Convergent evolution of the army ant syndrome and congruence in big-data phylogenetics – Supplementary figures and tables

Marek L. Borowiec

1 Harpegnathos_saltator_Genome Linepithema_humile_Genome 100 Camponotus_floridanus_Genome 100 Pogonomyrmex_barbatus_Genome Vollenhovia_emeryi_Genome 100 100 Cardiocondyla_obscurior_Genome 100 Solenopsis_invicta_Genome 100 Atta_cephalotes_Genome 100 Acromyrmex_echinatior_Genome Tanipone_scelesta_M159 100 Tanipone_zona_M182 100 Tanipone_hirsuta_M279 100 Tanipone_aglandula_M280 Lioponera_longitarsus_M193 Lioponera_vespula_M210 100100 Lioponera_nr_kraepelinii_M131 100 Lioponera_nr_mayri_M215 100 Lioponera_MY_M268 100 Lioponera_cf_suscitata_M267 100 Lioponera_PG_M250 100 Lioponera_marginata_M249 87 Lioponera_clarus_M137 100 100 Lioponera_ruficornis_M165 Lividopone_MG_M132 100 100 Lividopone_MG_M194 100Lividopone_MG_M216 66 Lividopone_MG_M294 Zasphinctus_wilsoni_M229 100 Zasphinctus_sarowiwai_M227 100 100 Zasphinctus_TH_M192 100 Zasphinctus_trux_M136 100 Zasphinctus_PG_M285 100 100 Zasphinctus_imbecilis_M170 Parasyscia_UG_M281 100 Parasyscia_MG_M212 Parasyscia_UG_M219 100 100 Parasyscia_UG_M218 100 100 Parasyscia_wittmeri_M282 83 Parasyscia_VN_M207 100 Parasyscia_PG_M204 100 Parasyscia_dohertyi_M142 Vicinopone_conciliatrix_M128 Simopone_grandidieri_M186 83 100 Simopone_cf_oculata_D0792 100 Simopone_dryas_M224 100 Simopone_marleyi_M171 100 Simopone_conradti_M144 93 Simopone_rex_M133 100 Simopone_trita_M185 Syscia_augustae_M196 100 Syscia_GT_M127 100 Syscia_typhla_D0841 100 Syscia_MY_M176 100 100 Syscia_MY_M147 Eusphinctus_TH_M158 83 93 Ooceraea_fragosa_D0842 Ooceraea_biroi_Genome 100 100 Ooceraea_australis_M138 100 Ooceraea_MY_M270 100 Ooceraea_PG_M248 100 Ooceraea_FJ06_M168 Eburopone_CM02_D0788 100 Eburopone_UG_M259 Eburopone_MG_M195 100 100 Eburopone_MG_M130 100 Eburopone_MG_M213 100 Eburopone_MG_M214 Yunodorylus_TH_M160 100 98 Yunodorylus_paradoxus_M190 100 Yunodorylus_TH_M191 100 Yunodorylus_eguchii_M247 100 Cerapachys_sulcinodis_M243 100 Cerapachys_MY_M264 100 Cerapachys_antennatus_M263 100 84 Cerapachys_TH_M203 Chrysapace_TH_M156 100 Chrysapace_cf_crawleyi_M262 100 Chrysapace_MG_M155 100 Chrysapace_cf_sauteri_M261 Aenictogiton_ZM02_M181 100 Aenictogiton_UG_M189 97 100 Dorylus_laevigatus_M157 Dorylus_orientalis_M244 99 100100 Dorylus_conradti_M178 100 Dorylus_fimbriatus_M288 Dorylus_cf_fulvus_M149 100 100 Dorylus_fulvus_M179 100 Dorylus_spininodis_M292 Dorylus_braunsi_M289 100100 Dorylus_affinis_M177 97 100Dorylus_kohli_M180 100Dorylus_mayri_M291 100Dorylus_molestus_M290 100Dorylus_rubellus_M287 93 Dorylus_UG_M153 Aenictus_silvestrii_M221 100 Aenictus_yamanei_M265 99 Aenictus_latifemoratus_M266 49 Aenictus_bobaiensis_M197 100 100 Aenictus_levior_M231 Aenictus_camposi_M222 Aenictus_UG_M143 100 100 Aenictus_ZA_M228 99 Aenictus_fergusoni_M223 100 100 Aenictus_hodgsoni_M198 100Aenictus_laeviceps_M269 100 Aenictus_rotundicollis_M232 100 Aenictus_turneri_M135 100Aenictus_fuchuanensis_M201 100 100 Aenictus_hoelldobleri_M200 Aenictus_currax_M245 100Aenictus_cornutus_M230 100 Aenictus_gracilis_M199 Neocerapachys_CR_M209 100 Neocerapachys_neotropicus_M134 100Neocerapachys_cf_splendens_M251 100 Neocerapachys_BR_M295 97 Cylindromyrmex_meinerti_D0778 100 Cylindromyrmex_brasiliensis_M140 100 Cylindromyrmex_whymperi_M271 100 100 Cylindromyrmex_darlingtoni_M211 Acanthostichus_AZ_M277 100 Acanthostichus_AZ_M278 100 Acanthostichus_BR_M252 100Acanthostichus_GF_M208 100 98 Acanthostichus_serratulus_M166 Leptanilloides_nubecula_M167 100 Leptanilloides_mckennae_D0228 100 Leptanilloides_femoralis_M188 100 Leptanilloides_gracilis_M187 100 Leptanilloides_erinys_M246 Sphinctomyrmex_stali_M253 100 Sphinctomyrmex_cf_marcoyi_M202 98 Cheliomyrmex_megalonyx_M146 100Cheliomyrmex_cf_andicola_M174 96 Cheliomyrmex_cf_morosus_M217 100 Labidus_coecus_M173 100 Labidus_spininodis_M172 100 97 Labidus_praedator_M152 Nomamyrmex_hartigii_M220 100 100 Nomamyrmex_esenbeckii_M129 100 Eciton_mexicanum_M238 61Eciton_vagans_M184 100 100Eciton_quadriglume_M254 Eciton_lucanoides_M239 100 100Eciton_burchellii_M273 100Eciton_hamatum_M293 100 Eciton_rapax_M145 Neivamyrmex_distans_M242 100 Neivamyrmex_alfaroi_M240 100 Neivamyrmex_swainsonii_M169 100 Neivamyrmex_adnepos_M236 100 Neivamyrmex_EC_M175 100 Neivamyrmex_gibbatus_M139 100 Neivamyrmex_impudens_M237 100 0.04 100 Neivamyrmex_melanocephalus_M154 Neivamyrmex_cf_nyensis_M296 combined data matrix 100 Neivamyrmex_compressinodis_M235 Neivamyrmex_sumichrasti_M151 100100 maximum likelihood tree Neivamyrmex_asper_M233 100Neivamyrmex_kiowapache_M275 RAxML 100Neivamyrmex_opacithorax_M276 96Neivamyrmex_texanus_M274 partitioned by locus GTR+4Gamma model 100 Neivamyrmex_californicus_M272 500 bootstrap replicates

Supplementary Figure S1: Maximum likelihood tree obtained from the combined data matrix par- titioned by locus. Scale is in number of substitutions per site. Nodal support in percent bootstrap.

2 Harpegnathos_saltator_Genome Linepithema_humile_Genome 100 Camponotus_floridanus_Genome 100 Pogonomyrmex_barbatus_Genome Vollenhovia_emeryi_Genome 100 100 Cardiocondyla_obscurior_Genome 100 Solenopsis_invicta_Genome 100 Atta_cephalotes_Genome 100 Acromyrmex_echinatior_Genome Aenictogiton_ZM02_M181 100 Aenictogiton_UG_M189 100 Dorylus_laevigatus_M157 Dorylus_orientalis_M244 100100 Dorylus_conradti_M178 100 Dorylus_fimbriatus_M288 Dorylus_fulvus_M179 100 100 Dorylus_cf_fulvus_M149 100 Dorylus_spininodis_M292 Dorylus_affinis_M177 100100 Dorylus_braunsi_M289 100Dorylus_kohli_M180 100Dorylus_mayri_M291 100Dorylus_molestus_M290 100Dorylus_rubellus_M287 100 Dorylus_UG_M153 Aenictus_silvestrii_M221 Aenictus_latifemoratus_M266 10090 Aenictus_yamanei_M265 96 Aenictus_bobaiensis_M197 100 100 Aenictus_levior_M231 Aenictus_camposi_M222 Aenictus_ZA_M228 100 100 Aenictus_UG_M143 Aenictus_fergusoni_M223 100 100 Aenictus_hodgsoni_M198 100Aenictus_laeviceps_M269 100 Aenictus_rotundicollis_M232 100 Aenictus_turneri_M135 100Aenictus_fuchuanensis_M201 100 100 100 Aenictus_hoelldobleri_M200 Aenictus_currax_M245 100Aenictus_cornutus_M230 100 100 Aenictus_gracilis_M199 Cheliomyrmex_megalonyx_M146 100Cheliomyrmex_cf_andicola_M174 100 Cheliomyrmex_cf_morosus_M217 100 Labidus_coecus_M173 100 Labidus_spininodis_M172 100 Labidus_praedator_M152 100 Nomamyrmex_hartigii_M220 100 Nomamyrmex_esenbeckii_M129 100 Eciton_mexicanum_M238 Eciton_vagans_M184 100100 Eciton_quadriglume_M254 100 100 Eciton_lucanoides_M239 100Eciton_burchellii_M273 100Eciton_hamatum_M293 100 Eciton_rapax_M145 Neivamyrmex_distans_M242 100 Neivamyrmex_alfaroi_M240 99 Neivamyrmex_swainsonii_M169 100 Neivamyrmex_adnepos_M236 100 Neivamyrmex_EC_M175 100 Neivamyrmex_gibbatus_M139 100 Neivamyrmex_impudens_M237 100 99 Neivamyrmex_melanocephalus_M154 Neivamyrmex_cf_nyensis_M296 82 100 Neivamyrmex_compressinodis_M235 Neivamyrmex_sumichrasti_M151 100100 Neivamyrmex_asper_M233 100Neivamyrmex_kiowapache_M275 100Neivamyrmex_opacithorax_M276 100Neivamyrmex_texanus_M274 100 Neivamyrmex_californicus_M272 Yunodorylus_TH_M160 100 Yunodorylus_paradoxus_M190 100 Yunodorylus_TH_M191 100 Yunodorylus_eguchii_M247 Chrysapace_TH_M156 100 100 Chrysapace_cf_crawleyi_M262 100 Chrysapace_MG_M155 100 89 Chrysapace_cf_sauteri_M261 Cerapachys_sulcinodis_M243 100 Cerapachys_MY_M264 100 Cerapachys_antennatus_M263 100 Cerapachys_TH_M203 Sphinctomyrmex_stali_M253 100 Sphinctomyrmex_cf_marcoyi_M202 Leptanilloides_nubecula_M167 96 100 Leptanilloides_mckennae_D0228 100 Leptanilloides_femoralis_M188 100 Leptanilloides_gracilis_M187 100 100 Leptanilloides_erinys_M246 100 Neocerapachys_CR_M209 100 Neocerapachys_neotropicus_M134 100Neocerapachys_cf_splendens_M251 100 Neocerapachys_BR_M295 96 Cylindromyrmex_meinerti_D0778 100 Cylindromyrmex_brasiliensis_M140 100 Cylindromyrmex_whymperi_M271 100 100 Cylindromyrmex_darlingtoni_M211 Acanthostichus_AZ_M277 100 Acanthostichus_AZ_M278 100 Acanthostichus_BR_M252 100Acanthostichus_GF_M208 100 100 Acanthostichus_serratulus_M166 Eburopone_CM02_D0788 100 Eburopone_UG_M259 Eburopone_MG_M195 100 100 Eburopone_MG_M130 100 Eburopone_MG_M213 100 Eburopone_MG_M214 Syscia_GT_M127 100 Syscia_augustae_M196 100 Syscia_typhla_D0841 100 Syscia_MY_M176 100 83 100 Syscia_MY_M147 Eusphinctus_TH_M158 96 Ooceraea_fragosa_D0842 Ooceraea_biroi_Genome 100 100 Ooceraea_australis_M138 100 Ooceraea_MY_M270 100 Ooceraea_FJ06_M168 100 Ooceraea_PG_M248 100 Vicinopone_conciliatrix_M128 Simopone_grandidieri_M186 64 100 Simopone_cf_oculata_D0792 100 Simopone_dryas_M224 Simopone_rex_M133 100 100 Simopone_trita_M185 100 Simopone_conradti_M144 100 Simopone_marleyi_M171 88 Tanipone_scelesta_M159 100 Tanipone_zona_M182 100 Tanipone_hirsuta_M279 100 Tanipone_aglandula_M280 Lioponera_longitarsus_M193 Lioponera_vespula_M210 100100 Lioponera_nr_kraepelinii_M131 100 64 Lioponera_nr_mayri_M215 100 Lioponera_MY_M268 100 Lioponera_cf_suscitata_M267 100 Lioponera_PG_M250 100 Lioponera_marginata_M249 41 Lioponera_clarus_M137 100 100 Lioponera_ruficornis_M165 Lividopone_MG_M132 100 Lividopone_MG_M194 100Lividopone_MG_M216 100 Lividopone_MG_M294 Zasphinctus_wilsoni_M229 100 Zasphinctus_sarowiwai_M227 100 100 Zasphinctus_TH_M192 100 Zasphinctus_trux_M136 100 Zasphinctus_PG_M285 100 100 Zasphinctus_imbecilis_M170 0.07 Parasyscia_UG_M281 100 Parasyscia_MG_M212 combined data matrix Parasyscia_UG_M219 100 100 Parasyscia_UG_M218 100 maximum likelihood tree 100 Parasyscia_wittmeri_M282 Parasyscia_VN_M207 RAxML 100 Parasyscia_PG_M204 100 k-means partitions GTR+4Gamma model Parasyscia_dohertyi_M142 500 bootstrap replicates

Supplementary Figure S2: Maximum likelihood tree obtained from the combined data matrix under k-means partitions. Scale is in number of substitutions per site. Nodal support in percent bootstrap.

3 HARPEGNATHOS_SALTATOR_GENOME LINEPITHEMA_HUMILE_GENOME 100 CAMPONOTUS_FLORIDANUS_GENOME 100 POGONOMYRMEX_BARBATUS_GENOME 100 VOLLENHOVIA_EMERYI_GENOME 100 CARDIOCONDYLA_OBSCURIOR_GENOME 100 SOLENOPSIS_INVICTA_GENOME 100 ACROMYRMEX_ECHINATIOR_GENOME 100 ATTA_CEPHALOTES_GENOME AENICTOGITON_UG_M189 100AENICTOGITON_ZM02_M181 100 DORYLUS_LAEVIGATUS_M157 DORYLUS_ORIENTALIS_M244 100100 DORYLUS_CONRADTI_M178 100 DORYLUS_FIMBRIATUS_M288 DORYLUS_CF_FULVUS_M149 100 100DORYLUS_FULVUS_M179 100 DORYLUS_SPININODIS_M292 100DORYLUS_AFFINIS_M177 100DORYLUS_BRAUNSI_M289 100DORYLUS_KOHLI_M180 100DORYLUS_MAYRI_M291 100DORYLUS_MOLESTUS_M290 100DORYLUS_UG_M153 98DORYLUS_RUBELLUS_M287 AENICTUS_SILVESTRII_M221 100 AENICTUS_YAMANEI_M265 100 AENICTUS_LATIFEMORATUS_M266 56 AENICTUS_LEVIOR_M231 100 100 AENICTUS_BOBAIENSIS_M197 AENICTUS_CAMPOSI_M222 AENICTUS_UG_M143 100 100 AENICTUS_ZA_M228 AENICTUS_FERGUSONI_M223 100 100 AENICTUS_HODGSONI_M198 100AENICTUS_ROTUNDICOLLIS_M232 100AENICTUS_LAEVICEPS_M269 100 AENICTUS_CURRAX_M245 100AENICTUS_CORNUTUS_M230 100 100 100 AENICTUS_GRACILIS_M199 AENICTUS_TURNERI_M135 100AENICTUS_HOELLDOBLERI_M200 99 100AENICTUS_FUCHUANENSIS_M201 CHELIOMYRMEX_MEGALONYX_M146 100CHELIOMYRMEX_CF_ANDICOLA_M174 99CHELIOMYRMEX_CF_MOROSUS_M217 LABIDUS_COECUS_M173 100 100 LABIDUS_SPININODIS_M172 100LABIDUS_PRAEDATOR_M152 100 NOMAMYRMEX_ESENBECKII_M129 100 NOMAMYRMEX_HARTIGII_M220 100 ECITON_MEXICANUM_M238 48ECITON_VAGANS_M184 100 100ECITON_QUADRIGLUME_M254 ECITON_LUCANOIDES_M239 100 100ECITON_BURCHELLII_M273 100ECITON_RAPAX_M145 100ECITON_HAMATUM_M293 NEIVAMYRMEX_DISTANS_M242 100 NEIVAMYRMEX_ALFAROI_M240 98 NEIVAMYRMEX_SWAINSONII_M169 100 NEIVAMYRMEX_EC_M175 100NEIVAMYRMEX_ADNEPOS_M236 100 NEIVAMYRMEX_GIBBATUS_M139 100 NEIVAMYRMEX_IMPUDENS_M237 100NEIVAMYRMEX_MELANOCEPHALUS_M154 99 98 NEIVAMYRMEX_CF_NYENSIS_M296 100 NEIVAMYRMEX_COMPRESSINODIS_M235 100 NEIVAMYRMEX_ASPER_M233 100NEIVAMYRMEX_SUMICHRASTI_M151 100NEIVAMYRMEX_KIOWAPACHE_M275 100NEIVAMYRMEX_OPACITHORAX_M276 96NEIVAMYRMEX_CALIFORNICUS_M272 100NEIVAMYRMEX_TEXANUS_M274 YUNODORYLUS_PARADOXUS_M190 100 YUNODORYLUS_TH_M160 100 YUNODORYLUS_EGUCHII_M247 100YUNODORYLUS_TH_M191 100 CERAPACHYS_SULCINODIS_M243 100 CERAPACHYS_MY_M264 100 CERAPACHYS_ANTENNATUS_M263 100 86 CERAPACHYS_TH_M203 CHRYSAPACE_TH_M156 100 CHRYSAPACE_CF_CRAWLEYI_M262 100 CHRYSAPACE_MG_M155 100 CHRYSAPACE_CF_SAUTERI_M261 SPHINCTOMYRMEX_STALI_M253 100 SPHINCTOMYRMEX_CF_MARCOYI_M202 92 LEPTANILLOIDES_NUBECULA_M167 100 LEPTANILLOIDES_MCKENNAE_D0228 100 LEPTANILLOIDES_FEMORALIS_M188 99 100 LEPTANILLOIDES_ERINYS_M246 100 LEPTANILLOIDES_GRACILIS_M187 100 NEOCERAPACHYS_CR_M209 100 NEOCERAPACHYS_NEOTROPICUS_M134 100 NEOCERAPACHYS_BR_M295 100NEOCERAPACHYS_CF_SPLENDENS_M251 91 CYLINDROMYRMEX_MEINERTI_D0778 100 CYLINDROMYRMEX_BRASILIENSIS_M140 100 CYLINDROMYRMEX_WHYMPERI_M271 100 100 CYLINDROMYRMEX_DARLINGTONI_M211 ACANTHOSTICHUS_AZ_M277 100 ACANTHOSTICHUS_AZ_M278 100 ACANTHOSTICHUS_BR_M252 99 100ACANTHOSTICHUS_GF_M208 100ACANTHOSTICHUS_SERRATULUS_M166 EBUROPONE_CM02_D0788 100 EBUROPONE_UG_M259 100 EBUROPONE_MG_M195 100EBUROPONE_MG_M130 100EBUROPONE_MG_M214 100EBUROPONE_MG_M213 SYSCIA_GT_M127 100SYSCIA_AUGUSTAE_M196 100 SYSCIA_TYPHLA_D0841 96 100 SYSCIA_MY_M147 100 100SYSCIA_MY_M176 EUSPHINCTUS_TH_M158 98 OOCERAEA_FRAGOSA_D0842 100 OOCERAEA_AUSTRALIS_M138 100 OOCERAEA_BIROI_GENOME 100 OOCERAEA_MY_M270 100 OOCERAEA_FJ06_M168 100 94 OOCERAEA_PG_M248 VICINOPONE_CONCILIATRIX_M128 TANIPONE_SCELESTA_M159 100 TANIPONE_ZONA_M182 100 TANIPONE_HIRSUTA_M279 100 63 TANIPONE_AGLANDULA_M280 SIMOPONE_CF_OCULATA_D0792 100 88 SIMOPONE_GRANDIDIERI_M186 100 SIMOPONE_DRYAS_M224 100 SIMOPONE_MARLEYI_M171 100 SIMOPONE_CONRADTI_M144 91 SIMOPONE_REX_M133 100SIMOPONE_TRITA_M185 51 LIOPONERA_LONGITARSUS_M193 LIOPONERA_VESPULA_M210 100100 LIOPONERA_NR_KRAEPELINII_M131 100LIOPONERA_NR_MAYRI_M215 100 LIOPONERA_CF_SUSCITATA_M267 100 LIOPONERA_MY_M268 100 LIOPONERA_PG_M250 100 LIOPONERA_MARGINATA_M249 93 100 LIOPONERA_CLARUS_M137 100 LIOPONERA_RUFICORNIS_M165 LIVIDOPONE_MG_M132 100 LIVIDOPONE_MG_M194 100LIVIDOPONE_MG_M294 62LIVIDOPONE_MG_M216 ZASPHINCTUS_WILSONI_M229 100 100 ZASPHINCTUS_SAROWIWAI_M227 100 ZASPHINCTUS_TH_M192 100 ZASPHINCTUS_TRUX_M136 100 100 ZASPHINCTUS_PG_M285 100 ZASPHINCTUS_IMBECILIS_M170 0.04 PARASYSCIA_UG_M281 combined data matrix 100 PARASYSCIA_MG_M212 PARASYSCIA_VN_M207 maximum likelihood tree 100 100 PARASYSCIA_PG_M204 100 100 PARASYSCIA_DOHERTYI_M142 RAxML PARASYSCIA_UG_M219 100 PARASYSCIA_UG_M218 unpartitioned GTR+4Gamma model 100 500 bootstrap replicates PARASYSCIA_WITTMERI_M282

