Papilionidae

Supplementary figure 1. Phylogenetic relationships of 408 swallowtail butterfly species (Papilionidae). Left phylogeny is inferred with the maximum-likelihood approach implemented with IQ-TREE, and right phylogeny is inferred with the Bayesian approach implemented with MrBayes. Both phylogenies show similar relationships except for the placement of the genus Teinopalpus, found as sister to Papilionini + Troidini with IQ-TREE and sister to Meandrusa (Papilionini) with MrBayes. Node support is indicated by ultrafast bootstrap and posterior probabilities on the maximum-likelihood and Bayesian phylogenies, respectively, with values of 95% and 0.95 considered as indicative of strong node support.

Choaspes benjaminii Hyblaea puera 37 Hyblaea puera 0.76 88 0.95 Macrosoma macrosoma 100 Macrosoma macrosoma Macrosoma tipulata Macrosoma tipulata Choaspes benjaminii Colias eurytheme 100 1 1 Hylephila phyleus 100 100 Pieris napi 1 Pyrgus communis 64 Pieris rapae 1 Erynnis montanus Hylephila phyleus 1 100 0.63 Erynnis tristis 100 Pyrgus communis Colias eurytheme 100 Erynnis montanus 1 Pieris napi 36 Erynnis tristis 1 Pieris rapae Coenonympha tullia 92 0.53 Coenonympha tullia 98 Libythea celtis 1 Libythea celtis Vanessa cardui 0.76 Vanessa cardui 99 Hamearis lucina 100 1 Hamearis lucina 100 Apodemia mormo 1 Apodemia mormo 92 Riodina lysippus 1 Riodina lysippus Lycaena helloides 1 100 Lycaena helloides 100 Favonius cognatus 1 Favonius cognatus Plebejus pylaon 1 Plebejus pylaon Baronia brevicornis Baronia Baronia brevicornis Archon apollinaris 100 0.93 Archon apollinaris 100 Archon bostanchii Archon bostanchii Archon apollinus1 Archon 1 100 1 Archon apollinus1 100 Archon apollinus2 1 Archon apollinus2 Luehdorfia japonica Luehdorfia japonica 100 Luehdorfia puziloi 1 Luehdorfia puziloi 100 Luehdorfia 0.98 100Luehdorfia chinensis Luehdorfia chinensis 99 100Luehdorfia longicaudata 1 1 Luehdorfia longicaudata Luehdorfia taibai 1 Luehdorfia taibai Sericinus montela Sericinus Sericinus montela Bhutanitis thaidina 100 Bhutanitis Bhutanitis thaidina 100 100 Bhutanitis lidderdalii 1 1 Bhutanitis lidderdalii Bhutanitis mansfieldi 1 Bhutanitis mansfieldi 100 100Zerynthia polyxena1 1 1 Zerynthia polyxena1 100 Zerynthia polyxena2 Zerynthia 1 Zerynthia polyxena2 100 Zerynthia rumina1 1 Zerynthia rumina1 100 Zerynthia rumina2 1 Zerynthia rumina2 Allancastria louristana Allancastria louristana 100 Allancastria deyrollei 1 Allancastria deyrollei 100 Allancastria 1 95 100 Allancastria cretica Allancastria cretica 100 Allancastria caucasica 1 1 Allancastria caucasica Allancastria cerisyi 1 Allancastria cerisyi 100 Hypermnestra helios1 Hypermnestra Hypermnestra helios1 Hypermnestra helios2 1 Hypermnestra helios2 100 Parnassius apollonius Parnassius apollonius Parnassius honrathi 1 Parnassius honrathi Parnassius dongalaicus Parnassius tianschanicus 100 100 Parnassius mercurius 0.83 100 0.98 Parnassius actius 100Parnassius epaphus Parnassius jacquemontii Parnassius nomion 1 0.75 Parnassius dongalaicus 100 54 Parnassius tianschanicus 1 Parnassius nomion 97 Parnassius actius 1 Parnassius epaphus 100 Parnassius jacquemontii 1 0.82 Parnassius mercurius Parnassius apollo3 1 54 Parnassius apollo3 99 99 Parnassius apollo1 1 Parnassius apollo2 88 Parnassius apollo5 0.57Parnassius apollo4 100Parnassius apollo4 Parnassius apollo1 100 Parnassius apollo2 1 1 Parnassius apollo5 100Parnassius bremeri 0.94Parnassius bremeri 100 Parnassius sacerdos Parnassius sacerdos 100Parnassius phoebus 1 100 Parnassius phoebus 100 100Parnassius behrii 1 Parnassius behrii Parnassius smintheus 1 1 Parnassius smintheus Parnassius boedromius Parnassius boedromius 100 Parnassius andreji 1 1 100 1 Parnassius andreji 100 Parnassius simo Parnassius 1 Parnassius simo 100 Parnassius simonius 1 Parnassius simonius Parnassius orleans Parnassius orleans 100 Parnassius nordmanni 1 Parnassius nordmanni 100 Parnassius clodius 1 Parnassius clodius 100 Parnassius eversmanni 0.99 Parnassius eversmanni Parnassius glacialis 100100 1 1 Parnassius glacialis 100 Parnassius hoenei 0.98 Parnassius hoenei 100 Parnassius stubbendorfii 1 Parnassius stubbendorfii Parnassius ariadne Parnassius ariadne 100 Parnassius mnemosyne3 1 80 100 0.77 Parnassius mnemosyne3 100 Parnassius mnemosyne1 0.94 Parnassius mnemosyne1 Parnassius mnemosyne2 0.98 Parnassius mnemosyne2 Parnassius hardwickii Parnassius hardwickii 100 Parnassius schultei 1 Parnassius schultei Parnassius acco Parnassius acco 100 100 1 100 Parnassius hannyngtoni 1 Parnassius hannyngtoni 98 Parnassius huberi 1 0.79 Parnassius huberi 99 Parnassius maharaja Parnassius maharaja 100 Parnassius cephalus 1 Parnassius cephalus 75 Parnassius szechenyii 0.63 1 Parnassius szechenyii 100Parnassius arctica Parnassius arctica Parnassius tenedius 1 Parnassius tenedius 100 Parnassius augustus Parnassius augustus Parnassius imperator 1 Parnassius imperator 100 Parnassius acdestis 1 Parnassius acdestis 73 100 Papilio inopinatus 0.6 Papilio inopinatus 89 Parnassius charltonius 0.72 1 Parnassius charltonius 98 Parnassius autocrator 0.97 100 1 Parnassius autocrator 100 Parnassius loxias 0.98 Parnassius davydovi 100 Parnassius davydovi 1 Parnassius loxias Parnassius staudingeri1 Parnassius staudingeri1 100 Parnassius staudingeri2 0.52 99 0.93 Parnassius staudingeri2 99 Parnassius patricius Parnassius patricius 94 Parnassius delphius 0.92 Parnassius delphius 93 Parnassius maximinus 0.8 Parnassius maximinus 100 Parnassius jacobsoni 1 100 0.99 Parnassius jacobsoni 100 Parnassius cardinal 1 Parnassius cardinal 100 Parnassius staudingeri3 1 Parnassius staudingeri3 Parnassius hide 70 0.92 Parnassius hide 100 Parnassius stenosemus Parnassius stenosemus Parnassius stoliczkanus 1 Parnassius stoliczkanus 100 Lamproptera meges Lamproptera Lamproptera curius Lamproptera curius 1 1 Lamproptera meges 100Iphiclides podalirius Iphiclides Iphiclides feisthamelii Iphiclides feisthamelii 1 Iphiclides podalirius Protographium philolaus Protographium philolaus 100 93 Protographium epidaus Protographium 0.94 0.83 Protographium epidaus 53 Protographium marcellus 1 Protographium marcellus 100 Protographium asius 95 0.91 Protographium asius 100 Mimoides euryleon 0.8 Mimoides euryleon 97 Mimoides pausanias Mimoides 0.83 Mimoides pausanias 100 100 Mimoides ilus 1 Mimoides ilus Mimoides lysithous 0.62 Mimoides lysithous 100 Eurytides serville “Eurytides” 0.99 1 Eurytides orabilis 99 Eurytides orabilis Eurytides serville 100 Protographium leucaspis 1 0.92 Protographium leucaspis 97 Protographium dioxippus Protographium dioxippus 99 Protographium thyastes 0.7 98 0.54 Protographium thyastes 97 Eurytides helioss “Eurytides” Eurytides helioss Protesilaus telesilaus 0.57 Protesilaus telesilaus 59 Protesilaus molops 1 99 Protesilaus 0.77Protesilaus molops 100 Protesilaus glaucolaus Protesilaus glaucolaus Protesilaus protesilaus 0.89Protesilaus protesilaus Graphium tynderaeus 1 Graphium macleayanus 100 Graphium latreillianus Graphium phidias 98 Graphium leonidas 99 98 Graphium leechi 100 Graphium adamastor 0.87 1 Graphium arycles 100 Graphium schubotzi Graphium evemon 100 Graphium angolanus 1 Graphium bathycles 56 Graphium ridleyanus 1 Graphium chironides Graphium nomius 1 Graphium doson Graphium macareus 0.52 Graphium eurypylus 100 Graphium ramaceus 98 92 Graphium meyeri 100 Graphium delessertii Graphium eurous Graphium xenocles 1 0.93 Graphium tamerlanus 99 0.98 98 Graphium decolor Graphium incertus 100 Graphium antiphates 0.81 0.78 Graphium glycerion 85 Graphium dorcus 0.52 Graphium sichuanica 100 Graphium androcles 0.81Graphium mandarinus 89 Graphium aristeus 0.53 Graphium timur 99 Graphium thule Graphium weiskei 100 Graphium agetes 0.6 Protographium leosthenes 100 Graphium stratiotes 0.61 Graphium wallacei Graphium phidias Graphium 0.71 Graphium agamemnon 42 Graphium leechi 0.8 Graphium macfarlanei 63 Graphium macleayanus Graphium codrus Graphium arycles 0.91 Graphium empedovana 63 100 Graphium evemon 0.6 1 Graphium cloanthus 100 100 Graphium bathycles 1 Graphium milon 100 Graphium chironides Graphium sarpedon 95 Graphium eurypylus Graphium nomius 95 Graphium doson Graphium adamastor 16 Graphium meyeri 0.85 Graphium schubotzi Graphium incertus 0.7 Graphium angolanus 98 94 Graphium glycerion 0.97 Graphium ridleyanus 100 Graphium sichuanica 99 0.58 Graphium tynderaeus 89 Graphium eurous 0.58 Graphium latreillianus 74 Graphium tamerlanus 0.63 Graphium leonidas 100Graphium mandarinus Graphium macareus Graphium timur 1 Graphium ramaceus 66 Graphium weiskei 0.99 Graphium delessertii 78 Protographium leosthenes 0.81 Graphium xenocles 79 Graphium wallacei 1 Graphium decolor 99 Graphium agamemnon 0.99 Graphium antiphates 79 98 Graphium macfarlanei 0.99 Graphium dorcus Graphium codrus 0.88 Graphium androcles 100 Graphium empedovana 1 Graphium aristeus 98 Graphium cloanthus 0.98 Graphium thule 100 0.93 Graphium agetes 100 Graphium sarpedon 1 Graphium milon 1 Graphium stratiotes 100Teinopalpus imperialis Teinopalpus Battus philenor Teinopalpus aureus 1 Battus polydamas Battus philenor 1 Battus polystictus 100 Battus polydamas 1 Battus belus 100 Battus polystictus Battus 0.93 Battus crassus 100 Battus belus 0.99 Battus ingenuus 100 Battus crassus Pharmacophagus antenor 100 Battus ingenuus Cressida cressida Pharmacophagus antenor Pharmacophagus 1 Losaria coon 100 Cressida cressida Cressida 0.92 Losaria neptunus Losaria neptunus 1 Pachliopta aristolochiae 99 Losaria coon Losaria 0.92 Pachliopta kotzebuea 100 Pachliopta aristolochiae 1 100 0.89 Pachliopta hector 100 Pachliopta kotzebuea 0.75 Pachliopta liris 100 Pachliopta hector Pachliopta 1 Pachliopta polydorus 100 Pachliopta polydorus 1 Atrophaneura dixoni 100 Pachliopta liris Atrophaneura horishana 99 Atrophaneura dixoni 1 Atrophaneura luchti 89 Atrophaneura horishana 0.9 Atrophaneura priapus 100100 Atrophaneura varuna Atrophaneura 1 0.61 Atrophaneura nox 100 83 Atrophaneura nox Atrophaneura varuna 99 99 Atrophaneura luchti Byasa impediens Atrophaneura priapus 1 1 Byasa plutonius Byasa impediens 0.951 Byasa mencius 100 Byasa plutonius Byasa polyeuctes Byasa mencius 0.77 98 100 Byasa 0.75 Byasa laos 98 Byasa polyeuctes 0.78 Byasa alcinous 99 Byasa laos Byasa dasarada 100 Byasa alcinous 1 Euryades corethrus 100 Byasa dasarada Euryades duponchelii 100 Euryades corethrus Euryades 0.81 Parides ascanius Euryades duponchelii 0.95 Parides bunichus 94 Parides ascanius Parides agavus 98 81 Parides bunichus 0.58 Parides montezuma 1 99 Parides montezuma Parides proneus 94 Parides agavus Parides iphidamas 64 Parides proneus 0.99 Parides aeneas Parides chabrias 0.58 0.98 Parides tros 71 Parides hahneli 0.99 1 Parides lysander 54 57 Parides childrenae 1 Parides burchellanus 78 Parides photinus 1 Parides panthonus 79 Parides panares 1 Parides neophilus 71 Parides sesostris 1 Parides eurimedes 100 79 Parides anchises 0.98 100 Parides Parides zacynthus 100 Parides erithalion 0.93 Parides chabrias Parides vertumnus 0.5 Parides hahneli Parides iphidamas 0.94 Parides childrenae 95 Parides aeneas 0.97 Parides photinus 73 97 Parides tros 1 Parides panares Parides lysander 0.96 Parides sesostris 92 100 0.6 100Parides burchellanus Parides anchises 94 Parides panthonus 0.98 Parides erithalion Parides neophilus 0.96 Parides vertumnus 95 Parides eurimedes Trogonoptera brookiana 95 Parides zacynthus 1 Trogonoptera trojana Trogonoptera brookiana Ornithoptera richmondia 100 Trogonoptera trojana Trogonoptera 1 Ornithoptera croesus Ornithoptera richmondia 0.94Ornithoptera aesacus 97 100 Ornithoptera croesus 0.6 Ornithoptera euphorion 55 Ornithoptera priamus 1 1 Ornithoptera priamus 96 Ornithoptera aesacus Ornithoptera alexandrae 100 93 1 100 Ornithoptera euphorion 0.75 Ornithoptera victoriae 99 Ornithoptera alexandrae Ornithoptera 1 Ornithoptera rothschildi Ornithoptera victoriae 1 Ornithoptera goliath 98 Ornithoptera rothschildi 0.72 Ornithoptera chimaera 99 Ornithoptera goliath 1 0.69 Ornithoptera tithonus 87 Ornithoptera chimaera 1 Ornithoptera meridionalis 100 87 Ornithoptera tithonus 0.96 Ornithoptera arfakensis 99 Ornithoptera meridionalis 1 Ornithoptera paradisea 100 Ornithoptera paradisea Troides hypolitus 100 Ornithoptera arfakensis Troides magellanus Troides hypolitus 1 Troides andromache 1 100 Troides magellanus 1 Troides cuneifera Troides andromache 0.54 1 Troides amphrysus 100 100 Troides miranda 97 Troides cuneifera 1 100 Troides amphrysus Troides plato 100 Troides miranda Troides prattorum Troides plato 1 Troides vandepolli Troides helena Troides helena 100100Troides oblongomaculatus 0.59 1 Troides oblongomaculatus 100 Troides vandepolli Troides aeacus 53 Troides prattorum Troides 0.98 Troides minos 54 Troides aeacus 0.7 Troides criton 100 Troides minos Troides rhadamantus 100 Troides criton 0.98 Troides riedeli Troides rhadamantus Troides haliphron 100 55 Troides riedeli 0.98Troides naias 100 0.99 Troides staudingeri 98 Troides haliphron 98 Troides naias 1 Meandrusa payeni Troides staudingeri 0.81 Meandrusa sciron 100 Meandrusa payeni Meandrusa 1 Teinopalpus aureus Meandrusa sciron Teinopalpus imperialis Papilio hyppason Papilio alexanor Papilio andraemon Papilio clytia 100 84 Papilio machaonides 0.99 Papilio paradoxa 100 Papilio paeon 1 Papilio agestor 84 100 Papilio aristor 0.53 1 1 Papilio epycides Papilio caiguanabus 1 Papilio slateri 95 100 Papilio thoas 1 Papilio laglaizei Papilio oviedo 0.8 Papilio osmana 95 Papilio melonius 1 Papilio veiovis 99 98 Papilio homothoas Papilio esperanza 98 Papilio cresphontes 0.94 Papilio troilus 100Papilio rumiko 1 Papilio palamedes Papilio astyalus 0.54 Papilio pilumnus 100 Papilio ornythion 1 Papilio elwesi 100 Papilio pallas 1Papilio maraho 98 58 Papilio aristodemus Papilio multicaudata 58 Papilio eurymedon 97 100 Papilio androgeus 0.94 1 1 Papilio thersites 0.87 Papilio rutulus Papilio torquatus 1 Papilio canadensis 96 Papilio himeros 1 Papilio appalachiensis Papilio hectorides 0.89 Papilio glaucus 68 100 Papilio lamarchei Papilio neyi 94 Papilio oxynius 0.87 Papilio scamander Papilio garleppi 0.57 0.89 Papilio zagreus 96 44 0.88 96 Papilio chiansiades 0.94 Papilio homerus 54 Papilio isidorus 0.97 Papilio warscewiczii Papilio pelaus 0.78 1 Papilio cacicus 84 Papilio pharnaces Papilio euterpinus 100Papilio rogeri Papilio garamas 84 Papilio anchisiades 0.96 Papilio birchallii 77 0.99 77 Papilio epenetus 1 Papilio menatius 100 Papilio erostratus Papilio victorinus 97 Papilio clytia Papilio hyppason Papilio paradoxa 1 0.99 Papilio andraemon 100 Papilio agestor Papilio machaonides 100 Papilio epycides Papilio paeon 100 Papilio slateri 0.99 Papilio aristor 100 0.91 1 Papilio caiguanabus 100 Papilio laglaizei 100 Papilio osmana 0.99 1 Papilio oviedo 99 Papilio veiovis Papilio thoas Papilio esperanza 0.95 Papilio melonius 98 1 0.5 Papilio homothoas 100 Papilio pilumnus Papilio palamedes 0.58 1 Papilio cresphontes 63 Papilio troilus Papilio rumiko 99 Papilio elwesi 1 Papilio androgeus 100Papilio maraho Papilio thersites Papilio multicaudata 1 Papilio aristodemus 100 Papilio eurymedon 0.68 Papilio astyalus 98 100Papilio rutulus 0.66 Papilio ornythion 100 0.97 1 Papilio pallas 100 Papilio canadensis 100Papilio glaucus 1 Papilio himeros 98 Papilio appalachiensis 0.99 Papilio torquatus Papilio scamander 1 Papilio hectorides 99 Papilio zagreus Papilio lamarchei 68 Papilio cacicus 0.83 Papilio oxynius 98 100 82 Papilio euterpinus 0.97 Papilio pelaus 69 Papilio neyi 0.87 Papilio chiansiades 80 Papilio warscewiczii 0.51 Papilio isidorus Papilio homerus Papilio anchisiades 71 Papilio garamas Papilio epenetus 100 0.6 Papilio erostratus 100 Papilio birchallii 100Papilio menatius 0.94 Papilio garleppi Papilio victorinus 1 Papilio pharnaces Papilio alexanor Papilio rogeri Papilio gigon Papilio anactus 100 Papilio demolion Papilio gigon 100 Papilio liomedon 0.88 1 Papilio demolion 100 1 98 Papilio noblei Papilio liomedon 100 Papilio delalandei 0.66 Papilio noblei 69 Papilio lormieri 1 Papilio delalandei 100 100 Papilio antimachus Papilio lormieri Papilio rex 1 1 Papilio antimachus 100 Papilio constantinus Papilio rex 100 Papilio phorcas 1 Papilio constantinus 99 Papilio meriones 1 Papilio phorcas 100 100 0.74 100 Papilio dardanus 1 Papilio meriones Papilio humbloti 0.97 Papilio dardanus Papilio anactus Papilio humbloti Papilio xuthus 1 1 Papilio benguetana 100 Papilio benguetana Papilio Papilio xuthus 100 Papilio indra 1 Papilio indra 100 100 Papilio polyxenes 1 1 Papilio polyxenes 68 Papilio zelicaon Papilio zelicaon 100 Papilio hospiton 1 Papilio hospiton 1 Papilio brevicauda 100 98 Papilio hippocrates 100Papilio brevicauda 1 Papilio hippocrates Papilio machaon 1 Papilio machaon 100Papilio oregonius Papilio oregonius 99 Papilio nireus Papilio nobilis Papilio nobilis 0.98 Papilio epiphorbas 87 Papilio zalmoxis 0.76 Papilio nireus 95 Papilio epiphorbas 1 Papilio oribazus 91 Papilio oribazus Papilio zalmoxis Papilio montrouzieri Papilio montrouzieri 100 1 Papilio ulysses3 1 Papilio ulysses3 82 100 Papilio ulysses1 1 Papilio ulysses1 100 Papilio ulysses2 Papilio ulysses2 Papilio crino Papilio crino Papilio blumei 1 Papilio blumei 98 100 1 Papilio daedalus 100 100 Papilio daedalus 1 100 Papilio buddha 0.55 Papilio buddha 100 Papilio palinurus 1 1 1 Papilio palinurus 80 Papilio neumoegeni Papilio neumoegeni 100 1 Papilio pericles 0.97 Papilio pericles 100 Papilio lorquinianus 1 Papilio lorquinianus 100 100 Papilio peranthus Papilio peranthus Papilio paris3 0.51 Papilio paris3 100 Papilio karna 1 Papilio karna 99 Papilio paris1 0.83 1 Papilio paris1 100Papilio paris2 Papilio paris2 100Papilio maackii 1 1 Papilio maackii 100 Papilio syfanius Papilio syfanius 100 1 Papilio krishna 100 Papilio krishna 0.99 Papilio arcturus 0.71 1 Papilio arcturus 100 Papilio hopponis Papilio hopponis 71 99 1 Papilio dialis 100 Papilio dialis 0.74 100Papilio chikae 1 Papilio chikae 100 Papilio hermeli 1 Papilio hermeli Papilio polyctor Papilio polyctor 100 1 Papilio bianor 0.62 Papilio bianor 100 Papilio dehaanii1 1 Papilio dehaanii1 100 Papilio dehaanii2 Papilio dehaanii2 Papilio morondavana Papilio morondavana 100 Papilio grosesmithi 1 Papilio grosesmithi 100 0.99 Papilio demoleus 0.87 Papilio demoleus 100 Papilio demodocus 1 Papilio demodocus 100 Papilio erithonioides Papilio erithonioides Papilio iswara Papilio ambrax 1 Papilio iswara 0.99 Papilio amynthor 99 Papilio amynthor 0.99 0.99 Papilio enganius 83 68 94 Papilio helenus Papilio helenus 95 Papilio enganius Papilio tydeus 48 Papilio tydeus 1 0.99Papilio aegeus 0.2 100 100Papilio aegeus 1 Papilio gambrisius2 Papilio gambrisius2 0.09 0.62 Papilio bridgei 99 Papilio bridgei 0.87 Papilio gambrisius1 99 98 Papilio gambrisius1 1 Papilio fuscus Papilio hipponous 100 Papilio fuscus 0.55 98 Papilio albinus 0.92 Papilio pitmani 98 Papilio heringi Papilio prexaspes 97 Papilio prexaspes Papilio albinus 98 0.68 89 Papilio hipponous Papilio heringi Papilio pitmani 0.55 Papilio ambrax Papilio polytes Papilio polytes Papilio nephelus 69 Papilio macilentus 1 Papilio dravidarum 0.74 Papilio dravidarum 61 100 Papilio nephelus 0.57 0.78Papilio castor 66 Papilio castor Papilio mahadeva 100Papilio mahadeva Papilio macilentus 57 Papilio protenor 1 Papilio demetrius 100Papilio demetrius 0.59 Papilio protenor Papilio bootes 1 Papilio bootes 92 99 Papilio forbesi 0.95 1 Papilio forbesi 100Papilio thaiwanus Papilio thaiwanus 100 Papilio deiphobus 1 Papilio deiphobus 100 1 Papilio rumanzovia 100 Papilio rumanzovia 1 Papilio oenomaus 0.87 Papilio oenomaus 100 Papilio memnon 1 Papilio memnon 100 Papilio polymnestor Papilio polymnestor Supplementary figure 2. Node support (ultrafast bootstrap) of the maximum-likelihood phylogeny. The histogram shows the distribution of node support for all Papilionidae, and indicates a high overall tree resolution with ~80% of nodes having ultrafast bootstrap values ≥ 95%.

