A. 90% missing taxa/locus Brachycephalus quiririensis Brachycephalidae

100 Adelophryne adiastola Phyzelaphryninae Phyzelaphryne miriame 9 7 100 100 johnstonei

9 8 Eleutherodactylus longipes Eleutherodactylinae 9 9 Diasporus gularis Diasporus vocator

8 8 9 7 Craugastor augusti

9 4 Craugastor longirostris Craugastoridae 9 3 Craugastor daryi

9 1 Strabomantis anomalus Strabomantinae Lynchius nebulanastes 100 Pristimantinae

100 Oreobates quixensis Strabomantidae Barycholos pulcher Holoadeninae 9 6 Pristimantis miyatai substitutions / site 100 Pristimantinae 0.3 Pristimantis simonsii B. 70% missing taxa/locus Brachycephalus quiririensis Brachycephalidae

9 8 Adelophryne adiastola Phyzelaphryne miriame Phyzelaphryninae 9 6 100 100 Eleutherodactylus johnstonei Eleutherodactylidae

9 9 Eleutherodactylus longipes

9 9 Diasporus vocator Eleutherodactylinae Diasporus gularis

8 9 9 9 Craugastor augusti Craugastor longirostris 8 5 Craugastoridae 9 2 Craugastor daryi

8 4 Strabomantis anomalus Strabomantinae

9 9 Lynchius nebulanastes Pristimantinae Oreobates quixensis 9 6 Strabomantidae Barycholos pulcher Holoadeninae 9 8

100 Pristimantis miyatai substitutions / site Pristimantinae 0.4 Pristimantis simonsii C. 60% missing taxa/locus

Brachycephalus quiririensis Brachycephalidae 100 Adelophryne adiastola Phyzelaphryninae Phyzelaphryne miriame 9 7 100 Eleutherodactylus johnstonei 100 Eleutherodactylidae 9 8 Eleutherodactylus longipes Eleutherodactylinae 9 9 Diasporus vocator Diasporus gularis

8 4 9 7 Craugastor augusti

8 5 Craugastor longirostris Craugastoridae

9 3 Craugastor daryi

8 5 Strabomantis anomalus Strabomantinae 100 Lynchius nebulanastes Pristimantinae Strabomantidae 100 Oreobates quixensis Barycholos pulcher Holoadeninae 9 6

100 Pristimantis miyatai substitutions / site Pristimantinae 0.3 Pristimantis simonsii D. 50% missing taxa/locus

Brachycephalus quiririensis Brachycephalidae

9 9 Adelophryne adiastola Phyzelaphryninae Phyzelaphryne miriame 9 0 100 9 9 Diasporus vocator Eleutherodactylidae 9 9 Diasporus gularis Eleutherodactylinae 100 Eleutherodactylus johnstonei Eleutherodactylus longipes

7 6 9 6 Craugastor augusti Craugastoridae 7 4 Craugastor longirostris

8 8 Craugastor daryi

7 6 Strabomantis anomalus Strabomantinae Lynchius nebulanastes 100 Pristimantinae 100 Oreobates quixensis Strabomantidae Barycholos pulcher Holoadeninae 100

100 Pristimantis miyatai substitutions / site Pristimantinae 0.4 Pristimantis simonsii E. 40% missing taxa/locus Brachycephalidae Brachycephalus quiririensis

9 8 Adelophryne adiastola Phyzelaphryninae Phyzelaphryne miriame 8 3 9 9 100 Eleutherodactylus johnstonei Eleutherodactylidae 9 9 Eleutherodactylus longipes Eleutherodactylinae 9 9 Diasporus vocator Diasporus gularis 6 6

9 3 Craugastor augusti

6 3 Craugastor longirostris Craugastoridae 8 8 Craugastor daryi

5 6 Strabomantis anomalus Strabomantinae

100 Lynchius nebulanastes Pristimantinae Oreobates quixensis 9 3 Strabomantidae Barycholos pulcher Holoadeninae 9 4

100 Pristimantis miyatai substitutions / site Pristimantinae 0.4 Pristimantis simonsii F. 30% missing taxa/locus

Brachycephalus quiririensis Brachycephalidae 6 4 Adelophryne adiastola Phyzelaphryne miriame Phyzelaphryninae 2 0 9 8 Eleutherodactylus johnstonei 8 0 Eleutherodactylidae 8 6 Eleutherodactylus longipes Eleutherodactylinae 9 4 Diasporus vocator Diasporus gularis 1 8

7 8 Craugastor augusti Craugastoridae 1 1 Craugastor longirostris

6 6 Craugastor daryi Strabomantis anomalus Strabomantinae 9 Lynchius nebulanastes 6 7 Pristimantinae Oreobates quixensis Strabomantidae 2 5 Barycholos pulcher Holoadeninae 6 4 substitutions / site 100 Pristimantis miyatai 0.4 Pristimantis simonsii Pristimantinae G. 20% missing taxa/locus

Stefania coxi Barycholos pulcher Diasporus vocator 1 0 Hyloxalus nexipus Dendropsophus leali 6 Leptodactylus dydimus Craugastor augusti 1 Espadarana prosoblepon 4 4 Diasporus gularis Lynchius nebulanastes

3 Phyzelaphryne_miriame

8 Craugastor longirostris 3 7 Craugastor daryi Eleutherodactylus longipes 1 6 Eleutherodactylus johnstonei 1 Adelophryne adiastola 7 Pristimantis miyatai

3 Pristimantis simonsii

3 Oreobates quixensis

2 1 Strabomantis_anomalus substitutions / site 8 1 Brachycephalus quiririensis 0.5 H. 10% missing taxa/locus

2 7 Hyloxalus nexipus

Diasporus vocator

Leptodactylus dydimus

2 0 Dendropsophus leali

6 Espadarana prosoblepon

2 7 2 2 Diasporus gularis

Craugastor augusti

8 Barycholos pulcher

Pristimantis simonsii 2 9 Stefania coxi 1 4

6 8 Eleutherodactylus johnstonei

Eleutherodactylus longipes

4 0 Adelophryne adiastola

Pristimantis miyatai 1 Craugastor longirostris 6 Phyzelaphryne miriame 4 Lynchius nebulanastes 2 0

substitutions / site 3 8 Brachycephalus quiririensis 0.7 Oreobates quixensis