Supplementary Figure S3: Maximum likelihood tree obtained from unpartitioned combined data matrix. Scale is in number of substitutions per site. Nodal support in percent bootstrap.

4 HARPEGNATHOS_SALTATOR_GENOME LINEPITHEMA_HUMILE_GENOME 1 CAMPON OTUS_FLORI DANUS_G ENOME 1 POGONOMYRMEX_BARBATUS_GENOME VOLLENHOVIA_EMERYI_GENOME 1 1 CARDIOCONDYLA_OBSCURIOR_GENOME 1 SOLENOPSIS_INVICTA_GENOME 1 A CRO MYRME X_ECHIN ATIOR_G ENOME 1 ATTA_CEPHALOTES_GENOME VICINOPONE_CONCILIATRIX_M128 SYSCIA_GT_M127 1 SYSCIA_AUGUSTAE_M196 1 SY SCIA_TYP HLA_D0841 1 SYSC IA_MY _M176 1 1 SYSC IA_MY _M147 1 EUSPHINCTUS_TH_M158 1 OOCERAEA_FRAGOSA_D0842 OOCERAEA_AUSTRALIS_M138 1 1 OOCERAEA_BIROI_GENOME 1 OOCERAEA_MY_M270 1 OOCE RAEA_ FJ06_M168 1 OOCERAEA_PG_M248 1 SIMOPONE_CF_OCULATA_D0792 1 SIMOPONE_GRANDIDIERI_M186 1 SIMOPONE_DRYAS_M224 SIM OPONE_CO NRAD TI_M144 1 0 . 7 9 SIMOPONE_MARLEYI_M171 1 SIMOPONE_TRITA_M185 1 SIMOPONE_REX_M133 TANIPONE_SCEL ESTA_M159 1 1 TANIPONE_ZONA_M182 1 T ANIPO NE_HI RSUT A_M279 1 TANIPONE_AGLANDULA_M280 LIOPONERA_LONGITARSUS_M193 L IOPO NERA_VES PULA_M210 11 L IOPONERA_NR_MAYRI _M215 0 . 5 7 1 LIOPONERA_NR_KRAEPELINII_M131 1 LIOPONERA_MY_M268 1 LIOPONERA_CF_SUSCITATA_M267 1 LIOPONERA_MARGINATA_M249 1 LIOPONERA_PG_M250 0 . 9 4 L IOPO NERA_CLARUS_M137 1 1 LIOPONERA_RUFICORNIS_M165 1 LIVIDOPONE_MG_M132 1 LIVIDOPONE_MG_M194 1 LIVIDOPONE_MG_M216 1 LIVIDOPONE_MG_M294 ZASPHI NCT US_WILSONI _M229 1 ZASPHINCTUS_TH_M192 1 1 ZASPHINCTUS_SAROWIWAI_M227 1 ZASPHINCTUS_TRUX_M136 1 ZASPHINCTUS_PG_M285 1 1 ZASPHINCTUS_IMBECILIS_M170 PARASYSC IA_UG _M281 1 PARASYSCIA_MG_M212 PARASYSCIA_VN_M207 1 1 PARASYSCIA_PG_M204 1 1 PARASYSCIA_DOHERTYI_M142 PARAS YSC IA_UG _M219 1 PARASYSCIA_WITTMERI_M282 1 PARASYSC IA_UG _M218 EBUROPONE_CM02_D0788 1 EBUROPONE_UG_M259 EBUROPONE_MG_M213 1 1 EBUROPONE_MG_M214 1 EBUROPONE_MG_M195 1 EBUROPONE_MG_M130 CERAPACHYS_SULCINODIS_M243 1 CERAPACHYS_MY_M264 1 CER APACHYS_T H_M203 1 01 . 9 7 CERAPACHYS_ANTENNATUS_M263 YUNODORYLUS_TH_M160 1 Y UNODORY LUS_ PARAD OXUS _M190 1 YUNODORYLUS_TH_M191 1 Y UNODORY LUS_ EGUCHII_M247 LEPT ANI LLOIDES_MCK ENNA E_D0228 1 LEPTANILLOIDES_NUBECULA_M167 1 LEPTANILLOIDES_FEMORALIS_M188 1 1 LEPTANILLOIDES_ERINYS_M246 1 LEPTANILLOIDES_GRACILIS_M187 SPHI NCTOMY RMEX_ STALI _M253 1 SPHINCTOMYRMEX_CF_MARCOYI_M202 NEOCERAPACHYS_CR_M209 1 1 NEOCERAPACHYS_NEOTROPICUS_M134 1 NEO CERAPACHYS_CF _SPLENDENS_M251 1 NEOCERAPACHYS_BR_M295 11 CYLINDROMYRMEX_MEINERTI_D077 8 1 CYLINDROMYRMEX_BRASILIENSIS_M140 1 CYLI NDRO MYRMEX_DARLIN GTONI _M211 1 1 CYLINDROMYRMEX_WHYMPERI_M271 ACANTHOSTICHUS_AZ_M278 1 ACANTHOSTICHUS_AZ_M277 1 ACANTH OSTICHUS_B R_M252 1 ACANTHOSTICHUS_GF_M208 1 ACANTHOSTICHUS_SERRATULUS_M166 0 . 7 1 CHRYSAPACE_MG_M155 1 CHRYSAPACE_CF _SAUT ERI _M261 1 CHRYSAPA CE_T H_M156 1 CHRYSAPACE_CF_CRAWLEYI_M262 AENICTOGITON_UG_M189 1 AENICTOGITON_ZM02_M181 1 DORYLUS_LAEVIGATUS_M157 DORYLUS_CONRADTI_M178 1 1 DORYLUS_ORIENTALIS_M244 1 DORYLUS_FIMBRIATUS_M288 DORYLUS_CF_FULVUS_M149 1 1 DORYLUS_FULVUS_M179 1 1 DORYLUS_SPININODIS_M292 DO RYLUS_B RAUNSI_M289 1 1 DORYLUS_AFFINIS_M177 1 DORYLUS_KOHLI_M180 1 DORYLUS_MAYRI_M291 1 DORYLUS_MOLESTUS_M290 1 DORYLUS_UG_M153 0 . 6 2 DORYLUS_RUBELLUS_M287 AENICTUS_SILVESTRII_M221 AENICTUS_LATIFEMORATUS_M266 1 10 . 9 9 AENICTUS_ YAMAN EI_M265 1 AENICTUS_LEVIOR_M231 1 1 AENICT US_BO BAI ENSI S_M197 AENICTUS_CAMPOSI_M222 AENICTUS_UG_M143 1 1 AENICTUS_ZA_M228 AENICTUS_FERGUSONI_M223 1 1 AENICTUS_HODGSONI_M198 1 AENICTUS_LAEVICEPS_M269 1 AENICTUS_ROTUNDICOLLIS_M232 1 AENICTUS_CURRAX_M245 1 AENICTUS_CORNUTUS_M230 1 1 AENICTUS_GRACILIS_M199 AENICT US_T URNERI _M135 1 AENICTUS_FUCHUANENSIS_M201 1 0 . 8 4 AENICTUS_HOELLDOBLERI_M200 CHELIOMYRMEX_MEGALONYX_M146 1 CHELIOMYRMEX_CF_MOROSUS_M217 1 CHELIOMYRMEX_CF_ANDICOLA_M174 LABIDUS_COECUS _M173 1 1 LABIDUS_PRAEDATOR_M152 1 LABIDUS_SPININODIS_M172 1 NOMAMYRMEX_ESENBECKII_M129 1 NO MAMYRME X_HAR TIGII_M220 1 ECITON_MEXICANUM_M238 0 . 4 ECITON_QUA DRIGLUME _M254 1 1 EC ITON_VAGANS _M184 ECITON_LUCANOIDES_M239 1 1 ECITON_BURCHELLII_M273 1 EC ITON_HA MAT UM_M293 1 ECITON_RAPAX_M145 NEIVAMYRMEX_DISTANS_M242 1 NEIVA MYRMEX _ALFAR OI_M240 0 . 9 9 NEIVAMYRMEX_SWAINSONII_M169 1 NEIVAMYRMEX_ADNEPOS_M236 1 NEIVAMYRMEX_EC_M175 1 NEIVAMYRMEX_GIBBATUS_M139 1 NEIVAMYRMEX_IMPUDENS_M237 1 N EIVAMY RME X_MELANOCE PHA LUS _M154 1 NEI VAMYRMEX_CF _NY ENSI S_M296 1 N EIVAMY RME X_COMPR ESSINOD IS_M235 NEIVAMYRMEX_SUMICHRASTI_M151 1 1 3 . 0 NEIVAMYRMEX_ASPER_M233 all loci 1 NEIVAMYRMEX_KIOWAPACHE_M275 1 NEIVAMYRMEX_OPACITHORAX_M276 weighted statistical binning 1 NEIVAMYRMEX_TEXANUS_M274 1 ASTRAL species tree NEIVAMYRMEX_CALIFORNICUS_M272

Supplementary Figure S4: Summary species tree obtained from all 2,166 loci using ASTRAL. Scale is in coalescent units. Nodal support in local posterior probabilities.

5 Harpegnathos_saltator_Genome Linepithema_humile_Genome 100 Camponotus_floridanus_Genome 100 Pogonomyrmex_barbatus_Genome Vollenhovia_emeryi_Genome 100 100 Cardiocondyla_obscurior_Genome 100 Solenopsis_invicta_Genome 100 Acromyrmex_echinatior_Genome 100 Atta_cephalotes_Genome Lioponera_longitarsus_M193 Lioponera_vespula_M210 10095 Lioponera_nr_kraepelinii_M131 100 Lioponera_nr_mayri_M215 98 Lioponera_cf_suscitata_M267 100 Lioponera_MY_M268 100 Lioponera_PG_M250 100 Lioponera_marginata_M249 48 Lioponera_ruficornis_M165 100 100 Lioponera_clarus_M137 Lividopone_MG_M132 100 Lividopone_MG_M294 100 Lividopone_MG_M194 67 Lividopone_MG_M216 Zasphinctus_wilsoni_M229 100 Zasphinctus_sarowiwai_M227 100 100 Zasphinctus_TH_M192 100 Zasphinctus_trux_M136 100 Zasphinctus_imbecilis_M170 100 94 Zasphinctus_PG_M285 Parasyscia_MG_M212 100 Parasyscia_UG_M281 Parasyscia_VN_M207 82 100 Parasyscia_dohertyi_M142 100 100 Parasyscia_PG_M204 Parasyscia_UG_M219 100 100 Parasyscia_UG_M218 99 Parasyscia_wittmeri_M282 Vicinopone_conciliatrix_M128 62 Tanipone_scelesta_M159 100 Tanipone_zona_M182 100 Tanipone_hirsuta_M279 100 53 Tanipone_aglandula_M280 Simopone_grandidieri_M186 100 Simopone_cf_oculata_D0792 100 Simopone_dryas_M224 Simopone_trita_M185 100 100 Simopone_rex_M133 100 Simopone_conradti_M144 66 Simopone_marleyi_M171 Eusphinctus_TH_M158 Syscia_GT_M127 100 Syscia_augustae_M196 100 100 39 Syscia_typhla_D0841 94 Syscia_MY_M147 100 77 Syscia_MY_M176 Ooceraea_fragosa_D0842 Ooceraea_biroi_Genome 100 75 Ooceraea_australis_M138 100 Ooceraea_MY_M270 100 Ooceraea_FJ06_M168 100 Ooceraea_PG_M248 Eburopone_CM02_D0788 100 Eburopone_UG_M259 Eburopone_MG_M214 58 100 100 Eburopone_MG_M213 100 Eburopone_MG_M195 100 Eburopone_MG_M130 Sphinctomyrmex_cf_marcoyi_M202 100 Sphinctomyrmex_stali_M253 Leptanilloides_mckennae_D0228 76 100 Leptanilloides_nubecula_M167 100 Leptanilloides_femoralis_M188 100 Leptanilloides_gracilis_M187 100 Leptanilloides_erinys_M246 64 Neocerapachys_CR_M209 100 57 Neocerapachys_neotropicus_M134 100 Neocerapachys_BR_M295 100 Neocerapachys_cf_splendens_M251 91 Cylindromyrmex_meinerti_D0778 100 Cylindromyrmex_brasiliensis_M140 100 Cylindromyrmex_whymperi_M271 100 100 Cylindromyrmex_darlingtoni_M211 Acanthostichus_AZ_M277 100 Acanthostichus_AZ_M278 100 Acanthostichus_BR_M252 100Acanthostichus_GF_M208 100 Acanthostichus_serratulus_M166 Cerapachys_sulcinodis_M243 100 Cerapachys_MY_M264 39 100 Cerapachys_antennatus_M263 100 Cerapachys_TH_M203 Chrysapace_TH_M156 88 100 Chrysapace_cf_crawleyi_M262 100 Chrysapace_MG_M155 100 Chrysapace_cf_sauteri_M261 37 Yunodorylus_eguchii_M247 100 Yunodorylus_TH_M191 100 Yunodorylus_TH_M160 100 Yunodorylus_paradoxus_M190 Aenictogiton_ZM02_M181 100 Aenictogiton_UG_M189 100 Dorylus_laevigatus_M157 Dorylus_conradti_M178 100100 Dorylus_orientalis_M244 45 95 Dorylus_fimbriatus_M288 Dorylus_cf_fulvus_M149 100 100 Dorylus_fulvus_M179 100 Dorylus_spininodis_M292 Dorylus_affinis_M177 100100 Dorylus_braunsi_M289 100Dorylus_kohli_M180 90Dorylus_mayri_M291 100Dorylus_molestus_M290 100Dorylus_UG_M153 91 Dorylus_rubellus_M287 Aenictus_silvestrii_M221 Aenictus_bobaiensis_M197 50 100 100 Aenictus_levior_M231 99 Aenictus_latifemoratus_M266 56 100 Aenictus_yamanei_M265 Aenictus_camposi_M222 Aenictus_UG_M143 100 100 Aenictus_ZA_M228 Aenictus_fergusoni_M223 100100 Aenictus_hodgsoni_M198 100Aenictus_laeviceps_M269 100 Aenictus_rotundicollis_M232 100 Aenictus_currax_M245 100Aenictus_gracilis_M199 100 100 Aenictus_cornutus_M230 Aenictus_turneri_M135 100Aenictus_hoelldobleri_M200 98 41 Aenictus_fuchuanensis_M201 Cheliomyrmex_megalonyx_M146 100Cheliomyrmex_cf_morosus_M217 100 Cheliomyrmex_cf_andicola_M174 100 Labidus_coecus_M173 100 Labidus_spininodis_M172 100 Labidus_praedator_M152 Nomamyrmex_esenbeckii_M129 100 100 Nomamyrmex_hartigii_M220 100 Eciton_mexicanum_M238 87Eciton_vagans_M184 100 100Eciton_quadriglume_M254 Eciton_lucanoides_M239 100 100Eciton_burchellii_M273 100Eciton_hamatum_M293 100 Eciton_rapax_M145 Neivamyrmex_distans_M242 100 Neivamyrmex_alfaroi_M240 65 Neivamyrmex_swainsonii_M169 100 Neivamyrmex_adnepos_M236 100 Neivamyrmex_EC_M175 100 Neivamyrmex_gibbatus_M139 100 Neivamyrmex_impudens_M237 100 83 Neivamyrmex_melanocephalus_M154 Neivamyrmex_cf_nyensis_M296 0.05 100 Neivamyrmex_compressinodis_M235 Neivamyrmex_asper_M233 high bootstrap loci 100100 Neivamyrmex_sumichrasti_M151 maximum likelihood tree 100Neivamyrmex_opacithorax_M276 RAxML 100Neivamyrmex_kiowapache_M275 57Neivamyrmex_californicus_M272 100 partitioned by locus GTR+4Gamma model Neivamyrmex_texanus_M274 500 bootstrap replicates

Supplementary Figure S5: Maximum likelihood tree obtained from high-bootstrap data matrix partitioned by locus. Scale is in number of substitutions per site. Nodal support in percent bootstrap.