350 79% of nodes have UFBS > 95 77% of nodes have UFBS = 100 mean of node support = 94 300 median of node support = 100

250

200

150 Number of nodes

100

0 20 40 60 80 100

Ultrafast bootstrap (UFBS) values

Supplementary figure 3. Bayesian estimates of divergence times for swallowtail butterflies. The first inference was performed with exponential priors on fossil calibrations, while the second inference was carried out with uniform priors. The analysis based on exponential priors estimated a crown age for the family at 55.4 Ma (95% CI: 47.8-71.0 Ma), while the analysis based on uniform priors estimated the origin at 67.2 Ma (95% CI: 47.8-112 Ma).

Cretaceous

70 Upper

Paleocene 60

50 Paleogene

Eocene

30 Oligocene

20 Neogene

Miocene

Quat. Pliocene Pleistocene 0 Holocene Papilio memnon Papilio polymnestor Papilio oenomaus Papilio deiphobus Papilio rumanzovia Papilio forbesi Papilio thaiwanus Papilio bootes Papilio demetrius Papilio protenor Papilio macilentus Papilio castor Papilio mahadeva Papilio dravidarum Papilio nephelus Papilio ambrax Papilio polytes Papilio albinus Papilio heringi Papilio prexaspes Papilio hipponous Papilio pitmani Papilio fuscus Papilio aegeus Papilio gambrisius2 Papilio bridgei Papilio gambrisius1 Papilio tydeus Papilio enganius Papilio helenus Papilio amynthor Papilio iswara Papilio demodocus Papilio erithonioides Papilio demoleus Papilio grosesmithi Papilio morondavana Papilio dehaanii1 Papilio dehaanii2 Papilio bianor Papilio polyctor Papilio chikae Papilio hermeli Papilio dialis Papilio arcturus Papilio hopponis Papilio krishna Papilio maackii Papilio syfanius Papilio paris1 Papilio paris2 Papilio karna Papilio paris3 Papilio buddha Papilio palinurus Papilio daedalus Papilio blumei Papilio lorquinianus Papilio peranthus Papilio pericles Papilio neumoegeni Papilio crino Papilio ulysses1 Papilio ulysses2 Papilio ulysses3 Papilio montrouzieri Papilio epiphorbas Papilio nireus Papilio oribazus Papilio zalmoxis Papilio nobilis Papilio machaon Papilio oregonius Papilio brevicauda Papilio hippocrates Papilio hospiton Papilio polyxenes Papilio zelicaon Papilio indra Papilio benguetana Papilio xuthus Papilio dardanus Papilio humbloti Papilio meriones Papilio phorcas Papilio constantinus Papilio antimachus Papilio rex Papilio delalandei Papilio lormieri Papilio demolion Papilio liomedon Papilio noblei Papilio gigon Papilio anactus Papilio alexanor Papilio erostratus Papilio garleppi Papilio pharnaces Papilio rogeri Papilio anchisiades Papilio epenetus Papilio chiansiades Papilio isidorus Papilio pelaus Papilio oxynius Papilio hectorides Papilio lamarchei Papilio himeros Papilio torquatus Papilio ornythion Papilio pallas Papilio astyalus Papilio aristodemus Papilio androgeus Papilio thersites Papilio cresphontes Papilio rumiko Papilio homothoas Papilio melonius Papilio oviedo Papilio thoas Papilio aristor Papilio caiguanabus Papilio paeon Papilio andraemon Papilio machaonides Papilio hyppason Papilio menatius Papilio victorinus Papilio birchallii Papilio garamas Papilio cacicus Papilio euterpinus Papilio warscewiczii Papilio homerus Papilio scamander Papilio zagreus Papilio neyi Papilio appalachiensis Papilio glaucus Papilio canadensis Papilio eurymedon Papilio rutulus Papilio multicaudata Papilio elwesi Papilio maraho Papilio palamedes Papilio pilumnus Papilio troilus Papilio esperanza Papilio osmana Papilio veiovis Papilio laglaizei Papilio epycides Papilio slateri Papilio agestor Papilio clytia Papilio paradoxa payeniMeandrusa sciron Meandrusa Troides naias Troides staudingeri Troides haliphron Troides riedeli Troides criton Troides rhadamantus Troides aeacus Troides minos Troides helena Troides oblongomaculatus Troides prattorum Troides vandepolli Troides plato Troides amphrysus Troides miranda Troides cuneifera Troides andromache Troides magellanus Troides hypolitus arfakensisOrnithoptera paradisea Ornithoptera meridionalis Ornithoptera tithonus Ornithoptera chimaera Ornithoptera goliath Ornithoptera rothschildi Ornithoptera alexandraeOrnithoptera victoriae Ornithoptera aesacus Ornithoptera euphorion Ornithoptera priamus Ornithoptera croesus Ornithoptera richmondia Ornithoptera Trogonoptera brookiana Trogonoptera trojana Parides burchellanus Parides panthonus Parides lysander Parides eurimedes Parides zacynthus Parides neophilus Parides aeneas Parides tros Parides iphidamas Parides erithalion Parides vertumnus Parides anchises Parides sesostris Parides panares Parides photinus Parides childrenae Parides chabrias Parides hahneli Parides agavus Parides montezuma Parides proneus Parides ascanius Parides bunichus corethrus Euryades duponchelii Euryades Cressida cressida Byasa alcinous Byasa dasarada Byasa laos Byasa mencius Byasa polyeuctes Byasa plutonius Byasa impediens Atrophaneura luchti Atrophaneura priapus Atrophaneura nox Atrophaneura varuna Atrophaneura dixoni Atrophaneura horishana Pachliopta liris Pachliopta polydorus Pachliopta hector Pachliopta aristolochiae Pachliopta kotzebuea coon Losaria neptunus Losaria antenor Pharmacophagus Battus crassus Battus ingenuus Battus belus Battus polystictus Battus philenor Battus polydamas Teinopalpus aureus Teinopalpus imperialis Graphium agamemnon Graphium macfarlanei Graphium wallacei Graphium weiskei Protographium leosthenes Graphium milon Graphium sarpedon Graphium cloanthus Graphium codrus Graphium empedovana Graphium glycerion Graphium sichuanica Graphium mandarinus Graphium timur Graphium incertus Graphium eurous Graphium tamerlanus Graphium doson Graphium eurypylus Graphium meyeri Graphium bathycles Graphium chironides Cretaceous

70 Upper

Paleocene 60

50 Paleogene

Eocene

30 Oligocene

20 Neogene

Miocene

Magnoliaceae Rosaceae Hernandiaceae Zygophyllaceae ( Fabaceae Secondary Papaveraceae Lauraceae Apiaceae Crassulaceae Annonaceae Rutaceae Aristolochiaceae host plants Main Legend

