Additional file 1 – Molecular phylogenetic trees with reconstructed shifts in geographic 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 Significant Evolutionary Character Changes Tree 1: Bruniaceae 90 Flowering Midpoint Time 93 (No significant changes) 74 92
Flowering Duration 92 (No significant changes) 99 100 Distributional Changes 98
100 Entering West Cape Leaving West Cape 98 65 Entering East Cape 100 Leaving East Cape 63 62 Sampling of Cape species: 85% 100 90 Bootstrap values: 98 Parsimony, 1000 replicates 71
79
100 99
81
69 67
85 85
54
80 53 67 100 100
99
58
100 69 97
clade 100
100
Cape 100 97 100 73 99 100 96 83 59
100 100
Non-Cape relatives Significant Evolutionary Character Changes Tree 2: Cyperaceae
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 94 Tetraria Sampling of Cape species Ficinia: 21% Tetraria: 19%
Boostrap values: Parsimony, 1000 replicates
95 92 79 100 Tetraria Ficinia
61 68
Non-Cape relatives Significant Evolutionary Character Changes Tree 3: Disa
Flowering Midpoint Time 98 100 100 Flowering Duration 100 (No significant changes) 100
Distributional Changes 100 100 100 Entering West Cape 100 100 Leaving West Cape
100 Entering East Cape 100 Leaving East Cape 100 99 Sampling of Cape species: 82% 79 96 Support values: 93 Bayesian posterior probability 81
100 100
100 100 100 91 100
100 97 100 100
64 100
68 100
100 100 100 62 100
79 83 91
100 100
98 100 100 100 100
100
100 100
100 100 99 100
56 100 100 95
100
99 100 100 100 57 100
100 78 78 100
84 100 52 100 100
100
100 100 98 100
100 100 95 100 91 100 90 100
100 100
100 100 100
100 100 100
100 100 93 100
100 100 100
100 100 100 100 100 100
98 100 100 100 100 100
100 100
100 100
Non-Cape relatives Significant Evolutionary Character Changes Tree 4: Ehrharta - there are no significant changes Flowering Midpoint Time 100 Flowering Duration
77 Distributional Changes
Entering West Cape 95 Leaving West Cape 89 Entering East Cape Leaving East Cape 83 100 Sampling of Cape species: 100% Bootstrap values: Parsimony, 300 replicates 95
100 71
74 97 Cape clade 60 79 75
Non-Cape relatives Significant Evolutionary Character Changes Tree 5: Genistoids
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
Sampling of Cape species: Crotalarieae: 43% Podalyrieae: 15%
Bootstrap values: Parsimony, 1000 replicates
87
92
97
94
61
93
63
87 61
82
61
74
62
71 + Allies
93 55
51
51 83 Aspalathus
96
97
83
69
76
52
92
96
82
82
56
54
93
81
70
89
75
55 100100
72
60
65
Podalyrieae 100
99
95
91
Non-Cape relatives Significant Evolutionary Character Changes Tree 6: Heliophila 100 Flowering Midpoint Time 95 58 Flowering Duration 100 81
Distributional Changes 68 97 Entering West Cape 88 73 Leaving West Cape Sampling of Cape species: 65% 61 Entering East Cape Support values: Bayesian posterior Leaving East Cape probabilities 96 98 87
80 100
60 100 89 100 100 79 53 100
100 100 62 68 100 100 86 Clade
Cape 97 97 100 100
87 90
100 100 100
Non-Cape relatives Significant Evolutionary Character Changes Tree 7: Indigofera
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
Sampling of Cape species: 20% Support values: Bayesian posterior probabilities
97
Cape clade 100 100 100 100 100
100
Non-Cape relatives Significant Evolutionary Character Changes Tree 8: Moraea
Flowering Midpoint Time (No significant change)
Flowering Duration 73 Distributional Changes 53
Entering West Cape 93 Leaving West Cape 91 Entering East Cape 72 Leaving East Cape 95 53 Sampling of Cape species: 39% Boostrap values: Parsimony, 1000 replicates
89
89 93
55
83
86 100
100 92 54
74 86 82 89
67
100 57 100 100 78 65 100 67