6 Harpegnathos_saltator_Genome Linepithema_humile_Genome 100 Camponotus_floridanus_Genome 100 Pogonomyrmex_barbatus_Genome Vollenhovia_emeryi_Genome 100 100 Cardiocondyla_obscurior_Genome 100 Solenopsis_invicta_Genome 100 Acromyrmex_echinatior_Genome 100 Atta_cephalotes_Genome Cheliomyrmex_megalonyx_M146 100Cheliomyrmex_cf_andicola_M174 100 Cheliomyrmex_cf_morosus_M217 100 Labidus_coecus_M173 100 Labidus_praedator_M152 100 Labidus_spininodis_M172 100 Nomamyrmex_hartigii_M220 100 Nomamyrmex_esenbeckii_M129 100 Eciton_mexicanum_M238 Eciton_vagans_M184 100100 Eciton_quadriglume_M254 100 100 Eciton_lucanoides_M239 100Eciton_burchellii_M273 100Eciton_hamatum_M293 100 Eciton_rapax_M145 Neivamyrmex_distans_M242 100 Neivamyrmex_alfaroi_M240 58 Neivamyrmex_swainsonii_M169 100 Neivamyrmex_adnepos_M236 100 Neivamyrmex_EC_M175 100 Neivamyrmex_gibbatus_M139 100 Neivamyrmex_impudens_M237 100 83 Neivamyrmex_melanocephalus_M154 Neivamyrmex_cf_nyensis_M296 100 Neivamyrmex_compressinodis_M235 Neivamyrmex_sumichrasti_M151 100100 Neivamyrmex_asper_M233 100Neivamyrmex_opacithorax_M276 100Neivamyrmex_kiowapache_M275 31Neivamyrmex_californicus_M272 100 100 Neivamyrmex_texanus_M274 Aenictogiton_UG_M189 100 Aenictogiton_ZM02_M181 100 Dorylus_laevigatus_M157 Dorylus_conradti_M178 100100 Dorylus_orientalis_M244 100 Dorylus_fimbriatus_M288 Dorylus_cf_fulvus_M149 100 100 Dorylus_fulvus_M179 100 Dorylus_spininodis_M292 Dorylus_affinis_M177 100100 Dorylus_braunsi_M289 100Dorylus_kohli_M180 90Dorylus_mayri_M291 100Dorylus_molestus_M290 100Dorylus_UG_M153 92 Dorylus_rubellus_M287 45 Aenictus_silvestrii_M221 Aenictus_latifemoratus_M266 10070 Aenictus_yamanei_M265 98 Aenictus_bobaiensis_M197 100 100 Aenictus_levior_M231 Aenictus_camposi_M222 Aenictus_ZA_M228 100 100 Aenictus_UG_M143 Aenictus_fergusoni_M223 100100 Aenictus_hodgsoni_M198 100Aenictus_rotundicollis_M232 100 Aenictus_laeviceps_M269 100 Aenictus_currax_M245 100Aenictus_gracilis_M199 100 100 Aenictus_cornutus_M230 71 Aenictus_turneri_M135 100Aenictus_hoelldobleri_M200 100 Aenictus_fuchuanensis_M201 Chrysapace_MG_M155 100 Chrysapace_cf_sauteri_M261 100 Chrysapace_TH_M156 100 Chrysapace_cf_crawleyi_M262 Cerapachys_sulcinodis_M243 100 Cerapachys_MY_M264 100 Cerapachys_antennatus_M263 100 100 Cerapachys_TH_M203 Yunodorylus_eguchii_M247 100 Yunodorylus_TH_M191 100 Yunodorylus_TH_M160 100 Yunodorylus_paradoxus_M190 Sphinctomyrmex_cf_marcoyi_M202 94 100 Sphinctomyrmex_stali_M253 Leptanilloides_nubecula_M167 91 100 Leptanilloides_mckennae_D0228 100 Leptanilloides_femoralis_M188 100 Leptanilloides_erinys_M246 100 Leptanilloides_gracilis_M187 78 Neocerapachys_CR_M209 85 100 Neocerapachys_neotropicus_M134 100 Neocerapachys_cf_splendens_M251 100 Neocerapachys_BR_M295 91 Cylindromyrmex_meinerti_D0778 100 Cylindromyrmex_brasiliensis_M140 100 Cylindromyrmex_darlingtoni_M211 100 100 Cylindromyrmex_whymperi_M271 Acanthostichus_AZ_M277 100 Acanthostichus_AZ_M278 100 Acanthostichus_BR_M252 100Acanthostichus_serratulus_M166 89 100 Acanthostichus_GF_M208 Eburopone_CM02_D0788 100 Eburopone_UG_M259 Eburopone_MG_M213 100 100 Eburopone_MG_M214 100 Eburopone_MG_M130 100 Eburopone_MG_M195 Eusphinctus_TH_M158 Syscia_GT_M127 100 100 Syscia_augustae_M196 100 Syscia_typhla_D0841 100 Syscia_MY_M176 41 100 30 Syscia_MY_M147 Ooceraea_fragosa_D0842 100 Ooceraea_australis_M138 100 Ooceraea_biroi_Genome 99 Ooceraea_MY_M270 100 Ooceraea_PG_M248 100 Ooceraea_FJ06_M168 Vicinopone_conciliatrix_M128 98 66 Tanipone_scelesta_M159 100 Tanipone_zona_M182 100 Tanipone_hirsuta_M279 100 49 Tanipone_aglandula_M280 Simopone_grandidieri_M186 100 Simopone_cf_oculata_D0792 100 Simopone_dryas_M224 Simopone_trita_M185 100 100 Simopone_rex_M133 100 Simopone_conradti_M144 100 Simopone_marleyi_M171 99 Lioponera_longitarsus_M193 Lioponera_vespula_M210 10058 Lioponera_nr_mayri_M215 100 Lioponera_nr_kraepelinii_M131 96 Lioponera_cf_suscitata_M267 100 Lioponera_MY_M268 100 Lioponera_marginata_M249 100 Lioponera_PG_M250 100 Lioponera_ruficornis_M165 100 100 Lioponera_clarus_M137 Lividopone_MG_M132 100 Lividopone_MG_M194 100Lividopone_MG_M294 100 Lividopone_MG_M216 Zasphinctus_wilsoni_M229 100 Zasphinctus_sarowiwai_M227 100 100 Zasphinctus_TH_M192 100 Zasphinctus_trux_M136 100 Zasphinctus_PG_M285 100 100 Zasphinctus_imbecilis_M170 0.08 Parasyscia_MG_M212 100 Parasyscia_UG_M281 high bootstrap loci Parasyscia_VN_M207 100 100 Parasyscia_PG_M204 maximum likelihood tree 100 100 Parasyscia_dohertyi_M142 RAxML Parasyscia_UG_M219 100 Parasyscia_wittmeri_M282 100 k-means partitions GTR+4Gamma model Parasyscia_UG_M218 500 bootstrap replicates

Supplementary Figure S6: Maximum likelihood tree obtained from high-bootstrap data matrix under k-means partitions. Scale is in number of substitutions per site. Nodal support in percent bootstrap.

7 Harpegnathos_saltator_Genome Linepithema_humile_Genome 100 Camponotus_floridanus_Genome 100 Pogonomyrmex_barbatus_Genome Vollenhovia_emeryi_Genome 100 100 Cardiocondyla_obscurior_Genome 100 Solenopsis_invicta_Genome 100 Atta_cephalotes_Genome 100 Acromyrmex_echinatior_Genome Aenictus_silvestrii_M221 Aenictus_latifemoratus_M266 10054 Aenictus_yamanei_M265 98 Aenictus_bobaiensis_M197 100 100 Aenictus_levior_M231 Aenictus_camposi_M222 Aenictus_ZA_M228 100 100 Aenictus_UG_M143 Aenictus_fergusoni_M223 100100 Aenictus_hodgsoni_M198 100Aenictus_laeviceps_M269 100 Aenictus_rotundicollis_M232 100 Aenictus_currax_M245 100Aenictus_cornutus_M230 100 100 Aenictus_gracilis_M199 Aenictus_turneri_M135 100Aenictus_fuchuanensis_M201 98 Aenictus_hoelldobleri_M200 Aenictogiton_ZM02_M181 100 Aenictogiton_UG_M189 100 Dorylus_laevigatus_M157 Dorylus_orientalis_M244 100100 Dorylus_conradti_M178 97 Dorylus_fimbriatus_M288 Dorylus_fulvus_M179 100 100 Dorylus_cf_fulvus_M149 100 Dorylus_spininodis_M292 Dorylus_affinis_M177 100100 Dorylus_braunsi_M289 100Dorylus_kohli_M180 85Dorylus_mayri_M291 100 100Dorylus_molestus_M290 100Dorylus_rubellus_M287 92 65 Dorylus_UG_M153 Cheliomyrmex_megalonyx_M146 100Cheliomyrmex_cf_andicola_M174 100 Cheliomyrmex_cf_morosus_M217 100 Labidus_coecus_M173 100 Labidus_praedator_M152 100 Labidus_spininodis_M172 Nomamyrmex_esenbeckii_M129 100 100 Nomamyrmex_hartigii_M220 100 Eciton_mexicanum_M238 86Eciton_vagans_M184 100 100Eciton_quadriglume_M254 Eciton_lucanoides_M239 100 100Eciton_burchellii_M273 100Eciton_rapax_M145 100 Eciton_hamatum_M293 Neivamyrmex_distans_M242 100 Neivamyrmex_alfaroi_M240 64 Neivamyrmex_swainsonii_M169 100 Neivamyrmex_EC_M175 100 Neivamyrmex_adnepos_M236 100 Neivamyrmex_gibbatus_M139 100 Neivamyrmex_impudens_M237 100 80 Neivamyrmex_melanocephalus_M154 Neivamyrmex_cf_nyensis_M296 59 100 Neivamyrmex_compressinodis_M235 Neivamyrmex_asper_M233 100100 Neivamyrmex_sumichrasti_M151 100Neivamyrmex_opacithorax_M276 100Neivamyrmex_kiowapache_M275 62Neivamyrmex_californicus_M272 100 Neivamyrmex_texanus_M274 Yunodorylus_TH_M160 100 Yunodorylus_paradoxus_M190 100 Yunodorylus_eguchii_M247 100 Yunodorylus_TH_M191 71 Cerapachys_sulcinodis_M243 100 Cerapachys_MY_M264 100 Cerapachys_antennatus_M263 100 56 Cerapachys_TH_M203 Chrysapace_cf_sauteri_M261 100 Chrysapace_MG_M155 100 Chrysapace_TH_M156 100 Chrysapace_cf_crawleyi_M262 Sphinctomyrmex_stali_M253 100 Sphinctomyrmex_cf_marcoyi_M202 Leptanilloides_nubecula_M167 90 100 Leptanilloides_mckennae_D0228 100 Leptanilloides_femoralis_M188 100 Leptanilloides_erinys_M246 80 100 Leptanilloides_gracilis_M187 64 Neocerapachys_CR_M209 100 Neocerapachys_neotropicus_M134 100 Neocerapachys_cf_splendens_M251 100 Neocerapachys_BR_M295 94 Cylindromyrmex_meinerti_D0778 100 Cylindromyrmex_brasiliensis_M140 100 Cylindromyrmex_whymperi_M271 100 100 Cylindromyrmex_darlingtoni_M211 Acanthostichus_AZ_M277 100 Acanthostichus_AZ_M278 100 Acanthostichus_BR_M252 100Acanthostichus_serratulus_M166 74 100 Acanthostichus_GF_M208 Eburopone_CM02_D0788 100 Eburopone_UG_M259 Eburopone_MG_M130 100 100 Eburopone_MG_M195 100 Eburopone_MG_M213 100 Eburopone_MG_M214 Eusphinctus_TH_M158 Syscia_augustae_M196 100 Syscia_GT_M127 100 100 Syscia_typhla_D0841 94 Syscia_MY_M176 29 100 63 Syscia_MY_M147 Ooceraea_fragosa_D0842 Ooceraea_biroi_Genome 100 72 Ooceraea_australis_M138 100 Ooceraea_MY_M270 100 Ooceraea_FJ06_M168 100 Ooceraea_PG_M248 Vicinopone_conciliatrix_M128 77 67 Tanipone_scelesta_M159 100 Tanipone_zona_M182 100 Tanipone_aglandula_M280 100 44 Tanipone_hirsuta_M279 Simopone_grandidieri_M186 100 Simopone_cf_oculata_D0792 100 Simopone_dryas_M224 Simopone_trita_M185 100 100 Simopone_rex_M133 100 Simopone_conradti_M144 59 Simopone_marleyi_M171 80 Lioponera_longitarsus_M193 Lioponera_vespula_M210 10096 Lioponera_nr_kraepelinii_M131 100 Lioponera_nr_mayri_M215 99 Lioponera_cf_suscitata_M267 100 Lioponera_MY_M268 100 Lioponera_marginata_M249 100 Lioponera_PG_M250 56 Lioponera_clarus_M137 100 100 Lioponera_ruficornis_M165 Lividopone_MG_M132 100 Lividopone_MG_M294 100Lividopone_MG_M216 59 Lividopone_MG_M194 Zasphinctus_wilsoni_M229 100 Zasphinctus_sarowiwai_M227 100 100 Zasphinctus_TH_M192 100 Zasphinctus_trux_M136 100 Zasphinctus_imbecilis_M170 100 93 Zasphinctus_PG_M285 Parasyscia_MG_M212 0.04 100 Parasyscia_UG_M281 high bootstrap loci Parasyscia_VN_M207 81 100 Parasyscia_PG_M204 100 maximum likelihood tree 100 Parasyscia_dohertyi_M142 Parasyscia_UG_M219 RAxML 100 Parasyscia_wittmeri_M282 100 unpartitioned GTR+4Gamma model Parasyscia_UG_M218 500 bootstrap replicates

Supplementary Figure S7: Maximum likelihood tree obtained from unpartitioned high-bootstrap data matrix. Scale is in number of substitutions per site. Nodal support in percent bootstrap.

8 Harpegnat hos_salt a t or_G enome Linepit hema_humile_G enome 1 Camponot u s _ f loridanus _ G enome 1 Pogonomyrmex_barbat u s _ G enome V ollenhov ia_emery i_G enome 1 0 . 9 9 Cardioc ondy la_obs curior_G enome 1 Solenops is_inv ict a_G enome 1 A cromy rmex _ec hinat ior_G enome 1 Atta_cephalot e s _ G enome Chry sapace_cf _saut eri_M261 1 Chrysapace_MG _M155 1 Chrysapac e_cf _ c rawleyi_M262 1 Chrysapac e_T H_M156 A enictogit on_UG _M189 1 Aenict ogit on_Z M02_M181 1 Dorylus_laevigat us_M157 Dorylus_c onradt i_M178 1 1 Dorylus_orient alis_M244 0 . 7 6 Dory lus _ f imbriat u s _M288 Dorylus_f ulvus_M179 1 1 Dory lus _ cf_ f ulv u s _M149 0 . 9 2 1 Dorylus _spininodis _M292 Dorylus_braunsi_M289 1 1 Dory lus_affinis _M177 1 Dory lus_k ohli_M180 0 . 9 6 Dory lus _mayri_M291 1 Dorylus_molest us_M290 1 Dorylus_UG _M153 0 . 4 5 Dorylus_rubellus_M287 A enict u s _ s ilvestrii_M221 0 . 9 5 1 A enict us_lat i f emorat u s _M266 0 . 9 7Aenict u s _ y amanei_M265 0 . 5 Aenict u s _lev ior_M231 1 1 A enictu s _bobaiens i s _M197 Aenict u s _ c amposi_M222 A enict u s _UG _M143 1 1 A enictus_ZA_M228 A enictu s _ f ergusoni_M223 1 1 A enictu s _hodgs oni_M198 1 Aenict us_laev iceps_M269 1 A enict u s _rot undic ollis_M232 1 A enictu s _ t urneri_M135 1 A enict us_f uchuanensis _M201 1 1 A enictus_hoelldobleri_M200 A enictu s _currax _M245 1 A enict us_grac ilis _M199 1 0 . 5 4 A enictu s _ c ornut u s _M230 Cheliomyrmex _megalonyx_M146 1 Cheliomy rmex_cf_moros u s _M217 1 Cheliomy rmex_cf_andic ola_M174 1 Labidus_c oecus _M173 1 Labidus_spininodis_M172 1 Labidus _praedat or_M152 1 Nomamy rmex _hart igii_M220 1 1 Nomamy rmex _es enbeck ii_M129 E c i t on_quadriglume_M254 1 1 Eci t on_v agans _M184 1 Ecit on_mexicanum_M238 0 . 4 7 E cit on_lucanoides_M239 1 1 Ecit on_burchellii_M273 1 E c i t on_hamat um_M293 1 Eci t on_rapax _M145 Neivamy rmex _alf aroi_M240 1 Neivamy rmex _dist ans _M242 0 . 9 2 Neivamy rmex _swains onii_M169 1 Neiv amy rmex _adnepos _M236 1 Neivamyrmex_EC_M175 1 Neiv amy rmex _gibbat u s _M139 1 Neiv amyrmex_melanocephalus_M154 1 Neivamyrmex_impudens_M237 0 . 9 1 Neiv amyrmex_cf _ny ens i s _M296 1 Neivamy rmex _ c ompressinodis _M235 Neiv amyrmex_s umichrast i_M151 1 0 . 9 9 Neivamyrmex_asper_M233 1 Neiv amy rmex _ k iowapac he_M275 1 Neiv amy rmex _opac i t horax _M276 0 . 5 6 Neivamyrmex _ t exanus_M274 1 Neivamyrmex_c alif ornicus_M272 Cerapac h ys_sulc inodis_M243 1 Cerapac h y s_MY_M264 1 Cerapac h ys_T H_M203 1 Cerapac h ys_ant ennat u s _M263 Neoc erapachy s_CR_M209 1 Neoc erapac h ys_neot ropic u s _M134 1 Neoc erapac hys _cf _splendens_M251 1 Neoc erapac h y s_BR_M295 00 . .9 9 6 7 Cylindromyrmex_meinert i_D0778 1 Cylindromyrmex_brasiliens i s _M140 1 Cylindromy rmex_whymperi_M271 1 1 Cylindromyrmex _darlingt oni_M211 A cant host i c hus_AZ_M278 1 A cant host i c hus_AZ_M277 1 Acant host ichus_BR_M252 1 Acant host i c hus _ GF_M208 0 . 8 6 1 A cant hostichus_s errat ulus_M166 E buropone_CM02_D0788 1 Eburopone_UG _M259 Eburopone_MG _M214 1 1 Eburopone_MG _M213 1 Eburopone_MG _M195 1 Eburopone_MG _M130 0 . 8 9 S phinct omyrmex _st ali_M253 1 S phinctomy rmex _cf_marc o y i_M202 Y unodory lus _ T H_M191 1 Yunodorylus _eguc hii_M247 1 Yunodorylus _paradoxus _M190 1 0 . 8 7 Y unodory lus _ T H_M160 Lept anilloides _mckennae_D0228 1 Lept anilloides _nubec ula_M167 1 Lept anilloides _ f emoralis_M188 0 . 6 3 1 Lept anilloides_erinys _M246 1 Lept anilloides _gracilis_M187 S y s cia_august ae_M196 1 Sys c ia_GT_M127 1 Syscia_t yphla_D0841 1 Syscia_MY _M147 0 . 8 8 1 1 Syscia_MY _M176 E u s phinctu s _ T H_M158 0 . 8 3 O oceraea_f ragos a_D0842 1 O oceraea_australis _M138 1 O o c eraea_biroi_G enome 0 . 6 1 O oceraea_MY _M270 1 1 O oceraea_FJ06_M168 1 O o c eraea_PG_M248 V i c inopone_c onciliat rix _M128 T anipone_s celest a_M159 1 T anipone_z ona_M182 1 T anipone_hirsut a_M279 1 0 . 8 5 T anipone_aglandula_M280 Simopone_cf _oculat a_D0792 1 S imopone_grandidieri_M186 1 Simopone_dryas_M224 0 . 9 9 Simopone_conradt i_M144 1 0 . 6 Simopone_marleyi_M171 1 S imopone_t rit a_M185 1 Simopone_rex _M133 Lioponera_longit ars u s _M193 Lioponera_ves pula_M210 0 . 4 6 1 0 . 9 6 Lioponera_nr_mayri_M215 1 Lioponera_nr_k raepelinii_M131 1 Lioponera_MY _M268 1 Lioponera_cf _ s u s cit a t a_M267 1 Lioponera_PG_M250 1 Lioponera_marginat a_M249 0 . 7 7 Lioponera_clarus _M137 1 1 Lioponera_ruf i c ornis _M165 Liv idopone_MG _M132 1 Liv idopone_MG _M194 1 Liv idopone_MG _M216 0 . 5 2 Liv idopone_MG _M294 Z asphinct us_wilsoni _M229 1 Z a s phinctu s _sarowiwai_M227 1 1 Z asphinct us_T H_M192 1 Z asphinct us_t rux_M136 1 Z asphinct us_imbecilis_M170 1 0 . 9 7 Z a s phinctus_PG _M285 P arasyscia_UG _M281 1 Parasy s c ia_MG _M212 Parasyscia_VN_M207 0 . 7 1 1 Paras yscia_dohertyi_M142 3 . 0 1 1 P arasyscia_PG_M204 high bootstrap loci P arasyscia_UG _M219 1 Parasysc ia_wittmeri_M282 0 . 9 9 weighted statistical binning P arasyscia_UG _M218 ASTRAL species tree

Supplementary Figure S8: Summary species tree obtained from 271 highest bootstrap loci using ASTRAL. Scale is in coalescent units. Nodal support in local posterior probabilities.