Acacia host plants host plants +

Saxifragaceae ) Ma Ma

50 50 Eocene

40 40 30 30 Oligocene

20 20

Miocene

10 10

Pl Pl

P 0 Ornithoptera_priamus Ornithoptera_aesacus Ornithoptera_euphorion Ornithoptera_alexandrae Ornithoptera_victoriae Ornithoptera_rothschildi Ornithoptera_goliath Ornithoptera_chimaera Ornithoptera_tithonus Ornithoptera_meridionalis Ornithoptera_arfakensis Ornithoptera_paradisea Troides_hypolitus Troides_magellanus Troides_andromache Troides_cuneifera Troides_amphrysus Troides_miranda Troides_plato Troides_prattorum Troides_vandepolli Troides_helena Troides_oblongomaculatus Troides_aeacus Troides_minos Troides_criton Troides_rhadamantus Troides_riedeli Troides_haliphron Troides_naias Troides_staudingeri Meandrusa_payeni Meandrusa_sciron Papilio_clytia Papilio_paradoxa Papilio_agestor Papilio_epycides Papilio_slateri Papilio_laglaizei Papilio_osmana Papilio_veiovis Papilio_esperanza Papilio_troilus Papilio_palamedes Papilio_pilumnus Papilio_elwesi Papilio_maraho Papilio_multicaudata Papilio_eurymedon Papilio_rutulus Papilio_canadensis Papilio_appalachiensis Papilio_glaucus Papilio_neyi Papilio_scamander Papilio_zagreus Papilio_garamas Papilio_birchallii Papilio_menatius Papilio_victorinus Papilio_homerus Papilio_warscewiczii Papilio_cacicus Papilio_euterpinus Papilio_hyppason Papilio_andraemon Papilio_machaonides Papilio_paeon Papilio_aristor Papilio_caiguanabus Papilio_oviedo Papilio_thoas Papilio_melonius Papilio_homothoas Papilio_cresphontes Papilio_rumiko Papilio_androgeus Papilio_thersites Papilio_aristodemus Papilio_astyalus Papilio_ornythion Papilio_pallas Papilio_himeros Papilio_torquatus Papilio_hectorides Papilio_lamarchei Papilio_oxynius Papilio_pelaus Papilio_chiansiades Papilio_isidorus Papilio_anchisiades Papilio_epenetus Papilio_erostratus Papilio_garleppi Papilio_pharnaces Papilio_rogeri Papilio_alexanor Papilio_anactus Papilio_gigon Papilio_noblei Papilio_demolion Papilio_liomedon Papilio_delalandei Papilio_lormieri Papilio_antimachus Papilio_rex Papilio_constantinus Papilio_phorcas Papilio_meriones Papilio_dardanus Papilio_humbloti Papilio_benguetana Papilio_xuthus Papilio_indra Papilio_polyxenes Papilio_zelicaon Papilio_hospiton Papilio_machaon Papilio_oregonius Papilio_brevicauda Papilio_hippocrates Papilio_nobilis Papilio_epiphorbas Papilio_nireus Papilio_oribazus Papilio_zalmoxis Papilio_montrouzieri Papilio_ulysses3 Papilio_ulysses1 Papilio_ulysses2 Papilio_crino Papilio_blumei Papilio_daedalus Papilio_buddha Papilio_palinurus Papilio_neumoegeni Papilio_pericles Papilio_lorquinianus Papilio_peranthus Papilio_paris3 Papilio_karna Papilio_paris1 Papilio_paris2 Papilio_maackii Papilio_syfanius Papilio_krishna Papilio_arcturus Papilio_hopponis Papilio_dialis Papilio_chikae Papilio_hermeli Papilio_polyctor Papilio_bianor Papilio_dehaanii1 Papilio_dehaanii2 Papilio_morondavana Papilio_grosesmithi Papilio_demoleus Papilio_demodocus Papilio_erithonioides Papilio_iswara Papilio_amynthor Papilio_enganius Papilio_helenus Papilio_tydeus Papilio_aegeus Papilio_gambrisius2 Papilio_bridgei Papilio_gambrisius1 Papilio_fuscus Papilio_hipponous Papilio_pitmani Papilio_prexaspes Papilio_albinus Papilio_heringi Papilio_ambrax Papilio_polytes Papilio_nephelus Papilio_dravidarum Papilio_castor Papilio_mahadeva Papilio_macilentus Papilio_demetrius Papilio_protenor Papilio_bootes Papilio_forbesi Papilio_thaiwanus Papilio_deiphobus Papilio_rumanzovia Papilio_oenomaus Papilio_memnon Papilio_polymnestor Baronia_brevicornis Archon_apollinaris Archon_bostanchii Archon_apollinus1 Archon_apollinus2 Luehdorfia_japonica Luehdorfia_puziloi Luehdorfia_chinensis Luehdorfia_longicaudata Luehdorfia_taibai Sericinus_montela Bhutanitis_thaidina Bhutanitis_lidderdalii Bhutanitis_mansfieldi Zerynthia_polyxena1 Zerynthia_polyxena2 Zerynthia_rumina1 Zerynthia_rumina2 Allancastria_louristana Allancastria_deyrollei Allancastria_cretica Allancastria_caucasica Allancastria_cerisyi Hypermnestra_helios1 Hypermnestra_helios2 Parnassius_apollonius Parnassius_honrathi Parnassius_tianschanicus Parnassius_actius Parnassius_jacquemontii Parnassius_dongalaicus Parnassius_nomion Parnassius_epaphus Parnassius_mercurius Parnassius_apollo3 Parnassius_apollo1 Parnassius_apollo5 Parnassius_apollo2 Parnassius_apollo4 Parnassius_bremeri Parnassius_sacerdos Parnassius_phoebus Parnassius_behrii Parnassius_smintheus Parnassius_boedromius Parnassius_andreji Parnassius_simo Parnassius_simonius Parnassius_orleans Parnassius_nordmanni Parnassius_clodius Parnassius_eversmanni Parnassius_glacialis Parnassius_hoenei Parnassius_stubbendorfii Parnassius_ariadne Parnassius_mnemosyne3 Parnassius_mnemosyne1 Parnassius_mnemosyne2 Parnassius_hardwickii Parnassius_schultei Parnassius_acco Parnassius_hannyngtoni Parnassius_huberi Parnassius_maharaja Parnassius_cephalus Parnassius_szechenyii Parnassius_arctica Parnassius_tenedius Parnassius_augustus Parnassius_imperator Parnassius_acdestis Parnassius_inopinatus Parnassius_charltonius Parnassius_autocrator Parnassius_davydovi Parnassius_loxias Parnassius_staudingeri1 Parnassius_staudingeri2 Parnassius_patricius Parnassius_delphius Parnassius_maximinus Parnassius_jacobsoni Parnassius_cardinal Parnassius_staudingeri3 Parnassius_hide Parnassius_stenosemus Parnassius_stoliczkanus Iphiclides_feisthamelii Iphiclides_podalirius Lamproptera_curius Lamproptera_meges Protographium_philolaus Protographium_epidaus Protographium_marcellus Mimoides_ilus Mimoides_lysithous Protographium_asius Mimoides_euryleon Mimoides_pausanias Eurytides_orabilis Eurytides_serville Protographium_leucaspis Protographium_dioxippus Protographium_thyastes Protesilaus_helios Protesilaus_telesilaus Protesilaus_molops Protesilaus_glaucolaus Protesilaus_protesilaus Graphium_macleayanus Graphium_phidias Graphium_nomius Graphium_adamastor Graphium_schubotzi Graphium_angolanus Graphium_ridleyanus Graphium_tynderaeus Graphium_latreillianus Graphium_leonidas Graphium_macareus Graphium_ramaceus Graphium_delessertii Graphium_xenocles Graphium_decolor Graphium_antiphates Graphium_dorcus Graphium_androcles Graphium_aristeus Graphium_thule Graphium_agetes Graphium_stratiotes Graphium_leechi Graphium_arycles Graphium_evemon Graphium_bathycles Graphium_chironides Graphium_meyeri Graphium_doson Graphium_eurypylus Graphium_eurous Graphium_tamerlanus Graphium_incertus Graphium_glycerion Graphium_sichuanica Graphium_mandarinus Graphium_timur Graphium_weiskei Protographium_leosthenes Graphium_wallacei Graphium_agamemnon Graphium_macfarlanei Graphium_codrus Graphium_empedovana Graphium_cloanthus Graphium_milon Graphium_sarpedon Teinopalpus_aureus Teinopalpus_imperialis Battus_philenor Battus_polydamas Battus_polystictus Battus_belus Battus_crassus Battus_ingenuus Pharmacophagus_antenor Losaria_coon Losaria_neptunus Pachliopta_aristolochiae Pachliopta_kotzebuea Pachliopta_hector Pachliopta_liris Pachliopta_polydorus Atrophaneura_dixoni Atrophaneura_horishana Atrophaneura_luchti Atrophaneura_priapus Atrophaneura_nox Atrophaneura_varuna Byasa_impediens Byasa_plutonius Byasa_mencius Byasa_polyeuctes Byasa_laos Byasa_alcinous Byasa_dasarada Cressida_cressida Euryades_corethrus Euryades_duponchelii Parides_ascanius Parides_bunichus Parides_proneus Parides_agavus Parides_montezuma Parides_iphidamas Parides_aeneas Parides_tros Parides_lysander Parides_burchellanus Parides_panthonus Parides_neophilus Parides_eurimedes Parides_zacynthus Parides_chabrias Parides_hahneli Parides_childrenae Parides_photinus Parides_panares Parides_sesostris Parides_anchises Parides_erithalion Parides_vertumnus Trogonoptera_brookiana Trogonoptera_trojana Ornithoptera_richmondia Ornithoptera_croesus

Lue. Zer. Parnassiini Leptociricini T. Troidini Papilionini possible states ZY SA RU RO PA MA LA HE FA AR AP AN Papilio_polymnestor 50 Papilio_memnon Papilio_oenomaus Legend Papilio_rumanzovia Papilio_deiphobus Papilio_thaiwanus Papilio_forbesi Papilio_bootes Papilio_protenor Papilio_demetrius Main host plants Papilio_macilentus Papilio_mahadeva Papilio_castor Papilio_dravidarum Aristolochiaceae Papilio_nephelus Papilio_polytes Papilio_ambrax Papilio_heringi Papilio_albinus Rutaceae Papilio_prexaspes Papilio_pitmani Papilio_hipponous Papilio_fuscus Papilio_gambrisius1 Papilio_bridgei Annonaceae Papilio_gambrisius2 Papilio_aegeus Papilio_tydeus Papilio_helenus Papilio_enganius Papilio_amynthor Crassulaceae + Saxifragaceae Papilio_iswara Papilio_erithonioides Papilio_demodocus Papilio_demoleus Papilio_grosesmithi Papilio_morondavana Apiaceae Papilio_dehaanii2 Papilio_dehaanii1 Papilio_bianor Papilio_polyctor Papilio_hermeli Papilio_chikae Lauraceae Papilio_dialis Papilio_hopponis Papilio_arcturus Papilio_krishna Papilio_syfanius Papilio_maackii Papaveraceae Papilio_paris2 Papilio_paris1 Papilio_karna Papilio_paris3 Papilio_peranthus Papilio_lorquinianus Papilio_pericles Papilio_neumoegeni Secondary host plants Papilio_palinurus Papilio_buddha Papilio_daedalus Papilio_blumei Papilio_crino Fabaceae (Acacia) Papilio_ulysses2 Papilio_ulysses1 Papilio_ulysses3 Papilio_montrouzieri Papilio_zalmoxis Papilio_oribazus Papilio_nireus Zygophyllaceae Papilio_epiphorbas Papilio_nobilis Papilio_hippocrates Papilio_brevicauda Papilio_oregonius Hernandiaceae Papilio_machaon Papilio_hospiton Papilio_zelicaon Papilio_polyxenes Papilio_indra Papilio_xuthus Rosaceae Papilio_benguetana Papilio_humbloti Papilio_dardanus Papilio_meriones Papilio_phorcas Papilio_constantinus Magnoliaceae Papilio_rex Papilio_antimachus

Parides_burchellanus Troidini Parides_lysander Parides_tros Parides_aeneas Parides_iphidamas Parides_montezuma MA Parides_agavus Parides_proneus Parides_bunichus Parides_ascanius Euryades_duponchelii Euryades_corethrus Cressida_cressida Byasa_dasarada Byasa_alcinous PA Byasa_laos Byasa_polyeuctes Byasa_mencius Byasa_plutonius Byasa_impediens Atrophaneura_varuna Atrophaneura_nox Atrophaneura_priapus Atrophaneura_luchti RO Atrophaneura_horishana Atrophaneura_dixoni Pachliopta_polydorus Pachliopta_liris Pachliopta_hector Pachliopta_kotzebuea Pachliopta_aristolochiae Losaria_neptunus Losaria_coon Pharmacophagus_antenor RU Battus_ingenuus Battus_crassus Battus_belus Battus_polystictus Battus_polydamas Battus_philenor

Teinopalpus_imperialis T. Teinopalpus_aureus Graphium_sarpedon SA Graphium_milon Graphium_cloanthus Graphium_empedovana Graphium_codrus Graphium_macfarlanei Graphium_agamemnon Graphium_wallacei Protographium_leosthenes Graphium_weiskei ZY Graphium_timur Graphium_mandarinus Graphium_sichuanica Graphium_glycerion Graphium_incertus Graphium_tamerlanus Graphium_eurous Graphium_eurypylus Graphium_doson Graphium_meyeri Graphium_chironides Graphium_bathycles Graphium_evemon Graphium_arycles Graphium_leechi Graphium_stratiotes Graphium_agetes Graphium_thule Graphium_aristeus Graphium_androcles Graphium_dorcus Graphium_antiphates Graphium_decolor Graphium_xenocles Graphium_delessertii Graphium_ramaceus Graphium_macareus Graphium_leonidas Graphium_latreillianus Graphium_tynderaeus Graphium_ridleyanus Graphium_angolanus Graphium_schubotzi

Graphium_adamastorLeptociricini Graphium_nomius Graphium_phidias Graphium_macleayanus Protesilaus_protesilaus Protesilaus_glaucolaus Protesilaus_molops Protesilaus_telesilaus Protesilaus_helios Protographium_thyastes Protographium_dioxippus Protographium_leucaspis Eurytides_serville Eurytides_orabilis Mimoides_pausanias Mimoides_euryleon Protographium_asius Mimoides_lysithous Mimoides_ilus Protographium_marcellus Protographium_epidaus Protographium_philolaus Lamproptera_meges Lamproptera_curius Iphiclides_podalirius Iphiclides_feisthamelii Parnassius_stoliczkanus Parnassius_stenosemus Parnassius_hide Parnassius_staudingeri3 Parnassius_cardinal Parnassius_jacobsoni Parnassius_maximinus Parnassius_delphius Parnassius_patricius Parnassius_staudingeri2 Parnassius_staudingeri1 Parnassius_loxias Parnassius_davydovi Parnassius_autocrator Parnassius_charltonius Parnassius_inopinatus Parnassius_acdestis Parnassius_imperator Parnassius_augustus Parnassius_tenedius Parnassius_arctica Parnassius_szechenyii Parnassius_cephalus Parnassius_maharaja Parnassius_huberi Parnassius_hannyngtoni Parnassius_acco Parnassius_schultei Parnassius_hardwickii Parnassius_mnemosyne2 Parnassius_mnemosyne1 Parnassius_mnemosyne3 Parnassius_ariadne Parnassius_stubbendorfii Parnassius_hoenei Parnassius_glacialis Parnassius_eversmanni Parnassius_clodius Parnassius_nordmanni Parnassius_orleans

Parnassius_simoniusParnassiini Parnassius_simo Parnassius_andreji Parnassius_boedromius Parnassius_smintheus Parnassius_behrii Parnassius_phoebus Parnassius_sacerdos Parnassius_bremeri Parnassius_apollo4 Parnassius_apollo2 Parnassius_apollo5 Parnassius_apollo1 Parnassius_apollo3 Parnassius_mercurius Parnassius_epaphus Parnassius_nomion Parnassius_dongalaicus Parnassius_jacquemontii Parnassius_actius Parnassius_tianschanicus Parnassius_honrathi Parnassius_apollonius Hypermnestra_helios2 Hypermnestra_helios1 Allancastria_cerisyi Allancastria_caucasica Allancastria_cretica Allancastria_deyrollei. Allancastria_louristana Zerynthia_rumina2 Zerynthia_rumina1 Zerynthia_polyxena2 Zerynthia_polyxena1 Bhutanitis_mansfieldiZer Bhutanitis_lidderdalii Bhutanitis_thaidina Sericinus_montela Luehdorfia_taibai Luehdorfia_longicaudata Luehdorfia_chinensis Luehdorfia_puziloi Luehdorfia_japonica Archon_apollinus2 Archon_apollinus1 Archon_bostanchii Archon_apollinarisLue. Baronia_brevicornis

Late K Paleocene Eocene Oligocene Miocene Pl P Ma 70 60 50 40 30 20 10 0 Supplementary figure 5. Estimation of ancestral host-plant preferences with the maximum- likelihood model of Markov 1-parameter (Mk) and the Bayesian approach of BayesTraits. The results are represented by pie charts indicating the relative probability for each state inferred at a given node. The results consistently show that (1) the family Aristolochiaceae is recovered as the ancestral feeding habit of the Papilionidae, and (2) the host-plant shifts are recovered at the same nodes, except at the root of Papilionini and at the root of Iphiclides + Lamproptera (due to the fact the the Mk model can include only 10 states).

Aristolochiaceae Lauraceae Hernandiaceae Magnoliaceae Rosaceae Annonaceae Zygophyllaceae Crassulaceae + Saxifragaceae Apiaceae Papaveraceae Rutaceae Fabaceae (Acacia) Markov 1−parameter BayesTraits

root of Papilionidae

root of Parnassiinae + Papilioninae

root of Parnassiinae

root of Zerynthiini + Luehdorfiini

root of Parnassiini

root of Papilioninae

root of Leptocircini

root of Papilionini + Troidini + Teinopalpini

root of Papilionini + Troidini

root of Troidini

root of Papilionini Aristolochiaceae Lauraceae Hernandiaceae Magnoliaceae Rosaceae Annonaceae Zygophyllaceae Crassulaceae + Saxifragaceae Apiaceae Papaveraceae Rutaceae Fabaceae (Acacia) Markov 1−parameter BayesTraits

root of Parnassius

root of Parnassius subgenus Parnassius

root of Parnassius other subgenera

root of Iphiclides + Lamproptera

root of Meandrusa

root of Papilio

root of New World Papilio

root of Papilio subgenera Pterourus and Chilasa

root of Papilio subgenus Heraclides

root of Old World Papilio

root of Papilio subgenus Papilio Supplementary figure 6. Estimation of ancestral host-plant preferences for the Aristolochiaceae feeders with the Dispersal-Extinction-Cladogenesis (DEC) model. The results show that the genus Aristolochia is the primary Aristolochiaceae host plant while being also recovered as the ancestral feeding habit of the Papilionidae.

