1: Beast2.1.3_r1

0.93 Canis adustus 0.89 Canis mesomelas 0.37 Canis simensis Canis arnensis 1 Lycaon pictus 1 Cuon javanicus 0.57 Xenocyon texanus 0.91 Canis antonii 0.96 0.35 Canis falconeri 1 Canis dirus 1 Canis armbrusteri 0.060.27 Canis lupus Canis chihliensis Canis etruscus 0.98 0.99 0.26 Canis variabilis 0.11 Canis edwardii 0.93 Canis mosbachensis 0.68 0.58 Canis latrans Canis aureus 0.94 Canis palmidens 0.94 Canis lepophagus 1 0.41 Canis thooides Canis ferox 0.99 Eucyon davisi 0.8 Cerdocyon texanus Vulpes stenognathus Leptocyon matthewi 0.98 Urocyon cinereoargenteus 0.85 Urocyon minicephalus 0.96 1 Urocyon citronus 1 Urocyon galushi 0.96 Urocyon webbi 1 1 Metalopex merriami 0.23 Metalopex macconnelli 0.68 Leptocyon vafer 1 Leptocyon leidyi Leptocyon vulpinus 0.7 Leptocyon gregorii 1 Leptocyon douglassi Leptocyon mollis 0.32 Borophagus dudleyi 1 Borophagus hilli 0.98 Borophagus diversidens 0.97 Borophagus secundus 0.18 Borophagus parvus 1 Borophagus pugnator 1 Borophagus orc 1 Borophagus littoralis 0.96 Epicyon haydeni 1 0.92 Epicyon saevus Epicyon aelurodontoides Protepicyon raki 0.98 0.28 Carpocyon limosus 0.96 Carpocyon webbi 0.97 0.98 Carpocyon robustus Carpocyon compressus 0.17 0.87 Paratomarctus euthos Paratomarctus temerarius Tomarctus brevirostris 0.31 0.85 0.35 Tomarctus hippophaga 0.17 Tephrocyon rurestris Protomarctus opatus 0.24 0.58 Microtomarctus conferta Metatomarctus canavus Psalidocyon marianae 0.79 1 Aelurodon taxoides 0.32 0.27 Aelurodon ferox 1 Aelurodon stirtoni 0.14 Aelurodon mcgrewi 0.33 Aelurodon asthenostylus 0.711 Euoplocyon brachygnathus 0.92 Euoplocyon spissidens 1 Cynarctus crucidens 1 Cynarctus voorhiesi 0.38 Cynarctus saxatilis 0.52 Cynarctus galushai 0.99 1 Cynarctus marylandica 0.54 1 Paracynarctus sinclari 0.91 Paracynarctus kelloggi Desmocyon matthewi 0.98 Desmocyon thomsoni Cormocyon copei Cormocyon haydeni 0.96 Phlaocyon mariae 0.53 0.88 Phlaocyon yatkolai 1 Phlaocyon leucosteus 0.9 0.94 Phlaocyon marshlandensis 1 1 Phlaocyon multicuspus Phlaocyon achoros 0.93 Phlaocyon annectens 0.18 Phlaocyon latidens Phlaocyon minor 0.89 0.8 1 Cynarctoides emryi 1 Cynarctoides accridens 1 Cynarctoides gawanae 1 0.69 Cynarctoides luskensis 0.69 Cynarctoides harlowi Cynarctoides lemur Cynarctoides roii Rhizocyon oreganensis 1 Otarocyon cooki 0.55 Otarocyon macdonaldi Oxetocyon cuspidatus 0.21 Osbornodon brachypus 1 Osbornodon iamonensis 0.18 0.22 Osbornodon fricki 0.26 Mesocyon brachyops 0.25 Mesocyon coryphaeus Cynodesmus martini 0.42 1 Paraenhydrocyon wallovianus 1 Paraenhydrocyon robustus 0.57 0.41 Paraenhydrocyon josephi Mesocyon temnodon Cynodesmus thooides 0.75 Enhydrocyon basilatus 0.64 Enhydrocyon stenocephalus 0.66 0.66 Enhydrocyon crassidens 1 Enhydrocyon pahinsintewakpa 1 0.59 Ectopocynus intermedius 0.65 0.93 Ectopocynus antiquus 0.98 0.77 Ectopocynus simplicidens Philotrox condoni 0.76 Sunkahetanka geringensis 0.27 Caedocyon tedfordi 0.65 Osbornodon sesnoni 0.9 Osbornodon renjiei Hesperocyon coloradensis 0.46 Hesperocyon gregarius 0.36 Archaeocyon falkenbachi 0.93 Archaeocyon pavidus Archaeocyon leptodus Prohesperocyon wilsoni outgroup

40 30 20 10 0 millions of years ago 2: Beast2.1.3_r2

0.93 Canis adustus 0.93 Canis mesomelas Canis simensis 0.66 Canis latrans 0.27 Canis aureus 0.92 Canis variabilis 0.4 Canis mosbachensis 0.26 Canis edwardii 0.34 1 Canis dirus 0.331 Canis armbrusteri Canis lupus Canis palmidens 0.18 1 Lycaon pictus 1 Cuon javanicus 0.98 0.65 0.64 Xenocyon texanus 0.8 Canis antonii 0.98 Canis falconeri 0.92 Canis chihliensis Canis etruscus 1 Canis arnensis 0.93 Canis lepophagus 1 Canis thooides 1 Canis ferox Eucyon davisi 0.99 Cerdocyon texanus 0.48 Vulpes stenognathus Leptocyon matthewi 0.99 Urocyon cinereoargenteus 0.72 0.75 Urocyon minicephalus 1 Urocyon citronus 1 Urocyon galushi 1 0.97 Urocyon webbi 1 Metalopex merriami 1 Metalopex macconnelli 0.92 Leptocyon vafer Leptocyon leidyi 1 Leptocyon vulpinus 0.98 Leptocyon gregorii 1 Leptocyon douglassi Leptocyon mollis 0.77 Borophagus diversidens 0.96 Borophagus hilli 0.95 Borophagus dudleyi 0.93 Borophagus secundus 1 Borophagus parvus 1 0.49 Borophagus orc Borophagus pugnator 1 Borophagus littoralis 0.98 Epicyon haydeni 1 0.95 Epicyon saevus Epicyon aelurodontoides 1 Protepicyon raki 0.32 Carpocyon limosus 1 Carpocyon robustus 0.97 1 Carpocyon webbi Carpocyon compressus 0.03 0.96 Paratomarctus euthos 0.04 Paratomarctus temerarius Psalidocyon marianae 0.07 Tephrocyon rurestris 0.07 0.86 Tomarctus brevirostris Tomarctus hippophaga 0.28 Protomarctus opatus 0.24 Microtomarctus conferta Metatomarctus canavus 1 Aelurodon taxoides 0.671 0.35 Aelurodon ferox 0.42 0.69 Aelurodon stirtoni 1 Aelurodon mcgrewi 0.45 Aelurodon asthenostylus 0.46 Euoplocyon brachygnathus 0.35 Euoplocyon spissidens 1 Cynarctus crucidens 1 Cynarctus voorhiesi 0.39 Cynarctus saxatilis 0.91 0.5 Cynarctus marylandica 1 Cynarctus galushai 1 1 Paracynarctus sinclari Paracynarctus kelloggi 0.98 Desmocyon matthewi 0.99 Desmocyon thomsoni Cormocyon copei Cormocyon haydeni 0.97 Phlaocyon mariae 0.55 0.06 0.95 Phlaocyon yatkolai 1 Phlaocyon leucosteus 0.81 Phlaocyon marshlandensis 1 0.99 Phlaocyon multicuspus Phlaocyon achoros 0.94 Phlaocyon annectens 0.98 Phlaocyon latidens 1 Cynarctoides emryi 1 Cynarctoides accridens 1 Cynarctoides gawanae 0.96 0.68 Cynarctoides luskensis 0.81 0.79 Cynarctoides harlowi 1 Cynarctoides lemur Phlaocyon minor Cynarctoides roii Rhizocyon oreganensis 1 Otarocyon cooki 0.62 Otarocyon macdonaldi Oxetocyon cuspidatus 0.63 Osbornodon fricki 1 Osbornodon brachypus 0.27 0.3 Osbornodon iamonensis 0.33 Mesocyon brachyops 0.27 Mesocyon coryphaeus Cynodesmus martini 0.92 1 Paraenhydrocyon wallovianus 1 Paraenhydrocyon robustus 0.93 0.38 Paraenhydrocyon josephi Mesocyon temnodon Cynodesmus thooides 0.72 Enhydrocyon basilatus 0.57 Enhydrocyon stenocephalus 0.91 0.6 Enhydrocyon crassidens 1 Enhydrocyon pahinsintewakpa 1 0.38 Ectopocynus intermedius 0.51 0.91 Ectopocynus antiquus 0.98 0.87 Ectopocynus simplicidens Philotrox condoni 0.76 Sunkahetanka geringensis 0.54 Caedocyon tedfordi 0.78 Osbornodon sesnoni 0.88 Osbornodon renjiei Hesperocyon gregarius 0.41 Hesperocyon coloradensis 0.65 Archaeocyon falkenbachi 0.94 Archaeocyon leptodus Archaeocyon pavidus Prohesperocyon wilsoni outgroup

40 30 20 10 0 millions of years ago 3: mb3.2.5_mb1_orig

Borophagus diversidens 1 0.35 Borophagus dudleyi 0.96 Borophagus hilli 0.96 Borophagus secundus 0.91 Borophagus parvus 1 0.75 Borophagus orc Borophagus pugnator 1 Borophagus littoralis 0.99 Epicyon haydeni 1 0.63 Epicyon saevus Epicyon aelurodontoides 1 Protepicyon raki 0.32 Carpocyon limosus 0.92 Carpocyon webbi 0.98 1 Carpocyon robustus Carpocyon compressus 0.95 Paratomarctus euthos 0.46 Paratomarctus temerarius 0.99 Tomarctus brevirostris 0.24 Tomarctus hippophaga 0.38 0.47 Protomarctus opatus Tephrocyon rurestris 0.3 0.78 Microtomarctus conferta Metatomarctus canavus Psalidocyon marianae 0.93 0.27 Aelurodon mcgrewi 0.26 Aelurodon asthenostylus 1 Aelurodon stirtoni 1 Aelurodon taxoides 0.53 Aelurodon ferox 1 Euoplocyon brachygnathus 0.76 Euoplocyon spissidens 1 Cynarctus crucidens 1 Cynarctus voorhiesi 0.41 Cynarctus saxatilis Cynarctus galushai 0.18 1 0.99 Paracynarctus sinclari 0.38 0.2 Paracynarctus kelloggi Cynarctus marylandica 0.67 Desmocyon matthewi 0.31 Desmocyon thomsoni Cormocyon copei Cormocyon haydeni 0.87 Phlaocyon mariae 0.16 Phlaocyon yatkolai 0.99 Phlaocyon multicuspus 0.26 0.65 Phlaocyon achoros 0.97 1 Phlaocyon leucosteus Phlaocyon marshlandensis 0.21 Phlaocyon annectens 0.3 Phlaocyon latidens Phlaocyon minor Cynarctoides emryi 0.23 1 0.25 1 Cynarctoides accridens 0.99 Cynarctoides gawanae 0.22 Cynarctoides luskensis 0.2 0.68 Cynarctoides harlowi 0.97 Cynarctoides lemur Cynarctoides roii 1 Otarocyon cooki 1 Otarocyon macdonaldi Oxetocyon cuspidatus Rhizocyon oreganensis 1 Lycaon pictus 1 Cuon javanicus 0.51 Xenocyon texanus 0.98 Canis antonii 0.55 Canis falconeri 1 Canis dirus 1 Canis armbrusteri 0.140.29 Canis lupus Canis chihliensis 0.98 Canis etruscus 0.02 Canis palmidens 0.12 Canis edwardii 0.75 Canis variabilis 0.45 Canis latrans 0.71 0.15 Canis aureus Canis mosbachensis 0.94 Canis adustus 1 0.71 Canis mesomelas 0.44 Canis simensis Canis arnensis 0.64 0.81 Canis lepophagus 0.93 Canis thooides 1 Canis ferox 1 0.95 Eucyon davisi Cerdocyon texanus 0.78 Vulpes stenognathus Leptocyon matthewi 0.93 Urocyon cinereoargenteus 0.79 Urocyon minicephalus 0.99 1 Urocyon citronus 1 Urocyon galushi 0.89 Urocyon webbi 1 0.49 Metalopex merriami 0.22 Metalopex macconnelli Leptocyon vafer 0.94 0.41 Leptocyon leidyi 1 Leptocyon gregorii Leptocyon vulpinus 0.82 0.33 Leptocyon douglassi Leptocyon mollis 0.23 Prohesperocyon wilsoni 0.35 Archaeocyon leptodus 0.9 Archaeocyon pavidus Archaeocyon falkenbachi 0.66 Ectopocynus intermedius 0.87 Ectopocynus antiquus 0.19 Ectopocynus simplicidens Caedocyon tedfordi 0.45 0.78 Enhydrocyon basilatus 0.92 Enhydrocyon stenocephalus 0.72 0.17 Enhydrocyon crassidens 0.3 Enhydrocyon pahinsintewakpa 0.5 Philotrox condoni 0.38 Sunkahetanka geringensis 0.5 Mesocyon coryphaeus 0.14 Mesocyon brachyops 0.57 Mesocyon temnodon 0.42 Cynodesmus martini 0.98 Cynodesmus thooides 0.69 Osbornodon fricki 1 Osbornodon brachypus 0.92 Osbornodon iamonensis 0.95 Osbornodon sesnoni 0.75 0.11 Osbornodon renjiei 0.87 Paraenhydrocyon wallovianus 0.83 Paraenhydrocyon robustus Paraenhydrocyon josephi 0.75 Hesperocyon coloradensis Hesperocyon gregarius outgroup

40 30 20 10 0 millions of years ago 4: mb3.2.5_mb2_orig

0.931 Canis adustus 0.881 Canis mesomelas Canis simensis 1 Lycaon pictus 1 Cuon javanicus Xenocyon texanus 0.291 1 Canis dirus 0.211 11 Canis armbrusteri 0.51 Canis lupus 0.74 0.891 Canis antonii Canis falconeri Canis chihliensis 0.561 0.341 Canis variabilis 0.931 0.281 Canis palmidens 0.2210.281 Canis latrans 11 Canis aureus 0.541 Canis edwardii 0.641 Canis mosbachensis Canis etruscus 0.961 Canis arnensis 0.26 Canis lepophagus 0.931 Canis thooides 1 Canis ferox Eucyon davisi Cerdocyon texanus 0.861 Urocyon cinereoargenteus 0.861 Urocyon minicephalus 0.61 0.931 Urocyon citronus 0.871 Urocyon galushi 0.841 Urocyon webbi 0.811 1 Metalopex merriami 0.431 Metalopex macconnelli 0.851 Vulpes stenognathus 0.99 Leptocyon matthewi Leptocyon vafer 0.71 Leptocyon leidyi 0.681 Leptocyon gregorii 1 Leptocyon vulpinus 0.83 0.311 Leptocyon douglassi Leptocyon mollis 0.121 Prohesperocyon wilsoni Archaeocyon falkenbachi 0.721 Borophagus diversidens 1 Borophagus dudleyi 0.971 Borophagus hilli 0.971 Borophagus secundus 0.371 Borophagus parvus 0.851 Borophagus orc 1 Borophagus pugnator 0.291 Borophagus littoralis 11 Epicyon aelurodontoides 0.99 0.921 Epicyon haydeni Epicyon saevus 11 Protepicyon raki 0.311 Carpocyon robustus Carpocyon webbi 0.261 0.571 0.12 Carpocyon limosus 0.99 Carpocyon compressus Paratomarctus euthos Paratomarctus temerarius 11 Aelurodon taxoides 0.221 0.721 Aelurodon ferox 1 Aelurodon stirtoni 1 Aelurodon mcgrewi 0.2110.971 Aelurodon asthenostylus 0.97 Tomarctus brevirostris 0.8 Tomarctus hippophaga 0.481 Protomarctus opatus Tephrocyon rurestris 0.26 Microtomarctus conferta 11 Euoplocyon brachygnathus 0.8610.241 Euoplocyon spissidens Psalidocyon marianae Metatomarctus canavus Cynarctus crucidens 0.771 0.981 1 Cynarctus voorhiesi 0.671 Cynarctus saxatilis 0.641 Cynarctus marylandica 0.981 1 Cynarctus galushai 11 Paracynarctus sinclari 0.981 Paracynarctus kelloggi 0.911 Desmocyon matthewi Desmocyon thomsoni 0.771 Cormocyon copei Cormocyon haydeni 0.981 Phlaocyon leucosteus 0.541 Phlaocyon marshlandensis 1 Phlaocyon multicuspus 0.951 Phlaocyon achoros 0.991 0.911 Phlaocyon mariae Phlaocyon yatkolai 0.941 0.98 Phlaocyon annectens 0.71 Phlaocyon latidens Phlaocyon minor 11 Cynarctoides emryi 0.561 11 Cynarctoides accridens 11 Cynarctoides gawanae 0.99 0.23 Cynarctoides luskensis 0.211 0.461 Cynarctoides lemur 0.24 Cynarctoides harlowi Cynarctoides roii 1 Otarocyon cooki 11 Otarocyon macdonaldi Oxetocyon cuspidatus Rhizocyon oreganensis 0.8 Enhydrocyon basilatus 0.761 Enhydrocyon stenocephalus 0.77 Enhydrocyon crassidens 0.9 Enhydrocyon pahinsintewakpa 0.731 Ectopocynus intermedius 0.51 0.63 Ectopocynus antiquus 0.32 Ectopocynus simplicidens Caedocyon tedfordi 0.711 0.05 Philotrox condoni 0.14 Sunkahetanka geringensis 0.11 Mesocyon coryphaeus 0.691 0.36 Cynodesmus martini Cynodesmus thooides 0.511 Mesocyon brachyops Mesocyon temnodon 0.51 0.05 Osbornodon brachypus 1 Osbornodon iamonensis 0.991 0.01 Osbornodon fricki 11 0.961 Osbornodon sesnoni Osbornodon renjiei 0.38 0.82 Paraenhydrocyon wallovian 0.761 Paraenhydrocyon robustus 0.971 Paraenhydrocyon josephi 0.13 Hesperocyon coloradensis Hesperocyon gregarius 0.2 Archaeocyon leptodus Archaeocyon pavidus outgroup

2 2 1 0 0 0 millions of years ago 5: mb3.2.5_mb2_mfixed

0.91 Canis adustus 0.851 Canis mesomelas Canis simensis 1 Lycaon pictus 11 Cuon javanicus 0.71 Xenocyon texanus 0.91 Canis antonii 0.161 Canis falconeri 11 Canis dirus 0.881 0.571 11 Canis armbrusteri Canis lupus Canis chihliensis 0.55 0.07 Canis variabilis 0.11 Canis aureus 0.281 0.261 Canis palmidens 0.991 0.1 Canis latrans 0.51 Canis mosbachensis 0.361 0.621 Canis edwardii Canis etruscus Canis arnensis 0.951 Canis lepophagus 0.921 Canis thooides 11 Canis ferox Eucyon davisi Cerdocyon texanus 0.881 Urocyon cinereoargenteus 0.881 Urocyon minicephalus 0.561 0.981 Urocyon citronus 0.951 Urocyon galushi 0.91 Urocyon webbi 0.821 11 Metalopex merriami 0.361 Metalopex macconnelli 0.91 Vulpes stenognathus 0.981 Leptocyon matthewi Leptocyon vafer 0.771 Leptocyon leidyi 0.621 Leptocyon gregorii 0.311 Leptocyon vulpinus 11 Leptocyon mollis 0.791 Leptocyon douglassi 0.241 Prohesperocyon wilsoni outgroup 0.741 Borophagus diversidens 11 Borophagus dudleyi 11 Borophagus hilli 0.991 Borophagus secundus 0.271 Borophagus parvus 0.861 Borophagus pugnator 11 Borophagus orc 0.361 Borophagus littoralis 11 Epicyon aelurodontoides 11 0.911 Epicyon haydeni Epicyon saevus 0.11 Protepicyon raki 0.021 Carpocyon robustus 110.161 Carpocyon compressus 0.261 Carpocyon webbi Carpocyon limosus 11 Paratomarctus temer Paratomarctus euthos 11 Aelurodon taxoides 0.241 0.721 Aelurodon ferox 11 Aelurodon stirtoni 1 Aelurodon mcgrewi 0.981 0.821 Aelurodon asthenostylus 0.971 Tomarctus brevirostris Tomarctus hippophaga 0.51 0.231 Tephrocyon rurestris Protomarctus opatus 0.3 Microtomarctus confer 11 Euoplocyon brachygnathus 0.910.31 Euoplocyon spissidens Psalidocyon marianae Metatomarctus canavus 0.821 0.981 Cynarctus crucidens 1 Cynarctus voorhiesi 0.641 Cynarctus saxatilis 0.641 Cynarctus marylandica 11 11 Cynarctus galushai 11 Paracynarctus sinclar 11 Paracynarctus kelloggi 0.931 Desmocyon matthewi Desmocyon thomsoni 0.841 Cormocyon copei Cormocyon haydeni 0.981 Phlaocyon leucosteus 0.61 Phlaocyon marshlandensis 11 Phlaocyon multicuspus 0.981 Phlaocyon achoros 11 0.921 Phlaocyon mariae 0.311 Phlaocyon yatkolai 11 Phlaocyon annectens 0.81 Phlaocyon latidens Phlaocyon minor 11 Cynarctoides emryi 0.22 11 Cynarctoides accridens 0.921 11 Cynarctoides gawanae 0.221 0.641 Cynarctoides luskensis 0.24 Cynarctoides lemur Cynarctoides harlowi 0.981 Cynarctoides roii 11 Otarocyon cooki 0.4 11 Otarocyon macdonaldi Oxetocyon cuspidatus Rhizocyon oreganensis Archaeocyon falkenbachi 0.831 Enhydrocyon basilatus 0.761 Enhydrocyon stenocephalus 0.721 Enhydrocyon crassidens 0.96 Enhydrocyon pahinsinte 0.641 Ectopocynus intermedius 0.33 0.591 Ectopocynus antiquus 0.221 Ectopocynus simplicidens Philotrox condoni 0.51 Caedocyon tedfordi 0.061 Sunkahetanka geringensis 0.381 0.141 Mesocyon coryphaeus 0.481 Mesocyon brachyops 0.340.31 Cynodesmus martini Cynodesmus thooides 0.31 Mesocyon temnodon 0.641 Paraenhydrocyon wallo 10.521 Paraenhydrocyon rob Paraenhydrocyon josephi 11 Osbornodon renjiei 0.931 Osbornodon fricki 11 Osbornodon brachypus 0.991 0.991 Osbornodon iamonensis Osbornodon sesnoni 0.220.361 Hesperocyon coloradensis Hesperocyon gregarius 0.181 Archaeocyon leptodus Archaeocyon pavidus

1 1 1 0 0 0 millions of years ago 6: mb3.2.5_mb3_orig

0.94 Borophagus diversidens 1 Borophagus dudleyi 0.97 Borophagus hilli 0.95 Borophagus secundus 11 Borophagus parvus 1 0.98 Borophagus orc Borophagus pugnator 1 Borophagus littoralis 1 Epicyon haydeni 1 0.81 Epicyon saevus Epicyon aelurodontoides 1 Protepicyon raki 1 Carpocyon limosus 11 Carpocyon robustus 0.99 1 Carpocyon webbi Carpocyon compressus 1 Paratomarctus euthos 0.71 Paratomarctus temerarius 0.99 Tomarctus brevirostris 0.17 Tomarctus hippophaga 0.5 0.51 Protomarctus opatus Tephrocyon rurestris 0.56 0.96 Microtomarctus conferta Metatomarctus canavus Psalidocyon marianae 0.9 0.51 Aelurodon mcgrewi 0.46 Aelurodon asthenostylus 1 Aelurodon stirtoni 1 Aelurodon taxoides 0.82 Aelurodon ferox 1 Euoplocyon brachygnathus 0.99 Euoplocyon spissidens 1 Cynarctus crucidens 1 Cynarctus voorhiesi 0.36 Cynarctus saxatilis 0.59 Cynarctus marylandica 0.9 1 Cynarctus galushai 0.3 1 Paracynarctus sinclari Paracynarctus kelloggi Desmocyon matthewi 0.98 Desmocyon thomsoni 0.65 Cormocyon copei 0.6 Cormocyon haydeni 0.99 Phlaocyon leucosteus 0.18 Phlaocyon marshlandensis 0.51 Phlaocyon multicuspus 1 Phlaocyon achoros 0.43 Phlaocyon mariae 1 0.17 Phlaocyon yatkolai 0.99 Phlaocyon annectens Phlaocyon latidens 1 Cynarctoides emryi 1 Cynarctoides accridens 0.83 Cynarctoides gawanae 1 0.25 Cynarctoides luskensis 0.86 Cynarctoides roii 0.46 Phlaocyon minor 0.44 0.98 Cynarctoides lemur Cynarctoides harlowi Rhizocyon oreganensis 1 Otarocyon cooki 1 Otarocyon macdonaldi Oxetocyon cuspidatus 0.54 Canis edwardii 0.28 Canis aureus 0.86 Canis variabilis 0.840.29 Canis latrans Canis mosbachensis Canis palmidens 0.58 1 Lycaon pictus 1 Cuon javanicus 0.9 Xenocyon texanus 0.13 0.92 Canis antonii Canis falconeri 0.66 Canis simensis 0.5 0.37 Canis arnensis Canis etruscus 1 Canis dirus 0.63 1 Canis armbrusteri 0.16 Canis lupus Canis chihliensis 1 0.96 Canis adustus Canis mesomelas Canis lepophagus 0.92 0.65 0.64 Canis thooides 1 1 Canis ferox Eucyon davisi 0.99 Cerdocyon texanus 0.29 0.96 Vulpes stenognathus Leptocyon matthewi Leptocyon vafer 1 Urocyon cinereoargenteus 0.65 Urocyon minicephalus 1 1 Urocyon galushi 1 Urocyon citronus 1 Urocyon webbi 0.34 1 Metalopex merriami 0.2 Metalopex macconnelli 0.73 Leptocyon leidyi Leptocyon gregorii 1 Leptocyon vulpinus 0.98 0.36 Leptocyon douglassi Leptocyon mollis Prohesperocyon wilsoni 0.56 Mesocyon coryphaeus 0.33 Mesocyon brachyops 0.34 Cynodesmus martini Cynodesmus thooides 0.54 1 Paraenhydrocyon wallovianus 1 Paraenhydrocyon robustus 0.42 Paraenhydrocyon josephi Mesocyon temnodon 0.34 0.19 0.58 Enhydrocyon basilatus 0.59 Enhydrocyon stenocephalus 0.5 Enhydrocyon crassidens 0.38 Enhydrocyon pahinsintewakpa 0.48 Sunkahetanka geringensis 0.76 Philotrox condoni 0.5 Ectopocynus simplicidens 0.5 Ectopocynus intermedius 0.5 Ectopocynus antiquus 0.3 Caedocyon tedfordi Osbornodon renjiei 0.25 0.42 0.74 Osbornodon fricki 1 Osbornodon brachypus 0.97 Osbornodon iamonensis Osbornodon sesnoni 0.46 Archaeocyon falkenbachi 0.89 Archaeocyon leptodus 0.4 Archaeocyon pavidus 0.19 Hesperocyon gregarius Hesperocyon coloradensis outgroup

40 30 20 10 0 millions of years ago 7: mb3.2.5_mb4_orig

0.96 Canis adustus Canis mesomelas 0.31 Canis edwardii 0.19 Canis aureus 0.5 Canis mosbachensis 0.50.26 Canis latrans 0.49 Canis variabilis 0.4 Canis palmidens Canis etruscus 0.04 1 Canis dirus 1 Canis armbrusteri 0.21 Canis lupus 0.98 Canis chihliensis 1 1 Lycaon pictus 1 Cuon javanicus 0.33 Xenocyon texanus 0.9 Canis antonii Canis falconeri 1 0.48 Canis simensis 0.2 Canis arnensis 0.47 Canis lepophagus 0.48 Canis thooides 0.97 Canis ferox 0.13 Eucyon davisi 0.26 Cerdocyon texanus 0.85 Vulpes stenognathus Leptocyon matthewi Leptocyon vafer 1 Urocyon cinereoargenteus 1 0.64 Urocyon minicephalus 1 Urocyon galushi 1 Urocyon citronus 1 0.75 Urocyon webbi 1 Metalopex merriami 0.15 Metalopex macconnelli 0.84 Leptocyon leidyi 1 Leptocyon vulpinus Leptocyon gregorii 0.98 0.3 Leptocyon douglassi Leptocyon mollis Prohesperocyon wilsoni 1 Borophagus diversidens 1 Borophagus dudleyi 0.97 Borophagus hilli 0.98 Borophagus secundus 1 Borophagus parvus 1 0.99 Borophagus orc Borophagus pugnator 1 Borophagus littoralis 1 Epicyon haydeni 1 0.73 Epicyon saevus Epicyon aelurodontoides 1 Protepicyon raki 1 Carpocyon limosus 1 Carpocyon robustus 0.99 1 Carpocyon webbi Carpocyon compressus 1 Paratomarctus euthos 0.78 Paratomarctus temerarius 0.99 Tomarctus brevirostris 0.4 Tomarctus hippophaga 0.5 0.55 Tephrocyon rurestris Protomarctus opatus 0.66 0.98 Microtomarctus conferta Metatomarctus canavus Psalidocyon marianae 0.82 0.47 Aelurodon stirtoni 0.53 Aelurodon mcgrewi 1 Aelurodon asthenostylus 1 Aelurodon taxoides 0.77 Aelurodon ferox 1 Euoplocyon brachygnathus 0.19 Euoplocyon spissidens 1 Cynarctus crucidens 1 Cynarctus voorhiesi 0.35 Cynarctus saxatilis 0.88 0.6 Cynarctus marylandica 1 Cynarctus galushai 1 Paracynarctus sinclari 0.81 1 Paracynarctus kelloggi Desmocyon matthewi 0.99 Desmocyon thomsoni 0.56 Cormocyon copei Cormocyon haydeni 0.31 0.55 Phlaocyon mariae 0.48 Phlaocyon multicuspus Phlaocyon achoros 0.5 1 Phlaocyon leucosteus 0.5 0.5 Phlaocyon marshlandensis Phlaocyon annectens 0.47 Phlaocyon latidens 1 Cynarctoides emryi 1 Cynarctoides accridens 0.8 Cynarctoides gawanae 0.5 0.74 Cynarctoides luskensis 0.51 Phlaocyon minor 0.88 0.95 Cynarctoides harlowi Cynarctoides lemur 0.72 Cynarctoides roii Rhizocyon oreganensis 0.5 Phlaocyon yatkolai 0.58 0.39 Archaeocyon falkenbachi 0.4 Archaeocyon leptodus 0.29 Archaeocyon pavidus Hesperocyon gregarius Hesperocyon coloradensis 0.64 Enhydrocyon basilatus 0.72 Enhydrocyon stenocephalus 1 Enhydrocyon crassidens 0.43 Enhydrocyon pahinsintewakpa 0.99 Philotrox condoni Sunkahetanka geringensis 0.65 0.15 0.21 Cynodesmus martini 0.34 Cynodesmus thooides 0.58 Mesocyon coryphaeus 0.74 Mesocyon brachyops 0.98 Paraenhydrocyon wallovianus 0.97 Paraenhydrocyon robustus 0.49 Paraenhydrocyon josephi Mesocyon temnodon 0.78 0.76 Ectopocynus simplicidens 0.53 1 Ectopocynus intermedius 0.98 Ectopocynus antiquus 0.75 Caedocyon tedfordi Osbornodon renjiei 0.61 0.84 Osbornodon fricki 1 Osbornodon brachypus 0.99 Osbornodon iamonensis Osbornodon sesnoni 1 Otarocyon cooki 1 Otarocyon macdonaldi Oxetocyon cuspidatus outgroup

40 30 20 10 0 millions of years ago 8: mb3.2.5_mb5_orig

0.92 Canis adustus 0.8 Canis mesomelas Cerdocyon texanus 0.55 Canis edwardii 0.4 Canis aureus 1 Canis mosbachensis 0.970.4 Canis latrans Canis variabilis Canis palmidens 0.34 11 Lycaon pictus 0.5 Cuon javanicus 0.5 Xenocyon texanus 0.5 0.49 Canis antonii 0.49 Canis falconeri 1 Canis dirus 1 Canis armbrusteri 0.2810.96 Canis lupus 0.53 Canis chihliensis 0.5 0.4 Canis etruscus Canis arnensis Canis simensis 0.44 0.33 0.33 Canis lepophagus 0.5 0.44 Canis thooides Canis ferox Eucyon davisi Vulpes stenognathus Leptocyon matthewi 0.1 1 Urocyon cinereoargenteus 1 Urocyon minicephalus 1 Urocyon galushi 1 0.46 Urocyon citronus 1 Urocyon webbi 1 Metalopex merriami 0.5 Metalopex macconnelli 0.49 Leptocyon vafer 0.5 Leptocyon leidyi Leptocyon vulpinus 0.5 Leptocyon gregorii 0.5 Leptocyon douglassi 0.49 Leptocyon mollis Prohesperocyon wilsoni 0.62 Borophagus diversidens 0.67 Borophagus dudleyi 0.67 Borophagus hilli 0.8 Borophagus secundus 0.82 Borophagus parvus 0.82 0.92 Borophagus orc Borophagus pugnator 0.82 Borophagus littoralis 1 Epicyon haydeni 0.82 0.9 Epicyon saevus Epicyon aelurodontoides 0.79 Protepicyon raki 0.59 Carpocyon limosus 0.61 Carpocyon robustus 0.78 0.61 Carpocyon webbi Carpocyon compressus 0.34 1 Paratomarctus euthos Paratomarctus temerarius Tomarctus brevirostris 0.61 0.99 0.5 Tomarctus hippophaga 0.21 Tephrocyon rurestris Protomarctus opatus 0.5 Psalidocyon marianae 0.9 Microtomarctus conferta Metatomarctus canavus 1 Aelurodon taxoides 0.79 0.42 Aelurodon ferox 1 Aelurodon stirtoni 0.78 0.37 Aelurodon mcgrewi Aelurodon asthenostylus 0.85 Euoplocyon brachygnathus Euoplocyon spissidens 0.55 1 Cynarctus crucidens 1 Cynarctus voorhiesi 0.58 Cynarctus saxatilis 0.34 Cynarctus galushai 0.47 0.82 1 Paracynarctus sinclari Paracynarctus kelloggi 0.61 0.49 Cynarctus marylandica 0.98 Desmocyon matthewi 0.15 Desmocyon thomsoni Cormocyon copei 0.65 Cormocyon haydeni Cynarctoides emryi 0.2 Phlaocyon mariae 0.09 Phlaocyon yatkolai Phlaocyon leucosteus 0.31 0.11 1 Phlaocyon marshlandensis 0.49 Phlaocyon annectens 0.45 0.27 Phlaocyon multicuspus Phlaocyon achoros Phlaocyon latidens 0.7 0.04 0.82 Cynarctoides accridens 0.82 Cynarctoides gawanae 0.05 Cynarctoides luskensis 0.7 0.67 0.46 Phlaocyon minor Cynarctoides harlowi Cynarctoides lemur 0.42 Cynarctoides roii Rhizocyon oreganensis Archaeocyon falkenbachi 0.35 0.54 0.66 Archaeocyon leptodus Archaeocyon pavidus Hesperocyon gregarius 0.52 Enhydrocyon basilatus 0.5 Enhydrocyon stenocephalus 0.79 Enhydrocyon crassidens 0.28 Enhydrocyon pahinsintewakpa 0.72 Sunkahetanka geringensis Philotrox condoni 0.1 0.77 Ectopocynus simplicidens 0.79 Ectopocynus intermedius 0.53 0.31 Ectopocynus antiquus Caedocyon tedfordi 0.67 Paraenhydrocyon wallovianus 0.15 0.67 Paraenhydrocyon robustus Paraenhydrocyon josephi 0.11 0.6 Mesocyon coryphaeus 0.17 0.4 0.23 Mesocyon brachyops 0.58 Mesocyon temnodon Cynodesmus martini 0.22 Cynodesmus thooides 0.73 Osbornodon renjiei 0.91 Osbornodon fricki 0.52 1 Osbornodon brachypus 0.66 Osbornodon iamonensis Osbornodon sesnoni Hesperocyon coloradensis 1 Otarocyon cooki 0.89 Otarocyon macdonaldi Oxetocyon cuspidatus outgroup

