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Additional file 1 – Molecular phylogenetic trees with reconstructed shifts in geographic distribution and flowering patterns (flowering durations and flowering midpoint) indicated.

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distribution and flowering patterns (flowering durations and flowering midpoint)

indicated.

Unless otherwise indicated, shifts in flowering patterns are in the direction consistent with

past climatic change; shifts in flowering midpoint are from the summer towards the spring,

and shifts in flowering duration are reductions in the number of months of flowering. Where

nodes optimised at different states are separated by nodes in which the ancestral state is

undetermined, we have marked on the basal-most possible location of the shift.

Bruniaceae (1 Cape clade): Tree 1

Cyperaceae (Ficinia & Tetraria): Tree 2

Disa (1 Cape clade): Tree 3

Ehrharta (1 Cape clade): Tree 4

Genistoids (Crotalarieae & Podalyrieae): Tree 5

Heliophila: Tree 6

Indigofera: Tree 7

Moraea: Tree 8

Muraltia: Tree 9

Oxalis: Tree 10

Pelargonium: Tree 11

Pentaschistis: Tree 12

Phylica: Tree 13

Restionaceae: Tree 14

Satyrium: Tree 15

Zygophyllum: Tree 16

(2)

Tree 1: Bruniaceae

Character Changes

Flowering Midpoint Time

(No significant changes)

Flowering Duration

(No significant changes)

Distributional Changes

Entering West Cape

Leaving West Cape

Entering East Cape

Leaving East Cape

Cape

clade

100

100

100

100

100

97

73

99

96

59

83

100

99

97

58

69

100

100

69

100

80

54

85 85

67

67

53

100

100

71

79

90

98

62

63

99

81

98

98

100

100

65

92

92

74

93

90

100

99

Sampling of Cape species: 85%

Bootstrap values:

(3)

Tree 2: Cyperaceae

Character Changes

Flowering Midpoint Time

(No significant changes)

Flowering Duration

(No significant changes)

Distributional Changes

Entering West Cape

Leaving West Cape

Entering East Cape

Leaving East Cape

Ficinia

Tetraria

Tetraria

95

92

79

100

94

68

61

Sampling of Cape species

Ficinia: 21%

Tetraria: 19%

(4)

Tree 3: Disa

Character Changes

Flowering Midpoint Time

Flowering Duration

(No significant changes)

Distributional Changes

Entering West Cape

Leaving West Cape

Entering East Cape

Leaving East Cape

100

100

100

100

100

100

100

100

100

100

98

100

100

100

100

100

100

100

100

100

100

100

100

100

95

100

100

100

91

90

100

100

100

98

100

100

100

84

100

100

52

78

100

78

100

100

100

100

56

95

100

100

99

100

100

100

100

100

100

100

98

100

100

100

83

91

79

100

100

100

99

57

62

100

100

100

100

68

100

100

64

97

100

100

96

100

100

100

100

100

91

100

99

79

81

93

100

100

100

100

100

100

100

98

100

100

100

100

100

100

100

100

100

100

100

100

100

93

100

Sampling of Cape species: 82%

Support values:

(5)

Tree 4: Ehrharta

- there are no significant changes

Character Changes

Flowering Midpoint Time

Flowering Duration

Distributional Changes

Entering West Cape

Leaving West Cape

Entering East Cape

Leaving East Cape

Non-Cape relatives

Cape clade

60

75

79

74

100

95

83

97

71

100

95

89

100

77

Sampling of Cape species: 100%

(6)

Tree 5: Genistoids

Character Changes

Flowering Midpoint Time

(Note the hollow triangle

is in the opposite

direction to that predicted

under climate change)

Flowering Duration

Distributional Changes

Entering West Cape

Leaving West Cape

Entering East Cape

Leaving East Cape

Podalyrieae

Crotalarieae

100100 55 70 89 75 81 54 82 56 93 95 91 100 65 99 72 60 92 82 96 52 76 69 83 96 97 51 83 51 55 93 71 62 74 61 82 87 92 97 94 8761 93 63 61

Sampling of Cape species:

Crotalarieae: 43%

Podalyrieae: 15%

(7)

Tree 6: Heliophila

Character Changes

Flowering Midpoint Time

Flowering Duration

Distributional Changes

Entering West Cape

Leaving West Cape

Entering East Cape

Leaving East Cape

Cape

Clade

100

100

100

100

87

100

90

100

97

97

100

86

100

62

100

68

53

100

100

79

89

100

100

60

87

100

80

61

98

96

88

68

73

97

100

58

81

95

100

Sampling of Cape species: 65%

Support values: Bayesian posterior

probabilities

(8)

Tree 7: Indigofera

Character Changes

Flowering Midpoint Time

(No significant change)