Legend

Aristolochia [AR]

Asarum [AS]

Tho.ea [TH]

Supplementary figure 7. Phylogenetic relationships within the Aristolochiaceae (perianth- bearing Piperales) for 247 species. The phylogeny is inferred with the Bayesian approach of MrBayes. Node support is indicated by posterior probabilities, with values > 0.95 considered as strong node support.

Gymnotheca_chinensis 0.94 1 Gymnotheca_involucrata Anemopsis_californica Saururus_cernuus 1 Saururus_chinensis Saururaceae 1 Saruma_henryi Asarum_cordifolium Saruma 0.83 1 Asarum_cardiophyllum 0.75 Asarum_caudigerum Asarum_pulchellum 1 Asarum_misandrum 0.32 0.13 Asarum_heterotropoides Asarum_versicolor 0.08 Asarum_mikuniense 0,64 0.13 Asarum_tohokuense 0.57 0.18 Asarum_maruyamae Asarum_dimidiatum 0.89 0.2 Asarum_patens Asarum_sieboldii 0.4 Asarum_glabrum 0.24 Asarum_maculatum 0.73 Asarum_himalaicum Asarum_caulescens Asarum_caudigerellum 1 1 Asarum_debile 1 Asarum_europaeum 0.27 0.99 Asarum_canadense 0.98 Asarum_hartwegii 0.83 Asarum_caudatum 0.99 Asarum_lemmonii 0.96 Asarum_dissitum 1 0.72 Asarum_monodoriflorum 0.850.34 Asarum_yaeyamense Asarum_geophilum 1 Asarum_epigynum 1 Asarum_yunnanense Asarum_arifolium 1 Asarum_speciosum 0.73 Asarum_lewisii 0.68 Asarum_shuttleworthii 0.91 Asarum_minus Asarum 0.1 Asarum_virginicum 0.12 Asarum_contractum 0.1 Asarum_heterophyllum 0.54 0.03 Asarum_memmingeri 0.09 Asarum_naniflorum Asarum_maximum 0.87 Asarum_campaniflorum 1 Asarum_insigne 0.87 Asarum_hongkongense 0.36 0.64 Asarum_sagittarioides 0.49 Asarum_magnificum 0.84 Asarum_longerhizomatosum 1 1 Asarum_wulingense Asarum_bashanense 0.34 Asarum_chengkouense 0.31 Asarum_nanchuanense Asarum_inflatum Perianth-bearing Piperales 0.98 0.41 Asarum_chinense 0.96 Asarum_ichangense 1 0.18 0.44 Asarum_crispulatum Asarum_chingchengense 0.76 1 Asarum_splendens 0.69 Asarum_delavayi 1 Asarum_porphyronotum Asarum_gusk Asarum_pellucidum 0.11 Asarum_trinacriforme 0.98 Asarum_tokarense 0.1 Asarum_yakusimense Asarum_forbesii 0.12 Asarum_muramatsui 0.16 0.55 Asarum_asaroides Asarum_senkakuinsulare 0.16 0.46 0.39 Asarum_unzen 0.73 Asarum_fudsinoi Asarum_kumageanum 0.72 Asarum_satsumense 0.87 Asarum_gelasinum 0.27 0.52 0.32 Asarum_hatsushimae 0.59 Asarum_okinawense 0.29 Asarum_simile Asarum_subglobosum 0.44 Asarum_tamaensis 0.3 Asarum_crassum Asarum_minamitanianum 0.29 Asarum_nipponicum 0.19 0.74 Asarum_savatieri 0.8 Asarum_takaoi 0.76 Asarum_sakawanum Asarum_fauriei 0.15 Asarum_tamaense 0.09 0.09 Asarum_costatum 0.08 Asarum_blumei 0.14 Asarum_hexalobum 0.54 Asarum_asperum 0.28 Asarum_megacalyx Lactoris_fernandeziana Thottea_tomentosLactorisa Thottea_piperiformis Thottea 1 0.99 Thottea_abrahamii Thottea_dinghoui 0.52 Thottea_barberi 0.26 Thottea_ponmudiana 0.9 Thottea_duchartrei 0.74 0,9Thottea_idukkian5 a 0.78 Thottea_dalzellii 0.95 0.19 Thottea_siliquosa 0.21 Thottea_sivarajanii Thottea_corymbosa 1 Thottea_parviflora 0.42 0.59 Thottea_borneensis 0.6 Thottea_macrantha 0.5 Thottea_penitilobata 0.37 Thottea_dependens 0.72 Thottea_grandiflora Aristolochia_reticulata 1 Aristolochia_serpentaria Aristolochia_panamensis Aristolochia_paracleta 1 Aristolochia_malacophylla 0.99 0.34 Aristolochia_stevensii 1 1 Aristolochia_salvadorensis 0.99 1 Aristolochia_impudica 1 Aristolochia_arborea 0.35 Aristolochia_kalebii 0.99 Aristolochia_chiapensis 0.96 0.55 Aristolochia_tricaudata 0.98 Aristolochia_asclepiadifolia 1 Aristolochia_veracruzana 0.67 Aristolochia_macrophylla Aristolochia_manshuriensis 0.86 Aristolochia_tomentosa Aristolochia_tubiflora 0.87 Aristolochia_californica Aristolochia_cucurbitoides 0.13 0.91 Aristolochia_wardiana 0.46 Aristolochia_moupinensis 0.28 Aristolochia_grandis 0.57 Aristolochia_saccata 0.47 0.83 Aristolochia_westlandii 0,24 0.99 Aristolochia_austroyunnanensis 0.4 Aristolochia_kwangsiensis Aristolochia_championii 1 0.3 Aristolochia_neolongifolia 0.2 Aristolochia_griffithii 0.91 Aristolochia_nakaoi 0,53 Aristolochia_kaempferi 0,97 Aristolochia_cucurbitifolia 0.16 Aristolochia_shimadai 0.24 Aristolochia_liukiuensis 0.17 Aristolochia_onoei Aristolochia_goldieana 1 Aristolochia_promissa 0.98 Aristolochia_triactina 1 Aristolochia_praevenosa 1 Pararistolochia_australopithecurus 0.53 Pararistolochia_laheyana Aristolochia_burelae Aristolochia_lindneri 1 Aristolochia_erecta 1 1 Aristolochia_pentandra 1 Aristolochia_micrantha 0.51 Aristolochia_nelsonii Aristolochia_rojasiana 1 0.88 Aristolochia_cauliflora 1 Aristolochia_leuconeura 0.83 Aristolochia_taliscana 0.98 Aristolochia_tentaculata 0.81 Aristolochia_passiflorifolia 1 Aristolochia_chilensis

1 Aristolochia_fimbriata Aristolochia Aristolochia_nummularifolia Aristolochia_chamissonis 0.85 1 Aristolochia_paulistana 1 Aristolochia_triangularis 0.24 Aristolochia_gibertii 0.95 Aristolochia_macroura 0.89 0.98 1 Aristolochia_trilobata 0.95 Aristolochia_ringens 0.21 Aristolochia_cymbifera 1 Aristolochia_maurorum 0.18 Aristolochia_esperanzae 0.09 Aristolochia_galeata 0.74 0.18 Aristolochia_labiata Aristolochia_arcuata 1 Aristolochia_pilosa 0.45 Aristolochia_cynanchifolia 0.52 Aristolochia_anguicida 0.54 1 Aristolochia_odoratissima 1 Aristolochia_gigantea 0.56 Aristolochia_elegans 0.37 0.89 Aristolochia_littoralis Aristolochia_argentina 0.16 Holostylis_reniformis 0.37 Aristolochia_holostylis 0.8 0.46 Aristolochia_reniformis Aristolochia_eriantha 0.73 Aristolochia_peruviana 0.95 Aristolochia_cordiflora 0.9 Aristolochia_cruenta Aristolochia_melastoma Aristolochia_maxima 1 1 Aristolochia_acutifolia 1 Aristolochia_ovalifolia 0.53 Aristolochia_tonduzii Aristolochia_grandiflora 1 Aristolochia_gorgona 0.57 1 Aristolochia_pichinchensis Aristolochia_kerrii Aristolochia_kankauensis 1 0.91 Aristolochia_zollingeriana 0.28 Aristolochia_pierrei 0.98 Aristolochia_acuminata 0.73 0,47 Aristolochia_tagala 1 Aristolochia_gaudichaudii 0.97 Aristolochia_bracteolata 0.57 Aristolochia_indica 0.99 Aristolochia_krisagathra 0.82 0.34 Aristolochia_heppii 0.99 Aristolochia_hockii 0.98 Aristolochia_jackii 0.91 Aristolochia_albida 0.36 Aristolochia_petersiana Aristolochia_rigida Aristolochia_clematitis 1 Aristolochia_debilis 0.44 Aristolochia_fordiana 0.73 0.88 Aristolochia_foveolata 0.53 Aristolochia_goliathiana 0.86 Aristolochia_papillifolia 0.32 Aristolochia_delavayi 0.85 Aristolochia_pistolochia Aristolochia_iberica 1 Aristolochia_pontica 0.5 Aristolochia_bottae 0.99 0.9 Aristolochia_hirta 1 Aristolochia_incisa Aristolochia_baetica 0.71 1 Aristolochia_sempervirens Aristolochia_clusii 0.03 0.36 1 Aristolochia_sicula 1 Aristolochia_tyrrhena Aristolochia_bianorii 0.51 1 Aristolochia_rotunda 1 Aristolochia_navicularis 1 Aristolochia_parvifolia 1 0.35 Aristolochia_elongata Aristolochia_microstoma 1 Aristolochia_merxmuelleri Aristolochia_lutea 0.98 1 Aristolochia_pallida Supplementary figure 8. Bayesian estimates of divergence times for Aristolochiaceae. The first inference was performed with exponential priors on fossil calibrations and 150 Ma as maximum age. The second inference was performed with exponential priors on fossil calibrations and 221 Ma as maximum age. The third inference was performed with uniform priors on fossil calibrations and 150 Ma as maximum age. The fourth inference was performed with uniform priors on fossil calibrations and 221 Ma as maximum age. The origin of the genus Aristolochia is estimated at 55.5 Ma (95% CI: 39.2-72.8 Ma) in the first analysis, at 58.8 Ma (95% CI: 42.5-76.2 Ma) in the second analysis, at 60.7 Ma (95% CI: 43.9-80.5 Ma) in the third analysis, and at 64.8 Ma (95% CI: 47.3-83.1 Ma) in the fourth analysis.

200

190 Lower

180 Jurassic

170 Middle

160 Upper 150

140

130 Lower 120 Cretaceous

110

100

90 Upper 80

60 Paleocene Paleogene 50 Eocene 40

30 Oligocene

20 Neogene Miocene 10 Pliocene 0 lutea Aristolochia pallida Aristolochia merxmuelleri Aristolochia elongata Aristolochia microstoma Aristolochia bianorii Aristolochia rotunda Aristolochia navicularis Aristolochia parvifolia Aristolochia sicula Aristolochia tyrrhena Aristolochia clusii Aristolochia baetica Aristolochia sempervirens Aristolochia hirta Aristolochia incisa Aristolochia bottae Aristolochia pontica Aristolochia iberica Aristolochia delavayiAristolochia pistolochia Aristolochia fordianaAristolochia foveolataAristolochia goliathiana Aristolochia papillifoliaAristolochia clematitis Aristolochia debilis Aristolochia rigida Aristolochia albida Aristolochia petersiana Aristolochia jackii Aristolochia heppii Aristolochia hockii Aristolochia indica Aristolochia krisagathra Aristolochia bracteolata Aristolochia gaudichaudii Aristolochia acuminata Aristolochia tagala Aristolochia pierrei Aristolochia kankauensis Aristolochia zollingeriana Aristolochia kerrii Aristolochia gorgona Aristolochia pichinchensis Aristolochia grandifloraAristolochia ovalifoliaAristolochia tonduzii Aristolochia acutifoliaAristolochia maxima Aristolochia melastoma Aristolochia anguicida Aristolochia odoratissima Aristolochia cynanchifoliaAristolochia elegans Aristolochia littoralis Aristolochia gigantea Aristolochia arcuata Aristolochia pilosa Aristolochia holostylis Aristolochia reniformis Aristolochia Holostylis reniformis argentina Aristolochia cordiflora Aristolochia cruenta Aristolochia peruviana Aristolochia eriantha Aristolochia galeata Aristolochia labiata Aristolochia esperanzae Aristolochia cymbiferaAristolochia maurorum Aristolochia ringens Aristolochia macroura Aristolochia trilobata Aristolochia gibertii Aristolochia triangularis Aristolochia chamissonis Aristolochia paulistana Aristolochia nummularifoliaAristolochia chilensis Aristolochia fimbriata Aristolochia passiflorifoliaAristolochia cauliflora Aristolochia leuconeura Aristolochia taliscana Aristolochia tentaculata Aristolochia rojasiana Aristolochia erecta Aristolochia pentandra Aristolochia micrantha Aristolochia nelsonii Aristolochia lindneri Aristolochia burelaeAristolochia promissa Aristolochia triactina Aristolochia goldieana Aristolochia Pararistolochia australopithecurus Pararistolochia laheyana praevenosaAristolochia austroyunnanensisAristolochia kwangsiensisAristolochia westlandii Aristolochia grandis Aristolochia saccata Aristolochia moupinensis Aristolochia cucurbitoides Aristolochia wardianaAristolochia californica Aristolochia cucurbitifoliaAristolochia shimadai Aristolochia liukiuensis Aristolochia onoei Aristolochia kaempferiAristolochia griffithii Aristolochia nakaoi Aristolochia neolongifoliaAristolochia championii Aristolochia tubiflora Aristolochia manshuriensis Aristolochia tomentosa Aristolochia macrophyllaAristolochia arborea Aristolochia kalebii Aristolochia impudica Aristolochia salvadorensisAristolochia asclepiadifoliaAristolochia veracruzanaAristolochia tricaudata Aristolochia chiapensis Aristolochia malacophyllaAristolochia stevensiiAristolochia paracleta Aristolochia panamensis Aristolochia reticulata Aristolochia serpentaria Aristolochia Thottea siliquosa Thottea sivarajanii Thottea dalzellii Thottea duchartrei Thottea idukkiana Thottea ponmudiana Thottea barberi Thottea dependens Thottea grandiflora Thottea penitilobata Thottea macrantha Thottea borneensis Thottea parviflora Thottea corymbosa Thottea abrahamii Thottea dinghoui Thottea piperiformis Thottea tomentosa fernandeziana Lactoris asperum Asarum megacalyx Asarum hexalobumAsarum blumeiAsarum costatum Asarum faurieiAsarum tamaense Asarum sakawanumAsarum savatieriAsarum takaoi Asarum nipponicum Asarum minamitanianum Asarum crassum Asarum subglobosum Asarum tamaensis Asarum gelasinum Asarum hatsushimae Asarum okinawenseAsarum simile Asarum satsumense Asarum kumageanum Asarum fudsinoi Asarum senkakuinsulare Asarum unzenAsarum asaroides Asarum muramatsuiAsarum forbesiiAsarum tokarense Asarum yakusimenseAsarum trinacriforme Asarum pellucidum Asarum gusk Asarum chingchengense Asarum splendens Asarum delavayiAsarum porphyronotum Asarum crispulatum Asarum chinense Asarum ichangense Asarum inflatum Asarum chengkouenseAsarum nanchuanense Asarum bashanense Asarum longerhizomatosumAsarum wulingense Asarum magnificum Asarum sagittarioides Asarum hongkongenseAsarum campaniflorum Asarum insigne Asarum maximum Asarum contractum Asarum heterophyllumAsarum memmingeri Asarum naniflorum Asarum minus Asarum virginicum Asarum shuttleworthii Asarum lewisiiAsarum arifoliumAsarum speciosum Asarum monodoriflorum Asarum yaeyamenseAsarum dissitum Asarum epigynum Asarum yunnanense Asar 200

190 Lower

180 Jurassic

170 Middle

160 Upper 150

140

130 Lower 120 Cretaceous

110

100

90 Upper 80

60 Paleocene Paleogene 50 Eocene 40

30 Oligocene

190 Lower

180 Jurassic

170 Middle

160 Upper 150

140

130 Lower 120 Cretaceous

110

100

90 Upper 80

60 Paleocene Paleogene 50 Eocene 40

30 Oligocene

190 Lower

180 Jurassic

170 Middle

160 Upper 150

140

130 Lower 120 Cretaceous

110

100

90 Upper 80

60 Paleocene Paleogene 50 Eocene 40

30 Oligocene

Ma Uniformpriors 150(max. Ma) Exponentialpriors 221(max. Ma) Exponentialpriors 150(max. Ma) Uniformpriors Exponentialpriors Uniformpriors 221(max. Ma) Dating analyses Dating 0 P

tre Aristo_BD_expo_150 Aristo_expo_221 Papilio_expo_H5 Papilio_unif_H5 Aristo_unif_221 Aristo_unif_150 10 Miocene 60.7Ma 58.8Ma 55.5Ma 67.2Ma 55.4Ma 64.8Ma 20 Estimatedages (95% CI: 47.8 – 112 Ma) (95%47.8 –112 CI: (95%43.9 –80.5CI: Ma) (95%42.5 –76.2CI: Ma) (95%39.2 –72.8CI: Ma) (95%47.8 –71.0CI: Ma) (95%47.3 –83.1CI: Ma) ● ● (95% credibility intervals) (95% credibility ● ● 30 ● ● ● Oligocene ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● 40 40