40 30 20 10 0 millions of years ago 9: mb3.2.5_mb6_orig

0.88 Canis adustus 0.68 Canis mesomelas 0.27 Canis simensis Canis arnensis 0.22 Canis variabilis 0.23 Canis palmidens 0.45 Canis latrans 0.71 0.5 Canis aureus 0.45 Canis mosbachensis 0.22 Canis edwardii 1 Canis dirus 1 Canis armbrusteri Canis lupus 1 1 Lycaon pictus 0.82 1 Cuon javanicus 0.55 Xenocyon texanus 0.34 0.97 Canis antonii Canis falconeri 0.06 0.36 Canis chihliensis Canis etruscus 0.83 Canis lepophagus 0.99 0.92 Canis thooides Canis ferox 0.92 Eucyon davisi 0.82 Cerdocyon texanus Vulpes stenognathus Leptocyon matthewi 0.93 Urocyon cinereoargenteus 0.3 0.8 Urocyon minicephalus 1 Urocyon citronus 0.99 Urocyon galushi 0.34 0.81 Urocyon webbi 1 Metalopex merriami 0.99 Metalopex macconnelli 0.51 Leptocyon vafer Leptocyon leidyi 0.89 Leptocyon gregorii 1 Leptocyon vulpinus 0.68 0.42 Leptocyon douglassi Leptocyon mollis Prohesperocyon wilsoni 0.35 Borophagus dudleyi 1 Borophagus hilli 0.98 Borophagus diversidens 0.96 Borophagus secundus 0.97 Borophagus parvus 1 0.72 Borophagus orc Borophagus pugnator 1 Borophagus littoralis 0.98 Epicyon haydeni 1 0.65 Epicyon saevus Epicyon aelurodontoides 0.98 Protepicyon raki 0.45 Carpocyon robustus 0.84 Carpocyon webbi 0.94 0.99 Carpocyon limosus Carpocyon compressus 0.09 0.96 Paratomarctus euthos Paratomarctus temerarius 0.44 Tephrocyon rurestris Protomarctus opatus 0.3 1 Aelurodon taxoides 0.82 Aelurodon ferox 1 0.55 Aelurodon stirtoni Aelurodon mcgrewi 0.34 0.13 Aelurodon asthenostylus 0.86 Tomarctus brevirostris Tomarctus hippophaga 0.91 0.73 Microtomarctus conferta Metatomarctus canavus 0.91 Euoplocyon brachygnathus 0.22 Euoplocyon spissidens Psalidocyon marianae 0.63 1 Cynarctus crucidens 1 Cynarctus voorhiesi 0.43 Cynarctus saxatilis 0.73 1 Cynarctus galushai 0.75 1 Paracynarctus sinclari 0.37 0.19 Paracynarctus kelloggi Cynarctus marylandica 0.54 Desmocyon matthewi Desmocyon thomsoni 0.68 Cormocyon copei Cormocyon haydeni 0.09 1 Cynarctoides emryi 1 Cynarctoides accridens 1 Cynarctoides gawanae 0.49 Cynarctoides luskensis 0.11 Phlaocyon minor 0.38 0.26 Cynarctoides harlowi Cynarctoides lemur 0.3 Cynarctoides roii 0.84 Phlaocyon mariae 0.3 Phlaocyon yatkolai 1 Phlaocyon leucosteus 0.61 0.72 Phlaocyon marshlandensis 0.96 1 Phlaocyon multicuspus Phlaocyon achoros 0.62 Phlaocyon annectens 0.91 Phlaocyon latidens Rhizocyon oreganensis 1 Otarocyon cooki 0.09 0.97 Otarocyon macdonaldi Oxetocyon cuspidatus 0.35 Archaeocyon falkenbachi 0.89 Archaeocyon leptodus Archaeocyon pavidus 0.78 Enhydrocyon basilatus 0.72 Enhydrocyon stenocephalus 0.88 Enhydrocyon crassidens 0.79 Enhydrocyon pahinsintewakpa 0.69 Ectopocynus intermedius 0.43 0.88 Ectopocynus antiquus Ectopocynus simplicidens 0.92 0.15 Caedocyon tedfordi 0.42 Philotrox condoni Sunkahetanka geringensis 0.44 0.45 Cynodesmus martini 0.08 Cynodesmus thooides 0.58 Mesocyon temnodon 0.54 Mesocyon coryphaeus 0.26 Mesocyon brachyops Paraenhydrocyon wallovianus 0.97 1 0.97 Paraenhydrocyon robustus Paraenhydrocyon josephi 0.13 Osbornodon fricki 1 0.68 Osbornodon iamonensis 0.92 Osbornodon brachypus 0.93 Osbornodon sesnoni Osbornodon renjiei 0.69 Hesperocyon coloradensis Hesperocyon gregarius outgroup

40 30 20 10 0 millions of years ago 10: mb3.2.5_mb7_orig

0.43 Borophagus diversidens 1 Borophagus dudleyi 0.99 Borophagus hilli 0.96 Borophagus secundus 0.13 Borophagus parvus 0.98 Borophagus pugnator 1 Borophagus orc 1 Borophagus littoralis 0.97 Epicyon haydeni 1 0.7 Epicyon saevus Epicyon aelurodontoides Protepicyon raki 0.99 0.32 Carpocyon limosus 0.87 Carpocyon robustus 0.95 0.98 Carpocyon webbi Carpocyon compressus 0.28 0.93 Paratomarctus euthos Paratomarctus temerarius 0.79 Tomarctus brevirostris 0.42 Tomarctus hippophaga 0.15 0.43 Tephrocyon rurestris Protomarctus opatus 0.72 Microtomarctus conferta 0.11 Metatomarctus canavus 0.96 Psalidocyon marianae 1 Aelurodon taxoides 0.86 Aelurodon ferox 1 0.65 Aelurodon stirtoni Aelurodon mcgrewi 0.31 Aelurodon asthenostylus 0.22 0.95 Euoplocyon brachygnathus Euoplocyon spissidens 1 Cynarctus crucidens 1 Cynarctus voorhiesi 0.36 Cynarctus saxatilis 0.77 0.56 Cynarctus marylandica 1 Cynarctus galushai 0.67 1 Paracynarctus sinclari Paracynarctus kelloggi 0.63 Desmocyon matthewi Desmocyon thomsoni 0.06 0.58 Cormocyon copei Cormocyon haydeni Cynarctoides roii 0.83 Phlaocyon mariae 0.34 Phlaocyon yatkolai 1 Phlaocyon leucosteus 0.3 0.66 Phlaocyon marshlandensis 0.98 0.99 Phlaocyon multicuspus Phlaocyon achoros 0.79 Phlaocyon annectens Phlaocyon latidens Cynarctoides emryi 0.2 1 0.6 1 Cynarctoides accridens 1 Cynarctoides gawanae 0.58 Cynarctoides luskensis 0.52 Cynarctoides harlowi 0.96 0.32 Cynarctoides lemur Phlaocyon minor Rhizocyon oreganensis 1 Otarocyon cooki 0.98 Otarocyon macdonaldi Oxetocyon cuspidatus 0.23 Canis variabilis 0.19 Canis palmidens 0.44 Canis latrans 0.71 Canis aureus 0.5 Canis mosbachensis 0.2 Canis edwardii 1 Canis dirus 0.11 1 Canis armbrusteri Canis lupus Canis etruscus 0.99 1 Lycaon pictus 1 Cuon javanicus Xenocyon texanus 0.22 0.33 0.99 Canis antonii 0.17 Canis falconeri 0.24 Canis chihliensis Canis arnensis 0.83 Canis adustus 0.71 0.6 Canis mesomelas Canis simensis Canis lepophagus 0.32 0.79 0.83 Canis thooides 1 Canis ferox 0.71 0.9 Eucyon davisi Cerdocyon texanus 0.73 Vulpes stenognathus Leptocyon matthewi 0.91 Urocyon cinereoargenteus 0.34 1 Urocyon minicephalus Urocyon citronus 0.99 0.17 Urocyon galushi 0.33 0.81 Urocyon webbi 1 Metalopex merriami 0.97 Metalopex macconnelli Leptocyon vafer 0.91 Leptocyon leidyi 0.32 0.28 Leptocyon gregorii 1 Leptocyon vulpinus Leptocyon douglassi 0.81 Leptocyon mollis 0.24 Prohesperocyon wilsoni 0.34 Archaeocyon leptodus 0.85 Archaeocyon pavidus Archaeocyon falkenbachi 0.74 Enhydrocyon basilatus 0.68 Enhydrocyon stenocephalus 0.93 Enhydrocyon crassidens 0.75 Enhydrocyon pahinsintewakpa 0.66 Ectopocynus intermedius 0.87 Ectopocynus antiquus 0.87 Ectopocynus simplicidens 0.49 Philotrox condoni 0.29 0.07 Sunkahetanka geringensis 0.37 Caedocyon tedfordi 0.1 Cynodesmus martini 0.1 Mesocyon coryphaeus 0.51 Cynodesmus thooides 0.45 0.58 Mesocyon brachyops Mesocyon temnodon 0.95 Paraenhydrocyon wallovianus 0.94 Paraenhydrocyon robustus 0.98 Paraenhydrocyon josephi 0.73 Osbornodon fricki 1 Osbornodon brachypus 0.62 0.9 Osbornodon iamonensis 0.94 Osbornodon sesnoni Osbornodon renjiei 0.77 Hesperocyon coloradensis Hesperocyon gregarius outgroup

40 30 20 10 0 millions of years ago 11: mb3.2.5_mb8_orig

0.9 Canis adustus 0.55 Canis mesomelas Canis simensis 0.5 Canis latrans 0.3 Canis aureus 0.05 Canis variabilis 0.5 Canis mosbachensis 0.1 Canis edwardii 0.25 1 Canis dirus 0.4 1 Canis armbrusteri Canis lupus Canis palmidens 0.2 1 Lycaon pictus 0.65 0.95 Cuon javanicus 0.4 Xenocyon texanus 0.9 0.55 0.95 Canis antonii Canis falconeri 0.9 Canis chihliensis Canis etruscus Canis arnensis 0.35 0.9 Canis lepophagus 0.85 Canis thooides 1 Canis ferox 1 Eucyon davisi Cerdocyon texanus 0.95 Vulpes stenognathus 0.251 Leptocyon matthewi Leptocyon vafer 1 Urocyon cinereoargenteus 0.4 1 Urocyon minicephalus Urocyon citronus 1 0.2 Urocyon galushi 1 0.95 Urocyon webbi 1 Metalopex merriami 0.6 Metalopex macconnelli Leptocyon leidyi 1 Leptocyon gregorii 0.3 Leptocyon douglassi 0.8 0.05 Leptocyon mollis Leptocyon vulpinus Prohesperocyon wilsoni 0.35 Borophagus diversidens 1 Borophagus dudleyi 0.95 Borophagus hilli 0.95 Borophagus secundus 0.95 Borophagus parvus 1 0.8 Borophagus orc Borophagus pugnator 1 Borophagus littoralis 0.1 Epicyon saevus 1 0.75 Epicyon aelurodontoides Epicyon haydeni 0.95 Protepicyon raki 0.55 Carpocyon robustus 0.95 Carpocyon webbi 0.95 1 Carpocyon limosus Carpocyon compressus 0.95 Paratomarctus euthos 0.15 Paratomarctus temerarius 1 Aelurodon taxoides 0.95 Aelurodon ferox 1 0.65 Aelurodon stirtoni 0.25 Aelurodon mcgrewi Aelurodon asthenostylus 0.9 Tomarctus brevirostris 0.25 0.05 Tomarctus hippophaga 0.55 Protomarctus opatus 0.1 Tephrocyon rurestris 0.6 Microtomarctus conferta 1 Metatomarctus canavus Psalidocyon marianae 0.9 Euoplocyon brachygnathus Euoplocyon spissidens 1 Cynarctus crucidens 0.8 1 Cynarctus voorhiesi 0.8 0.55 Cynarctus saxatilis 0.25 Cynarctus galushai 1 1 Paracynarctus sinclari 0.2 Paracynarctus kelloggi 0.15 Cynarctus marylandica 0.85 0.3 Desmocyon matthewi Desmocyon thomsoni Cormocyon copei Cormocyon haydeni 1 Phlaocyon leucosteus 0.3 Phlaocyon marshlandensis 1 Phlaocyon multicuspus 0.45 0.6 Phlaocyon achoros 1 0.75 Phlaocyon mariae Phlaocyon yatkolai 0.85 Phlaocyon annectens Phlaocyon latidens 1 Cynarctoides emryi 0.9 0.15 1 Cynarctoides accridens 1 Cynarctoides gawanae 0.6 Cynarctoides luskensis 0.3 Phlaocyon minor 0.7 0.55 Cynarctoides lemur 0.85 Cynarctoides harlowi Cynarctoides roii Rhizocyon oreganensis 1 Otarocyon cooki 1 Otarocyon macdonaldi Oxetocyon cuspidatus 0.75 Enhydrocyon basilatus 0.95 Enhydrocyon stenocephalus 0.2 Enhydrocyon crassidens 0.6 Enhydrocyon pahinsintewakpa 0.85 Ectopocynus intermedius 0.2 0.85 Ectopocynus antiquus 0.15 Ectopocynus simplicidens Philotrox condoni 0.41 Sunkahetanka geringensis 0.1 0.45 Mesocyon coryphaeus 0.25 Mesocyon brachyops 0.5 0.65 Mesocyon temnodon 0.35 Cynodesmus martini Cynodesmus thooides Caedocyon tedfordi 1 0.7 Osbornodon fricki 1 Osbornodon brachypus 0.85 Osbornodon iamonensis 0.95 Osbornodon sesnoni 0.8 0.1 Osbornodon renjiei 1 Paraenhydrocyon wallovianus 1 Paraenhydrocyon robustus Paraenhydrocyon josephi 0.4 0.7 Hesperocyon coloradensis Hesperocyon gregarius 0.3 Archaeocyon falkenbachi 0.9 Archaeocyon leptodus Archaeocyon pavidus outgroup

40 30 20 10 0 millions of years ago 12: mb3.2.5_mb9_orig

0.95 Canis adustus 0.9 Canis mesomelas Canis simensis 0.15 Canis latrans 0.15 Canis aureus 0.95 Canis variabilis 0.90.45 Canis mosbachensis 0.15 Canis edwardii Canis palmidens 0.1 1 Lycaon pictus 0.5 Cuon javanicus 0.25 Xenocyon texanus 0.3 Canis antonii 0.450.45 Canis falconeri 1 Canis dirus 1 Canis armbrusteri 0.15 Canis lupus 0.5 0.1 Canis chihliensis Canis etruscus Canis arnensis 0.5 0.75 Canis lepophagus 0.45 Canis thooides 0.5 Canis ferox 0.5 Eucyon davisi Cerdocyon texanus 0.45 Vulpes stenognathus 0.1 Leptocyon matthewi Leptocyon vafer 1 Urocyon cinereoargenteus 0.5 1 Urocyon minicephalus 1 Urocyon citronus 1 Urocyon galushi 0.5 0.9 Urocyon webbi 1 Metalopex merriami 0.35 Metalopex macconnelli 0.5 Leptocyon leidyi Leptocyon vulpinus 0.5 Leptocyon gregorii 0.5 Leptocyon douglassi Leptocyon mollis 0.2 Borophagus diversidens 1 Borophagus hilli 1 Borophagus dudleyi 0.95 Borophagus secundus 1 Borophagus parvus 1 0.75 Borophagus orc Borophagus pugnator 1 Borophagus littoralis 0.95 Epicyon haydeni 1 0.95 Epicyon saevus Epicyon aelurodontoides 1 Protepicyon raki 0.3 Carpocyon limosus 1 Carpocyon webbi 1 1 Carpocyon robustus Carpocyon compressus 0.4 1 Paratomarctus euthos Paratomarctus temerarius Tomarctus brevirostris 0.4 1 0.35 Tomarctus hippophaga 0.35 Tephrocyon rurestris Protomarctus opatus 0.8 0.5 Microtomarctus conferta Metatomarctus canavus Psalidocyon marianae 1 Aelurodon taxoides 0.9 0.35 Aelurodon ferox 0.3 1 Aelurodon stirtoni 0.8 0.35 Aelurodon mcgrewi Aelurodon asthenostylus 0.9 Euoplocyon brachygnathus Euoplocyon spissidens 0.9 1 Cynarctus crucidens 1 Cynarctus voorhiesi 0.35 Cynarctus saxatilis 0.2 Cynarctus galushai 0.6 1 1 Paracynarctus sinclari Paracynarctus kelloggi 0.55 0.6 Cynarctus marylandica Desmocyon matthewi Desmocyon thomsoni Cormocyon copei 1 Cynarctoides emryi 0.15 1 Cynarctoides accridens 0.2 1 Cynarctoides gawanae 0.1 Cynarctoides luskensis 0.95 Cynarctoides lemur 0.05 0.4 Phlaocyon minor Cynarctoides harlowi 0.45 Cormocyon haydeni 0.95 Phlaocyon mariae 0.85 Phlaocyon yatkolai 1 Phlaocyon leucosteus 0.6 0.5 Phlaocyon marshlandensis 1 0.9 Phlaocyon multicuspus Phlaocyon achoros 0.9 0.5 Phlaocyon annectens Phlaocyon latidens Cynarctoides roii Rhizocyon oreganensis 1 Otarocyon cooki 1 Otarocyon macdonaldi Oxetocyon cuspidatus 0.9 Osbornodon fricki 1 Osbornodon brachypus 0.35 0.15 Osbornodon iamonensis 0.3 Mesocyon coryphaeus 0.25 Mesocyon brachyops Cynodesmus martini 0.55 1 Paraenhydrocyon wallovianus 1 Paraenhydrocyon robustus 0.6 0.4 Paraenhydrocyon josephi Mesocyon temnodon Cynodesmus thooides 0.4 Enhydrocyon basilatus 0.85 Enhydrocyon stenocephalus 0.35 0.3 Enhydrocyon crassidens 1 Enhydrocyon pahinsintewakpa 1 0.7 Ectopocynus simplicidens 0.8 0.85 Ectopocynus intermedius 0.85 0.9 Ectopocynus antiquus Philotrox condoni 0.55 Sunkahetanka geringensis 0.25 Caedocyon tedfordi 0.25 Osbornodon sesnoni 0.5 Osbornodon renjiei Hesperocyon gregarius 0.15 Hesperocyon coloradensis 0.25 Archaeocyon falkenbachi 0.85 Archaeocyon leptodus Archaeocyon pavidus Prohesperocyon wilsoni outgroup

40 30 20 10 0 millions of years ago 13: mb3.2.5_mb1_root_unif

0.17 Borophagus diversidens 1 Borophagus hilli 0.97 Borophagus dudleyi 0.95 Borophagus secundus 0.9 Borophagus parvus 1 0.73 Borophagus orc Borophagus pugnator 0.17 Borophagus littoralis 1 Epicyon aelurodontoides 1 0.98 Epicyon haydeni Epicyon saevus Protepicyon raki 0.99 0.4 Carpocyon robustus 0.88 Carpocyon webbi 0.96 1 Carpocyon limosus Carpocyon compressus 0.96 Paratomarctus euthos 0.11 Paratomarctus temerarius 1 Aelurodon taxoides 0.74 Aelurodon ferox 1 0.79 Aelurodon stirtoni Aelurodon mcgrewi 0.29 Aelurodon asthenostylus 0.88 Tomarctus brevirostris 0.44 Tomarctus hippophaga 0.11 0.44 Tephrocyon rurestris 0.14 Protomarctus opatus 0.73 Microtomarctus conferta 0.96 Metatomarctus canavus 1 Euoplocyon brachygnathus Euoplocyon spissidens Psalidocyon marianae 0.99 Cynarctus crucidens 0.8 1 Cynarctus voorhiesi 0.43 Cynarctus saxatilis 0.51 Cynarctus galushai 0.75 1 Cynarctus marylandica 0.45 1 Paracynarctus sinclari Paracynarctus kelloggi 0.59 Desmocyon matthewi Desmocyon thomsoni 0.03 0.65 Cormocyon copei Cormocyon haydeni Cynarctoides roii 0.01 0.08 Rhizocyon oreganensis 1 Otarocyon cooki 1 Otarocyon macdonaldi Oxetocyon cuspidatus 1 Phlaocyon leucosteus 0.35 Phlaocyon marshlandensis 0.94 1 Phlaocyon multicuspus 0.6 Phlaocyon achoros 0.99 0.87 Phlaocyon mariae Phlaocyon yatkolai 0.62 Phlaocyon annectens Phlaocyon latidens Cynarctoides emryi 0.18 1 1 Cynarctoides accridens 0.99 Cynarctoides gawanae 0.36 Cynarctoides luskensis 0.61 Cynarctoides harlowi 0.37 Cynarctoides lemur Phlaocyon minor 1 Lycaon pictus 1 Cuon javanicus 0.44 Xenocyon texanus 0.99 Canis antonii 0.08 Canis falconeri 1 Canis dirus 0.5 1 Canis armbrusteri Canis lupus Canis chihliensis 0.47 Canis mosbachensis 0.99 0.03 Canis edwardii 0.5 Canis aureus 0.68 0.13 Canis latrans Canis variabilis 0.460.32 Canis palmidens Canis etruscus 0.9 Canis adustus 0.61 1 Canis mesomelas 0.31 Canis simensis 1 Canis arnensis 0.54 0.77 Canis lepophagus 0.93 Canis thooides 1 Canis ferox 0.95 Eucyon davisi Cerdocyon texanus 0.78 Vulpes stenognathus Leptocyon matthewi 0.93 Urocyon cinereoargenteus 0.29 0.76 Urocyon minicephalus 1 Urocyon citronus 1 Urocyon galushi 0.9 0.97 Urocyon webbi 1 Metalopex merriami Metalopex macconnelli 0.46 0.4 Leptocyon vafer 0.89 Leptocyon leidyi 0.35 Leptocyon gregorii Leptocyon vulpinus 1 Leptocyon douglassi 0.79 Leptocyon mollis Prohesperocyon wilsoni 0.3 0.37 Archaeocyon leptodus 0.8 Archaeocyon pavidus 0.22 Archaeocyon falkenbachi 0.85 Hesperocyon coloradensis Hesperocyon gregarius 0.52 Cynodesmus martini 0.56 Cynodesmus thooides Mesocyon coryphaeus 0.56 0.55 Mesocyon brachyops 0.29 0.18 Mesocyon temnodon 0.97 Paraenhydrocyon wallovianus 0.96 Paraenhydrocyon robustus Paraenhydrocyon josephi 0.06 0.73 Osbornodon fricki 1 Osbornodon brachypus 0.93 Osbornodon iamonensis 0.97 Osbornodon sesnoni Osbornodon renjiei 0.71 Enhydrocyon basilatus 0.99 0.74 Enhydrocyon stenocephalus 0.9 Enhydrocyon crassidens 0.79 Enhydrocyon pahinsintewakpa 0.74 Ectopocynus intermedius 0.11 0.87 Ectopocynus antiquus Ectopocynus simplicidens 0.94 0.49 Philotrox condoni Sunkahetanka geringensis Caedocyon tedfordi outgroup

40 30 20 10 0 millions of years ago 14: mb3.2.5_mb1_fixed_root_unif

0.46 Borophagus diversidens 1 Borophagus dudleyi 0.97 Borophagus hilli 0.96 Borophagus secundus 0.89 Borophagus parvus 1 0.74 Borophagus orc Borophagus pugnator 1 Borophagus littoralis 0.99 Epicyon haydeni 1 0.64 Epicyon saevus Epicyon aelurodontoides 0.99 Protepicyon raki 0.29 Carpocyon limosus 0.85 Carpocyon robustus 0.96 0.99 Carpocyon webbi Carpocyon compressus 0.96 Paratomarctus euthos 0.17 Paratomarctus temerarius 1 Aelurodon taxoides 0.79 Aelurodon ferox 1 0.83 Aelurodon stirtoni 0.33 Aelurodon mcgrewi Aelurodon asthenostylus 0.9 Tomarctus brevirostris 0.44 Tomarctus hippophaga 0.94 0.47 Tephrocyon rurestris Protomarctus opatus 1 Euoplocyon brachygnathus 0.17 0.25 Euoplocyon spissidens 0.07 Psalidocyon marianae 0.72 Microtomarctus conferta Metatomarctus canavus Desmocyon matthewi 0.78 1 Cynarctus crucidens 1 Cynarctus voorhiesi 0.45 Cynarctus saxatilis 0.49 0.75 Cynarctus galushai 1 Cynarctus marylandica 1 Paracynarctus sinclari 0.54 Paracynarctus kelloggi Desmocyon thomsoni 0.65 Cormocyon copei Cormocyon haydeni Cynarctoides emryi 0.06 1 1 Cynarctoides accridens 0.99 Cynarctoides gawanae 0.03 Cynarctoides luskensis 0.38 Phlaocyon minor 0.31 0.64 Cynarctoides harlowi Cynarctoides lemur Cynarctoides roii 0.41 1 Phlaocyon leucosteus 0.33 Phlaocyon marshlandensis 0.99 Phlaocyon multicuspus 0.62 Phlaocyon achoros 1 0.83 Phlaocyon mariae Phlaocyon yatkolai 0.94 0.67 Phlaocyon annectens 0.04 Phlaocyon latidens 1 Otarocyon cooki 1 Otarocyon macdonaldi Oxetocyon cuspidatus Rhizocyon oreganensis 0.19 Canis variabilis 0.15 Canis palmidens 0.39 Canis latrans 0.68 Canis aureus 0.39 Canis mosbachensis 0.17 Canis edwardii 1 Canis dirus 1 Canis armbrusteri Canis lupus 0.17 1 Lycaon pictus 1 Cuon javanicus 0.41 Xenocyon texanus 1 0.26 0.99 Canis antonii Canis falconeri 0.15 Canis chihliensis Canis etruscus 0.55 Canis arnensis 0.9 Canis adustus 0.75 1 Canis mesomelas Canis simensis Canis lepophagus 0.54 0.11 0.91 Canis ferox 1 Canis thooides Eucyon davisi 1 0.96 Cerdocyon texanus 0.8 Vulpes stenognathus Leptocyon matthewi 0.94 Urocyon cinereoargenteus 0.3 0.79 Urocyon minicephalus 1 Urocyon citronus 1 Urocyon galushi 0.33 0.9 Urocyon webbi 1 Metalopex merriami 0.99 Metalopex macconnelli 0.43 Leptocyon vafer Leptocyon leidyi 0.93 Leptocyon gregorii 0.19 Leptocyon vulpinus 1 Leptocyon mollis 0.78 Leptocyon douglassi 0.23 Prohesperocyon wilsoni 0.33 Archaeocyon falkenbachi 0.29 0.8 Archaeocyon leptodus Archaeocyon pavidus 0.85 Hesperocyon coloradensis Hesperocyon gregarius 0.74 Enhydrocyon basilatus 0.75 Enhydrocyon stenocephalus 0.88 Enhydrocyon crassidens 0.7 Enhydrocyon pahinsintewakpa 0.71 Ectopocynus intermedius 0.15 0.87 Ectopocynus antiquus Ectopocynus simplicidens 0.27 0.93 Philotrox condoni 0.11 Caedocyon tedfordi 0.21 Sunkahetanka geringensis 0.51 Cynodesmus martini 0.43 0.56 Cynodesmus thooides 0.54 Mesocyon coryphaeus Mesocyon brachyops Mesocyon temnodon 0.23 0.76 Osbornodon fricki 1 Osbornodon brachypus 0.93 Osbornodon iamonensis 0.98 0.95 Osbornodon sesnoni Osbornodon renjiei 0.98 Paraenhydrocyon wallovianus 0.96 Paraenhydrocyon robustus Paraenhydrocyon josephi outgroup

50 40 30 20 10 0 millions of years ago 15: mb3.2.5_mb2_root_unif

0.771 Borophagus diversidens 11 Borophagus dudleyi 0.981 Borophagus hilli 0.961 Borophagus secundus 0.831 Borophagus parvus 11 0.281 Borophagus orc Borophagus pugnator 11 Borophagus littoralis 0.921 Epicyon haydeni 0.991 0.41 Epicyon saevus Epicyon aelurodontoides 11 Protepicyon raki 0.261 Carpocyon robustus 0.161 Carpocyon webbi 11 0.571 Carpocyon compressus Carpocyon limosus 0.221 0.441 Paratomarctus euthos 0.191 Paratomarctus temer Tephrocyon rurestris Protomarctus opatus 11 Aelurodon taxoides 0.871 0.731 Aelurodon ferox 11 Aelurodon stirtoni 1 Aelurodon mcgrewi 0.571 0.981 Aelurodon asthenostylus 0.981 Tomarctus brevirostris 0.371 Tomarctus hippophaga 0.31 Microtomarctus confer Psalidocyon marianae 0.871 11 Euoplocyon brachygnathus Euoplocyon spissidens Metatomarctus canavus 0.811 0.991 Cynarctus crucidens 1 Cynarctus voorhiesi 0.271 Cynarctus saxatilis Cynarctus galushai 11 11 11 Paracynarctus sinclar 0.091 Paracynarctus kelloggi 0.931 Cynarctus marylandica 0.731 Desmocyon matthewi Desmocyon thomsoni 0.591 Cormocyon copei Cormocyon haydeni 0.961 Phlaocyon leucosteus 0.561 Phlaocyon marshlandensis 0.981 Phlaocyon multicuspus 0.951 Phlaocyon achoros 11 0.851 Phlaocyon mariae Phlaocyon yatkolai 0.991 0.641 Phlaocyon annectens 0.771 Phlaocyon latidens 0.061 Phlaocyon minor Cynarctoides lemur 0.141 11 Cynarctoides emryi 11 Cynarctoides accridens 0.991 0.681 0.651 Cynarctoides gawanae Cynarctoides luskensis Cynarctoides harlowi 0.1810.291 Cynarctoides roii 1 Otarocyon cooki 11 Otarocyon macdonaldi Oxetocyon cuspidatus Rhizocyon oreganensis 1 Lycaon pictus 11 Cuon javanicus 0.691 Xenocyon texanus 0.881 Canis antonii 0.611 Canis falconeri 11 Canis dirus 11 Canis armbrusteri 0.261 Canis lupus 0.411 Canis chihliensis 0.221 Canis variabilis 0.181 Canis palmidens 0.211 Canis latrans 11 0.151 Canis aureus 0.361 Canis edwardii 0.391 Canis mosbachensis Canis etruscus 0.8410.11 Canis adustus 0.841 Canis simensis 0.281 Canis mesomelas 0.651 Canis arnensis Canis thooides 0.911 Canis lepophagus 0.921 Canis ferox 11 Eucyon davisi 0.531 Cerdocyon texanus Vulpes stenognathus 0.861 Urocyon cinereoargenteus 0.661 0.881 Urocyon minicephalus 0.921 Urocyon citronus 0.831 Urocyon galushi 0.831 0.791 Urocyon webbi 1 Metalopex merriami 0.861 Metalopex macconnelli 0.911 Leptocyon matthewi Leptocyon vafer 0.611 Leptocyon leidyi 0.441 Leptocyon gregorii 0.161 Leptocyon vulpinus 1 Leptocyon mollis 0.561 Leptocyon douglassi Prohesperocyon wilsoni 0.81 Enhydrocyon basilatus 0.71 Enhydrocyon stenocephalus 0.691 Enhydrocyon crassidens 0.94 Enhydrocyon pahinsinte 0.691 Ectopocynus intermedius 0.421 0.711 Ectopocynus antiquus 0.231 Ectopocynus simplicidens Caedocyon tedfordi 0.541 Philotrox condoni 0.251 Sunkahetanka geringensis 0.121 Cynodesmus martini 0.081 0.08 Cynodesmus thooides 0.531 Mesocyon brachyops 0.371 Mesocyon coryphaeus Mesocyon temnodon 0.371 0.871 Osbornodon fricki 11 Osbornodon brachypus 0.971 Osbornodon iamonensis 0.9910.971 Osbornodon sesnoni 0.03 Osbornodon renjiei 0.421 0.71 Paraenhydrocyon wallo 0.591 Paraenhydrocyon rob 0.941 Paraenhydrocyon josephi Hesperocyon coloradensis 0.081 Hesperocyon gregarius 0.091 Archaeocyon falkenbachi 0.031 Archaeocyon pavidus Archaeocyon leptodus outgroup