Flowering Duration

(No significant change)

Distributional Changes

Entering West Cape

Leaving West Cape

Entering East Cape

Leaving East Cape

Cape

clade

Non-Cape relatives

100

97

100

100

100

100

100

Sampling of Cape species: 20%

Support values: Bayesian posterior

probabilities

(9)

Tree 7: Indigofera

Character Changes

Flowering Midpoint Time

(No significant change)

Flowering Duration

(No significant change)

Distributional Changes

Entering West Cape

Leaving West Cape

Entering East Cape

Leaving East Cape

Cape

clade

Non-Cape relatives

100

97

100

100

100

100

100

Sampling of Cape species: 20%

Support values: Bayesian posterior

probabilities

(10)

Tree 8: Moraea

Character Changes

Flowering Midpoint Time

(No significant change)

Flowering Duration

Distributional Changes

Entering West Cape

Leaving West Cape

Entering East Cape

Leaving East Cape

Cape

Clade

100

89

88

84

55

67

65

57

100

100

100

78

100

82

67

100

92

54

74

86

89

86

100

55

83

93

89

89

93

72

95

91

53

73

53

Sampling of Cape species: 39%

(11)

Tree 9: Muraltia

Character Changes

Flowering Midpoint Time

Flowering Duration

(No significant change)

Distributional Changes

Entering West Cape

Leaving West Cape

Entering East Cape

Leaving East Cape

100

83

98

99

56

56

55

84

96

100

100

73

100

100

96

86

97

100

100

59

100

88

100

65

98

99

63

54

54

92

95

84

70

60

97

77

68

60

59

55

53

96

57

60

64

63

85

100

60

60

Sampling of Cape species: 64%

(12)

Tree 10: Oxalis

Character Changes

Flowering Midpoint time

(Note that the hollow blue

triangle represents a shift

from late-autumn towards

the winter)

Flowering Duration

Distributional Changes

Entering West Cape

Leaving West Cape

Entering East Cape

Leaving East Cape

Non-Cape relatives

Cape

clade

64

100

61

100

79

59

100

89

93

57

64

69

100

88

75

100

94

83

91

51

100

96

100

99

96

62

54

60

98

86

97

77

100

100

90

88

95

100

91

75

79

52

100

85

81

81

88

85

82

73

62

93

62

60

100

100

99

97

96

97

77

100

57

88

59

60

87

75

75

85

100

78

61

99

100

100

78

91

100

98

Sampling of Cape species: 78%

(13)

Tree 11: Pelargonium

- no significant changes

Character Changes

Flowering Midpoint Time

Flowering Duration

Distributional Changes

Entering West Cape

Leaving West Cape

Entering East Cape

Leaving East Cape

Cape clade

Non-Cape relatives

90

87

77

84 67

87

86

69

64

90

91

66

69

92

58

61

56

82

54

81

57

67

Sampling of Cape species: 53%

(14)

Tree 12: Pentaschistis

Character Changes

Flowering Midpoint Time

(No significant changes)

Flowering Duration

Distributional Changes

Entering West Cape

Leaving West Cape

Entering East Cape

Leaving East Cape

Cape clade

89

100

65

100

89

100

100

96

96

100

100

92

86

78

96

100

100

100

63

77

100

100

100

63

100

98

62

99

100

100

100

100

100

100

100

94

100

100

100

100

100

96

83

100

72

100

98

71

99

100

100

100

83

100

77

100

100

100

98

100

98

100

100

100

100

100

55

100

Sampling of Cape species: 96%

Support values:

(15)

Tree 13: Phylica

Character Changes

Flowering Midpoint Time

(No significant change)

Flowering Duration

Distributional Changes

Entering West Cape

Leaving West Cape

Entering East Cape

Leaving East Cape

Non-Cape relatives

Cape clade

100

78

71

73

100

64

87

95

64

86

100

98

87

Sampling of Cape species: 10%

(16)

Baloskion tetraphyllum Sporodanthus tasmanicus Anthochortus crinalis Anthochortus graminifolius Anthochortus singularis Cannomois arenicola Cannomois dolichocaryon Cannomois parviflora Cannomois saundersii Cannomois schlechteri Cannomois scirpoides Ceratocaryum argenteum Ceratocaryum caespitosum Ceratocaryum fimbriatum Ceratocaryum fistulosum Ceratocaryum pulchrum Ceratocaryum xerophilum Hypodiscus aristatus Hypodiscus montanus Hypodiscus squamosus Mastersiella purpurea Mastersiella spathulata Nevillea obtusissima Willdenowia arescens Willdenowia glomerata

