Supplementary Material

ZooKeys

Systematics of Neotropical microteiid lizards (Gymnophthalmidae, Cercosaurinae), with the description of a new genus and species from the Andean montane forests

Jiří Moravec, Jiří Šmíd, Jan Štundl, Edgar Lehr

SUPPLEMENTARY MATERIAL

Contents:

Figure S1. A complete tree of Cercosaurinae and outgroup taxa resulting from the ML analysis.

Figure S2. A 50% majority-rule consensus tree of Cercosaurinae and outgroup taxa resulting from the MrBayes analysis.

Figure S3. An MCC tree of Cercosaurinae and outgroup taxa resulting from the BEAST analysis.

Table S1. Samples of the Cercosaurinae and outgroup species used for the phylogenetic analyses and their respective GenBank accession numbers. Sample codes are those shown in tree figures. Voucher numbers correspond to those given in the original references.

References to Table S1.

P90roctoporus_pachyurus_Proc_pa_2 89Proctoporus_pachyurus_Proc_pa_3 95Proctoporus_pachyurus_Pro_pach_5 54Proctoporus_pachyurus_Pro_pach_4 18 Proctoporus_pachyurus_Proc_pa_1 69Proctoporus_oreades_Proc_or_1 Proctoporus_oreades_Proc_or_2100 Proctoporus_oreades_Proc_or_3 7 Proctoporus_spinalis_Proc_sp_396 Proctoporus_spinalis_Proc_sp_1100 96Proctoporus_spinalis_Proc_sp_2 3 Proctoporus_spinalis_Proc_sp_4 49 50Proctoporus_spinalis_IWU119 36Proctoporus_spinalis_IWU120 Proctoporus_spinalis_Proc_sp_5 70 Proctoporus_sp_1_Proc_s1_395 Proctoporus_sp_1_Proc_s1_2100 Proctoporus_sp_1_Proc_s1_1 Proctoporus_sp_5 _Pro_pach_3 42 Proctoporus_rahmi_Proc_ra_386 Proctoporus_rahmi_Proc_ra_1100 100Proctoporus_rahmi_Proc_ra_2 89 Proctoporus_rahmi_Pro_pach_1 Proctoporus_sp _Pro_pach_2 Proctoporus_chasqui_IWU5025 48 Proctoporus_chasqui_IWU8210 Proctoporus_chasqui_IWU24100 Proctoporus_chasqui_IWU25 41 Proctoporus_chasqui_Pro_chas_187 99Proctoporus_chasqui_Pro_chas_2 86 Proctoporus_chasqui_Pro_chas_3 90Proctoporus_chasqui_Proc_ch_1 88 98 62Proctoporus_chasqui_Proc_ch_2 Proctoporus_chasqui_IWU133 Proctoporus_chasqui_Proc_ch_3 66Proctoporus_chasqui_Pro_sp_1 Proctoporus_sucullucu_Pro_suc_290 31 85Proctoporus_sucullucu_Pro_suc_3 100Proctoporus_sucullucu_Pro_suc_4 100 Proctoporus_sucullucu_Pro_suc_1 Proctoporus_sucullucu_Pro_suc_5 98 Proctoporus_xestus_Pro_xes_1 Proctoporus_xestus_Pro_xes_2 Proctoporus_81 kiziriani _Proc_ca_1 Proctoporus_77 kiziriani _Proc_ca_3 35Proctoporus_kiziriani _Proc_ca_2 Proctoporus_30 kiziriani _Pro_bol_47 Proctoporus_kiziriani _Pro_bol_45 58 99Proctoporus_kiziriani _Pro_bol_48 86 Proctoporus_kiziriani _Pro_bol_50 Proctoporus_kiziriani _Pro_bol_49 99 89Proctoporus_kiziriani _Pro_bol_43 Proctoporus_64 kiziriani _Pro_bol_44 33Proctoporus_kiziriani _Pro_bol_41 34 52Proctoporus_kiziriani _Pro_bol_42 43 Proctoporus_kiziriani _Pro_bol_40 Proctoporus_16 kiziriani _Pro_bol_46 Proctoporus_61 carabaya _Pro_bol_37 92Proctoporus_carabaya _Pro_bol_38 100Proctoporus_carabaya _Pro_bol_39 Proctoporus_carabaya _Pro_bol_36 48Proctoporus_iridescens _Pro_bol_23 1Proctoporus_iridescens _Pro_bol_31 1Proctoporus_iridescens _Pro_bol_20 67 Proctoporus_99 iridescens _Pro_bol_21 Proctoporus_iridescens _Pro_bol_22 99 Proctoporus_81 iridescens _Pro_bol_29 98Proctoporus_iridescens _Pro_bol_28 15 Proctoporus_iridescens _Pro_bol_30 97Proctoporus_iridescens _Pro_bol_27 Proctoporus_70 iridescens _Pro_bol_26 98 27 100Proctoporus_iridescens _Pro_bol_25 Proctoporus_iridescens _Pro_bol_24 24 Proctoporus_iridescens _Pro_bol_34 15 100Proctoporus_iridescens _Pro_bol_35 100Proctoporus_iridescens _Pro_bol_32 Proctoporus_iridescens _Pro_bol_33 88Proctoporus_lacertus _Pro_bol_52 100Proctoporus_lacertus _Pro_bol_51 Proctoporus_lacertus _Pro_bol_53 Proctoporus_bolivianus_Pro_bol_653 63Proctoporus_bolivianus_Pro_bol_4 95Proctoporus_bolivianus_Pro_bol_5 100Proctoporus_bolivianus_Pro_bol_3 100 Proctoporus_bolivianus_Pro_bol_7 Proctoporus_bolivianus_Pro_bol_1100 Proctoporus_bolivianus_Pro_bol_2 80 Proctoporus_bolivianus_Pro_bol_1521 Proctoporus_bolivianus_Pro_bol_1315 Proctoporus_bolivianus_Pro_bol_12100 13 100 Proctoporus_bolivianus_Pro_bol_14100 Proctoporus_bolivianus_Pro_bol_11 81Proctoporus_bolivianus_Pro_bol_8 93 Proctoporus_bolivianus_Pro_bol_10100 Proctoporus_bolivianus_Pro_bol_9 98Proctoporus_Ca1 _Pro_bol_16 100 Proctoporus_Ca1 _Pro_bol_18 Proctoporus_Ca1 _Pro_bol_17 Proctoporus_sp_2_Proc_s2_131 Proctoporus_sp_2_Proc_s2_39 Proctoporus_sp_2_Proc_s2_2100 Proctoporus_sp_2_Proc_s2_4 51 43 Proctoporus_unsaacae_Pro_uns_4 71 Proctoporus_unsaacae_Pro_uns_3 99 Proctoporus_unsaacae_Proc_un_1 100 Proctoporus_guentheri_Pro_gue_2 Proctoporus_guentheri_Pro_gue_1 96 Proctoporus_sp_3_Proc_s3_2100 79 Proctoporus_sp_3_Proc_s3_1 Proctoporus_sp_4_IWU358 96 Proctoporus_laudahnae_Proc_la_1100 75 Proctoporus_laudahnae_Proc_la_2 Proctoporus_Ca2 _Pro_bol_19 Potamites_trachodus_Pota_tr_382 100Potamites_trachodus_Pota_tr_4 81 Potamites_trachodus_Pota_tr_2 88 Potamites_strangulatus_Pota_st_1 48 Potamites_strangulatus_Pot_str_1 64 Potamites_ecpleopus_Pota_ec_4 100 Potamites_ecpleopus_Pota_ec_3 Potamites_ecpleopus_Pota_ec_2 28 36 96Potamites_ecpleopus_186_1 88 Potamites_ecpleopus_186_2 88 Potamites_ecpleopus_Pota_ec_1 79 Potamites_ecpleopus_Pot_ecp_1 100Potamites_erythrocularis_Pota_er_2 93 Potamites_erythrocularis_Pota_er_1 60Potamites_juruazensis_Pota_ju_2 100Potamites_juruazensis_Pota_ju_5 Potamites_juruazensis_Pota_ju_485 99 Potamites_juruazensis_Pota_ju_3 69 96 Potamites_juruazensis_Pot_jur_1 Potamites_juruazensis_Pota_ju_1 Potamites_montanicola_Pota_mo_1 47 S34elvasaur a_brava_IWU340 S95elvasaur a_brava_IWU381 S100elvasaur a_brava_IWU382 82Selvasaur a_brava_IWU339 71 Selvasaur a_brava_IWU380 31 52 Selvasaur a_sp _Cerc_s3_5 S21elvasaur a_sp _Cerc_s3_1 96 S100elvasaur a_sp _Cerc_s3_3 Selvasaur a_sp _Cerc_s3_2 Selvasaur a_sp _Cerc_s3_4 91 Unnamed_clade_IV_ML1352 Unnamed_clade_IV_EL409 94Cercosaura_oshaughnessyi _155_2 71 Cercosaura_oshaughnessyi _160_1 Cercosaura_oshaughnessyi_Cer_osh_1 100 Cercosaura_oshaughnessyi_Cerc_os_1100 69 99 Cercosaura_oshaughnessyi _Cer_arg_1 100 Cercosaura_oshaughnessyi_Cerc_os_2 Cercosaura_argulus_Cer_arg_4 19 49 97 Cercosaura_argulus_Cer_arg_2 97 Cercosaura_argulus_184 71 Cercosaura_argulus_Cer_arg_3 94 Cercosaura_parkeri_Cer_par_2 50 Cercosaura_schreibersii_Cer_schr_1 100 Cercosaura_parkeri_Cer_par_1 89 Cercosaura_schreibersii_albostrigatus_Cer_schr_2 46 Cercosaura_eigenmanni_Cer_eig_2 70 Cercosaura_eigenmanni_Cer_eig_112 100 Cercosaura_eigenmanni_Cer_eig_609 85 Cercosaura_eigenmanni_Cer_eig_1 43 99 Cercosaura_bassleri _Cerc_oc_1 88 Cercosaura_bassleri_Cerc_ba_1 78 Cercosaura_ocellata_Cer_oce_1 Cercosaura_quadrilineata_Cer_qua_1 60 100 Cercosaura_manicata_Cerc_ma_2 100 Cercosaura_manicata_Cerc_ma_1 Cercosaura_doanae_Cerc_do_1 Unnamed_clade_II_90100 25 Unnamed_clade_II_91 53 Unnamed_clade_II_Cerc_s2_1 93 Unnamed_clade_II_Cerc_s2_3 38 Unnamed_clade_II_Cerc_s2_2 14 Unnamed_clade_II_IWU114 34 Unnamed_clade_II_IWU57 26 Unnamed_clade_II_IWU165 100 Unnamed_clade_II_IWU29663 Unnamed_clade_II_IWU325100 48 Unnamed_clade_II_IWU320 Unnamed_clade_II_IWU28899 Unnamed_clade_II_IWU287 67 Petracola_ventrimaculatus_Pet_ven_1 93 Petracola_ventrimaculatus_Pet_ven_2 Petracola_waka_Petr_wa_1 "100Oreosaurus " _ serranus _Oreo_SN2 "Oreosaurus " _ serranus _Oreo_SN1 Pholidobolus_montium_Pho_mon_597 98Pholidobolus_montium_Pho_mon_1 100Pholidobolus_montium_Pho_mon_2 88 Pholidobolus_montium_Pho_mon_3 Pholidobolus_affinis_Pho_aff_1 25 100Pholidobolus_affinis_Pho_aff_2 100Pholidobolus_prefrontalis_Pho_pre_2 Pholidobolus_prefrontalis_Pho_pre_1 85 100Pholidobolus_macbrydei_Pho_mac_3 98 Pholidobolus_macbrydei_Pho_mac_1 34 19 Pholidobolus_macbrydei_Pho_mac_2 63 Pholidobulus_vertebralis_Phol_ve_1 Pholidobulus_dicrus_Phol_di_1 63 Pholidobolus_hillisi_Pho_hil_381 Pholidobolus_hillisi_Pho_hil_1100 Pholidobolus_hillisi_Pho_hil_2 82 Pholidobolus_sp1_84391 93Pholidobolus_sp1_JCM239 66 Pholidobolus_sp1_JCM238 100 Pholidobolus_ulisesi _Phol_sp 98 Pholidobolus_ulisesi _JCM310 Macropholidus_annectens_Mac_ann_1100 100 Macropholidus_annectens_Mac_ann_2 64 Macropholidus_sp_Macr_sp Macropholidus_ruthveni_Mac_rut_1 21 92 Macropholidus_huancabambae_Mac_hua_1100 Macropholidus_huancabambae_Mac_hua_2100 100 Macropholidus_huancabambae_Mac_hua_3 Euspondylus_excelsum_Cerc_s1_1100 98 Euspondylus_excelsum_Cerc_s1_2 35 Euspondylus_excelsum_IWU234 46 "Echinosaura_sulcarostrum " _Echi_sul_1 49Anadia_rhombifera_Anad_rhomb 100 Anadia_rhombifera_Anad_rhomb5 100 Anadia_rhombifera_Anad_rhomb2 Anadia_rhombifera_Anad_rhomb6 100 Anadia_rhombifera_Anad_rhomb3100 62 83 Anadia_rhombifera_Anad_rhomb4 100 Anadia_rhombifera_Anad_rhomb7 91 Anadia_petersi_Anad_rhomb_peters 70 Anadia_petersi_Anad_rhomb_peters2 Anadia_ocellata_SMF90095 31 Oreosaurus_shrevei_Oreo_shr 64 Oreosaurus_Venezuela_Oreo_Ven 80 Oreosaurus_achlyens_Oreo_ach Oreosaurus_mcdiarmidi_Ore_mcd_1 100Gelanesaurus_flavogularis_Gela_fl_2 100 Gelanesaurus_flavogularis_Gela_fl_1 100Gelanesaurus_cochranae_Gela_co_2 Gelanesaurus_cochranae_Gela_co_1 Andinosaura_vespertina_Andin_ves_1100 23 96 Andinosaura_vespertina_Andin_ves_2 Andinosaura_aurea_Andin_aur_2100 100 Andinosaura_aurea_Andin_aur_1 100 Andinosaura_kiziriani_Andin_kiz_2 Andinosaura_kiziriani_Andin_kiz_1 72 100 Andinosaura_crypta_Andin_cry_2 52 Andinosaura_crypta_Andin_cry_1 100Andinosaura_oculata_Andin_ocu_2 36 Andinosaura_oculata_Andin_ocu_1 86 100 Andinosaura_hyposticta_Andin_hyp_1 Andinosaura_hyposticta_Andin_hyp_2 Andinosaura_afrania_Andin_afr_1100 100 Andinosaura_afrania_Andin_afr_2 100 Andinosaura_laevis_Andin_lae Andinosaura_vieta_Andin_vie_2100 63 Andinosaura_vieta_Andin_vie_1 100Echinosaura_keyi_Echi_ke_2 40 Echinosaura_keyi_Echi_ke_1 Echinosaura_orcesi_Echi_or_1100 59 Echinosaura_orcesi_Echi_or_2 100 Echinosaura_brachycephala_Echi_br_1 100Echinosaura_horrida_Echi_ho_2 Echinosaura_horrida_Echi_ho_1 Riama_meleagris_Ria_mel_227 Riama_meleagris_Ria_mel_566 Riama_meleagris_Ria_mel_1100 Riama_meleagris_Ria_mel_365 Riama_meleagris_Ria_mel_4 85 49Riama_stigmatoral_Ria_stig_4 100Riama_stigmatoral_Ria_stig_2 100 Riama_stigmatoral_Ria_stig_3 76 25 Riama_stigmatoral_Ria_stig_1 100Riama_yumborum_Ria_yum_2 47 Riama_yumborum_Ria_yum_1 89 Riama_labionis_Ria_lab_1 Riama_labionis_Ria_lab_2100 Riama_cashcaensis_Ria_cas_3100 Riama_cashcaensis_Ria_cas_2 Riama_unicolor_Ria_uni_187 Riama_unicolor_Ria_uni_285 100 14Riama_unicolor_Ria_uni_6 28Riama_unicolor_Ria_uni_9 Riama_unicolor_Ria_uni_780 52Riama_unicolor_Ria_uni_8 Riama_unicolor_Ria_uni_484 95Riama_unicolor_Ria_uni_3 100 Riama_unicolor_Ria_uni_10 84Riama_unicolor_Ria_uni_5 97 Riama_unicolor_Ria_uni_11 100Riama_Narino_Ria_N1 47 Riama_Narino_Ria_N2 71Riama_colomaromani_Ria_col_2 95 Riama_colomaromani_Ria_col_1 78Riama_simotera_Ria_sp_1 100 70Riama_simotera_Ria_sim_2 90 Riama_simotera_Ria_sim_1 100Riama_anatoloros_Ria_an_3 73 Riama_anatoloros_Ria_an_1 84 Riama_anatoloros_Ria_an_2 100 99 Riama_raneyi_Ria_ran_1 Riama_raneyi_Ria_ran_2 100 Riama_columbiana_Ria_columb_2 100 Riama_columbiana_Ria_columb_1 Riama_Cordillera_Central_Ria_CC1100 65 Riama_Cordillera_Central_Ria_CC2 100 Riama_striata_Ria_str_2 100 Riama_striata_Ria_str_1 Riama_Cordillera_Occidental_Ria_CO1 100 Riama_orcesi_Ria_orc_294 100Riama_orcesi_Ria_orc_3 100 Riama_orcesi_Ria_orc_1 Riama_balneator_Ria_ba_2 100 Riama_balneator_Ria_ba_1 Neusticurus_aff_rudis_Neu_rud_6 81 67Neusticurus_aff_rudis_Neu_rud_15 35 23 Neusticurus_aff_rudis_Neu_rud_16 Neusticurus_aff_rudis_Neu_rud_1374 100Neusticurus_aff_rudis_Neu_rud_11 85 Neusticurus_aff_rudis_Neu_rud_12 Neusticurus_aff_rudis_Neu_rud_8 79 Neusticurus_aff_rudis_Neu_rud_398 Neusticurus_aff_rudis_Neu_rud_280 95 Neusticurus_aff_rudis_Neu_rud_10 Neusticurus_aff_rudis_Neu_rud_498 44 Neusticurus_aff_rudis_Neu_rud_5 98 Neusticurus_aff_rudis_Neu_rud_9 Neusticurus_aff_rudis_Neu_rud_7 100 100 65 Neusticurus_rudis_Neu_rud_1 Neusticurus_bicarinatus_Neu_bic_1 100 Placosoma_glabellum_Pla_gla_1 Placosoma_cordylinum_Pla_cor_1 57 Gymnophthalmus_leucomystax_Gymn_le_1 13 Rhachisaurus_brachylepis_Rhac_br_1 Bachia_scaea_Bach_sca_3100 Bachia_scaea_Bach_sca_2100 41 Bachia_scaea_Bach_sca_1 38 Bachia_dorbignyi_Bach_dor_1 32 Bachia_trisanale_Bach_tri_1 33Bachia_monodactylus_Bach_mon_2 12 Bachia_panoplia_Bach_pan_1 9 Bachia_peruana_Bach_per_1 15 Bachia_bicolor_Bach_bic_1 16 Bachia_barbouri_Bach_bar_1 22 Bachia_intermedia_Bach_int_1 Bachia_monodactylus_parkerii_Bach_mon_1 69 100Bachia_huallagana_Bach_hua_1 38 Bachia_scolecoides_Bach_sco_1 59 32 Bachia_heteropa_Bach_het_1 100 Bachia_heteropa_Bach_het_2 Bachia_bresslaui_Bach_bre_1 Bachia_flavescens_Bach_fla_1 99Riolama_leucosticta_Rio_leu_1 100 Riolama_leucosticta_Rio_leu_2 100 Riolama_leucosticta_Rio_leu_3 28 Riolama_inopinata_Rio_ino_1 Ecpleopus_gaudichaudii_Ecpl_ga_1 Alopoglossus_viridiceps_Alop_vi_1