Eocene 50

60 Paleoc. ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● 70 ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● crown ages crown ages ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● 80 ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● 80 ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● Posterior distributions of of distributions Posterior ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● Late Cretaceous ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● age ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● 90 ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● 100 ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● 110 ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● 120 ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● 120 ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● Early Cretaceous ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● 130 ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● 140 ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● 150 Clade Late J Aristolochia Papilionidae 160 160 tre Aristo_BD_expo_150 Aristo_expo_221 Aristo_unif_150 Aristo_unif_221 Papilio_expo_H5 Papilio_unif_H5 Supplementary figure 10. Estimation of the historical biogeography for the two molecular dated trees of Papilionidae with the Dispersal-Extinction-Cladogenesis (DEC) model. For each tree, two DEC analyses were performed: one with time-stratified palaeogeographic constraints, and one without such constraints. The swallowtail butterflies originated in a northern region centred around the Bering land bridge. K = Cretaceous, Pl = Pliocene, P = Pleistocene.

a) a) Dating Papilionidae Papilionidae Early (95% CI: 47.8-70.9 Ma) CI: (95% 47.8-70.9 Color Viewed Ancestral area area Ancestral of Papilionidae Origin

with Eocene Legend code for areas Global

exponential

from appeared

paleogeography paleogeography

North Ma Ma

Pole 55.4 Ma 55.4 priors

(max. 150 Ma) and Ma) and (max. 150

25 Ma 25 50 Eocene biogeographic

inference 30 Oligocene

with

adjacency

matrix 20

Miocene

Pl Pl

Lue. Zer. Parnassiini Leptociricini T. Troidini Papilionini possible states WP WN WA SA MD IN EP EN CA AU AF b) b) Dating Papilionidae Papilionidae (95% CI: 47.8-70.9 Ma) CI: (95% 47.8-70.9 Color Ancestral area area Ancestral of Papilionidae Origin

with Legend code for areas Global

exponential appeared paleogeography

Ma Ma

55.4 Ma 55.4 priors

(max. 150 Ma) and Ma) and (max. 150

25 Ma 25 50 Eocene biogeographic

inference 30 Oligocene

with

unconstrained

20 matrix

Miocene

Pl Pl

Lue. Zer. Parnassiini Leptociricini T. Troidini Papilionini possible states WP WN WA SA MD IN EP EN CA AU AF Papilio_polymnestor c) Dating with uniform priors (max. 150 Ma) and biogeographic inference with adjacency matrix Papilio_memnon Papilio_oenomaus Papilio_rumanzovia Papilio_deiphobus Papilio_thaiwanus Papilio_forbesi Papilio_bootes Papilio_protenor Papilio_demetrius Papilio_macilentus Global paleogeography 25 Ma Papilio_mahadeva Papilio_castor Papilio_dravidarum Papilio_nephelus Papilio_polytes Papilio_ambrax Papilio_heringi Papilio_albinus Papilio_prexaspes Papilio_pitmani Papilio_hipponous Papilio_fuscus Papilio_gambrisius1 Papilio_bridgei Papilio_gambrisius2 Papilio_aegeus Papilio_tydeus Papilio_helenus Papilio_enganius Papilio_amynthor Papilio_iswara Papilio_erithonioides Papilio_demodocus Papilio_demoleus Papilio_grosesmithi Papilio_morondavana Papilio_dehaanii2 Papilio_dehaanii1 Papilio_bianor Papilio_polyctor Papilio_hermeli Papilio_chikae Papilio_dialis Papilio_hopponis Papilio_arcturus Papilio_krishna Papilio_syfanius Papilio_maackii Papilio_paris2 Papilio_paris1 Papilio_karna Papilio_paris3 Papilio_peranthus Papilio_lorquinianus Papilio_pericles Papilio_neumoegeni Papilio_palinurus Papilio_buddha Papilio_daedalus Papilio_blumei Papilio_crino Papilio_ulysses2 Papilio_ulysses1 Papilio_ulysses3 Papilio_montrouzieri Papilio_zalmoxis Papilio_oribazus Papilio_nireus Papilio_epiphorbas Papilio_nobilis Papilio_hippocrates Papilio_brevicauda Papilio_oregonius Papilio_machaon Papilio_hospiton Papilio_zelicaon Papilio_polyxenes Papilio_indra Papilio_xuthus Papilio_benguetana Papilio_humbloti Papilio_dardanus Papilio_meriones Papilio_phorcas Papilio_constantinus Papilio_rex Papilio_antimachus

Parides_burchellanus Troidini IN Viewed from North Pole Parides_lysander Parides_tros Parides_aeneas Parides_iphidamas Parides_montezuma Parides_agavus Parides_proneus Parides_bunichus Parides_ascanius Euryades_duponchelii MD Euryades_corethrus Cressida_cressida Byasa_dasarada Byasa_alcinous Byasa_laos Byasa_polyeuctes Byasa_mencius Byasa_plutonius Byasa_impediens SA Atrophaneura_varuna Atrophaneura_nox Atrophaneura_priapus Atrophaneura_luchti Atrophaneura_horishana Atrophaneura_dixoni Pachliopta_polydorus Pachliopta_liris Pachliopta_hector WA Pachliopta_kotzebuea Pachliopta_aristolochiae Losaria_neptunus Losaria_coon Legend Pharmacophagus_antenor Battus_ingenuus Battus_crassus Battus_belus Battus_polystictus WN Battus_polydamas Battus_philenor

Teinopalpus_imperialis T. Teinopalpus_aureus Graphium_sarpedon Graphium_milon Origin of Papilionidae Graphium_cloanthus Graphium_empedovana Graphium_codrus WP Graphium_macfarlanei Graphium_agamemnon Graphium_wallacei Protographium_leosthenes Graphium_weiskei Graphium_timur Graphium_mandarinus Graphium_sichuanica Graphium_glycerion Graphium_incertus Graphium_tamerlanus Graphium_eurous Ancestral area Graphium_eurypylus Graphium_doson Graphium_meyeri Graphium_chironides Graphium_bathycles Graphium_evemon Graphium_arycles Graphium_leechi Graphium_stratiotes Graphium_agetes Graphium_thule Graphium_aristeus Graphium_androcles Graphium_dorcus Graphium_antiphates Graphium_decolor Color code for areas Graphium_xenocles Graphium_delessertii Graphium_ramaceus Graphium_macareus Graphium_leonidas Graphium_latreillianus Graphium_tynderaeus Graphium_ridleyanus Graphium_angolanus Graphium_schubotzi

Late K Paleocene Eocene Oligocene Miocene Pl P Ma 70 60 50 40 30 20 10 0 Papilio_polymnestor d) Dating with uniform priors (max. 150 Ma) and biogeographic inference with unconstrained matrix Papilio_memnon Papilio_oenomaus Papilio_rumanzovia Papilio_deiphobus Papilio_thaiwanus Papilio_forbesi Papilio_bootes Papilio_protenor Papilio_demetrius Papilio_macilentus Global paleogeography 25 Ma Papilio_mahadeva Papilio_castor Papilio_dravidarum Papilio_nephelus Papilio_polytes Papilio_ambrax Papilio_heringi Papilio_albinus Papilio_prexaspes Papilio_pitmani Papilio_hipponous Papilio_fuscus Papilio_gambrisius1 Papilio_bridgei Papilio_gambrisius2 Papilio_aegeus Papilio_tydeus Papilio_helenus Papilio_enganius Papilio_amynthor Papilio_iswara Papilio_erithonioides Papilio_demodocus Papilio_demoleus Papilio_grosesmithi Papilio_morondavana Papilio_dehaanii2 Papilio_dehaanii1 Papilio_bianor Papilio_polyctor Papilio_hermeli Papilio_chikae Papilio_dialis Papilio_hopponis Papilio_arcturus Papilio_krishna Papilio_syfanius Papilio_maackii Papilio_paris2 Papilio_paris1 Papilio_karna Papilio_paris3 Papilio_peranthus Papilio_lorquinianus Papilio_pericles Papilio_neumoegeni Papilio_palinurus Papilio_buddha Papilio_daedalus Papilio_blumei Papilio_crino Papilio_ulysses2 Papilio_ulysses1 Papilio_ulysses3 Papilio_montrouzieri Papilio_zalmoxis Papilio_oribazus Papilio_nireus Papilio_epiphorbas Papilio_nobilis Papilio_hippocrates Papilio_brevicauda Papilio_oregonius Papilio_machaon Papilio_hospiton Papilio_zelicaon Papilio_polyxenes Papilio_indra Papilio_xuthus Papilio_benguetana Papilio_humbloti Papilio_dardanus Papilio_meriones Papilio_phorcas Papilio_constantinus Papilio_rex Papilio_antimachus

Papilio_lormieriPapilionini Papilio_delalandei Papilio_liomedon Papilio_demolion Papilio_noblei Papilio_gigon Papilio_anactus Papilio_alexanor Papilio_rogeri Papilio_pharnaces Papilio_garleppi Papilio_erostratus Papilio_epenetus Papilio_anchisiades Papilionidae appeared 67.2 Ma Papilio_isidorus Papilio_chiansiades Papilio_pelaus Papilio_oxynius Papilio_lamarchei Papilio_hectorides (95% CI: 47.8-112 Ma) Papilio_torquatus Papilio_himeros Papilio_pallas Papilio_ornythion Papilio_astyalus Papilio_aristodemus Papilio_thersites Papilio_androgeus Papilio_rumiko Papilio_cresphontes Papilio_homothoas Papilio_melonius Papilio_thoas Papilio_oviedo Papilio_caiguanabus Papilio_aristor Papilio_paeon Papilio_machaonides Papilio_andraemon Papilio_hyppason Papilio_euterpinus Papilio_cacicus Papilio_warscewiczii Papilio_homerus Papilio_victorinus Papilio_menatius Papilio_birchallii Papilio_garamas Papilio_zagreus Papilio_scamander Papilio_neyi Papilio_glaucus Papilio_appalachiensis Papilio_canadensis Papilio_rutulus Papilio_eurymedon Papilio_multicaudata Papilio_maraho Papilio_elwesi Papilio_pilumnus Papilio_palamedes Papilio_troilus Papilio_esperanza Papilio_veiovis Papilio_osmana Papilio_laglaizei Papilio_slateri possible states Papilio_epycides Papilio_agestor Papilio_paradoxa Papilio_clytia Meandrusa_sciron Meandrusa_payeni Troides_staudingeri Troides_naias Troides_haliphron Troides_riedeli AF Troides_rhadamantus Troides_criton Troides_minos Troides_aeacus Troides_oblongomaculatus Troides_helena Troides_vandepolli Troides_prattorum Troides_plato AU Troides_miranda Troides_amphrysus Troides_cuneifera Troides_andromache Troides_magellanus Troides_hypolitus Ornithoptera_paradisea Ornithoptera_arfakensis Ornithoptera_meridionalis CA Ornithoptera_tithonus Ornithoptera_chimaera Ornithoptera_goliath Ornithoptera_rothschildi Ornithoptera_victoriae Ornithoptera_alexandrae Ornithoptera_euphorion Ornithoptera_aesacus Ornithoptera_priamus EN Ornithoptera_croesus Ornithoptera_richmondia Trogonoptera_trojana Trogonoptera_brookiana Parides_vertumnus Parides_erithalion Parides_anchises Parides_sesostris Parides_panares EP Parides_photinus Parides_childrenae Parides_hahneli Parides_chabrias Parides_zacynthus Parides_eurimedes Parides_neophilus Parides_panthonus Parides_burchellanus Troidini IN Parides_lysander Parides_tros Parides_aeneas Parides_iphidamas Parides_montezuma Parides_agavus Parides_proneus Parides_bunichus Parides_ascanius Euryades_duponchelii MD Euryades_corethrus Cressida_cressida Byasa_dasarada Byasa_alcinous Byasa_laos Byasa_polyeuctes Byasa_mencius Byasa_plutonius Byasa_impediens SA Atrophaneura_varuna Atrophaneura_nox Atrophaneura_priapus Atrophaneura_luchti Atrophaneura_horishana Atrophaneura_dixoni Pachliopta_polydorus Pachliopta_liris Pachliopta_hector WA Pachliopta_kotzebuea Pachliopta_aristolochiae Losaria_neptunus Losaria_coon Legend Pharmacophagus_antenor Battus_ingenuus Battus_crassus Battus_belus Battus_polystictus WN Battus_polydamas Battus_philenor Teinopalpus_imperialis T. Teinopalpus_aureus Graphium_sarpedon Graphium_milon Origin of Papilionidae Graphium_cloanthus Graphium_empedovana Graphium_codrus WP Graphium_macfarlanei Graphium_agamemnon Graphium_wallacei Protographium_leosthenes Graphium_weiskei Graphium_timur Graphium_mandarinus Graphium_sichuanica Graphium_glycerion Graphium_incertus Graphium_tamerlanus Graphium_eurous Ancestral area Graphium_eurypylus Graphium_doson Graphium_meyeri Graphium_chironides Graphium_bathycles Graphium_evemon Graphium_arycles Graphium_leechi Graphium_stratiotes Graphium_agetes Graphium_thule Graphium_aristeus Graphium_androcles Graphium_dorcus Graphium_antiphates Graphium_decolor Color code for areas Graphium_xenocles Graphium_delessertii Graphium_ramaceus Graphium_macareus Graphium_leonidas Graphium_latreillianus Graphium_tynderaeus Graphium_ridleyanus Graphium_angolanus Graphium_schubotzi

Late K Paleocene Eocene Oligocene Miocene Pl P Ma 70 60 50 40 30 20 10 0 Supplementary figure 11. Estimation of the historical biogeography for the four molecular dated trees of Aristolochiaceae with the Dispersal-Extinction-Cladogenesis (DEC) model. For each tree, two DEC analyses were performed: one with time-stratified palaeogeographic constraints, and one without such constraints. The genus Aristolochia originated in a northern region centred around the Bering land bridge. J = Jurassic, K = Cretaceous, Pl = Pliocene, P = Pleistocene.

a) a) Dating Early Ancestral area area Ancestral of Origin Color Viewed

Eocene

with Legend code for areas Global Aristolochia Aristolochia

exponential from

paleogeography

paleogeography North

Pole Ma Ma

priors (max. 150 Ma) and Ma) and (max. 150 110

Early 25 Ma 25 K 100 Aristolochia (95% CI: 39.2-72.8 Ma) CI: (95% 39.2-72.8 90 biogeographic Late appeared appeared

Cretaceous 80

55.5 Ma 55.5

70 inference

Paleoc 60

Lactoris with .