Clade 55
84
Cape 88 89 100
Non-Cape relatives Significant Evolutionary Tree 9: Muraltia Character Changes
Flowering Midpoint Time 85 Flowering Duration (No significant change)
Distributional Changes
Entering West Cape 60 63 Leaving West Cape 64
Entering East Cape 60 Leaving East Cape 53 57 Sampling of Cape species: 64% Bootstrap values: Parsimony, 500 replicates
55 96
100 59
60
60 68 63 77
97 60 54 70 99 84 54 95 98 92 65
88 100
97 100 59 100 100
100 96 84 100 100 55
56 100 100
56 96 73 86
83
99 98
Non-Cape relatives Significant Evolutionary Character Changes Tree 10: Oxalis 59 Flowering Midpoint time 60 (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 88
Entering East Cape 100 Leaving East Cape
Sampling of Cape species: 78% 57 Bootstrap values: Likelihood, 100 replicates 96 97 77 97
100 99
60
100
62
93
73
85 82 88
100 81 62 81 85
100 78 91
87 75
100 75
85 78
100 98
61 99 100
100 100 94 88 75 51 83
91
99 100 96
100 96 88
95 100
91 75
62 54
60 69 98
86 97 77
100 100 64 90
57 79 52 clade
100 93 89 100 59 Cape 61 79
64 100
Non-Cape relatives
Significant Evolutionary Tree 12: Pentaschistis Character Changes 89 99 Flowering Midpoint Time 100 100
Flowering Duration 100 83 Distributional Changes 100
Entering West Cape 100 100 Leaving West Cape 77
Entering East Cape 100 100 Leaving East Cape 98
Sampling of Cape species: 96% 100 98 Support values: 100 Bayesian posterior probabilities 100 55 Note: Depending on the nodes considered, 100 100 the basal-most node in the radiation is the location of either a slight backward shift in 100 flowering midpoint (marked with a hollow 98 triangle) or a slight forward one (marked in 71 100 100 parentheses). 72
83
100 100 100
94 96
100 100
100 100 100 100 100 100 100
99
62
98 63 100 100
100 100 100 100 63 77 Cape clade 96 100 96
96 100 78
86 92 100 100
100 ( ) 89 65 100 100 100 100 Non-Cape relatives Significant Evolutionary Character Changes Tree 13: Phylica
Flowering Midpoint Time (No significant change)
Flowering Duration
Distributional Changes 87 Entering West Cape Leaving West Cape 98 Entering East Cape Leaving East Cape 86 100 Sampling of Cape species: 10% Bootstrap values: Parsimony, 1000 replicates 64
95
87
100 64
78 73 Cape clade 100 71
Non-Cape relatives Significant Evolutionary Character Changes Tree 14: Restionaceae Flowering Midpoint Time (No significant changes)
Baloskion tetraphyllum Flowering Duration Non-Cape relatives Sporodanthus tasmanicus Anthochortus crinalis
97 83 Anthochortus graminifolius Anthochortus singularis 74 Nevillea obtusissima Hypodiscus aristatus 57 99 Hypodiscus montanus Hypodiscus squamosus 71 Distributional Changes 79 100 Mastersiella purpurea
Cape clade 74 Mastersiella spathulata 99 Cannomois dolichocaryon 100 39 Cannomois scirpoides Cannomois saundersii 100 61 Cannomois schlechteri Entering West Cape 72 Cannomois arenicola 43 Cannomois parviflora 100 Willdenowia arescens Leaving West Cape Willdenowia glomerata 93 100 Ceratocaryum fimbriatum
95 Ceratocaryum fistulosum Ceratocaryum xerophilum 100 Ceratocaryum caespitosum 100 100 Entering East Cape 78 Ceratocaryum argenteum Ceratocaryum pulchrum Leaving East Cape Restio ambiguus 100 Platycaulos depauperatus Platycaulos subcompressus Restio galpinii 92 46 58 Restio mahonii ssp mahonii 63 Restio mlanjiensis 39 78 Restio mahonii ssp humbertii Sampling of Cape species: 89% Restio quartziticola Platycaulos anceps 98 100 Platycaulos compressus Bootstrap values: Parsimony 24 Platycaulos major 61 Platycaulos acutus 86 Platycaulos callistachyus Platycaulos cascadensis Ischyrolepis fuscidula 3 Staberoha stokoei 100 Staberoha