0.06 Figure S1. A complete tree of Cercosaurinae and outgroup taxa resulting from the ML analysis. 2

Proctoporus_spinalis_Proc_sp_1 1Proctoporus_spinalis_Proc_sp_2 1Proctoporus_spinalis_Proc_sp_3 0.94Proctoporus_spinalis_Proc_sp_4 0.82 Proctoporus_spinalis_Proc_sp_5 0.84Proctoporus_spinalis_IWU119 0.56 Proctoporus_spinalis_IWU120 Proctoporus_sp_1_Proc_s1_1 1Proctoporus_sp_1_Proc_s1_2 Proctoporus_sp_1_Proc_s1_3 Proctoporus_pachyurus_Pro_pach_5 1Proctoporus_pachyurus_Proc_pa_2 0.86 Proctoporus_pachyurus_Proc_pa_3 1Proctoporus_pachyurus_Pro_pach_4 Proctoporus_pachyurus_Proc_pa_1 0.95 Proctoporus_oreades_Proc_or_1 1Proctoporus_oreades_Proc_or_2 Proctoporus_oreades_Proc_or_3 0.95 Proctoporus_sp_5 _Pro_pach_3 Proctoporus_rahmi_Proc_ra_1 1Proctoporus_rahmi_Proc_ra_2 1 Proctoporus_rahmi_Proc_ra_3 1 Proctoporus_rahmi_Pro_pach_1 Proctoporus_sp _Pro_pach_2 Proctoporus_chasqui_IWU24 0.71 Proctoporus_chasqui_IWU25 0.99Proctoporus_chasqui_IWU50 Proctoporus_chasqui_IWU82 0.98Proctoporus_chasqui_Pro_chas_1 0.921Proctoporus_chasqui_Pro_chas_2 Proctoporus_chasqui_Pro_chas_3 Proctoporus_chasqui_Proc_ch_1 1 0.99 1 0.92Proctoporus_chasqui_Proc_ch_2 Proctoporus_chasqui_IWU133 Proctoporus_chasqui_Pro_sp_1 1 Proctoporus_chasqui_Proc_ch_3 Proctoporus_sucullucu_Pro_suc_2 0.76 0.61Proctoporus_sucullucu_Pro_suc_3 1 Proctoporus_sucullucu_Pro_suc_4 1 Proctoporus_sucullucu_Pro_suc_1 Proctoporus_sucullucu_Pro_suc_5 1 Proctoporus_xestus_Pro_xes_1 Proctoporus_xestus_Pro_xes_2 Proctoporus_iridescens _Pro_bol_20 Proctoporus_iridescens _Pro_bol_21 1Proctoporus_iridescens _Pro_bol_22 Proctoporus_iridescens _Pro_bol_23 1 Proctoporus_iridescens _Pro_bol_31 0.56Proctoporus_iridescens _Pro_bol_28 1Proctoporus_iridescens _Pro_bol_30 Proctoporus_iridescens _Pro_bol_29 0.76 0.51Proctoporus_iridescens _Pro_bol_26 0.98Proctoporus_iridescens _Pro_bol_27 1Proctoporus_iridescens _Pro_bol_25 Proctoporus_iridescens _Pro_bol_24 0.98 0.62 1Proctoporus_iridescens _Pro_bol_32 0.7 Proctoporus_iridescens _Pro_bol_33 1 Proctoporus_iridescens _Pro_bol_34 Proctoporus_iridescens _Pro_bol_35 0.51 1Proctoporus_kiziriani _Pro_bol_48 1 Proctoporus_kiziriani _Pro_bol_50 Proctoporus_kiziriani _Pro_bol_49 Proctoporus_kiziriani _Proc_ca_1 0.72Proctoporus_kiziriani _Proc_ca_2 0.59Proctoporus_kiziriani _Proc_ca_3 Proctoporus_kiziriani _Pro_bol_45 Proctoporus_kiziriani _Pro_bol_47 1 1 Proctoporus_kiziriani _Pro_bol_40 Proctoporus_kiziriani _Pro_bol_41 0.58Proctoporus_kiziriani _Pro_bol_42 Proctoporus_kiziriani _Pro_bol_43 0.74Proctoporus_kiziriani _Pro_bol_44 Proctoporus_kiziriani _Pro_bol_46 1 Proctoporus_carabaya _Pro_bol_37 0.95 0.84Proctoporus_carabaya _Pro_bol_38 1Proctoporus_carabaya _Pro_bol_39 Proctoporus_carabaya _Pro_bol_36 0.59Proctoporus_lacertus _Pro_bol_51 1 Proctoporus_lacertus _Pro_bol_52 Proctoporus_lacertus _Pro_bol_53 Proctoporus_bolivianus_Pro_bol_3 Proctoporus_bolivianus_Pro_bol_4 1Proctoporus_bolivianus_Pro_bol_5 1 Proctoporus_bolivianus_Pro_bol_6 1 Proctoporus_bolivianus_Pro_bol_7 1Proctoporus_bolivianus_Pro_bol_1 Proctoporus_bolivianus_Pro_bol_2 0.82 Proctoporus_bolivianus_Pro_bol_11 Proctoporus_bolivianus_Pro_bol_12 1Proctoporus_bolivianus_Pro_bol_13 1 0.95 Proctoporus_bolivianus_Pro_bol_14 Proctoporus_bolivianus_Pro_bol_15 Proctoporus_bolivianus_Pro_bol_10 1 1Proctoporus_bolivianus_Pro_bol_8 Proctoporus_bolivianus_Pro_bol_9 1Proctoporus_Ca1 _Pro_bol_16 1 Proctoporus_Ca1 _Pro_bol_18 Proctoporus_Ca1 _Pro_bol_17 Proctoporus_sp_2_Proc_s2_1 1Proctoporus_sp_2_Proc_s2_2 Proctoporus_sp_2_Proc_s2_3 0.75 Proctoporus_sp_2_Proc_s2_4 0.55 Proctoporus_unsaacae_Pro_uns_3 1 0.98 Proctoporus_unsaacae_Pro_uns_4 Proctoporus_unsaacae_Proc_un_1 1 Proctoporus_guentheri_Pro_gue_1 Proctoporus_guentheri_Pro_gue_2 1 1Proctoporus_laudahnae_Proc_la_1 0.99 Proctoporus_laudahnae_Proc_la_2 Proctoporus_Ca2 _Pro_bol_19 1 1Proctoporus_sp_3_Proc_s3_1 1 Proctoporus_sp_3_Proc_s3_2 Proctoporus_sp_4_IWU358 0.68Potamites_trachodus_Pota_tr_3 1Potamites_trachodus_Pota_tr_4 1 Potamites_trachodus_Pota_tr_2 0.99 Potamites_strangulatus_Pot_str_1 0.9 Potamites_strangulatus_Pota_st_1 0.87 Potamites_ecpleopus_Pota_ec_3 1 Potamites_ecpleopus_Pota_ec_4 Potamites_ecpleopus_Pota_ec_2 0.76 Potamites_ecpleopus_186_1 1 1 0.97 Potamites_ecpleopus_186_2 1 Potamites_ecpleopus_Pota_ec_1 1 Potamites_ecpleopus_Pot_ecp_1 1 Potamites_erythrocularis_Pota_er_1 1 Potamites_erythrocularis_Pota_er_2 Potamites_juruazensis_Pota_ju_2 0.93Potamites_juruazensis_Pota_ju_5 1Potamites_juruazensis_Pota_ju_3 1 Potamites_juruazensis_Pota_ju_4 1 Potamites_juruazensis_Pot_jur_1 1 Potamites_juruazensis_Pota_ju_1 Potamites_montanicola_Pota_mo_1 0.55 0.98Selvasaur a_brava_IWU339 Selvasaur a_brava_IWU380 1Selvasaur a_brava_IWU340 Selvasaur a_brava_IWU381 0.73 Selvasaur a_brava_IWU382 0.85 0.67 Selvasaur a_sp _Cerc_s3_5 Selvasaur a_sp _Cerc_s3_1 1 1Selvasaur a_sp _Cerc_s3_2 Selvasaur a_sp _Cerc_s3_3 Selvasaur a_sp _Cerc_s3_4 1 Unnamed_clade_IV_EL409 Unnamed_clade_IV_ML1352 1Cercosaura_oshaughnessyi _Cer_arg_1 1 Cercosaura_oshaughnessyi_Cerc_os_1 Cercosaura_oshaughnessyi_Cerc_os_2 1 1 Cercosaura_oshaughnessyi _155_2 Cercosaura_oshaughnessyi _160_1 1 0.86 1 Cercosaura_oshaughnessyi_Cer_osh_1 Cercosaura_argulus_Cer_arg_2 0.99 0.58 1 Cercosaura_argulus_Cer_arg_4 1 Cercosaura_argulus_184 0.97 Cercosaura_argulus_Cer_arg_3 1 Cercosaura_parkeri_Cer_par_2 Cercosaura_schreibersii_Cer_schr_1 1 Cercosaura_parkeri_Cer_par_1 1 Cercosaura_schreibersii_albostrigatus_Cer_schr_2 0.55 Cercosaura_eigenmanni_112 0.88 Cercosaura_eigenmanni_Cer_eig_2 1 Cercosaura_eigenmanni_609 1 Cercosaura_eigenmanni_Cer_eig_1 0.72 1 Cercosaura_bassleri_Cerc_ba_1 1 Cercosaura_bassleri _Cerc_oc_1 1 Cercosaura_ocellata_Cer_oce_1 Cercosaura_quadrilineata_Cer_qua_1 0.99 1 Cercosaura_manicata_Cerc_ma_1 1 Cercosaura_manicata_Cerc_ma_2 Cercosaura_doanae_Cerc_do_1 Unnamed_clade_II_Cerc_s2_2 1 Unnamed_clade_II_Cerc_s2_3 0.79 Unnamed_clade_II_90 1Unnamed_clade_II_91 0.63 Unnamed_clade_II_Cerc_s2_1 Unnamed_clade_II_IWU114 Unnamed_clade_II_IWU296 0.76 1Unnamed_clade_II_IWU320 0.88 Unnamed_clade_II_IWU325 1 1 Unnamed_clade_II_IWU287 Unnamed_clade_II_IWU288 Unnamed_clade_II_IWU165 Unnamed_clade_II_IWU57 0.85 Petracola_ventrimaculatus_Pet_ven_1 1 Petracola_ventrimaculatus_Pet_ven_2 Petracola_waka_Petr_wa_1 1"Oreosaurus " _ serranus _Oreo_SN1 "Oreosaurus " _ serranus _Oreo_SN2 0.88Pholidobolus_montium_Pho_mon_1 0.63Pholidobolus_montium_Pho_mon_5 1Pholidobolus_montium_Pho_mon_2 1 Pholidobolus_montium_Pho_mon_3 1 Pholidobolus_affinis_Pho_aff_1 Pholidobolus_affinis_Pho_aff_2 1Pholidobolus_macbrydei_Pho_mac_1 Pholidobolus_macbrydei_Pho_mac_3 1 1 0.6 Pholidobolus_macbrydei_Pho_mac_2 1 Pholidobulus_dicrus_Phol_di_1 Pholidobulus_vertebralis_Phol_ve_1 0.82 1Pholidobolus_prefrontalis_Pho_pre_1 Pholidobolus_prefrontalis_Pho_pre_2 0.97 Pholidobolus_hillisi_Pho_hil_1 1Pholidobolus_hillisi_Pho_hil_2 Pholidobolus_hillisi_Pho_hil_3 0.91 0.97Pholidobolus_sp1_843 1Pholidobolus_sp1_JCM239 0.93 Pholidobolus_sp1_JCM238 1 Pholidobolus_ulisesi _Phol_sp 1 Pholidobolus_ulisesi _JCM310 1Macropholidus_annectens_Mac_ann_1 1 Macropholidus_annectens_Mac_ann_2 0.84 Macropholidus_sp_Macr_sp Macropholidus_ruthveni_Mac_rut_1 1 Macropholidus_huancabambae_Mac_hua_1 0.73 1Macropholidus_huancabambae_Mac_hua_2 Macropholidus_huancabambae_Mac_hua_3 1 0.71Anadia_rhombifera_Anad_rhomb 1 Anadia_rhombifera_Anad_rhomb5 1 Anadia_rhombifera_Anad_rhomb2 Anadia_rhombifera_Anad_rhomb6 1 1Anadia_rhombifera_Anad_rhomb3 0.97 0.98 Anadia_rhombifera_Anad_rhomb4 1 Anadia_rhombifera_Anad_rhomb7 1 Anadia_petersi_Anad_rhomb_peters 0.75 Anadia_petersi_Anad_rhomb_peters2 1 Anadia_ocellata_SMF90095 1Euspondylus_excelsum_Cerc_s1_1 1 Euspondylus_excelsum_Cerc_s1_2 0.96 Euspondylus_excelsum_IWU234 "Echinosaura_sulcarostrum " _Echi_sul_1 0.6 Oreosaurus_achlyens_Oreo_ach 0.91 Oreosaurus_Venezuela_Oreo_Ven 1 Oreosaurus_shrevei_Oreo_shr Oreosaurus_mcdiarmidi_Ore_mcd_1 1 Gelanesaurus_cochranae_Gela_co_1 1 Gelanesaurus_cochranae_Gela_co_2 1Gelanesaurus_flavogularis_Gela_fl_1 Gelanesaurus_flavogularis_Gela_fl_2 0.97Riama_meleagris_Ria_mel_3 Riama_meleagris_Ria_mel_4 Riama_meleagris_Ria_mel_11 Riama_meleagris_Ria_mel_2 Riama_meleagris_Ria_mel_5 1 0.53Riama_stigmatoral_Ria_stig_3 1Riama_stigmatoral_Ria_stig_4 1 Riama_stigmatoral_Ria_stig_2 Riama_stigmatoral_Ria_stig_1 1Riama_labionis_Ria_lab_1 1 Riama_labionis_Ria_lab_2 0.54 Riama_yumborum_Ria_yum_1 1Riama_yumborum_Ria_yum_2 Riama_cashcaensis_Ria_cas_2 1Riama_cashcaensis_Ria_cas_3 Riama_unicolor_Ria_uni_1 0.98Riama_unicolor_Ria_uni_2 1 Riama_unicolor_Ria_uni_6 1Riama_unicolor_Ria_uni_7 Riama_unicolor_Ria_uni_8 0.85Riama_unicolor_Ria_uni_9 0.99Riama_unicolor_Ria_uni_3 1 Riama_unicolor_Ria_uni_4 Riama_unicolor_Ria_uni_10 1 Riama_unicolor_Ria_uni_5 1 Riama_unicolor_Ria_uni_11 0.99Riama_simotera_Ria_sim_2 0.7Riama_simotera_Ria_sp_1 0.51 Riama_simotera_Ria_sim_1 1Riama_Narino_Ria_N1 0.51 Riama_Narino_Ria_N2 0.99 1 Riama_colomaromani_Ria_col_2 1 Riama_colomaromani_Ria_col_1 1 1 Riama_anatoloros_Ria_an_1 0.97 Riama_anatoloros_Ria_an_3 0.99 Riama_anatoloros_Ria_an_2 1 Riama_raneyi_Ria_ran_1 Riama_raneyi_Ria_ran_2 1 1 Riama_columbiana_Ria_columb_1 Riama_columbiana_Ria_columb_2 0.94Riama_orcesi_Ria_orc_2 1 Riama_orcesi_Ria_orc_3 1 Riama_orcesi_Ria_orc_1 1Riama_balneator_Ria_ba_1 Riama_balneator_Ria_ba_2 1 1Riama_Cordillera_Central_Ria_CC1 0.87 Riama_Cordillera_Central_Ria_CC2 Riama_striata_Ria_str_1 1 1 Riama_striata_Ria_str_2 Riama_Cordillera_Occidental_Ria_CO1 0.96Andinosaura_afrania_Andin_afr_1 1 Andinosaura_afrania_Andin_afr_2 1 Andinosaura_laevis_Andin_lae 1Andinosaura_vieta_Andin_vie_1 0.57 Andinosaura_vieta_Andin_vie_2 1 Andinosaura_hyposticta_Andin_hyp_1 Andinosaura_hyposticta_Andin_hyp_2 0.52 1Andinosaura_aurea_Andin_aur_1 Andinosaura_aurea_Andin_aur_2 1 Andinosaura_vespertina_Andin_ves_1 1 1 1 Andinosaura_vespertina_Andin_ves_2 Andinosaura_kiziriani_Andin_kiz_1 1 1 Andinosaura_kiziriani_Andin_kiz_2 Andinosaura_crypta_Andin_cry_1 1 Andinosaura_crypta_Andin_cry_2 1Andinosaura_oculata_Andin_ocu_1 0.75 Andinosaura_oculata_Andin_ocu_2 1Echinosaura_horrida_Echi_ho_1 0.74 Echinosaura_horrida_Echi_ho_2 0.51 Echinosaura_brachycephala_Echi_br_1 1Echinosaura_keyi_Echi_ke_1 1 Echinosaura_keyi_Echi_ke_2 1Echinosaura_orcesi_Echi_or_1 Echinosaura_orcesi_Echi_or_2 Neusticurus_aff_rudis_Neu_rud_11 0.52Neusticurus_aff_rudis_Neu_rud_12 0.63 Neusticurus_aff_rudis_Neu_rud_13 1 0.76Neusticurus_aff_rudis_Neu_rud_15 0.95 Neusticurus_aff_rudis_Neu_rud_6 0.96 Neusticurus_aff_rudis_Neu_rud_16 0.96Neusticurus_aff_rudis_Neu_rud_3 0.99 Neusticurus_aff_rudis_Neu_rud_8 Neusticurus_aff_rudis_Neu_rud_10 Neusticurus_aff_rudis_Neu_rud_2 1 0.84Neusticurus_aff_rudis_Neu_rud_4 Neusticurus_aff_rudis_Neu_rud_5 1 Neusticurus_aff_rudis_Neu_rud_9 1 Neusticurus_rudis_Neu_rud_1 1 0.58 Neusticurus_aff_rudis_Neu_rud_7 Neusticurus_bicarinatus_Neu_bic_1 1 Placosoma_cordylinum_Pla_cor_1 Placosoma_glabellum_Pla_gla_1 0.93 Gymnophthalmus_leucomystax_Gymn_le_1 Rhachisaurus_brachylepis_Rhac_br_1 Bachia_scaea_Bach_sca_1 1Bachia_scaea_Bach_sca_2 0.98 Bachia_scaea_Bach_sca_3 0.97 Bachia_trisanale_Bach_tri_1 0.98Bachia_monodactylus_Bach_mon_2 Bachia_panoplia_Bach_pan_1 1 0.97Bachia_barbouri_Bach_bar_1 Bachia_peruana_Bach_per_1 0.97 Bachia_bicolor_Bach_bic_1 0.97 Bachia_intermedia_Bach_int_1 Bachia_monodactylus_parkerii_Bach_mon_1 0.99 0.98 Bachia_dorbignyi_Bach_dor_1 0.98 Bachia_heteropa_Bach_het_1 0.99Bachia_huallagana_Bach_hua_1 0.89 0.98 Bachia_scolecoides_Bach_sco_1 1 Bachia_heteropa_Bach_het_2 Bachia_bresslaui_Bach_bre_1 Bachia_flavescens_Bach_fla_1 1 Riolama_leucosticta_Rio_leu_1 1 Riolama_leucosticta_Rio_leu_2 1 Riolama_leucosticta_Rio_leu_3 0.54 Riolama_inopinata_Rio_ino_1 Ecpleopus_gaudichaudii_Ecpl_ga_1 Alopoglossus_viridiceps_Alop_vi_1

0.1 Figure S2. A 50% majority-rule consensus tree of Cercosaurinae and outgroup taxa resulting from the MrBayes analysis. 3