Askidiosperma albo aristata Askidiosperma alticolum Askidiosperma andreaeanum Askidiosperma capitatum Askidiosperma chartaceum Askidiosperma delicatulum Askidiosperma esterhuyseniae Askidiosperma insigne Askidiosperma longiflorum Askidiosperma nitidum Askidiosperma paniculatum Askidiosperma rugosum Calopsis adpressa Calopsis andreaeana Calopsis aspera Calopsis burchellii Calopsis clandestina Calopsis dura Calopsis esterhuyseniae Calopsis filiformis Calopsis fruticosa Calopsis gracilis Calopsis hyalina Calopsis impolita Calopsis levynsiae Calopsis marlothii Calopsis membranacea Calopsis monostylis Calopsis muirii Calopsis nudiflora Calopsis paniculata Calopsis pulchra Calopsis rigida Calopsis rigorata Calopsis sparsa Calopsis viminea Chondropetalum acockii Chondropetalum aggregatum Chondropetalum decipiens Chondropetalum deustum Chondropetalum ebracteatum Chondropetalum elephantinum Chondropetalum hookerianum Chondropetalum marlothii Chondropetalum microcarpum Chondropetalum mucronatum Chondropetalum nudum Chondropetalum rectum Chondropetalum tectorum Dovea macrocarpa Elegia altigena Elegia amoena Elegia asperiflora Elegia atratiflora Elegia caespitosa Elegia capensis Elegia coleura Elegia cuspidata Elegia equisetacea Elegia esterhuyseniae Elegia extensa Elegia fastigiata Elegia fenestrata Elegia filacea Elegia fistulosa Elegia fucata Elegia galpinii Elegia glomerata Elegia grandis Elegia grandispicata Elegia hutchinsonii Elegia intermedia Elegia juncea Elegia muirii Elegia neesii Elegia persistens Elegia prominens Elegia racemosa Elegia rigida Elegia spathacea Elegia squamosa Elegia stipularis Elegia stokoei Elegia thyrsifera Elegia thyrsoidea Elegia vaginulata Elegia verreauxii Ischyrolepis affinis Ischyrolepis anomala Ischyrolepis arida Ischyrolepis caespitosa Ischyrolepis capensis Ischyrolepis cincinnata Ischyrolepis coactilis Ischyrolepis constipata Ischyrolepis curvibracteata Ischyrolepis curviramis Ischyrolepis duthieae Ischyrolepis eleocharis Ischyrolepis elsieae Ischyrolepis esterhuyseniae Ischyrolepis feminea Ischyrolepis fraterna Ischyrolepis fuscidula Ischyrolepis gossypina Ischyrolepis helenae Ischyrolepis hystrix Ischyrolepis karooica Ischyrolepis laniger Ischyrolepis leptoclados Ischyrolepis longiaristata Ischyrolepis macer Ischyrolepis marlothii Ischyrolepis monanthos Ischyrolepis nana Ischyrolepis ocreata Ischyrolepis paludosa Ischyrolepis papillosa Ischyrolepis parthenocarpos Ischyrolepis pratensis Ischyrolepis pygmaea Ischyrolepis rivula Ischyrolepis rottboellioides Ischyrolepis sabulosa Ischyrolepis saxatilis Ischyrolepis schoenoides Ischyrolepis setiger Ischyrolepis sieberi Ischyrolepis sporadica Ischyrolepis subverticellata Ischyrolepis tenuis Ischyrolepis tenuissima Ischyrolepis triflora Ischyrolepis vilis Ischyrolepis virgea Ischyrolepis wallichii Ischyrolepis wittebergensis Platycaulos acutus Platycaulos anceps Platycaulos callistachyus Platycaulos cascadensis Platycaulos compressus Platycaulos depauperatus Platycaulos major Platycaulos subcompressus Restio acockii Restio alticola Restio ambiguus Restio arcuatus Restio aureolus Restio bifarius Restio bifidus Restio bifurcus Restio bolusii Restio brachiatus Restio brunneus Restio burchellii Restio capillaris Restio colliculospermus Restio communis Restio confusus Restio corneolus Restio cymosus Restio debilis Restio decipiens Restio degenerans Restio dispar Restio distans Restio distichus

Restio dodii var dodii Restio dodii var purpurascens Restio echinatus Restio egregius Restio ejuncidus Restio festuciformis Restio filiformis Restio fragilis Restio fusiformis Restio galpinii Restio harveyi Restio implicatus Restio inconspicuus Restio ingens Restio insignis Restio inveteratus Restio involutus Restio leptostachyus Restio mahonii ssp humbertii