remota 95 Staberoha aemula Note: Backward shifts in flowering 100 100 98 Staberoha cernua 100 Staberoha distachyos Staberoha banksii 100 are indicated with a hollow green Staberoha multispicula 2 55 59 Staberoha ornata Staberoha vaginata triangle and precede forward shifts 100 Restio pedicellatus Re sp affp 69 66 Restio stereocaulis that concern much smaller numbers 65 Restio subtilis 98 45 Restio confusus Restio miser 90 Calopsis esterhuyseniae of species and are marked in 69 Calopsis monostylis Restio papyraceus 55 Restio echinatus 52 94 Restio nuwebergensis parentheses. 80 80 Restio bifarius Restio bifidus 75 Restio egregius Restio micans
97 Rhodocoma vleibergensis 100 Rhodocoma alpina
100 Rhodocoma fruticosa 100 Rhodocoma foliosa 99 Rhodocoma gigantea
58 Rhodocoma arida 86 Rhodocoma capensis 49 Rhodocoma gracilis 86 Thamnochortus levynsiae Thamnochortus pulcher 97 Thamnochortus gracilis 100 Thamnochortus nutans 48 Thamnochortus karooica Thamnochortus muirii 11 67 97 38 Thamnochortus paniculatus 45 Thamnochortus spicigerus 22 Thamnochortus fraternus Thamnochortus pluristachyus 86 Thamnochortus cinereus 92 92 Thamnochortus rigidus Thamnochortus glaber 34 Thamnochortus amoena 33 51 Thamnochortus papyraceus 99 Thamnochortus acuminatus 54 Thamnochortus fruticosus
94 Thamnochortus guthrieae 87 ( ) 96 Thamnochortus erectus Thamnochortus insignis 65 19 Thamnochortus arenarius 31 Thamnochortus ellipticus 43 Thamnochortus pellucidus 45 65 Thamnochortus stokoei 65 Thamnochortus dumosus
24 Thamnochortus lucens 78 Thamnochortus platypteris Thamnochortus schlechteri 89 97 Thamnochortus obtusus 84 Thamnochortus sporadicus 79 Thamnochortus bachmannii Thamnochortus punctatus 100 Askidiosperma esterhuyseniae
81 Askidiosperma rugosum Askidiosperma chartaceum 87 100 Askidiosperma andreaeanum ( ) 66 87 Askidiosperma alticolum Askidiosperma paniculatum 100 Askidiosperma albo aristata
69 Askidiosperma nitidum Askidiosperma insigne 74 73 Askidiosperma longiflorum 46 Askidiosperma capitatum
70 Askidiosperma delicatulum 73 Chondropetalum mucronatum Elegia cuspidata
94 Chondropetalum nudum 94 Chondropetalum elephantinum Chondropetalum tectorum 28 Chondropetalum marlothii 53 Chondropetalum decipiens 100 16 63 Chondropetalum hookerianum 43 Chondropetalum aggregatum 19 Chondropetalum ebracteatum Chondropetalum deustum 17 Chondropetalum acockii 56 100 Chondropetalum microcarpum 54 100 Chondropetalum rectum Elegia verreauxii ( ) Dovea macrocarpa 60 99 Elegia esterhuyseniae 0 81 Elegia capensis 94 Elegia hutchinsonii Elegia neesii 98 25 Elegia muirii 32 37 Elegia grandis Elegia prominens 100 Elegia galpinii Elegia thyrsoidea Elegia extensa Elegia asperiflora 80 92 100 Elegia caespitosa Elegia glomerata 81 49 Elegia intermedia 48 39 Elegia fastigiata 68 Elegia fucata Elegia fistulosa 81 Elegia coleura 36 89 Elegia rigida 36 Elegia spathacea 21 23 Elegia grandispicata Elegia thyrsifera 99 Elegia amoena
39 Elegia racemosa Elegia persistens 30 35 Elegia altigena 99 62 Elegia stipularis Elegia stokoei 43 Elegia atratiflora
66 Elegia squamosa Elegia fenestrata 79 28 Elegia juncea 76 Elegia vaginulata 43 Elegia equisetacea Elegia filacea 88 Restio inveteratus
32 Restio obscurus Restio fusiformis 43 58 Restio acockii 53 Restio praeacutus 69 Restio rupicola Restio perseverans
64 Restio aureolus 61 Restio perplexus 24 17 Restio pulvinatus Restio cymosus 58 Restio capillaris 22 Restio patens 0 36 29 Restio brachiatus Restio occultus Restio filiformis