0.51Proctoporus_pachyurus_Proc_pa_2 1Proctoporus_pachyurus_Proc_pa_3 1 Proctoporus_pachyurus_Pro_pach_5 0.76Proctoporus_pachyurus_Pro_pach_4 0.53 Proctoporus_pachyurus_Proc_pa_1 0.22Proctoporus_oreades_Proc_or_1 1Proctoporus_oreades_Proc_or_3 0.33 Proctoporus_oreades_Proc_or_2 0.23Proctoporus_sp_1_Proc_s1_1 1Proctoporus_sp_1_Proc_s1_2 Proctoporus_sp_1_Proc_s1_3 0.72 0.33Proctoporus_spinalis_Proc_sp_1 1Proctoporus_spinalis_Proc_sp_3 1 Proctoporus_spinalis_Proc_sp_2 0.96 0.99 Proctoporus_spinalis_Proc_sp_4 0.67 Proctoporus_spinalis_Proc_sp_5 Proctoporus_spinalis_IWU119 0.95 Proctoporus_spinalis_IWU120 0.72 Proctoporus_sp_5 _Pro_pach_3 0.32Proctoporus_rahmi_Proc_ra_2 1Proctoporus_rahmi_Proc_ra_3 1 Proctoporus_rahmi_Proc_ra_1 1 Proctoporus_rahmi_Pro_pach_1 Proctoporus_sp _Pro_pach_2 0.22Proctoporus_chasqui_IWU24 0.96 1Proctoporus_chasqui_IWU82 0.22Proctoporus_chasqui_IWU25 0.41 Proctoporus_chasqui_IWU50 0.99Proctoporus_chasqui_Pro_chas_1 1Proctoporus_chasqui_Pro_chas_2 0.86 Proctoporus_chasqui_Pro_chas_3 1 Proctoporus_chasqui_Proc_ch_1 1 1 0.95 Proctoporus_chasqui_Proc_ch_2 Proctoporus_chasqui_IWU133 Proctoporus_chasqui_Pro_sp_1 1 Proctoporus_chasqui_Proc_ch_3 Proctoporus_sucullucu_Pro_suc_1 0.59 0.05 1 Proctoporus_sucullucu_Pro_suc_3 0.25Proctoporus_sucullucu_Pro_suc_2 1 Proctoporus_sucullucu_Pro_suc_4 Proctoporus_sucullucu_Pro_suc_5 1 Proctoporus_xestus_Pro_xes_1 Proctoporus_xestus_Pro_xes_2 0.07Proctoporus_kiziriani _Pro_bol_47 0.43Proctoporus_kiziriani _Proc_ca_2 0.3Proctoporus_kiziriani _Proc_ca_1 0.47Proctoporus_kiziriani _Proc_ca_3 0.59Proctoporus_kiziriani _Pro_bol_45 0.55Proctoporus_kiziriani _Pro_bol_49 1 Proctoporus_kiziriani _Pro_bol_48 Proctoporus_kiziriani _Pro_bol_50 1 0.2Proctoporus_kiziriani _Pro_bol_41 0.48Proctoporus_kiziriani _Pro_bol_42 0.47Proctoporus_kiziriani _Pro_bol_43 0.96Proctoporus_kiziriani _Pro_bol_44 0.88 0.89 0.39Proctoporus_kiziriani _Pro_bol_40 Proctoporus_kiziriani _Pro_bol_46 0.57Proctoporus_carabaya _Pro_bol_37 0.78Proctoporus_carabaya _Pro_bol_38 1 Proctoporus_carabaya _Pro_bol_39 0.37 Proctoporus_carabaya _Pro_bol_36 0.14Proctoporus_iridescens _Pro_bol_22 0.13Proctoporus_iridescens _Pro_bol_23 1Proctoporus_iridescens _Pro_bol_21 0.12Proctoporus_iridescens _Pro_bol_20 0.26 1 Proctoporus_iridescens _Pro_bol_31 0.34Proctoporus_iridescens _Pro_bol_29 1 Proctoporus_iridescens _Pro_bol_30 Proctoporus_iridescens _Pro_bol_28 1 Proctoporus_iridescens _Pro_bol_32 1 0.5 Proctoporus_iridescens _Pro_bol_33 1 Proctoporus_iridescens _Pro_bol_34 Proctoporus_iridescens _Pro_bol_35 0.4Proctoporus_iridescens _Pro_bol_25 0.85 1 0.97Proctoporus_iridescens _Pro_bol_26 1Proctoporus_iridescens _Pro_bol_27 Proctoporus_iridescens _Pro_bol_24 0.82Proctoporus_lacertus _Pro_bol_51 1 Proctoporus_lacertus _Pro_bol_52 Proctoporus_lacertus _Pro_bol_53 0.25Proctoporus_bolivianus_Pro_bol_5 0.34Proctoporus_bolivianus_Pro_bol_6 0.95Proctoporus_bolivianus_Pro_bol_3 1 Proctoporus_bolivianus_Pro_bol_4 1 Proctoporus_bolivianus_Pro_bol_7 Proctoporus_bolivianus_Pro_bol_1 1Proctoporus_bolivianus_Pro_bol_2 0.89 0.22Proctoporus_bolivianus_Pro_bol_12 Proctoporus_bolivianus_Pro_bol_13 0.6Proctoporus_bolivianus_Pro_bol_14 10.22 0.51 1 Proctoporus_bolivianus_Pro_bol_15 Proctoporus_bolivianus_Pro_bol_11 0.2Proctoporus_bolivianus_Pro_bol_8 1 1 Proctoporus_bolivianus_Pro_bol_9 Proctoporus_bolivianus_Pro_bol_10 1 Proctoporus_Ca1 _Pro_bol_16 1 Proctoporus_Ca1 _Pro_bol_18 Proctoporus_Ca1 _Pro_bol_17 0.23Proctoporus_sp_2_Proc_s2_3 0.17Proctoporus_sp_2_Proc_s2_4 1Proctoporus_sp_2_Proc_s2_2 Proctoporus_sp_2_Proc_s2_1 0.29 0.35 Proctoporus_unsaacae_Pro_uns_3 0.98 Proctoporus_unsaacae_Pro_uns_4 1 Proctoporus_unsaacae_Proc_un_1 1 Proctoporus_guentheri_Pro_gue_1 Proctoporus_guentheri_Pro_gue_2 1 0.48 1Proctoporus_laudahnae_Proc_la_1 0.99 Proctoporus_laudahnae_Proc_la_2 Proctoporus_Ca2 _Pro_bol_19 1 1Proctoporus_sp_3_Proc_s3_1 1 Proctoporus_sp_3_Proc_s3_2 Proctoporus_sp_4_IWU358 1 Unnamed_clade_II_Cerc_s2_2 0.37 Unnamed_clade_II_Cerc_s2_3 1 Unnamed_clade_II_90 0.51 Unnamed_clade_II_91 0.84 Unnamed_clade_II_Cerc_s2_1 0.67 Unnamed_clade_II_IWU114 Unnamed_clade_II_IWU165 0.69 0.56Unnamed_clade_II_IWU296 1Unnamed_clade_II_IWU325 1 0.99 Unnamed_clade_II_IWU320 1 Unnamed_clade_II_IWU287 Unnamed_clade_II_IWU288 0.42 Unnamed_clade_II_IWU57 1 Unnamed_clade_IV_EL409 Unnamed_clade_IV_ML1352 1 0.86Potamites_juruazensis_Pota_ju_3 0.11Potamites_juruazensis_Pota_ju_4 1Potamites_juruazensis_Pota_ju_2 1 Potamites_juruazensis_Pota_ju_5 Potamites_juruazensis_Pot_jur_1 1 1 Potamites_juruazensis_Pota_ju_1 Potamites_montanicola_Pota_mo_1 0.97 1 Potamites_ecpleopus_186_1 0.89 Potamites_ecpleopus_186_2 1 Potamites_ecpleopus_Pota_ec_1 1 Potamites_ecpleopus_Pot_ecp_1 1 Potamites_erythrocularis_Pota_er_1 1 Potamites_erythrocularis_Pota_er_2 0.83Potamites_trachodus_Pota_tr_3 1Potamites_trachodus_Pota_tr_4 1 Potamites_trachodus_Pota_tr_2 1 Potamites_strangulatus_Pot_str_1 0.82 Potamites_strangulatus_Pota_st_1 0.97 Potamites_ecpleopus_Pota_ec_3 1 Potamites_ecpleopus_Pota_ec_4 0.89 Potamites_ecpleopus_Pota_ec_2 0.34Selvasaur a_brava_IWU381 0.95Selvasaur a_brava_IWU382 1 Selvasaur a_brava_IWU340 0.83Selvasaur a_brava_IWU339 0.78 Selvasaur a_brava_IWU380 1 0.84 Selvasaur a_ sp_Cerc_s3_5 0.32Selvasaur a_ sp_Cerc_s3_1 1 1Selvasaur a_ sp_Cerc_s3_3 Selvasaur a_ sp_Cerc_s3_2 Selvasaur a_ sp_Cerc_s3_4 1Cercosaura_oshaughnessyi _Cer_arg_1 1 Cercosaura_oshaughnessyi_Cerc_os_1 Cercosaura_oshaughnessyi_Cerc_os_2 1 1 Cercosaura_oshaughnessyi _155_2 0.83 Cercosaura_oshaughnessyi _160_1 1 Cercosaura_oshaughnessyi_Cer_osh_1 0.57 Cercosaura_argulus_Cer_arg_2 1 Cercosaura_argulus_Cer_arg_4 1 Cercosaura_argulus_184 0.69 Cercosaura_argulus_Cer_arg_3 0.96 1 Cercosaura_parkeri_Cer_par_2 0.3 Cercosaura_schreibersii_Cer_schr_1 0.7 1 Cercosaura_schreibersii_albostrigatus_Cer_schr_2 Cercosaura_parkeri_Cer_par_1 1 Cercosaura_bassleri_Cerc_ba_1 1 Cercosaura_bassleri _Cerc_oc_1 1 