adjacency

50 Eocene matrix

40 Oligocene 30

20 Saruma

Miocene

Pl Pl

P 0 Aristolochia_cucurbitoides Aristolochia_wardiana Aristolochia_moupinensis Aristolochia_grandis Aristolochia_saccata Aristolochia_westlandii Aristolochia_austroyunnanensis Aristolochia_kwangsiensis Aristolochia_championii Aristolochia_neolongifolia Aristolochia_griffithii Aristolochia_nakaoi Aristolochia_kaempferi Aristolochia_cucurbitifolia Aristolochia_shimadai Aristolochia_liukiuensis Aristolochia_onoei Aristolochia_goldieana Aristolochia_promissa Aristolochia_triactina Aristolochia_praevenosa Pararistolochia_australopithecurus Pararistolochia_laheyana Aristolochia_burelae Aristolochia_lindneri Aristolochia_erecta Aristolochia_pentandra Aristolochia_micrantha Aristolochia_nelsonii Aristolochia_rojasiana Aristolochia_cauliflora Aristolochia_leuconeura Aristolochia_taliscana Aristolochia_tentaculata Aristolochia_passiflorifolia Aristolochia_chilensis Aristolochia_fimbriata Aristolochia_nummularifolia Aristolochia_chamissonis Aristolochia_paulistana Aristolochia_triangularis Aristolochia_gibertii Aristolochia_macroura Aristolochia_trilobata Aristolochia_ringens Aristolochia_cymbifera Aristolochia_maurorum Aristolochia_esperanzae Aristolochia_galeata Aristolochia_labiata Aristolochia_arcuata Aristolochia_pilosa Aristolochia_cynanchifolia Aristolochia_anguicida Aristolochia_odoratissima Aristolochia_gigantea Aristolochia_elegans Aristolochia_littoralis Aristolochia_argentina Holostylis_reniformis Aristolochia_holostylis Aristolochia_reniformis Aristolochia_eriantha Aristolochia_peruviana Aristolochia_cordiflora Aristolochia_cruenta Aristolochia_melastoma Aristolochia_maxima Aristolochia_acutifolia Aristolochia_ovalifolia Aristolochia_tonduzii Aristolochia_grandiflora Aristolochia_gorgona Aristolochia_pichinchensis Aristolochia_kerrii Aristolochia_kankauensis Aristolochia_zollingeriana Aristolochia_pierrei Aristolochia_acuminata Aristolochia_tagala Aristolochia_gaudichaudii Aristolochia_bracteolata Aristolochia_indica Aristolochia_krisagathra Aristolochia_heppii Aristolochia_hockii Aristolochia_jackii Aristolochia_albida Aristolochia_petersiana Aristolochia_rigida Aristolochia_clematitis Aristolochia_debilis Aristolochia_fordiana Aristolochia_foveolata Aristolochia_goliathiana Aristolochia_papillifolia Aristolochia_delavayi Aristolochia_pistolochia Aristolochia_iberica Aristolochia_pontica Aristolochia_bottae Aristolochia_hirta Aristolochia_incisa Aristolochia_baetica Aristolochia_sempervirens Aristolochia_clusii Aristolochia_sicula Aristolochia_tyrrhena Aristolochia_bianorii Aristolochia_rotunda Aristolochia_navicularis Aristolochia_parvifolia Aristolochia_elongata Aristolochia_microstoma Aristolochia_merxmuelleri Aristolochia_lutea Aristolochia_pallida Saruma_henryi Asarum_cordifolium Asarum_cardiophyllum Asarum_caudigerum Asarum_pulchellum Asarum_misandrum Asarum_heterotropoides Asarum_versicolor Asarum_mikuniense Asarum_tohokuense Asarum_maruyamae Asarum_dimidiatum Asarum_patens Asarum_sieboldii Asarum_glabrum Asarum_maculatum Asarum_himalaicum Asarum_caulescens Asarum_caudigerellum Asarum_debile Asarum_europaeum Asarum_canadense Asarum_hartwegii Asarum_caudatum Asarum_lemmonii Asarum_dissitum Asarum_monodoriflorum Asarum_yaeyamense Asarum_geophilum Asarum_epigynum Asarum_yunnanense Asarum_arifolium Asarum_speciosum Asarum_lewisii Asarum_shuttleworthii Asarum_minus Asarum_virginicum Asarum_contractum Asarum_heterophyllum Asarum_memmingeri Asarum_naniflorum Asarum_maximum Asarum_campaniflorum Asarum_insigne Asarum_hongkongense Asarum_sagittarioides Asarum_magnificum Asarum_longerhizomatosum Asarum_wulingense Asarum_bashanense Asarum_chengkouense Asarum_nanchuanense Asarum_inflatum Asarum_chinense Asarum_ichangense Asarum_crispulatum Asarum_chingchengense Asarum_splendens Asarum_delavayi Asarum_porphyronotum Asarum_gusk Asarum_pellucidum Asarum_trinacriforme Asarum_tokarense Asarum_yakusimense Asarum_forbesii Asarum_muramatsui Asarum_asaroides Asarum_senkakuinsulare Asarum_unzen Asarum_fudsinoi Asarum_kumageanum Asarum_satsumense Asarum_gelasinum Asarum_hatsushimae Asarum_okinawense Asarum_simile Asarum_subglobosum Asarum_tamaensis Asarum_crassum Asarum_minamitanianum Asarum_nipponicum Asarum_savatieri Asarum_takaoi Asarum_sakawanum Asarum_fauriei Asarum_tamaense Asarum_costatum Asarum_blumei Asarum_hexalobum Asarum_asperum Asarum_megacalyx Lactoris_fernandeziana Thottea_tomentosa Thottea_piperiformis Thottea_abrahamii Thottea_dinghoui Thottea_barberi Thottea_ponmudiana Thottea_duchartrei Thottea_idukkiana Thottea_dalzellii Thottea_siliquosa Thottea_sivarajanii Thottea_corymbosa Thottea_parviflora Thottea_borneensis Thottea_macrantha Thottea_penitilobata Thottea_dependens Thottea_grandiflora Aristolochia_reticulata Aristolochia_serpentaria Aristolochia_panamensis Aristolochia_paracleta Aristolochia_malacophylla Aristolochia_stevensii Aristolochia_salvadorensis Aristolochia_impudica Aristolochia_arborea Aristolochia_kalebii Aristolochia_chiapensis Aristolochia_tricaudata Aristolochia_asclepiadifolia Aristolochia_veracruzana Aristolochia_macrophylla Aristolochia_manshuriensis Aristolochia_tomentosa Aristolochia_tubiflora Aristolochia_californica

Asarum Thottea Aristolochia possible states WP WN WA SA IN EP EN CA AU AF b) b) Dating Ancestral area area Ancestral of Origin Color

with Legend code for areas Global Aristolochia Aristolochia

exponential

paleogeography

Ma Ma

priors (max. 150 Ma) and Ma) and (max. 150 110 Early 25 Ma 25 K 100 Aristolochia (95% CI: 39.2-72.8 Ma) CI: (95% 39.2-72.8 90 biogeographic Late appeared appeared

Cretaceous 80

55.5 Ma 55.5

70 inference

Paleoc 60

Lactoris with .

unconstrained

50 Eocene

40 matrix Oligocene 30

20 Saruma

Miocene

Pl Pl

Asarum Thottea Aristolochia possible states CA AU AF WP WN WA SA IN EP EN c) Dating with exponential priors (max. 221 Ma) and biogeographic inference with adjacency matrix Global paleogeography 25 Ma Aristolochia

Aristolochia appeared 58.8 Ma (95% CI: 42.5-76.2 Ma) possible states

AF AU CA Late Paleocene paleogeography EN Viewed from North Pole EP IN SA Legend WA Origin of Aristolochia WN

Thottea WP Ancestral area Lactoris

Color code for areas Asarum

Saruma

Late J Early Cretaceous Late Cretaceous Paleoc. Eocene Oligocene Miocene Pl P Ma 150 140 130 120 110 100 90 80 70 60 50 40 30 20 10 0 d) Dating with exponential priors (max. 221 Ma) and biogeographic inference with unconstrained matrix Global paleogeography 25 Ma Aristolochia

Aristolochia appeared 58.8 Ma (95% CI: 42.5-76.2 Ma) possible states

AF AU CA EN EP IN SA Legend WA Origin of Aristolochia WN

Thottea WP Ancestral area Lactoris

Color code for areas Asarum

Saruma

Late J Early Cretaceous Late Cretaceous Paleoc. Eocene Oligocene Miocene Pl P Ma 150 140 130 120 110 100 90 80 70 60 50 40 30 20 10 0 Aristolochia_pallida e) Dating with uniform priors (max. 150 Ma) and biogeographic inference with adjacency matrix Aristolochia_lutea Aristolochia_merxmuelleri Aristolochia_microstoma Aristolochia_elongata Aristolochia_parvifolia Aristolochia_navicularis Global paleogeography 25 Ma Aristolochia_rotunda Aristolochia_bianorii Aristolochia_tyrrhena Aristolochia_sicula Aristolochia_clusii Aristolochia_sempervirens Aristolochia_baetica Aristolochia_incisa Aristolochia_hirta Aristolochia_bottae Aristolochia_pontica Aristolochia_iberica Aristolochia_pistolochia Aristolochia_delavayi Aristolochia_papillifolia Aristolochia_goliathiana Aristolochia_foveolata Aristolochia_fordiana Aristolochia_debilis Aristolochia_clematitis Aristolochia_rigida Aristolochia_petersiana Aristolochia_albida Aristolochia_jackii Aristolochia_hockii Aristolochia_heppii Aristolochia_krisagathra Aristolochia_indica Aristolochia_bracteolata Aristolochia_gaudichaudii Aristolochia_tagala Aristolochia_acuminata Aristolochia_pierrei Aristolochia_zollingeriana Aristolochia_kankauensis Aristolochia_kerrii Aristolochia_pichinchensis Aristolochia_gorgona Aristolochia_grandiflora Aristolochia_tonduzii Aristolochia_ovalifolia Aristolochia_acutifolia Aristolochia_maxima Aristolochia_melastoma Aristolochia_cruenta Aristolochia_cordiflora Aristolochia_peruviana Aristolochia_eriantha Aristolochia_reniformis Aristolochia_holostylis Holostylis_reniformis Aristolochia_argentina Aristolochia_littoralis Aristolochia_elegans

Aristolochia_gigantea Aristolochia_odoratissima Aristolochia_anguicida Aristolochia_cynanchifolia Aristolochia_pilosa Aristolochia_arcuata Aristolochia_labiata Aristolochia_galeata Aristolochia_esperanzae Aristolochia_maurorum Aristolochia_cymbifera Aristolochia_ringens Aristolochia_trilobata Aristolochia_macrouraAristolochia Aristolochia_gibertii Aristolochia_triangularis Aristolochia_paulistana Aristolochia_chamissonis Aristolochia_nummularifolia Aristolochia_fimbriata Aristolochia_chilensis Aristolochia_passiflorifolia Aristolochia_tentaculata Aristolochia_taliscana Aristolochia_leuconeura Aristolochia_cauliflora Aristolochia_rojasiana Aristolochia_nelsonii Aristolochia_micrantha Aristolochia appeared 60.7 Ma Aristolochia_pentandra Aristolochia_erecta Aristolochia_lindneri Aristolochia_burelae (95% CI: 43.9-80.5 Ma) Pararistolochia_laheyana Pararistolochia_australopithecurus Aristolochia_praevenosapossible states Aristolochia_triactina Aristolochia_promissa Aristolochia_goldieana Aristolochia_onoei Aristolochia_liukiuensis Aristolochia_shimadai AF Aristolochia_cucurbitifolia Aristolochia_kaempferi Aristolochia_nakaoi Aristolochia_griffithii Aristolochia_neolongifolia AU Aristolochia_championii Aristolochia_kwangsiensis Aristolochia_austroyunnanensis Aristolochia_westlandii Aristolochia_saccata Aristolochia_grandis CA Aristolochia_moupinensis Aristolochia_wardiana Aristolochia_cucurbitoides Aristolochia_californica Late Paleocene paleogeography Aristolochia_tubiflora EN Aristolochia_tomentosa Aristolochia_manshuriensis Viewed from North Pole Aristolochia_macrophylla Aristolochia_veracruzana Aristolochia_asclepiadifolia Aristolochia_tricaudata EP Aristolochia_chiapensis Aristolochia_kalebii Aristolochia_arborea Aristolochia_impudica Aristolochia_salvadorensis IN Aristolochia_stevensii Aristolochia_malacophylla Aristolochia_paracleta Aristolochia_panamensis Aristolochia_serpentaria Aristolochia_reticulata SA Thottea_grandiflora Thottea_dependens Thottea_penitilobata Legend Thottea_macrantha Thottea_borneensis WA Thottea_parviflora Thottea_corymbosa Thottea_sivarajanii Thottea_siliquosa Origin of Aristolochia Thottea_dalzellii Thottea_idukkiana WN Thottea_duchartrei Thottea_ponmudiana Thottea_barberiThottea Thottea_dinghoui Thottea_abrahamii WP Thottea_piperiformis Thottea_tomentosa Ancestral area Lactoris_fernandeziana Asarum_megacalyx Lactoris Asarum_asperum Asarum_hexalobum Asarum_blumei Asarum_costatum Asarum_tamaense Asarum_fauriei Color code for areas Asarum_sakawanum Asarum_takaoi Asarum_savatieri Asarum_nipponicum Asarum_minamitanianum Asarum_crassum Asarum_tamaensis Asarum_subglobosum Asarum_simile Asarum_okinawense Asarum_hatsushimae Asarum_gelasinum Asarum_satsumense Asarum_kumageanum Asarum_fudsinoi Asarum_unzen Asarum_senkakuinsulare Asarum_asaroides Asarum_muramatsui Asarum_forbesii Asarum_yakusimense Asarum_tokarense Asarum_trinacriforme Asarum_pellucidum Asarum_gusk Asarum_porphyronotum Asarum_delavayi Asarum_splendens Asarum_chingchengense Asarum_crispulatum Asarum_ichangense Asarum_chinense Asarum_inflatum Asarum_nanchuanense Asarum_chengkouense Asarum_bashanense Asarum_wulingense Asarum_longerhizomatosum Asarum_magnificum Asarum_sagittarioides Asarum_hongkongense Asarum_insigne

Asarum_campaniflorumAsarum Asarum_maximum Asarum_naniflorum Asarum_memmingeri Asarum_heterophyllum Asarum_contractum Asarum_virginicum Asarum_minus Asarum_shuttleworthii Asarum_lewisii Asarum_speciosum Asarum_arifolium Asarum_yunnanense Asarum_epigynum Asarum_geophilum Asarum_yaeyamense Asarum_monodoriflorum Asarum_dissitum Asarum_lemmonii Asarum_caudatum Asarum_hartwegii Asarum_canadense Asarum_europaeum Asarum_debile Asarum_caudigerellum Asarum_caulescens Asarum_himalaicum Asarum_maculatum Asarum_glabrum Asarum_sieboldii Asarum_patens Asarum_dimidiatum Asarum_maruyamae Asarum_tohokuense Asarum_mikuniense Asarum_versicolor Asarum_heterotropoides Asarum_misandrum Asarum_pulchellum Asarum_caudigerum Asarum_cardiophyllum Saruma Asarum_cordifolium Saruma_henryi

Early Cretaceous Late Cretaceous Paleoc. Eocene Oligocene Miocene Pl P Ma 120 110 100 90 80 70 60 50 40 30 20 10 0 Aristolochia_pallida f) Dating with uniform priors (max. 150 Ma) and biogeographic inference with unconstrained matrix Aristolochia_lutea Aristolochia_merxmuelleri Aristolochia_microstoma Aristolochia_elongata Aristolochia_parvifolia Aristolochia_navicularis Global paleogeography 25 Ma Aristolochia_rotunda Aristolochia_bianorii Aristolochia_tyrrhena Aristolochia_sicula Aristolochia_clusii Aristolochia_sempervirens Aristolochia_baetica Aristolochia_incisa Aristolochia_hirta Aristolochia_bottae Aristolochia_pontica Aristolochia_iberica Aristolochia_pistolochia Aristolochia_delavayi Aristolochia_papillifolia Aristolochia_goliathiana Aristolochia_foveolata Aristolochia_fordiana Aristolochia_debilis Aristolochia_clematitis Aristolochia_rigida Aristolochia_petersiana Aristolochia_albida Aristolochia_jackii Aristolochia_hockii Aristolochia_heppii Aristolochia_krisagathra Aristolochia_indica Aristolochia_bracteolata Aristolochia_gaudichaudii Aristolochia_tagala Aristolochia_acuminata Aristolochia_pierrei Aristolochia_zollingeriana Aristolochia_kankauensis Aristolochia_kerrii Aristolochia_pichinchensis Aristolochia_gorgona Aristolochia_grandiflora Aristolochia_tonduzii Aristolochia_ovalifolia Aristolochia_acutifolia Aristolochia_maxima Aristolochia_melastoma Aristolochia_cruenta Aristolochia_cordiflora Aristolochia_peruviana Aristolochia_eriantha Aristolochia_reniformis Aristolochia_holostylis Holostylis_reniformis Aristolochia_argentina Aristolochia_littoralis Aristolochia_elegans