1 1 1 0 0 0 millions of years ago 16: mb3.2.5_mb3_root_unif

0.94 Canis adustus 0.461 Canis mesomelas Canis simensis 0.35 Canis latrans 0.27 Canis edwardii 0.94 Canis mosbachensis 0.940.27 Canis variabilis 0.49 Canis aureus 0.46 Canis palmidens 0.1 0.84 Canis antonii Canis falconeri Canis etruscus 1 Lycaon pictus 0.65 1 Cuon javanicus 1 Xenocyon texanus 0.39 1 Canis dirus 0.15 1 Canis armbrusteri Canis lupus 0.89 Canis chihliensis 0.21 Canis arnensis 0.48 Canis lepophagus 1 0.49 Canis thooides Canis ferox 0.37 Eucyon davisi 0.94 Cerdocyon texanus Vulpes stenognathus Leptocyon matthewi 0.99 Urocyon cinereoargenteus 0.26 0.49 Urocyon minicephalus 1 Urocyon citronus 1 Urocyon galushi 0.97 1 Urocyon webbi 1 Metalopex merriami 0.93 Metalopex macconnelli 0.57 Leptocyon vafer 0.98 Leptocyon leidyi Leptocyon vulpinus 1 Leptocyon gregorii 1 0.46 Leptocyon douglassi Leptocyon mollis Prohesperocyon wilsoni 0.83 Borophagus diversidens 1 Borophagus dudleyi 0.98 Borophagus hilli 0.98 Borophagus secundus 1 Borophagus parvus 1 1 Borophagus orc Borophagus pugnator 1 Borophagus littoralis 1 Epicyon haydeni 1 0.71 Epicyon saevus Epicyon aelurodontoides 1 Protepicyon raki 1 Carpocyon limosus 11 Carpocyon robustus 0.99 1 Carpocyon webbi Carpocyon compressus 1 Paratomarctus euthos 0.8 Paratomarctus temerarius 1 Tomarctus brevirostris 0.35 Tomarctus hippophaga 0.63 0.55 Tephrocyon rurestris Protomarctus opatus 0.59 0.97 Microtomarctus conferta Metatomarctus canavus Psalidocyon marianae 0.97 0.61 Aelurodon mcgrewi 0.46 Aelurodon asthenostylus 1 Aelurodon stirtoni 1 Aelurodon taxoides 0.9 Aelurodon ferox 1 Euoplocyon brachygnathus 0.25 Euoplocyon spissidens 1 Cynarctus crucidens 1 Cynarctus voorhiesi 0.34 Cynarctus saxatilis 1 0.56 Cynarctus marylandica 1 Cynarctus galushai 1 Paracynarctus sinclari 1 0.88 Paracynarctus kelloggi Desmocyon matthewi 0.95 Desmocyon thomsoni 0.59 Cormocyon copei Cormocyon haydeni 0.71 Phlaocyon mariae 0.24 Phlaocyon yatkolai 0.99 Phlaocyon leucosteus 1 0.08 Phlaocyon marshlandensis 1 0.43 Phlaocyon multicuspus Phlaocyon achoros 0.91 Phlaocyon annectens 0.2 Phlaocyon latidens 0.62 Phlaocyon minor 1 0.88 Cynarctoides harlowi Cynarctoides lemur 0.17 1 Cynarctoides emryi 1 Cynarctoides accridens 0.92 Cynarctoides gawanae 0.82 0.37 Cynarctoides luskensis Cynarctoides roii Rhizocyon oreganensis 0.83 Archaeocyon falkenbachi 10.84 Archaeocyon leptodus Archaeocyon pavidus 0.71 Enhydrocyon basilatus 0.91 Enhydrocyon stenocephalus 1 Enhydrocyon crassidens 0.87 Enhydrocyon pahinsintewakpa 0.98 Sunkahetanka geringensis Philotrox condoni 0.24 0.6 0.69 Mesocyon coryphaeus 0.36 Mesocyon brachyops 0.48 Cynodesmus martini 0.69 Cynodesmus thooides 1 Paraenhydrocyon wallovianus 1 Paraenhydrocyon robustus 0.45 Paraenhydrocyon josephi Mesocyon temnodon 0.72 1 Ectopocynus simplicidens 1 Ectopocynus intermedius 0.46 1 Ectopocynus antiquus 0.77 Caedocyon tedfordi Osbornodon renjiei 0.59 0.65 0.86 Osbornodon fricki 1 Osbornodon brachypus 1 Osbornodon iamonensis Osbornodon sesnoni 0.1 Hesperocyon coloradensis Hesperocyon gregarius 1 Otarocyon cooki 1 Otarocyon macdonaldi Oxetocyon cuspidatus outgroup

50 40 30 20 10 0 millions of years ago 17: mb3.2.5_mb4_root_unif

0.95 Canis adustus 0.81 Canis mesomelas Canis simensis 1 Lycaon pictus 1 Cuon javanicus 0.38 Xenocyon texanus 0.99 0.97 Canis antonii 0.23 Canis falconeri 1 Canis dirus 0.99 Canis armbrusteri 0.33 Canis lupus Canis chihliensis 1 0.11 Canis edwardii 0.11 Canis aureus 1 0.5 Canis mosbachensis 0.5 0.17 Canis latrans Canis variabilis 0.35 Canis palmidens 0.9 Canis etruscus 0.29 Canis arnensis 0.97 Canis lepophagus 1 0.99 Canis thooides Canis ferox 0.91 Eucyon davisi Cerdocyon texanus 0.43 Vulpes stenognathus Leptocyon matthewi 0.27 1 Urocyon cinereoargenteus 0.72 Urocyon minicephalus 1 Urocyon galushi 1 Urocyon citronus 1 1 Urocyon webbi 1 Metalopex merriami 0.83 Metalopex macconnelli 0.56 Leptocyon vafer 0.97 Leptocyon leidyi Leptocyon vulpinus 1 Leptocyon gregorii 0.98 0.59 Leptocyon douglassi Leptocyon mollis Prohesperocyon wilsoni 0.92 Borophagus diversidens 1 Borophagus dudleyi 0.98 Borophagus hilli 0.95 Borophagus secundus 1 Borophagus parvus 1 0.98 Borophagus orc Borophagus pugnator 1 Borophagus littoralis 1 Epicyon haydeni 1 0.71 Epicyon saevus Epicyon aelurodontoides 0.99 Protepicyon raki 0.95 Carpocyon limosus 1 Carpocyon robustus 0.99 1 Carpocyon webbi Carpocyon compressus 1 Paratomarctus euthos 0.72 Paratomarctus temerarius 0.95 Tomarctus brevirostris 0.38 Tomarctus hippophaga 0.49 0.55 Tephrocyon rurestris Protomarctus opatus 0.5 0.92 Microtomarctus conferta Metatomarctus canavus Psalidocyon marianae 0.98 0.53 Aelurodon mcgrewi 0.37 Aelurodon asthenostylus 1 Aelurodon stirtoni 1 Aelurodon taxoides 0.79 Aelurodon ferox 1 Euoplocyon brachygnathus 1 Euoplocyon spissidens 1 Cynarctus crucidens 1 1 Cynarctus voorhiesi 0.58 Cynarctus saxatilis 0.11 Cynarctus marylandica 1 0.9 Cynarctus galushai 0.32 1 Paracynarctus sinclari Paracynarctus kelloggi Desmocyon matthewi 0.98 Desmocyon thomsoni 0.61 Cormocyon copei Cormocyon haydeni 1 Cynarctoides emryi 0.46 1 Cynarctoides accridens 0.94 Cynarctoides gawanae 0.38 Cynarctoides luskensis 0.36 Phlaocyon minor 0.54 0.69 Cynarctoides harlowi Cynarctoides lemur Cynarctoides roii 0.49 0.98 Phlaocyon leucosteus 0.08 0.12 Phlaocyon marshlandensis 0.5 Phlaocyon multicuspus 0.49 Phlaocyon achoros 0.37 0.33 0.22 Phlaocyon mariae Phlaocyon annectens Phlaocyon latidens Rhizocyon oreganensis 1 Otarocyon cooki 1 Otarocyon macdonaldi Oxetocyon cuspidatus 0.76 Enhydrocyon basilatus 0.93 Enhydrocyon stenocephalus 1 Enhydrocyon crassidens 0.93 Enhydrocyon pahinsintewakpa 1 Sunkahetanka geringensis Philotrox condoni 0.24 0.74 Mesocyon coryphaeus 0.46 0.41 Mesocyon brachyops 0.55 Cynodesmus martini 0.91 Cynodesmus thooides 1 Paraenhydrocyon wallovianus 1 Paraenhydrocyon robustus 0.55 Paraenhydrocyon josephi Mesocyon temnodon 0.99 0.99 Ectopocynus simplicidens 1 Ectopocynus intermedius 1 Ectopocynus antiquus 0.99 Caedocyon tedfordi Osbornodon renjiei 0.89 0.75 Osbornodon fricki 0.34 1 Osbornodon brachypus 1 Osbornodon iamonensis Osbornodon sesnoni 0.49 Phlaocyon yatkolai 0.38 Archaeocyon falkenbachi 0.47 Archaeocyon leptodus 0.32 Archaeocyon pavidus 0.21 Hesperocyon gregarius Hesperocyon coloradensis outgroup

50 40 30 20 10 0 millions of years ago 18: mb3.2.5_mb5_root_unif

1 Canis adustus 0.96 Canis mesomelas Cerdocyon texanus 0.52 Canis edwardii 0.37 Canis aureus 0.95 Canis variabilis 0.880.42 Canis latrans Canis mosbachensis 0.33 Canis palmidens 0.5 Xenocyon texanus 0.49 0.250.5 Canis antonii Canis falconeri 0.46 Canis chihliensis 1 Canis dirus 1 Canis armbrusteri 0.260.39 Canis lupus 0.5 Canis etruscus 0.5 Canis arnensis 0.38 Canis simensis 0.66 0.5 Canis thooides 0.5 0.19 Canis lepophagus Canis ferox Eucyon davisi Vulpes stenognathus Leptocyon matthewi 0.33 1 Urocyon cinereoargenteus 0.5 Urocyon minicephalus 1 Urocyon galushi 1 Urocyon citronus 0.5 1 Urocyon webbi 1 Metalopex merriami 0.39 0.49 Metalopex macconnelli Leptocyon vafer 0.5 Leptocyon leidyi 0.5 Leptocyon vulpinus Leptocyon gregorii 0.5 Leptocyon douglassi 0.5 Leptocyon mollis Prohesperocyon wilsoni 0.19 Borophagus diversidens 0.5 Borophagus hilli 0.5 Borophagus dudleyi 0.49 Borophagus secundus 0.74 Borophagus parvus 0.74 0.44 Borophagus orc Borophagus pugnator 0.74 Borophagus littoralis 1 Epicyon haydeni 0.74 0.86 Epicyon saevus Epicyon aelurodontoides 0.5 Protepicyon raki 0.5 Carpocyon robustus 0.5 0.5 Carpocyon webbi Carpocyon compressus 0.25 1 Paratomarctus euthos Paratomarctus temerarius 1 Tomarctus brevirostris 0.480.47 Tomarctus hippophaga 0.32 Tephrocyon rurestris Protomarctus opatus 0.31 0.89 Microtomarctus conferta Metatomarctus canavus 0.48 Psalidocyon marianae 0.54 Euoplocyon brachygnathus Euoplocyon spissidens 0.11 1 Cynarctus crucidens 1 Cynarctus voorhiesi 0.35 Cynarctus saxatilis 0.59 Cynarctus marylandica 0.32 1 Cynarctus galushai 1 Paracynarctus sinclari Paracynarctus kelloggi 0.41 Desmocyon matthewi 0.39 1 Lycaon pictus 0.49 0.37 Cuon javanicus 0.12 Desmocyon thomsoni Cormocyon copei Cormocyon haydeni 0.44 Phlaocyon mariae 0.24 0.32 Phlaocyon yatkolai 0.48 Phlaocyon multicuspus 1 Phlaocyon achoros 0.99 Phlaocyon leucosteus 0.7 0.48 Phlaocyon marshlandensis Phlaocyon annectens 0.5 Phlaocyon latidens 0.5 Cynarctoides emryi 0.5 Cynarctoides accridens 0.5 Cynarctoides gawanae 0.5 0.31 Cynarctoides luskensis 0.17 Phlaocyon minor 0.29 0.53 Cynarctoides harlowi Cynarctoides lemur 0.41 Cynarctoides roii Rhizocyon oreganensis 0.32 0.46 Archaeocyon falkenbachi 0.82 Archaeocyon pavidus Archaeocyon leptodus Hesperocyon gregarius 1 Aelurodon taxoides 0.56 Aelurodon ferox 0.71 0.99 Aelurodon stirtoni 1 Aelurodon mcgrewi 0.5 Aelurodon asthenostylus Philotrox condoni 0.5 0.76 Enhydrocyon basilatus 0.95 Enhydrocyon stenocephalus 1 Enhydrocyon crassidens 1 Enhydrocyon pahinsintewakpa 0.37 0.45 Sunkahetanka geringensis 0.15 Cynodesmus martini 0.4 Cynodesmus thooides 0.7 Mesocyon coryphaeus Mesocyon brachyops 0.59 1 Paraenhydrocyon wallovianus 1 Paraenhydrocyon robustus 0.58 0.48 Paraenhydrocyon josephi Mesocyon temnodon 0.5 Carpocyon limosus 0.47 Osbornodon fricki 0.5 Osbornodon brachypus 0.5 Osbornodon iamonensis 0.33 Osbornodon sesnoni 0.41 1 Ectopocynus simplicidens 1 Ectopocynus intermedius 1 Ectopocynus antiquus 0.91 Caedocyon tedfordi Osbornodon renjiei Hesperocyon coloradensis 1 Otarocyon cooki 0.94 Otarocyon macdonaldi Oxetocyon cuspidatus outgroup

50 40 30 20 10 0 millions of years ago 19: mb3.2.5_mb6_root_unif

0.43 Borophagus diversidens 1 Borophagus dudleyi 0.96 Borophagus hilli 0.94 Borophagus secundus 0.93 Borophagus parvus 1 0.73 Borophagus orc Borophagus pugnator 1 Borophagus littoralis 0.97 Epicyon haydeni 1 0.67 Epicyon saevus Epicyon aelurodontoides 0.98 Protepicyon raki 0.27 Carpocyon limosus 0.77 Carpocyon robustus 0.96 0.99 Carpocyon webbi Carpocyon compressus 0.97 Paratomarctus euthos Paratomarctus temerarius 0.3 1 Aelurodon taxoides 0.29 Aelurodon ferox 0.93 Aelurodon stirtoni 1 Aelurodon mcgrewi Aelurodon asthenostylus 0.45 0.1 0.94 Tomarctus brevirostris 0.49 Tomarctus hippophaga 0.47 Tephrocyon rurestris 0.92 Protomarctus opatus 0.8 Microtomarctus conferta Metatomarctus canavus 0.98 Euoplocyon brachygnathus 0.35 Euoplocyon spissidens Psalidocyon marianae 0.71 1 Cynarctus crucidens 1 Cynarctus voorhiesi 0.27 Cynarctus saxatilis 0.48 Cynarctus marylandica 1 0.36 Cynarctus galushai 0.39 1 Paracynarctus sinclari Paracynarctus kelloggi Desmocyon matthewi 0.06 0.31 Desmocyon thomsoni 0.3 Cormocyon copei Cormocyon haydeni Rhizocyon oreganensis 0.81 Phlaocyon mariae 0.16 Phlaocyon yatkolai 0.35 1 Phlaocyon multicuspus 0.56 Phlaocyon achoros 0.97 1 Phlaocyon leucosteus Phlaocyon marshlandensis 0.54 Phlaocyon annectens Phlaocyon latidens Cynarctoides emryi 0.19 1 1 Cynarctoides accridens 0.87 1 Cynarctoides gawanae Cynarctoides luskensis 0.3 0.09 Cynarctoides harlowi 0.02 Cynarctoides roii 0.1 Phlaocyon minor Cynarctoides lemur 1 Otarocyon cooki 1 Otarocyon macdonaldi Oxetocyon cuspidatus 1 Canis dirus 1 Canis armbrusteri 0.03 Canis lupus 0.06 0.99 Canis antonii Canis falconeri 0.54 Canis chihliensis 1 Lycaon pictus 1 Cuon javanicus Xenocyon texanus 0.99 0.04 Canis latrans 0.23 Canis palmidens 0.1 Canis variabilis 0.74 Canis aureus 0.35 0.35 0.42 Canis mosbachensis Canis edwardii Canis etruscus 0.79 Canis adustus 0.75 0.66 Canis mesomelas 0.24 Canis simensis Canis arnensis 0.29 0.78 Canis lepophagus 0.91 Canis thooides 0.99 Canis ferox 0.85 Eucyon davisi Cerdocyon texanus 0.7 Vulpes stenognathus Leptocyon matthewi 0.91 Urocyon cinereoargenteus 0.34 0.78 Urocyon minicephalus 1 Urocyon citronus 0.99 Urocyon galushi 0.98 1 Urocyon webbi 0.2 Metalopex merriami Metalopex macconnelli 0.77 0.57 Leptocyon vafer Leptocyon leidyi 1 0.54 Leptocyon gregorii Leptocyon vulpinus 0.69 0.59 Leptocyon douglassi Leptocyon mollis 0.06 Prohesperocyon wilsoni 0.88 Hesperocyon coloradensis 0.33 Hesperocyon gregarius 0.36 Archaeocyon leptodus 0.21 0.82 Archaeocyon pavidus Archaeocyon falkenbachi outgroup 0.75 Enhydrocyon basilatus 0.74 Enhydrocyon stenocephalus 0.9 Enhydrocyon crassidens 0.73 Enhydrocyon pahinsintewakpa 0.7 Ectopocynus intermedius 0.44 0.85 Ectopocynus antiquus Ectopocynus simplicidens 0.26 0.84 Caedocyon tedfordi 0.56 Philotrox condoni Sunkahetanka geringensis 0.33 0.5 Cynodesmus martini 0.58 Cynodesmus thooides Mesocyon coryphaeus 0.55 0.54 0.32 Mesocyon brachyops Mesocyon temnodon 0.91 Paraenhydrocyon wallovianus 0.89 Paraenhydrocyon robustus 0.94 Paraenhydrocyon josephi 0.11 Osbornodon fricki 1 Osbornodon iamonensis 0.92 Osbornodon brachypus 0.94 Osbornodon sesnoni Osbornodon renjiei

50 40 30 20 10 0 millions of years ago 20: mb3.2.5_mb7_root_unif

0.43 Borophagus diversidens 1 Borophagus dudleyi 0.98 Borophagus hilli 0.96 Borophagus secundus 0.94 Borophagus parvus 1 0.73 Borophagus orc Borophagus pugnator 1 Borophagus littoralis 0.99 Epicyon haydeni 0.99 0.63 Epicyon saevus Epicyon aelurodontoides 0.98 Protepicyon raki 0.24 Carpocyon limosus 0.72 Carpocyon robustus 0.95 0.98 Carpocyon webbi Carpocyon compressus 0.95 Paratomarctus euthos Paratomarctus temerarius 1 Aelurodon taxoides 0.32 0.93 Aelurodon ferox 1 0.6 Aelurodon stirtoni Aelurodon mcgrewi 0.12 Aelurodon asthenostylus 0.42 0.9 Tomarctus brevirostris 0.13 Tomarctus hippophaga 0.5 Tephrocyon rurestris Protomarctus opatus 0.93 0.76 Microtomarctus conferta Metatomarctus canavus 0.97 Euoplocyon brachygnathus 0.34 Euoplocyon spissidens Psalidocyon marianae 0.68 0.99 Cynarctus crucidens 1 Cynarctus voorhiesi 0.47 Cynarctus saxatilis Cynarctus galushai 0.75 1 1 Paracynarctus sinclari 0.37 0.22 Paracynarctus kelloggi Cynarctus marylandica Desmocyon matthewi Desmocyon thomsoni 0.81 Phlaocyon mariae 0.15 Phlaocyon yatkolai 1 Phlaocyon multicuspus 0.54 Phlaocyon achoros 0.95 1 Phlaocyon leucosteus 0.36 Phlaocyon marshlandensis 0.56 Phlaocyon annectens 0.01 Phlaocyon latidens 0.72 Cormocyon copei Cormocyon haydeni 1 Cynarctoides emryi 0.05 1 Cynarctoides accridens 1 0.83 Cynarctoides gawanae 0.07 Cynarctoides luskensis 0.39 0.12 Phlaocyon minor 0.33 0.58 Cynarctoides harlowi Cynarctoides lemur Cynarctoides roii Rhizocyon oreganensis 1 Otarocyon cooki 0.98 Otarocyon macdonaldi Oxetocyon cuspidatus 1 Lycaon pictus 1 Cuon javanicus Xenocyon texanus 0.33 0.99 Canis antonii 0.21 Canis falconeri 0.53 Canis chihliensis 1 Canis dirus 0.13 1 Canis armbrusteri Canis lupus Canis etruscus 0.971 0.33 Canis variabilis 0.13 Canis edwardii Canis palmidens 0.16 0.73 0.42 Canis latrans 0.17 Canis aureus 0.3 Canis mosbachensis Canis arnensis 0.93 Canis adustus 0.76 0.46 Canis mesomelas Canis simensis 0.11 Canis thooides 0.95 0.92 Canis ferox Canis lepophagus 0.89 0.51 Eucyon davisi 0.64 Cerdocyon texanus Vulpes stenognathus 0.17 Leptocyon matthewi 0.6 Leptocyon vafer Leptocyon leidyi 0.92 Urocyon cinereoargenteus 0.97 0.79 Urocyon minicephalus 1 Urocyon citronus 0.98 Urocyon galushi 0.43 0.78 Urocyon webbi 1 Metalopex merriami 0.74 Metalopex macconnelli Leptocyon gregorii 1 Leptocyon vulpinus 0.72 0.62 Leptocyon douglassi 0.17 Leptocyon mollis Prohesperocyon wilsoni outgroup 0.73 Enhydrocyon basilatus 0.77 Enhydrocyon stenocephalus 0.88 Enhydrocyon crassidens 0.67 Enhydrocyon pahinsintewakpa 0.63 Ectopocynus intermedius 0.39 0.92 Ectopocynus antiquus Ectopocynus simplicidens 0.81 Caedocyon tedfordi 0.46 Philotrox condoni Sunkahetanka geringensis 0.05 0.35 0.83 Osbornodon fricki 1 Osbornodon brachypus 0.91 Osbornodon iamonensis 0.97 Osbornodon sesnoni 0.99 Osbornodon renjiei 0.52 Cynodesmus martini 0.51 Cynodesmus thooides 0.49 Mesocyon coryphaeus Mesocyon brachyops 0.52 0.19 0.89 Paraenhydrocyon wallovianus 0.87 Paraenhydrocyon robustus 0.17 Paraenhydrocyon josephi 0.18 Mesocyon temnodon 0.85 Hesperocyon coloradensis Hesperocyon gregarius 0.29 Archaeocyon falkenbachi 0.79 Archaeocyon pavidus Archaeocyon leptodus

50 40 30 20 10 0 millions of years ago 21: mb3.2.5_mb8_root_unif

0.47 Borophagus diversidens 1 Borophagus dudleyi 0.97 Borophagus hilli 0.96 Borophagus secundus 0.97 Borophagus parvus 1 0.71 Borophagus orc Borophagus pugnator 1 Borophagus littoralis 0.97 Epicyon haydeni 1 0.68 Epicyon saevus Epicyon aelurodontoides 0.99 Protepicyon raki 0.28 Carpocyon limosus 0.86 Carpocyon webbi 0.95 0.99 Carpocyon robustus Carpocyon compressus 0.05 0.94 Paratomarctus euthos Paratomarctus temerarius 0.31 0.92 Tomarctus brevirostris Tomarctus hippophaga 0.22 0.41 Tephrocyon rurestris Protomarctus opatus 0.72 Microtomarctus conferta 0.31 Metatomarctus canavus 1 Aelurodon taxoides 0.94 Aelurodon ferox 1 0.59 Aelurodon stirtoni 0.95 Aelurodon mcgrewi Aelurodon asthenostylus 0.96 Euoplocyon brachygnathus 0.27 Euoplocyon spissidens Psalidocyon marianae 0.75 1 Cynarctus crucidens 1 Cynarctus voorhiesi 0.42 Cynarctus saxatilis 0.13 Cynarctus galushai 0.63 1 1 Paracynarctus sinclari Paracynarctus kelloggi 0.36 Cynarctus marylandica 0.59 Desmocyon matthewi Desmocyon thomsoni 0.63 Cormocyon copei Cormocyon haydeni 1 Phlaocyon leucosteus 0.33 Phlaocyon marshlandensis Phlaocyon multicuspus 0.26 0.99 0.54 Phlaocyon achoros 0.98 0.83 Phlaocyon mariae Phlaocyon yatkolai 0.66 Phlaocyon annectens Phlaocyon latidens 1 Cynarctoides emryi 1 0.67 0.19 Cynarctoides accridens 1 Cynarctoides gawanae 0.07 Cynarctoides luskensis 0.49 Phlaocyon minor 0.41 0.56 Cynarctoides harlowi 0.9 Cynarctoides lemur Cynarctoides roii Rhizocyon oreganensis 1 Otarocyon cooki 0.96 Otarocyon macdonaldi Oxetocyon cuspidatus 0.56 Canis mosbachensis 0.06 Canis edwardii 0.43 Canis latrans 0.78 0.15 Canis variabilis Canis aureus Canis palmidens 0.12 1 Canis dirus 1 Canis armbrusteri 0.04 Canis lupus 0.99 Canis etruscus 1 Lycaon pictus 1 Cuon javanicus 0.54 Xenocyon texanus 0.35 0.98 Canis antonii 0.46 Canis falconeri Canis chihliensis 0.9 Canis adustus 0.83 0.66 Canis mesomelas 0.25 Canis simensis Canis arnensis 0.97 0.82 Canis lepophagus 0.89 Canis thooides 0.92 Canis ferox 0.41 Eucyon davisi 0.83 Cerdocyon texanus Vulpes stenognathus Leptocyon matthewi 0.94 Urocyon cinereoargenteus 0.29 0.81 Urocyon minicephalus 1 Urocyon citronus 0.99 Urocyon galushi 0.35 0.84 Urocyon webbi 1 Metalopex merriami 0.99 Metalopex macconnelli Leptocyon vafer 0.86 Leptocyon leidyi 0.22 0.3 Leptocyon gregorii 1 Leptocyon vulpinus Leptocyon mollis 0.67 Leptocyon douglassi 0.15 Prohesperocyon wilsoni 0.07 outgroup 0.3 Archaeocyon falkenbachi 0.88 Archaeocyon pavidus Archaeocyon leptodus 0.77 Enhydrocyon basilatus 0.68 Enhydrocyon stenocephalus 0.92 Enhydrocyon crassidens 0.72 Enhydrocyon pahinsintewakpa 0.65 Ectopocynus intermedius 0.41 0.89 Ectopocynus antiquus 0.09 Ectopocynus simplicidens Caedocyon tedfordi 0.27 0.8 Philotrox condoni Sunkahetanka geringensis 0.37 0.08 Mesocyon brachyops 0.15 Mesocyon temnodon 0.65 Mesocyon coryphaeus 0.43 Cynodesmus martini Cynodesmus thooides 0.98 0.14 Osbornodon fricki 1 Osbornodon iamonensis 0.88 Osbornodon brachypus 0.94 Osbornodon sesnoni 0.45 0.13 Osbornodon renjiei 0.9 Paraenhydrocyon wallovianus 0.88 Paraenhydrocyon robustus Paraenhydrocyon josephi 0.81 Hesperocyon coloradensis Hesperocyon gregarius

50 40 30 20 10 0 millions of years ago 22: mb3.2.5_mb9_root_unif

0.98 Canis adustus 0.28 Canis mesomelas Cerdocyon texanus 0.53 Canis edwardii 0.33 Canis aureus 0.99 Canis mosbachensis 0.32 Canis latrans Canis variabilis 0.08 Canis palmidens 0.4 Canis antonii 0.5 Canis falconeri Xenocyon texanus 0.49 1 Canis dirus 1 Canis armbrusteri 0.47 Canis lupus 0.36 Canis etruscus 0.3 0.5 Canis chihliensis 0.48 Canis simensis 0.12 Canis arnensis 0.3 0.25 Canis thooides 10.5 0.14 Canis lepophagus Canis ferox Eucyon davisi Vulpes stenognathus Leptocyon matthewi 0.46 1 Urocyon cinereoargenteus 0.8 Urocyon minicephalus 1 Urocyon galushi 1 Urocyon citronus 0.5 1 Urocyon webbi 1 Metalopex merriami 10.45 0.47 Metalopex macconnelli Leptocyon vafer 0.5 Leptocyon leidyi 0.5 Leptocyon vulpinus Leptocyon gregorii 0.5 Leptocyon douglassi 0.5 Leptocyon mollis Prohesperocyon wilsoni 0.59 Borophagus diversidens 1 Borophagus dudleyi 1 Borophagus hilli 0.94 Borophagus secundus 1 Borophagus parvus 1 0.89 Borophagus orc Borophagus pugnator 11 Borophagus littoralis 0.99 Epicyon haydeni 11 0.92 Epicyon saevus Epicyon aelurodontoides 1 Protepicyon raki 0.93 Carpocyon limosus 1 Carpocyon robustus 1 11 Carpocyon webbi Carpocyon compressus 0.15 1 Paratomarctus euthos Paratomarctus temerarius 0.030.99 Tomarctus brevirostris 0.72 Tomarctus hippophaga Protomarctus opatus 0.31 Tephrocyon rurestris 0.65 Psalidocyon marianae 0.85 Microtomarctus conferta Metatomarctus canavus 1 Aelurodon taxoides 0.46 0.62 Aelurodon ferox 1 0.44 Aelurodon stirtoni Aelurodon mcgrewi 0.36 Aelurodon asthenostylus 1 Lycaon pictus 0.41 0.5 Cuon javanicus Euoplocyon brachygnathus 0.36 Euoplocyon spissidens 1 Cynarctus crucidens 1 Cynarctus voorhiesi 0.34 Cynarctus saxatilis 0.55 0.48 Cynarctus marylandica 11 Cynarctus galushai 0.59 1 Paracynarctus sinclari 0.99 0.49 Paracynarctus kelloggi Desmocyon matthewi 0.48 Desmocyon thomsoni Cormocyon copei Cormocyon haydeni 0.75 Phlaocyon mariae 0.25 0.43 Phlaocyon yatkolai Phlaocyon leucosteus 0.39 0.99 Phlaocyon marshlandensis 1 Phlaocyon annectens 0.99 0.58 Phlaocyon multicuspus Phlaocyon achoros 0.5 Phlaocyon latidens 1 Cynarctoides emryi 1 Cynarctoides accridens 1 Cynarctoides gawanae 0.5 0.98 Cynarctoides luskensis 0.54 Phlaocyon minor 0.3 0.66 Cynarctoides harlowi Cynarctoides lemur 0.49 Cynarctoides roii Rhizocyon oreganensis 0.41 0.64 Archaeocyon falkenbachi 0.88 Archaeocyon leptodus Archaeocyon pavidus Hesperocyon gregarius 1 Paraenhydrocyon wallovianus 1 Paraenhydrocyon robustus 0.4 Paraenhydrocyon josephi 0.49 Mesocyon temnodon 0.44 Mesocyon coryphaeus 0.59 0.21 Mesocyon brachyops Cynodesmus martini 0.45 Cynodesmus thooides 0.45 0.61 Enhydrocyon basilatus 0.63 Enhydrocyon stenocephalus 1 Enhydrocyon crassidens 0.62 Enhydrocyon pahinsintewakpa 0.98 Sunkahetanka geringensis Philotrox condoni 0.98 0.89 Ectopocynus simplicidens 1 Ectopocynus intermedius 0.28 1 Ectopocynus antiquus 0.4 Caedocyon tedfordi 0.66 Osbornodon renjiei 0.2 0.95 Osbornodon fricki 1 Osbornodon brachypus 0.6 Osbornodon iamonensis Osbornodon sesnoni Hesperocyon coloradensis 1 Otarocyon cooki 1 Otarocyon macdonaldi Oxetocyon cuspidatus outgroup

50 40 30 20 10 0 millions of years ago 23: mb3.2.0_mb6

0.41 Borophagus diversidens 1 Borophagus dudleyi 0.96 Borophagus hilli 0.91 Borophagus secundus 1 Borophagus parvus 0.59 Borophagus orc 0.24 Borophagus pugnator 1 Borophagus littoralis 0.96 Epicyon haydeni 0.96 0.58 Epicyon saevus Epicyon aelurodontoides Protepicyon raki 0.05 1 Aelurodon taxoides 0.29 Aelurodon ferox 0.91 Aelurodon stirtoni 0.15 1 Aelurodon mcgrewi Aelurodon asthenostylus 0.63 Carpocyon robustus 0.26 0.97 Carpocyon webbi 0.23 Carpocyon limosus Carpocyon compressus 0.3 0.93 Paratomarctus euthos Paratomarctus temerarius 0.87 Tomarctus brevirostris 0 0.31 Tomarctus hippophaga 0.44 Tephrocyon rurestris 0.45 Protomarctus opatus Metatomarctus canavus 0.91 Microtomarctus conferta 0.99 Euoplocyon brachygnathus 0.44 Euoplocyon spissidens Psalidocyon marianae 0.2 0.98 Cynarctus crucidens 1 Cynarctus voorhiesi 0.45 Cynarctus saxatilis 0.73 1 Cynarctus galushai 1 Paracynarctus sinclari 0.24 Paracynarctus kelloggi 0.62 Cynarctus marylandica 0.3 Desmocyon matthewi Desmocyon thomsoni 0.65 Cormocyon copei 0.08 Cormocyon haydeni 1 Otarocyon cooki 0.99 Otarocyon macdonaldi Oxetocyon cuspidatus 0.66 Phlaocyon mariae 0.19 Phlaocyon yatkolai Phlaocyon leucosteus 0.5 1 0.52 Phlaocyon marshlandensis 0.94 1 Phlaocyon multicuspus Phlaocyon achoros 0.65 Phlaocyon annectens Phlaocyon latidens 1 Cynarctoides emryi 0.58 0.26 1 Cynarctoides accridens 1 Cynarctoides gawanae 0.29 Cynarctoides luskensis 0.44 Cynarctoides harlowi 0.34 0.15 Cynarctoides lemur Phlaocyon minor Cynarctoides roii Rhizocyon oreganensis 1 Lycaon pictus 1 Cuon javanicus 0.43 Xenocyon texanus 0.99 Canis antonii 0.5 Canis falconeri 1 Canis dirus 1 Canis armbrusteri 0.17 0.2 Canis lupus Canis chihliensis Canis etruscus 0.99 0.45 Canis variabilis 0.16 Canis palmidens 0.42 Canis latrans 0.73 Canis aureus 0.52 0.48 Canis mosbachensis Canis edwardii 0.64 Canis lepophagus 0.9 Canis thooides 0.78 0.32 Canis ferox 0.29 Canis arnensis 0.92 Canis simensis 0.89 Canis adustus 1 Canis mesomelas 0.68 0.58 Eucyon davisi 0.28 Cerdocyon texanus Vulpes stenognathus Leptocyon matthewi 0.74 Urocyon cinereoargenteus 0.61 Urocyon minicephalus 0.23 0.95 Urocyon citronus 0.68 Urocyon galushi 0.37 Urocyon webbi 0.84 1 Metalopex merriami 0.06 Metalopex macconnelli 0.2 Leptocyon vafer Leptocyon leidyi 1 Leptocyon gregorii 0.83 Leptocyon douglassi 0.42 0.19 Leptocyon mollis Leptocyon vulpinus 0.12 Prohesperocyon wilsoni 0.31 Archaeocyon falkenbachi 0.54 Archaeocyon pavidus Archaeocyon leptodus 0.72 Enhydrocyon basilatus 0.75 Enhydrocyon stenocephalus 0.66 Enhydrocyon crassidens 0.73 Enhydrocyon pahinsintewakpa 0.67 Ectopocynus intermedius 0.27 0.85 Ectopocynus antiquus Ectopocynus simplicidens 0.86 Caedocyon tedfordi 0.22 0.07 0.39 Philotrox condoni Sunkahetanka geringensis 0.55 0.42 Mesocyon coryphaeus Mesocyon brachyops 0.69 Cynodesmus martini Cynodesmus thooides 0.71 Osbornodon fricki 0.97 1 Osbornodon brachypus 0.91 Osbornodon iamonensis 0.91 Osbornodon sesnoni 0.15 Osbornodon renjiei 0.6 0.13 Mesocyon temnodon 0.96 Paraenhydrocyon wallovianus 0.92 Paraenhydrocyon robustus Paraenhydrocyon josephi 0.76 Hesperocyon coloradensis Hesperocyon gregarius outgroup