9 Harpegnathos_saltator_Genome Linepithema_humile_Genome 100 Camponotus_floridanus_Genome 100 Pogonomyrmex_barbatus_Genome Vollenhovia_emeryi_Genome 100 100 Cardiocondyla_obscurior_Genome 100 Solenopsis_invicta_Genome 100 Acromyrmex_echinatior_Genome 100 Atta_cephalotes_Genome Vicinopone_conciliatrix_M128 Tanipone_scelesta_M159 100 Tanipone_zona_M182 100Tanipone_aglandula_M280 100 86 Tanipone_hirsuta_M279 Simopone_grandidieri_M186 100 Simopone_cf_oculata_D0792 100 Simopone_dryas_M224 100 Simopone_marleyi_M171 100Simopone_conradti_M144 83 Simopone_trita_M185 100 Simopone_rex_M133 35 Lioponera_vespula_M210 91 Lioponera_nr_kraepelinii_M131 100 Lioponera_nr_mayri_M215 100 Lioponera_longitarsus_M193 Lioponera_cf_suscitata_M267 38 100 Lioponera_MY_M268 100 Lioponera_PG_M250 100 100 Lioponera_marginata_M249 98 Lioponera_ruficornis_M165 100 100 Lioponera_clarus_M137 Lividopone_MG_M132 100 Lividopone_MG_M294 100Lividopone_MG_M216 63 Lividopone_MG_M194 Zasphinctus_wilsoni_M229 100 Zasphinctus_TH_M192 100 100 Zasphinctus_sarowiwai_M227 100 Zasphinctus_trux_M136 100 Zasphinctus_PG_M285 100 100 Zasphinctus_imbecilis_M170 Parasyscia_UG_M281 100 Parasyscia_MG_M212 Parasyscia_VN_M207 100100 Parasyscia_dohertyi_M142 100 100 Parasyscia_PG_M204 Parasyscia_UG_M219 100 Parasyscia_wittmeri_M282 40 100 Parasyscia_UG_M218 Syscia_augustae_M196 100 Syscia_GT_M127 100 Syscia_typhla_D0841 100 Syscia_MY_M147 100 100 Syscia_MY_M176 Eusphinctus_TH_M158 92 Ooceraea_fragosa_D0842 Ooceraea_australis_M138 100100 Ooceraea_biroi_Genome 100 Ooceraea_MY_M270 100 Ooceraea_FJ06_M168 100 Ooceraea_PG_M248 Eburopone_CM02_D0788 100 Eburopone_UG_M259 Eburopone_MG_M214 100 100 Eburopone_MG_M213 100 Eburopone_MG_M195 100 Eburopone_MG_M130 Aenictogiton_ZM02_M181 100 Aenictogiton_UG_M189 100 Dorylus_laevigatus_M157 Dorylus_orientalis_M244 68 100100 Dorylus_conradti_M178 98 Dorylus_fimbriatus_M288 62 Dorylus_fulvus_M179 98 100 Dorylus_cf_fulvus_M149 100 Dorylus_spininodis_M292 Dorylus_affinis_M177 100100 Dorylus_braunsi_M289 100 100Dorylus_kohli_M180 93Dorylus_mayri_M291 100Dorylus_molestus_M290 100Dorylus_UG_M153 57 Dorylus_rubellus_M287 Aenictus_silvestrii_M221 Aenictus_latifemoratus_M266 10078 Aenictus_yamanei_M265 59 Aenictus_bobaiensis_M197 100 100 Aenictus_levior_M231 Aenictus_camposi_M222 Aenictus_UG_M143 100 100 Aenictus_ZA_M228 Aenictus_fergusoni_M223 100 78 100 Aenictus_hodgsoni_M198 100Aenictus_rotundicollis_M232 100 Aenictus_laeviceps_M269 100 Aenictus_turneri_M135 100 Aenictus_hoelldobleri_M200 100 100 Aenictus_fuchuanensis_M201 Aenictus_currax_M245 100Aenictus_gracilis_M199 100 Aenictus_cornutus_M230 Cerapachys_sulcinodis_M243 100 Cerapachys_MY_M264 100 Cerapachys_antennatus_M263 100 Cerapachys_TH_M203 Yunodorylus_TH_M160 100 100 Yunodorylus_paradoxus_M190 100 Yunodorylus_eguchii_M247 100 Yunodorylus_TH_M191 85 Chrysapace_cf_sauteri_M261 100 Chrysapace_MG_M155 100 Chrysapace_cf_crawleyi_M262 100 Chrysapace_TH_M156 Neocerapachys_CR_M209 100 Neocerapachys_neotropicus_M134 63 100Neocerapachys_BR_M295 100 Neocerapachys_cf_splendens_M251 72 Cylindromyrmex_meinerti_D0778 100 Cylindromyrmex_brasiliensis_M140 100 Cylindromyrmex_whymperi_M271 100 100 Cylindromyrmex_darlingtoni_M211 Acanthostichus_AZ_M277 100 Acanthostichus_AZ_M278 100 Acanthostichus_BR_M252 100Acanthostichus_GF_M208 100 100 Acanthostichus_serratulus_M166 Sphinctomyrmex_marcoyi_M202 100 Sphinctomyrmex_stali_M253 Leptanilloides_mckennae_D0228 100 Leptanilloides_nubecula_M167 100 Leptanilloides_femoralis_M188 100 Leptanilloides_gracilis_M187 100 100 Leptanilloides_erinys_M246 Cheliomyrmex_megalonyx_M146 100Cheliomyrmex_cf_morosus_M217 69 Cheliomyrmex_cf_andicola_M174 100 Labidus_coecus_M173 62 100 Labidus_praedator_M152 100 Labidus_spininodis_M172 100 Nomamyrmex_esenbeckii_M129 100 Nomamyrmex_hartigii_M220 100 Eciton_mexicanum_M238 Eciton_vagans_M184 100100 Eciton_quadriglume_M254 94 100 Eciton_lucanoides_M239 98 Eciton_burchellii_M273 100Eciton_rapax_M145 100 Eciton_hamatum_M293 Neivamyrmex_distans_M242 100 Neivamyrmex_alfaroi_M240 82 Neivamyrmex_swainsonii_M169 100 Neivamyrmex_EC_M175 100 Neivamyrmex_adnepos_M236 100 Neivamyrmex_gibbatus_M139 100 Neivamyrmex_melanocephalus_M154 100 94 Neivamyrmex_impudens_M237 0.02 Neivamyrmex_cf_nyensis_M296 100 Neivamyrmex_compressinodis_M235 slow-evolving loci Neivamyrmex_asper_M233 10099 Neivamyrmex_sumichrasti_M151 maximum likelihood tree 100Neivamyrmex_opacithorax_M276 RAxML 100Neivamyrmex_kiowapache_M275 52Neivamyrmex_californicus_M272 100 partitioned by locus GTR+4Gamma model Neivamyrmex_texanus_M274 500 bootstrap replicates

Supplementary Figure S9: Maximum likelihood tree obtained from slow-evolving data matrix par- titioned by locus. Scale is in number of substitutions per site. Nodal support in percent bootstrap.

10 Harpegnathos_saltator_Genome Linepithema_humile_Genome 100 Camponotus_floridanus_Genome 100 Pogonomyrmex_barbatus_Genome Vollenhovia_emeryi_Genome 100 100 Cardiocondyla_obscurior_Genome 100 Solenopsis_invicta_Genome 100 Acromyrmex_echinatior_Genome 100 Atta_cephalotes_Genome Eburopone_CM02_D0788 100 Eburopone_UG_M259 Eburopone_MG_M195 100 100 Eburopone_MG_M130 100 Eburopone_MG_M214 100 Eburopone_MG_M213 Vicinopone_conciliatrix_M128 Syscia_augustae_M196 100 Syscia_GT_M127 100 Syscia_typhla_D0841 100 Syscia_MY_M176 100 100 Syscia_MY_M147 Eusphinctus_TH_M158 94 Ooceraea_fragosa_D0842 Ooceraea_biroi_Genome 100100 Ooceraea_australis_M138 100 100 Ooceraea_MY_M270 100 Ooceraea_FJ06_M168 100 Ooceraea_PG_M248 Tanipone_scelesta_M159 100 Tanipone_zona_M182 31 100Tanipone_hirsuta_M279 100 91 Tanipone_aglandula_M280 Simopone_cf_oculata_D0792 100 Simopone_grandidieri_M186 100 Simopone_dryas_M224 100 Simopone_marleyi_M171 100Simopone_conradti_M144 38 Simopone_rex_M133 100 Simopone_trita_M185 45 Lioponera_longitarsus_M193 Lioponera_vespula_M210 35 100100 Lioponera_nr_kraepelinii_M131 100 Lioponera_nr_mayri_M215 98 Lioponera_MY_M268 100 Lioponera_cf_suscitata_M267 100 Lioponera_PG_M250 100 Lioponera_marginata_M249 100 Lioponera_clarus_M137 100 100 Lioponera_ruficornis_M165 Lividopone_MG_M132 100 Lividopone_MG_M194 100Lividopone_MG_M216 100 Lividopone_MG_M294 Zasphinctus_wilsoni_M229 100 Zasphinctus_TH_M192 100 100 Zasphinctus_sarowiwai_M227 100 Zasphinctus_trux_M136 100 Zasphinctus_imbecilis_M170 100 100 Zasphinctus_PG_M285 Parasyscia_UG_M281 100 Parasyscia_MG_M212 Parasyscia_UG_M219 100100 Parasyscia_UG_M218 100 100 Parasyscia_wittmeri_M282 Parasyscia_VN_M207 100 Parasyscia_PG_M204 100 24 Parasyscia_dohertyi_M142 Yunodorylus_TH_M191 100 Yunodorylus_eguchii_M247 100 Yunodorylus_TH_M160 100 Yunodorylus_paradoxus_M190 Chrysapace_cf_sauteri_M261 100 100 Chrysapace_MG_M155 100 Chrysapace_cf_crawleyi_M262 100 31 Chrysapace_TH_M156 Cerapachys_sulcinodis_M243 100 Cerapachys_MY_M264 100 Cerapachys_TH_M203 100 Cerapachys_antennatus_M263 Aenictogiton_UG_M189 100 Aenictogiton_ZM02_M181 68 100 Dorylus_laevigatus_M157 Dorylus_orientalis_M244 100100 Dorylus_conradti_M178 92 Dorylus_fimbriatus_M288 Dorylus_fulvus_M179 92 100 Dorylus_cf_fulvus_M149 100 Dorylus_spininodis_M292 Dorylus_braunsi_M289 100100 Dorylus_affinis_M177 100 100Dorylus_kohli_M180 95Dorylus_mayri_M291 100Dorylus_molestus_M290 100Dorylus_UG_M153 69 Dorylus_rubellus_M287 Aenictus_latifemoratus_M266 81 Aenictus_yamanei_M265 100 Aenictus_silvestrii_M221 24 Aenictus_bobaiensis_M197 100 100 Aenictus_levior_M231 Aenictus_camposi_M222 Aenictus_UG_M143 100 100 Aenictus_ZA_M228 69 Aenictus_fergusoni_M223 100 100 Aenictus_hodgsoni_M198 100Aenictus_laeviceps_M269 100 Aenictus_rotundicollis_M232 100 Aenictus_turneri_M135 100 Aenictus_hoelldobleri_M200 100 100 Aenictus_fuchuanensis_M201 Aenictus_currax_M245 100Aenictus_gracilis_M199 100 Aenictus_cornutus_M230 Neocerapachys_CR_M209 100 Neocerapachys_neotropicus_M134 100Neocerapachys_cf_splendens_M251 100 Neocerapachys_BR_M295 88 Cylindromyrmex_meinerti_D0778 100 Cylindromyrmex_brasiliensis_M140 100 Cylindromyrmex_whymperi_M271 100 100 Cylindromyrmex_darlingtoni_M211 Acanthostichus_AZ_M277 100 Acanthostichus_AZ_M278 100 Acanthostichus_BR_M252 100Acanthostichus_GF_M208 100 100 Acanthostichus_serratulus_M166 Leptanilloides_nubecula_M167 100 Leptanilloides_mckennae_D0228 100 Leptanilloides_femoralis_M188 100 Leptanilloides_erinys_M246 100 Leptanilloides_gracilis_M187 Sphinctomyrmex_stali_M253 100 Sphinctomyrmex_cf_marcoyi_M202 100 Cheliomyrmex_megalonyx_M146 100Cheliomyrmex_cf_andicola_M174 100 Cheliomyrmex_cf_morosus_M217 100 Labidus_coecus_M173 100 Labidus_spininodis_M172 100 65 Labidus_praedator_M152 100 Nomamyrmex_esenbeckii_M129 100 Nomamyrmex_hartigii_M220 100 Eciton_mexicanum_M238 Eciton_vagans_M184 100100 Eciton_quadriglume_M254 97 100 Eciton_lucanoides_M239 97 Eciton_burchellii_M273 100Eciton_rapax_M145 100 Eciton_hamatum_M293 Neivamyrmex_alfaroi_M240 100 Neivamyrmex_distans_M242 78 Neivamyrmex_swainsonii_M169 100 Neivamyrmex_adnepos_M236 100 Neivamyrmex_EC_M175 100 Neivamyrmex_gibbatus_M139 100 Neivamyrmex_impudens_M237 100 97 Neivamyrmex_melanocephalus_M154 0.04 Neivamyrmex_cf_nyensis_M296 100 Neivamyrmex_compressinodis_M235 Neivamyrmex_sumichrasti_M151 slow-evolving loci 10099 Neivamyrmex_asper_M233 maximum likelihood tree 100Neivamyrmex_opacithorax_M276 RAxML 100Neivamyrmex_kiowapache_M275 88Neivamyrmex_californicus_M272 100 k-means partitions GTR+4Gamma model Neivamyrmex_texanus_M274 500 bootstrap replicates

Supplementary Figure S10: Maximum likelihood tree obtained from slow-evolving data matrix under k-means partitions. Scale is in number of substitutions per site. Nodal support in percent bootstrap.

11 HARPEGNATHOS_SALTATOR_GENOME LINEPITHEMA_HUMILE_GENOME 100 CAMPONOTUS_FLORIDANUS_GENOME 100 POGONOMYRMEX_BARBATUS_GENOME 100 VOLLENHOVIA_EMERYI_GENOME 100 CARDIOCONDYLA_OBSCURIOR_GENOME 100 SOLENOPSIS_INVICTA_GENOME 100 ACROMYRMEX_ECHINATIOR_GENOME 100 ATTA_CEPHALOTES_GENOME VICINOPONE_CONCILIATRIX_M128 TANIPONE_SCELESTA_M159 100 TANIPONE_ZONA_M182 100TANIPONE_HIRSUTA_M279 100 87 TANIPONE_AGLANDULA_M280 SIMOPONE_GRANDIDIERI_M186 100 SIMOPONE_CF_OCULATA_D0792 100 SIMOPONE_DRYAS_M224 100 SIMOPONE_MARLEYI_M171 100 SIMOPONE_CONRADTI_M144 80 SIMOPONE_TRITA_M185 100SIMOPONE_REX_M133 32 LIOPONERA_LONGITARSUS_M193 LIOPONERA_VESPULA_M210 10095 LIOPONERA_NR_MAYRI_M215 100LIOPONERA_NR_KRAEPELINII_M131 85 LIOPONERA_MY_M268 100 LIOPONERA_CF_SUSCITATA_M267 100 LIOPONERA_PG_M250 100 100 LIOPONERA_MARGINATA_M249 100 100 LIOPONERA_RUFICORNIS_M165 100 LIOPONERA_CLARUS_M137 LIVIDOPONE_MG_M132 100 LIVIDOPONE_MG_M294 100 LIVIDOPONE_MG_M194 56LIVIDOPONE_MG_M216 ZASPHINCTUS_WILSONI_M229 100 100 ZASPHINCTUS_SAROWIWAI_M227 100 ZASPHINCTUS_TH_M192 100 ZASPHINCTUS_TRUX_M136 100 100 ZASPHINCTUS_IMBECILIS_M170 100 ZASPHINCTUS_PG_M285 PARASYSCIA_UG_M281 100 PARASYSCIA_MG_M212 PARASYSCIA_VN_M207 100100 PARASYSCIA_DOHERTYI_M142 100 100 PARASYSCIA_PG_M204 PARASYSCIA_UG_M219 33 100 PARASYSCIA_UG_M218 96 PARASYSCIA_WITTMERI_M282 SYSCIA_AUGUSTAE_M196 100SYSCIA_GT_M127 100 SYSCIA_TYPHLA_D0841 100 SYSCIA_MY_M147 100 100 SYSCIA_MY_M176 EUSPHINCTUS_TH_M158 90 OOCERAEA_FRAGOSA_D0842 100 OOCERAEA_AUSTRALIS_M138 100 OOCERAEA_BIROI_GENOME 100 OOCERAEA_MY_M270 100 OOCERAEA_FJ06_M168 100 OOCERAEA_PG_M248 EBUROPONE_CM02_D0788 100 EBUROPONE_UG_M259 100 EBUROPONE_MG_M214 100EBUROPONE_MG_M213 100 EBUROPONE_MG_M195 100EBUROPONE_MG_M130 AENICTOGITON_ZM02_M181 100AENICTOGITON_UG_M189 100 DORYLUS_LAEVIGATUS_M157 38 DORYLUS_CONRADTI_M178 100100 DORYLUS_ORIENTALIS_M244 96 DORYLUS_FIMBRIATUS_M288 55 DORYLUS_CF_FULVUS_M149 96 100DORYLUS_FULVUS_M179 100 DORYLUS_SPININODIS_M292 100DORYLUS_AFFINIS_M177 100DORYLUS_BRAUNSI_M289 100 100DORYLUS_KOHLI_M180 95DORYLUS_MAYRI_M291 100DORYLUS_MOLESTUS_M290 100DORYLUS_RUBELLUS_M287 57DORYLUS_UG_M153 AENICTUS_YAMANEI_M265 73 AENICTUS_LATIFEMORATUS_M266 100 AENICTUS_SILVESTRII_M221 31 AENICTUS_LEVIOR_M231 100 100 AENICTUS_BOBAIENSIS_M197 AENICTUS_CAMPOSI_M222 AENICTUS_ZA_M228 100 100 AENICTUS_UG_M143 AENICTUS_FERGUSONI_M223 100 AENICTUS_HODGSONI_M198 50 100 100AENICTUS_ROTUNDICOLLIS_M232 100AENICTUS_LAEVICEPS_M269 100 AENICTUS_TURNERI_M135 100 AENICTUS_HOELLDOBLERI_M200 100 100 AENICTUS_FUCHUANENSIS_M201 AENICTUS_CURRAX_M245 100AENICTUS_CORNUTUS_M230 100AENICTUS_GRACILIS_M199 CERAPACHYS_SULCINODIS_M243 100 CERAPACHYS_MY_M264 100 CERAPACHYS_ANTENNATUS_M263 100 CERAPACHYS_TH_M203 100 CHRYSAPACE_CF_SAUTERI_M261 100 CHRYSAPACE_MG_M155 100 CHRYSAPACE_CF_CRAWLEYI_M262 100 CHRYSAPACE_TH_M156 91 YUNODORYLUS_TH_M160 100 YUNODORYLUS_PARADOXUS_M190 100 YUNODORYLUS_EGUCHII_M247 100YUNODORYLUS_TH_M191 NEOCERAPACHYS_CR_M209 100 NEOCERAPACHYS_NEOTROPICUS_M134 31 100NEOCERAPACHYS_BR_M295 100NEOCERAPACHYS_CF_SPLENDENS_M251 85 CYLINDROMYRMEX_MEINERTI_D0778 100 CYLINDROMYRMEX_BRASILIENSIS_M140 100 CYLINDROMYRMEX_WHYMPERI_M271 100 100 CYLINDROMYRMEX_DARLINGTONI_M211 ACANTHOSTICHUS_AZ_M277 100 ACANTHOSTICHUS_AZ_M278 100 ACANTHOSTICHUS_BR_M252 100ACANTHOSTICHUS_GF_M208 100 100ACANTHOSTICHUS_SERRATULUS_M166 SPHINCTOMYRMEX_CF_MARCOYI_M202 100 SPHINCTOMYRMEX_STALI_M253 LEPTANILLOIDES_MCKENNAE_D0228 100 LEPTANILLOIDES_NUBECULA_M167 100 LEPTANILLOIDES_FEMORALIS_M188 100 LEPTANILLOIDES_GRACILIS_M187 100 100 LEPTANILLOIDES_ERINYS_M246 CHELIOMYRMEX_MEGALONYX_M146 100CHELIOMYRMEX_CF_ANDICOLA_M174 78CHELIOMYRMEX_CF_MOROSUS_M217 100 LABIDUS_COECUS_M173 65 100 LABIDUS_SPININODIS_M172 100LABIDUS_PRAEDATOR_M152 100 NOMAMYRMEX_ESENBECKII_M129 100 NOMAMYRMEX_HARTIGII_M220 100 ECITON_MEXICANUM_M238 100ECITON_VAGANS_M184 100ECITON_QUADRIGLUME_M254 96 ECITON_LUCANOIDES_M239 100 98 ECITON_BURCHELLII_M273 100ECITON_HAMATUM_M293 100ECITON_RAPAX_M145 NEIVAMYRMEX_ALFAROI_M240 100 NEIVAMYRMEX_DISTANS_M242 76 NEIVAMYRMEX_SWAINSONII_M169 100 NEIVAMYRMEX_EC_M175 100NEIVAMYRMEX_ADNEPOS_M236 100 NEIVAMYRMEX_GIBBATUS_M139 100 NEIVAMYRMEX_IMPUDENS_M237 100NEIVAMYRMEX_MELANOCEPHALUS_M154 96 NEIVAMYRMEX_CF_NYENSIS_M296 0.03 100 NEIVAMYRMEX_COMPRESSINODIS_M235 slow-evolving loci 100 NEIVAMYRMEX_ASPER_M233 99NEIVAMYRMEX_SUMICHRASTI_M151 maximum likelihood tree 100NEIVAMYRMEX_OPACITHORAX_M276 RAxML 100NEIVAMYRMEX_KIOWAPACHE_M275 53NEIVAMYRMEX_CALIFORNICUS_M272 100 unpartitioned GTR+4Gamma model NEIVAMYRMEX_TEXANUS_M274 500 bootstrap replicates

