123	120	124	94-150
campanulids	123	±0.3	123	122	123	123	120	124	94-150	121	±1.7	121	119	120	120	116	120	92-146
Aquifoliales	121	±1.7	121	119	120	120	116	120	92-146	113	±2.4	112	111	110	110	110	111	88-136
core campanulids	121	±1.7	121	119	120	120	116	120	92-146	114	±2.0	114	112	113	113	108	112	90-138
Columelliaceae	110	±1.5	109-110	107	106	105	104	107	85-132	64	±2.1	63-64	62	66	66	61	63	50-77
Paracryphiaceae	111	±4.7	111-112	109	111	110	106	95	87-134	101	±23.3	102	99	102	102	98	60	79-122
Apiales	113	±1.0	113-114	111	112	111	107	104	88-136	84	±1.2	84	84	81	81	84	77	76-96
Dipsacales	111	±4.7	111-112	109	111	110	106	95	87-134	101	±3.1	101	94	95	95	95	85	79-122
Caprifoliaceae	101	±3.1	101	94	95	95	95	85	79-122	75	±5.2	75	62	75	74	70	65	59-90
Asterales	112	±0.9	111-112	110	111	110	106	110	87-135	93	±1.8	93-94	89	90	89	86	97	73-112
Calyceraceae	51	±1.1	51	41	45	45	46	55	40-61	26	±0.7	25	21	20	20	25	25	19-31
lamiids	123	±0.3	123	122	123	123	120	124	94-150	119	±2.8	119	117	120	119	114	120	91-145
Icacinaceae	119	±2.4	114-119	117	120	119	114	120	91-144	115	±2.4	115	113	115	115	110	114	88-139
Garryales	114	±12.3	113-114	112	112	112	110	99	87-138	-	-	-	-	-	-	-	-	-
core lamiids	119	±2.4	114-119	117	120	119	114	120	91-144	108	±2.1	108-109	104	107	106	100	114	83-131
Gentianales	108	±2.1	107-109	104	107	106	100	114	83-131	78	±7.3	76-79	66	80	80	74	90	60-95
Solanales	106	±0	106-107	100	105	105	97	112	81-128	100	±1.7	100-101	96	99	99	92	108	77-121
Montiniaceae	92	±0.7	92	88	91	90	85	101	70-111	42	±7.5	42	40	38	38	38	51	32-50
Lamiales	106	±0	106-107	100	105	105	97	112	81-128	97	±1.9	96-97	91	95	94	86	100	74-116
Acanthaceae	67	±7.1	67-68	64	65	63	50	63	53-79	54	±4.2	54-55	52	51	49	40	54	43-64
Gesneriaceae	78	±0.4	78	74	74	72	62	78	60-92	71	±1.3	71-72	68	67	66	57	71	55-85
Orobanchaceae	64	±3.4	64-65	64	60	58	49	62	50-76	48	±2.1	48-49	47	43	42	36	49	38-57
Plantaginaceae	76	±1.2	76-77	73	72	71	60	77	59-91	66	±7.5	67	63	62	61	52	70	26-70
Scrophulariaceae	75	±1.4	75	71	70	69	50	63	58-89	68	±1.3	68-69	66	64	62	54	64	53-81
Tetrachondraceae	87	±2.6	88	84	84	83	74	89	68-104	46	±11.6	46	44	46	46	40	47	35-55