40 30 20 10 0 millions of years ago 24: mb3.2.0_mb7

0.86 Canis adustus Canis mesomelas 1 Lycaon pictus 1 Cuon javanicus 0.44 Xenocyon texanus 0.98 Canis antonii 0.44 Canis falconeri 1 Canis dirus 1 Canis armbrusteri 0.76 0.16 Canis lupus Canis chihliensis 0.98 0.46 Canis variabilis 0.37 Canis palmidens 0.35 Canis latrans 0.76 0.16 Canis aureus 0.27 0.47 Canis mosbachensis 0.05 Canis edwardii Canis etruscus 0.42 Canis arnensis 0.22 Canis lepophagus 0.96 0.91 Canis ferox 0.15 Canis thooides Canis simensis Cerdocyon texanus Eucyon davisi 0.38 0.77 Urocyon cinereoargenteus 0.67 Urocyon minicephalus 0.93 Urocyon citronus 0.6 Urocyon galushi 1 Urocyon webbi 0.77 0.3 0.61 Metalopex merriami Metalopex macconnelli Vulpes stenognathus 0.34 0.57 Leptocyon vafer 0.17 Leptocyon leidyi Leptocyon matthewi 1 0.67 Leptocyon gregorii Leptocyon vulpinus 0.86 Leptocyon douglassi Leptocyon mollis 0.38 Borophagus dudleyi 1 Borophagus hilli 0.96 Borophagus diversidens 0.921 Borophagus secundus 0.1 Borophagus parvus 0.57 Borophagus pugnator 1 Borophagus orc 0.18 Borophagus littoralis 1 Epicyon aelurodontoides 0.93 0.95 Epicyon haydeni Epicyon saevus Protepicyon raki 0.92 0.16 Carpocyon limosus 0.06 Carpocyon webbi 0.86 0.96 Carpocyon compressus Carpocyon robustus 0.9 Paratomarctus euthos Paratomarctus temerarius 0.31 1 Aelurodon taxoides 0.3 Aelurodon ferox 0.96 Aelurodon stirtoni 1 Aelurodon mcgrewi Aelurodon asthenostylus 0.1 0.06 Tephrocyon rurestris 0.88 0.12 Microtomarctus conferta 0.56 0.08 Protomarctus opatus 0.75 Tomarctus brevirostris Tomarctus hippophaga 0.99 Euoplocyon brachygnathus 0.21 Euoplocyon spissidens 0.2 Metatomarctus canavus 0.74 Psalidocyon marianae 0.97 Cynarctus crucidens 1 Cynarctus voorhiesi 0.06 Cynarctus saxatilis 0.641 0.99 Paracynarctus sinclari 1 Paracynarctus kelloggi 0.42 0.17 Cynarctus marylandica 0.24 Cynarctus galushai Desmocyon matthewi Desmocyon thomsoni 0.62 Cormocyon copei Cormocyon haydeni 0.73 Phlaocyon mariae 0.22 Phlaocyon yatkolai 0.09 1 Phlaocyon leucosteus 0.63 0.39 Phlaocyon marshlandensis 0.96 0.99 Phlaocyon multicuspus Phlaocyon achoros 0.69 Phlaocyon annectens 0.07 Phlaocyon latidens 1 Otarocyon cooki 0.99 Otarocyon macdonaldi Oxetocyon cuspidatus 0.51 1 Cynarctoides emryi 0.15 1 Cynarctoides accridens 1 Cynarctoides gawanae 0.34 Cynarctoides luskensis 0.5 Cynarctoides harlowi 0.33 0.14 Cynarctoides lemur Phlaocyon minor Cynarctoides roii Rhizocyon oreganensis 0.27 Archaeocyon leptodus 0.55 Archaeocyon pavidus 0.22 1 Archaeocyon falkenbachi Prohesperocyon wilsoni 0.69 Enhydrocyon basilatus 0.7 Enhydrocyon stenocephalus 0.64 Enhydrocyon crassidens 0.78 Enhydrocyon pahinsintewakpa 0.59 Ectopocynus intermedius 0.27 0.86 Ectopocynus antiquus Ectopocynus simplicidens 0.74 Caedocyon tedfordi 0.07 0.42 Philotrox condoni Sunkahetanka geringensis 0.5 0.45 Mesocyon coryphaeus Mesocyon brachyops 0.66 Cynodesmus martini Cynodesmus thooides 0.73 Osbornodon fricki 0.99 1 Osbornodon brachypus 0.9 Osbornodon iamonensis 0.91 Osbornodon sesnoni 0.15 Osbornodon renjiei 0.64 0.13 Mesocyon temnodon 0.89 Paraenhydrocyon wallovianus 0.82 Paraenhydrocyon robustus Paraenhydrocyon josephi 0.72 Hesperocyon coloradensis Hesperocyon gregarius outgroup

40 30 20 10 0 10 millions of years ago 25: mb3.2.0_mb8

0.43 Borophagus diversidens 0.99 Borophagus dudleyi 0.97 Borophagus hilli 0.94 Borophagus secundus 0.67 Borophagus parvus 1 0.63 Borophagus orc Borophagus pugnator 0.99 Borophagus littoralis 0.95 Epicyon haydeni 0.92 0.59 Epicyon saevus Epicyon aelurodontoides 0.95 Protepicyon raki 0.16 Carpocyon limosus 0.43 Carpocyon webbi 0.85 0.95 Carpocyon robustus Carpocyon compressus 0.92 Paratomarctus euthos Paratomarctus temerarius 0.84 Tomarctus brevirostris 0.48 0.12 Tomarctus hippophaga 0.35 Tephrocyon rurestris 0.15 Protomarctus opatus 0.78 Microtomarctus conferta Metatomarctus canavus 0.07 0.94 1 Aelurodon taxoides 0.32 Aelurodon ferox 0.9 Aelurodon stirtoni 1 Aelurodon mcgrewi Aelurodon asthenostylus 0.97 Euoplocyon brachygnathus 0.42 Euoplocyon spissidens 0.75 Psalidocyon marianae 0.98 Cynarctus crucidens 1 Cynarctus voorhiesi 0.43 Cynarctus saxatilis 0.68 0.12 Cynarctus galushai 1 1 Paracynarctus sinclari Paracynarctus kelloggi 0.46 0.35 Cynarctus marylandica Desmocyon matthewi Desmocyon thomsoni 0.65 Cormocyon copei Cormocyon haydeni 1 Phlaocyon leucosteus 0.37 Phlaocyon marshlandensis 0.11 0.99 Phlaocyon multicuspus 0.52 Phlaocyon achoros 0.98 0.69 Phlaocyon mariae Phlaocyon yatkolai 0.6 Phlaocyon annectens Phlaocyon latidens 1 Cynarctoides emryi 1 Cynarctoides accridens 0.24 0.5 1 Cynarctoides gawanae 0.24 Cynarctoides luskensis 0.24 0.42 Cynarctoides harlowi Cynarctoides lemur 0.29 0.69 Phlaocyon minor Cynarctoides roii 1 Otarocyon cooki 0.99 Otarocyon macdonaldi Oxetocyon cuspidatus Rhizocyon oreganensis 0.1 Canis variabilis 0.16 Canis aureus 0.31 Canis latrans 0.72 Canis palmidens 0.27 0.44 Canis mosbachensis Canis edwardii 0 Canis etruscus 1 Lycaon pictus 1 Cuon javanicus 0.94 Xenocyon texanus 1 Canis dirus 1 Canis armbrusteri Canis lupus 0.08 0.07 0.98 Canis antonii 0.21 Canis falconeri 0.38 Canis chihliensis 0.18 Canis simensis Canis arnensis 0.88 0.88 Canis adustus Canis mesomelas 0.62 Canis lepophagus 0.96 0.93 Canis thooides Canis ferox 0.65 1 0.66 Eucyon davisi 0.38 Cerdocyon texanus Vulpes stenognathus Leptocyon matthewi 0.77 Urocyon cinereoargenteus 0.89 0.96 Urocyon minicephalus Urocyon citronus 0.78 0.26 Urocyon galushi 1 Urocyon webbi 0.58 0.51 Metalopex merriami 0.22 Metalopex macconnelli 0.62 Leptocyon vafer 1 Leptocyon leidyi 0.69 Leptocyon gregorii Leptocyon vulpinus 0.49 0.79 Leptocyon douglassi Leptocyon mollis 0.16 Prohesperocyon wilsoni 0.31 Archaeocyon falkenbachi 0.54 Archaeocyon leptodus Archaeocyon pavidus 0.73 Enhydrocyon basilatus 0.67 Enhydrocyon stenocephalus 0.7 Enhydrocyon crassidens 0.63 Enhydrocyon pahinsintewakpa 0.61 Ectopocynus intermedius 0.84 Ectopocynus antiquus 0.82 Ectopocynus simplicidens 0.43 Philotrox condoni 0.24 0.12 Sunkahetanka geringensis 0.45 Caedocyon tedfordi 0.58 Cynodesmus martini 0.18 Cynodesmus thooides 0.56 0.26 Mesocyon coryphaeus Mesocyon brachyops 0.96 Paraenhydrocyon wallovianus 0.92 Paraenhydrocyon robustus 0.28 Paraenhydrocyon josephi 0.99 Mesocyon temnodon 0.72 Osbornodon fricki 1 Osbornodon brachypus 0.68 0.91 Osbornodon iamonensis 0.92 Osbornodon sesnoni Osbornodon renjiei 0.74 Hesperocyon coloradensis Hesperocyon gregarius outgroup

40 30 20 10 0 millions of years ago 26: mb3.2.2_mb5

0.91 Canis adustus 0.87 Canis mesomelas 0.38 Canis simensis Canis arnensis 0.46 Canis latrans 0.22 Canis aureus 0.8 Canis mosbachensis 0.4 Canis variabilis 0.17 Canis edwardii 0.77 1 Canis dirus 0.21 1 Canis armbrusteri Canis lupus Canis palmidens 0.28 1 Lycaon pictus 1 Cuon javanicus 0.89 0.52 Xenocyon texanus 0.99 0.26 0.94 Canis antonii Canis falconeri Canis chihliensis 0.76 Canis etruscus 0.92 Canis lepophagus 1 0.66 Canis thooides Canis ferox 1 Eucyon davisi 0.88 Cerdocyon texanus Vulpes stenognathus Leptocyon matthewi 0.9 Urocyon cinereoargenteus 0.44 0.83 Urocyon minicephalus 1 Urocyon citronus 1 Urocyon galushi 0.65 0.9 Urocyon webbi 1 Metalopex merriami 1 Metalopex macconnelli 0.64 Leptocyon vafer Leptocyon leidyi 0.99 Leptocyon vulpinus 1 Leptocyon gregorii 0.76 0.23 Leptocyon douglassi Leptocyon mollis Prohesperocyon wilsoni 0.35 Borophagus dudleyi 1 Borophagus hilli 0.99 Borophagus diversidens 0.97 Borophagus secundus 0.16 Borophagus parvus 1 Borophagus orc 1 Borophagus pugnator 1 Borophagus littoralis 0.97 Epicyon haydeni 1 0.81 Epicyon saevus Epicyon aelurodontoides Protepicyon raki 0.99 0.32 Carpocyon limosus 0.94 Carpocyon webbi 0.98 0.99 Carpocyon robustus Carpocyon compressus 0.9 Paratomarctus euthos Paratomarctus temerarius 0.08 1 Aelurodon taxoides 0.9 Aelurodon ferox 10.37 Aelurodon stirtoni Aelurodon mcgrewi 0.41 0.41 Aelurodon asthenostylus 0.47 Tomarctus brevirostris Tomarctus hippophaga 0.031 Protomarctus opatus 0.93 0.06 Microtomarctus conferta Tephrocyon rurestris 0.86 Euoplocyon brachygnathus 0.05 Euoplocyon spissidens 0.15 Psalidocyon marianae 0.29 Metatomarctus canavus 1 Cynarctus crucidens 1 Cynarctus voorhiesi 0.34 Cynarctus saxatilis 0.91 0.55 Cynarctus marylandica 1 Cynarctus galushai 0.91 1 Paracynarctus sinclari Paracynarctus kelloggi 1 0.76 Desmocyon matthewi 0.97 Desmocyon thomsoni Cormocyon copei Cormocyon haydeni 0.97 Phlaocyon mariae 0.68 Phlaocyon yatkolai 1 Phlaocyon leucosteus 0.87 0.6 Phlaocyon marshlandensis 1 1 Phlaocyon multicuspus Phlaocyon achoros 0.82 Phlaocyon annectens 0.26 Phlaocyon latidens Phlaocyon minor 0.92 0.61 1 Cynarctoides emryi 1 Cynarctoides accridens 1 Cynarctoides gawanae 1 0.51 Cynarctoides luskensis 0.65 Cynarctoides harlowi Cynarctoides lemur 0.44 Cynarctoides roii Rhizocyon oreganensis 0.41 Archaeocyon falkenbachi 0.87 Archaeocyon pavidus Archaeocyon leptodus 0.72 Enhydrocyon basilatus 0.83 Enhydrocyon stenocephalus 0.71 Enhydrocyon crassidens 0.99 Enhydrocyon pahinsintewakpa 0.66 Ectopocynus intermedius 0.55 0.96 Ectopocynus antiquus 0.49 Ectopocynus simplicidens 0.26 Philotrox condoni 0.91 Sunkahetanka geringensis Caedocyon tedfordi 1 Paraenhydrocyon wallovianus 0.79 1 Paraenhydrocyon robustus 0.56 Paraenhydrocyon josephi 0.15 Mesocyon temnodon 0.11 Cynodesmus martini 0.54 0.42 Mesocyon coryphaeus 0.99 Mesocyon brachyops 0.32 Cynodesmus thooides 0.85 Osbornodon fricki 1 Osbornodon brachypus 0.94 0.83 Osbornodon iamonensis 0.75 Osbornodon sesnoni Osbornodon renjiei 0.38 Hesperocyon coloradensis Hesperocyon gregarius 1 Otarocyon cooki 0.97 Otarocyon macdonaldi Oxetocyon cuspidatus outgroup

50 40 30 20 10 0 millions of years ago 27: mb3.2.2_mb6

0.87 Canis adustus 0.37 Canis mesomelas Canis simensis 0.44 Canis variabilis 0.42 Canis palmidens 0.06 0.37 Canis latrans Canis aureus 0.77 0.11 Canis mosbachensis 0.25 Canis edwardii 1 Canis dirus 0.1 1 Canis armbrusteri Canis lupus Canis etruscus 0.98 1 Lycaon pictus 0.76 1 Cuon javanicus Xenocyon texanus 0.37 0.99 Canis antonii 0.26 Canis falconeri 0.91 Canis chihliensis 0.18 Canis thooides 0.91 Canis ferox 0.37 Canis lepophagus 0.62 Canis arnensis 0.62 Eucyon davisi Cerdocyon texanus Vulpes stenognathus 0.4 0.71 Urocyon cinereoargenteus 0.62 Urocyon minicephalus 0.9 Urocyon citronus 0.51 Urocyon galushi 0.3 0.17 Urocyon webbi 1 Metalopex merriami Metalopex macconnelli 0.18 Leptocyon matthewi 1 Leptocyon vafer 0.9 Leptocyon douglassi 0.23 Leptocyon mollis 0.71 Leptocyon vulpinus 0.21 Leptocyon gregorii Leptocyon leidyi 0.42 Borophagus dudleyi 0.99 Borophagus hilli 0.96 Borophagus diversidens 0.92 Borophagus secundus 0.49 Borophagus parvus 1 0.55 Borophagus orc Borophagus pugnator 0.21 Borophagus littoralis 0.99 0.96 Epicyon haydeni Epicyon saevus 0.93 Epicyon aelurodontoides 0.89 Protepicyon raki 0.17 Carpocyon limosus 0.97 Carpocyon robustus 0.78 0.11 Carpocyon webbi 0.31 Carpocyon compressus 0.93 Paratomarctus euthos 0.28 Paratomarctus temerarius 1 Aelurodon taxoides 0.93 Aelurodon ferox 1 0.55 Aelurodon stirtoni 0.34 Aelurodon mcgrewi Aelurodon asthenostylus 0.82 Tomarctus brevirostris 0.17 Tomarctus hippophaga 0.9 0.32 Protomarctus opatus Tephrocyon rurestris 0.99 Euoplocyon brachygnathus 0.42 Euoplocyon spissidens 0.12 Psalidocyon marianae 0.69 Microtomarctus conferta 0.74 Metatomarctus canavus 0.96 Cynarctus crucidens 1 Cynarctus voorhiesi 0.42 Cynarctus saxatilis 0.87 0.62 1 Cynarctus galushai 1 Paracynarctus sinclari 0.43 0.22 Paracynarctus kelloggi Cynarctus marylandica Desmocyon matthewi Desmocyon thomsoni 1 Phlaocyon leucosteus 0.13 Phlaocyon marshlandensis Phlaocyon mariae 0.42 0.99 Phlaocyon multicuspus 0.95 0.04 Phlaocyon achoros Phlaocyon yatkolai 0.18 Phlaocyon annectens 0.48 Phlaocyon latidens Phlaocyon minor 0.2 1 Cynarctoides emryi 1 Cynarctoides accridens 0.99 Cynarctoides gawanae 0.16 Cynarctoides luskensis 0.34 Cynarctoides lemur 0.09 0.24 Cynarctoides harlowi Cynarctoides roii 0.71 Cormocyon copei 0.12 Cormocyon haydeni 1 Rhizocyon oreganensis 0.03 1 Otarocyon cooki 1 Otarocyon macdonaldi Oxetocyon cuspidatus 0.76 Enhydrocyon basilatus 0.75 Enhydrocyon stenocephalus 0.7 Enhydrocyon crassidens 0.83 Enhydrocyon pahinsintewakpa 0.15 Ectopocynus simplicidens 0.16 0.85 Ectopocynus intermedius Ectopocynus antiquus 0.8 0.45 Philotrox condoni Sunkahetanka geringensis 0.51 Caedocyon tedfordi 0.7 Cynodesmus martini 0.6 Cynodesmus thooides 0.39 Mesocyon coryphaeus Mesocyon brachyops 0.99 0.7 Osbornodon fricki 1 Osbornodon brachypus 0.85 Osbornodon iamonensis 0.9 Osbornodon sesnoni 0.18 Osbornodon renjiei 0.16 Mesocyon temnodon 0.51 0.88 Paraenhydrocyon wallovianus 0.84 Paraenhydrocyon robustus Paraenhydrocyon josephi 0.3 Archaeocyon falkenbachi 0.49 Archaeocyon pavidus 0.29 Archaeocyon leptodus 0.51 Prohesperocyon wilsoni 0.83 Hesperocyon coloradensis Hesperocyon gregarius outgroup

60 50 40 30 20 10 0 millions of years ago 28: mb3.2.2_mb7

0.87 Canis adustus Canis mesomelas 1 Lycaon pictus 1 Cuon javanicus 0.48 Xenocyon texanus 0.98 Canis antonii 0.48 Canis falconeri 1 Canis dirus 0.76 1 Canis armbrusteri 0.18 Canis lupus Canis chihliensis 0.99 0.46 Canis mosbachensis 0.04 Canis edwardii 0.37 Canis latrans 0.76 Canis aureus 0.28 0.5 Canis variabilis 0.94 0.54 Canis palmidens Canis etruscus 0.23 Canis lepophagus 0.94 Canis ferox 0.02 0.34 Canis thooides 0.28 Canis arnensis Canis simensis 0.64 Eucyon davisi Cerdocyon texanus Leptocyon matthewi 0.38 0.27 Urocyon citronus 0.08 Urocyon galushi 0.92 Urocyon cinereoargenteus 0.54 Urocyon minicephalus 0.31 1 Urocyon webbi 0.39 0.75 Metalopex merriami 0.57 Metalopex macconnelli Vulpes stenognathus Leptocyon vafer 1 Leptocyon leidyi 0.91 Leptocyon douglassi 0.23 Leptocyon mollis 0.71 Leptocyon vulpinus Leptocyon gregorii 0.37 Borophagus diversidens 1 Borophagus dudleyi 0.97 Borophagus hilli 0.91 Borophagus secundus 0.47 Borophagus parvus 1 0.54 Borophagus orc Borophagus pugnator 0.2 Borophagus littoralis 0.99 Epicyon aelurodontoides 0.94 0.96 Epicyon haydeni Epicyon saevus 0.9 Protepicyon raki 0.65 Carpocyon robustus 0.96 Carpocyon webbi 0.83 0.27 Carpocyon limosus 0.45 Carpocyon compressus 0.93 Paratomarctus euthos 0.23 Paratomarctus temerarius 1 Aelurodon taxoides 0.28 Aelurodon ferox 0.96 Aelurodon stirtoni 1 0.23 Aelurodon mcgrewi Aelurodon asthenostylus 0.63 Tomarctus brevirostris 0.21 Tomarctus hippophaga Tephrocyon rurestris 0.08 0.51 0.94 Protomarctus opatus Microtomarctus conferta 1 Euoplocyon brachygnathus 0.44 Euoplocyon spissidens 0.15 Psalidocyon marianae 0.81 Metatomarctus canavus 0.95 Cynarctus crucidens 1 Cynarctus voorhiesi 0.42 Cynarctus saxatilis 0.48 Cynarctus galushai 0.67 0.58 1 Cynarctus marylandica 0.49 1 Paracynarctus sinclari Paracynarctus kelloggi Desmocyon matthewi Desmocyon thomsoni 0.99 Phlaocyon leucosteus 0.37 Phlaocyon marshlandensis 0.99 Phlaocyon multicuspus 0.45 Phlaocyon achoros 0.97 0.64 Phlaocyon mariae Phlaocyon yatkolai 0.48 Phlaocyon annectens Phlaocyon latidens 0.89 1 Cynarctoides emryi 0.14 1 Cynarctoides accridens 1 Cynarctoides gawanae 0.24 Cynarctoides luskensis 0.2 0.2 0.45 Cynarctoides harlowi Cynarctoides lemur Phlaocyon minor 0.11 Cynarctoides roii 1 Otarocyon cooki 0.99 Otarocyon macdonaldi 0.09 Oxetocyon cuspidatus 0.74 Cormocyon copei Cormocyon haydeni Rhizocyon oreganensis 0.7 Ectopocynus intermedius 0.84 Ectopocynus antiquus 0.14 Ectopocynus simplicidens 0.88 Enhydrocyon pahinsintewakpa 1 0.72 Enhydrocyon basilatus 0.23 0.7 Enhydrocyon stenocephalus 0.07 Enhydrocyon crassidens Caedocyon tedfordi 0.82 Philotrox condoni Sunkahetanka geringensis 0.49 0.05 Cynodesmus martini 0.17 Mesocyon brachyops 0.54 Cynodesmus thooides Mesocyon coryphaeus 0.99 0.7 Osbornodon fricki 1 Osbornodon brachypus 0.86 Osbornodon iamonensis 0.87 Osbornodon sesnoni Osbornodon renjiei 0.32 0.17 0.97 Paraenhydrocyon wallovianus 0.94 Paraenhydrocyon robustus 0.24 Paraenhydrocyon josephi Mesocyon temnodon 0.45 0.82 Hesperocyon coloradensis Hesperocyon gregarius 0.28 Archaeocyon falkenbachi 0.44 Archaeocyon pavidus 0.27 Archaeocyon leptodus Prohesperocyon wilsoni outgroup

60 50 40 30 20 10 0 millions of years ago 29: mb3.2.2_mb8

Borophagus diversidens 1 0.38 Borophagus dudleyi 0.96 Borophagus hilli 0.87 Borophagus secundus 1 Borophagus parvus 0.55 Borophagus orc 0.3 Borophagus pugnator 0.98 Borophagus littoralis 0.94 Epicyon haydeni 0.94 0.56 Epicyon saevus Epicyon aelurodontoides 0.91 Protepicyon raki 0.65 Carpocyon robustus Carpocyon webbi 0.8 0.95 0.24 Carpocyon limosus Carpocyon compressus 0.95 Paratomarctus euthos Paratomarctus temerarius 0.21 1 Aelurodon taxoides 0.82 Aelurodon ferox 1 0.51 Aelurodon stirtoni Aelurodon mcgrewi Aelurodon asthenostylus 0.33 0.1 0.86 Tomarctus brevirostris 0.33 Tomarctus hippophaga 0.48 Tephrocyon rurestris 0.91 Protomarctus opatus 0.65 Microtomarctus conferta Metatomarctus canavus 0.94 Euoplocyon brachygnathus 0.37 Euoplocyon spissidens Psalidocyon marianae 0.75 0.98 Cynarctus crucidens 1 Cynarctus voorhiesi 0.3 Cynarctus saxatilis 0.08 Cynarctus marylandica 0.611 1 1 Paracynarctus sinclari Paracynarctus kelloggi 0.47 Cynarctus galushai 0.26 Desmocyon matthewi Desmocyon thomsoni 0.61 Cormocyon copei Cormocyon haydeni 0.69 Phlaocyon mariae 0.16 Phlaocyon yatkolai 0.99 Phlaocyon multicuspus 0.49 Phlaocyon achoros 0.39 0.97 1 Phlaocyon leucosteus Phlaocyon marshlandensis 0.52 Phlaocyon annectens Phlaocyon latidens 1 Cynarctoides emryi 1 Cynarctoides accridens 0.231 1 Cynarctoides gawanae 0.1 Cynarctoides luskensis 0.53 0.34 0.27 Cynarctoides harlowi 0.12 Cynarctoides roii 0.26 Cynarctoides lemur Phlaocyon minor 1 Otarocyon cooki 0.99 Otarocyon macdonaldi Oxetocyon cuspidatus Rhizocyon oreganensis 1 Lycaon pictus 1 Cuon javanicus Xenocyon texanus 0.45 0.99 Canis antonii 0.24 Canis falconeri 0.43 Canis chihliensis 1 Canis dirus 1 Canis armbrusteri Canis lupus 0.98 0.46 Canis variabilis 0.38 Canis palmidens 0.38 Canis latrans 0.75 Canis aureus 0.04 0.25 0.4 Canis mosbachensis Canis edwardii Canis etruscus 0.49 0.59 Canis lepophagus 0.9 Canis thooides Canis ferox 0.97 0.19 Canis simensis Canis arnensis Canis adustus 1 0.86 0.59 0.03 Canis mesomelas 0.08 Eucyon davisi Cerdocyon texanus Vulpes stenognathus 0.43 0.07 Urocyon cinereoargenteus 0.64 Urocyon citronus 0.95 Urocyon minicephalus 0.65 Urocyon galushi 0.73 1 Urocyon webbi 0.6 Metalopex merriami Metalopex macconnelli 0.15 0.58 Leptocyon vafer 0.21 Leptocyon leidyi 11 Leptocyon matthewi Leptocyon gregorii Leptocyon douglassi 0.3 0.82 0.25 Leptocyon mollis Leptocyon vulpinus Prohesperocyon wilsoni 0.67 Ectopocynus intermedius 0.81 Ectopocynus antiquus 0.11 Ectopocynus simplicidens 0.79 Enhydrocyon pahinsintewakpa 0.11 Enhydrocyon stenocephalus 0.09 0.64 Enhydrocyon crassidens Enhydrocyon basilatus 0.83 0.09 Caedocyon tedfordi Philotrox condoni 0.51 Sunkahetanka geringensis 0.4 Mesocyon coryphaeus 0.16 0.09 Mesocyon brachyops 0.56 Cynodesmus thooides 0.07 Cynodesmus martini 0.65 Osbornodon fricki 1 Osbornodon brachypus 0.81 Osbornodon iamonensis 0.99 0.81 Osbornodon sesnoni Osbornodon renjiei 0.96 Paraenhydrocyon wallovianus 0.52 0.95 Paraenhydrocyon robustus 0.3 Paraenhydrocyon josephi Mesocyon temnodon 0 0.8 Hesperocyon coloradensis Hesperocyon gregarius 0.09 0.32 Archaeocyon falkenbachi Archaeocyon leptodus Archaeocyon pavidus outgroup

50 40 30 20 10 0 millions of years ago 30: mb3.2.2_mb9

0.94 Canis adustus 0.8 Canis mesomelas 0.48 Canis simensis Canis arnensis 0.47 Canis latrans 0.34 Canis aureus 0.74 Canis variabilis 0.49 Canis mosbachensis Canis edwardii 0.9410.32 1 Canis dirus 1 Canis armbrusteri 0.06 Canis lupus 0.35 Canis palmidens 1 Lycaon pictus 1 0.38 Cuon javanicus Xenocyon texanus 0.990.38 0.91 Canis antonii 0.15 Canis falconeri 0.98 Canis chihliensis Canis etruscus 0.91 0.96 Canis lepophagus Canis thooides 1 Canis ferox 1 Eucyon davisi Cerdocyon texanus 0.92 Vulpes stenognathus Leptocyon matthewi 0.96 Urocyon cinereoargenteus 0.81 Urocyon minicephalus 0.91 1 Urocyon citronus 1 Urocyon galushi 0.97 Urocyon webbi 1 1 Metalopex merriami 0.25 Metalopex macconnelli 1 Leptocyon vafer Leptocyon leidyi 0.12 0.08 Leptocyon gregorii 1 Leptocyon vulpinus Leptocyon mollis 0.5 Leptocyon douglassi Prohesperocyon wilsoni 0.4 Borophagus diversidens 1 Borophagus dudleyi 0.98 Borophagus hilli 0.96 Borophagus secundus 1 Borophagus parvus 1 0.62 Borophagus orc Borophagus pugnator 1 Borophagus littoralis 0.95 Epicyon haydeni 1 0.87 Epicyon saevus Epicyon aelurodontoides 1 Protepicyon raki 0.33 Carpocyon limosus 0.96 Carpocyon webbi 0.99 0.99 Carpocyon robustus Carpocyon compressus 0.08 0.89 Paratomarctus euthos Paratomarctus temerarius 0.03 0.69 Tomarctus brevirostris 0.22 Tomarctus hippophaga Protomarctus opatus Tephrocyon rurestris 0.36 1 Aelurodon taxoides 0.85 Aelurodon ferox 1 0.53 Aelurodon stirtoni 0.23 Aelurodon mcgrewi Aelurodon asthenostylus 0.38 0.48 Microtomarctus conferta 0.83 Metatomarctus canavus Psalidocyon marianae 0.75 Euoplocyon brachygnathus Euoplocyon spissidens 1 Cynarctus crucidens 0.84 1 Cynarctus voorhiesi 0.39 0.15 Cynarctus saxatilis 0.58 Cynarctus galushai 0.98 1 Cynarctus marylandica 0.53 1 Paracynarctus sinclari Paracynarctus kelloggi 0.88 Desmocyon matthewi 0.98 Desmocyon thomsoni Cormocyon copei Cormocyon haydeni 0.97 Phlaocyon mariae 0.8 Phlaocyon yatkolai 1 Phlaocyon leucosteus 0.87 0.91 Phlaocyon marshlandensis 1 1 Phlaocyon multicuspus Phlaocyon achoros 0.95 Phlaocyon annectens Phlaocyon latidens 1 Cynarctoides emryi 0.92 0.69 1 Cynarctoides accridens 1 Cynarctoides gawanae 0.44 Cynarctoides luskensis 1 0.83 0.59 Cynarctoides harlowi Cynarctoides lemur Phlaocyon minor 0.48 Cynarctoides roii Rhizocyon oreganensis 0.37 Archaeocyon falkenbachi 0.87 Archaeocyon leptodus 1 Archaeocyon pavidus 0.7 Enhydrocyon basilatus 0.62 Enhydrocyon stenocephalus 0.72 Enhydrocyon crassidens 0.99 Enhydrocyon pahinsintewakpa 0.32 Ectopocynus simplicidens 0.54 0.93 Ectopocynus intermedius 0.63 Ectopocynus antiquus Philotrox condoni 0.83 0.29 Sunkahetanka geringensis Caedocyon tedfordi 0.49 Mesocyon coryphaeus 0.63 0.22 Mesocyon brachyops 0.09 Cynodesmus martini 0.48 Mesocyon temnodon 1 Paraenhydrocyon wallovianus 0.66 0.99 Paraenhydrocyon robustus 0.98 Paraenhydrocyon josephi Cynodesmus thooides 0.71 Osbornodon fricki 0.36 1 Osbornodon brachypus 0.62 Osbornodon iamonensis 0.52 Osbornodon sesnoni 0.75 Osbornodon renjiei Hesperocyon gregarius Hesperocyon coloradensis 1 Otarocyon cooki 0.8 Otarocyon macdonaldi Oxetocyon cuspidatus outgroup