Supplementary Figure S11: Maximum likelihood tree obtained from unpartitioned slow-evolving data matrix. Scale is in number of substitutions per site. Nodal support in percent bootstrap.

12 HARPEGNATHOS_SALTATOR_GENOME LINEPITHEMA_HUMILE_GENOME 1 CAMPON OTUS_FLORI DANUS_G ENOME 1 POGONOMYRMEX_BARBATUS_GENOME CARDIOCONDYLA_OBSCURIOR_GENOME 1 1 VOLLENHOVIA_EMERYI_GENOME 1 SOLENOPSIS_INVICTA_GENOME 1 A CRO MYRME X_ECHI NATIOR_GENOME 1 ATTA_CEPHALOTES_GENOME EBUROPONE_CM02_D0788 1 EBUROPONE_UG_M259 EBUROPONE_MG_M213 1 1 EBUROPONE_MG_M214 1 EBUROPONE_MG_M195 1 EBUROPONE_MG_M130 0 . 5 2 VICINOPONE_CONCILIATRIX_M128 TAN IPONE_SCEL ESTA_M159 1 TANIPONE_ZONA_M182 1 T ANIPONE _HI RSUTA_M279 1 0 . 2 8 TANIPONE_AGLANDULA_M280 SIMOPONE_GRANDIDIERI_M186 1 SIMOPONE_CF_OCULATA_D0792 1 SIMOPONE_DRYAS_M224 0 . 4 8 1 SIMOPONE_MARLEYI_M171 1 SIM OPONE_CO NRAD TI_M144 0 . 9 9 SIMOPONE_REX_M133 1 SIMOPONE_TRITA_M185 LIOPONERA_LONGITARSUS_M193 L IOPO NERA _VESP ULA _M210 0 . 4 4 11 L IOPONERA_NR_MAYRI _M215 1 LIOPONERA_NR_KRAEPELINII_M131 0 . 8 7 LIOPONERA_MY_M268 1 LIOPONERA_CF_SUSCITATA_M267 1 LIOPONERA_PG_M250 1 LIOPONERA_MARGINATA_M249 0 . 9 5 L IOPO NERA_CLARUS_M137 1 1 LIOPONERA_RUFICORNIS_M165 LIVIDOPONE_MG_M132 1 LIVIDOPONE_MG_M294 1 LIVIDOPONE_MG_M216 0 . 9 6 LIVIDOPONE_MG_M194 ZASPHI NCT US_WILSONI _M229 1 ZASPHINCTUS_TH_M192 1 1 ZASPHINCTUS_SAROWIWAI_M227 1 1 ZASPHINCTUS_TRUX_M136 1 ZASPHINCTUS_PG_M285 1 1 ZASPHINCTUS_IMBECILIS_M170 PARASYSC IA_UG _M281 1 PARASYSCIA_MG_M212 PARASYSC IA_UG _M218 0 . 9 3 1 PARASYSCIA_WITTMERI_M282 0 . 8 4 1 PARASYSC IA_UG _M219 PARASYSCIA_VN_M207 1 PARASYSCIA_PG_M204 1 PARASYSCIA_DOHERTYI_M142 SYSCIA_GT_M127 1 SYSCIA_AUGUSTAE_M196 1 SY SCIA_TYP HLA_D0841 1 SYSC IA_MY _M147 1 1 SYSC IA_MY _M176 EUSPHINCTUS_TH_M158 1 OOCERAEA_FRAGOSA_D0842 OOCERAEA_AUSTRALIS_M138 1 1 OOCERAEA_BIROI_GENOME 1 OOCERAEA_MY_M270 1 OOCERAEA_PG_M248 1 OOCE RAEA_ FJ06_M168 CERAPACHYS_SULCINODIS_M243 1 CERAPACHYS_MY_M264 1 CER APACHYS_T H_M203 1 CERAPACHYS_ANTENNATUS_M263 CHRYSA PACE_T H_M156 1 1 CHRYSAPACE_CF_CRAWLEYI_M262 1 CHRY SAPACE _CF_S AUT ERI _M261 0 . 6 5 1 CHRYSAPACE_MG_M155 0 . 8 6 YUNODORYLUS_TH_M191 1 Y UNODORY LUS _EG UCHII_M247 1 Y UNODORY LUS_ PARAD OXUS _M190 1 YUNODORYLUS_TH_M160 AENICTOGITON_UG_M189 1 AENICTOGITON_ZM02_M181 1 DORYLUS_FIMBRIATUS_M288 1 DORYLUS_LAEVIGATUS_M157 DORYLUS_ORIENTALIS_M244 1 0 . 8 7 DORYLUS_CONRADTI_M178 DORYLUS_FULVUS_M179 1 1 DORYLUS_CF_FULVUS_M149 1 DORYLUS_SPININODIS_M292 1 DORYLUS_AFFINIS_M177 1 1 DO RYLUS_BRA UNSI _M289 0 . 9 7 1 DORYLUS_KOHLI_M180 0 . 9 9 DORYLUS_MAYRI_M291 1 DORYLUS_UG_M153 1 DORYLUS_RUBELLUS_M287 0 . 6 9 DORYLUS_MOLESTUS_M290 AENICTUS_SILVESTRII_M221 1 AENICTUS_LATIFEMORATUS_M266 1 AENICTUS_ YAMAN EI_M265 0 . 3 7 AENICTUS_LEVIOR_M231 1 1 AENICT US_BO BAI ENSI S_M197 AENICTUS_CAMPOSI_M222 AENICTUS_ZA_M228 1 1 AENICTUS_UG_M143 AENICTUS_FERGUSONI_M223 1 1 AENICTUS_HODGSONI_M198 0 . 9 7 1 AENICTUS_ROTUNDICOLLIS_M232 1 AENICTUS_LAEVICEPS_M269 1 AENICTUS_CURRAX_M245 1 AENICTUS_GRACILIS_M199 1 1 AENICTUS_CORNUTUS_M230 AENICT US_T URNERI _M135 1 AENICTUS_FUCHUANENSIS_M201 1 AENICTUS_HOELLDOBLERI_M200 NEOCERAPACHYS_CR_M209 1 NEOCERAPACHYS_NEOTROPICUS_M134 1 NEO CERAPACHYS_CF _SPLENDENS _M251 1 NEOCERAPACHYS_BR_M295 CYLINDROMYRMEX_MEINERTI_D0778 1 CYLINDROMYRMEX_BRASILIENSIS_M140 1 CYLINDROMYRMEX_WHYMPERI_M271 1 1 1 CYLI NDRO MYRMEX_DARLIN GTONI _M211 ACANTHOSTICHUS_AZ_M278 1 ACANTHOSTICHUS_AZ_M277 1 ACANTH OSTICHUS_B R_M252 1 ACANTHOSTICHUS_GF_M208 1 ACANTHOSTICHUS_SERRATULUS_M166 0 . 4 9 SPHINCTOMYRMEX_CF_MARCOYI_M202 1 S PHI NCTOMYRME X_ST ALI _M253 LEPT ANI LLOIDES_MCK ENNA E_D0228 1 LEPTANILLOIDES_NUBECULA_M167 1 LEPTANILLOIDES_FEMORALIS_M188 1 LEPTANILLOIDES_GRACILIS_M187 1 1 LEPTANILLOIDES_ERINYS_M246 CHELIOMYRMEX_MEGALONYX_M146 1 CHELIOMYRMEX_CF_ANDICOLA_M174 1 CHELIOMYRMEX_CF_MOROSUS_M217 1 LABIDUS_COECUS _M173 0 . 9 9 1 LABIDUS_PRAEDATOR_M152 1 LABIDUS_SPININODIS_M172 1 NO MAMYRME X_HAR TIGII_M220 1 NOMAMYRMEX_ESENBECKII_M129 1 ECITON_MEXICANUM_M238 ECITON_QUA DRIGLUME_M254 1 1 EC ITON_VAGANS _M184 1 0 . 4 9ECITON_LUCANOIDES_M239 1 ECITON_BURCHELLII_M273 1 EC ITON_HA MAT UM_M293 1 ECITON_RAPAX_M145 NEIVAMYRMEX_DISTANS_M242 1 NEIVA MYRMEX _ALFAR OI_M240 NEIVAMYRMEX_SWAINSONII_M169 11 NEIVAMYRMEX_EC_M175 1 NEIVAMYRMEX_ADNEPOS_M236 0 . 6 4 NEIVAMYRMEX_GIBBATUS_M139 1 N EIVAMY RME X_MELANOCE PHA LUS _M154 1 NEIVAMYRMEX_IMPUDENS_M237 1 NEI VAMYRMEX_CF _NYEN SIS_M296 1 N EIVAMY RME X_COMPR ESSINOD IS_M235 NEIVAMYRMEX_ASPER_M233 1 1 4 . 0 NEIVAMYRMEX_SUMICHRASTI_M151 slow-evolving loci 1 NEIVAMYRMEX_OPACITHORAX_M276 1 NEIVAMYRMEX_KIOWAPACHE_M275 weighted statistical binning 1 NEIVAMYRMEX_CALIFORNICUS_M272 1 ASTRAL species tree NEIVAMYRMEX_TEXANUS_M274

Supplementary Figure S12: Summary species tree obtained from 580 slow-evolving loci using ASTRAL. Scale is in coalescent units. Nodal support in local posterior probabilities.

13 Harpegnathos_saltator_Genome Linepithema_humile_Genome 99 Camponotus_floridanus_Genome 100 Pogonomyrmex_barbatus_Genome Vollenhovia_emeryi_Genome 100 100 Cardiocondyla_obscurior_Genome 100 Solenopsis_invicta_Genome 100 Atta_cephalotes_Genome 100 Acromyrmex_echinatior_Genome Aenictogiton_ZM02_M181 100 Aenictogiton_UG_M189 100 Dorylus_fimbriatus_M288 Dorylus_laevigatus_M157 10035 Dorylus_orientalis_M244 100 Dorylus_conradti_M178 35 Dorylus_cf_fulvus_M149 100 Dorylus_fulvus_M179 100 Dorylus_spininodis_M292 Dorylus_braunsi_M289 100100 Dorylus_affinis_M177 72 100Dorylus_kohli_M180 93Dorylus_mayri_M291 100Dorylus_rubellus_M287 100Dorylus_molestus_M290 100 Dorylus_UG_M153 Aenictus_silvestrii_M221 100 Aenictus_latifemoratus_M266 76 Aenictus_yamanei_M265 48 Aenictus_bobaiensis_M197 100 100 Aenictus_levior_M231 Aenictus_camposi_M222 Aenictus_UG_M143 100 100 Aenictus_ZA_M228 Aenictus_fergusoni_M223 100 100 Aenictus_hodgsoni_M198 100Aenictus_laeviceps_M269 100 Aenictus_rotundicollis_M232 100 Aenictus_turneri_M135 100 Aenictus_fuchuanensis_M201 100 100 Aenictus_hoelldobleri_M200 Aenictus_currax_M245 100Aenictus_cornutus_M230 100 Aenictus_gracilis_M199 Tanipone_scelesta_M159 100 Tanipone_zona_M182 100 Tanipone_hirsuta_M279 100 89 Tanipone_aglandula_M280 Simopone_grandidieri_M186 100 Simopone_cf_oculata_D0792 100 Simopone_dryas_M224 100 Simopone_marleyi_M171 100 100 Simopone_conradti_M144 100 Simopone_rex_M133 43 100 Simopone_trita_M185 Vicinopone_conciliatrix_M128 Lioponera_longitarsus_M193 Lioponera_vespula_M210 10099 Lioponera_nr_kraepelinii_M131 100 Lioponera_nr_mayri_M215 67 99 Lioponera_MY_M268 100 Lioponera_cf_suscitata_M267 100 Lioponera_marginata_M249 100 Lioponera_PG_M250 100 Lioponera_clarus_M137 100 100 Lioponera_ruficornis_M165 Lividopone_MG_M132 100 Lividopone_MG_M294 100Lividopone_MG_M194 37 Lividopone_MG_M216 Zasphinctus_wilsoni_M229 100 Zasphinctus_sarowiwai_M227 100 100 Zasphinctus_TH_M192 100 Zasphinctus_trux_M136 100 Zasphinctus_PG_M285 100 100 Zasphinctus_imbecilis_M170 Parasyscia_UG_M281 100 Parasyscia_MG_M212 Parasyscia_UG_M219 100100 Parasyscia_UG_M218 98 100 Parasyscia_wittmeri_M282 Parasyscia_VN_M207 56 100 Parasyscia_PG_M204 100 Parasyscia_dohertyi_M142 Cerapachys_sulcinodis_M243 100 Cerapachys_MY_M264 100 Cerapachys_antennatus_M263 100 Cerapachys_TH_M203 Chrysapace_TH_M156 100 100 Chrysapace_cf_crawleyi_M262 100 Chrysapace_MG_M155 100 Chrysapace_cf_sauteri_M261 65 Yunodorylus_TH_M160 100 Yunodorylus_paradoxus_M190 100 Yunodorylus_TH_M191 100 70 Yunodorylus_eguchii_M247 Eburopone_CM02_D0788 100 Eburopone_UG_M259 Eburopone_MG_M195 100 100 Eburopone_MG_M130 100 Eburopone_MG_M213 100 Eburopone_MG_M214 73 Syscia_augustae_M196 100 Syscia_GT_M127 100 Syscia_typhla_D0841 100 Syscia_MY_M176 100 100 Syscia_MY_M147 Eusphinctus_TH_M158 78 Ooceraea_fragosa_D0842 Ooceraea_biroi_Genome 100100 69 Ooceraea_australis_M138 100 Ooceraea_MY_M270 100 Ooceraea_PG_M248 100 Ooceraea_FJ06_M168 Neocerapachys_CR_M209 100 Neocerapachys_neotropicus_M134 100Neocerapachys_cf_splendens_M251 100 Neocerapachys_BR_M295 83 Cylindromyrmex_meinerti_D0778 100 Cylindromyrmex_brasiliensis_M140 100 Cylindromyrmex_whymperi_M271 100 100 Cylindromyrmex_darlingtoni_M211 Acanthostichus_AZ_M277 100 Acanthostichus_AZ_M278 100 Acanthostichus_BR_M252 100Acanthostichus_GF_M208 100 100 Acanthostichus_serratulus_M166 Leptanilloides_nubecula_M167 100 Leptanilloides_mckennae_D0228 100 Leptanilloides_femoralis_M188 100 Leptanilloides_gracilis_M187 100 Leptanilloides_erinys_M246 Sphinctomyrmex_stali_M253 100 Sphinctomyrmex_cf_marcoyi_M202 100 Cheliomyrmex_cf_morosus_M217 100Cheliomyrmex_cf_andicola_M174 100 Cheliomyrmex_megalonyx_M146 100 Labidus_coecus_M173 100 Labidus_spininodis_M172 100 85 Labidus_praedator_M152 Nomamyrmex_hartigii_M220 100 100 Nomamyrmex_esenbeckii_M129 100 Eciton_mexicanum_M238 93 Eciton_vagans_M184 100 100Eciton_quadriglume_M254 Eciton_lucanoides_M239 100 97 Eciton_burchellii_M273 100Eciton_hamatum_M293 100 Eciton_rapax_M145 Neivamyrmex_distans_M242 100 Neivamyrmex_alfaroi_M240 76 Neivamyrmex_swainsonii_M169 100 Neivamyrmex_adnepos_M236 100 Neivamyrmex_EC_M175 100 Neivamyrmex_gibbatus_M139 100 Neivamyrmex_impudens_M237 100 Neivamyrmex_melanocephalus_M154 81 Neivamyrmex_cf_nyensis_M296 0.03 100 Neivamyrmex_compressinodis_M235 Neivamyrmex_sumichrasti_M151 compositionally homogeneous loci 100100 Neivamyrmex_asper_M233 100Neivamyrmex_texanus_M274 maximum likelihood tree 100 Neivamyrmex_californicus_M272 100 RAxML Neivamyrmex_opacithorax_M276 61 partitioned by locus GTR+4Gamma model Neivamyrmex_kiowapache_M275 500 bootstrap replicates

Supplementary Figure S13: Maximum likelihood tree obtained from compositionally homoge- neous data matrix partitioned by locus. Scale is in number of substitutions per site. Nodal support in percent bootstrap.