Aristolochia_gigantea Aristolochia_odoratissima Aristolochia_anguicida Aristolochia_cynanchifolia Aristolochia_pilosa Aristolochia_arcuata Aristolochia_labiata Aristolochia_galeata Aristolochia_esperanzae Aristolochia_maurorum Aristolochia_cymbifera Aristolochia_ringens Aristolochia_trilobata Aristolochia_macrouraAristolochia Aristolochia_gibertii Aristolochia_triangularis Aristolochia_paulistana Aristolochia_chamissonis Aristolochia_nummularifolia Aristolochia_fimbriata Aristolochia_chilensis Aristolochia_passiflorifolia Aristolochia_tentaculata Aristolochia_taliscana Aristolochia_leuconeura Aristolochia_cauliflora Aristolochia_rojasiana Aristolochia_nelsonii Aristolochia_micrantha Aristolochia appeared 60.7 Ma Aristolochia_pentandra Aristolochia_erecta Aristolochia_lindneri Aristolochia_burelae (95% CI: 43.9-80.5 Ma) Pararistolochia_laheyana Pararistolochia_australopithecurus Aristolochia_praevenosapossible states Aristolochia_triactina Aristolochia_promissa Aristolochia_goldieana Aristolochia_onoei Aristolochia_liukiuensis Aristolochia_shimadai AF Aristolochia_cucurbitifolia Aristolochia_kaempferi Aristolochia_nakaoi Aristolochia_griffithii Aristolochia_neolongifolia AU Aristolochia_championii Aristolochia_kwangsiensis Aristolochia_austroyunnanensis Aristolochia_westlandii Aristolochia_saccata Aristolochia_grandis CA Aristolochia_moupinensis Aristolochia_wardiana Aristolochia_cucurbitoides Aristolochia_californica Aristolochia_tubiflora EN Aristolochia_tomentosa Aristolochia_manshuriensis Aristolochia_macrophylla Aristolochia_veracruzana Aristolochia_asclepiadifolia Aristolochia_tricaudata EP Aristolochia_chiapensis Aristolochia_kalebii Aristolochia_arborea Aristolochia_impudica Aristolochia_salvadorensis IN Aristolochia_stevensii Aristolochia_malacophylla Aristolochia_paracleta Aristolochia_panamensis Aristolochia_serpentaria Aristolochia_reticulata SA Thottea_grandiflora Thottea_dependens Thottea_penitilobata Legend Thottea_macrantha Thottea_borneensis WA Thottea_parviflora Thottea_corymbosa Thottea_sivarajanii Thottea_siliquosa Origin of Aristolochia Thottea_dalzellii Thottea_idukkiana WN Thottea_duchartrei Thottea_ponmudiana Thottea_barberiThottea Thottea_dinghoui Thottea_abrahamii WP Thottea_piperiformis Thottea_tomentosa Ancestral area Lactoris_fernandeziana Asarum_megacalyx Lactoris Asarum_asperum Asarum_hexalobum Asarum_blumei Asarum_costatum Asarum_tamaense Asarum_fauriei Color code for areas Asarum_sakawanum Asarum_takaoi Asarum_savatieri Asarum_nipponicum Asarum_minamitanianum Asarum_crassum Asarum_tamaensis Asarum_subglobosum Asarum_simile Asarum_okinawense Asarum_hatsushimae Asarum_gelasinum Asarum_satsumense Asarum_kumageanum Asarum_fudsinoi Asarum_unzen Asarum_senkakuinsulare Asarum_asaroides Asarum_muramatsui Asarum_forbesii Asarum_yakusimense Asarum_tokarense Asarum_trinacriforme Asarum_pellucidum Asarum_gusk Asarum_porphyronotum Asarum_delavayi Asarum_splendens Asarum_chingchengense Asarum_crispulatum Asarum_ichangense Asarum_chinense Asarum_inflatum Asarum_nanchuanense Asarum_chengkouense Asarum_bashanense Asarum_wulingense Asarum_longerhizomatosum Asarum_magnificum Asarum_sagittarioides Asarum_hongkongense Asarum_insigne

Early Cretaceous Late Cretaceous Paleoc. Eocene Oligocene Miocene Pl P Ma 120 110 100 90 80 70 60 50 40 30 20 10 0 Aristolochia_pallida g) Dating with uniform priors (max. 221 Ma) and biogeographic inference with adjacency matrix Aristolochia_lutea Aristolochia_merxmuelleri Aristolochia_microstoma Aristolochia_elongata Aristolochia_parvifolia Aristolochia_navicularis Global paleogeography 25 Ma Aristolochia_rotunda Aristolochia_bianorii Aristolochia_tyrrhena Aristolochia_sicula Aristolochia_clusii Aristolochia_sempervirens Aristolochia_baetica Aristolochia_incisa Aristolochia_hirta Aristolochia_bottae Aristolochia_pontica Aristolochia_iberica Aristolochia_pistolochia Aristolochia_delavayi Aristolochia_papillifolia Aristolochia_goliathiana Aristolochia_foveolata Aristolochia_fordiana Aristolochia_debilis Aristolochia_clematitis Aristolochia_rigida Aristolochia_petersiana Aristolochia_albida Aristolochia_jackii Aristolochia_hockii Aristolochia_heppii Aristolochia_krisagathra Aristolochia_indica Aristolochia_bracteolata Aristolochia_gaudichaudii Aristolochia_tagala Aristolochia_acuminata Aristolochia_pierrei Aristolochia_zollingeriana Aristolochia_kankauensis Aristolochia_kerrii Aristolochia_pichinchensis Aristolochia_gorgona Aristolochia_grandiflora Aristolochia_tonduzii Aristolochia_ovalifolia Aristolochia_acutifolia Aristolochia_maxima Aristolochia_melastoma Aristolochia_cruenta Aristolochia_cordiflora Aristolochia_peruviana Aristolochia_eriantha Aristolochia_reniformis Aristolochia_holostylis Holostylis_reniformis Aristolochia_argentina Aristolochia_littoralis Aristolochia_elegans Aristolochia_gigantea Aristolochia_odoratissima Aristolochia_anguicida Aristolochia_cynanchifolia Aristolochia_pilosa Aristolochia_arcuata Aristolochia_labiata Aristolochia_galeata Aristolochia_esperanzae Aristolochia_maurorum Aristolochia_cymbifera Aristolochia_ringens Aristolochia_trilobata

Aristolochia_macrouraAristolochia Aristolochia_gibertii Aristolochia_triangularis Aristolochia_paulistana Aristolochia_chamissonis Aristolochia_nummularifolia Aristolochia_fimbriata Aristolochia_chilensis Aristolochia_passiflorifolia Aristolochia_tentaculata Aristolochia_taliscana Aristolochia_leuconeura Aristolochia_cauliflora Aristolochia_rojasiana Aristolochia_nelsonii Aristolochia_micrantha Aristolochia_pentandra Aristolochia appeared 64.8 Ma Aristolochia_erecta Aristolochia_lindneri Aristolochia_burelae (95% CI: 47.3-83.1 Ma) Pararistolochia_laheyana Pararistolochia_australopithecurus Aristolochia_praevenosapossible states Aristolochia_triactina Aristolochia_promissa Aristolochia_goldieana Aristolochia_onoei Aristolochia_liukiuensis Aristolochia_shimadai AF Aristolochia_cucurbitifolia Aristolochia_kaempferi Aristolochia_nakaoi Aristolochia_griffithii Aristolochia_neolongifolia AU Aristolochia_championii Aristolochia_kwangsiensis Aristolochia_austroyunnanensis Aristolochia_westlandii Aristolochia_saccata Aristolochia_grandis CA Aristolochia_moupinensis Aristolochia_wardiana Aristolochia_cucurbitoides Aristolochia_californica Early Paleocene paleogeography Aristolochia_tubiflora EN Aristolochia_tomentosa Aristolochia_manshuriensis Viewed from North Pole Aristolochia_macrophylla Aristolochia_veracruzana Aristolochia_asclepiadifolia Aristolochia_tricaudata EP Aristolochia_chiapensis Aristolochia_kalebii Aristolochia_arborea Aristolochia_impudica Aristolochia_salvadorensis IN Aristolochia_stevensii Aristolochia_malacophylla Aristolochia_paracleta Aristolochia_panamensis Aristolochia_serpentaria Aristolochia_reticulata SA Thottea_grandiflora Thottea_dependens Thottea_penitilobata Legend Thottea_macrantha Thottea_borneensis WA Thottea_parviflora Thottea_corymbosa Thottea_sivarajanii Thottea_siliquosa Thottea_dalzellii Origin of Aristolochia Thottea_idukkiana WN Thottea_duchartrei Thottea_ponmudiana Thottea_barberi Thottea_dinghouiThottea Thottea_abrahamii WP Thottea_piperiformis Thottea_tomentosa Lactoris_fernandeziana Ancestral area Asarum_megacalyx Asarum_asperum Lactoris Asarum_hexalobum Asarum_blumei Asarum_costatum Asarum_tamaense Asarum_fauriei Color code for areas Asarum_sakawanum Asarum_takaoi Asarum_savatieri Asarum_nipponicum Asarum_minamitanianum Asarum_crassum Asarum_tamaensis Asarum_subglobosum Asarum_simile Asarum_okinawense Asarum_hatsushimae Asarum_gelasinum Asarum_satsumense Asarum_kumageanum Asarum_fudsinoi Asarum_unzen Asarum_senkakuinsulare Asarum_asaroides Asarum_muramatsui Asarum_forbesii Asarum_yakusimense Asarum_tokarense Asarum_trinacriforme Asarum_pellucidum Asarum_gusk Asarum_porphyronotum Asarum_delavayi Asarum_splendens Asarum_chingchengense Asarum_crispulatum Asarum_ichangense Asarum_chinense Asarum_inflatum Asarum_nanchuanense Asarum_chengkouense Asarum_bashanense Asarum_wulingense Asarum_longerhizomatosum Asarum_magnificum Asarum_sagittarioides Asarum_hongkongense Asarum_insigne Asarum_campaniflorum

Asarum_maximumAsarum Asarum_naniflorum Asarum_memmingeri Asarum_heterophyllum Asarum_contractum Asarum_virginicum Asarum_minus Asarum_shuttleworthii Asarum_lewisii Asarum_speciosum Asarum_arifolium Asarum_yunnanense Asarum_epigynum Asarum_geophilum Asarum_yaeyamense Asarum_monodoriflorum Asarum_dissitum Asarum_lemmonii Asarum_caudatum Asarum_hartwegii Asarum_canadense Asarum_europaeum Asarum_debile Asarum_caudigerellum Asarum_caulescens Asarum_himalaicum Asarum_maculatum Asarum_glabrum Asarum_sieboldii Asarum_patens Asarum_dimidiatum Asarum_maruyamae Asarum_tohokuense Asarum_mikuniense Asarum_versicolor Asarum_heterotropoides Asarum_misandrum Asarum_pulchellum Asarum_caudigerum Asarum_cardiophyllum Asarum_cordifolium Saruma Saruma_henryi

M. J Late J Early Cretaceous Late Cretaceous Paleoc. Eocene Oligocene Miocene Pl P Ma 160 150 140 130 120 110 100 90 80 70 60 50 40 30 20 10 0 Aristolochia_pallida h) Dating with uniform priors (max. 221 Ma) and biogeographic inference with unconstrained matrix Aristolochia_lutea Aristolochia_merxmuelleri Aristolochia_microstoma Aristolochia_elongata Aristolochia_parvifolia Aristolochia_navicularis Global paleogeography 25 Ma Aristolochia_rotunda Aristolochia_bianorii Aristolochia_tyrrhena Aristolochia_sicula Aristolochia_clusii Aristolochia_sempervirens Aristolochia_baetica Aristolochia_incisa Aristolochia_hirta Aristolochia_bottae Aristolochia_pontica Aristolochia_iberica Aristolochia_pistolochia Aristolochia_delavayi Aristolochia_papillifolia Aristolochia_goliathiana Aristolochia_foveolata Aristolochia_fordiana Aristolochia_debilis Aristolochia_clematitis Aristolochia_rigida Aristolochia_petersiana Aristolochia_albida Aristolochia_jackii Aristolochia_hockii Aristolochia_heppii Aristolochia_krisagathra Aristolochia_indica Aristolochia_bracteolata Aristolochia_gaudichaudii Aristolochia_tagala Aristolochia_acuminata Aristolochia_pierrei Aristolochia_zollingeriana Aristolochia_kankauensis Aristolochia_kerrii Aristolochia_pichinchensis Aristolochia_gorgona Aristolochia_grandiflora Aristolochia_tonduzii Aristolochia_ovalifolia Aristolochia_acutifolia Aristolochia_maxima Aristolochia_melastoma Aristolochia_cruenta Aristolochia_cordiflora Aristolochia_peruviana Aristolochia_eriantha Aristolochia_reniformis Aristolochia_holostylis Holostylis_reniformis Aristolochia_argentina Aristolochia_littoralis Aristolochia_elegans Aristolochia_gigantea Aristolochia_odoratissima Aristolochia_anguicida Aristolochia_cynanchifolia Aristolochia_pilosa Aristolochia_arcuata Aristolochia_labiata Aristolochia_galeata Aristolochia_esperanzae Aristolochia_maurorum Aristolochia_cymbifera Aristolochia_ringens Aristolochia_trilobata

Aristolochia_macrouraAristolochia Aristolochia_gibertii Aristolochia_triangularis Aristolochia_paulistana Aristolochia_chamissonis Aristolochia_nummularifolia Aristolochia_fimbriata Aristolochia_chilensis Aristolochia_passiflorifolia Aristolochia_tentaculata Aristolochia_taliscana Aristolochia_leuconeura Aristolochia_cauliflora Aristolochia_rojasiana Aristolochia_nelsonii Aristolochia_micrantha Aristolochia_pentandra Aristolochia appeared 64.8 Ma Aristolochia_erecta Aristolochia_lindneri Aristolochia_burelae (95% CI: 47.3-83.1 Ma) Pararistolochia_laheyana Pararistolochia_australopithecurus Aristolochia_praevenosapossiblepossible states states Aristolochia_triactina Aristolochia_promissa Aristolochia_goldieana Aristolochia_onoei Aristolochia_liukiuensis Aristolochia_shimadai AF AF Aristolochia_cucurbitifolia Aristolochia_kaempferi Aristolochia_nakaoi Aristolochia_griffithii Aristolochia_neolongifolia AU AU Aristolochia_championii Aristolochia_kwangsiensis Aristolochia_austroyunnanensis Aristolochia_westlandii Aristolochia_saccata Aristolochia_grandis CA CA Aristolochia_moupinensis Aristolochia_wardiana Aristolochia_cucurbitoides Aristolochia_californica Aristolochia_tubiflora EN EN Aristolochia_tomentosa Aristolochia_manshuriensis Aristolochia_macrophylla Aristolochia_veracruzana Aristolochia_asclepiadifolia Aristolochia_tricaudata EP EP Aristolochia_chiapensis Aristolochia_kalebii Aristolochia_arborea Aristolochia_impudica Aristolochia_salvadorensis IN IN Aristolochia_stevensii Aristolochia_malacophylla Aristolochia_paracleta Aristolochia_panamensis Aristolochia_serpentaria Aristolochia_reticulata SA SA Thottea_grandiflora Thottea_dependens Thottea_penitilobata Legend Thottea_macrantha Thottea_borneensis WA WA Thottea_parviflora Thottea_corymbosa Thottea_sivarajanii Thottea_siliquosa Thottea_dalzellii Origin of Aristolochia Thottea_idukkiana WN WN Thottea_duchartrei Thottea_ponmudiana Thottea_barberi Thottea_dinghouiThottea Thottea_abrahamii WP WP Thottea_piperiformis Thottea_tomentosa Lactoris_fernandeziana Ancestral area Asarum_megacalyx Lactoris Asarum_asperum Asarum_hexalobum Asarum_blumei Asarum_costatum Asarum_tamaense Asarum_fauriei Color code for areas Asarum_sakawanum Asarum_takaoi Asarum_savatieri Asarum_nipponicum Asarum_minamitanianum Asarum_crassum Asarum_tamaensis Asarum_subglobosum Asarum_simile Asarum_okinawense Asarum_hatsushimae Asarum_gelasinum Asarum_satsumense Asarum_kumageanum Asarum_fudsinoi Asarum_unzen Asarum_senkakuinsulare Asarum_asaroides Asarum_muramatsui Asarum_forbesii Asarum_yakusimense Asarum_tokarense Asarum_trinacriforme Asarum_pellucidum Asarum_gusk Asarum_porphyronotum Asarum_delavayi Asarum_splendens Asarum_chingchengense Asarum_crispulatum Asarum_ichangense Asarum_chinense Asarum_inflatum Asarum_nanchuanense Asarum_chengkouense Asarum_bashanense Asarum_wulingense Asarum_longerhizomatosum Asarum_magnificum Asarum_sagittarioides Asarum_hongkongense Asarum_insigne Asarum_campaniflorum

M. J Late J Early Cretaceous Late Cretaceous Paleoc. Eocene Oligocene Miocene Pl P Ma 160 150 140 130 120 110 100 90 80 70 60 50 40 30 20 10 0 Supplementary figure 12. Trait-dependent diversification of Papilionidae linked to their host plant. a, Bayesian inferences made with the full MuSSE model showed that speciation rates vary according to the host-plant trait. b, Boxplots showing the increase of diversification rates following host-plant shifts from the ancestral state (Aristolochiaceae). Only the species-poor swallowtail lineages feeding on Fabaceae, Zygophyllaceae and Magnoliaceae show decrease of diversification rates.