50 40 30 20 10 0 millions of years ago 31: mb3.2.5_mb1

Borophagus diversidens 1 0.39 Borophagus dudleyi 0.96 Borophagus hilli 0.94 Borophagus secundus 0.92 Borophagus parvus 1 0.7 Borophagus orc Borophagus pugnator 1 Borophagus littoralis 0.98 Epicyon haydeni 1 0.6 Epicyon saevus Epicyon aelurodontoides 0.99 Protepicyon raki 0.29 Carpocyon limosus 0.88 Carpocyon webbi 0.95 0.99 Carpocyon robustus Carpocyon compressus 0.95 Paratomarctus euthos 0.47 Paratomarctus temerarius 1 Tomarctus brevirostris 0.24 Tomarctus hippophaga 0.37 0.5 Tephrocyon rurestris Protomarctus opatus 0.84 Microtomarctus conferta Metatomarctus canavus 0.12 0.3 Aelurodon mcgrewi 0.29 Aelurodon asthenostylus 1 Aelurodon stirtoni 0.98 1 Aelurodon taxoides 0.62 Aelurodon ferox 1 Euoplocyon brachygnathus Euoplocyon spissidens Psalidocyon marianae 0.73 1 Cynarctus crucidens 1 Cynarctus voorhiesi 0.3 Cynarctus saxatilis 0.51 Cynarctus marylandica 0.73 1 Cynarctus galushai 0.39 1 Paracynarctus sinclari Paracynarctus kelloggi 0.72 Desmocyon matthewi Desmocyon thomsoni 0.12 0.64 Cormocyon copei Cormocyon haydeni Rhizocyon oreganensis 1 Phlaocyon leucosteus 0.34 Phlaocyon marshlandensis 1 Phlaocyon multicuspus 0.65 1 Phlaocyon achoros 0.85 Phlaocyon mariae 0.7 0.09 Phlaocyon yatkolai Phlaocyon annectens Phlaocyon latidens 1 Cynarctoides emryi 0.21 1 Cynarctoides accridens 0.97 0.99 Cynarctoides gawanae 0.25 Cynarctoides luskensis 0.241 0.68 Cynarctoides harlowi Cynarctoides lemur 0.37 Cynarctoides roii Phlaocyon minor 1 Otarocyon cooki 1 Otarocyon macdonaldi Oxetocyon cuspidatus 1 Lycaon pictus 1 Cuon javanicus 0.48 Xenocyon texanus 0.99 Canis antonii 0.52 Canis falconeri 1 Canis dirus 1 Canis armbrusteri 0.25 Canis lupus Canis chihliensis 0.99 0.56 Canis mosbachensis 0.05 Canis edwardii 0.46 Canis latrans 0.72 Canis aureus 0.710.33 0.23 Canis variabilis Canis palmidens Canis etruscus 0.93 Canis adustus 1 0.75 Canis mesomelas 0.52 Canis simensis Canis arnensis 0.65 0.78 Canis lepophagus 0.92 Canis thooides 1 1 Canis ferox 0.96 Eucyon davisi Cerdocyon texanus 0.82 Vulpes stenognathus Leptocyon matthewi 0.92 Urocyon cinereoargenteus 0.8 Urocyon minicephalus 0.99 1 Urocyon citronus 0.99 Urocyon galushi 0.9 Urocyon webbi 1 0.46 Metalopex merriami 0.21 Metalopex macconnelli Leptocyon vafer 0.94 0.41 Leptocyon leidyi 0.21 Leptocyon gregorii 1 Leptocyon vulpinus Leptocyon mollis 0.84 Leptocyon douglassi 0.26 Prohesperocyon wilsoni 0.31 Archaeocyon falkenbachi 0.89 Archaeocyon leptodus Archaeocyon pavidus 0.76 Enhydrocyon basilatus 0.7 Enhydrocyon stenocephalus 0.9 Enhydrocyon crassidens 0.69 Enhydrocyon pahinsintewakpa 0.69 Ectopocynus intermedius 0.17 0.88 Ectopocynus antiquus Ectopocynus simplicidens 0.85 Philotrox condoni 0.12 Caedocyon tedfordi 0.29 Sunkahetanka geringensis 0.41 0.56 Mesocyon coryphaeus 0.04 Mesocyon brachyops Cynodesmus thooides 0.64 0.05 Mesocyon temnodon 0.25 Cynodesmus martini 0.64 Osbornodon fricki 1 Osbornodon brachypus 0.92 0.97 Osbornodon iamonensis 0.93 Osbornodon sesnoni Osbornodon renjiei 0.08 0.92 Paraenhydrocyon wallovianus 0.92 Paraenhydrocyon robustus 0.68 Paraenhydrocyon josephi Hesperocyon coloradensis Hesperocyon gregarius outgroup

50 40 30 20 10 0 millions of years ago 32: mb3.2.5_mb5

1 Canis adustus 0.91 Canis mesomelas Cerdocyon texanus 0.57 Canis edwardii Canis aureus 1 Canis variabilis 0.98 Canis latrans Canis mosbachensis 0.46 Canis palmidens 0.49 Xenocyon texanus 0.49 Canis antonii 0.5 0.5 Canis falconeri 1 Canis dirus 1 Canis armbrusteri 0.85 0.46 Canis lupus 0.77 Canis chihliensis Canis etruscus 0.5 0.27 0.96 Canis simensis Canis arnensis 0.49 0.63 Canis lepophagus 0.5 0.49 Canis thooides Canis ferox Eucyon davisi 0.15 Vulpes stenognathus Leptocyon matthewi Leptocyon vafer 1 Urocyon cinereoargenteus 0.34 0.88 Urocyon minicephalus 1 Urocyon citronus 1 Urocyon galushi 0.5 1 Urocyon webbi 1 Metalopex merriami 0.5 Metalopex macconnelli 0.5 Leptocyon leidyi Leptocyon vulpinus 0.5 Leptocyon gregorii 0.5 Leptocyon douglassi 0.5 Leptocyon mollis Prohesperocyon wilsoni 0.86 Borophagus diversidens 0.92 Borophagus dudleyi 0.92 Borophagus hilli 0.97 Borophagus secundus 0.99 Borophagus parvus 0.99 0.93 Borophagus orc Borophagus pugnator 0.99 Borophagus littoralis 1 Epicyon haydeni 0.99 0.86 Epicyon saevus Epicyon aelurodontoides 1 Protepicyon raki 0.99 Carpocyon limosus 0.99 Carpocyon robustus 1 0.99 Carpocyon webbi Carpocyon compressus 0.39 1 Paratomarctus euthos Paratomarctus temerarius Tomarctus brevirostris 0.76 0.97 0.4 Tomarctus hippophaga 0.51 Tephrocyon rurestris Protomarctus opatus 0.59 0.88 Microtomarctus conferta Metatomarctus canavus 0.49 Psalidocyon marianae 0.72 Euoplocyon brachygnathus Euoplocyon spissidens 1 Cynarctus crucidens 0.38 1 Cynarctus voorhiesi 0.35 Cynarctus saxatilis 0.57 Cynarctus marylandica 0.42 1 Cynarctus galushai 0.85 1 Paracynarctus sinclari Paracynarctus kelloggi 0.44 Desmocyon matthewi 0.5 Desmocyon thomsoni Cormocyon copei Cormocyon haydeni 1 1 Phlaocyon leucosteus 0.41 0.03 Phlaocyon marshlandensis 0.2 Phlaocyon multicuspus 0.5 Phlaocyon achoros 0.5 0.2 Phlaocyon mariae Phlaocyon annectens 0.5 Phlaocyon latidens 1 Cynarctoides emryi 1 Cynarctoides accridens 1 Cynarctoides gawanae Cynarctoides luskensis 0.5 0.72 0.41 Phlaocyon minor 0.63 0.56 Cynarctoides lemur Cynarctoides harlowi 0.35 Cynarctoides roii Rhizocyon oreganensis 0.27 0.53 Archaeocyon falkenbachi 0.79 Archaeocyon leptodus 0.12 Archaeocyon pavidus Hesperocyon gregarius Hesperocyon coloradensis 1 Aelurodon taxoides 0.59 Aelurodon ferox 0.83 Aelurodon stirtoni 1 Aelurodon mcgrewi 0.5 Aelurodon asthenostylus Philotrox condoni 0.49 0.76 Enhydrocyon basilatus 0.95 Enhydrocyon stenocephalus 0.3 0.9 Enhydrocyon crassidens 0.89 Enhydrocyon pahinsintewakpa Sunkahetanka geringensis 0.39 0.35 Phlaocyon yatkolai 0.36 Mesocyon brachyops 0.2 Mesocyon coryphaeus 0.2 Cynodesmus martini Cynodesmus thooides 0.27 1 Paraenhydrocyon wallovianus 1 Paraenhydrocyon robustus 0.49 Paraenhydrocyon josephi 0.49 Mesocyon temnodon 0.19 1 Lycaon pictus 0.5 Cuon javanicus 0.49 Ectopocynus simplicidens 0.5 Ectopocynus intermedius 0.5 Ectopocynus antiquus 0.43 Caedocyon tedfordi Osbornodon renjiei 0.37 0.96 Osbornodon fricki 1 Osbornodon brachypus 1 Osbornodon iamonensis Osbornodon sesnoni 1 Otarocyon cooki 0.99 Otarocyon macdonaldi Oxetocyon cuspidatus outgroup

50 40 30 20 10 0 millions of years ago 33: mb3.2.5_mb6

0.85 Canis adustus Canis mesomelas 0.42 Canis variabilis 0.16 Canis palmidens 0.83 Canis edwardii 0.36 Canis latrans 0.09 Canis aureus 0.24 Canis mosbachensis 1 Canis dirus 0.11 1 0.78 Canis armbrusteri Canis lupus Canis etruscus 0.94 1 Lycaon pictus 1 Cuon javanicus Xenocyon texanus 0.35 1 Canis antonii 0.25 0.96 0.22 Canis falconeri Canis chihliensis 0.56 Canis lepophagus 0.44 0.93 Canis thooides 0.49 0.63 Canis ferox Canis arnensis Canis simensis 0.73 Eucyon davisi Cerdocyon texanus 0.31 Vulpes stenognathus 0.33 Urocyon citronus 0.06 Urocyon galushi 0.94 Urocyon cinereoargenteus 0.6 Urocyon minicephalus 0.56 1 Urocyon webbi 0.8 Metalopex merriami Metalopex macconnelli 0.61 Leptocyon vafer 1 0.22 Leptocyon leidyi Leptocyon matthewi 0.87 Leptocyon douglassi 0.04 Leptocyon mollis 0.81 Leptocyon gregorii Leptocyon vulpinus 0.46 Borophagus diversidens 1 Borophagus dudleyi 0.96 Borophagus hilli Borophagus secundus 1 0.12 Borophagus orc 0.53 Borophagus littoralis 0.18 0.11 Borophagus pugnator Borophagus parvus 1 Epicyon aelurodontoides 0.92 0.97 Epicyon haydeni Epicyon saevus 0.84 Protepicyon raki 0.7 Carpocyon robustus 0.98 Carpocyon webbi 0.66 0.28 Carpocyon limosus Carpocyon compressus 0.07 0.99 Paratomarctus euthos Paratomarctus temerarius 0.92 Tomarctus brevirostris 0.9 0.46 Tomarctus hippophaga 0.02 0.52 Tephrocyon rurestris Protomarctus opatus 0.71 Microtomarctus conferta 0.12 Metatomarctus canavus 0.95 Psalidocyon marianae 1 Aelurodon taxoides 0.93 Aelurodon ferox 1 0.67 Aelurodon stirtoni Aelurodon mcgrewi 0.07 Aelurodon asthenostylus 0.99 Euoplocyon brachygnathus 0.66 Euoplocyon spissidens 0.97 Cynarctus crucidens 1 Cynarctus voorhiesi 0.44 Cynarctus saxatilis 1 Cynarctus galushai 1 Paracynarctus sinclari 0.42 0.24 Paracynarctus kelloggi 0.25 Cynarctus marylandica Desmocyon matthewi Desmocyon thomsoni 0.68 Phlaocyon mariae 0.16 Phlaocyon yatkolai 1 Phlaocyon leucosteus 0.4 Phlaocyon marshlandensis 0.47 0.99 1 Phlaocyon multicuspus Phlaocyon achoros 0.47 Phlaocyon annectens Phlaocyon latidens 1 Cynarctoides emryi 0.15 1 Cynarctoides accridens 1 Cynarctoides gawanae 1 0.21 Cynarctoides luskensis 0.11 Phlaocyon minor 0.1 0.22 0.11 Cynarctoides lemur Cynarctoides harlowi Cynarctoides roii Cormocyon copei 0.2 0.76 0.2 Cormocyon haydeni Rhizocyon oreganensis 1 Otarocyon cooki 0.98 Otarocyon macdonaldi Oxetocyon cuspidatus 0.75 Enhydrocyon basilatus 0.66 Enhydrocyon stenocephalus 0.86 Enhydrocyon crassidens 0.7 Enhydrocyon pahinsintewakpa 0.67 Ectopocynus intermedius 0.81 Ectopocynus antiquus 0.67 Ectopocynus simplicidens 0.6 Philotrox condoni 0.16 Sunkahetanka geringensis 0.25 Caedocyon tedfordi 0.59 Cynodesmus martini 0.22 0.59 Cynodesmus thooides 0.42 Mesocyon coryphaeus Mesocyon brachyops Mesocyon temnodon 0.18 0.73 Osbornodon fricki 1 Osbornodon brachypus 0.79 Osbornodon iamonensis 0.99 0.9 Osbornodon sesnoni Osbornodon renjiei 0.83 Paraenhydrocyon wallovianus 0.75 Paraenhydrocyon robustus 0.63 Paraenhydrocyon josephi 0.36 Archaeocyon leptodus 0.59 Archaeocyon pavidus Archaeocyon falkenbachi 0.86 0.87 Hesperocyon coloradensis 0.29 Hesperocyon gregarius Prohesperocyon wilsoni outgroup

70 60 50 40 30 20 10 0 millions of years ago 34: mb3.2.5_mb7

0.89 Canis adustus Canis mesomelas 1 Lycaon pictus 1 Cuon javanicus 0.48 Xenocyon texanus 0.99 Canis antonii 0.5 Canis falconeri 1 Canis dirus 0.83 1 Canis armbrusteri 0.19 Canis lupus Canis chihliensis 0.99 0.41 Canis latrans 0.19 Canis aureus 0.39 Canis variabilis 0.79 Canis palmidens 0.55 Canis mosbachensis 0.97 0.36 0.54 Canis edwardii Canis etruscus 0.56 Canis lepophagus 0.92 Canis thooides 0.52 Canis ferox 0.41 Canis arnensis Canis simensis 0.44 0.81 Eucyon davisi Cerdocyon texanus 0.7 Urocyon cinereoargenteus 0.95 Urocyon minicephalus 0.37 Urocyon citronus 0.3 1 Urocyon galushi 0.87 Metalopex merriami 0.37 0.55 Metalopex macconnelli 0.54 Urocyon webbi Vulpes stenognathus Leptocyon matthewi 1 0.59 Leptocyon vafer Leptocyon leidyi 0.68 Leptocyon gregorii 0.75 Leptocyon vulpinus 0.88 Leptocyon douglassi Leptocyon mollis 0.42 Borophagus dudleyi 0.99 Borophagus hilli 0.93 Borophagus diversidens 0.88 Borophagus secundus 0.05 Borophagus parvus 0.37 Borophagus orc 1 Borophagus pugnator 0.99 Borophagus littoralis 0.98 Epicyon haydeni 0.93 0.62 Epicyon saevus Epicyon aelurodontoides 0.87 Protepicyon raki 0.65 Carpocyon robustus 0.97 Carpocyon webbi 0.7 0.29 Carpocyon limosus Carpocyon compressus 0.09 0.98 Paratomarctus euthos Paratomarctus temerarius 0.9 Tomarctus brevirostris 0.44 Tomarctus hippophaga 0.55 Tephrocyon rurestris 0.42 Protomarctus opatus 1 Aelurodon taxoides 0.86 Aelurodon ferox 0.81 1 0.57 Aelurodon stirtoni Aelurodon mcgrewi 0.95 0.01 Aelurodon asthenostylus 0.74 Microtomarctus conferta Metatomarctus canavus 1 Euoplocyon brachygnathus 0.45 Euoplocyon spissidens Psalidocyon marianae 0.62 0.98 Cynarctus crucidens 1 Cynarctus voorhiesi 0.34 Cynarctus saxatilis 0.51 Cynarctus marylandica 0.74 1 Cynarctus galushai 0.46 1 Paracynarctus sinclari 0.06 Paracynarctus kelloggi Desmocyon matthewi Desmocyon thomsoni 0.78 Cormocyon copei Cormocyon haydeni 1 Phlaocyon leucosteus 0.1 Phlaocyon marshlandensis 0.2 Phlaocyon mariae 1 Phlaocyon multicuspus 0.11 0.97 Phlaocyon achoros 0.54 0.18 Phlaocyon yatkolai Phlaocyon annectens Phlaocyon latidens 0.14 1 Cynarctoides emryi 1 Cynarctoides accridens 1 Cynarctoides gawanae 1 0.57 Cynarctoides luskensis 0.04 0.26 0.52 Cynarctoides harlowi 0.16 Cynarctoides lemur Phlaocyon minor 0.12 Cynarctoides roii Rhizocyon oreganensis 1 Otarocyon cooki 0.99 Otarocyon macdonaldi Oxetocyon cuspidatus 0.73 Ectopocynus intermedius 0.74 Ectopocynus antiquus 0.08 Ectopocynus simplicidens 0.78 Enhydrocyon pahinsintewakpa 0.8 Enhydrocyon basilatus 0.43 0.65 Enhydrocyon stenocephalus Enhydrocyon crassidens 0.74 Caedocyon tedfordi 0.63 Philotrox condoni 0.26 Sunkahetanka geringensis 0.09 Cynodesmus thooides 0.58 Mesocyon coryphaeus 0.04 Cynodesmus martini 0.15 Mesocyon brachyops 0.73 Osbornodon fricki 1 Osbornodon brachypus 0.79 Osbornodon iamonensis 0.97 0.89 Osbornodon sesnoni 0.09 Osbornodon renjiei Mesocyon temnodon 0.98 Paraenhydrocyon wallovianus 0.6 0.89 Paraenhydrocyon robustus Paraenhydrocyon josephi 0.28 Archaeocyon falkenbachi 0.6 Archaeocyon leptodus Archaeocyon pavidus 0.81 0.89 Hesperocyon coloradensis 0.32 Hesperocyon gregarius Prohesperocyon wilsoni outgroup

60 40 20 0 millions of years ago 35: mb3.2.5_mb8

0.83 Canis adustus 0.45 Canis mesomelas Canis simensis 0.43 Canis variabilis 0.35 Canis palmidens 0.38 Canis latrans 0.84 Canis aureus 0.52 Canis mosbachensis 0.23 Canis edwardii 0.8 1 Canis dirus 1 Canis armbrusteri Canis lupus 0.97 1 Lycaon pictus 1 Cuon javanicus 0.47 Xenocyon texanus 0.37 0.99 Canis antonii 0.99 Canis falconeri 0.29 0.09 Canis chihliensis Canis etruscus 0.63 Canis lepophagus 0.72 0.91 Canis thooides 0.56 Canis ferox Canis arnensis 0.75 Eucyon davisi Cerdocyon texanus 0.3 Vulpes stenognathus 0.78 Urocyon cinereoargenteus 0.68 Urocyon minicephalus 0.96 Urocyon citronus 0.75 Urocyon galushi 0.86 1 Urocyon webbi 0.73 Metalopex merriami Metalopex macconnelli 1 0.75 Leptocyon vafer 0.34 Leptocyon leidyi Leptocyon matthewi 0.79 Leptocyon gregorii 0.5 Leptocyon vulpinus 0.88 Leptocyon douglassi Leptocyon mollis 0.19 Borophagus diversidens 0.99 Borophagus hilli 0.93 Borophagus dudleyi 0.88 Borophagus secundus 0.53 Borophagus parvus 1 0.64 Borophagus orc Borophagus pugnator 0.99 Borophagus littoralis 0.96 Epicyon haydeni 0.92 0.64 Epicyon saevus Epicyon aelurodontoides 0.83 Protepicyon raki 0.14 Carpocyon limosus 0.43 Carpocyon webbi 0.02 0.98 Carpocyon robustus 0.21 0.69 Carpocyon compressus Paratomarctus temerarius Paratomarctus euthos 0.081 0.82 Tomarctus brevirostris 0.17 Tomarctus hippophaga 0.45 Protomarctus opatus 0.21 Tephrocyon rurestris 0.45 0.79 Microtomarctus conferta Metatomarctus canavus 1 Aelurodon taxoides 0.85 Aelurodon ferox 0.96 1 0.63 Aelurodon stirtoni Aelurodon mcgrewi Aelurodon asthenostylus 0.03 0.98 Euoplocyon brachygnathus 0.41 Euoplocyon spissidens 0.19 Psalidocyon marianae 0.99 Cynarctus crucidens 1 Cynarctus voorhiesi 0.49 Cynarctus saxatilis 0.71 0.21 Cynarctus marylandica 1 Cynarctus galushai 0.59 1 Paracynarctus sinclari Paracynarctus kelloggi Desmocyon matthewi Desmocyon thomsoni 1 Otarocyon cooki 0.21 0.99 Otarocyon macdonaldi 0.05 Oxetocyon cuspidatus 0.68 Cormocyon copei Cormocyon haydeni 1 Phlaocyon leucosteus 0.38 Phlaocyon marshlandensis Phlaocyon multicuspus 0.15 0.98 Phlaocyon achoros 0.99 Phlaocyon mariae 0.47 0.14 Phlaocyon yatkolai 0.63 Phlaocyon annectens Phlaocyon latidens 1 Cynarctoides emryi 0.2 1 Cynarctoides accridens 1 Cynarctoides gawanae 0.07 Cynarctoides luskensis 0.11 Phlaocyon minor 0.26 Cynarctoides lemur 0.23 Cynarctoides harlowi Cynarctoides roii Rhizocyon oreganensis 0.77 Enhydrocyon basilatus 0.74 Enhydrocyon stenocephalus 0.77 Enhydrocyon crassidens 0.81 Enhydrocyon pahinsintewakpa 0.74 Ectopocynus intermedius 0.87 Ectopocynus antiquus 0.81 1 Ectopocynus simplicidens 0.07 Caedocyon tedfordi 0.23 Philotrox condoni 0.32 Sunkahetanka geringensis 0.63 Cynodesmus martini 0.12 Cynodesmus thooides 0.54 Mesocyon brachyops 0.21 Mesocyon coryphaeus 0.68 Osbornodon fricki 1 Osbornodon brachypus 0.89 Osbornodon iamonensis 0.97 0.92 Osbornodon sesnoni 0.1 Osbornodon renjiei Mesocyon temnodon 0.37 0.96 Paraenhydrocyon wallovianus 0.92 Paraenhydrocyon robustus Paraenhydrocyon josephi 0.89 Hesperocyon coloradensis 0.44 Hesperocyon gregarius 0.37 Archaeocyon leptodus 0.04 Archaeocyon pavidus 0.25 Prohesperocyon wilsoni Archaeocyon falkenbachi outgroup

50 40 30 20 10 0 10 millions of years ago 36: mb3.2.5_mb9

0.98 Canis adustus 0.6 Canis mesomelas Cerdocyon texanus 0.44 Canis edwardii 0.1 Canis aureus 0.99 Canis variabilis 0.960.17 Canis latrans Canis mosbachensis 0.71 Canis palmidens 0.11 Canis antonii 0.220.96 Canis falconeri 1 Xenocyon texanus 1 Canis chihliensis 1 Canis dirus 1 Canis armbrusteri 0.260.31 Canis lupus Canis etruscus 1 0.52 Canis arnensis 0.441 Canis lepophagus 0.65 0.4 Canis thooides 0.99 0.64 Canis simensis Canis ferox Eucyon davisi Vulpes stenognathus Leptocyon matthewi 0.31 1 Urocyon cinereoargenteus 0.69 Urocyon minicephalus 1 Urocyon galushi 1 0.89 Urocyon citronus 1 Urocyon webbi 1 Metalopex merriami 1 Metalopex macconnelli 0.92 Leptocyon vafer 1 Leptocyon leidyi Leptocyon vulpinus 1 Leptocyon gregorii 1 Leptocyon douglassi 0.97 Leptocyon mollis Prohesperocyon wilsoni 0.26 Borophagus diversidens 1 Borophagus hilli 1 Borophagus dudleyi 0.96 Borophagus secundus 1 Borophagus parvus 1 0.91 Borophagus orc Borophagus pugnator 1 Borophagus littoralis 1 Epicyon haydeni 1 0.89 Epicyon saevus Epicyon aelurodontoides 1 Protepicyon raki 0.83 Carpocyon limosus 1 Carpocyon robustus 0.98 1 Carpocyon webbi Carpocyon compressus 0.43 1 Paratomarctus euthos Paratomarctus temerarius Tomarctus brevirostris 0.64 0.96 0.46 Tomarctus hippophaga 0.32 Tephrocyon rurestris Protomarctus opatus 0.59 Psalidocyon marianae 0.88 Microtomarctus conferta Metatomarctus canavus 1 Aelurodon taxoides 0.87 0.33 Aelurodon ferox 0.7 Aelurodon stirtoni 11 Aelurodon mcgrewi 0.72 Aelurodon asthenostylus 0.8 Euoplocyon brachygnathus Euoplocyon spissidens 0.88 1 Cynarctus crucidens 1 Cynarctus voorhiesi 0.38 Cynarctus saxatilis 0.59 Cynarctus marylandica 0.99 11 Cynarctus galushai 0.68 1 Paracynarctus sinclari Paracynarctus kelloggi Desmocyon matthewi 0.98 1 1 Lycaon pictus 1 Cuon javanicus 0.99 Desmocyon thomsoni Cormocyon copei Cormocyon haydeni 0.68 Phlaocyon mariae 0.38 Phlaocyon yatkolai 0.4 0.6 Phlaocyon multicuspus 0.99 Phlaocyon achoros 0.99 Phlaocyon leucosteus 0.94 0.38 Phlaocyon marshlandensis Phlaocyon annectens Phlaocyon latidens Cynarctoides emryi 1 0.27 1 1 Cynarctoides accridens 1 Cynarctoides gawanae 0.9 Cynarctoides luskensis 1 0.39 Phlaocyon minor 0.6 Cynarctoides harlowi Cynarctoides lemur 0.95 Cynarctoides roii Rhizocyon oreganensis 0.82 0.68 Archaeocyon falkenbachi 0.89 Archaeocyon pavidus Archaeocyon leptodus Hesperocyon gregarius 1 Paraenhydrocyon wallovianus 1 Paraenhydrocyon robustus 0.52 Paraenhydrocyon josephi 0.23 Mesocyon temnodon 0.75 0.56 Mesocyon coryphaeus Mesocyon brachyops 0.93 Cynodesmus martini Cynodesmus thooides 0.86 0.6 Enhydrocyon basilatus 0.73 0.55 Enhydrocyon stenocephalus 1 Enhydrocyon crassidens 0.43 Enhydrocyon pahinsintewakpa 0.99 0.36 Sunkahetanka geringensis Philotrox condoni 0.96 Ectopocynus simplicidens 0.4 1 Ectopocynus intermedius 1 Ectopocynus antiquus 0.45 Caedocyon tedfordi 0.89 Osbornodon renjiei 0.9 Osbornodon fricki 0.62 1 Osbornodon brachypus 0.96 Osbornodon iamonensis Osbornodon sesnoni Hesperocyon coloradensis 1 Otarocyon cooki 11 Otarocyon macdonaldi Oxetocyon cuspidatus outgroup

50 40 30 20 10 0 millions of years ago 37: mb3.2.5_mb10

0.97 Canis adustus 0.84 Canis mesomelas 0.55 Canis simensis Canis arnensis 1 Lycaon pictus 1 Cuon javanicus Xenocyon texanus 0.23 1 Canis dirus 0.92 0.091 Canis armbrusteri Canis lupus 0.410.96 Canis antonii Canis falconeri Canis chihliensis 0.48 Canis latrans 0.99 0.42 0.98 Canis aureus 0.81 Canis variabilis 0.7 0.61 Canis mosbachensis Canis edwardii 0.23 Canis palmidens 0.94 Canis etruscus 0.97 Canis lepophagus 0.99 0.72 Canis thooides Canis ferox 1 Eucyon davisi 0.93 Cerdocyon texanus Vulpes stenognathus Leptocyon matthewi 0.98 Urocyon cinereoargenteus 0.37 0.82 Urocyon minicephalus 1 Urocyon citronus 1 Urocyon galushi 0.88 0.96 Urocyon webbi 1 Metalopex merriami 1 Metalopex macconnelli 0.77 Leptocyon vafer Leptocyon leidyi 1 Leptocyon vulpinus 0.75 Leptocyon gregorii 1 Leptocyon douglassi Leptocyon mollis 0.49 Borophagus diversidens 1 Borophagus dudleyi 0.98 Borophagus hilli 0.96 Borophagus secundus 1 Borophagus parvus 1 0.7 Borophagus orc Borophagus pugnator 1 Borophagus littoralis 0.95 Epicyon haydeni 1 0.9 Epicyon saevus Epicyon aelurodontoides 0.99 Protepicyon raki 0.32 Carpocyon limosus 0.97 Carpocyon robustus 0.99 1 Carpocyon webbi Carpocyon compressus 0.95 Paratomarctus euthos 0.44 Paratomarctus temerarius 0.97 Tomarctus brevirostris 0.11 Tomarctus hippophaga 0.270.21 Protomarctus opatus Tephrocyon rurestris 0.54 0.51 Microtomarctus conferta Metatomarctus canavus Psalidocyon marianae 1 Aelurodon taxoides 0.9 0.17 0.59 Aelurodon ferox 1 0.53 Aelurodon stirtoni Aelurodon mcgrewi 0.54 Aelurodon asthenostylus 0.74 Euoplocyon brachygnathus 0.2 Euoplocyon spissidens 1 Cynarctus crucidens 1 Cynarctus voorhiesi 0.36 Cynarctus saxatilis 0.8 0.11 Cynarctus galushai 1 1 Paracynarctus sinclari 0.98 Paracynarctus kelloggi Cynarctus marylandica 0.87 Desmocyon matthewi 0.98 Desmocyon thomsoni Cormocyon copei Cormocyon haydeni 0.94 Phlaocyon mariae 0.28 0.82 Phlaocyon yatkolai 1 Phlaocyon leucosteus 0.88 0.83 Phlaocyon marshlandensis 1 1 Phlaocyon multicuspus Phlaocyon achoros 0.91 Phlaocyon annectens Phlaocyon latidens 1 Cynarctoides emryi 0.92 0.62 1 Cynarctoides accridens 0.99 Cynarctoides gawanae 0.11 Cynarctoides luskensis 1 0.88 Phlaocyon minor 0.56 Cynarctoides harlowi Cynarctoides lemur Cynarctoides roii Rhizocyon oreganensis 1 Otarocyon cooki 0.92 Otarocyon macdonaldi Oxetocyon cuspidatus 0.74 Enhydrocyon basilatus 0.69 Enhydrocyon stenocephalus 0.84 Enhydrocyon crassidens 1 0.97 Enhydrocyon pahinsintewakpa 0.55 Ectopocynus intermedius 0.57 0.95 Ectopocynus antiquus 0.64 Ectopocynus simplicidens Philotrox condoni 0.85 Sunkahetanka geringensis Caedocyon tedfordi 0.46 Mesocyon coryphaeus 0.42 0.24 Mesocyon brachyops 0.09 Cynodesmus martini 0.35 Mesocyon temnodon 1 Paraenhydrocyon wallovianus 0.46 1 Paraenhydrocyon robustus 0.97 Paraenhydrocyon josephi Cynodesmus thooides 0.7 Osbornodon fricki 1 Osbornodon brachypus 0.4 0.07 Osbornodon iamonensis 0.42 Osbornodon sesnoni Osbornodon renjiei Archaeocyon falkenbachi 0.29 0.39 0.9 Archaeocyon leptodus 0.19 Archaeocyon pavidus 0.17 Hesperocyon gregarius Hesperocyon coloradensis Prohesperocyon wilsoni outgroup