14 Harpegnathos_saltator_Genome Linepithema_humile_Genome 100 Camponotus_floridanus_Genome 100 Pogonomyrmex_barbatus_Genome Vollenhovia_emeryi_Genome 100 100 Cardiocondyla_obscurior_Genome 100 Solenopsis_invicta_Genome 97 Acromyrmex_echinatior_Genome 100 Atta_cephalotes_Genome Aenictogiton_UG_M189 100 Aenictogiton_ZM02_M181 100 Dorylus_fimbriatus_M288 Dorylus_laevigatus_M157 10066 Dorylus_orientalis_M244 100 Dorylus_conradti_M178 66 Dorylus_fulvus_M179 100 Dorylus_cf_fulvus_M149 100 Dorylus_spininodis_M292 Dorylus_affinis_M177 100100 Dorylus_braunsi_M289 83 100Dorylus_kohli_M180 95Dorylus_mayri_M291 100Dorylus_rubellus_M287 100Dorylus_molestus_M290 100 Dorylus_UG_M153 Aenictus_silvestrii_M221 100 Aenictus_latifemoratus_M266 66 Aenictus_yamanei_M265 47 Aenictus_levior_M231 100 100 Aenictus_bobaiensis_M197 Aenictus_camposi_M222 Aenictus_UG_M143 100 100 Aenictus_ZA_M228 Aenictus_fergusoni_M223 100 100 Aenictus_hodgsoni_M198 100Aenictus_laeviceps_M269 100 Aenictus_rotundicollis_M232 100 Aenictus_currax_M245 100Aenictus_cornutus_M230 100 100 Aenictus_gracilis_M199 Aenictus_turneri_M135 100 Aenictus_fuchuanensis_M201 100 Aenictus_hoelldobleri_M200 Tanipone_scelesta_M159 100 Tanipone_zona_M182 100 Tanipone_aglandula_M280 100 60 Tanipone_hirsuta_M279 Simopone_cf_oculata_D0792 100 Simopone_grandidieri_M186 100 Simopone_dryas_M224 100 Simopone_marleyi_M171 100 100 Simopone_conradti_M144 100 Simopone_rex_M133 26 100 Simopone_trita_M185 Vicinopone_conciliatrix_M128 Lioponera_longitarsus_M193 Lioponera_vespula_M210 10098 Lioponera_nr_kraepelinii_M131 100 Lioponera_nr_mayri_M215 41 96 Lioponera_cf_suscitata_M267 100 Lioponera_MY_M268 100 Lioponera_marginata_M249 100 Lioponera_PG_M250 100 Lioponera_clarus_M137 100 100 Lioponera_ruficornis_M165 Lividopone_MG_M132 100 Lividopone_MG_M216 100Lividopone_MG_M194 92 Lividopone_MG_M294 Zasphinctus_wilsoni_M229 100 Zasphinctus_sarowiwai_M227 100 100 Zasphinctus_TH_M192 100 Zasphinctus_trux_M136 100 Zasphinctus_imbecilis_M170 100 100 Zasphinctus_PG_M285 Parasyscia_UG_M281 100 Parasyscia_MG_M212 Parasyscia_UG_M219 100100 Parasyscia_UG_M218 100 100 Parasyscia_wittmeri_M282 Parasyscia_VN_M207 40 100 Parasyscia_PG_M204 100 Parasyscia_dohertyi_M142 Yunodorylus_eguchii_M247 100 Yunodorylus_TH_M191 100 Yunodorylus_paradoxus_M190 100 Yunodorylus_TH_M160 100 Cerapachys_sulcinodis_M243 100 Cerapachys_MY_M264 100 Cerapachys_antennatus_M263 100 51 Cerapachys_TH_M203 Chrysapace_MG_M155 100 Chrysapace_cf_sauteri_M261 100 Chrysapace_cf_crawleyi_M262 100 51 Chrysapace_TH_M156 Eburopone_CM02_D0788 100 Eburopone_UG_M259 Eburopone_MG_M195 100 100 Eburopone_MG_M130 100 Eburopone_MG_M213 100 Eburopone_MG_M214 57 Syscia_augustae_M196 100 Syscia_GT_M127 100 Syscia_typhla_D0841 100 Syscia_MY_M176 100 100 Syscia_MY_M147 Eusphinctus_TH_M158 95 Ooceraea_fragosa_D0842 Ooceraea_biroi_Genome 100100 32 Ooceraea_australis_M138 100 Ooceraea_MY_M270 100 Ooceraea_FJ06_M168 100 Ooceraea_PG_M248 Neocerapachys_CR_M209 100 Neocerapachys_neotropicus_M134 100Neocerapachys_cf_splendens_M251 100 Neocerapachys_BR_M295 65 Cylindromyrmex_meinerti_D0778 100 Cylindromyrmex_brasiliensis_M140 100 Cylindromyrmex_whymperi_M271 100 100 Cylindromyrmex_darlingtoni_M211 Acanthostichus_AZ_M277 100 Acanthostichus_AZ_M278 100 Acanthostichus_BR_M252 100Acanthostichus_GF_M208 100 100 Acanthostichus_serratulus_M166 Leptanilloides_nubecula_M167 100 Leptanilloides_mckennae_D0228 100 Leptanilloides_femoralis_M188 100 Leptanilloides_erinys_M246 100 Leptanilloides_gracilis_M187 Sphinctomyrmex_cf_marcoyi_M202 100 Sphinctomyrmex_stali_M253 100 Cheliomyrmex_cf_morosus_M217 100Cheliomyrmex_cf_andicola_M174 100 Cheliomyrmex_megalonyx_M146 100 Labidus_coecus_M173 100 Labidus_spininodis_M172 100 91 Labidus_praedator_M152 Nomamyrmex_hartigii_M220 100 100 Nomamyrmex_esenbeckii_M129 100 Eciton_mexicanum_M238 77 Eciton_vagans_M184 100 100Eciton_quadriglume_M254 Eciton_lucanoides_M239 100 98 Eciton_burchellii_M273 100Eciton_hamatum_M293 100 Eciton_rapax_M145 Neivamyrmex_distans_M242 100 Neivamyrmex_alfaroi_M240 78 Neivamyrmex_swainsonii_M169 100 Neivamyrmex_adnepos_M236 100 Neivamyrmex_EC_M175 100 Neivamyrmex_gibbatus_M139 100 Neivamyrmex_melanocephalus_M154 100 Neivamyrmex_impudens_M237 86 Neivamyrmex_cf_nyensis_M296 0.04 100 Neivamyrmex_compressinodis_M235 Neivamyrmex_asper_M233 compositionally homogeneous loci 100100 Neivamyrmex_sumichrasti_M151 maximum likelihood tree 100Neivamyrmex_texanus_M274 100 Neivamyrmex_californicus_M272 RAxML 100 Neivamyrmex_opacithorax_M276 44 k-means partitions GTR+4Gamma model Neivamyrmex_kiowapache_M275 500 bootstrap replicates

Supplementary Figure S14: Maximum likelihood tree obtained from compositionally homoge- neous data matrix under k-means partitions. Scale is in number of substitutions per site. Nodal support in percent bootstrap.

15 Harpegnathos_saltator_Genome Linepithema_humile_Genome 99 Camponotus_floridanus_Genome 99 Pogonomyrmex_barbatus_Genome Cardiocondyla_obscurior_Genome 100 100 Vollenhovia_emeryi_Genome 100 Solenopsis_invicta_Genome 100 Atta_cephalotes_Genome 100 Acromyrmex_echinatior_Genome Aenictogiton_UG_M189 100 Aenictogiton_ZM02_M181 100 Dorylus_fimbriatus_M288 Dorylus_laevigatus_M157 10039 Dorylus_orientalis_M244 100 Dorylus_conradti_M178 39 Dorylus_cf_fulvus_M149 100 Dorylus_fulvus_M179 100 Dorylus_spininodis_M292 Dorylus_affinis_M177 100100 Dorylus_braunsi_M289 69 100Dorylus_kohli_M180 95Dorylus_mayri_M291 100Dorylus_rubellus_M287 100Dorylus_molestus_M290 100 Dorylus_UG_M153 Aenictus_silvestrii_M221 100 Aenictus_latifemoratus_M266 69 Aenictus_yamanei_M265 39 Aenictus_bobaiensis_M197 100 100 Aenictus_levior_M231 Aenictus_camposi_M222 Aenictus_UG_M143 100 100 Aenictus_ZA_M228 Aenictus_fergusoni_M223 100 100 Aenictus_hodgsoni_M198 100Aenictus_laeviceps_M269 100 Aenictus_rotundicollis_M232 100 Aenictus_turneri_M135 100 Aenictus_fuchuanensis_M201 100 100 Aenictus_hoelldobleri_M200 Aenictus_currax_M245 100Aenictus_cornutus_M230 100 Aenictus_gracilis_M199 Tanipone_scelesta_M159 100 Tanipone_zona_M182 100 Tanipone_aglandula_M280 100 85 Tanipone_hirsuta_M279 Simopone_grandidieri_M186 100 Simopone_cf_oculata_D0792 100 Simopone_dryas_M224 100 Simopone_marleyi_M171 100 100 Simopone_conradti_M144 100 Simopone_rex_M133 30 100 Simopone_trita_M185 Vicinopone_conciliatrix_M128 Lioponera_longitarsus_M193 Lioponera_vespula_M210 100100 Lioponera_nr_kraepelinii_M131 100 Lioponera_nr_mayri_M215 60 100 Lioponera_cf_suscitata_M267 100 Lioponera_MY_M268 100 Lioponera_marginata_M249 100 Lioponera_PG_M250 100 Lioponera_clarus_M137 100 100 Lioponera_ruficornis_M165 Lividopone_MG_M132 100 Lividopone_MG_M294 100Lividopone_MG_M216 33 Lividopone_MG_M194 Zasphinctus_wilsoni_M229 100 Zasphinctus_TH_M192 100 100 Zasphinctus_sarowiwai_M227 100 Zasphinctus_trux_M136 100 Zasphinctus_imbecilis_M170 100 99 Zasphinctus_PG_M285 Parasyscia_UG_M281 100 Parasyscia_MG_M212 Parasyscia_VN_M207 100100 Parasyscia_PG_M204 100 100 Parasyscia_dohertyi_M142 Parasyscia_UG_M219 63 100 Parasyscia_wittmeri_M282 98 Parasyscia_UG_M218 Cerapachys_sulcinodis_M243 100 Cerapachys_MY_M264 100 Cerapachys_TH_M203 100 Cerapachys_antennatus_M263 Yunodorylus_TH_M160 100 100 Yunodorylus_paradoxus_M190 100 Yunodorylus_eguchii_M247 100 Yunodorylus_TH_M191 60 Chrysapace_TH_M156 100 Chrysapace_cf_crawleyi_M262 100 Chrysapace_MG_M155 100 71 Chrysapace_cf_sauteri_M261 Eburopone_CM02_D0788 100 Eburopone_UG_M259 Eburopone_MG_M214 100 100 Eburopone_MG_M213 100 Eburopone_MG_M195 100 Eburopone_MG_M130 69 Syscia_GT_M127 100 Syscia_augustae_M196 100 Syscia_typhla_D0841 100 Syscia_MY_M176 100 100 Syscia_MY_M147 Eusphinctus_TH_M158 82 Ooceraea_fragosa_D0842 Ooceraea_biroi_Genome 100100 66 Ooceraea_australis_M138 100 Ooceraea_MY_M270 100 Ooceraea_FJ06_M168 100 Ooceraea_PG_M248 Neocerapachys_CR_M209 100 Neocerapachys_neotropicus_M134 100Neocerapachys_BR_M295 100 Neocerapachys_cf_splendens_M251 78 Cylindromyrmex_meinerti_D0778 100 Cylindromyrmex_brasiliensis_M140 100 Cylindromyrmex_whymperi_M271 100 100 Cylindromyrmex_darlingtoni_M211 Acanthostichus_AZ_M277 100 Acanthostichus_AZ_M278 100 Acanthostichus_BR_M252 100 Acanthostichus_serratulus_M166 100 100 Acanthostichus_GF_M208 Leptanilloides_nubecula_M167 100 Leptanilloides_mckennae_D0228 100 Leptanilloides_femoralis_M188 100 Leptanilloides_gracilis_M187 100 Leptanilloides_erinys_M246 Sphinctomyrmex_stali_M253 100 Sphinctomyrmex_cf_marcoyi_M202 100 Cheliomyrmex_cf_morosus_M217 100Cheliomyrmex_cf_andicola_M174 100 Cheliomyrmex_megalonyx_M146 100 Labidus_coecus_M173 100Labidus_praedator_M152 100 89 Labidus_spininodis_M172 Nomamyrmex_esenbeckii_M129 100 100 Nomamyrmex_hartigii_M220 100 Eciton_mexicanum_M238 93 Eciton_vagans_M184 100 100Eciton_quadriglume_M254 Eciton_lucanoides_M239 100 98 Eciton_burchellii_M273 100Eciton_hamatum_M293 100 Eciton_rapax_M145 Neivamyrmex_distans_M242 100 Neivamyrmex_alfaroi_M240 76 Neivamyrmex_swainsonii_M169 100 Neivamyrmex_EC_M175 100 Neivamyrmex_adnepos_M236 100 Neivamyrmex_gibbatus_M139 100 Neivamyrmex_melanocephalus_M154 100 Neivamyrmex_impudens_M237 78 Neivamyrmex_cf_nyensis_M296 0.03 100 Neivamyrmex_compressinodis_M235 Neivamyrmex_sumichrasti_M151 compositionally homogeneous loci 100100 Neivamyrmex_asper_M233 maximum likelihood tree 100Neivamyrmex_californicus_M272 100 Neivamyrmex_texanus_M274 RAxML 100 Neivamyrmex_opacithorax_M276 53 unpartitioned GTR+4Gamma model Neivamyrmex_kiowapache_M275 500 bootstrap replicates

Supplementary Figure S15: Maximum likelihood tree obtained from unpartitioned compositionally homogeneous data matrix. Scale is in number of substitutions per site. Nodal support in percent bootstrap.

16 Harpegnathos_saltator_Genome Camponotus_floridanus_Genome 99 Linepithema_humile_Genome 99 Pogonomyrmex_barbatus_Genome Atta_cephalotes_Genome 100 100 Acromyrmex_echinatior_Genome 100 Vollenhovia_emeryi_Genome 33 Solenopsis_invicta_Genome 60 Cardiocondyla_obscurior_Genome Tanipone_scelesta_M159 100 Tanipone_zona_M182 100Tanipone_hirsuta_M279 100 Tanipone_aglandula_M280 Vicinopone_conciliatrix_M128 Eburopone_CM02_D0788 100 Eburopone_UG_M259 Eburopone_MG_M213 67 100 Eburopone_MG_M214 100 100 Eburopone_MG_M195 100 Eburopone_MG_M130 Lioponera_longitarsus_M193 Lioponera_vespula_M210 100100 Lioponera_nr_kraepelinii_M131 100 Lioponera_nr_mayri_M215 100 Lioponera_MY_M268 100 96 Lioponera_cf_suscitata_M267 100 Lioponera_PG_M250 100 Lioponera_marginata_M249 100 Lioponera_clarus_M137 100 100 Lioponera_ruficornis_M165 Lividopone_MG_M132 100 Lividopone_MG_M194 100Lividopone_MG_M294 27 Lividopone_MG_M216 Zasphinctus_wilsoni_M229 100 Zasphinctus_sarowiwai_M227 100 100 Zasphinctus_TH_M192 45 100 Zasphinctus_trux_M136 100 Zasphinctus_imbecilis_M170 100 100 Zasphinctus_PG_M285 Parasyscia_UG_M281 100 Parasyscia_MG_M212 Parasyscia_VN_M207 100 99 Parasyscia_PG_M204 100 100 Parasyscia_dohertyi_M142 Parasyscia_UG_M218 100 Parasyscia_wittmeri_M282 100 Parasyscia_UG_M219 Neocerapachys_CR_M209 100 Neocerapachys_neotropicus_M134 100 Neocerapachys_cf_splendens_M251 100 Neocerapachys_BR_M295 69 Cylindromyrmex_meinerti_D0778 100 Cylindromyrmex_brasiliensis_M140 100 Cylindromyrmex_whymperi_M271 100 100 Cylindromyrmex_darlingtoni_M211 Acanthostichus_AZ_M277 100 Acanthostichus_AZ_M278 100 Acanthostichus_BR_M252 19 100Acanthostichus_GF_M208 100 63 Acanthostichus_serratulus_M166 Leptanilloides_nubecula_M167 100 Leptanilloides_mckennae_D0228 100 Leptanilloides_femoralis_M188 100 Leptanilloides_erinys_M246 100 Leptanilloides_gracilis_M187 Sphinctomyrmex_cf_marcoyi_M202 100 Sphinctomyrmex_stali_M253 58 Cheliomyrmex_cf_andicola_M174 100Cheliomyrmex_megalonyx_M146 94 Cheliomyrmex_cf_morosus_M217 100 Labidus_praedator_M152 100 Labidus_coecus_M173 76 63 Labidus_spininodis_M172 Nomamyrmex_hartigii_M220 100100 Nomamyrmex_esenbeckii_M129 Eciton_burchellii_M273 100 72Eciton_rapax_M145 100 Eciton_hamatum_M293 100Eciton_vagans_M184 100 51 Eciton_quadriglume_M254 58 Eciton_mexicanum_M238 69 Eciton_lucanoides_M239 Neivamyrmex_swainsonii_M169 99 Neivamyrmex_EC_M175 100 Neivamyrmex_adnepos_M236 Neivamyrmex_alfaroi_M240 88 100 Neivamyrmex_distans_M242 52 Neivamyrmex_gibbatus_M139 34 98 Neivamyrmex_melanocephalus_M154 100 31 Neivamyrmex_impudens_M237 Neivamyrmex_cf_nyensis_M296 100 Neivamyrmex_compressinodis_M235 Neivamyrmex_asper_M233 100 100 Neivamyrmex_sumichrasti_M151 100Neivamyrmex_kiowapache_M275 100Neivamyrmex_opacithorax_M276 67Neivamyrmex_texanus_M274 44 Neivamyrmex_californicus_M272 Simopone_grandidieri_M186 100 Simopone_cf_oculata_D0792 100 Simopone_dryas_M224 100 Simopone_marleyi_M171 100 Simopone_conradti_M144 100 Simopone_rex_M133 100 40 Simopone_trita_M185 Eusphinctus_TH_M158 Syscia_augustae_M196 100 Syscia_GT_M127 100 100 Syscia_typhla_D0841 100 Syscia_MY_M176 100 100 Syscia_MY_M147 Ooceraea_fragosa_D0842 Ooceraea_australis_M138 100 100 Ooceraea_biroi_Genome 100 Ooceraea_MY_M270 100 Ooceraea_FJ06_M168 100 Ooceraea_PG_M248 21 Cerapachys_sulcinodis_M243 100 Cerapachys_MY_M264 100 Cerapachys_antennatus_M263 99 Cerapachys_TH_M203 Chrysapace_TH_M156 94 100 Chrysapace_cf_crawleyi_M262 100 Chrysapace_cf_sauteri_M261 100 Chrysapace_MG_M155 92 Yunodorylus_eguchii_M247 100 Yunodorylus_TH_M191 100 Yunodorylus_TH_M160 100 Yunodorylus_paradoxus_M190 Aenictogiton_UG_M189 100 Aenictogiton_ZM02_M181 36 100 Dorylus_laevigatus_M157 Dorylus_fimbriatus_M288 10078 Dorylus_orientalis_M244 100 Dorylus_conradti_M178 81 Dorylus_cf_fulvus_M149 100 Dorylus_fulvus_M179 100Dorylus_spininodis_M292 Dorylus_braunsi_M289 100100 Dorylus_affinis_M177 73 100Dorylus_kohli_M180 100Dorylus_mayri_M291 100Dorylus_rubellus_M287 100Dorylus_UG_M153 91 Dorylus_molestus_M290 Aenictus_silvestrii_M221 Aenictus_latifemoratus_M266 10047 Aenictus_yamanei_M265 31 Aenictus_levior_M231 100 100 Aenictus_bobaiensis_M197 Aenictus_camposi_M222 Aenictus_UG_M143 100 100 Aenictus_ZA_M228 Aenictus_fergusoni_M223 100 100 Aenictus_hodgsoni_M198 100Aenictus_laeviceps_M269 100 Aenictus_rotundicollis_M232 amino acid alignment 100 Aenictus_currax_M245 100Aenictus_gracilis_M199 maximum likelihood tree 97 100Aenictus_cornutus_M230 RAxML Aenictus_hoelldobleri_M200 100 Aenictus_turneri_M135 76 partitioned by locus GTR+4Gamma model Aenictus_fuchuanensis_M201 100 bootstrap replicates

0.02 Supplementary Figure S16: Maximum likelihood tree obtained from amino acid data matrix parti- tioned by locus. Scale is in number of substitutions per site. Nodal support in percent bootstrap.

