A. 90% missing taxa/locus Brachycephalus quiririensis miriame 100 adiastola Phyzelaphryninae vocator 100 100 100 Diasporus gularis Eleutherodactylinae 100 johnstonei 100 Eleutherodactylus longipes 5 8 100 anomalus Strabomantinae Craugastortor daryi 100 Craugastor augusti 100 Craugastor longirostris 100 nebulanastes 100 Pristimantinae quixensis 100 pulcher Holoadeninae Strabomantidae 100 simonsii substitutions / site 100 Pristimantinae 0.005 Pristimantis miyatai

B. 70% missing taxa/locus

Brachycephalus quiririensis Brachycephalidae Phyzelaphryne miriame Phyzelaphryninae 100 Adelophryne adiastola Diasporus vocator 100 Eleutherodactylidae 100 100 Diasporus gularis Eleutherodactylinae 100 Eleutherodactylus johnstonei 100 Eleutherodactylus longipes 6 7 100 Strabomantis anomalus Strabomantinae Strabomantidae Craugastortor daryi

100 Craugastor augusti Craugastoridae 9 6 Craugastor longirostris 100 Lynchius nebulanastes Pristimantinae 100 Strabomantidae 100 Barycholos pulcher Holoadeninae Pristimantis simonsii 100 Pristimantinae substitutions / site 100 Pristimantis miyatai 0.004

C. 60% missing taxa/locus

Brachycephalus quiririensis Brachycephalidae Adelophryne adiastola 100 Phyzelaphryninae 100 Phyzelaphryne miriame Diasporus gularis Eleutherodactylidae 100 100 Diasporus vocator Eleutherodactylinae 100 Eleutherodactylus longipes 100 Eleutherodactylus johnstonei 7 4 9 9 Strabomantis anomalus Strabomantinae Strabomantidae Craugastortor daryi 9 9 Craugastor longirostris Craugastoridae 9 6 Craugastor augusti 100 Oreobates quixensis Pristimantinae 100 Lynchius nebulanastes 100 Barycholos pulcher Holoadeninae Strabomantidae

100 Pristimantis simonsii substitutions / site Pristimantinae 100 0.005 Pristimantis miyatai

D. 50% missing taxa/locus

Brachycephalus quiririensis Brachycephalidae Phyzelaphryne miriame Phyzelaphryninae 9 4 Adelophryne adiastola 9 4 Eleutherodactylus johnstonei 100 100 Eleutherodactylus longipes Eleutherodactylidae Eleutherodactylinae 100 Diasporus gularis 100 Diasporus vocator 8 5 8 8 Strabomantis anomalus Strabomantinae Strabomantidae Craugastortor daryi

9 2 Craugastor longirostris Craugastoridae 100 Craugastor augusti 8 7 100 Oreobates quixensis Pristimantinae Lynchius nebulanastes 9 6 Barycholos pulcher Holoadeninae Strabomantidae 100 Pristimantis miyatai substitutions / site 100 Pristimantinae 0.003 Pristimantis simonsii E. 40% missing taxa/locus

Brachycephalus quiririensis Brachycephalidae Phyzelaphryne miriame 9 4 Phyzelaphryninae 9 4 Adelophryne adiastola Eleutherodactylus johnstonei 100 Eleutherodactylidae 100 Eleutherodactylus longipes Eleutherodactylinae 100 Diasporus gularis 100 Diasporus vocator 8 4 8 9 Strabomantis anomalus Strabomantinae Strabomantidae Craugastortor daryi

9 2 Craugastor augusti Craugastoridae 100 Craugastor longirostris 9 0 100 Lynchius nebulanastes Pristimantinae Oreobates quixensis 9 4 Barycholos pulcher Holoadeninae Strabomantidae Pristimantis simonsii 100 Pristimantinae 100 Pristimantis miyatai 0.003

F. 30% missing taxa/locus

Brachycephalus quiririensis 3 2 Adelophryne adiastola Craugastortor daryi 3 9 Phyzelaphrynee miriame 2 5 8 9 Diasporus vocator 6 8 Diasporus gularis 5 2 Eleutherodactylus johnstonei 8 4 3 4 Eleutherodactylus longipes 4 5 Craugastor augusti Strabomantis anomalus 3 7 Craugastor longirostris 1 8 Barycholos pulcher Pristimantis miyatai 4 0 100 Pristimantis simonsii 5 6 Lynchius nebulanastes 4 8 Oreobates quixensis substitutions / site 0.003 G. 20% missing taxa/locus

Dendropsophus leali Stefania coxi Eleutherodactylus longipes 4 5 Eleutherodactylus johnstonei 7 5 Pristimantis miyatai 5 4 Espadarana prosoblepon 8 0 Diasporus gularis 3 0 Craugastor augusti Barycholos pulcher 7 2

1 0 Adelophryne adiastola 7 2 Diasporus vocator 9 0 Hyloxalus nexipus 1 0 Leptodactylus dydimus 1 2 Phyzelaphryne miriame 2 6 Brachycephalus quiririensis 3 6 2 Craugastor longirostris Craugastortor daryi 8 Lynchius nebulanastes 1 6 Pristimantis simonsii

2 2 Strabomantis anomalus 6 7 Oreobates quixensis

substitutions / site 0.007 H. 10% missing taxa/locus

Adelophryne adiastola

Brachycephalus quiririensis

Barycholos pulcher

Lynchius nebulanastes 5 8 Pristimantis simonsii 6 0 1 5 Oreobates quixensis 6 3 Pristimantis miyatai

3 Dendropsophus leali 2 Diasporus gularis 0 Eleutherodactylus longipes 8 Espadarana prosoblepon 5 6

0 Craugastor longirostris Craugastor augusti 1 1 Eleutherodactylus johnstonei

0 Phyzelaphryne miriame 3 9 Stefania coxi 1 Hyloxalus nexipus 8 Leptodactylus dydimus 1 8 Diasporus vocator substitutions / site 0.01