50 40 30 20 10 0 millions of years ago 36a: mb3.2.5_mb9a

0.97 Canis adustus 0.84 Canis mesomelas Canis simensis 1 Lycaon pictus 1 Cuon javanicus 0.4 Xenocyon texanus 0.42 0.84 Canis antonii 0.28 Canis falconeri 1 Canis dirus 1 Canis armbrusteri 0.3 Canis lupus Canis chihliensis 0.98 Canis latrans 0.85 0.54 0.29 Canis aureus 0.96 Canis variabilis 0.76 0.51 Canis mosbachensis Canis edwardii 0.98 0.21 Canis palmidens Canis etruscus Canis arnensis 0.95 0.94 Canis lepophagus 0.71 Canis thooides 1 Canis ferox 1 Eucyon davisi Cerdocyon texanus 0.98 Vulpes stenognathus 0.46 Leptocyon matthewi Leptocyon vafer 0.98 Urocyon cinereoargenteus 0.79 0.87 Urocyon minicephalus 1 Urocyon citronus 1 Urocyon galushi 1 0.97 Urocyon webbi 1 Metalopex merriami 0.78 Metalopex macconnelli 1 Leptocyon leidyi Leptocyon vulpinus 0.88 Leptocyon gregorii 1 Leptocyon douglassi 0.77 Leptocyon mollis Prohesperocyon wilsoni 0.21 Borophagus diversidens 1 Borophagus hilli 0.99 Borophagus dudleyi 0.96 Borophagus secundus 1 Borophagus parvus 1 0.72 Borophagus orc Borophagus pugnator 1 Borophagus littoralis 0.98 Epicyon haydeni 1 0.92 Epicyon saevus Epicyon aelurodontoides 1 Protepicyon raki 0.17 Carpocyon robustus 0.99 Carpocyon webbi 1 1 Carpocyon limosus Carpocyon compressus 0.97 Paratomarctus euthos 0.29 Paratomarctus temerarius 0.9 Tomarctus brevirostris 0.17 Tomarctus hippophaga 0.26 Tephrocyon rurestris 0.110.18 Microtomarctus conferta 0.61 Protomarctus opatus Psalidocyon marianae Metatomarctus canavus 0.91 1 Aelurodon taxoides 0.77 Aelurodon ferox 1 0.6 Aelurodon stirtoni Aelurodon mcgrewi 0.110.79 Aelurodon asthenostylus 0.431 Euoplocyon brachygnathus Euoplocyon spissidens Desmocyon matthewi 0.66 1 Cynarctus crucidens 1 Cynarctus voorhiesi 0.4 0.34 Cynarctus saxatilis 0.63 0.97 Cynarctus galushai 1 Cynarctus marylandica Paracynarctus sinclari 0.78 1 Paracynarctus kelloggi 0.99 Desmocyon thomsoni Cormocyon copei Cormocyon haydeni 0.95 Phlaocyon mariae 0.78 Phlaocyon yatkolai 1 Phlaocyon leucosteus 0.92 0.82 Phlaocyon marshlandensis 1 0.99 Phlaocyon multicuspus Phlaocyon achoros 0.93 Phlaocyon annectens Phlaocyon latidens 0.51 1 Cynarctoides emryi 0.94 1 Cynarctoides accridens 1 Cynarctoides gawanae 0.91 Cynarctoides luskensis 1 0.42 Cynarctoides harlowi 0.44 Cynarctoides lemur Phlaocyon minor 0.79 Cynarctoides roii Rhizocyon oreganensis 0.53 0.39 Archaeocyon falkenbachi 0.89 Archaeocyon leptodus 1 0.23 Archaeocyon pavidus Hesperocyon gregarius Hesperocyon coloradensis 0.73 Enhydrocyon basilatus 0.6 Enhydrocyon stenocephalus 0.88 Enhydrocyon crassidens 0.94 Enhydrocyon pahinsintewakpa 0.41 Ectopocynus intermedius 0.62 0.94 Ectopocynus antiquus Ectopocynus simplicidens 0.71 0.74 Philotrox condoni 0.72 Sunkahetanka geringensis Caedocyon tedfordi 0.09 Cynodesmus martini 0.67 0.59 Mesocyon brachyops Mesocyon coryphaeus 0.34 0.23 Mesocyon temnodon 0.8 Cynodesmus thooides 1 Paraenhydrocyon wallovianus 0.97 1 Paraenhydrocyon robustus Paraenhydrocyon josephi 0.65 Osbornodon fricki 1 Osbornodon brachypus 0.74 Osbornodon iamonensis 0.73 Osbornodon sesnoni Osbornodon renjiei 1 Otarocyon cooki 0.9 Otarocyon macdonaldi Oxetocyon cuspidatus outgroup

50 40 30 20 10 0 millions of years ago 36b: mb3.2.5_mb9b

0.99 Canis adustus 0.86 Canis mesomelas Canis simensis 1 Lycaon pictus 1 Cuon javanicus 0.36 Xenocyon texanus 1 Canis antonii 0.51 Canis falconeri 0.79 1 Canis dirus 1 Canis armbrusteri 0.43 Canis lupus Canis chihliensis 0.99 0.57 Canis latrans 0.32 Canis aureus 0.05 Canis variabilis 0.95 1 0.16 Canis mosbachensis 0.9 Canis edwardii 0.4 Canis palmidens Canis etruscus 0.92 Canis arnensis 0.95 Canis lepophagus 1 0.82 Canis thooides Canis ferox 1 Eucyon davisi 0.98 Cerdocyon texanus Vulpes stenognathus 0.58 Leptocyon matthewi 0.28 Leptocyon vafer Leptocyon leidyi 0.99 Urocyon cinereoargenteus 1 0.85 Urocyon minicephalus 1 Urocyon citronus 1 Urocyon galushi 0.82 0.94 Urocyon webbi 1 Metalopex merriami 1 Metalopex macconnelli 0.8 Leptocyon vulpinus Leptocyon gregorii 1 Leptocyon douglassi 0.74 Leptocyon mollis Prohesperocyon wilsoni 0.26 Borophagus dudleyi 1 Borophagus hilli 0.98 Borophagus diversidens 0.95 Borophagus secundus 1 Borophagus parvus 1 0.73 Borophagus orc Borophagus pugnator 1 Borophagus littoralis 0.99 Epicyon haydeni 1 0.89 Epicyon saevus Epicyon aelurodontoides 1 Protepicyon raki 0.38 Carpocyon limosus 0.99 Carpocyon robustus 0.98 1 Carpocyon webbi Carpocyon compressus 0.99 Paratomarctus euthos 0.54 Paratomarctus temerarius 0.99 Tomarctus brevirostris 0.47 Tomarctus hippophaga 0.310.31 Tephrocyon rurestris Protomarctus opatus 0.85 0.52 Microtomarctus conferta Metatomarctus canavus Psalidocyon marianae 0.93 1 Aelurodon taxoides 0.87 Aelurodon ferox 1 0.73 Aelurodon stirtoni Aelurodon mcgrewi 0.96 Aelurodon asthenostylus 0.5 Euoplocyon brachygnathus 0.9 Euoplocyon spissidens 1 Cynarctus crucidens 1 Cynarctus voorhiesi 0.62 Cynarctus saxatilis 0.62 0.34 Cynarctus marylandica 0.03 1 Cynarctus galushai Paracynarctus sinclari 0.29 1 Paracynarctus kelloggi 0.96 0.57 Desmocyon matthewi Desmocyon thomsoni Cormocyon haydeni Cormocyon copei 0.95 Phlaocyon mariae 0.77 Phlaocyon yatkolai 0.94 1 Phlaocyon leucosteus 0.83 Phlaocyon marshlandensis 1 1 Phlaocyon multicuspus Phlaocyon achoros 0.96 Phlaocyon annectens Phlaocyon latidens Cynarctoides emryi 0.92 1 0.53 1 Cynarctoides accridens 1 Cynarctoides gawanae 0.19 Cynarctoides luskensis 1 0.95 0.44 Cynarctoides harlowi Cynarctoides lemur Phlaocyon minor 0.74 Cynarctoides roii Rhizocyon oreganensis 0.63 0.34 Archaeocyon falkenbachi 0.95 Archaeocyon pavidus 1 0.34 Archaeocyon leptodus Hesperocyon gregarius Hesperocyon coloradensis 0.81 Enhydrocyon basilatus 0.67 Enhydrocyon stenocephalus 0.97 Enhydrocyon crassidens 0.98 Enhydrocyon pahinsintewakpa 0.37 Ectopocynus simplicidens 0.63 0.95 Ectopocynus intermedius Ectopocynus antiquus 0.76 0.72 Philotrox condoni 0.74 Sunkahetanka geringensis Caedocyon tedfordi 0.36 Mesocyon coryphaeus 0.56 0.48 Mesocyon brachyops 0.89 Mesocyon temnodon 0.57 Cynodesmus martini 0.71 Cynodesmus thooides 1 Paraenhydrocyon wallovianus 0.96 0.98 Paraenhydrocyon robustus Paraenhydrocyon josephi 0.62 Osbornodon fricki 1 Osbornodon brachypus 0.56 Osbornodon iamonensis 0.64 Osbornodon sesnoni Osbornodon renjiei 1 Otarocyon cooki 0.89 Otarocyon macdonaldi Oxetocyon cuspidatus outgroup

50 40 30 20 10 0 millions of years ago 36c: mb3.2.5_mb9c

0.97 Canis adustus 0.87 Canis mesomelas Canis simensis 1 Canis dirus 1 Canis armbrusteri 0.29 Canis lupus 0.11 Canis chihliensis 1 Lycaon pictus 0.281 Cuon javanicus 0.91 Xenocyon texanus 0.78 Canis antonii Canis falconeri 0.38 0.47 Canis latrans 0.25 Canis aureus 0.93 Canis variabilis 0.97 0.97 0.74 0.52 Canis mosbachensis Canis edwardii 0.17 Canis palmidens Canis etruscus 0.95 Canis arnensis 0.96 Canis lepophagus 1 0.63 Canis thooides Canis ferox 1 Eucyon davisi 0.96 Cerdocyon texanus Vulpes stenognathus 0.44 Leptocyon matthewi Leptocyon vafer 1 Urocyon cinereoargenteus 0.79 0.9 Urocyon minicephalus 1 Urocyon citronus 1 Urocyon galushi 1 0.96 Urocyon webbi 1 Metalopex merriami 0.81 Metalopex macconnelli 1 Leptocyon leidyi Leptocyon vulpinus 0.88 Leptocyon gregorii 1 Leptocyon douglassi 0.75 Leptocyon mollis Prohesperocyon wilsoni 0.22 Borophagus dudleyi 1 Borophagus hilli 0.99 Borophagus diversidens 0.97 Borophagus secundus 1 Borophagus parvus 1 0.71 Borophagus orc Borophagus pugnator 1 Borophagus littoralis 0.97 Epicyon haydeni 1 0.91 Epicyon saevus Epicyon aelurodontoides 1 Protepicyon raki 0.47 Carpocyon limosus 0.99 Carpocyon robustus 0.99 1 Carpocyon webbi Carpocyon compressus 0.21 0.96 Paratomarctus euthos Paratomarctus temerarius 0.43 0.99 Tomarctus brevirostris 0.38 Tomarctus hippophaga 0.23 Tephrocyon rurestris Protomarctus opatus 0.77 0.44 Microtomarctus conferta Metatomarctus canavus Psalidocyon marianae 1 Aelurodon taxoides 0.89 0.27 Aelurodon ferox 0.72 Aelurodon stirtoni 1 Aelurodon mcgrewi 0.55 Aelurodon asthenostylus 0.98 Euoplocyon brachygnathus Euoplocyon spissidens 0.54 1 Cynarctus crucidens 1 Cynarctus voorhiesi 0.63 Cynarctus saxatilis 0.23 Cynarctus marylandica 0.95 1 Cynarctus galushai 0.36 1 Paracynarctus sinclari 0.98 Paracynarctus kelloggi Desmocyon matthewi 0.43 Desmocyon thomsoni 0.26 Cormocyon copei Cormocyon haydeni 0.94 Phlaocyon mariae 0.74 Phlaocyon yatkolai 0.92 1 Phlaocyon leucosteus 0.77 Phlaocyon marshlandensis 0.99 1 Phlaocyon multicuspus Phlaocyon achoros 0.93 Phlaocyon annectens Phlaocyon latidens Cynarctoides emryi 0.92 1 0.6 1 Cynarctoides accridens 1 Cynarctoides gawanae 0.24 Cynarctoides luskensis 1 0.91 0.4 Cynarctoides harlowi Cynarctoides lemur Phlaocyon minor 0.8 Cynarctoides roii Rhizocyon oreganensis 0.43 Archaeocyon falkenbachi 0.89 Archaeocyon pavidus Archaeocyon leptodus 0.71 Enhydrocyon basilatus 0.57 1 Enhydrocyon stenocephalus 0.9 Enhydrocyon crassidens 0.93 Enhydrocyon pahinsintewakpa 0.41 Ectopocynus intermedius 0.94 0.03 0.57 Ectopocynus antiquus 0.67 Ectopocynus simplicidens Philotrox condoni 0.71 Sunkahetanka geringensis Caedocyon tedfordi 1 Paraenhydrocyon wallovianus 0.41 0.97 Paraenhydrocyon robustus 0.04 Paraenhydrocyon josephi Cynodesmus thooides 0.19 0.5 0.36 Mesocyon coryphaeus 0.34 Mesocyon brachyops 0.96 0.51 Mesocyon temnodon Cynodesmus martini 0.66 Osbornodon fricki 0.7 1 Osbornodon brachypus 0.08 Osbornodon iamonensis 0.42 Osbornodon renjiei Osbornodon sesnoni Hesperocyon gregarius Hesperocyon coloradensis 1 Otarocyon cooki 0.88 Otarocyon macdonaldi Oxetocyon cuspidatus outgroup

50 40 30 20 10 0 millions of years ago 36x1: mb3.2.5_run1_v1

0.93 Canis adustus 0.47 Canis mesomelas 0.38 Canis simensis Canis arnensis 0.33 Canis latrans 0.28 Canis edwardii 0.97 Canis mosbachensis 0.930.29 Canis variabilis 0.44 Canis aureus Canis palmidens 0.67 1 Lycaon pictus 1 Cuon javanicus 0.93 Xenocyon texanus 0.95 Canis antonii 0.590.96 Canis falconeri 1 Canis dirus 1 Canis armbrusteri 0.64 Canis lupus 0.79 0.46 Canis chihliensis Canis etruscus 0.82 0.51 Canis lepophagus Canis thooides 1 Canis ferox 1 Eucyon davisi 0.97 Cerdocyon texanus Vulpes stenognathus Leptocyon matthewi 1 Urocyon cinereoargenteus 0.32 0.65 Urocyon minicephalus 1 Urocyon galushi 1 Urocyon citronus 0.96 1 Urocyon webbi 1 Metalopex merriami 1 Metalopex macconnelli 0.9 Leptocyon vafer 1 Leptocyon leidyi Leptocyon vulpinus 1 Leptocyon gregorii 1 Leptocyon douglassi 0.98 Leptocyon mollis 0.09 Prohesperocyon wilsoni 1 Otarocyon cooki 0.98 Otarocyon macdonaldi Oxetocyon cuspidatus 0.65 Borophagus diversidens 1 Borophagus dudleyi 1 Borophagus hilli 0.97 Borophagus secundus 1 Borophagus parvus 1 0.86 Borophagus orc Borophagus pugnator 1 Borophagus littoralis 1 Epicyon haydeni 1 0.94 Epicyon saevus Epicyon aelurodontoides 1 Protepicyon raki 0.81 Carpocyon limosus 1 Carpocyon robustus 0.99 1 Carpocyon webbi Carpocyon compressus 0.2 1 Paratomarctus euthos 0.35 Paratomarctus temerarius Tephrocyon rurestris 0.52 0.92 Tomarctus brevirostris Tomarctus hippophaga 0.5 Protomarctus opatus 0.84 Microtomarctus conferta 0.13 Metatomarctus canavus Psalidocyon marianae 0.84 1 Aelurodon taxoides 0.68 Aelurodon ferox 1 0.46 Aelurodon stirtoni Aelurodon mcgrewi 0.67 Aelurodon asthenostylus 0.36 Euoplocyon brachygnathus 0.81 Euoplocyon spissidens 1 Cynarctus crucidens 1 Cynarctus voorhiesi 1 0.13 Cynarctus saxatilis 0.98 1 Paracynarctus sinclari 1 0.05 Paracynarctus kelloggi 0.62 Cynarctus galushai 0.98 Cynarctus marylandica Desmocyon matthewi 0.98 Desmocyon thomsoni Cormocyon copei Cormocyon haydeni 0.65 Phlaocyon mariae 0.31 Phlaocyon yatkolai 1 Phlaocyon leucosteus 0.59 0.28 Phlaocyon marshlandensis 0.99 Phlaocyon annectens 0.97 0.4 Phlaocyon multicuspus Phlaocyon achoros Phlaocyon latidens 0.25 0.99 Cynarctoides emryi 1 0.99 Cynarctoides accridens 0.99 Cynarctoides gawanae 0.93 Cynarctoides luskensis 1 0.42 Phlaocyon minor 0.6 Cynarctoides harlowi Cynarctoides lemur 0.95 Cynarctoides roii Rhizocyon oreganensis 0.81 0.49 Archaeocyon falkenbachi 0.87 Archaeocyon pavidus Archaeocyon leptodus Hesperocyon gregarius 0.86 Osbornodon fricki 1 Osbornodon brachypus 0.32 Osbornodon iamonensis 0.23 Mesocyon coryphaeus Mesocyon brachyops 0.15 0.98 Paraenhydrocyon wallovianus 0.98 Paraenhydrocyon robustus 0.51 0.43 Paraenhydrocyon josephi 0.85 0.57 Mesocyon temnodon Cynodesmus martini Cynodesmus thooides 0.45 0.58 Enhydrocyon basilatus 0.48 Enhydrocyon stenocephalus 0.96 Enhydrocyon crassidens 0.32 0.4 Enhydrocyon pahinsintewakpa 0.88 Sunkahetanka geringensis Philotrox condoni 0.95 Osbornodon renjiei 0.86 Ectopocynus simplicidens 0.97 Ectopocynus intermedius 0.61 0.89 Ectopocynus antiquus 0.33 Caedocyon tedfordi Osbornodon sesnoni Hesperocyon coloradensis outgroup

50 40 30 20 10 0 millions of years ago 36x2: mb3.2.5_run1_v2

0.92 Canis adustus 0.48 Canis mesomelas 0.4 Canis simensis Canis arnensis 0.48 Canis edwardii 0.38 Canis aureus 0.97 Canis mosbachensis 0.920.38 Canis latrans 0.52 Canis variabilis Canis palmidens 0.66 1 Lycaon pictus 1 Cuon javanicus 0.94 Xenocyon texanus 0.95 Canis antonii 0.590.96 Canis falconeri 1 Canis dirus 1 Canis armbrusteri 0.61 Canis lupus 0.76 0.44 Canis chihliensis Canis etruscus 0.78 0.66 Canis lepophagus Canis thooides 1 Canis ferox 1 Eucyon davisi Cerdocyon texanus Vulpes stenognathus 1 Urocyon cinereoargenteus 0.03 0.57 Urocyon minicephalus 1 Urocyon galushi 1 Urocyon citronus 0.33 1 Urocyon webbi 1 Metalopex merriami 1 Metalopex macconnelli Leptocyon matthewi 0.89 0.01 Leptocyon vafer 1 Leptocyon leidyi 1 Leptocyon vulpinus Leptocyon gregorii 1 Leptocyon douglassi 0.97 Leptocyon mollis Prohesperocyon wilsoni 0.67 Borophagus diversidens 1 Borophagus dudleyi 1 Borophagus hilli 0.97 Borophagus secundus 1 Borophagus parvus 1 0.88 Borophagus orc Borophagus pugnator 1 Borophagus littoralis 1 Epicyon haydeni 1 0.92 Epicyon saevus Epicyon aelurodontoides 1 Protepicyon raki 0.78 Carpocyon limosus 1 Carpocyon robustus 0.99 1 Carpocyon webbi Carpocyon compressus 0.38 0.99 Paratomarctus euthos Paratomarctus temerarius 0.53 0.94 Tomarctus brevirostris 0.45 Tomarctus hippophaga 0.24 Tephrocyon rurestris Protomarctus opatus 0.58 0.84 Microtomarctus conferta Metatomarctus canavus Psalidocyon marianae 1 Aelurodon taxoides 0.85 0.64 Aelurodon ferox 1 0.49 Aelurodon stirtoni Aelurodon mcgrewi 0.68 Aelurodon asthenostylus 0.76 Euoplocyon brachygnathus Euoplocyon spissidens 0.81 1 Cynarctus crucidens 1 Cynarctus voorhiesi 0.39 Cynarctus saxatilis 0.38 0.57 Cynarctus marylandica 0.98 1 Cynarctus galushai 0.61 1 Paracynarctus sinclari 0.98 Paracynarctus kelloggi Desmocyon matthewi 0.97 Desmocyon thomsoni Cormocyon copei Cormocyon haydeni 0.7 Phlaocyon mariae 0.5 0.3 Phlaocyon yatkolai 0.27 1 Phlaocyon leucosteus Phlaocyon marshlandensis 0.99 Phlaocyon annectens 0.97 0.38 Phlaocyon multicuspus 0.67 Phlaocyon achoros Phlaocyon latidens 0.98 Cynarctoides emryi 0.98 Cynarctoides accridens 0.98 1 Cynarctoides gawanae 0.92 Cynarctoides luskensis 0.44 Phlaocyon minor 1 0.62 Cynarctoides lemur Cynarctoides harlowi 0.94 Cynarctoides roii Rhizocyon oreganensis 0.46 Archaeocyon falkenbachi 0.8 0.88 Archaeocyon pavidus 1 Archaeocyon leptodus Hesperocyon gregarius 0.88 Osbornodon fricki 1 Osbornodon brachypus 0.28 Osbornodon iamonensis 0.16 Mesocyon temnodon 0.2 0.28 Mesocyon coryphaeus Mesocyon brachyops 0.69 Cynodesmus martini 0.99 Paraenhydrocyon wallovianus 0.76 0.87 0.99 Paraenhydrocyon robustus Paraenhydrocyon josephi Cynodesmus thooides 0.59 0.58 Enhydrocyon basilatus 0.47 Enhydrocyon stenocephalus 0.96 Enhydrocyon crassidens 0.44 0.38 Enhydrocyon pahinsintewakpa 0.88 Sunkahetanka geringensis Philotrox condoni 0.95 Osbornodon renjiei 0.86 Ectopocynus simplicidens 0.98 Ectopocynus intermedius 0.64 0.88 Ectopocynus antiquus 0.44 Caedocyon tedfordi Osbornodon sesnoni Hesperocyon coloradensis 1 Otarocyon cooki 0.98 Otarocyon macdonaldi Oxetocyon cuspidatus outgroup

50 40 30 20 10 0 millions of years ago 36x3: mb3.2.5_run1_v3

0.92 Canis adustus 0.47 Canis mesomelas 0.39 Canis simensis Canis arnensis 0.35 Canis latrans 0.29 Canis edwardii 0.95 Canis mosbachensis 0.90.31 Canis variabilis 0.48 Canis aureus Canis palmidens 0.67 1 Lycaon pictus 1 Cuon javanicus 0.93 Xenocyon texanus 0.96 Canis antonii 0.60.98 Canis falconeri 1 Canis dirus 1 Canis armbrusteri 0.54 Canis lupus 0.81 0.41 Canis chihliensis Canis etruscus 0.82 0.58 Canis lepophagus Canis thooides 1 Canis ferox 1 Eucyon davisi 0.97 Cerdocyon texanus Vulpes stenognathus Leptocyon matthewi 1 Urocyon cinereoargenteus 0.49 Urocyon minicephalus 0.95 1 Urocyon galushi 1 Urocyon citronus 1 Urocyon webbi 1 1 Metalopex merriami 0.46 Metalopex macconnelli 0.92 Leptocyon vafer 1 Leptocyon leidyi 1 Leptocyon vulpinus Leptocyon gregorii 1 Leptocyon douglassi 0.97 Leptocyon mollis Prohesperocyon wilsoni 0.69 Borophagus diversidens 1 Borophagus dudleyi 1 Borophagus hilli 0.96 Borophagus secundus 1 Borophagus parvus 1 0.86 Borophagus orc Borophagus pugnator 1 Borophagus littoralis 1 Epicyon haydeni 1 0.94 Epicyon saevus Epicyon aelurodontoides 1 Protepicyon raki 0.79 Carpocyon limosus 1 Carpocyon robustus 0.99 1 Carpocyon webbi Carpocyon compressus 0.2 1 Paratomarctus euthos 0.35 Paratomarctus temerarius Tephrocyon rurestris 0.53 0.93 Tomarctus brevirostris Tomarctus hippophaga 0.54 Protomarctus opatus 0.84 Microtomarctus conferta 0.15 Metatomarctus canavus Psalidocyon marianae 0.87 0.45 Aelurodon stirtoni 0.1 Aelurodon mcgrewi 1 Aelurodon asthenostylus 0.65 1 Aelurodon taxoides 0.7 Aelurodon ferox Euoplocyon brachygnathus 0.84 Euoplocyon spissidens 1 Cynarctus crucidens 1 Cynarctus voorhiesi 0.42 Cynarctus saxatilis 0.36 0.98 1 Cynarctus galushai 1 Paracynarctus sinclari 0.63 0.19 Paracynarctus kelloggi 0.98 Cynarctus marylandica Desmocyon matthewi 0.97 Desmocyon thomsoni Cormocyon copei Cormocyon haydeni 0.71 Phlaocyon mariae 0.38 Phlaocyon yatkolai 0.99 Phlaocyon leucosteus 0.68 0.37 Phlaocyon marshlandensis 0.99 Phlaocyon annectens 0.97 0.48 Phlaocyon multicuspus Phlaocyon achoros Phlaocyon latidens 0.32 0.99 Cynarctoides emryi 1 0.99 Cynarctoides accridens 0.99 Cynarctoides gawanae 0.93 Cynarctoides luskensis 1 0.44 Phlaocyon minor 0.59 Cynarctoides harlowi Cynarctoides lemur 0.95 Cynarctoides roii Rhizocyon oreganensis 0.82 0.5 Archaeocyon falkenbachi 0.88 Archaeocyon pavidus 1 Archaeocyon leptodus Hesperocyon gregarius 0.89 Osbornodon fricki 1 Osbornodon brachypus 0.35 Osbornodon iamonensis 0.31 Mesocyon coryphaeus 0.18 Mesocyon brachyops 0.18 Mesocyon temnodon 1 Paraenhydrocyon wallovianus 0.73 1 Paraenhydrocyon robustus 0.85 0.82 Paraenhydrocyon josephi Cynodesmus martini Cynodesmus thooides 0.61 0.6 Enhydrocyon basilatus 0.94 Enhydrocyon stenocephalus 0.46 0.3 Enhydrocyon crassidens 0.44 Enhydrocyon pahinsintewakpa 0.84 Sunkahetanka geringensis Philotrox condoni 0.95 Osbornodon renjiei 0.83 Ectopocynus simplicidens 0.96 Ectopocynus intermedius 0.64 0.84 Ectopocynus antiquus 0.45 Caedocyon tedfordi Osbornodon sesnoni Hesperocyon coloradensis 1 Otarocyon cooki 0.99 Otarocyon macdonaldi Oxetocyon cuspidatus outgroup

50 40 30 20 10 0 millions of years ago 36x4: mb3.2.5_run1_v4

0.92 Canis adustus 0.35 Canis mesomelas 0.33 Canis simensis Canis arnensis 0.51 Canis edwardii 0.4 Canis aureus 0.97 Canis mosbachensis 0.940.39 Canis latrans Canis variabilis 0.47 Canis palmidens 0.64 1 Lycaon pictus 0.95 Cuon javanicus 0.86 Xenocyon texanus 0.89 0.19 Canis antonii 0.51 Canis falconeri 1 Canis dirus 0.93 1 Canis armbrusteri 0.58 Canis lupus 0.72 Canis chihliensis Canis etruscus 0.74 0.62 Canis lepophagus Canis thooides 0.95 Canis ferox 0.95 Eucyon davisi 0.93 Cerdocyon texanus Vulpes stenognathus Leptocyon matthewi 1 Urocyon cinereoargenteus 0.3 0.61 Urocyon minicephalus 1 Urocyon galushi 1 Urocyon citronus 0.91 1 Urocyon webbi 1 Metalopex merriami 0.95 Metalopex macconnelli 0.87 Leptocyon vafer 0.95 Leptocyon leidyi Leptocyon vulpinus 0.95 Leptocyon gregorii 0.95 Leptocyon douglassi 0.92 Leptocyon mollis Prohesperocyon wilsoni 0.66 Borophagus diversidens 1 Borophagus dudleyi 1 Borophagus hilli 0.96 Borophagus secundus 1 Borophagus parvus 1 0.87 Borophagus orc Borophagus pugnator 1 Borophagus littoralis 1 Epicyon haydeni 1 0.94 Epicyon saevus Epicyon aelurodontoides 1 Protepicyon raki 0.18 Carpocyon limosus 1 Carpocyon webbi 0.99 1 Carpocyon robustus Carpocyon compressus 0.99 Paratomarctus euthos 0.53 Paratomarctus temerarius 0.92 Tomarctus brevirostris 0.44 0.24 Tomarctus hippophaga 0.11 Tephrocyon rurestris Protomarctus opatus 0.53 0.86 Microtomarctus conferta Metatomarctus canavus Psalidocyon marianae 1 Aelurodon taxoides 0.86 0.7 Aelurodon ferox 1 0.47 Aelurodon stirtoni Aelurodon mcgrewi 0.64 0.07 Aelurodon asthenostylus 0.7 Euoplocyon brachygnathus Euoplocyon spissidens Desmocyon matthewi 0.8 1 Cynarctus crucidens 1 Cynarctus voorhiesi 0.36 Cynarctus saxatilis 0.58 0.93 Cynarctus marylandica 1 Cynarctus galushai 0.93 1 Paracynarctus sinclari 1 Paracynarctus kelloggi 0.92 Desmocyon thomsoni Cormocyon copei Cormocyon haydeni 0.72 Phlaocyon mariae 0.28 Phlaocyon yatkolai 0.27 Phlaocyon multicuspus 0.66 1 Phlaocyon achoros 1 Phlaocyon leucosteus 0.98 0.26 Phlaocyon marshlandensis Phlaocyon annectens Phlaocyon latidens 0.3 0.97 Cynarctoides emryi 0.95 0.98 Cynarctoides accridens 0.98 Cynarctoides gawanae 0.92 Cynarctoides luskensis 0.95 0.5 Phlaocyon minor 0.6 Cynarctoides lemur Cynarctoides harlowi 0.91 Cynarctoides roii Rhizocyon oreganensis 0.49 Archaeocyon falkenbachi 0.89 Archaeocyon pavidus Archaeocyon leptodus 0.88 Osbornodon fricki 1 Osbornodon brachypus 0.15 Osbornodon iamonensis 0.34 Mesocyon brachyops 0.19 Mesocyon coryphaeus 0.21 Cynodesmus martini 0.67 Mesocyon temnodon 0.98 Paraenhydrocyon wallovianus 0.79 0.98 0.81 Paraenhydrocyon robustus Paraenhydrocyon josephi Cynodesmus thooides 0.68 0.37 Enhydrocyon crassidens 0.1 Enhydrocyon pahinsintewakpa 0.98 Enhydrocyon stenocephalus 0.49 0.49 Enhydrocyon basilatus 0.9 Philotrox condoni Sunkahetanka geringensis 0.46 0.95 Osbornodon renjiei 0.86 Ectopocynus simplicidens 0.99 Ectopocynus intermedius 0.63 0.91 Ectopocynus antiquus 0.51 Caedocyon tedfordi 0.12 Osbornodon sesnoni Hesperocyon coloradensis Hesperocyon gregarius 1 Otarocyon cooki 0.98 Otarocyon macdonaldi Oxetocyon cuspidatus outgroup

50 40 30 20 10 0 millions of years ago 36x5: mb3.2.5_defaults_v1

0.93 Canis adustus 0.41 Canis mesomelas 0.34 Canis simensis Canis arnensis 0.49 Canis edwardii 0.36 Canis aureus 0.98 Canis mosbachensis 0.930.36 Canis latrans 0.44 Canis variabilis Canis palmidens 0.68 1 Lycaon pictus 0.99 Cuon javanicus 0.92 Xenocyon texanus 0.95 Canis antonii 0.530.95 Canis falconeri 1 Canis dirus 1 Canis armbrusteri 0.59 Canis lupus 0.77 0.46 Canis chihliensis Canis etruscus 0.79 0.58 Canis lepophagus Canis thooides 0.99 Canis ferox 0.99 Eucyon davisi 0.97 Cerdocyon texanus Vulpes stenognathus Leptocyon matthewi 1 Urocyon cinereoargenteus 0.49 Urocyon minicephalus 0.94 1 Urocyon citronus 1 Urocyon galushi 1 Urocyon webbi 0.99 1 Metalopex merriami 0.46 Metalopex macconnelli 0.9 Leptocyon vafer 0.99 Leptocyon leidyi 0.99 Leptocyon vulpinus Leptocyon gregorii 0.99 Leptocyon douglassi 0.96 Leptocyon mollis Prohesperocyon wilsoni 0.67 Borophagus diversidens 1 Borophagus dudleyi 1 Borophagus hilli 0.96 Borophagus secundus 1 Borophagus parvus 1 0.86 Borophagus orc 0.03 Borophagus pugnator Borophagus littoralis 1 Epicyon aelurodontoides 1 1 Epicyon haydeni Epicyon saevus Protepicyon raki 1 0.78 Carpocyon limosus 1 Carpocyon robustus 1 1 Carpocyon webbi Carpocyon compressus 0.38 1 Paratomarctus euthos Paratomarctus temerarius Tomarctus brevirostris 0.54 0.93 0.42 Tomarctus hippophaga 0.25 Tephrocyon rurestris Protomarctus opatus 0.55 0.85 Microtomarctus conferta Metatomarctus canavus Psalidocyon marianae 1 Aelurodon taxoides 0.85 0.66 Aelurodon ferox 1 0.45 Aelurodon stirtoni Aelurodon mcgrewi 0.65 Aelurodon asthenostylus 0.74 Euoplocyon brachygnathus 0.82 Euoplocyon spissidens 1 Cynarctus crucidens 1 Cynarctus voorhiesi 0.57 Cynarctus saxatilis 0.13 Cynarctus marylandica 0.97 1 Cynarctus galushai 0.64 1 Paracynarctus sinclari 0.98 Paracynarctus kelloggi 1 Desmocyon matthewi 0.98 Desmocyon thomsoni Cormocyon copei Cormocyon haydeni 0.71 Phlaocyon mariae 0.52 0.14 Phlaocyon yatkolai 0.3 Phlaocyon annectens 1 Phlaocyon leucosteus 0.99 Phlaocyon marshlandensis 0.96 0.42 Phlaocyon multicuspus 0.61 Phlaocyon achoros Phlaocyon latidens 1 Cynarctoides emryi 1 Cynarctoides accridens 1 0.99 Cynarctoides gawanae 0.92 Cynarctoides luskensis 0.47 Phlaocyon minor 0.99 0.6 Cynarctoides lemur Cynarctoides harlowi 0.04 Cynarctoides roii Rhizocyon oreganensis 0.94 0.5 Archaeocyon falkenbachi 0.79 Archaeocyon leptodus Archaeocyon pavidus Hesperocyon gregarius 0.87 Osbornodon fricki 1 Osbornodon brachypus 0.26 Osbornodon iamonensis 0.22 Mesocyon coryphaeus 0.11 Mesocyon brachyops Cynodesmus martini 0.47 0.99 Paraenhydrocyon wallovianus 0.99 Paraenhydrocyon robustus 0.54 0.38 Paraenhydrocyon josephi 0.83 Mesocyon temnodon Cynodesmus thooides 0.46 0.59 Enhydrocyon basilatus 0.95 Enhydrocyon stenocephalus 0.46 0.33 Enhydrocyon crassidens 0.32 Enhydrocyon pahinsintewakpa 0.89 Philotrox condoni Sunkahetanka geringensis 0.46 0.95 Osbornodon renjiei 0.88 Ectopocynus simplicidens 0.96 Ectopocynus intermedius 0.63 0.9 Ectopocynus antiquus 0.33 Caedocyon tedfordi Osbornodon sesnoni Hesperocyon coloradensis 1 Otarocyon cooki 0.98 Otarocyon macdonaldi Oxetocyon cuspidatus outgroup