17 Harpegnathos_saltator_Genome Linepithema_humile_Genome 100 Camponotus_floridanus_Genome 100 Pogonomyrmex_barbatus_Genome Cardiocondyla_obscurior_Genome 100 100 Vollenhovia_emeryi_Genome 100 Solenopsis_invicta_Genome 100 Acromyrmex_echinatior_Genome 100 Atta_cephalotes_Genome Aenictogiton_UG_M189 100 Aenictogiton_ZM02_M181 100 Dorylus_laevigatus_M157 Dorylus_conradti_M178 100100 Dorylus_orientalis_M244 100 Dorylus_fimbriatus_M288 Dorylus_fulvus_M179 100 100 Dorylus_cf_fulvus_M149 100 Dorylus_spininodis_M292 Dorylus_affinis_M177 100100 Dorylus_braunsi_M289 100Dorylus_kohli_M180 100Dorylus_mayri_M291 100Dorylus_molestus_M290 100Dorylus_rubellus_M287 98 Dorylus_UG_M153 Yunodorylus_paradoxus_M190 100 Yunodorylus_TH_M160 100 Yunodorylus_TH_M191 100 Yunodorylus_eguchii_M247 Chrysapace_cf_sauteri_M261 100 100 Chrysapace_MG_M155 100 Chrysapace_cf_crawleyi_M262 100 100 98 Chrysapace_TH_M156 Cerapachys_sulcinodis_M243 100 Cerapachys_MY_M264 100 Cerapachys_antennatus_M263 100 Cerapachys_TH_M203 Neocerapachys_CR_M209 100 Neocerapachys_neotropicus_M134 100 Neocerapachys_BR_M295 100 Neocerapachys_cf_splendens_M251 97 Cylindromyrmex_meinerti_D0778 100 Cylindromyrmex_brasiliensis_M140 100 Cylindromyrmex_darlingtoni_M211 100 100 Cylindromyrmex_whymperi_M271 Acanthostichus_AZ_M277 100 Acanthostichus_AZ_M278 100 Acanthostichus_BR_M252 100Acanthostichus_serratulus_M166 100 97 Acanthostichus_GF_M208 Leptanilloides_mckennae_D0228 100 96 Leptanilloides_nubecula_M167 100 Leptanilloides_femoralis_M188 100 Leptanilloides_erinys_M246 100 Leptanilloides_gracilis_M187 Sphinctomyrmex_stali_M253 100 Sphinctomyrmex_cf_marcoyi_M202 97 Cheliomyrmex_megalonyx_M146 100Cheliomyrmex_cf_andicola_M174 100 Cheliomyrmex_cf_morosus_M217 100 Labidus_coecus_M173 100 Labidus_praedator_M152 100 97 Labidus_spininodis_M172 100 Nomamyrmex_hartigii_M220 100 Nomamyrmex_esenbeckii_M129 100 Eciton_mexicanum_M238 Eciton_vagans_M184 100100 Eciton_quadriglume_M254 100 100 Eciton_lucanoides_M239 100Eciton_burchellii_M273 100Eciton_hamatum_M293 100 Eciton_rapax_M145 Neivamyrmex_distans_M242 100 56 Neivamyrmex_alfaroi_M240 99 Neivamyrmex_swainsonii_M169 100 Neivamyrmex_EC_M175 100 Neivamyrmex_adnepos_M236 100 Neivamyrmex_gibbatus_M139 100 Neivamyrmex_melanocephalus_M154 100 Neivamyrmex_impudens_M237 100 Neivamyrmex_cf_nyensis_M296 100 Neivamyrmex_compressinodis_M235 Neivamyrmex_sumichrasti_M151 100100 Neivamyrmex_asper_M233 100Neivamyrmex_kiowapache_M275 100Neivamyrmex_opacithorax_M276 100Neivamyrmex_californicus_M272 100 Neivamyrmex_texanus_M274 Eburopone_CM02_D0788 100 Eburopone_UG_M259 Eburopone_MG_M195 100 100 Eburopone_MG_M130 100 Eburopone_MG_M213 100 Eburopone_MG_M214 Syscia_GT_M127 100 Syscia_augustae_M196 100 Syscia_typhla_D0841 100 Syscia_MY_M147 57 100 100 Syscia_MY_M176 Eusphinctus_TH_M158 96 Ooceraea_fragosa_D0842 Ooceraea_australis_M138 100 100 Ooceraea_biroi_Genome 100 Ooceraea_MY_M270 100 Ooceraea_PG_M248 100 Ooceraea_FJ06_M168 98 Vicinopone_conciliatrix_M128 Simopone_cf_oculata_D0792 63 100 Simopone_grandidieri_M186 100 Simopone_dryas_M224 Simopone_rex_M133 100 100 Simopone_trita_M185 100 Simopone_conradti_M144 100 Simopone_marleyi_M171 82 Tanipone_scelesta_M159 100 Tanipone_zona_M182 100 Tanipone_aglandula_M280 100 Tanipone_hirsuta_M279 Lioponera_longitarsus_M193 Lioponera_vespula_M210 100100 Lioponera_nr_mayri_M215 100 62 Lioponera_nr_kraepelinii_M131 100 Lioponera_MY_M268 100 Lioponera_cf_suscitata_M267 100 Lioponera_PG_M250 100 Lioponera_marginata_M249 32 Lioponera_ruficornis_M165 100 100 Lioponera_clarus_M137 Lividopone_MG_M132 100 Lividopone_MG_M194 100Lividopone_MG_M294 100 Lividopone_MG_M216 Zasphinctus_wilsoni_M229 100 Zasphinctus_sarowiwai_M227 100 100 Zasphinctus_TH_M192 100 Zasphinctus_trux_M136 100 Zasphinctus_PG_M285 100 100 0.07 Zasphinctus_imbecilis_M170 Parasyscia_UG_M281 combined data matrix 100 Parasyscia_MG_M212 no Aenictus Parasyscia_UG_M219 100 100 Parasyscia_wittmeri_M282 100 maximum likelihood tree 100 Parasyscia_UG_M218 Parasyscia_VN_M207 RAxML 100 Parasyscia_PG_M204 100 k-means partitions GTR+4Gamma model Parasyscia_dohertyi_M142 500 bootstrap replicates

Supplementary Figure S17: Maximum likelihood tree obtained under from complete data matrix with Aenictus removed under k-means partitioning. Scale is in number of substitutions per site. Nodal support in percent bootstrap.

18 Harpegnathos_saltator_Genome Linepithema_humile_Genome 1 Camponotus_floridanus_Genome 1 Pogonomyrmex_barbatus_Genome Vollenhovia_emeryi_Genome 1 1 Cardiocondyla_obscurior_Genome 1 Solenopsis_invicta_Genome 1 Atta_cephalotes_Genome 1 Acromyrmex_echinatior_Genome Vicinopone_conciliatrix_M128 Tanipone_scelesta_M159 1 Tanipone_zona_M182 1 Tanipone_hirsuta_M279 1 0.52 Tanipone_aglandula_M280 Simopone_cf_oculata_D0792 1 0.98 Simopone_grandidieri_M186 1 Simopone_dryas_M224 1 Simopone_marleyi_M171 1 Simopone_conradti_M144 1 Simopone_rex_M133 1 Simopone_trita_M185 0.52 Lioponera_longitarsus_M193 Lioponera_vespula_M210 1 1 Lioponera_nr_mayri_M215 1 Lioponera_nr_kraepelinii_M131 1 Lioponera_cf_suscitata_M267 1 Lioponera_MY_M268 1 Lioponera_PG_M250 1 Lioponera_marginata_M249 1 Lioponera_ruficornis_M165 1 1 Lioponera_clarus_M137 Lividopone_MG_M132 1 Lividopone_MG_M194 1 Lividopone_MG_M294 1 Lividopone_MG_M216 Zasphinctus_wilsoni_M229 1 Zasphinctus_TH_M192 1 1 Zasphinctus_sarowiwai_M227 1 Zasphinctus_trux_M136 1 Zasphinctus_PG_M285 1 1 Zasphinctus_imbecilis_M170 1 Parasyscia_UG_M281 1 Parasyscia_MG_M212 Parasyscia_VN_M207 1 1 Parasyscia_dohertyi_M142 1 1 Parasyscia_PG_M204 Parasyscia_UG_M219 1 Parasyscia_wittmeri_M282 1 Parasyscia_UG_M218 Syscia_augustae_M196 1 Syscia_GT_M127 1 Syscia_typhla_D0841 1 Syscia_MY_M147 1 1 Syscia_MY_M176 Eusphinctus_TH_M158 1 Ooceraea_fragosa_D0842 Ooceraea_australis_M138 1 1 Ooceraea_biroi_Genome 1 Ooceraea_MY_M270 1 Ooceraea_FJ06_M168 1 Ooceraea_PG_M248 Eburopone_CM02_D0788 1 Eburopone_UG_M259 Eburopone_MG_M195 1 1 Eburopone_MG_M130 1 Eburopone_MG_M213 1 Eburopone_MG_M214 Yunodorylus_TH_M191 1 0.98 Yunodorylus_eguchii_M247 1 Yunodorylus_paradoxus_M190 1 Yunodorylus_TH_M160 Chrysapace_TH_M156 1 1 Chrysapace_cf_crawleyi_M262 1 Chrysapace_cf_sauteri_M261 1 1 Chrysapace_MG_M155 Cerapachys_sulcinodis_M243 1 Cerapachys_MY_M264 1 Cerapachys_antennatus_M263 1 Cerapachys_TH_M203 Aenictogiton_ZM02_M181 1 Aenictogiton_UG_M189 1 1 Dorylus_laevigatus_M157 Dorylus_conradti_M178 1 1 1 Dorylus_orientalis_M244 0.98 Dorylus_fimbriatus_M288 Dorylus_fulvus_M179 1 1 Dorylus_cf_fulvus_M149 1 Dorylus_spininodis_M292 Dorylus_braunsi_M289 1 1 Dorylus_affinis_M177 1 1 Dorylus_kohli_M180 1 Dorylus_mayri_M291 1Dorylus_molestus_M290 1Dorylus_rubellus_M287 1 Dorylus_UG_M153 Aenictus_silvestrii_M221 Aenictus_latifemoratus_M266 11 Aenictus_yamanei_M265 1 Aenictus_levior_M231 1 1 Aenictus_bobaiensis_M197 Aenictus_camposi_M222 Aenictus_ZA_M228 1 1 Aenictus_UG_M143 1 Aenictus_fergusoni_M223 1 1 Aenictus_hodgsoni_M198 1 Aenictus_laeviceps_M269 1 Aenictus_rotundicollis_M232 1 Aenictus_turneri_M135 1 Aenictus_fuchuanensis_M201 1 1 Aenictus_hoelldobleri_M200 Aenictus_currax_M245 1 Aenictus_cornutus_M230 1 Aenictus_gracilis_M199 Neocerapachys_CR_M209 1 Neocerapachys_neotropicus_M134 1 Neocerapachys_BR_M295 1 Neocerapachys_cf_splendens_M251 1 Cylindromyrmex_meinerti_D00778 1 Cylindromyrmex_brasiliensis_M140 1 Cylindromyrmex_whymperi_M271 1 1 Cylindromyrmex_darlingtoni_M211 Acanthostichus_AZ_M277 1 Acanthostichus_AZ_M278 1 Acanthostichus_BR_M252 1 Acanthostichus_serratulus_M166 1 1 Acanthostichus_GF_M208 Leptanilloides_nubecula_M167 1 Leptanilloides_mckennae_D0228 1 Leptanilloides_femoralis_M188 1 Leptanilloides_erinys_M246 1 Leptanilloides_gracilis_M187 Sphinctomyrmex_stali_M253 1 Sphinctomyrmex_cf_marcoyi_M202 1 Cheliomyrmex_megalonyx_M146 1 Cheliomyrmex_cf_morosus_M217 1 Cheliomyrmex_cf_andicola_M174 1 Labidus_coecus_M173 1 Labidus_spininodis_M172 1 1 Labidus_praedator_M152 Nomamyrmex_esenbeckii_M129 1 1 Nomamyrmex_hartigii_M220 1 Eciton_mexicanum_M238 1 Eciton_vagans_M184 1 1 Eciton_quadriglume_M254 Eciton_lucanoides_M239 1 1 Eciton_burchellii_M273 1 Eciton_rapax_M145 1 Eciton_hamatum_M293 Neivamyrmex_distans_M242 1 Neivamyrmex_alfaroi_M240 1 Neivamyrmex_swainsonii_M169 1 Neivamyrmex_EC_M175 1 Neivamyrmex_adnepos_M236 1 Neivamyrmex_gibbatus_M139 1 Neivamyrmex_impudens_M237 1 1 Neivamyrmex_melanocephalus_M154 0.04 Neivamyrmex_cf_nyensis_M296 1 Neivamyrmex_compressinodis_M235 combined data matrix Neivamyrmex_asper_M233 1 1 Bayesian posterior consensus tree Neivamyrmex_sumichrasti_M151 1 Neivamyrmex_kiowapache_M275 ExaBayes 1 Neivamyrmex_opacithorax_M276 1 Neivamyrmex_texanus_M274 k-means partitions GTR+4Gamma model 1 Neivamyrmex_californicus_M272

Supplementary Figure S18: Bayesian posterior consensus tree obtained from complete data matrix under k-means partitioning. Scale is in number of substitutions per site. Nodal support in posterior probability.

19 Neivamyrmex_californicus_M272 2.1 2.71 Neivamyrmex_texanus_M274 2.89 Neivamyrmex_kiowapache_M275 3.88 Neivamyrmex_opacithorax_M276 Neivamyrmex_sumichrasti_M151 2.85 6.43 Neivamyrmex_asper_M233 8.7 Neivamyrmex_compressinodis_M235 Neivamyrmex_cf_nyensis_M296 14.44 Neivamyrmex_impudens_M237 4.81 10.52 Neivamyrmex_melanocephalus_M154 Neivamyrmex_gibbatus_M139 19.51 Neivamyrmex_adnepos_M236 2.42 9.28 Neivamyrmex_EC_M175 14.37 Neivamyrmex_swainsonii_M169 Neivamyrmex_alfaroi_M240 8.91 Neivamyrmex_distans_M242 Eciton_rapax_M145 0.98 3.12 Eci t on_hamat um_M293 3.65 Eciton_burchellii_M273 27.36 4.46 Eciton_lucanoides_M239 E c i t on_vagans_M184 3.36 5.55 Eciton_quadriglume_M254 12.25 Eciton_mexicanum_M238 Nomamyrmex_esenbeckii_M129 6.64 18.06 Nomamyrmex_hartigii_M220 44.36 Labidus_spininodis_M172 6.11 10.7 Labidus_praedator_M152 23.8 Labidus_coecus_M173 Cheliomyrmex_cf_andicola_M174 5.87 9.78 Cheliomy rmex _ cf_moros u s _M217 51.98 Cheliomyrmex_megalonyx_M146 Sphinctomyrmex_stali_M253 19.98 Sphinct omyrmex_marc o y i_M202 Leptanilloides_erinys_M246 12.36 18.03 Leptanilloides_gracilis_M187 32.92 Leptanilloides_femoralis_M188 Leptanilloides_nubecula_M167 15.1 Leptanilloides_mckennae_D0228 A c ant hostichus _ GF_M208 60.11 6.07 11.67 Acanthostichus_serratulus_M166 25.63 Acanthostichus_BR_M252 Acanthostichus_AZ_M278 12.35 Acanthostichus_AZ_M277 39.72 Cylindromyrmex_whymperi_M271 8.45 20.62 Cylindromyrmex_darlingtoni_M211 28.25 Cylindromyrmex_brasiliensis_M140 51.52 Cylindromyrmex_meinerti_D0778 Neocerapachys_cf_splendens_M251 7.39 15.7 Neocerapachys_BR_M295 22.75 Neocerapachys_neotropicus_M134 Neoc erapac h ys_CR_M209 Aenict us_grac ilis _M199 1.99 3.21 Aenictus_cornutus_M230 Aenictus_currax_M245 8.09 Aenictus_hoelldobleri_M200 3.2 4.18 Aenictus_fuchuanensis_M201 9.67 Aenictus_turneri_M135 Aenictus_laeviceps_M269 1.79 2.84 Aenictus_rotundicollis_M232 13.08 5.36 Aenictus_hodgsoni_M198 70.42 Aenictus_fergusoni_M223 19.31 Aenictus_UG_M143 6.43 Aenictus_ZA_M228 Aenictus_camposi_M222 33.52 Aenictus_bobaiensis_M197 6.58 13.32 Aenictus_levior_M231 23.45 Aenictus_silvestrii_M221 Aenictus_latifemoratus_M266 13.2 Aenictus_yamanei_M265 Dorylus _UG _M153 1.14 1.4Dorylus_rubellus_M281 7 1.9Dorylus_molestus_M295 0 2.65Dorylus_mayri_M291 54.18 2.87 Dorylus _ k ohli_M180 Dorylus_braunsi_M289 1.84 4.11 Dorylus_affinis_M177 6.49 Dory lus_spininodis_M292 Dorylus_fulvus_M179 8.46 1.05 Dorylus_cf _ f ulvus_M149 11.27 Dorylus _ f imbriat u s _M288 Dory lus_orient alis _M244 14.68 6.66 Dorylus_conradti_M178 62.67 37.53 Dorylus_laevigatus_M157 Aenictogiton_UG_M189 13.71 Aenictogiton_ZM02_M181 Cerapachys_T H_M203 8.34 13.05 Cerapachys_antennatus_M263 24.95 Cerapachys_MY_M264 Cerapachys_sulcinodis_M243 43.37 Chrysapace_cf_crawleyi_M262 14.26 Chrysapace_T H_M156 26.22 Chrysapace_cf_sauteri_M261 14.45 54.73 Chrysapace_MG_M155 Y unodory lus _ T H_M160 18.04 Yunodorylus_paradoxus_M190 35.76 Y unodory lus _ T H_M191 16.15 Yunodory lus_eguchii_M247 80.43 Parasyscia_PG_M204 3.67 5.86 Paras ysc ia_dohert yi_M142 Parasyscia_VN_M207 6.93 Parasyscia_UG_M218 6.01 8.26.35 6 Parasyscia_wittmeri_M282 Parasyscia_UG_M219 9.33 Parasyscia_MG_M212 Parasyscia_UG_M281 Zasphinctus_imbecilis_M170 18.57 3.15 3.93 Zasphinctus_PG_M285 7.44 Zasphinctus_trux_M136 Zasphinctus_TH_M192 9.62 2.54 23.09 Z asphinct us_sarowiwai_M227 Zasphinctus_wilsoni_M229 Lividopone_MG_M216 3.18 4.13 Lividopone_MG_M294 11.8 Lividopone_MG_M194 Lividopone_MG_M132 Lioponera_clarus_M137 33.4 5.45 6.27 Lioponera_ruficornis_M165 6.81 Lioponera_marginata_M249 8.52 Lioponera_PG_M250 Lioponera_MY_M268 6.34 11.79 Lioponera_cf_suscitata_M267 Lioponera_nr_kraepelinii_M131 2.66 91.03 14.61 8.43 Lioponera_nr_mayri_M215 Lioponera_vespula_M210 46.34 Lioponera_longit ars us_M193 S imopone_rex _M133 1.85 5.58 Simopone_trita_M185 6.53 Simopone_conradti_M144 9.92 Simopone_marleyi_M171 18.5 Simopone_dryas_M224 Simopone_cf_oculata_D0792 11.07 Simopone_grandidieri_M186 36.06 T anipone_hirsut a_M279 4.76 60.98 8.79 Tanipone_aglandula_M280 14.21 Tanipone_zona_M182 T anipone_sc elest a_M159 Ooceraea_FJ06_M168 5.77 Ooceraea_PG_M248 97.48 6.56 8.27 Ooceraea_MY_M270 Ooceraea_biroi_Genome 6.66 11.2 Ooceraea_australis_M138 22.72 O o c eraea_f ragos a_D0842 Eusphinctus_TH_M158 Syscia_MY_M176 41.35 5.6 14.03 Syscia_MY_M147 25.34 Syscia_typhla_D0841 Sys cia_august ae_M196 12.22 Syscia_GT_M127 Vicinopone_conciliatrix_M128 Eburopone_MG_M214 118.62 7.5 Eburopone_MG_M213 14.98 Eburopone_MG_M195 8.23 27.58 Eburopone_MG_M130 50.21 Eburopone_UG_M259 E buropone_CM02_D0788 Acromyrmex_echinatior_Genome 10.91 28.47 Atta_cephalotes_Genome 47.67 Solenopsis_invicta_Genome Vollenhovia_emeryi_Genome 28.07 70.34 Cardiocondyla_obscurior_Genome 103.75 Pogonomy rmex _barbat us_G enome 108.04 Camponot u s _ f loridanus_G enome Linepit hema_humile_G enome