11 10 Restio brunneus 24 Restio burchellii 19 Restio insignis Restio pachystachyus 69 Restio strobilifer 26 4 32 Restio nodosus 86 Restio bifurcus Restio bolusii Restio quinquefarius 65 52 Restio similis 84 Restio debilis Restio distans 99 Calopsis levynsiae 66 Calopsis rigida
100 Calopsis paniculata 74 Restio quadratus Restio tetragonus
36 Restio distichus 90 Calopsis pulchra
65 Restio harveyi 57 Calopsis aspera 8 53 Calopsis membranacea
89 Calopsis hyalina 83 Calopsis impolita Restio versatilis 66 Restio strictus 40 Restio triticeus
76 Restio verrucosus 49 92 Restio pumilis 13 Restio zwartbergensis
55 Calopsis sparsa 86 Calopsis clandestina 28 Calopsis nudiflora 13 Restio pillansii 87 Restio corneolus 89 57 Restio saroclados 48 Restio ejuncidus 24 Restio leptostachyus Restio rarus 3 Restio degenerans 3 3 Restio singularis 15 Restio alticola Restio scaber Restio montanus 11 54 Restio multiflorus Restio tuberculatus 20 65 Restio scaberulus 42 Restio sejunctus Restio stokoei Restio peculiaris 19 39 32 Restio arcuatus 48 Restio inconspicuus 37 Restio vallis simius 12 Restio secundus 36 Restio decipiens 33 24 46 Restio fragilis 44 Restio colliculospermus Restio implicatus 23 Restio festuciformis Restio zuluensis 15 100 Restio dodii var dodii
58 Restio dodii var purpurascens Restio dispar 52 Restio purpurascens 21 33 Restio ingens 11 Restio involutus 65 Restio communis Restio paludicola Calopsis andreaeana Calopsis filiformis 97 66 100 Calopsis fruticosa 75 Calopsis burchellii 54 Calopsis muirii Calopsis gracilis 98 Calopsis rigorata 100 73 Calopsis marlothii Calopsis viminea
17 68 Calopsis adpressa Calopsis dura 100 Ischyrolepis anomala 72 Ischyrolepis feminea
92 Ischyrolepis wallichii 82 Ischyrolepis rivula Ischyrolepis tenuissima Ischyrolepis longiaristata 25 Ischyrolepis sabulosa 100 100 Ischyrolepis rottboellioides 100 Ischyrolepis paludosa 47 Ischyrolepis papillosa Ischyrolepis marlothii 1 78 81 Ischyrolepis schoenoides 52 Ischyrolepis constipata Ischyrolepis virgea 28 Ischyrolepis pratensis 38 Ischyrolepis saxatilis
62 Ischyrolepis sporadica 7 67 Ischyrolepis macer 93 Ischyrolepis pygmaea 31 Ischyrolepis caespitosa 30 Ischyrolepis cincinnata
97 Ischyrolepis curviramis 85 Ischyrolepis duthieae Ischyrolepis nana Ischyrolepis vilis 15 4 93 Ischyrolepis laniger 49 Ischyrolepis coactilis 17 Ischyrolepis karooica Ischyrolepis sieberi 29 12 Ischyrolepis monanthos 27 Ischyrolepis parthenocarpos Ischyrolepis tenuis 3 Ischyrolepis hystrix 2 Ischyrolepis esterhuyseniae
10 19 Ischyrolepis fraterna Ischyrolepis gossypina 26 26 Ischyrolepis affinis 73 Ischyrolepis elsieae 19 Ischyrolepis ocreata 8 Ischyrolepis arida 17 9 Ischyrolepis capensis 29 Ischyrolepis curvibracteata Ischyrolepis wittebergensis 37 Ischyrolepis eleocharis Ischyrolepis leptoclados 18 95 Ischyrolepis subverticellata Ischyrolepis triflora 23 12 Ischyrolepis helenae Ischyrolepis setiger 43 45 Ischyrolepis nubigena 100 Ischyrolepis gaudi var gaudi 38 Ischyrolepis gaudi var luxurian
55 Ischyrolepis venustulus 79 Ischyrolepis distracta Ischyrolepis unispicata Significant Evolutionary Character Changes Tree 15: Satyrium - There are no significant 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: 90% Bootstrap values: Parsimony, 1000 replicates
82 94 98 57
82 99 86 80
87
64 96 Cape Clade 98 64 98
71 53 58
100
Non-Cape relatives Significant Evolutionary Character Changes Tree 16: Zygophyllum - There are no significant changes Flowering Midpoint Time 100 Flowering Duration
Distributional Changes
Entering West Cape Leaving West Cape 100 Entering East Cape Leaving East Cape
Sampling of Cape species: 79% Support values: Bayesian posterior probabilities Cape Clade 100 100 100
100 100
Non-Cape relatives