50 40 30 20 10 0 millions of years ago 36x6: mb3.2.5_defaults_v2

0.92 Canis adustus 0.45 Canis mesomelas 0.38 Canis simensis Canis arnensis 0.47 Canis edwardii 0.39 Canis aureus 0.99 Canis mosbachensis 0.940.38 Canis latrans 0.44 Canis variabilis Canis palmidens 0.68 1 Lycaon pictus 1 Cuon javanicus 0.93 Xenocyon texanus 0.94 Canis antonii 0.580.96 Canis falconeri 1 Canis dirus 1 Canis armbrusteri 0.66 Canis lupus 0.8 0.45 Canis chihliensis Canis etruscus 0.82 0.52 Canis lepophagus Canis thooides 1 Canis ferox 1 Eucyon davisi 0.96 Cerdocyon texanus Vulpes stenognathus Leptocyon matthewi 1 Urocyon cinereoargenteus 0.33 0.45 Urocyon minicephalus 1 Urocyon citronus 1 Urocyon galushi 0.95 1 Urocyon webbi 1 Metalopex merriami 1 Metalopex macconnelli 0.91 Leptocyon vafer 1 Leptocyon leidyi Leptocyon vulpinus 1 Leptocyon gregorii 1 Leptocyon douglassi 0.96 Leptocyon mollis Prohesperocyon wilsoni 0.65 Borophagus diversidens 1 Borophagus dudleyi 1 Borophagus hilli 0.97 Borophagus secundus 1 Borophagus parvus 1 0.87 Borophagus orc Borophagus pugnator 1 Borophagus littoralis 1 Epicyon haydeni 1 0.93 Epicyon saevus Epicyon aelurodontoides 1 Protepicyon raki 0.75 Carpocyon limosus 1 Carpocyon robustus 0.99 1 Carpocyon webbi Carpocyon compressus 0.4 1 Paratomarctus euthos Paratomarctus temerarius 0.6 0.95 Tomarctus brevirostris 0.46 Tomarctus hippophaga 0.27 Tephrocyon rurestris Protomarctus opatus 0.87 Microtomarctus conferta Metatomarctus canavus 1 Aelurodon taxoides 0.86 0.32 Aelurodon ferox 0.66 Aelurodon stirtoni 1 Aelurodon mcgrewi 0.67 Aelurodon asthenostylus 0.76 Euoplocyon brachygnathus 0.03 Euoplocyon spissidens 0.81 Psalidocyon marianae 1 Cynarctus crucidens 1 Cynarctus voorhiesi 0.38 Cynarctus saxatilis 0.59 0.98 Cynarctus marylandica 1 Cynarctus galushai 0.66 1 Paracynarctus sinclari 0.98 Paracynarctus kelloggi 1 Desmocyon matthewi 0.98 Desmocyon thomsoni Cormocyon copei Cormocyon haydeni 0.64 Phlaocyon mariae 0.52 0.34 Phlaocyon yatkolai 0.32 Phlaocyon multicuspus 0.99 Phlaocyon achoros 0.99 Phlaocyon leucosteus 0.97 0.32 Phlaocyon marshlandensis 0.61 Phlaocyon annectens Phlaocyon latidens 0.99 Cynarctoides emryi 1 Cynarctoides accridens 1 1 Cynarctoides gawanae 0.94 Cynarctoides luskensis 0.46 Phlaocyon minor 1 0.61 Cynarctoides lemur Cynarctoides harlowi 0.95 Cynarctoides roii Rhizocyon oreganensis 0.5 Archaeocyon falkenbachi 0.79 0.89 Archaeocyon leptodus Archaeocyon pavidus Hesperocyon gregarius 0.98 Paraenhydrocyon wallovianus 0.97 Paraenhydrocyon robustus 0.37 Paraenhydrocyon josephi 0.25 Mesocyon temnodon 0.3 Mesocyon coryphaeus 0.29 0.18 Mesocyon brachyops Cynodesmus martini Cynodesmus thooides 0.83 0.22 0.62 Enhydrocyon basilatus 0.51 Enhydrocyon stenocephalus 0.97 Enhydrocyon crassidens 0.49 Enhydrocyon pahinsintewakpa 0.07 0.91 Philotrox condoni Sunkahetanka geringensis 0.88 Osbornodon fricki 1 Osbornodon brachypus 0.31 0.46 0.93 Osbornodon iamonensis Osbornodon sesnoni 0.85 Ectopocynus simplicidens 0.98 Ectopocynus intermedius 0.62 0.91 Ectopocynus antiquus 0.23 Caedocyon tedfordi Osbornodon renjiei Hesperocyon coloradensis 1 Otarocyon cooki 0.98 Otarocyon macdonaldi Oxetocyon cuspidatus outgroup

50 40 30 20 10 0 millions of years ago 36x7: mb3.2.5_defaults_v3

0.93 Canis adustus 0.42 Canis mesomelas 0.37 Canis simensis Canis arnensis 0.49 Canis edwardii 0.37 Canis aureus 0.98 Canis mosbachensis 0.940.37 Canis latrans 0.48 Canis variabilis Canis palmidens 0.69 1 Lycaon pictus 0.98 Cuon javanicus 0.91 0.17 Xenocyon texanus 0.93 Canis antonii 0.58 Canis falconeri 0.94 Canis chihliensis 1 Canis dirus 1 Canis armbrusteri 0.8 0.32 Canis lupus Canis etruscus 0.81 0.57 Canis lepophagus Canis thooides 0.98 Canis ferox 0.98 Eucyon davisi 0.94 Cerdocyon texanus Vulpes stenognathus Leptocyon matthewi 1 Urocyon cinereoargenteus 0.32 0.6 Urocyon minicephalus 1 Urocyon galushi 1 Urocyon citronus 0.93 1 Urocyon webbi 1 Metalopex merriami 0.98 Metalopex macconnelli 0.9 Leptocyon vafer 0.98 Leptocyon leidyi Leptocyon vulpinus 0.98 Leptocyon gregorii 0.98 Leptocyon douglassi 0.96 Leptocyon mollis Prohesperocyon wilsoni 0.67 Borophagus diversidens 1 Borophagus dudleyi 1 Borophagus hilli 0.97 Borophagus secundus 1 Borophagus parvus 1 0.87 Borophagus orc Borophagus pugnator 1 Borophagus littoralis 1 Epicyon haydeni 1 0.92 Epicyon saevus Epicyon aelurodontoides 1 Protepicyon raki 0.79 Carpocyon limosus 0.99 Carpocyon robustus 0.99 1 Carpocyon webbi Carpocyon compressus 0.41 0.99 Paratomarctus euthos Paratomarctus temerarius 0.59 0.95 Tomarctus brevirostris 0.44 Tomarctus hippophaga 0.29 Tephrocyon rurestris Protomarctus opatus 0.59 0.85 Microtomarctus conferta Metatomarctus canavus Psalidocyon marianae 1 Aelurodon taxoides 0.84 0.33 Aelurodon ferox 1 Aelurodon stirtoni 0.71 0.23 Aelurodon mcgrewi Aelurodon asthenostylus 0.79 Euoplocyon brachygnathus Euoplocyon spissidens 0.8 1 Cynarctus crucidens 1 Cynarctus voorhiesi 0.45 Cynarctus saxatilis 0.58 Cynarctus galushai 0.96 1 Cynarctus marylandica 0.63 1 Paracynarctus sinclari 0.97 Paracynarctus kelloggi Desmocyon matthewi 0.96 Desmocyon thomsoni 1 Cormocyon copei Cormocyon haydeni 0.99 Cynarctoides emryi 0.14 0.99 Cynarctoides accridens 0.99 Cynarctoides gawanae 0.09 Cynarctoides luskensis 0.92 0.44 Phlaocyon minor Cynarctoides harlowi 0.62 Cynarctoides lemur 0.68 Phlaocyon mariae 0.3 Phlaocyon yatkolai 0.28 0.99 Phlaocyon leucosteus Phlaocyon marshlandensis 0.96 0.99 Phlaocyon annectens 0.97 0.37 Phlaocyon multicuspus 0.97 Phlaocyon achoros Phlaocyon latidens Cynarctoides roii 0.93 Rhizocyon oreganensis 0.49 Archaeocyon falkenbachi 0.79 0.85 Archaeocyon leptodus Archaeocyon pavidus Hesperocyon gregarius 0.86 Osbornodon fricki 1 Osbornodon brachypus 0.21 Osbornodon iamonensis 0.12 Mesocyon temnodon 0.99 Paraenhydrocyon wallovianus 0.99 Paraenhydrocyon robustus 0.54 Paraenhydrocyon josephi 0.14 0.08 Cynodesmus martini 0.62 0.17 Mesocyon coryphaeus Mesocyon brachyops Cynodesmus thooides 0.54 0.6 Enhydrocyon basilatus 0.48 Enhydrocyon stenocephalus 0.92 Enhydrocyon crassidens 0.4 0.43 Enhydrocyon pahinsintewakpa 0.85 0.9 Sunkahetanka geringensis Philotrox condoni 0.95 Osbornodon renjiei 0.82 Ectopocynus simplicidens 0.93 Ectopocynus intermedius 0.47 0.91 Ectopocynus antiquus 0.42 Caedocyon tedfordi Osbornodon sesnoni Hesperocyon coloradensis 1 Otarocyon cooki 0.98 Otarocyon macdonaldi Oxetocyon cuspidatus outgroup

50 40 30 20 10 0 millions of years ago 36x8: mb3.2.5_defaults_v4 0.94 Canis adustus 0.42 Canis mesomelas Canis simensis 0.47 Canis edwardii 0.12 Canis aureus 0.96 Canis variabilis 0.920.18 Canis latrans Canis mosbachensis 0.46 Canis palmidens 0.67 1 Lycaon pictus 1 Cuon javanicus 0.93 Xenocyon texanus 0.95 Canis antonii 0.97 Canis falconeri 0.55 1 Canis dirus 1 Canis armbrusteri 0.1 0.55 Canis lupus 0.42 Canis chihliensis 0.76 Canis etruscus Canis arnensis 0.78 0.56 Canis lepophagus Canis thooides 1 Canis ferox 1 Eucyon davisi 0.96 Cerdocyon texanus Vulpes stenognathus Leptocyon matthewi 1 Urocyon cinereoargenteus 0.45 Urocyon minicephalus 0.95 1 Urocyon citronus 1 Urocyon galushi 0.99 Urocyon webbi 1 1 Metalopex merriami 0.45 Metalopex macconnelli 0.9 Leptocyon vafer 1 Leptocyon leidyi 1 Leptocyon vulpinus Leptocyon gregorii 1 Leptocyon douglassi 0.97 Leptocyon mollis Prohesperocyon wilsoni 0.65 Borophagus diversidens 1 Borophagus dudleyi 1 Borophagus hilli 0.96 Borophagus secundus 1 Borophagus parvus 1 0.86 Borophagus orc Borophagus pugnator 1 Borophagus littoralis 1 Epicyon haydeni 1 0.93 Epicyon saevus Epicyon aelurodontoides 1 Protepicyon raki 0.77 Carpocyon limosus 1 Carpocyon robustus 0.99 1 Carpocyon webbi Carpocyon compressus 0.39 1 Paratomarctus euthos Paratomarctus temerarius 0.54 0.94 Tomarctus brevirostris 0.42 Tomarctus hippophaga Tephrocyon rurestris 0.53 Protomarctus opatus 0.82 Microtomarctus conferta 0.14 Metatomarctus canavus 0.19 Psalidocyon marianae 1 Aelurodon taxoides 0.67 Aelurodon ferox 0.84 1 0.45 Aelurodon stirtoni Aelurodon mcgrewi Aelurodon asthenostylus 0.31 Euoplocyon brachygnathus Euoplocyon spissidens 0.82 1 Cynarctus crucidens 1 Cynarctus voorhiesi 0.43 Cynarctus saxatilis 0.57 Cynarctus galushai 0.98 1 Cynarctus marylandica 0.63 1 Paracynarctus sinclari 0.99 Paracynarctus kelloggi 1 Desmocyon matthewi 0.99 Desmocyon thomsoni Cormocyon copei Cormocyon haydeni 0.7 Phlaocyon mariae 0.54 0.27 Phlaocyon yatkolai 0.25 1 Phlaocyon leucosteus Phlaocyon marshlandensis 0.99 Phlaocyon annectens 0.97 0.35 Phlaocyon multicuspus Phlaocyon achoros 0.99 Phlaocyon latidens 1 Cynarctoides emryi 1 Cynarctoides accridens 1 Cynarctoides gawanae 1 0.93 Cynarctoides luskensis 0.49 Phlaocyon minor 0.32 0.62 Cynarctoides lemur Cynarctoides harlowi 0.95 Cynarctoides roii Rhizocyon oreganensis 0.8 0.51 Archaeocyon falkenbachi 0.87 Archaeocyon leptodus Archaeocyon pavidus Hesperocyon gregarius 0.87 Osbornodon fricki 1 Osbornodon brachypus 0.22 Osbornodon iamonensis 0.12 Mesocyon temnodon 0.99 Paraenhydrocyon wallovianus 0.2 0.99 Paraenhydrocyon robustus Paraenhydrocyon josephi 0.7 0.22 Mesocyon coryphaeus 0.85 0.8 Mesocyon brachyops Cynodesmus martini Cynodesmus thooides 0.65 0.34 Enhydrocyon crassidens 0.1 Enhydrocyon pahinsintewakpa 0.97 Enhydrocyon basilatus 0.46 0.48 Enhydrocyon stenocephalus 0.88 Philotrox condoni 0.45 Sunkahetanka geringensis 0.95 Osbornodon renjiei 0.87 Ectopocynus simplicidens 0.99 Ectopocynus intermedius 0.63 0.89 Ectopocynus antiquus 0.47 Caedocyon tedfordi Osbornodon sesnoni Hesperocyon coloradensis 1 Otarocyon cooki 0.98 Otarocyon macdonaldi Oxetocyon cuspidatus outgroup

50 40 30 20 10 0 millions of years ago 36x9: mb3.2.5_nruns1_v1_temp0.5

0.95 Canis adustus 0.49 Canis mesomelas Cerdocyon texanus 0.54 Canis edwardii 0.42 Canis aureus 0.95 Canis mosbachensis 0.910.43 Canis latrans Canis variabilis 0.67 Canis palmidens 0.92 Xenocyon texanus 0.96 Canis antonii 1 0.98 Canis falconeri 1 Canis dirus 1 Canis armbrusteri 0.61 0.35 Canis lupus 0.44 Canis chihliensis Canis etruscus 1 0.43 0.49 Canis simensis Canis arnensis 0.53 0.56 Canis lepophagus 0.99 0.53 Canis thooides Canis ferox 0.24 Eucyon davisi Vulpes stenognathus Leptocyon matthewi Leptocyon vafer Urocyon cinereoargenteus 0.95 1 0.5 Urocyon minicephalus 1 Urocyon galushi 1 Urocyon citronus 1 1 Urocyon webbi 1 Metalopex merriami 0.91 Metalopex macconnelli 1 Leptocyon leidyi 1 Leptocyon vulpinus Leptocyon gregorii 1 Leptocyon douglassi 0.97 Leptocyon mollis Prohesperocyon wilsoni 0.7 Borophagus diversidens 1 Borophagus dudleyi 1 Borophagus hilli 0.97 Borophagus secundus 1 Borophagus parvus 1 0.89 Borophagus orc Borophagus pugnator 1 Borophagus littoralis 1 Epicyon haydeni 1 0.89 Epicyon saevus Epicyon aelurodontoides 1 Protepicyon raki 0.84 Carpocyon limosus 1 Carpocyon robustus 0.99 1 Carpocyon webbi Carpocyon compressus 1 Paratomarctus euthos 0.5 Paratomarctus temerarius 0.92 Tomarctus brevirostris 0.4 0.25 Tomarctus hippophaga 0.12 Tephrocyon rurestris Protomarctus opatus 0.49 0.87 Microtomarctus conferta Metatomarctus canavus Psalidocyon marianae 1 Aelurodon taxoides 0.45 0.39 Aelurodon ferox 0.68 Aelurodon stirtoni 1 Aelurodon mcgrewi 0.28 Aelurodon asthenostylus 0.33 Euoplocyon brachygnathus 0.42 Euoplocyon spissidens 1 Cynarctus crucidens 1 Cynarctus voorhiesi 0.41 Cynarctus saxatilis 0.4 1 Cynarctus galushai 0.98 1 Paracynarctus sinclari 0.61 0.19 Paracynarctus kelloggi Cynarctus marylandica 0.99 Desmocyon matthewi 1 Lycaon pictus 0.5 Cuon javanicus 0.99 Desmocyon thomsoni Cormocyon copei Cormocyon haydeni 0.7 Phlaocyon mariae 0.53 0.31 Phlaocyon yatkolai 0.29 0.99 Phlaocyon leucosteus Phlaocyon marshlandensis 0.99 Phlaocyon annectens 0.98 0.43 Phlaocyon multicuspus 0.59 Phlaocyon achoros Phlaocyon latidens 1 Cynarctoides emryi 1 Cynarctoides accridens 1 1 Cynarctoides gawanae 0.94 Cynarctoides luskensis 0.47 Phlaocyon minor 1 0.64 Cynarctoides harlowi Cynarctoides lemur 0.96 Cynarctoides roii Rhizocyon oreganensis 0.52 Archaeocyon falkenbachi 0.81 1 0.85 Archaeocyon leptodus Archaeocyon pavidus Hesperocyon gregarius 0.52 Mesocyon coryphaeus 0.28 Mesocyon brachyops 0.05 Cynodesmus martini Cynodesmus thooides 0.84 0.99 Paraenhydrocyon wallovianus 0.99 Paraenhydrocyon robustus 0.46 Paraenhydrocyon josephi 0.85 Mesocyon temnodon 0.46 0.6 Enhydrocyon basilatus 0.07 Enhydrocyon stenocephalus 0.83 Enhydrocyon pahinsintewakpa 0.42 Enhydrocyon crassidens 0.78 Philotrox condoni 0.91 Sunkahetanka geringensis 0.77 Ectopocynus simplicidens 0.84 Ectopocynus intermedius 0.79 Ectopocynus antiquus 0.29 Caedocyon tedfordi 0.6 Osbornodon renjiei 0.19 0.89 Osbornodon fricki 1 Osbornodon brachypus 0.86 Osbornodon iamonensis Osbornodon sesnoni Hesperocyon coloradensis 1 Otarocyon cooki 0.99 Otarocyon macdonaldi Oxetocyon cuspidatus outgroup

50 40 30 20 10 0 millions of years ago 36x10: mb3.2.5_nruns1_v2_temp0.5

0.92 Canis adustus 0.51 Canis mesomelas 0.41 Canis simensis Canis arnensis 0.3 Canis latrans 0.27 Canis edwardii 0.95 Canis mosbachensis 0.90.28 Canis variabilis Canis aureus 0.53 Canis palmidens 0.67 1 Lycaon pictus 1 Cuon javanicus 0.92 Xenocyon texanus 0.94 0.12 Canis antonii Canis falconeri 0.53 1 Canis dirus 0.98 1 Canis armbrusteri 0.58 Canis lupus 0.77 Canis chihliensis Canis etruscus 0.79 0.67 Canis lepophagus Canis thooides 1 Canis ferox 1 Eucyon davisi 0.97 Cerdocyon texanus Vulpes stenognathus 0.22 Leptocyon matthewi Leptocyon vafer 1 Urocyon cinereoargenteus 0.95 0.57 Urocyon minicephalus 1 Urocyon galushi 1 Urocyon citronus 1 1 Urocyon webbi 1 Metalopex merriami 0.91 Metalopex macconnelli 1 Leptocyon leidyi 1 Leptocyon vulpinus Leptocyon gregorii 1 Leptocyon douglassi 0.98 Leptocyon mollis Prohesperocyon wilsoni 0.26 Borophagus diversidens 1 Borophagus hilli 1 Borophagus dudleyi 0.97 Borophagus secundus 1 Borophagus parvus 1 0.87 Borophagus orc Borophagus pugnator 1 Borophagus littoralis 1 Epicyon haydeni 1 0.92 Epicyon saevus Epicyon aelurodontoides 1 Protepicyon raki 0.86 Carpocyon limosus 1 Carpocyon robustus 1 1 Carpocyon webbi Carpocyon compressus 0.39 1 Paratomarctus euthos Paratomarctus temerarius 0.57 0.91 Tomarctus brevirostris 0.44 Tomarctus hippophaga 0.27 Tephrocyon rurestris Protomarctus opatus 0.58 0.87 Microtomarctus conferta Metatomarctus canavus Psalidocyon marianae 0.88 1 Aelurodon taxoides 0.67 Aelurodon ferox 1 0.48 Aelurodon stirtoni Aelurodon mcgrewi 0.74 Aelurodon asthenostylus 0.3 Euoplocyon brachygnathus 0.81 Euoplocyon spissidens 1 Cynarctus crucidens 1 Cynarctus voorhiesi 0.43 Cynarctus saxatilis 0.99 1 Cynarctus galushai 1 Paracynarctus sinclari 0.64 0.21 Paracynarctus kelloggi 0.99 Cynarctus marylandica 1 Desmocyon matthewi 0.99 Desmocyon thomsoni Cormocyon copei Cormocyon haydeni 0.75 Phlaocyon mariae 0.37 Phlaocyon yatkolai 0.99 Phlaocyon leucosteus 0.62 0.35 Phlaocyon marshlandensis 1 Phlaocyon annectens 0.98 0.51 Phlaocyon multicuspus Phlaocyon achoros Phlaocyon latidens 0.28 1 Cynarctoides emryi 1 1 Cynarctoides accridens 1 Cynarctoides gawanae 0.95 Cynarctoides luskensis 1 0.47 Phlaocyon minor 0.62 Cynarctoides harlowi Cynarctoides lemur 0.97 Cynarctoides roii Rhizocyon oreganensis 0.78 0.4 Archaeocyon falkenbachi 0.89 Archaeocyon pavidus Archaeocyon leptodus Hesperocyon gregarius 0.61 Enhydrocyon basilatus 0.54 Enhydrocyon stenocephalus 0.93 Enhydrocyon crassidens 0.48 Enhydrocyon pahinsintewakpa 0.76 Sunkahetanka geringensis Philotrox condoni 0.22 0.83 Ectopocynus simplicidens 0.96 Ectopocynus intermedius 0.78 0.87 Ectopocynus antiquus Caedocyon tedfordi 1 Paraenhydrocyon wallovianus 0.27 1 Paraenhydrocyon robustus 0.45 Paraenhydrocyon josephi 0.16 Mesocyon temnodon 0.26 0.52 0.46 Mesocyon coryphaeus 0.63 Mesocyon brachyops Cynodesmus martini 0.49 0.86 Cynodesmus thooides Osbornodon renjiei 0.87 Osbornodon fricki 0.61 1 Osbornodon brachypus 0.62 Osbornodon iamonensis Osbornodon sesnoni Hesperocyon coloradensis 1 Otarocyon cooki 0.99 Otarocyon macdonaldi Oxetocyon cuspidatus outgroup

50 40 30 20 10 0 millions of years ago 36x11: mb3.2.5_nruns1_v3_temp0.5

0.92 Canis adustus 0.52 Canis mesomelas 0.41 Canis simensis Canis arnensis 0.46 Canis edwardii 0.38 Canis aureus 0.99 Canis mosbachensis 0.940.38 Canis latrans 0.52 Canis variabilis Canis palmidens 0.67 1 Lycaon pictus 1 Cuon javanicus 0.89 Xenocyon texanus 0.92 Canis antonii 0.560.97 Canis falconeri 1 Canis dirus 1 Canis armbrusteri 0.58 Canis lupus 0.83 0.46 Canis chihliensis Canis etruscus 0.85 0.62 Canis lepophagus Canis thooides 1 Canis ferox 1 Eucyon davisi 0.96 Cerdocyon texanus Vulpes stenognathus 0.21 Leptocyon matthewi Leptocyon vafer 1 Urocyon cinereoargenteus 0.96 0.6 Urocyon minicephalus 1 Urocyon galushi 1 Urocyon citronus 1 1 Urocyon webbi 1 Metalopex merriami 0.91 Metalopex macconnelli 1 Leptocyon leidyi 1 Leptocyon vulpinus Leptocyon gregorii 1 Leptocyon douglassi 0.98 Leptocyon mollis Prohesperocyon wilsoni 0.63 Borophagus diversidens 1 Borophagus dudleyi 1 Borophagus hilli 0.98 Borophagus secundus 1 Borophagus parvus 1 0.89 Borophagus orc Borophagus pugnator 1 Borophagus littoralis 1 Epicyon haydeni 1 0.93 Epicyon saevus Epicyon aelurodontoides 1 Protepicyon raki 0.81 Carpocyon limosus 1 Carpocyon robustus 0.99 1 Carpocyon webbi Carpocyon compressus 0.15 1 Paratomarctus euthos Paratomarctus temerarius 0.410.93 Tomarctus brevirostris 0.59 Tomarctus hippophaga Tephrocyon rurestris 0.6 Protomarctus opatus 0.86 Microtomarctus conferta 0.13 Metatomarctus canavus Psalidocyon marianae 0.87 1 Aelurodon taxoides 0.63 Aelurodon ferox 1 0.46 Aelurodon stirtoni Aelurodon mcgrewi 0.7 Aelurodon asthenostylus 0.79 Euoplocyon brachygnathus Euoplocyon spissidens 0.99 1 Cynarctus crucidens 1 Cynarctus voorhiesi 0.4 0.38 Cynarctus saxatilis 0.6 Cynarctus marylandica 1 1 Cynarctus galushai 0.67 1 Paracynarctus sinclari 0.13 Paracynarctus kelloggi 0.99 Desmocyon matthewi Desmocyon thomsoni Cormocyon copei Cormocyon haydeni 0.72 Phlaocyon mariae 0.55 0.39 Phlaocyon yatkolai 0.35 1 Phlaocyon leucosteus Phlaocyon marshlandensis 0.99 Phlaocyon annectens 0.97 0.5 Phlaocyon multicuspus Phlaocyon achoros 1 Phlaocyon latidens 1 Cynarctoides emryi 1 Cynarctoides accridens 1 Cynarctoides gawanae 1 0.94 Cynarctoides luskensis 0.44 Phlaocyon minor 0.35 0.63 Cynarctoides harlowi Cynarctoides lemur 0.95 Cynarctoides roii Rhizocyon oreganensis 0.81 0.46 Archaeocyon falkenbachi 0.87 Archaeocyon pavidus 1 Archaeocyon leptodus Hesperocyon gregarius 1 Paraenhydrocyon wallovianus 1 Paraenhydrocyon robustus 0.41 Paraenhydrocyon josephi 0.13 Mesocyon temnodon 0.39 0.37 Mesocyon coryphaeus 0.46 Mesocyon brachyops Cynodesmus martini 0.86 Cynodesmus thooides 0.55 Enhydrocyon basilatus 0.31 0.1 Enhydrocyon stenocephalus 0.99 Enhydrocyon pahinsintewakpa 0.35 Enhydrocyon crassidens 0.91 Sunkahetanka geringensis Philotrox condoni 0.94 0.88 Ectopocynus simplicidens 1 Ectopocynus intermedius 0.92 Ectopocynus antiquus 0.25 Caedocyon tedfordi 0.64 Osbornodon renjiei 0.12 0.89 Osbornodon fricki 1 Osbornodon brachypus 0.47 Osbornodon iamonensis Osbornodon sesnoni Hesperocyon coloradensis 1 Otarocyon cooki 0.99 Otarocyon macdonaldi Oxetocyon cuspidatus outgroup

50 40 30 20 10 0 millions of years ago 36x12: mb3.2.5_nruns1_v4_temp0.5

0.94 Canis adustus 0.21 Canis mesomelas 0.26 Canis arnensis Canis simensis 0.34 Canis latrans 0.33 Canis edwardii 0.98 Canis mosbachensis 0.940.33 Canis variabilis 0.41 Canis aureus Canis palmidens 0.62 1 Lycaon pictus 1 Cuon javanicus 0.85 0.26 Xenocyon texanus 0.9 Canis antonii 0.52 Canis falconeri 0.93 Canis chihliensis 1 Canis dirus 1 Canis armbrusteri 0.74 0.52 Canis lupus Canis etruscus 0.77 0.52 Canis lepophagus Canis thooides 1 Canis ferox 1 Eucyon davisi 0.95 Cerdocyon texanus Vulpes stenognathus Leptocyon matthewi 1 Urocyon cinereoargenteus 0.56 Urocyon minicephalus 0.96 1 Urocyon galushi 1 Urocyon citronus 1 Urocyon webbi 1 1 Metalopex merriami 0.44 Metalopex macconnelli 0.93 Leptocyon vafer 1 Leptocyon leidyi 1 Leptocyon vulpinus Leptocyon gregorii 1 Leptocyon douglassi 0.98 Leptocyon mollis Prohesperocyon wilsoni 0.71 Borophagus diversidens 1 Borophagus dudleyi 1 Borophagus hilli 0.95 Borophagus secundus 1 Borophagus parvus 1 0.89 Borophagus orc Borophagus pugnator 1 Borophagus littoralis 1 Epicyon haydeni 1 0.92 Epicyon saevus Epicyon aelurodontoides 1 Protepicyon raki 0.77 Carpocyon limosus 1 Carpocyon robustus 0.99 1 Carpocyon webbi Carpocyon compressus 0.2 1 Paratomarctus euthos Paratomarctus temerarius 0.57 Tephrocyon rurestris 0.9 Tomarctus brevirostris 0.280.07 Tomarctus hippophaga Protomarctus opatus 0.56 0.84 Microtomarctus conferta Metatomarctus canavus Psalidocyon marianae 1 Aelurodon taxoides 0.85 0.64 Aelurodon ferox 1 0.45 Aelurodon stirtoni Aelurodon mcgrewi 0.65 Aelurodon asthenostylus 0.72 Euoplocyon brachygnathus 0.84 Euoplocyon spissidens 1 Cynarctus crucidens 1 Cynarctus voorhiesi 0.37 Cynarctus saxatilis 0.55 Cynarctus marylandica 0.99 1 Cynarctus galushai 0.61 1 Paracynarctus sinclari 0.99 Paracynarctus kelloggi Desmocyon matthewi 0.99 Desmocyon thomsoni 1 Cormocyon copei Cormocyon haydeni 0.12 1 Cynarctoides emryi 1 Cynarctoides accridens 1 Cynarctoides gawanae 0.94 Cynarctoides luskensis 0.5 Phlaocyon minor 0.6 Cynarctoides harlowi 0.62 Cynarctoides lemur 0.73 Phlaocyon mariae 0.29 Phlaocyon yatkolai 0.29 Phlaocyon multicuspus 1 1 Phlaocyon achoros 0.99 Phlaocyon leucosteus 0.97 0.28 Phlaocyon marshlandensis 1 Phlaocyon annectens Phlaocyon latidens 0.96 Cynarctoides roii Rhizocyon oreganensis 0.47 Archaeocyon falkenbachi 0.81 0.87 Archaeocyon pavidus Archaeocyon leptodus Hesperocyon gregarius 0.88 Osbornodon fricki 1 Osbornodon brachypus 0.25 Osbornodon iamonensis 0.21 Mesocyon coryphaeus 0.11 Mesocyon brachyops 0.13 Cynodesmus martini 0.44 Mesocyon temnodon 0.15 1 Paraenhydrocyon wallovianus 0.49 1 Paraenhydrocyon robustus Paraenhydrocyon josephi Cynodesmus thooides 0.43 0.36 Enhydrocyon crassidens 0.1 Enhydrocyon pahinsintewakpa 0.98 Enhydrocyon basilatus 0.3 0.45 Enhydrocyon stenocephalus 0.87 0.86 Philotrox condoni Sunkahetanka geringensis 0.91 Osbornodon renjiei 0.86 Ectopocynus simplicidens 0.99 Ectopocynus intermedius 0.47 0.87 Ectopocynus antiquus 0.31 Caedocyon tedfordi Osbornodon sesnoni Hesperocyon coloradensis 1 Otarocyon cooki 0.98 Otarocyon macdonaldi Oxetocyon cuspidatus outgroup