Cercosaura_ocellata_Cer_oce_1 0.56 Cercosaura_eigenmanni_112 1 0.81 Cercosaura_eigenmanni_Cer_eig_2 1 Cercosaura_eigenmanni_609 Cercosaura_eigenmanni_Cer_eig_1 1 Cercosaura_quadrilineata_Cer_qua_1 1 Cercosaura_manicata_Cerc_ma_1 1 Cercosaura_manicata_Cerc_ma_2 Cercosaura_doanae_Cerc_do_1 0.95 Petracola_ventrimaculatus_Pet_ven_1 1 Petracola_ventrimaculatus_Pet_ven_2 Petracola_waka_Petr_wa_1 0.95Pholidobolus_montium_Pho_mon_1 0.86Pholidobolus_montium_Pho_mon_5 1 Pholidobolus_montium_Pho_mon_2 1 Pholidobolus_montium_Pho_mon_3 Pholidobolus_affinis_Pho_aff_1 0.58 1 Pholidobolus_affinis_Pho_aff_2 1 Pholidobolus_prefrontalis_Pho_pre_1 0.32 0.99 Pholidobolus_prefrontalis_Pho_pre_2 1 Pholidobolus_macbrydei_Pho_mac_1 1 1 Pholidobolus_macbrydei_Pho_mac_3 Pholidobolus_macbrydei_Pho_mac_2 1 Pholidobulus_dicrus_Phol_di_1 Pholidobulus_vertebralis_Phol_ve_1 0.96 0.33Pholidobolus_hillisi_Pho_hil_2 1Pholidobolus_hillisi_Pho_hil_3 Pholidobolus_hillisi_Pho_hil_1 0.93 0.98Pholidobolus_sp1_843 1 Pholidobolus_sp1_JCM239 0.98 Pholidobolus_sp1_JCM238 1 1 Pholidobolus_ulisesi _Phol_sp Pholidobolus_ulisesi _JCM310 1Macropholidus_annectens_Mac_ann_1 1 Macropholidus_annectens_Mac_ann_2 0.98 Macropholidus_sp_Macr_sp Macropholidus_ruthveni_Mac_rut_1 0.92 1 0.38Macropholidus_huancabambae_Mac_hua_1 1 1Macropholidus_huancabambae_Mac_hua_2 Macropholidus_huancabambae_Mac_hua_3 1Euspondylus_excelsum_Cerc_s1_1 1 Euspondylus_excelsum_Cerc_s1_2 0.92 Euspondylus_excelsum_IWU234 0.96 "Echinosaura_sulcarostrum " _Echi_sul_1 0.14Anadia_rhombifera_Anad_rhomb 1 Anadia_rhombifera_Anad_rhomb5 1 Anadia_rhombifera_Anad_rhomb2 Anadia_rhombifera_Anad_rhomb6 1 1Anadia_rhombifera_Anad_rhomb3 1 Anadia_rhombifera_Anad_rhomb4 1 1 Anadia_rhombifera_Anad_rhomb7 0.99 Anadia_petersi_Anad_rhomb_peters 0.78 Anadia_petersi_Anad_rhomb_peters2 Anadia_ocellata_SMF90095 0.51 Oreosaurus_shrevei_Oreo_shr 0.87 Oreosaurus_Venezuela_Oreo_Ven 1 Oreosaurus_achlyens_Oreo_ach 0.3 Oreosaurus_mcdiarmidi_Ore_mcd_1 1"Oreosaurus " _ serranus _Oreo_SN1 "Oreosaurus " _ serranus _Oreo_SN2 1 Gelanesaurus_cochranae_Gela_co_1 1 Gelanesaurus_cochranae_Gela_co_2 1Gelanesaurus_flavogularis_Gela_fl_1 Gelanesaurus_flavogularis_Gela_fl_2 Andinosaura_aurea_Andin_aur_1 0.85 1 1 Andinosaura_aurea_Andin_aur_2 1Andinosaura_vespertina_Andin_ves_1 1 Andinosaura_vespertina_Andin_ves_2 1 Andinosaura_kiziriani_Andin_kiz_1 Andinosaura_kiziriani_Andin_kiz_2 1 1 Andinosaura_hyposticta_Andin_hyp_1 0.25 Andinosaura_hyposticta_Andin_hyp_2 1Andinosaura_oculata_Andin_ocu_1 0.89 Andinosaura_oculata_Andin_ocu_2 1 1 Andinosaura_crypta_Andin_cry_1 Andinosaura_crypta_Andin_cry_2 1 Andinosaura_afrania_Andin_afr_1 1 Andinosaura_afrania_Andin_afr_2 1 Andinosaura_laevis_Andin_lae 1Andinosaura_vieta_Andin_vie_1 1 Andinosaura_vieta_Andin_vie_2 1Echinosaura_keyi_Echi_ke_1 0.42 Echinosaura_keyi_Echi_ke_2 Echinosaura_orcesi_Echi_or_1 0.8 1Echinosaura_orcesi_Echi_or_2 1 Echinosaura_brachycephala_Echi_br_1 1Echinosaura_horrida_Echi_ho_1 Echinosaura_horrida_Echi_ho_2 0.32Riama_meleagris_Ria_mel_1 0.61Riama_meleagris_Ria_mel_5 1Riama_meleagris_Ria_mel_2 0.94Riama_meleagris_Ria_mel_3 Riama_meleagris_Ria_mel_4 1 0.88Riama_stigmatoral_Ria_stig_3 1 Riama_stigmatoral_Ria_stig_4 1 1 Riama_stigmatoral_Ria_stig_2 1 Riama_stigmatoral_Ria_stig_1 1Riama_cashcaensis_Ria_cas_2 0.87 Riama_cashcaensis_Ria_cas_3 1Riama_labionis_Ria_lab_1 0.51 Riama_labionis_Ria_lab_2 Riama_yumborum_Ria_yum_1 1Riama_yumborum_Ria_yum_2 0.16Riama_unicolor_Ria_uni_1 1 1Riama_unicolor_Ria_uni_6 Riama_unicolor_Ria_uni_2 1 0.34Riama_unicolor_Ria_uni_7 0.54Riama_unicolor_Ria_uni_9 0.88Riama_unicolor_Ria_uni_8 1Riama_unicolor_Ria_uni_3 1 Riama_unicolor_Ria_uni_4 1 Riama_unicolor_Ria_uni_10 0.95Riama_unicolor_Ria_uni_5 1 Riama_unicolor_Ria_uni_11 0.75 Riama_colomaromani_Ria_col_1 0.47 Riama_colomaromani_Ria_col_2 1 Riama_Narino_Ria_N1 1 Riama_Narino_Ria_N2 0.97Riama_simotera_Ria_sim_2 0.37 1 Riama_simotera_Ria_sp_1 1 Riama_simotera_Ria_sim_1 1 Riama_raneyi_Ria_ran_1 1 Riama_raneyi_Ria_ran_2 1 Riama_anatoloros_Ria_an_1 0.92 0.93 Riama_anatoloros_Ria_an_3 Riama_anatoloros_Ria_an_2 1 Riama_columbiana_Ria_columb_1 1 Riama_columbiana_Ria_columb_2 1 Riama_orcesi_Ria_orc_2 1 Riama_orcesi_Ria_orc_3 1 Riama_orcesi_Ria_orc_1 1Riama_balneator_Ria_ba_1 Riama_balneator_Ria_ba_2 1 1Riama_Cordillera_Central_Ria_CC1 0.76 Riama_Cordillera_Central_Ria_CC2 1 Riama_striata_Ria_str_1 1 Riama_striata_Ria_str_2 Riama_Cordillera_Occidental_Ria_CO1 0.97Neusticurus_aff_rudis_Neu_rud_4 0.98 Neusticurus_aff_rudis_Neu_rud_5 0.41 Neusticurus_aff_rudis_Neu_rud_9 0.96 Neusticurus_aff_rudis_Neu_rud_10 0.39 Neusticurus_aff_rudis_Neu_rud_2 1 Neusticurus_aff_rudis_Neu_rud_3 Neusticurus_aff_rudis_Neu_rud_8 1 0.75Neusticurus_aff_rudis_Neu_rud_11 0.99 Neusticurus_aff_rudis_Neu_rud_13 Neusticurus_aff_rudis_Neu_rud_12 1 0.22 0.99Neusticurus_aff_rudis_Neu_rud_15 0.95 Neusticurus_aff_rudis_Neu_rud_6 Neusticurus_aff_rudis_Neu_rud_16 1 1 1 Neusticurus_rudis_Neu_rud_1 Neusticurus_aff_rudis_Neu_rud_7 1 Neusticurus_bicarinatus_Neu_bic_1 1 Placosoma_cordylinum_Pla_cor_1 Placosoma_glabellum_Pla_gla_1 0.5 Bachia_heteropa_Bach_het_2 0.5 Bachia_monodactylus_parkerii_Bach_mon_1 0.35 Bachia_intermedia_Bach_int_1 0.18 Bachia_barbouri_Bach_bar_1 0.5 Bachia_bicolor_Bach_bic_1 0.04 Bachia_peruana_Bach_per_1 0.48 Bachia_monodactylus_Bach_mon_2 Bachia_panoplia_Bach_pan_1 0.5 0.33Bachia_scaea_Bach_sca_1 1 Bachia_scaea_Bach_sca_2 0.91 Bachia_scaea_Bach_sca_3 0.91 0.99 Bachia_dorbignyi_Bach_dor_1 Bachia_trisanale_Bach_tri_1 Bachia_huallagana_Bach_hua_1 0.99 1 1 Bachia_scolecoides_Bach_sco_1 1 Bachia_heteropa_Bach_het_1 Bachia_bresslaui_Bach_bre_1 0.32 Bachia_flavescens_Bach_fla_1 Ecpleopus_gaudichaudii_Ecpl_ga_1 0.93 1 Riolama_leucosticta_Rio_leu_1 1 Riolama_leucosticta_Rio_leu_2 1 Riolama_leucosticta_Rio_leu_3 0.96 0.77 Riolama_inopinata_Rio_ino_1 Alopoglossus_viridiceps_Alop_vi_1 1 Gymnophthalmus_leucomystax_Gymn_le_1 Rhachisaurus_brachylepis_Rhac_br_1