Restio mahonii ssp mahonii

Restio micans Restio miser Restio mlanjiensis Restio montanus Restio multiflorus Restio nodosus Restio nuwebergensis Restio obscurus Restio occultus Restio pachystachyus Restio paludicola Restio papyraceus Restio patens Restio peculiaris Restio pedicellatus Restio perplexus Restio perseverans Restio pillansii Restio praeacutus Restio pulvinatus Restio pumilis Restio purpurascens Restio quadratus Restio quartziticola Restio quinquefarius Restio rarus Restio rupicola Restio saroclados Restio scaber Restio scaberulus Restio secundus Restio sejunctus Restio similis Re sp affp Restio singularis Restio stereocaulis Restio stokoei Restio strictus Restio strobilifer Restio subtilis Restio tetragonus Restio triticeus Restio tuberculatus

Restio vallis simius Restio verrucosus Restio versatilis Restio zuluensis Restio zwartbergensis Rhodocoma alpina Rhodocoma arida Rhodocoma capensis Rhodocoma foliosa Rhodocoma fruticosa Rhodocoma gigantea Rhodocoma gracilis Rhodocoma vleibergensis Staberoha aemula Staberoha banksii Staberoha cernua Staberoha distachyos Staberoha multispicula Staberoha ornata Staberoha remota Staberoha stokoei Staberoha vaginata Thamnochortus acuminatus Thamnochortus amoena Thamnochortus arenarius Thamnochortus bachmannii Thamnochortus cinereus Thamnochortus dumosus Thamnochortus ellipticus Thamnochortus erectus Thamnochortus fraternus Thamnochortus fruticosus Thamnochortus glaber Thamnochortus gracilis Thamnochortus guthrieae Thamnochortus insignis Thamnochortus karooica Thamnochortus levynsiae Thamnochortus lucens Thamnochortus muirii Thamnochortus nutans Thamnochortus obtusus Thamnochortus paniculatus Thamnochortus papyraceus Thamnochortus pellucidus Thamnochortus platypteris Thamnochortus pluristachyus Thamnochortus pulcher Thamnochortus punctatus Thamnochortus rigidus Thamnochortus schlechteri Thamnochortus spicigerus Thamnochortus sporadicus Thamnochortus stokoei 100 58 39 63 46 100 86 61 24 98 78 92 59 55 100 98 100 100 100 100 3 100 66 98 65 69 80 80 52 55 90 69 45 2 24 10 86 32 26 69 19 11 29 36 22 58 61 64 17 0 24 88 53 58 43 32 69 84 52 65 74 100 99 66 42 65 20 54 23 100 33 65 11 21 52 58 15 44 46 33 36 48 32 37 39 24 19 15 3 3 3 11 66 92 76 40 48 57 89 87 86 55 28 13 24 90 36 83 89 57 53 65 49 82 92 100 72 100 100 100 52 81 78 47 28 67 62 38 85 97 31 30 93 27 12 29 49 93 17 4 37 95 12 23 18 19 29 9 17 73 26 19 26 10 2 8 3 15 7 1 25 75 100 66 100 68 73 98 54 97 17 12 13 8 4 75 86 97 48 38 22 45 67 96 94 43 65 65 78 97 79 84 89 24 19 45 65 86 99 51 33 34 92 54 92 97 100 100 86 58 99 100 97 100 49 73 100 39 49 89 23 36 36 81 68 100 92 81 28 43 76 79 43 66 99 99 35 30 39 62 21 48 80 32 25 98 81 99 94 60 37 94 94 53 43 63 100 100 56 17 19 16 28 54 100 100 66 100 87 81 46 73 74 100 69 87 70 31 11 0 87 94 95 99 100 99 74 71 100 100 78 100 100 95 93 72 61 100 43 39 79 57 83 74 97 100 100

Tree 14: Restionaceae

Character Changes

Flowering Midpoint Time

(No significant changes)

Flowering Duration

(No significant changes)

Distributional Changes

Entering West Cape

Leaving West Cape

Entering East Cape

Leaving East Cape

Sampling of Cape species: 89%

Bootstrap values: Parsimony

Cape clade

(17)

Tree 15: Satyrium

- There are no significant changes

Character Changes

Flowering Midpoint Time

(No significant changes)

Flowering Duration

(No significant changes)

Distributional Changes

Entering West Cape

Leaving West Cape

Entering East Cape

Leaving East Cape

Cape Clade

Non-Cape relatives

82

57

82

98

96

64

64

87

100

71

53

58

98

99

86

80

94

98

Sampling of Cape species: 90%

(18)

Tree 16: Zygophyllum

- There are no significant changes

Character Changes

Flowering Midpoint Time

Flowering Duration

Distributional Changes

Entering West Cape

Leaving West Cape

Entering East Cape

Leaving East Cape

Non-Cape relatives

Cape Clade

100

100

100

100

100

100

100

Sampling of Cape species: 79%

Support values: Bayesian

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