50 40 30 20 10 0 millions of years ago 37x1: mb3.2.6_run1_v1

0.93 Canis adustus 0.83 Canis mesomelas 0.45 Canis simensis Canis arnensis 0.28 Canis latrans 0.19 Canis aureus 0.93 Canis variabilis 0.690.42 Canis mosbachensis Canis edwardii 0.89 Canis palmidens 0.18 1 Lycaon pictus 1 Cuon javanicus 0.55 Xenocyon texanus 0.450.67 Canis antonii Canis falconeri 0.98 1 Canis dirus 0.96 1 Canis armbrusteri 0.15 Canis lupus Canis chihliensis 0.96 Canis etruscus 0.92 Canis lepophagus 1 0.4 Canis thooides Canis ferox 1 Eucyon davisi 0.93 Cerdocyon texanus Vulpes stenognathus Leptocyon matthewi 0.99 Urocyon cinereoargenteus 0.44 0.93 Urocyon minicephalus 1 Urocyon citronus 1 Urocyon galushi 0.93 0.99 Urocyon webbi 1 Metalopex merriami 1 Metalopex macconnelli 0.7 Leptocyon vafer 1 Leptocyon leidyi Leptocyon vulpinus 0.96 Leptocyon gregorii 1 Leptocyon douglassi Leptocyon mollis 0.6 Borophagus diversidens 1 Borophagus dudleyi 1 Borophagus hilli 0.97 Borophagus secundus 1 Borophagus parvus 1 0.68 Borophagus orc Borophagus pugnator 1 Borophagus littoralis 0.98 Epicyon haydeni 1 0.91 Epicyon saevus Epicyon aelurodontoides 1 Protepicyon raki 0.41 Carpocyon limosus 1 Carpocyon webbi 0.99 1 Carpocyon robustus Carpocyon compressus 0.95 Paratomarctus euthos 0.17 Paratomarctus temerarius 0.89 Tomarctus brevirostris 0.28 0.38 Tomarctus hippophaga 0.11 Tephrocyon rurestris 0.46 Microtomarctus conferta Protomarctus opatus 0.12 Psalidocyon marianae Metatomarctus canavus 0.88 1 Aelurodon taxoides 0.69 Aelurodon ferox 1 0.47 Aelurodon stirtoni Aelurodon mcgrewi 0.64 Aelurodon asthenostylus 0.67 Euoplocyon brachygnathus 0.81 Euoplocyon spissidens 1 Cynarctus crucidens 1 Cynarctus voorhiesi 0.43 Cynarctus saxatilis 0.99 1 Cynarctus galushai 1 Paracynarctus sinclari 0.54 0.18 Paracynarctus kelloggi 0.95 Cynarctus marylandica 0.2 Desmocyon matthewi 0.99 Desmocyon thomsoni Cormocyon copei Cormocyon haydeni 0.92 Phlaocyon mariae 0.81 Phlaocyon yatkolai 1 Phlaocyon leucosteus 0.85 0.74 Phlaocyon marshlandensis 0.990.97 Phlaocyon multicuspus 0.96 Phlaocyon achoros Phlaocyon annectens Phlaocyon latidens 1 Cynarctoides emryi 0.94 0.52 1 Cynarctoides accridens 1 Cynarctoides gawanae 0.15 Cynarctoides luskensis 1 0.92 Phlaocyon minor 0.47 Cynarctoides harlowi Cynarctoides lemur 0.67 Cynarctoides roii Rhizocyon oreganensis 0.44 Archaeocyon falkenbachi 0.86 Archaeocyon leptodus Archaeocyon pavidus 0.63 Enhydrocyon basilatus 0.85 Enhydrocyon stenocephalus 1 0.27 Enhydrocyon crassidens 0.76 Enhydrocyon pahinsintewakpa 0.67 Ectopocynus simplicidens 0.37 0.93 Ectopocynus intermedius 0.04 Ectopocynus antiquus 0.47 0.67 Philotrox condoni Caedocyon tedfordi Sunkahetanka geringensis 0.99 Paraenhydrocyon wallovianus 0.64 0.98 Paraenhydrocyon robustus 0.46 Paraenhydrocyon josephi 0.58 Mesocyon temnodon 0.5 Mesocyon coryphaeus 0.73 0.28 Mesocyon brachyops 0.95 Cynodesmus martini 0.28 Cynodesmus thooides 0.77 Osbornodon fricki 1 Osbornodon brachypus 0.47 0.7 Osbornodon iamonensis 0.56 Osbornodon sesnoni Osbornodon renjiei 0.12 Hesperocyon coloradensis Hesperocyon gregarius 1 Otarocyon cooki 0.91 Otarocyon macdonaldi Oxetocyon cuspidatus Prohesperocyon wilsoni outgroup

50 40 30 20 10 0 millions of years ago 37x2: mb3.2.6_run1_v2

0.94 Canis adustus 0.86 Canis mesomelas Canis simensis 0.21 Canis latrans 0.22 Canis variabilis 0.88 Canis aureus 0.640.42 Canis mosbachensis Canis edwardii 0.320.18 Canis palmidens 0.59 Canis antonii Canis falconeri 0.48 1 Lycaon pictus 1 Cuon javanicus 0.9 0.16 Xenocyon texanus Canis dirus 0.97 1 0.11 1 Canis armbrusteri Canis lupus 0.48 Canis chihliensis Canis etruscus 0.97 Canis arnensis 0.94 Canis lepophagus 0.97 Canis thooides 1 Canis ferox 1 Eucyon davisi Cerdocyon texanus 0.94 Vulpes stenognathus Leptocyon matthewi 0.99 Urocyon cinereoargenteus 0.45 0.94 Urocyon minicephalus 1 Urocyon citronus 1 Urocyon galushi 0.93 0.99 Urocyon webbi 1 Metalopex merriami 1 Metalopex macconnelli 0.25 Leptocyon vafer 1 Leptocyon leidyi Leptocyon gregorii 0.96 Leptocyon vulpinus 1 Leptocyon douglassi 0.56 Leptocyon mollis 0.06 Prohesperocyon wilsoni 1 Otarocyon cooki 0.89 Otarocyon macdonaldi Oxetocyon cuspidatus 0.58 Borophagus diversidens 1 Borophagus dudleyi 1 Borophagus hilli 0.96 Borophagus secundus 1 Borophagus parvus 1 0.68 Borophagus orc Borophagus pugnator 1 Borophagus littoralis 0.98 Epicyon haydeni 1 0.9 Epicyon saevus Epicyon aelurodontoides 1 Protepicyon raki 0.4 Carpocyon limosus 0.99 Carpocyon webbi 0.99 1 Carpocyon robustus Carpocyon compressus 0.29 0.95 Paratomarctus euthos Paratomarctus temerarius 0.4 0.93 Tomarctus brevirostris 0.36 Tomarctus hippophaga 0.2 Tephrocyon rurestris Protomarctus opatus 0.52 0.44 Microtomarctus conferta Metatomarctus canavus Psalidocyon marianae 1 Aelurodon taxoides 0.87 0.66 Aelurodon ferox 1 0.46 Aelurodon stirtoni Aelurodon mcgrewi 0.71 Aelurodon asthenostylus 0.75 Euoplocyon brachygnathus 0.24 Euoplocyon spissidens 1 Cynarctus crucidens 1 Cynarctus voorhiesi 1 0.39 Cynarctus saxatilis 0.98 0.62 Cynarctus galushai 1 Cynarctus marylandica 1 Paracynarctus sinclari 0.94 Paracynarctus kelloggi 0.11 Desmocyon matthewi 0.99 Desmocyon thomsoni Cormocyon copei Cormocyon haydeni 0.23 1 Cynarctoides emryi 1 Cynarctoides accridens 1 Cynarctoides gawanae 0.91 Cynarctoides luskensis 0.25 Phlaocyon minor 0.39 Cynarctoides harlowi 0.86 Cynarctoides lemur 0.91 Phlaocyon mariae 0.79 Phlaocyon yatkolai 1 Phlaocyon leucosteus 0.73 0.92 Phlaocyon marshlandensis 0.990.97 Phlaocyon multicuspus 0.95 Phlaocyon achoros 1 Phlaocyon annectens Phlaocyon latidens 0.68 Cynarctoides roii Rhizocyon oreganensis 0.41 Archaeocyon falkenbachi 0.86 Archaeocyon pavidus Archaeocyon leptodus 0.65 Enhydrocyon basilatus 0.47 Enhydrocyon stenocephalus 0.81 Enhydrocyon crassidens 0.84 Enhydrocyon pahinsintewakpa 0.67 Ectopocynus simplicidens 0.17 0.95 Ectopocynus intermedius Ectopocynus antiquus 0.69 Sunkahetanka geringensis 0.49 0.01 Caedocyon tedfordi Philotrox condoni 1 Paraenhydrocyon wallovianus 0.63 0.99 Paraenhydrocyon robustus 0.4 Paraenhydrocyon josephi 0.54 Mesocyon temnodon 0.5 Mesocyon coryphaeus 0.71 0.29 Mesocyon brachyops 0.96 Cynodesmus martini Cynodesmus thooides 0.71 Osbornodon fricki 0.3 1 Osbornodon brachypus 0.69 Osbornodon iamonensis 0.55 0.46 Osbornodon sesnoni Osbornodon renjiei Hesperocyon coloradensis Hesperocyon gregarius outgroup

50 40 30 20 10 0 millions of years ago 37x3: mb3.2.6_run1_v3

0.95 Canis adustus 0.84 Canis mesomelas Canis simensis 0.34 Canis latrans 0.19 Canis aureus 0.88 Canis variabilis 0.670.43 Canis mosbachensis Canis edwardii 0.31 0.2 Canis palmidens 0.68 Canis antonii 0.17 Canis falconeri 1 Lycaon pictus 1 Cuon javanicus 0.48 0.91 Xenocyon texanus 1 Canis dirus 0.98 1 Canis armbrusteri 0.19 Canis lupus 0.44 Canis chihliensis Canis etruscus 0.98 Canis arnensis 0.94 Canis lepophagus 0.97 Canis thooides 1 Canis ferox 1 Eucyon davisi Cerdocyon texanus 0.94 Vulpes stenognathus 0.3 Leptocyon matthewi Leptocyon vafer 1 Urocyon cinereoargenteus 0.93 0.93 Urocyon minicephalus 1 Urocyon citronus 1 Urocyon galushi 1 0.99 Urocyon webbi 1 Metalopex merriami 0.69 Metalopex macconnelli 1 Leptocyon leidyi 0.97 Leptocyon vulpinus Leptocyon gregorii 1 Leptocyon douglassi 0.56 Leptocyon mollis Prohesperocyon wilsoni 0.61 Borophagus diversidens 1 Borophagus dudleyi 1 Borophagus hilli 0.96 Borophagus secundus 0.17 Borophagus parvus 1 Borophagus pugnator 1 Borophagus orc 1 Borophagus littoralis 0.98 Epicyon haydeni 1 0.91 Epicyon saevus Epicyon aelurodontoides 1 Protepicyon raki 0.53 Carpocyon limosus 0.99 Carpocyon robustus 0.99 1 Carpocyon webbi Carpocyon compressus 0.3 0.94 Paratomarctus euthos Paratomarctus temerarius 0.37 0.93 Tomarctus brevirostris 0.39 Tomarctus hippophaga 0.19 Tephrocyon rurestris Protomarctus opatus 0.43 Microtomarctus conferta Metatomarctus canavus 1 Aelurodon taxoides 0.85 0.66 Aelurodon ferox 1 0.45 Aelurodon stirtoni Aelurodon mcgrewi 0.68 Aelurodon asthenostylus 0.73 Euoplocyon brachygnathus 0.03 Euoplocyon spissidens 0.82 Psalidocyon marianae 1 Cynarctus crucidens 1 Cynarctus voorhiesi 0.41 Cynarctus saxatilis 0.22 0.98 1 Cynarctus galushai 1 Paracynarctus sinclari 0.53 0.17 Paracynarctus kelloggi 0.93 Cynarctus marylandica Desmocyon matthewi 0.99 Desmocyon thomsoni Cormocyon copei Cormocyon haydeni 0.22 1 Cynarctoides emryi 1 Cynarctoides accridens 1 Cynarctoides gawanae 0.91 Cynarctoides luskensis 0.3 Phlaocyon minor 0.37 Cynarctoides harlowi 0.85 Cynarctoides lemur 0.91 Phlaocyon mariae 0.8 Phlaocyon yatkolai 1 Phlaocyon leucosteus 0.77 0.92 Phlaocyon marshlandensis 1 0.98 Phlaocyon multicuspus 0.96 Phlaocyon achoros 1 Phlaocyon annectens Phlaocyon latidens 0.65 Cynarctoides roii Rhizocyon oreganensis 0.45 Archaeocyon falkenbachi 0.85 Archaeocyon leptodus 1 Archaeocyon pavidus 0.68 Enhydrocyon basilatus 0.55 Enhydrocyon stenocephalus 0.83 Enhydrocyon crassidens 0.1 Enhydrocyon pahinsintewakpa 0.22 Philotrox condoni Sunkahetanka geringensis 0.69 0.61 Ectopocynus simplicidens 0.92 Ectopocynus intermedius 0.21 0.47 Ectopocynus antiquus Caedocyon tedfordi 0.61 0.97 Paraenhydrocyon wallovianus 0.98 Paraenhydrocyon robustus 0.39 Paraenhydrocyon josephi 0.53 Mesocyon temnodon 0.49 Mesocyon coryphaeus 0.69 0.26 Mesocyon brachyops 0.95 Cynodesmus martini Cynodesmus thooides 0.74 Osbornodon fricki 0.24 1 Osbornodon brachypus 0.7 Osbornodon iamonensis 0.57 0.45 Osbornodon sesnoni Osbornodon renjiei Hesperocyon gregarius Hesperocyon coloradensis 1 Otarocyon cooki 0.91 Otarocyon macdonaldi Oxetocyon cuspidatus outgroup

50 40 30 20 10 0 millions of years ago 37x4: mb3.2.6_run1_v4

0.93 Canis adustus 0.86 Canis mesomelas 0.45 Canis simensis Canis arnensis 1 Lycaon pictus 1 Cuon javanicus 0.17 Xenocyon texanus 1 Canis dirus 0.121 Canis armbrusteri 0.9 Canis lupus 0.12 Canis chihliensis 0.6 Canis antonii Canis falconeri 0.45 0.31 Canis latrans 0.2 Canis aureus 0.98 0.91 Canis variabilis 0.98 0.680.46 Canis mosbachensis Canis edwardii Canis palmidens 0.97 Canis etruscus 0.95 Canis lepophagus 1 0.46 Canis thooides Canis ferox 1 Eucyon davisi 0.94 Cerdocyon texanus Vulpes stenognathus Leptocyon matthewi 0.99 Urocyon cinereoargenteus 0.91 0.93 Urocyon minicephalus 1 Urocyon citronus 1 Urocyon galushi 0.99 Urocyon webbi 1 1 Metalopex merriami 0.23 Metalopex macconnelli 0.67 Leptocyon vafer 1 Leptocyon leidyi 0.95 Leptocyon vulpinus Leptocyon gregorii 1 Leptocyon douglassi 0.57 Leptocyon mollis Prohesperocyon wilsoni 0.58 Borophagus diversidens 1 Borophagus dudleyi 1 Borophagus hilli 0.97 Borophagus secundus 1 Borophagus parvus 1 0.7 Borophagus orc Borophagus pugnator 1 Borophagus littoralis 0.98 Epicyon haydeni 1 0.91 Epicyon saevus Epicyon aelurodontoides 1 Protepicyon raki 0.49 Carpocyon limosus 1 Carpocyon robustus 0.99 1 Carpocyon webbi Carpocyon compressus 0.95 Paratomarctus euthos 0.17 Paratomarctus temerarius 0.91 Tomarctus brevirostris 0.270.36 Tomarctus hippophaga 0.13 Tephrocyon rurestris 0.25 Microtomarctus conferta 0.52 Protomarctus opatus Psalidocyon marianae Metatomarctus canavus 1 Aelurodon taxoides 0.86 0.33 Aelurodon ferox 1 Aelurodon stirtoni 0.64 0.22 Aelurodon mcgrewi 0.7 Aelurodon asthenostylus Euoplocyon brachygnathus Euoplocyon spissidens 0.82 1 Cynarctus crucidens 1 Cynarctus voorhiesi 0.4 Cynarctus saxatilis 0.13 Cynarctus galushai 0.98 1 1 Paracynarctus sinclari 0.54 Paracynarctus kelloggi 0.94 Cynarctus marylandica 1 Desmocyon matthewi 0.99 Desmocyon thomsoni Cormocyon copei Cormocyon haydeni 0.91 Phlaocyon mariae 0.8 Phlaocyon yatkolai 1 Phlaocyon leucosteus 0.86 0.75 Phlaocyon marshlandensis 0.990.97 Phlaocyon multicuspus 0.96 Phlaocyon achoros Phlaocyon annectens Phlaocyon latidens 1 Cynarctoides emryi 0.94 0.52 1 Cynarctoides accridens 1 Cynarctoides gawanae 0.27 Cynarctoides luskensis 1 0.92 0.46 Cynarctoides harlowi Cynarctoides lemur Phlaocyon minor 0.68 Cynarctoides roii Rhizocyon oreganensis 0.45 Archaeocyon falkenbachi 0.86 Archaeocyon leptodus Archaeocyon pavidus 0.68 Enhydrocyon basilatus 0.83 Enhydrocyon stenocephalus 0.26 Enhydrocyon crassidens 0.79 Enhydrocyon pahinsintewakpa 0.68 Ectopocynus simplicidens 0.17 0.93 Ectopocynus intermedius 0.53 Ectopocynus antiquus 0.7 Sunkahetanka geringensis 0.51 Philotrox condoni Caedocyon tedfordi 0.98 Paraenhydrocyon wallovianus 0.63 0.98 Paraenhydrocyon robustus 0.46 Paraenhydrocyon josephi 0.56 Mesocyon temnodon 0.49 Mesocyon coryphaeus 0.72 0.27 Mesocyon brachyops 0.95 Cynodesmus martini 0.27 Cynodesmus thooides 0.09 Osbornodon brachypus 1 0.21 Osbornodon iamonensis 0.7 Osbornodon fricki 0.57 0.44 Osbornodon sesnoni Osbornodon renjiei Hesperocyon gregarius Hesperocyon coloradensis 1 Otarocyon cooki 0.9 Otarocyon macdonaldi Oxetocyon cuspidatus outgroup

50 40 30 20 10 0 millions of years ago 37x5: mb3.2.6_defaults1_v1

0.94 Canis adustus 0.84 Canis mesomelas Canis simensis 1 Lycaon pictus 1 Cuon javanicus 0.58 Xenocyon texanus 0.31 0.64 Canis antonii 0.14 Canis falconeri 1 Canis dirus 1 Canis armbrusteri 0.22 Canis lupus Canis chihliensis 0.98 0.43 Canis mosbachensis 0.89 0.18 Canis edwardii 0.940.31 Canis latrans Canis aureus 0.75 Canis variabilis 0.98 0.06 Canis palmidens Canis etruscus Canis arnensis 0.97 0.92 Canis lepophagus 0.43 Canis thooides 1 Canis ferox 1 Eucyon davisi 0.94 Cerdocyon texanus Vulpes stenognathus Leptocyon matthewi 0.99 Urocyon cinereoargenteus 0.44 0.92 Urocyon minicephalus 1 Urocyon citronus 1 Urocyon galushi 0.94 1 Urocyon webbi 1 Metalopex merriami 1 Metalopex macconnelli 0.68 Leptocyon vafer 1 Leptocyon leidyi Leptocyon vulpinus 0.96 Leptocyon gregorii 1 Leptocyon douglassi 0.57 Leptocyon mollis Prohesperocyon wilsoni 0.14 Borophagus dudleyi 1 Borophagus hilli 1 Borophagus diversidens 0.96 Borophagus secundus 1 Borophagus parvus 1 0.71 Borophagus orc Borophagus pugnator 1 Borophagus littoralis 0.98 Epicyon haydeni 1 0.91 Epicyon saevus Epicyon aelurodontoides 1 Protepicyon raki 0.49 Carpocyon limosus 1 Carpocyon robustus 0.99 1 Carpocyon webbi Carpocyon compressus 0.06 0.93 Paratomarctus euthos Paratomarctus temerarius 0.29 Protomarctus opatus 0.93 Tomarctus brevirostris 0.37 0.23 Tomarctus hippophaga 0.13 Tephrocyon rurestris 0.51 Microtomarctus conferta Psalidocyon marianae Metatomarctus canavus 1 Aelurodon taxoides 0.86 0.66 Aelurodon ferox 1 0.45 Aelurodon stirtoni Aelurodon mcgrewi 0.69 Aelurodon asthenostylus 0.74 Euoplocyon brachygnathus 0.84 Euoplocyon spissidens 1 Cynarctus crucidens 1 Cynarctus voorhiesi 0.4 Cynarctus saxatilis Cynarctus galushai 0.98 1 1 Paracynarctus sinclari 0.58 0.19 Paracynarctus kelloggi 0.94 Cynarctus marylandica 1 Desmocyon matthewi 0.99 Desmocyon thomsoni Cormocyon copei Cormocyon haydeni 0.9 Phlaocyon mariae 0.79 Phlaocyon yatkolai 1 Phlaocyon leucosteus 0.86 0.76 Phlaocyon marshlandensis 0.990.97 Phlaocyon multicuspus 0.96 Phlaocyon achoros Phlaocyon annectens Phlaocyon latidens 1 Cynarctoides emryi 0.93 0.51 1 Cynarctoides accridens 1 Cynarctoides gawanae 0.29 Cynarctoides luskensis 1 0.91 0.48 Cynarctoides harlowi Cynarctoides lemur Phlaocyon minor 0.69 Cynarctoides roii Rhizocyon oreganensis 0.46 Archaeocyon falkenbachi 0.86 Archaeocyon leptodus Archaeocyon pavidus 0.66 Enhydrocyon basilatus 0.53 Enhydrocyon stenocephalus 0.84 Enhydrocyon crassidens 0.8 Enhydrocyon pahinsintewakpa 0.67 Ectopocynus simplicidens 0.42 0.94 Ectopocynus intermedius 0.53 Ectopocynus antiquus Philotrox condoni 0.5 Sunkahetanka geringensis 0.45 Mesocyon coryphaeus 0.1 0.16 Mesocyon brachyops 0.24 Mesocyon temnodon 0.49 Cynodesmus martini 0.56 1 Paraenhydrocyon wallovianus 0.62 0.99 Paraenhydrocyon robustus Paraenhydrocyon josephi Cynodesmus thooides 0.29 0.96 Caedocyon tedfordi 0.73 Osbornodon fricki 1 Osbornodon brachypus 0.45 0.6 Osbornodon iamonensis 0.47 Osbornodon sesnoni Osbornodon renjiei 0.12 Hesperocyon coloradensis Hesperocyon gregarius 1 Otarocyon cooki 0.91 Otarocyon macdonaldi Oxetocyon cuspidatus outgroup

50 40 30 20 10 0 millions of years ago 37x6: mb3.2.6_defaults1_v2

0.92 Canis adustus 0.86 Canis mesomelas Canis simensis 0.36 Canis latrans 0.1 Canis aureus 0.88 Canis mosbachensis 0.13 Canis variabilis 0.19 Canis edwardii 1 Canis dirus 0.910.271 Canis armbrusteri Canis lupus 0.14 Canis palmidens 1 Lycaon pictus 1 Cuon javanicus 0.490.980.6 Xenocyon texanus 0.61 Canis antonii 0.18 Canis falconeri 0.07 Canis chihliensis 0.97 Canis etruscus Canis arnensis 0.97 0.94 Canis lepophagus Canis thooides 1 Canis ferox 1 Eucyon davisi 0.94 Cerdocyon texanus Vulpes stenognathus Leptocyon matthewi 1 Urocyon cinereoargenteus 0.44 0.92 Urocyon minicephalus 1 Urocyon citronus 1 Urocyon galushi 0.94 0.99 Urocyon webbi 1 Metalopex merriami 1 Metalopex macconnelli 0.71 Leptocyon vafer 1 Leptocyon leidyi Leptocyon vulpinus 0.95 Leptocyon gregorii 1 Leptocyon douglassi 0.54 Leptocyon mollis Prohesperocyon wilsoni 0.58 Borophagus diversidens 1 Borophagus dudleyi 1 Borophagus hilli 0.95 Borophagus secundus 1 Borophagus parvus 1 0.68 Borophagus orc Borophagus pugnator 1 Borophagus littoralis 0.99 Epicyon haydeni 1 0.91 Epicyon saevus Epicyon aelurodontoides 1 Protepicyon raki 0.38 Carpocyon limosus 1 Carpocyon webbi 0.99 1 Carpocyon robustus Carpocyon compressus 0.33 0.95 Paratomarctus euthos Paratomarctus temerarius 0.45 0.95 Tomarctus brevirostris 0.4 Tomarctus hippophaga 0.23 Tephrocyon rurestris Protomarctus opatus 0.55 0.49 Microtomarctus conferta Metatomarctus canavus Psalidocyon marianae 1 Aelurodon taxoides 0.88 0.3 Aelurodon ferox 0.65 Aelurodon stirtoni 1 Aelurodon mcgrewi 0.73 Aelurodon asthenostylus 0.77 Euoplocyon brachygnathus Euoplocyon spissidens 0.83 1 Cynarctus crucidens 1 Cynarctus voorhiesi 0.25 0.41 Cynarctus saxatilis 0.59 Cynarctus marylandica 0.98 1 Cynarctus galushai 0.58 1 Paracynarctus sinclari 0.95 Paracynarctus kelloggi Desmocyon matthewi 0.98 Desmocyon thomsoni Cormocyon copei Cormocyon haydeni 0.9 Phlaocyon mariae 0.79 Phlaocyon yatkolai 1 Phlaocyon leucosteus 0.86 0.77 Phlaocyon marshlandensis 1 0.97 Phlaocyon multicuspus 0.97 Phlaocyon achoros Phlaocyon annectens Phlaocyon latidens 1 Cynarctoides emryi 0.93 0.53 1 Cynarctoides accridens 1 Cynarctoides gawanae 0.09 Cynarctoides luskensis 1 0.93 Cynarctoides lemur 0.28 Phlaocyon minor Cynarctoides harlowi 0.65 Cynarctoides roii Rhizocyon oreganensis 0.42 Archaeocyon falkenbachi 0.85 1 Archaeocyon pavidus Archaeocyon leptodus 0.68 Enhydrocyon basilatus 0.52 Enhydrocyon stenocephalus 0.85 Enhydrocyon crassidens 0.77 Enhydrocyon pahinsintewakpa 0.65 Ectopocynus simplicidens 0.16 0.95 Ectopocynus intermedius 0.49 Ectopocynus antiquus 0.48 0.71 Sunkahetanka geringensis Philotrox condoni Caedocyon tedfordi 0.1 Cynodesmus martini 0.62 0.03 Mesocyon coryphaeus 0.26 Mesocyon temnodon 0.58 Mesocyon brachyops 0.99 Paraenhydrocyon wallovianus 0.73 0.99 Paraenhydrocyon robustus 0.95 Paraenhydrocyon josephi Cynodesmus thooides 0.74 Osbornodon fricki 1 Osbornodon brachypus 0.46 0.69 Osbornodon iamonensis 0.55 Osbornodon sesnoni Osbornodon renjiei 0.13 Hesperocyon coloradensis Hesperocyon gregarius 1 Otarocyon cooki 0.9 Otarocyon macdonaldi Oxetocyon cuspidatus outgroup

50 40 30 20 10 0 millions of years ago 37x7: mb3.2.6_defaults1_v3

0.94 Canis adustus 0.85 Canis mesomelas Canis simensis 1 Lycaon pictus 1 Cuon javanicus 0.54 Xenocyon texanus 0.67 Canis antonii Canis falconeri 0.310.17 1 Canis dirus 1 Canis armbrusteri 0.21 Canis lupus 0.45 Canis chihliensis 0.47 Canis mosbachensis 0.89 0.23 Canis edwardii 0.39 Canis latrans 0.97 0.92 Canis aureus 0.7 Canis variabilis 0.98 Canis palmidens Canis etruscus Canis arnensis 0.98 0.93 Canis lepophagus 0.47 Canis thooides 1 Canis ferox 1 Eucyon davisi 0.95 Cerdocyon texanus Vulpes stenognathus Leptocyon matthewi 0.99 Urocyon cinereoargenteus 0.43 0.91 Urocyon minicephalus 1 Urocyon citronus 1 Urocyon galushi 0.91 0.99 Urocyon webbi 1 Metalopex merriami 1 Metalopex macconnelli 0.69 Leptocyon vafer 1 Leptocyon leidyi Leptocyon vulpinus 0.94 Leptocyon gregorii 1 Leptocyon douglassi 0.58 Leptocyon mollis Prohesperocyon wilsoni 0.16 Borophagus dudleyi 1 Borophagus hilli 1 Borophagus diversidens 0.96 Borophagus secundus 0.19 Borophagus parvus 1 Borophagus pugnator 1 Borophagus orc 1 Borophagus littoralis 0.97 Epicyon haydeni 1 0.89 Epicyon saevus Epicyon aelurodontoides 1 Protepicyon raki 0.38 Carpocyon limosus 0.99 Carpocyon webbi 0.99 1 Carpocyon robustus Carpocyon compressus 0.29 0.96 Paratomarctus euthos Paratomarctus temerarius 0.43 0.92 Tomarctus brevirostris 0.38 Tomarctus hippophaga 0.22 Tephrocyon rurestris Protomarctus opatus 0.54 0.48 Microtomarctus conferta Metatomarctus canavus Psalidocyon marianae 1 Aelurodon taxoides 0.89 0.69 Aelurodon ferox 1 0.51 Aelurodon stirtoni Aelurodon mcgrewi 0.62 Aelurodon asthenostylus 0.73 Euoplocyon brachygnathus 0.22 Euoplocyon spissidens 1 Cynarctus crucidens 1 Cynarctus voorhiesi 0.43 Cynarctus saxatilis 0.74 0.61 Cynarctus marylandica 1 Cynarctus galushai 0.98 1 Paracynarctus sinclari Paracynarctus kelloggi 1 0.89 Desmocyon matthewi 0.98 Desmocyon thomsoni Cormocyon copei Cormocyon haydeni 0.91 Phlaocyon mariae 0.8 Phlaocyon yatkolai 1 Phlaocyon leucosteus 0.76 0.87 Phlaocyon marshlandensis 1 0.97 Phlaocyon multicuspus 0.95 Phlaocyon achoros Phlaocyon annectens Phlaocyon latidens 1 Cynarctoides emryi 0.93 0.54 1 Cynarctoides accridens 1 Cynarctoides gawanae 0.26 Cynarctoides luskensis 1 0.92 0.43 Cynarctoides harlowi Cynarctoides lemur Phlaocyon minor 0.7 Cynarctoides roii Rhizocyon oreganensis 0.31 0.44 Archaeocyon falkenbachi 0.87 Archaeocyon leptodus Archaeocyon pavidus Hesperocyon gregarius 0.66 Enhydrocyon basilatus 0.11 Enhydrocyon stenocephalus 0.88 Enhydrocyon pahinsintewakpa 0.79 Enhydrocyon crassidens 0.62 Ectopocynus simplicidens 0.14 0.94 Ectopocynus intermedius 0.52 Ectopocynus antiquus Sunkahetanka geringensis 0.52 Philotrox condoni 1 Paraenhydrocyon wallovianus 1 0.13 Paraenhydrocyon robustus 0.38 Paraenhydrocyon josephi 0.03 Mesocyon temnodon 0.55 0.64 Mesocyon brachyops 0.77 0.11 Cynodesmus martini Mesocyon coryphaeus Cynodesmus thooides 0.27 0.96 Caedocyon tedfordi 0.69 Osbornodon fricki 1 Osbornodon brachypus 0.28 0.73 Osbornodon iamonensis 0.61 Osbornodon sesnoni Osbornodon renjiei Hesperocyon coloradensis 1 Otarocyon cooki 0.91 Otarocyon macdonaldi Oxetocyon cuspidatus outgroup

50 40 30 20 10 0 millions of years ago 37x8: mb3.2.6_defaults1_v4

0.94 Canis adustus 0.84 Canis mesomelas 0.45 Canis simensis Canis arnensis 1 Lycaon pictus 1 Cuon javanicus 0.57 Xenocyon texanus 0.9 0.66 Canis antonii 0.14 Canis falconeri 1 Canis dirus 1 Canis armbrusteri 0.19 Canis lupus Canis chihliensis 0.98 0.35 Canis latrans 0.98 0.21 Canis aureus 0.93 Canis variabilis 0.710.46 Canis mosbachensis 0.06 Canis edwardii 0.97 Canis palmidens Canis etruscus 0.94 Canis lepophagus 1 0.43 Canis thooides Canis ferox 1 Eucyon davisi 0.93 Cerdocyon texanus Vulpes stenognathus Leptocyon matthewi 1 Urocyon cinereoargenteus 0.44 0.93 Urocyon minicephalus 1 Urocyon citronus 1 Urocyon galushi 0.93 0.99 Urocyon webbi 1 Metalopex merriami 1 Metalopex macconnelli 0.7 Leptocyon vafer 1 Leptocyon leidyi Leptocyon vulpinus 0.95 Leptocyon gregorii 1 Leptocyon douglassi 0.07 Leptocyon mollis 1 Otarocyon cooki 0.9 Otarocyon macdonaldi Oxetocyon cuspidatus 0.59 Borophagus diversidens 1 Borophagus dudleyi 1 Borophagus hilli 0.96 Borophagus secundus 1 Borophagus parvus 1 0.68 Borophagus orc Borophagus pugnator 1 Borophagus littoralis 0.98 Epicyon haydeni 1 0.91 Epicyon saevus Epicyon aelurodontoides 1 Protepicyon raki 0.37 Carpocyon limosus 1 Carpocyon webbi 0.99 1 Carpocyon robustus Carpocyon compressus 0.94 Paratomarctus euthos 0.43 Paratomarctus temerarius 0.95 Tomarctus brevirostris 0.4 Tomarctus hippophaga 0.55 0.09 Tephrocyon rurestris Protomarctus opatus 0.46 Microtomarctus conferta 0.09 Metatomarctus canavus Psalidocyon marianae 0.87 1 Aelurodon taxoides 0.64 Aelurodon ferox 1 0.47 Aelurodon stirtoni Aelurodon mcgrewi 0.72 Aelurodon asthenostylus 0.77 Euoplocyon brachygnathus 0.83 Euoplocyon spissidens 1 Cynarctus crucidens 1 Cynarctus voorhiesi 0.16 0.41 Cynarctus saxatilis 0.61 0.99 Cynarctus galushai 1 Cynarctus marylandica 0.56 1 Paracynarctus sinclari 0.94 Paracynarctus kelloggi Desmocyon matthewi 0.98 Desmocyon thomsoni Cormocyon copei Cormocyon haydeni 0.92 Phlaocyon mariae 0.8 Phlaocyon yatkolai 1 Phlaocyon leucosteus 0.87 0.77 Phlaocyon marshlandensis 1 0.98 Phlaocyon multicuspus 0.96 Phlaocyon achoros Phlaocyon annectens Phlaocyon latidens 1 Cynarctoides emryi 0.94 0.53 1 Cynarctoides accridens 1 Cynarctoides gawanae 0.28 Cynarctoides luskensis 1 0.91 0.44 Cynarctoides harlowi Cynarctoides lemur Phlaocyon minor 0.68 Cynarctoides roii Rhizocyon oreganensis 0.46 Archaeocyon falkenbachi 1 0.86 Archaeocyon leptodus Archaeocyon pavidus 0.1 Enhydrocyon stenocephalus 0.51 Enhydrocyon crassidens 0.86 Enhydrocyon basilatus 0.79 Enhydrocyon pahinsintewakpa 0.26 Ectopocynus intermedius 0.4 0.93 Ectopocynus antiquus 0.5 Ectopocynus simplicidens 0.71 Philotrox condoni 0.49 Sunkahetanka geringensis Caedocyon tedfordi 1 Paraenhydrocyon wallovianus 0.59 0.99 Paraenhydrocyon robustus 0.43 Paraenhydrocyon josephi 0.55 Mesocyon temnodon 0.48 Mesocyon coryphaeus 0.68 0.27 Mesocyon brachyops 0.96 Cynodesmus martini Cynodesmus thooides 0.73 Osbornodon fricki 1 0.24 Osbornodon brachypus 0.65 Osbornodon iamonensis 0.52 0.45 Osbornodon sesnoni Osbornodon renjiei Hesperocyon gregarius Hesperocyon coloradensis Prohesperocyon wilsoni outgroup

50 40 30 20 10 0 millions of years ago