0.04 Figure S3. An MCC tree of Cercosaurinae and outgroup taxa resulting from the BEAST analysis. 4

GenBank Accession Genus Species Sample code Voucher Source 12S 16S cytb ND4 c-mos Anadia A. ocellata SMF90095 SMF90095 MH579588 MH579625 MH579659 This study Anadia A. petersi Anad_rhomb_peters QCAZ 5068 KU902127 KU902208 KU902283 KU902048 Torres-Carvajal et al. 2016 Anadia A. petersi Anad_rhomb_peters2 QCAZ 10087 KU902130 KU902211 KU902286 KU902050 Torres-Carvajal et al. 2016 Anadia A. rhombifera Anad_rhomb QCAZ 5782 KU902128 KU902209 KU902284 Torres-Carvajal et al. 2016 Anadia A. rhombifera Anad_rhomb2 QCAZ 6873 KU902129 KU902210 KU902285 KU902049 Torres-Carvajal et al. 2016 Anadia A. rhombifera Anad_rhomb3 QCAZ 10537 KU902131 KU902212 KU902287 Torres-Carvajal et al. 2016 Anadia A. rhombifera Anad_rhomb4 QCAZ 10556 KU902132 KU902213 KU902288 KU902051 Torres-Carvajal et al. 2016 Anadia A. rhombifera Anad_rhomb5 QCAZ 11061 KU902133 KU902214 KU902289 KU902052 Torres-Carvajal et al. 2016 Anadia A. rhombifera Anad_rhomb6 QCAZ 11510 KU902134 KU902215 KU902290 Torres-Carvajal et al. 2016 Anadia A. rhombifera Anad_rhomb7 QCAZ 11862 KU902135 KU902216 KU902291 KU902053 Torres-Carvajal et al. 2016 Andinosaura A. afrania Andin_afr_1 RH KY670680 KY681098 Sanchez-Pacheco et al. 2017 Andinosaura A. afrania Andin_afr_2 RM KY670681 KY681099 Sanchez-Pacheco et al. 2017 Andinosaura A. aurea Andin_aur_1 QCAZ9649 KY670682 KY681100 KY710831 KY670647 Sanchez-Pacheco et al. 2017 Andinosaura A. aurea Andin_aur_2 QCAZ9650 KY670683 KY681101 KY710832 KY670648 Sanchez-Pacheco et al. 2017 Andinosaura A. crypta Andin_cry_1 QCAZ10455 KY670684 KY681102 KY710833 KY670649 Sanchez-Pacheco et al. 2017 Andinosaura A. crypta Andin_cry_2 QCAZ6154 KY670685 KY681103 KY710834 KY670650 Sanchez-Pacheco et al. 2017 Andinosaura A. hyposticta Andin_hyp_1 PSO-CZ85 KY670686 KY681104 Sanchez-Pacheco et al. 2017 Andinosaura A. hyposticta Andin_hyp_2 DHMECN1360 KY670687 KY681105 KY670651 Sanchez-Pacheco et al. 2017 Andinosaura A. kiziriani Andin_kiz_2 QCAZ9667 KY670689 KY681107 KY710836 KY670653 Sanchez-Pacheco et al. 2017 Andinosaura A. kiziriani Andin_kiz_1 QCAZ9607 KY670688 KY681106 KY710835 KY670652 Sanchez-Pacheco et al. 2017 Andinosaura A. laevis Andin_lae WB1330 KY670690 KY681108 KY799165 KY670654 Sanchez-Pacheco et al. 2017 Andinosaura A. oculata Andin_ocu_1 QCAZ10410 KY670691 KY681109 KY710837 KY670655 Sanchez-Pacheco et al. 2017 Andinosaura A. oculata Andin_ocu_2 QCAZ5474 KY670692 KY681110 KY710838 KY670656 Sanchez-Pacheco et al. 2017 Andinosaura A. vespertina Andin_ves_1 QCAZ10286 KY670693 KY681111 KY710839 KY670657 Sanchez-Pacheco et al. 2017 Andinosaura A. vespertina Andin_ves_2 QCAZ10306 KY670694 KY681112 KY710840 KY670658 Sanchez-Pacheco et al. 2017 Andinosaura A. vieta Andin_vie_1 QCAZ10456 KY670695 KY681113 KY710841 KY670659 Sanchez-Pacheco et al. 2017 Andinosaura A. vieta Andin_vie_2 QCAZ5287 KY670696 KY681114 KY710842 KY670660 Sanchez-Pacheco et al. 2017 Cercosaura C. argulus Cer_arg_2 QCAZ 4888 KP874738 KP874790 KP874900 KP874842 Torres-Carvajal et al. 2016 Cercosaura C. argulus Cer_arg_3 MPEG21580 KY555149 KY555221 KY555431 KY555359 Sturaro et al. 2017 Cercosaura C. argulus Cer_arg_4 MPEG21540 KY555148 KY555220 KY555362 KY555360 Sturaro et al. 2017

GenBank Accession Genus Species Sample code Voucher Source 12S 16S cytb ND4 c-mos Cercosaura C. argulus 184 NMP6V 72184 MH579589 MH579626 MH579660 MH579686 This study Cercosaura C. bassleri Cerc_ba_1 CORBIDI 15187 KU902136 KU902217 KU902292 KU902054 Torres-Carvajal et al. 2016 Cercosaura C. bassleri Cerc_oc_1 CORBIDI 11218 KP874744 KP874796 KP874906 KP874848 Torres-Carvajal et al. 2016 Cercosaura C. doanae Cerc_do_1 CORBIDI 650 KP874773 KP874825 KP874935 KP874875 Torres-Carvajal et al. 2016 Cercosaura C. eigenmanni 112 NMP6V 73112 MH579591 MH579628 MH579661 This study Cercosaura C. eigenmanni 609 NMP6V 72609 MH579590 MH579627 This study Cercosaura C. eigenmanni Cer_eig_1 MRT 976979 AF420690 AF420728 AF420895 AF420828 Pellegrino et al. 2001 Cercosaura C. eigenmanni Cer_eig_2 MPEG21550 KY555150 KY555222 KY555361 KY555358 Sturaro et al. 2017 Cercosaura C. manicata Cerc_ma_1 CORBIDI 8837 KP874745 KP874797 KP874907 KP874849 Torres-Carvajal et al. 2016 Cercosaura C. manicata Cerc_ma_2 QCAZ 5793 KP874746 KP874798 KP874908 KP874850 Torres-Carvajal et al. 2016 Cercosaura C. ocellata Cer_oce_1 MRT 977406 AF420677 AF420731 AF420883 AF420834 Pellegrino et al. 2001 Pellegrino et al. 2001 Cercosaura C. oshaughnessyi Cer_arg_1 LSUMZ H12591 AF420698 AF420751 AF420896 AF420838 Torres-Carvajal et al. 2016 Cercosaura C. oshaughnessyi Cer_osh_1 LSUMZ H13584 AF420696 AF420750 AF420893 AF420852 Pellegrino et al. 2001 Pellegrino et al. 2001 Cercosaura C. oshaughnessyi Cerc_os_1 LSUMZ H12591 AF420698 AF420751 AF420896 AF420838 Torres-Carvajal et al. 2016 Cercosaura C. oshaughnessyi Cerc_os_2 QCAZ 4623 KP874748 KP874800 KP874910 KP874852 Torres-Carvajal et al. 2016 Cercosaura C. oshaughnessyi 155/2 NMP6V 71155/2 MH579592 This study Cercosaura C. oshaughnessyi 160/1 NMP6V 71160/1 MH579593 MH579629 MH579662 MH579687 This study Cercosaura C. parkeri Cer_par_1 LG1560 KY555219 KY555290 KY555378 KY555291 Sturaro et al. 2017 Cercosaura C. parkeri Cer_par_2 LG1553 KY555218 KY555289 KY555363 KY555292 Sturaro et al. 2017 Cercosaura C. quadrilineata Cer_qua_1 LG 936 AF420672 AF420717 AF420880 AF420830 Pellegrino et al. 2001 Cercosaura C. schreibersii Cer_schr_1 LG 927 AF420686 AF420749 AF420911 AF420817 Goicoechea et al. 2012 Cercosaura C. s. albostrigatus Cer_schr_2 LG 1168 AF420658 AF420729 AF420882 AF420856 Pellegrino et al. 2001 Echinosaura E. brachycephala Echi_br_1 QCAZ 10824 KU902137 KU902218 KU902293 KU902055 Torres-Carvajal et al. 2016 Echinosaura E. horrida Echi_ho_1 QCAZ 6666 KU902138 KU902219 KU902294 KU902056 Torres-Carvajal et al. 2016 Echinosaura E. horrida Echi_ho_2 QCAZ 8788 KU902139 KU902220 KU902295 KU902057 Torres-Carvajal et al. 2016 Echinosaura E. keyi Echi_ke_1 QCAZ 8074 KU902140 KU902221 KU902296 KU902058 Torres-Carvajal et al. 2016 Echinosaura E. keyi Echi_ke_2 QCAZ 12485 KU902141 KU902222 KU902297 KU902059 Torres-Carvajal et al. 2016 Echinosaura E. orcesi Echi_or_1 QCAZ 6299 KU902142 KU902223 KU902298 KU902060 Torres-Carvajal et al. 2016 Echinosaura E. orcesi Echi_or_2 QCAZ 10022 KU902143 KU902224 KU902299 KU902061 Torres-Carvajal et al. 2016 Fu 2000 "Echinosaura" E. sulcarostrum Echi_sul_1 ROM 22892 AF206584 AF206584 AF206528 redetermined by Kok 2015 Euspondylus E. excelsum Cerc_s1_1 CORBIDI 14965 KU902198 KU902273 KU902354 KU902117 Torres-Carvajal et al. 2016 Euspondylus E. excelsum Cerc_s1_2 CORBIDI 15573 KU902199 KU902274 KU902355 KU902118 Torres-Carvajal et al. 2016