Aristolochiaceae Annonaceae 40 30 30 a 20 20 10 10 0 0

0.00 0.05 0.10 0.15 0.20 0.25 0.30 0.00 0.05 0.10 0.15 0.20 0.25 0.30

Lauraceae Apiaceae 30 12 25 10 20 8 15 6 10 4 5 2 0 0

0.00 0.05 0.10 0.15 0.20 0.25 0.30 0.00 0.05 0.10 0.15 0.20 0.25 0.30

Rutaceae Crassulaceae 10 30 8 20 6 4 10 2 0 0 Posterior density Posterior 0.00 0.05 0.10 0.15 0.20 0.25 0.30 0.00 0.05 0.10 0.15 0.20 0.25 0.30

Papaveraceae Fabaceae

15 30 10 20 5 10 0 0

0.00 0.05 0.10 0.15 0.20 0.25 0.30 0.00 0.05 0.10 0.15 0.20 0.25 0.30

Zygophyllaceae Magnoliaceae 12 10 10 8 8 6 6 4 4 2 2 0 0

0.00 0.05 0.10 0.15 0.20 0.25 0.30 0.00 0.05 0.10 0.15 0.20 0.25 0.30 Rate (events/Myr/lineage)

● b 0.30

● 0.25 ●

● ● ● ● 0.20

● ● ● 0.15 ● ● ● ● ● ● ●

0.10 ● Rate (events/Myr/lineage) ●

● ● ● ● ● ● ● 0.05

0.00

Apiaceae Lauraceae Rutaceae Fabaceae Annonaceae CrassulaceaePapaveraceae Magnoliaceae Aristolochiaceae Zygophyllaceae Supplementary figure 13. Time-dependent diversification of Papilionidae after shifting to new host plants. Diversification is inferred with the RPANDA models, and the best-fit model is plotted showing rates through time for each clade. A model with increasing diversification over time best fits the Aristolochiaceae feeders. A model with a slowdown of diversification through time explained the diversification of Annonaceae feeders, Lauraceae feeders, and Papaveraceae feeders. A model with constant rates through time best fits the diversification of Apiaceae feeders, Crassulaceae feeders, and Rutaceae feeders. K = Cretaceous, Pl = Pliocene, P = Pleistocene.

0.5

Papaveraceae%feeders%

0.4 %rates%

0.3

diversiﬁa6on Lauraceae%feeders%

%net% Crassulaceae%feeders% 0.2 Net diversification rate Net diversification speciﬁc Rutaceae%feeders% Apiaceae%feeders% Annonaceae%feeders% Clade- 0.1 Aristolochiaceae%feeders%

0.0

P P K% Paleoc.% Eocene% Oligocene% Miocene% l% −60 −50 −40 −30 −20 −10 0 66% 56% 33.9% 23.03% 5.33% 0%

Time%(Ma)% Supplementary figure 14. Bayesian analysis of clade-specific and time-dependent diversification of Papilionidae obtained with BAMM. a, Phylorate plot showing that global diversification rates increase through time in Papilionidae with no significant rate shifts detected by BAMM (the inset plot indicates the posterior probability for the estimated number of shifts). b, Rate-through-time plots for selected swallowtail lineages feeding on distinct host-plant families. The results also show an overall diversification increase through time for each group of swallowtails. P = Palaeocene, E = Eocene, O = Oligocene, M = Miocene.

prior

0.5 posterior

0.4

0.3

0.2

0.1

0.0 0 1 2 3 4 5 6 7

n shifts

Papilionini 0.11

0.1

0.085 Troidini

Papilioninae Teinopalpini

0.0093

Leptocircini

Parnassiini Parnassiinae Zerynthiini Baroniinae Luehdorﬁini

P E O M 66 56 33.9 23 5.3 0 Time (Ma) 0.15 0.15 All Papilionidae Aristolochiaceae feeders (ancestral host plant)

0.10 0.10

0.05 0.05 net diversification rate net diversification rate net diversification

0.00 0.00 P 60 50 E 40 30O 20 M 10 0 P 60 50 E 40 30O 20 M 10 0 time before present time before present 66 56 33.9 23 5.3 0 66 56 33.9 23 5.3 0

0.15 0.15 Crassulaceae and Saxifragaceae feeders (shift in Parnassius) Papaveraceae feeders (shift in Parnassius)

0.10 0.10

0.05 0.05 net diversification rate net diversification rate net diversification

0.00 0.00 P 60 50 E 40 30O 20 M 10 0 P 60 50 E 40 30O 20 M 10 0 time before present time before present 66 56 33.9 23 5.3 0 66 56 33.9 23 5.3 0

0.15 0.15 Annonaceae feeders (shift in Leptocircini) Rutaceae feeders (shift in Papilio)

0.10 0.10

0.05 0.05 net diversification rate net diversification rate net diversification

0.00 0.00 P 60 50 E 40 30O 20 M 10 0 P 60 50 E 40 30O 20 M 10 0 time before present time before present 66 56 33.9 23 5.3 0 66 56 33.9 23 5.3 0

0.15 0.15 Lauraceae feeders (shifts in Papilio, Meandrusa and Teinopalpus) Apiaceae feeders (shift in Papilio)

0.10 0.10

0.05 0.05 net diversification rate net diversification rate net diversification

0.00 0.00 P 60 50 E 40 30O 20 M 10 0 P 60 50 E 40 30O 20 M 10 0 time before present time before present 66 56 33.9 23 5.3 0 66 56 33.9 23 5.3 0 Time (Ma) Time (Ma) Supplementary figure 15. Bayesian analysis of branch-specific and time-dependent diversification of Papilionidae obtained with RevBayes. The median rates of diversification are plotted along each branch of the phylogeny, which shows a global increase of diversification rates through time in Papilionidae. Contrary to BAMM, this approach detected shifts in diversification rates in particular within the genera Parnassius and Papilio that have both shifted to new host-plant families. P = Palaeocene, E = Eocene, O = Oligocene, M = Miocene.

branch_net_div 0.173 0,173 branch_net_div 0,173

0.046 0,046

0,046

Papilionini

Troidini

Papilioninae Teinopalpini

Leptocircini

Parnassiini Parnassiinae Zerynthiini Luehdorﬁini -70 -60 Baroniinae-50 -40 -30 -20 -10 0

-70 P -60 -50 E -40 -30 O -20 M -10 0 66 56 33.9 23 5.3 0 Time (Ma) Supplementary figure 16. Bayesian analysis of episodic diversification of Papilionidae obtained with CoMET. The four plots represent speciation, extinction, net diversification, and relative extinction rates through time for the whole family. The result indicates a global increase of diversification rates over time, notably starting ~40 Ma. P = Palaeocene, E = Eocene, O = Oligocene, M = Miocene.

speciationSpecia'on rates rates netNet diversiﬁca'on rates −diversification rates

0.14

) 0.15 ) 0.12

lineage lineage 0.10 0.10 0.08 /Myr/ /Myr/ rate rate 0.06 events 0.05 events 0.04

Rates ( Rates ( 0.02 0.00 0.00 P E O M P E O M 66 60 56 50 40 33.9 30 23 20 10 5.3 00 66 60 56 50 40 33.9 30 23 20 10 5.3 00

million years ago million years ago

extinctionEx'nc'on rates rates relativeRela've ex'nc'on rates −extinction rates

0.7

) 0.15 ) 0.6

lineage lineage 0.5 0.10 0.4 /Myr/ /Myr/ rate rate 0.3 events 0.05 events 0.2

Rates ( Rates ( 0.1 0.00 0.0 P E O M P E O M 66 60 56 50 40 33.9 30 23 20 10 5.3 00 66 60 56 50 40 33.9 30 23 20 10 5.3 00

millionTime (Ma) years ago millionTime (Ma) years ago Supplementary figure 17. Number of host plants consumed through time by Papilionidae. Using the estimation of ancestral host-plant preferences (Fig. S4), we plotted the time at which a new host-plant family was colonised. This result shows that the swallowtail butterflies have a steady increase in the number of host families consumed over time. This ecological diversification can be paralleled with the global increase in diversification rates estimated by birth-death models (Figs. S13-16). K = Cretaceous, Pl = Pliocene, P = Pleistocene.

● 12

● ●

● ● 10

● 8

● %host%plants%

6 ● family %of% t$plant.species ● Number 4

2 ●

● ● ●

P Paleoc.% Eocene% Oligocene% Miocene% P 0 10 20 30 40 50 l 60 66% 56% 33.9% 23.03% 5.33% 0% rev(t$time) Time%(Ma)% Supplementary figure 18. Genus-level phylogenomic tree of Papilionidae showing the 14 selected branches with host-plant shifts and the 14 selected branches without host-plant shifts (control branches). The selection of these branches is based on the estimation of ancestral state models using the species-level phylogenies and current host-plant preferences (Figs. S4, S5).

Br 19 Br 29 Br 21 Br 26 Br 25 Br 5 Br 22 Br 1

Br 28

Br 20 Br 31

Br 7 Br 32

Br 23 Br 6 Br 30 Br 9 Br 12 Br 15 Br 8 Br 11 Br 17 Br 18 Br 16 Br 24 Br 13 Br 14

Br 10

0.03 Branch ID Plant shift Climate shift Plant and climate shifts Branch1 Host-plant shift No shift Host shift only Branch5 No shift No shift No shift Branch6 No shift No shift No shift Branch7 Host-plant shift No shift Host shift only Branch8 No shift No shift No shift Branch9 Host-plant shift No shift Host shift only Branch10 No shift No shift No shift Branch11 Host-plant shift No shift Host shift only Branch12 No shift No shift No shift Branch13 No shift No shift No shift Branch14 Host-plant shift Climate shift Host and climate shifts Branch15 Host-plant shift Climate shift Host and climate shifts Branch16 No shift No shift No shift Branch17 Host-plant shift Climate shift Host and climate shifts Branch18 No shift No shift No shift Branch19 Host-plant shift No shift Host shift only Branch20 No shift No shift No shift Branch21 Host-plant shift No shift Host shift only Branch22 No shift No shift No shift Branch23 Host-plant shift No shift Host shift only Branch24 No shift No shift No shift Branch25 Host-plant shift Climate shift Host and climate shifts Branch26 No shift No shift No shift Branch28 No shift No shift No shift Branch29 Host-plant shift No shift Host shift only Branch30 Host-plant shift No shift Host shift only Branch31 Host-plant shift Climate shift Host and climate shifts Branch32 No shift No shift No shift Supplementary figure 19. Violin plots of the percentage of missing data (“N” or “-”) and proportion of GC at third codon position (GC3) in alignment were positive selection have been detected (“Yes”) and positive selection have not been detected (“No”). Panels a and b are dataset 1 with 520 genes, and panels c and d are dataset 2 with 1533 genes.

Dataset 1 (n = 520 genes) a 30 b 0.8

20 0.6

10 0.4 % of missing data % of missing Porportion of GC3

0.2 No Yes No Yes Positive selection Positive selection Dataset 2 (n = 1533 genes) c d 50 0.8 40

30 0.6

20 0.4 10 % of missing data % of missing Porportion of GC3

0 0.2 No Yes No Yes Positive selection Positive selection Supplementary figure 20. The percentage of missing data (“N” or “-”) per genes across species computed for dataset 1 and dataset 2.

Dataset 1 (n = 520 genes)

Species

Papilio_xuthus Papilio_antimachus Protographium_marcellus 60 Papilio_machaon_gb Papilio_joanae Iphiclides_podalirius Troides_plateni Mimoides_lysithaus Eurytides_dolicaon Papilio_glaucus_gb Baronia_brevicornis Losaria_neptunus Ornithoptera_priamus Parnassius_orleans Ornithoptera_richmondia Papilio_polytes_gb Papilio_slateri Trogonoptera_brookiana 40 Byasa_alcinous Papilio_thoas Lamproptera_meges Papilio_alexanor Cressida_cressida Archon_apollinus Pachliopta_kotzebuea Euryades_corethrus Protesilaus_protesilaus Parides_ascanius Meandrusa_sciron Graphium_sarpedon Atrophaneura_dixoni Parnassius_smintheus Zerynthia_polyxena % of missing data missing % of 20 Pharmacophagus_antenor Graphium_androcles Bhutanitis_mansfieldi Parnassius_honrati Battus_polydamus Hypermnestra_helios Sericinus_montela Luehdorfia_japonica Teinopalpus_imperialis Papilio_zelicaon 0 Dataset 2 (n = 1533 genes)

Species

Papilio_xuthus Parnassius_honrati Luehdorfia_japonica 60 Papilio_machaon_gb Teinopalpus_imperialis Iphiclides_podalirius Papilio_polytes_gb Papilio_thoas Eurytides_dolicaon Ornithoptera_priamus Mimoides_lysithaus Ornithoptera_richmondia Papilio_glaucus_gb Baronia_brevicornis Losaria_neptunus Troides_plateni Papilio_slateri Trogonoptera_brookiana 40 Papilio_alexanor Cressida_cressida Lamproptera_meges Byasa_alcinous Parnassius_orleans Archon_apollinus Pachliopta_kotzebuea Meandrusa_sciron Protesilaus_protesilaus Atrophaneura_dixoni Euryades_corethrus Graphium_sarpedon Parides_ascanius Papilio_zelicaon Zerynthia_polyxena % of missing data missing % of 20 Pharmacophagus_antenor Parnassius_smintheus Bhutanitis_mansfieldi Papilio_antimachus Battus_polydamus Hypermnestra_helios Papilio_joanae Protographium_marcellus Sericinus_montela Graphium_androcles 0 Supplementary figure 21. The percentage of missing data (“N” or “-”) per branch for the branches with (“Yes”, n = 14) and without (“No”, n = 14) host-plant shift. For a given branch, the percentage of missing data is the mean value of the species of a clade for which the branch is the root.

Dataset 1 (n = 520 genes)

Branch29 40

% of missing data 10

0 No Yes Host−plant shift

Dataset 2 (n = 1533 genes)

Branch29 40

% of missing data 10

0 No Yes Host−plant shift Supplementary figure 22. Relationship between the percentage of missing data (“N” or “-”) and the number of positively selected genes per branch. For a given branch, the percentage of missing data is the mean value of the species of a clade for which the branch is the root.

Dataset 1 (n = 520 genes)

30 Host−plant shift No 20 Yes

% of missing data 10

0 10 20 30 40 Number of genes positively selected Dataset 2 (n = 1533 genes)

30 Host−plant shift No 20 Yes

% of missing data 10

0 10 20 30 40 Number of genes positively selected Supplementary figure 23. The percentage of GC at third codon position (GC3) per gene across species computed for dataset 1 and dataset 2.

Dataset 1 (n = 520 genes)

1.00 Species

Parnassius_honrati Ornithoptera_richmondia Eurytides_dolicaon Parnassius_smintheus Trogonoptera_brookiana Graphium_androcles Hypermnestra_helios Papilio_polytes_gb Protesilaus_protesilaus 0.75 Baronia_brevicornis Troides_plateni Meandrusa_sciron Parnassius_orleans Papilio_xuthus Papilio_alexanor Zerynthia_polyxena Papilio_zelicaon Lamproptera_meges Cressida_cressida Papilio_joanae Losaria_neptunus Bhutanitis_mansfieldi Pachliopta_kotzebuea Papilio_thoas 0.50 Sericinus_montela Battus_polydamus Papilio_slateri Archon_apollinus Papilio_machaon_gb Protographium_marcellus Luehdorfia_japonica Atrophaneura_dixoni Iphiclides_podalirius Proportion of GC3 Teinopalpus_imperialis Pharmacophagus_antenor Papilio_antimachus Parides_ascanius Mimoides_lysithaus Graphium_sarpedon 0.25 Ornithoptera_priamus Byasa_alcinous Euryades_corethrus Papilio_glaucus_gb

Dataset 2 (n = 1533 genes)

1.00 Species

Parnassius_smintheus Troides_plateni Papilio_alexanor Parnassius_honrati Archon_apollinus Mimoides_lysithaus Zerynthia_polyxena Pachliopta_kotzebuea Eurytides_dolicaon 0.75 Baronia_brevicornis Ornithoptera_richmondia Papilio_glaucus_gb Parnassius_orleans Papilio_polytes_gb Lamproptera_meges Hypermnestra_helios Papilio_xuthus Iphiclides_podalirius Bhutanitis_mansfieldi Battus_polydamus Meandrusa_sciron Luehdorfia_japonica Pharmacophagus_antenor Papilio_thoas 0.50 Cressida_cressida Atrophaneura_dixoni Papilio_antimachus Sericinus_montela Papilio_joanae Papilio_slateri Teinopalpus_imperialis Papilio_zelicaon Protographium_marcellus Proportion of GC3 Ornithoptera_priamus Papilio_machaon_gb Losaria_neptunus Euryades_corethrus Byasa_alcinous Graphium_sarpedon 0.25 Trogonoptera_brookiana Graphium_androcles Parides_ascanius Protesilaus_protesilaus Supplementary figure 24. The percentage of GC at third codon position (GC3) per branch for the branches with (“Yes”, n = 14) and without (“No”, n = 14) host-plant shift. For a given branch, the percentage of GC3 is the mean value of the species of a clade for which the branch is the root.

Dataset 1 (n = 520 genes)

0.46

0.44

0.42

Proportion of GC3 0.40

No Yes Host plant shift

Dataset 2 (n = 1533 genes)

0.44

0.42 Proportion of GC3 0.40

No Yes Host plant shift Supplementary figure 25. Relationship between the percentage of GC at third codon position (GC3) and the number of positively selected genes per branch. For a given branch, the percentage of GC3 is the mean value of the species of a clade for which the branch is the root.

Dataset 1 (n = 520 genes)

0.46

0.44

Host−plant shift

0.42 No Yes

Proportion of GC3 0.40

10 20 30 40 Number of genes positively selected Dataset 2 (n = 1533 genes)

0.44

Host−plant shift 0.42 No Yes Proportion of GC3 0.40

10 20 30 40 Number of genes positively selected