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Molecular Phylogenetic Trees with Reconstructed Shifts in Geographic Distribution and Flowering Patterns (Flowering Durations and Flowering Midpoint) Indicated

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Molecular Phylogenetic Trees with Reconstructed Shifts in Geographic Distribution and Flowering Patterns (Flowering Durations and Flowering Midpoint) Indicated 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
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