GenBank Accession Genus Species Sample code Voucher Source 12S 16S cytb ND4 c-mos Euspondylus E. excelsum IWU234 IWU 234 MH579594 MH579630 MH579688 This study Gelanesaurus G. cochranae Gela_co_1 QCAZ 5587 KU902144 KU902225 KU902300 KU902062 Torres-Carvajal et al. 2016 Gelanesaurus G. cochranae Gela_co_2 QCAZ 6120 KU902145 KU902226 KU902301 KU902063 Torres-Carvajal et al. 2016 Gelanesaurus G. flavogularis Gela_fl_1 QCAZ 4611 KU902146 KU902227 KU902302 KU902064 Torres-Carvajal et al. 2016 Gelanesaurus G. flavogularis Gela_fl_2 QCAZ 6943 KU902147 KU902228 KU902303 KU902065 Torres-Carvajal et al. 2016 Macropholidus M. annectens Mac_ann_1 QCAZ 11120 KC894341 KC894355 KC894369 Torres-Carvajal and Mafla-Endara 2013 Macropholidus M. annectens Mac_ann_2 QCAZ 11121 KC894342 KC894356 KC894370 KP874877 Torres-Carvajal and Mafla-Endara 2013 Macropholidus M. huancabambae Mac_hua_1 CORBIDI 10492 KC894343 KC894357 KC894371 Torres-Carvajal and Mafla-Endara 2013 Macropholidus M. huancabambae Mac_hua_2 CORBIDI 10493 KC894344 KC894358 KC894372 KP874879 Torres-Carvajal and Mafla-Endara 2013 Macropholidus M. huancabambae Mac_hua_3 CORBIDI 10496 KC894345 KC894359 KC894373 Torres-Carvajal and Mafla-Endara 2013 Macropholidus M. ruthveni Mac_rut_1 CORBIDI 4281 KC894354 KC894368 KC894382 Torres-Carvajal and Mafla-Endara 2013 Macropholidus M. sp. Macr_sp CORBIDI 12932 KP874774 KP874826 KP874936 KP874881 Torres-Carvajal et al. 2016 Neusticurus N. aff. rudis Neu_rud_10 ROM42644 JQ742249 Kok et al. 2012 Neusticurus N. aff. rudis Neu_rud_11 IRSNB18109 JQ742251 Kok et al. 2012 Neusticurus N. aff. rudis Neu_rud_12 IRSNB18110 JQ742252 Kok et al. 2012 Neusticurus N. aff. rudis Neu_rud_13 IRSNB18111 JQ742253 Kok et al. 2012 Neusticurus N. aff. rudis Neu_rud_15 IRSNB18150 JQ742240 Kok et al. 2012 Neusticurus N. aff. rudis Neu_rud_16 IRSNB18151 JQ742241 Kok et al. 2012 Neusticurus N. aff. rudis Neu_rud_2 IRSNB17344 JQ742242 Kok et al. 2012 Neusticurus N. aff. rudis Neu_rud_3 IRSNB17345 JQ742243 Kok et al. 2012 Neusticurus N. aff. rudis Neu_rud_4 IRSNB18146 JQ742244 Kok et al. 2012 Neusticurus N. aff. rudis Neu_rud_5 IRSNB18147 JQ742245 Kok et al. 2012 Neusticurus N. aff. rudis Neu_rud_6 PK2058V JQ742246 Kok et al. 2012 Neusticurus N. aff. rudis Neu_rud_7 IRSNB18149 JQ742250 Kok et al. 2012 Neusticurus N. aff. rudis Neu_rud_8 ROM20514 JQ742247 Kok et al. 2012 Neusticurus N. aff. rudis Neu_rud_9 ROM39498 JQ742248 Kok et al. 2012 Neusticurus N. bicarinatus Neu_bic_1 MRT 968462 AF420671 AF420708 AF420816 Goicoechea et al. 2012 Neusticurus N. rudis Neu_rud_1 MRT 926008 AF420689 AF420709 AF420905 Goicoechea et al. 2012 Oreosaurus O. "Venezuela" Oreo_Ven GAR5962 KY670701 KY681119 KY799161 Sanchez-Pacheco et al. 2017 Oreosaurus O. achlyens Oreo_ach ENS11010 KY670697 KY681115 KY799160 Sanchez-Pacheco et al. 2017 Oreosaurus O. mcdiarmidi Ore_mcd_1 IRSNB 2674 JQ742263 KP283392 KP283385 Kok 2015 Oreosaurus O. shrevei Oreo_shr UWIZM2011.7 KY670700 KY681118 KY670663 Sanchez-Pacheco et al. 2017 "Oreosaurus" O. serranus Oreo_SN2 JJS548 KY670699 KY681117 KY799164 KY670662 Sanchez-Pacheco et al. 2017 "Oreosaurus" O. serranus Oreo_SN1 JJS543 KY670698 KY681116 KY799163 KY670661 Sanchez-Pacheco et al. 2017

GenBank Accession Genus Species Sample code Voucher Source 12S 16S cytb ND4 c-mos Petracola P. ventrimaculatus Pet_ven_1 KU219838 AY507863 AY507883 AY507894 AY507910 Doan et al. 2005 Petracola P. ventrimaculatus Pet_ven_2 CORBIDI 9235 KJ948193 KJ948144 KJ948145 KJ948220 Aguirre-Penafiel et al. 2014 Petracola P. waka Petr_wa_1 KU212687 AY507864 AY507876 AY507903 Castoe et al. 2004 Pholidobolus P. affinis Pho_aff_1 QCAZ 9641 KC894348 KC894362 KC894376 KP874883 Torres-Carvajal and Mafla-Endara 2013 Pholidobolus P. affinis Pho_aff_2 QCAZ 9900 KC894349 KC894363 KC894377 Torres-Carvajal and Mafla-Endara 2013 Pholidobolus P. dicrus Phol_di_1 QCAZ 5304 KP874776 KP874828 KP874938 KP874885 Torres-Carvajal et al. 2016 Pholidobolus P. hillisi Pho_hil_1 KP090167 KP090170 KP090173 Torres-Carvajal et al. 2014 Pholidobolus P. hillisi Pho_hil_2 QCAZ 5000 KP090168 KP090171 KP090174 KP874888 Torres-Carvajal et al. 2014 Pholidobolus P. hillisi Pho_hil_3 KP090169 KP090172 KP090175 Torres-Carvajal et al. 2014 Pholidobolus P. macbrydei Pho_mac_1 KU218406 AY507848 AY507867 AY507886 AY507896 Doan et al. 2005 Pholidobolus P. macbrydei Pho_mac_2 QCAZ 9914 KC894352 KC894366 KC894380 Torres-Carvajal and Mafla-Endara 2013 Pholidobolus P. macbrydei Pho_mac_3 QCAZ 9932 KC894353 KC894367 KC894381 KP874889 Torres-Carvajal and Mafla-Endara 2013 Pholidobolus P. montium Pho_mon_1 AF420701 AF420756 AF420884 AF420820 Goicoechea et al. 2012 Pholidobolus P. montium Pho_mon_2 QCAZ 4051 KC894346 KC894360 KC894374 KP874890 Torres-Carvajal and Mafla-Endara 2013 Pholidobolus P. montium Pho_mon_3 QCAZ 9044 KC894347 KC894361 KC894375 Torres-Carvajal and Mafla-Endara 2013 Pholidobolus P. montium Pho_mon_5 QCAZ8056 KJ948194 KJ948143 KJ948146 KJ948221 Aguirre-Penafiel et al. 2014 Pholidobolus P. prefrontalis Pho_pre_1 QCAZ 9908 KC894350 KC894364 KC894378 Torres-Carvajal and Mafla-Endara 2013 Pholidobolus P. prefrontalis Pho_pre_2 QCAZ 9951 KC894351 KC894365 KC894379 Torres-Carvajal and Mafla-Endara 2013 Pholidobolus P. sp.1 843 MUSM 31843 MH579597 MH579633 MH579665 MH579691 This study Pholidobolus P. sp.1 JCM238 JCM 238 MH579595 MH579631 MH579663 MH579689 This study Pholidobolus P. sp.1 JCM239 JCM 239 MH579596 MH579632 MH579664 MH579690 This study Pholidobolus P. ulisesi JCM310 JCM 310 MH579598 MH579634 MH579666 MH579692 This study Pholidobolus P. ulisesi Phol_sp CORBIDI 12737 KP874788 KP874840 KP874949 KP874898 Torres-Carvajal et al. 2016 Pholidobolus P. vertebralis Phol_ve_1 QCAZ 8688 KP874780 KP874832 KP874942 KP874892 Torres-Carvajal et al. 2016 Placosoma P. cordylinum Pla_cor_1 LG 1006 AF420673 AF420734 AF420879 AF420823 Goicoechea et al. 2012 Placosoma P. glabellum Pla_gla_1 AF420674 AF420742 AF420907 AF420833 Goicoechea et al. 2012 Potamites P. ecpleopus 186/1 NMP6V 73186/1 MH579599 MH579635 This study Potamites P. ecpleopus 186/2 NMP6V 73186/2 MH579600 MH579636 This study Potamites P. ecpleopus Pot_ecp_1 MRT 0472 AF420656 AF420748 AF420890 AF420829 Goicoechea et al. 2012 Potamites P. ecpleopus Pota_ec_1 CORBIDI 14382 KU902148 KU902229 KU902304 KU902066 Torres-Carvajal et al. 2016 Potamites P. ecpleopus Pota_ec_2 QCAZ 4699 KU902149 KU902230 KU902305 KU902067 Torres-Carvajal et al. 2016 Potamites P. ecpleopus Pota_ec_3 QCAZ 5208 KU902150 KU902231 KU902306 KU902068 Torres-Carvajal et al. 2016 Potamites P. ecpleopus Pota_ec_4 QCAZ 10071 KU902151 KU902232 KU902307 KU902069 Torres-Carvajal et al. 2016 Potamites P. erythrocularis Pota_er_1 CORBIDI 15153 KU902152 KU902233 KU902308 KU902070 Torres-Carvajal et al. 2016

GenBank Accession Genus Species Sample code Voucher Source 12S 16S cytb ND4 c-mos Potamites P. erythrocularis Pota_er_2 MHNC 10946 KU902153 KU902234 KU902309 KU902071 Torres-Carvajal et al. 2016 Potamites P. juruazensis Pot_jur_1 AF420878 AF420857 Pellegrino et al. 2001 Potamites P. juruazensis Pota_ju_1 CORBIDI 9951 KU902154 KU902235 KU902310 KU902072 Torres-Carvajal et al. 2016 Potamites P. juruazensis Pota_ju_2 CORBIDI 15504 KU902155 KU902237 KU902312 KU902074 Torres-Carvajal et al. 2016 Potamites P. juruazensis Pota_ju_3 CORBIDI 15550 KU902156 KU902238 KU902313 KU902075 Torres-Carvajal et al. 2016 Potamites P. juruazensis Pota_ju_4 CORBIDI 15579 KU902157 KU902239 KU902314 KU902076 Torres-Carvajal et al. 2016 Potamites P. juruazensis Pota_ju_5 CORBIDI 15479 KU902236 KU902311 KU902073 Torres-Carvajal et al. 2016 Potamites P. montanicola Pota_mo_1 CORBIDI 10791 KU902158 KU902240 KU902315 KU902077 Torres-Carvajal et al. 2016 Potamites P. strangulatus Pot_str_1 KU21677 AY507847 AY507866 AY507885 Doan et al. 2005 Potamites P. strangulatus Pota_st_1 QCAZ 6133 KU902159 KU902241 KU902316 KU902078 Torres-Carvajal et al. 2016 Potamites P. trachodus Pota_tr_2 CORBIDI 15489 KU902160 KU902242 KU902317 KU902079 Torres-Carvajal et al. 2016 Potamites P. trachodus Pota_tr_3 CORBIDI 15514 KU902161 KU902243 KU902318 KU902080 Torres-Carvajal et al. 2016 Potamites P. trachodus Pota_tr_4 CORBIDI 15515 KU902162 KU902244 KU902319 KU902081 Torres-Carvajal et al. 2016 Proctoporus P. bolivianus Pro_bol_1 UTA R-52944 AY968826 AY968833 AY968814 Doan et al. 2005 Proctoporus P. bolivianus Pro_bol_10 MNCN43664 JX435938 JX435999 JX436038 Goicoechea et al. 2012 Proctoporus P. bolivianus Pro_bol_11 MNCN43678 JX435939 JX436067 JX436039 Goicoechea et al. 2012 Proctoporus P. bolivianus Pro_bol_12 MNCN 8989 JX435940 JX435994 JX436071 JX436040 Goicoechea et al. 2012 Proctoporus P. bolivianus Pro_bol_13 MNCN 8990 JX435941 JX435995 JX436070 JX436041 Goicoechea et al. 2012 Proctoporus P. bolivianus Pro_bol_14 MNCN8991 JX435942 JX435996 JX436068 JX436042 Goicoechea et al. 2012 Proctoporus P. bolivianus Pro_bol_15 MNCN43679 JX435943 JX435997 JX436069 JX436043 Goicoechea et al. 2012 Proctoporus P. bolivianus Pro_bol_2 UTA R-52946 AY968822 AY968831 AY968811 Doan et al. 2005 Proctoporus P. bolivianus Pro_bol_3 MNCN43660 JX435931 JX435989 JX436061 Goicoechea et al. 2012 Proctoporus P. bolivianus Pro_bol_4 MHNC5333 JX435932 JX435990 JX436064 JX436033 Goicoechea et al. 2012 Proctoporus P. bolivianus Pro_bol_5 MHNC5334 JX435933 JX435991 JX436062 Goicoechea et al. 2012 Proctoporus P. bolivianus Pro_bol_6 MHNC5348 JX435935 JX435992 JX436034 Goicoechea et al. 2012 Proctoporus P. bolivianus Pro_bol_7 MNCN43662 JX435934 JX435993 JX436063 JX436035 Goicoechea et al. 2012 Proctoporus P. bolivianus Pro_bol_8 MHNC5357 JX435936 JX435998 JX436065 JX436036 Goicoechea et al. 2012 Proctoporus P. bolivianus Pro_bol_9 MNCN43663 JX435937 JX436000 JX436066 JX436037 Goicoechea et al. 2012 Proctoporus P. Ca1 Pro_bol_16 MHNC5346 JX435944 JX436099 Goicoechea et al. 2012 Proctoporus P. Ca1 Pro_bol_17 MHNC5322 JX435945 JX435988 JX436045 Goicoechea et al. 2012 Proctoporus P. Ca1 Pro_bol_18 UTA R-52945 AY968825 AY968832 AY968813 Doan et al. 2005 Proctoporus P. Ca2 Pro_bol_19 AMNH R-150695 AY507851 AY968828 AY968812 Doan et al. 2005 Goicoechea et al. 2012 Proctoporus P. carabaya Pro_bol_36 MHNC5428 JX435912 JX435979 JX436083 JX436016 Torres-Carvajal et al. 2016

