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