GenBank Accession Genus Species Sample code Voucher Source 12S 16S cytb ND4 c-mos Goicoechea et al. 2012 Proctoporus P. carabaya Pro_bol_37 MNCN43675 JX435913 JX435980 JX436084 JX436017 Torres-Carvajal et al. 2016 Goicoechea et al. 2012 Proctoporus P. carabaya Pro_bol_38 MNCN43676 JX435914 JX435981 JX436085 JX436018 Torres-Carvajal et al. 2016 Goicoechea et al. 2012 Proctoporus P. carabaya Pro_bol_39 MHNC5429 JX435915 JX435982 JX436086 JX436019 Torres-Carvajal et al. 2016 Proctoporus P. chasqui IWU133 MUSM 31172 MH579605 MH579641 MH579671 MH579697 This study Proctoporus P. chasqui IWU24 MUSM 31108 MH579601 MH579637 MH579667 MH579693 This study Proctoporus P. chasqui IWU25 MUSM 31109 MH579602 MH579638 MH579668 MH579694 This study Proctoporus P. chasqui IWU50 MUSM 31123 MH579603 MH579639 MH579669 MH579695 This study Proctoporus P. chasqui IWU82 MUSM 31142 MH579604 MH579640 MH579670 MH579696 This study Proctoporus P. chasqui Pro_chas_1 MNCN6771 JX435887 JX435946 JX436051 JX436003 Goicoechea et al. 2012 Proctoporus P. chasqui Pro_chas_2 MNCN44407 JX435888 JX435947 JX436052 JX436004 Goicoechea et al. 2012 Proctoporus P. chasqui Pro_chas_3 MNCN44408 JX435889 JX435948 JX436053 JX436005 Goicoechea et al. 2012 Proctoporus P. chasqui Proc_ch_1 CORBIDI 8416 KU902166 KU902246 KU902323 KU902085 Torres-Carvajal et al. 2016 Proctoporus P. chasqui Proc_ch_2 CORBIDI 8431 KU902167 KU902247 KU902324 KU902086 Torres-Carvajal et al. 2016 Proctoporus P. chasqui Proc_ch_3 CORBIDI 8478 KU902168 KU902248 KU902325 KU902087 Torres-Carvajal et al. 2016 Proctoporus P. chasqui Pro_sp_1 MHNC6834 JX435890 JX435949 JX436054 JX436006 Goicoechea et al. 2012 Proctoporus P. guentheri Pro_gue_1 UTA R-51515 AY507849 AY507872 AY225185 AY507900 Goicoechea et al. 2012 Proctoporus P. guentheri Pro_gue_2 UTA R-51517 AY507854 AY507873 AY225169 AY507901 Goicoechea et al. 2012 Proctoporus P. iridescens Pro_bol_21 MHNC5359 JX435923 JX435958 JX436074 JX436009 Goicoechea et al. 2012 Proctoporus P. iridescens Pro_bol_22 MHNC6360 JX435924 JX435959 JX436075 JX436010 Goicoechea et al. 2012 Proctoporus P. iridescens Pro_bol_23 MHNC5361 JX435925 JX435960 JX436076 Goicoechea et al. 2012 Proctoporus P. iridescens Pro_bol_25 MHNC5417 JX435916 JX435963 JX436088 JX436015 Goicoechea et al. 2012 Proctoporus P. iridescens Pro_bol_26 MHNC5421 JX435917 JX435964 JX436087 Goicoechea et al. 2012 Proctoporus P. iridescens Pro_bol_27 MNCN43669 JX435918 JX435965 JX436090 JX436031 Goicoechea et al. 2012 Proctoporus P. iridescens Pro_bol_28 MNCN44222 JX435919 JX435985 JX436077 Goicoechea et al. 2012 Proctoporus P. iridescens Pro_bol_29 MNCN44223 JX435926 JX435986 JX436020 Goicoechea et al. 2012 Proctoporus P. iridescens Pro_bol_32 MHNC4600 JX435928 JX435974 JX436080 JX436025 Goicoechea et al. 2012 Proctoporus P. iridescens Pro_bol_33 MHNC4661 JX435929 JX435975 JX436081 JX436027 Goicoechea et al. 2012 Proctoporus P. iridescens Pro_bol_34 MHNC4629 JX435930 JX435976 JX436082 Goicoechea et al. 2012 Proctoporus P. iridescens Pro_bol_35 MHNC6005 JX435927 JX435966 JX436079 JX436049 Goicoechea et al. 2012 Goicoechea et al. 2012 Proctoporus P. iridescens Pro_bol_20 MNCN43666 JX435922 JX435957 JX436072 JX436008 Torres-Carvajal et al. 2016 Goicoechea et al. 2012 Proctoporus P. iridescens Pro_bol_24 MNCN43668 JX435911 JX435962 JX436089 JX436014 Torres-Carvajal et al. 2016

GenBank Accession Genus Species Sample code Voucher Source 12S 16S cytb ND4 c-mos Goicoechea et al. 2012 Proctoporus P. iridescens Pro_bol_30 MNCN44224 JX435920 JX435987 JX436078 JX436021 Torres-Carvajal et al. 2016 Goicoechea et al. 2012 Proctoporus P. iridescens Pro_bol_31 MHNC5651 JX435921 JX435961 JX436073 Torres-Carvajal et al. 2016 Proctoporus P. kiziriani Proc_ca_1 CORBIDI 14709 KU902163 KU902320 KU902082 Torres-Carvajal et al. 2016 Proctoporus P. kiziriani Proc_ca_2 CORBIDI 14710 KU902164 KU902245 KU902321 KU902083 Torres-Carvajal et al. 2016 Proctoporus P. kiziriani Proc_ca_3 CORBIDI 14711 KU902165 KU902322 KU902084 Torres-Carvajal et al. 2016 Proctoporus P. kiziriani Pro_bol_40 MNCN43670 JX435906 JX435967 JX436032 Goicoechea et al. 2012 Proctoporus P. kiziriani Pro_bol_41 MHNC5367 JX435907 JX435978 JX436091 JX436011 Goicoechea et al. 2012 Proctoporus P. kiziriani Pro_bol_42 MHNC43671 JX435910 JX435968 JX436012 Goicoechea et al. 2012 Proctoporus P. kiziriani Pro_bol_43 MHNC5370 JX435909 JX435970 JX436092 Goicoechea et al. 2012 Proctoporus P. kiziriani Pro_bol_44 MHNC5371 JX435908 JX435969 JX436093 JX436013 Goicoechea et al. 2012 Proctoporus P. kiziriani Pro_bol_45 MNCN44216 JX435900 JX435972 JX436096 JX436022 Goicoechea et al. 2012 Proctoporus P. kiziriani Pro_bol_46 MNCN44217 JX435905 JX435971 JX436094 Goicoechea et al. 2012 Goicoechea et al. 2012 Proctoporus P. kiziriani Pro_bol_47 MNCN44218 JX435903 JX435973 JX436023 Torres-Carvajal et al. 2016 Proctoporus P. kiziriani Pro_bol_48 MHNC4750 JX435901 JX435984 JX436098 JX436046 Goicoechea et al. 2012 Goicoechea et al. 2012 Proctoporus P. kiziriani Pro_bol_49 MHNC4751 JX435904 JX435977 JX436097 JX436048 Torres-Carvajal et al. 2016 Goicoechea et al. 2012 Proctoporus P. kiziriani Pro_bol_50 MNCN4221 JX435902 JX435983 JX436095 JX436047 Torres-Carvajal et al. 2016 Doan et al. 2005 Proctoporus P. lacertus Pro_bol_51 UTA R-51484 AY968820 AY968827 Goicoechea et al. 2012 Torres-Carvajal et al. 2016 Proctoporus P. lacertus Pro_bol_52 UTA R-51487 AY507850 AY507868 AY225180 AY507897 Goicoechea et al. 2012 Proctoporus P. lacertus Pro_bol_53 UTA R-51506 AY507851 AY507869 AY225175 AY507898 Goicoechea et al. 2012 Proctoporus P. laudahnae Proc_la_1 CORBIDI 15558 KU902171 KU902250 KU902328 KU902090 Torres-Carvajal et al. 2016 Proctoporus P. laudahnae Proc_la_2 CORBIDI 15743 KU902172 KU902251 KU902329 KU902091 Torres-Carvajal et al. 2016 Proctoporus P. oreades Proc_or_1 CORBIDI 7217 KU902173 KU902252 KU902330 KU902092 Torres-Carvajal et al. 2016 Proctoporus P. oreades Proc_or_2 CORBIDI 7218 KU902174 KU902253 KU902331 KU902093 Torres-Carvajal et al. 2016 Proctoporus P. oreades Proc_or_3 CORBIDI 7225 KU902175 KU902254 KU902332 KU902094 Torres-Carvajal et al. 2016 Proctoporus P. pachyurus Pro_pach_4 UTA R-52949 AY968824 AY968834 AY968816 Doan et al. 2005 Proctoporus P. pachyurus Pro_pach_5 MHNC TMD1203 AY968823 AY968829 AY968815 Doan et al. 2005 Proctoporus P. pachyurus Proc_pa_1 CORBIDI 11807 KU902176 KU902333 KU902095 Torres-Carvajal et al. 2016 Proctoporus P. pachyurus Proc_pa_2 CORBIDI 11810 KU902177 KU902334 KU902096 Torres-Carvajal et al. 2016 Proctoporus P. pachyurus Proc_pa_3 CORBIDI 11811 KU902178 KU902255 KU902335 KU902097 Torres-Carvajal et al. 2016 Proctoporus P. rahmi Pro_pach_1 MHNC11439 JX435893 JX435950 JX436056 JX436050 Goicoechea et al. 2012

GenBank Accession Genus Species Sample code Voucher Source 12S 16S cytb ND4 c-mos Proctoporus P. rahmi Proc_ra_1 CORBIDI 14705 KU902179 KU902256 KU902336 KU902098 Torres-Carvajal et al. 2016 Proctoporus P. rahmi Proc_ra_2 CORBIDI 14706 KU902180 KU902257 KU902337 KU902099 Torres-Carvajal et al. 2016 Proctoporus P. rahmi Proc_ra_3 CORBIDI 14707 KU902181 KU902258 KU902338 KU902100 Torres-Carvajal et al. 2016 Proctoporus P. sp. Pro_pach_2 MHNC4599 JX435891 JX435952 JX436055 JX436024 Goicoechea et al. 2012 Proctoporus P. sp. 1 Proc_s1_1 CORBIDI 14624 KU902188 KU902263 KU902344 KU902107 Torres-Carvajal et al. 2016 Proctoporus P. sp. 1 Proc_s1_2 CORBIDI 14625 KU902189 KU902264 KU902345 KU902108 Torres-Carvajal et al. 2016 Proctoporus P. sp. 1 Proc_s1_3 CORBIDI 14626 KU902190 KU902265 KU902346 KU902109 Torres-Carvajal et al. 2016 Proctoporus P. sp. 2 Proc_s2_1 CORBIDI 9636 KU902191 KU902266 KU902347 KU902110 Torres-Carvajal et al. 2016 Proctoporus P. sp. 2 Proc_s2_2 CORBIDI 10753 KU902192 KU902267 KU902348 KU902111 Torres-Carvajal et al. 2016 Proctoporus P. sp. 2 Proc_s2_3 CORBIDI 10754 KU902193 KU902268 KU902349 KU902112 Torres-Carvajal et al. 2016 Proctoporus P. sp. 2 Proc_s2_4 CORBIDI 10755 KU902194 KU902269 KU902350 KU902113 Torres-Carvajal et al. 2016 Proctoporus P. sp. 3 Proc_s3_1 CORBIDI 14692 KU902169 KU902326 KU902088 Torres-Carvajal et al. 2016 Proctoporus P. sp. 3 Proc_s3_2 CORBIDI 14693 KU902170 KU902249 KU902327 KU902089 Torres-Carvajal et al. 2016 Proctoporus P. sp. 4 IWU358 MUSM 32727 MH579606 MH579642 MH579672 MH579698 This study Proctoporus P. sp. 5 Pro_pach_3 MHNC4689 JX435892 JX435951 JX436057 JX436026 Goicoechea et al. 2012 Proctoporus P. spinalis IWU119 MUSM 31162 MH579607 MH579643 This study Proctoporus P. spinalis IWU120 IWU 120 MH579608 MH579644 MH579699 This study Proctoporus P. spinalis Proc_sp_1 CORBIDI 7234 KU902182 KU902259 KU902339 KU902101 Torres-Carvajal et al. 2016 Proctoporus P. spinalis Proc_sp_2 CORBIDI 7241 KU902183 KU902260 KU902340 KU902102 Torres-Carvajal et al. 2016 Proctoporus P. spinalis Proc_sp_3 CORBIDI 7246 KU902184 KU902261 KU902341 KU902103 Torres-Carvajal et al. 2016 Proctoporus P. spinalis Proc_sp_4 CORBIDI 11573 KU902185 KU902342 KU902104 Torres-Carvajal et al. 2016 Proctoporus P. spinalis Proc_sp_5 CORBIDI 11575 KU902186 KU902343 KU902105 Torres-Carvajal et al. 2016 Proctoporus P. sucullucu Pro_suc_1 MNCN44474 JX435894 JX435953 JX436028 Goicoechea et al. 2012 Proctoporus P. sucullucu Pro_suc_2 MNCN44475 JX435895 JX435954 JX436058 JX436029 Goicoechea et al. 2012 Proctoporus P. sucullucu Pro_suc_3 MNCN44476 JX435897 JX435955 JX436060 JX436030 Goicoechea et al. 2012 Proctoporus P. sucullucu Pro_suc_4 MNCN44478 JX435896 JX435956 JX436059 JX436044 Goicoechea et al. 2012 Proctoporus P. sucullucu Pro_suc_5 UTA R-52950 AY968830 AY968817 Doan et al. 2005 Proctoporus P. unsaacae Pro_uns_3 UTA R-51488 AY507859 AY507882 AY225186 AY507908 Doan et al. 2005 Proctoporus P. unsaacae Pro_uns_4 UTA R-51477 AY507860 AY507881 AY225170 AY507909 Doan et al. 2005 Proctoporus P. unsaacae Proc_un_1 CORBIDI 10562 KU902187 KU902262 KU902106 Torres-Carvajal et al. 2016 Proctoporus P. xestus Pro_xes_1 MNCN 6160 JX435898 JX436002 JX436101 Goicoechea et al. 2012 Proctoporus P. xestus Pro_xes_2 MNCN 2425 JX435899 JX436001 JX436100 JX436007 Goicoechea et al. 2012 Riama R. "Cordillera Central" Ria_CC1 A1 KY670708 KY681126 KY670670 Sanchez-Pacheco et al. 2017 Riama R. "Cordillera Central" Ria_CC2 A2 KY670709 KY681127 KY670671 Sanchez-Pacheco et al. 2017

GenBank Accession Genus Species Sample code Voucher Source 12S 16S cytb ND4 c-mos Riama R. "Narino" Ria_N1 SSP58 KY670711 KY681129 KY710849 KY670673 Sanchez-Pacheco et al. 2017 Riama R. "Narino" Ria_N2 SSP76 KY670712 KY681130 KY710850 KY670674 Sanchez-Pacheco et al. 2017 Riama R. “Cordillera Occidental" Ria_CO1 JJM2251 KY670710 KY681128 KY799162 KY670672 Sanchez-Pacheco et al. 2017 Riama R. anatoloros Ria_an_2 QCAZ9169 KY670702 KY681120 KY710843 KY670664 Sanchez-Pacheco et al. 2017 Riama R. anatoloros Ria_an_3 QCAZ9201 KY670703 KY681121 KY710844 KY670665 Sanchez-Pacheco et al. 2017 Riama R. anatoloros Ria_an_1 QCAZ 9203 KU902195 KU902270 KU902351 KU902114 Torres-Carvajal et al. 2016 Riama R. balneator Ria_ba_1 QCAZ 11099 KU902196 KU902271 KU902352 KU902115 Torres-Carvajal et al. 2016 Riama R. balneator Ria_ba_2 QCAZ11101 KY670704 KY681122 KY710845 KY670666 Sanchez-Pacheco et al. 2017 Riama R. cashcaensis Ria_cas_2 QCAZ10686 KJ948180 KJ948122 KJ948162 KJ948210 Aguirre-Penafiel et al. 2014 Riama R. cashcaensis Ria_cas_3 QCAZ 10754 KJ948181 KJ948126 KJ948163 KJ948219 Aguirre-Penafiel et al. 2014 Riama R. colomaromani Ria_col_1 KU217209 AY507853 AY507871 AY507888 AY507899 Doan et al. 2005 Riama R. colomaromani Ria_col_2 QCAZ8753 KY670705 KY681123 KY710846 KY670667 Sanchez-Pacheco et al. 2017 Riama R. columbiana Ria_columb_1 ICN11298 KY670706 KY681124 KY710847 KY670668 Sanchez-Pacheco et al. 2017 Riama R. columbiana Ria_columb_2 ICN11294 KY670707 KY681125 KY710848 KY670669 Sanchez-Pacheco et al. 2017 Riama R. labionis Ria_lab_2 QCAZ10412 KJ948172 KJ948121 KJ948148 KJ948207 Aguirre-Penafiel et al. 2014 Riama R. labionis Ria_lab_1 QCAZ 10411 KJ948171 KJ948120 KJ948147 KJ948218 Aguirre-Penafiel et al. 2014 Riama R. meleagris Ria_mel_1 QCAZ9841 KJ948185 KJ948130 KJ948165 KJ948211 Aguirre-Penafiel et al. 2014 Riama R. meleagris Ria_mel_2 QCAZ9842 KJ948191 KJ948131 KJ948166 KJ948198 Aguirre-Penafiel et al. 2014 Riama R. meleagris Ria_mel_3 QCAZ9845 KJ948184 KJ948132 KJ948167 KJ948197 Aguirre-Penafiel et al. 2014 Riama R. meleagris Ria_mel_4 QCAZ9846 KJ948183 KJ948133 KJ948168 KJ948212 Aguirre-Penafiel et al. 2014 Riama R. meleagris Ria_mel_5 QCAZ 9840 KJ948182 KJ948129 KJ948164 KJ948214 Aguirre-Penafiel et al. 2014 Riama R. orcesi Ria_orc_1 KU221772 AY507855 AY507874 AY507889 Doan et al. 2005 Riama R. orcesi Ria_orc_2 QCAZ 10569 KU902197 KU902272 KU902353 KU902116 Torres-Carvajal et al. 2016 Riama R. orcesi Ria_orc_3 QCAZ9035 KY670713 KY681131 KY710851 KY670675 Sanchez-Pacheco et al. 2017 Riama R. raneyi Ria_ran_1 QCAZ10090 KY670714 KY681132 KY710852 Sanchez-Pacheco et al. 2017 Riama R. raneyi Ria_ran_2 QCAZ9034 KY670715 KY681133 KY710853 Sanchez-Pacheco et al. 2017 Riama R. simotera Ria_sim_1 KU 217207 AY507856 AY507875 AY507890 AY507902 Aguirre-Penafiel et al. 2014 Riama R. simotera Ria_sim_2 QCAZ4120 KY670716 KY681134 KY710854 KY670676 Sanchez-Pacheco et al. 2017 Riama R. simotera Ria_sp_1 QCAZ 879 AY507861 AY507877 AY507904 Castoe et al. 2004 Riama R. stigmatoral Ria_stig_1 QCAZ7374 KJ948187 KJ948128 KJ948161 KJ948217 Aguirre-Penafiel et al. 2014 Riama R. stigmatoral Ria_stig_2 QCAZ9946 KJ948192 KJ948123 KJ948160 KJ948208 Aguirre-Penafiel et al. 2014 Riama R. stigmatoral Ria_stig_3 QCAZ 11412 KJ948189 KJ948124 KJ948158 KJ948209 Aguirre-Penafiel et al. 2014 Riama R. stigmatoral Ria_stig_4 QCAZ11415 KJ948190 KJ948127 KJ948159 KJ948215 Aguirre-Penafiel et al. 2014 Riama R. striata Ria_str_1 MAR333 KY670717 KY681135 KY670677 Sanchez-Pacheco et al. 2017

GenBank Accession Genus Species Sample code Voucher Source 12S 16S cytb ND4 c-mos Riama R. striata Ria_str_2 MAR933 KY670718 KY681136 KY710855 KY670678 Sanchez-Pacheco et al. 2017 Riama R. unicolor Ria_uni_1 QCAZ8405 KJ948173 KJ948139 KJ948149 KJ948201 Aguirre-Penafiel et al. 2014 Riama R. unicolor Ria_uni_10 KU 217211 AY507862 AY507880 AY507893 AY507907 Castoe et al. 2004 Riama R. unicolor Ria_uni_11 QCAZ9662 KY670719 KY681137 KY710856 KY670679 Sanchez-Pacheco et al. 2017 Riama R. unicolor Ria_uni_2 QCAZ8407 KJ948175 KJ948135 KJ948151 KJ948206 Aguirre-Penafiel et al. 2014 Riama R. unicolor Ria_uni_3 QCAZ8409 KJ948179 KJ948136 KJ948152 KJ948199 Aguirre-Penafiel et al. 2014 Riama R. unicolor Ria_uni_4 QCAZ8411 KJ948178 KJ948141 KJ948153 KJ948200 Aguirre-Penafiel et al. 2014 Riama R. unicolor Ria_uni_5 QCAZ8800 KJ948174 KJ948134 KJ948155 KJ948203 Aguirre-Penafiel et al. 2014 Riama R. unicolor Ria_uni_6 QCAZ9664 KJ948196 KJ948119 KJ948150 KJ948222 Aguirre-Penafiel et al. 2014 Riama R. unicolor Ria_uni_7 QCAZ9681 KJ948177 KJ948140 KJ948154 KJ948202 Aguirre-Penafiel et al. 2014 Riama R. unicolor Ria_uni_8 QCAZ 9682 KJ948188 KJ948138 KJ948157 KJ948205 Aguirre-Penafiel et al. 2014 Riama R. unicolor Ria_uni_9 QCAZ9684 KJ948176 KJ948137 KJ948156 KJ948204 Aguirre-Penafiel et al. 2014 Riama R. yumborum Ria_yum_1 QCAZ10822 KJ948186 KJ948125 KJ948169 KJ948213 Aguirre-Penafiel et al. 2014 Riama R. yumborum Ria_yum_2 QCAZ 10827 KJ948195 KJ948142 KJ948170 KJ948216 Aguirre-Penafiel et al. 2014 Selvasaura S. brava IWU339 MUSM 32718 MH579609 MH579645 MH579673 MH579700 This study Selvasaura S. brava IWU340 NMP6V 75655 MH579610 MH579646 MH579674 MH579701 This study Selvasaura S. brava IWU380 NMP6V 75653 MH579611 MH579647 MH579675 MH579702 This study Selvasaura S. brava IWU381 MUSM 32738 MH579612 MH579648 MH579676 MH579703 This study Selvasaura S. brava IWU382 NMP6V 75654 MH579613 MH579649 MH579677 MH579704 This study Selvasaura S. sp. Cerc_s3_1 CORBIDI 15117 KU902203 KU902278 KU902359 KU902122 Torres-Carvajal et al. 2016 Selvasaura S. sp. Cerc_s3_2 CORBIDI 15118 KU902204 KU902279 KU902360 KU902123 Torres-Carvajal et al. 2016 Selvasaura S. sp. Cerc_s3_3 CORBIDI 15119 KU902205 KU902280 KU902361 KU902124 Torres-Carvajal et al. 2016 Selvasaura S. sp. Cerc_s3_4 QCAZ 12798 KU902206 KU902281 KU902362 KU902125 Torres-Carvajal et al. 2016 Selvasaura S. sp. Cerc_s3_5 QCAZ 12891 KU902207 KU902282 KU902363 KU902126 Torres-Carvajal et al. 2016 Unnamed clade 2 90 NMP6V 75090 MH579621 MH579656 This study Unnamed clade 2 91 NMP6V 75091 MH579622 MH579657 This study Unnamed clade 2 Cerc_s2_1 CORBIDI 8815 KU902200 KU902275 KU902356 KU902119 Torres-Carvajal et al. 2016 Unnamed clade 2 Cerc_s2_2 CORBIDI 13634 KU902201 KU902276 KU902357 KU902120 Torres-Carvajal et al. 2016 Unnamed clade 2 Cerc_s2_3 CORBIDI 13636 KU902202 KU902277 KU902358 KU902121 Torres-Carvajal et al. 2016 Unnamed clade 2 IWU114 MUSM 31160 MH579614 MH579679 MH579706 This study Unnamed clade 2 IWU165 MUSM 31188 MH579615 MH579651 MH579680 MH579707 This study Unnamed clade 2 IWU287 MUSM 32973 MH579616 MH579708 This study Unnamed clade 2 IWU288 NMP6V 75084 MH579617 MH579652 MH579681 MH579709 This study Unnamed clade 2 IWU296 MUSM 31978 MH579618 MH579653 MH579682 This study

GenBank Accession Genus Species Sample code Voucher Source 12S 16S cytb ND4 c-mos Unnamed clade 2 IWU320 MUSM 31991 MH579619 MH579654 MH579683 MH579710 This study Unnamed clade 2 IWU325 MUSM 31994 MH579620 MH579655 MH579684 MH579711 This study Unnamed clade 2 IWU57 MUSM 31127 MH579650 MH579678 MH579705 This study Unnamed clade 4 EL409 MUSM 27610 MH579623 This study Unnamed clade 4 ML1352 MUSM 25345 MH579624 MH579658 MH579685 This study outgroup Alopoglossus A. viridiceps Alop_vi_1 QCAZ 10670 KP874789 KP874841 KJ705316 KP874899 Torres-Carvajal et al. 2014 Bachia B. barbouri Bach_bar_1 DQ383205 DQ383216 DQ383193 Kohlsdorf and Wagner 2006 Bachia B. bicolor Bach_bic_1 DQ383217 DQ383194 Kohlsdorf and Wagner 2006 Bachia B. bresslaui Bach_bre_1 MRT 916883 AF420755 AF420876 AF420860 Pellegrino et al. 2001 Pellegrino et al. 2001 Bachia B. dorbignyi Bach_dor_1 MRT 977273 AF420688 AF420754 AF420892 Teixeira et al. 2013 Pellegrino et al. 2001 Bachia B. flavescens Bach_fla_1 LSUMZ H12977 AF420705 AF420753 AF420869 AF420859 Teixeira et al. 2013 Bachia B. heteropa Bach_het_1 DQ383202 DQ383222 DQ383199 Kohlsdorf and Wagner 2006 Bachia B. heteropa Bach_het_2 DQ383210 DQ383213 DQ383190 Kohlsdorf and Wagner 2006 Bachia B. huallagana Bach_hua_1 DQ383212 DQ383224 DQ383201 Kohlsdorf and Wagner 2006 Bachia B. intermedia Bach_int_1 DQ383204 DQ383215 DQ383192 Kohlsdorf and Wagner 2006 Bachia B. monodactylus Bach_mon_2 DQ383208 DQ383220 DQ383191 Kohlsdorf and Wagner 2006 Bachia B. m. parkerii Bach_mon_1 DQ383203 DQ383214 DQ383197 Kohlsdorf and Wagner 2006 Bachia B. panoplia Bach_pan_1 DQ383207 DQ383219 DQ383196 Kohlsdorf and Wagner 2006 Bachia B. peruana Bach_per_1 DQ383206 DQ383218 DQ383195 Kohlsdorf and Wagner 2006 Bachia B. scaea Bach_sca_1 H1119 KC597259 KC597262 KC597265 Teixeira et al. 2013 Bachia B. scaea Bach_sca_2 H1978 KC597258 KC597261 KC597264 Teixeira et al. 2013 Bachia B. scaea Bach_sca_3 H510 KC597257 KC597260 KC597263 Teixeira et al. 2013 Bachia B. scolecoides Bach_sco_1 DQ383211 DQ383223 DQ383200 Kohlsdorf and Wagner 2006 Bachia B. trisanale Bach_tri_1 DQ383209 DQ383221 DQ383198 Kohlsdorf and Wagner 2006 Ecpleopus E. gaudichaudii Ecpl_ga_1 LG 1356 AF420660 AF420738 AF420901 AF420855 Pellegrino et al. 2001 Gymnophthalmus G. leucomystax Gymn_le_1 MRT 946613 AF420675 AF420715 AF420906 AF420824 Pellegrino et al. 2001 Rhachisaurus R. brachylepis Rhac_br_1 MRT 887336 AF420665 AF420737 AF420877 AF420853 Pellegrino et al. 2001 Riolama R. inopinata Rio_ino_1 IRSNB 2680 KP283384 KP283395 KP283388 Kok 2015 Riolama R. leucosticta Rio_leu_1 IRSNB18152 JQ742254 KP283398 KP283391 Kok 2015 Riolama R. leucosticta Rio_leu_2 IRSNB18153 JQ742255 KP283397 KP283390 Kok 2015 Riolama R. leucosticta Rio_leu_3 VUB 3767 JQ742256 KP283396 KP283389 Kok 2015

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