120.0 100.0 80.0 60.0 40.0 20.0 0.0 Supplementary Figure S19: Summary tree with mean ages from 100 analyses under penalized likelihood in Chronos.

20 Neivamyrmex_impudens_M237 4.52 10.31 Neivamyrmex_melanocephalus_M154 12.52 Neivamyrmex_gibbatus_M139 Neivamyrmex_alfaroi_M240 10.57 13.04 Neivamyrmex_distans_M242 Neivamyrmex_EC_M175 1.33 11.6 Neivamyrmex_adnepos_M236 Neivamyrmex_swainsonii_M169 Neivamyrmex_californicus_M272 2.13 13.37 3.01 Neivamyrmex_texanus_M274 3.44 Neivamyrmex_kiowapache_M275 4.3 Neivamyrmex_opacithorax_M276 Neivamyrmex_asper_M233 3.86 9.34 Neivamyrmex_sumichrasti_M151 11.29 Neivamyrmex_compressinodis_M235 Neivamyrmex_cf_nyensis_M296 Eci t on_hamat um_M293 0.79 3.37 Eciton_rapax_M145 27.5 4.34 Eciton_burchellii_M273 4.71 Eciton_lucanoides_M239 Eciton_quadriglume_M254 4.15 4.91 E c i t on_vagans_M184 13.23 Eciton_mexicanum_M238 Nomamyrmex_esenbeckii_M129 7.92 18.46 Nomamyrmex_hartigii_M220 Labidus_praedator_M152 56.66 5.21 6.91 Labidus_spininodis_M172 23.31 Labidus_coec u s _M173 Cheliomyrmex_cf_andicola_M174 3.53 4.36 Cheliomy rmex _cf _moros u s _M217 Cheliomyrmex_megalonyx_M146 59.16 Leptanilloides_erinys_M246 20.07 24.35 Leptanilloides_gracilis_M187 34.69 Leptanilloides_femoralis_M188 Leptanilloides_mckennae_D0228 8.26 Leptanilloides_nubecula_M167 Sphinct omyrmex _cf_marc oyi_M202 23.24 Sphinctomyrmex_stali_M253 A c ant hostichus_GF_M208 60.35 3.17 4.94 Acanthostichus_serratulus_M166 19.46 Acanthostichus_BR_M252 Acanthostichus_AZ_M277 8.14 Acanthostichus_AZ_M278 41.84 Cylindromyrmex_darlingtoni_M211 7.33 22.57 Cylindromyrmex_whymperi_M271 27.43 Cylindromyrmex_brasiliensis_M140 58.83 Cylindromyrmex_meinerti_D0778 Neocerapachys_BR_M295 3.33 7.32 Neocerapachys_cf_splendens_M251 9.85 Neocerapachys_neotropicus_M134 Neoc erapachys_CR_M209 Aenictus_cornutus_M230 2.09 3.96 Aenict us_gracilis_M199 Aenictus_currax_M245 10.55 Aenictus_fuchuanensis_M201 3.86 4.73 Aenictus_hoelldobleri_M200 Aenictus_turneri_M135 13.25 Aenictus_laeviceps_M269 2.26 3.55 Aenictus_rotundicollis_M232 15.61 7.81 Aenictus_hodgsoni_M198 Aenictus_fergusoni_M223 61.53 19.9 Aenictus_UG_M143 7 Aenictus_ZA_M228 Aenictus_camposi_M222 23.25 Aenictus_bobaiensis_M197 7.06 13.07 Aenictus_levior_M231 13.88 Aenictus_latifemoratus_M266 14.9 Aenictus_yamanei_M265 Aenictus_silvestrii_M221 Dorylus _UG _M153 1.14 1.4Dorylus_rubellus_M286 7 3.29 Dorylus_molestus_M290 Dorylus_mayri_M291 57.71 4.94 Dorylus_affinis _M177 2.49 6.654.52 Dorylus_braunsi_M289 Dorylus _kohli_M 180 10.6 Dory lus_spininodis_M292 Dorylus_cf _ f ulv u s _M149 14.1 0.88 Dorylus_fulvus_M179 15.6 Dorylus _ f imbriat u s _M288 Dorylus_conradti_M178 8.79 63.23 Dory lus_orient alis _M244 44.38 14.18 60.29 Dorylus_laevigatus_M157 Aenictogiton_UG_M189 4.68 Aenictogiton_ZM02_M181 Chrysapace_MG_M155 15.52 Chrysapace_cf_sauteri_M261 25.97 Chrysapace_T H_M156 16.85 Chrysapace_cf_crawleyi_M262 56.83 Y unodory lus _ T H_M160 14.88 Yunodorylus_paradoxus_M190 29.08 Y unodory lus _ T H_M191 3.52 58.56 Yunodory lus_eguchii_M247 Cerapachys_T H_M203 8.97 11.03 Cerapachys_antennatus_M263 15.12 Cerapachys_MY_M264 65.27 Cerapachys_sulcinodis_M243 Eburopone_MG_M130 3.76 Eburopone_MG_M195 6.32 Eburopone_MG_M213 1.64 28.7 Eburopone_MG_M214 33.58 Eburopone_UG_M259 E buropone_CM02_D0788 Ooceraea_FJ06_M168 12.25 15.01 Ooceraea_PG_M248 20.19 Ooceraea_MY_M270 Ooceraea_australis_M138 17.85 27.44 Ooceraea_biroi_Genome O o c eraea_f ragos a_D0842 67.14 48.76 Syscia_MY_M147 2.94 16.18 Syscia_MY_M176 Syscia_typhla_D0841 50.96 19.56 Syscia_GT_M127 5.31 Sys cia_august ae_M196 Eusphinctus_TH_M158 Simopone_conradti_M144 9.38 Simopone_marleyi_M171 10.44 S imopone_rex _M133 69.16 3.46 12.54 Simopone_trita_M185 21.7 Simopone_dryas_M224 Simopone_cf_oculata_D0792 13.63 Simopone_grandidieri_M186 63.2 Tanipone_aglandula_M280 3.41 7.73 T anipone_hirs u t a_M279 19.28 Tanipone_zona_M182 T anipone_scelest a_M159 Vicinopone_conciliatrix_M128 Parasyscia_PG_M204 6.88 13.33 Paras ysc ia_dohertyi_M142 Parasyscia_VN_M207 16.86 Parasyscia_UG_M218 12.84 Parasyscia_wittmeri_M282 73.8 22.53 14.19 Parasyscia_UG_M219 25.37 Parasyscia_MG_M212 Parasyscia_UG_M281 Zasphinctus_PG_M285 52.49 8.74 11.01 Zasphinctus_imbecilis_M170 22.42 Zasphinctus_trux_M136 Zasphinctus_TH_M192 6.34 27.67 Z asphinct u s _sarowiwai_M227 58.53 Zasphinctus_wilsoni_M229 Lividopone_MG_M194 5.03 6.34 Lividopone_MG_M216 26.65 Lividopone_MG_M294 Lividopone_MG_M132 Lioponera_clarus_M137 69.58 10.89 13.12 Lioponera_ruficornis_M165 13.87 Lioponera_marginata_M249 16.6 Lioponera_PG_M250 Lioponera_MY_M268 12.46 20.87 Lioponera_cf_suscitata_M267 Lioponera_nr_kraepelinii_M131 6.12 24.48 19.78 Lioponera_nr_mayri_M215 Lioponera_vespula_M210 Lioponera_longit arsus_M193

80.0 70.0 60.0 50.0 40.0 30.0 20.0 10.0 0.0 Supplementary Figure S20: Mean ages and their 95% confidence intervals on the consensus BEAST tree inferred under fossilized birth-death process. All ages in Ma.

21 Neivamyrmex_impudens_M237 1 1 Neivamyrmex_melanocephalus_M154 0.9862 Neivamyrmex_gibbatus_M139 Neivamyrmex_alfaroi_M240 1 0.6657 Neivamyrmex_distans_M242 Neivamyrmex_EC_M175 1 1 Neivamyrmex_adnepos_M236 Neivamyrmex_swainsonii_M169 Neivamyrmex_californicus_M272 1 1 0.9998 Neivamyrmex_texanus_M274 1 Neivamyrmex_kiowapache_M275 1 Neivamyrmex_opacithorax_M276 Neivamyrmex_asper_M233 1 1 Neivamyrmex_sumichrasti_M151 1 Neivamyrmex_compressinodis_M235 Neivamyrmex_cf_nyensis_M296 Eci t on_hamat um_M293 1 1 Eciton_rapax_M145 1 1 Eciton_burchellii_M273 0.8854 Eciton_lucanoides_M239 Eciton_quadriglume_M254 1 1 E c i t on_vagans_M184 1 Eciton_mexicanum_M238 Nomamyrmex_esenbeckii_M129 1 1 Nomamyrmex_hartigii_M220 Labidus_praedator_M152 0.9999 1 1 Labidus_spininodis_M172 1 Labidus_coecus_M173 Cheliomyrmex_cf_andicola_M174 0.8933 1 Cheliomy rmex _ cf_moros u s _M217 Cheliomyrmex_megalonyx_M146 1 Leptanilloides_erinys_M246 1 1 Leptanilloides_gracilis_M187 1 Leptanilloides_femoralis_M188 Leptanilloides_mckennae_D0228 1 Leptanilloides_nubecula_M167 Sphinct omyrmex_cf_marcoy i_M202 1 Sphinctomyrmex_stali_M253 A c ant hostichus _ GF_M208 1 1 1 Acanthostichus_serratulus_M166 Acanthostichus_BR_M252 1 Acanthostichus_AZ_M277 1 Acanthostichus_AZ_M278 1 Cylindromyrmex_darlingtoni_M211 1 1 Cylindromyrmex_whymperi_M271 1 Cylindromyrmex_brasiliensis_M140 1 Cylindromyrmex_meinerti_D0778 Neocerapachys_BR_M295 1 1 Neocerapachys_cf_splendens_M251 1 Neocerapachys_neotropicus_M134 Neoc erapac h ys_CR_M209 Aenictus_cornutus_M230 1 1 Aenict us_grac ilis _M199 Aenictus_currax_M245 1 Aenictus_fuchuanensis_M201 1 1 Aenictus_hoelldobleri_M200 Aenictus_turneri_M135 1 Aenictus_laeviceps_M269 1 1 Aenictus_rotundicollis_M232 1 1 Aenictus_hodgsoni_M198 Aenictus_fergusoni_M223 1 1 Aenictus_UG_M143 1 Aenictus_ZA_M228 Aenictus_camposi_M222 1 Aenictus_bobaiensis_M197 1 0.569 Aenictus_levior_M231 0.9999 Aenictus_latifemoratus_M266 1 Aenictus_yamanei_M265 Aenictus_silvestrii_M221 Dorylus _UG _M153 0.9974 1 Dorylus_rubellus_M287 1 Dorylus_molestus_M290 Dorylus_mayri_M291 1 1 Dorylus_affinis_M177 1 1 0.9998 Dorylus_braunsi_M289 Dorylus _ k ohli_M180 1 Dory lus_spininodis_M292 Dorylus_cf _ f ulvus_M149 0.9373 1 Dorylus_fulvus_M179 1 Dorylus _ f imbriat u s _M288 Dorylus_conradti_M178 1 1 Dory lus_orient alis _M244 1 0.8747 1 Dorylus_laevigatus_M157 Aenictogiton_UG_M189 1 Aenictogiton_ZM02_M181 Chrysapace_MG_M155 1 Chrysapace_cf_sauteri_M261 1 Chrysapace_T H_M156 1 Chrysapace_cf_crawleyi_M262 0.5869 Y unodory lus _ T H_M160 1 Yunodorylus_paradoxus_M190 1 Y unodory lus _ T H_M191 1 1 Yunodory lus_eguchii_M247 Cerapachys_T H_M203 1 1 Cerapachys_antennatus_M263 1 Cerapachys_MY_M264 0.9997 Cerapachys_sulcinodis_M243 Eburopone_MG_M130 1 Eburopone_MG_M195 1 Eburopone_MG_M213 1 1 Eburopone_MG_M214 1 Eburopone_UG_M259 E buropone_CM02_D0788 Ooceraea_FJ06_M168 1 1 Ooceraea_PG_M248 1 Ooceraea_MY_M270 Ooceraea_australis_M138 1 1 Ooceraea_biroi_Genome O o c eraea_f ragos a_D0842 0.9523 0.999 Syscia_MY_M147 1 1 Syscia_MY_M176 Syscia_typhla_D0841 1 1 Syscia_GT_M127 1 Sys cia_august ae_M196 Eusphinctus_TH_M158 Simopone_conradti_M144 0.9983 Simopone_marleyi_M171 1 S imopone_rex _M133 0.7991 1 1 Simopone_trita_M185 1 Simopone_dryas_M224 Simopone_cf_oculata_D0792 1 Simopone_grandidieri_M186 0.97 Tanipone_aglandula_M280 1 1 T anipone_hirsut a_M279 1 Tanipone_zona_M182 T anipone_sc elest a_M159 Vicinopone_conciliatrix_M128 Parasyscia_PG_M204 1 1 Paras ysc ia_dohert yi_M142 Parasyscia_VN_M207 1 Parasyscia_UG_M218 1 Parasyscia_wittmeri_M282 1 1 1 Parasyscia_UG_M219 1 Parasyscia_MG_M212 Parasyscia_UG_M281 Zasphinctus_PG_M285 1 1 1 Zasphinctus_imbecilis_M170 Zasphinctus_trux_M136 1 Zasphinctus_TH_M192 1 1 Z asphinct us_sarowiwai_M227 1 Zasphinctus_wilsoni_M229 Lividopone_MG_M194 1 1 Lividopone_MG_M216 1 Lividopone_MG_M294 Lividopone_MG_M132 Lioponera_clarus_M137 1 1 0.9991 Lioponera_ruficornis_M165 1 Lioponera_marginata_M249 1 Lioponera_PG_M250 Lioponera_MY_M268 1 1 Lioponera_cf_suscitata_M267 Lioponera_nr_kraepelinii_M131 1 1 0.9997 Lioponera_nr_mayri_M215 Lioponera_vespula_M210 Lioponera_longit ars us_M193

70.0 60.0 50.0 40.0 30.0 20.0 10.0 0.0

Supplementary Figure S21: Posterior probabilities on the consensus BEAST tree inferred under fossilized birth-death process. Red dots reflect monophyly constraints used in the dating analysis. All ages in Ma.

22 Neivamyrmex_texanus_M274 Neivamyrmex_californicus_M272 Neivamyrmex_kiowapache_M275 Neivamyrmex_opacithorax_M276 Neivamyrmex_sumichrasti_M151 Neivamyrmex_asper_M233 Neivamyrmex_compressinodis_M235 Neivamyrmex_cf_nyensis_M296 Neivamyrmex_melanocephalus_M154 Neivamyrmex_impudens_M237 Neivamyrmex_gibbatus_M139 Neivamyrmex_distans_M242 Neivamyrmex_alfaroi_M240 Neivamyrmex_adnepos_M236 Neivamyrmex_EC_M175 Neivamyrmex_swainsonii_M169 Eciton_rapax_M145 Eciton_hamatum_M293 Eciton_burchellii_M273 Eciton_lucanoides_M239 Eciton_vagans_M184 Eciton_quadriglume_M254 Eciton_mexicanum_M238 Nomamyrmex_hartigii_M220 Nomamyrmex_esenbeckii_M129 Labidus_spininodis_M172 Labidus_praedator_M152 Labidus_coecus_M173 Cheliomyrmex_cf_morosus_M217 Cheliomyrmex_cf_andicola_M174 Cheliomyrmex_megalonyx_M146 Leptanilloides_gracilis_M187 Leptanilloides_erinys_M246 Leptanilloides_femoralis_M188 Leptanilloides_nubecula_M167 Leptanilloides_mckennae_D0228 Sphinctomyrmex_stali_M253 Sphinctomyrmex_cf_marcoyi_M202 Acanthostichus_serratulus_M166 Acanthostichus_GF_M208 Acanthostichus_BR_M252 Acanthostichus_AZ_M278 Acanthostichus_AZ_M277 Cylindromyrmex_whympe ri_M271 Cylindromyrmex_darlingtoni_M211 Cylindromyrmex_brasiliensis_M140 Cylindromyrmex_meinerti_D0778 Neocerapachys_cf_splendens_M251 Neocerapachys_BR_M295 Neocerapachys_neotropicus_M134 Neocerapachys_CR_M209 Aenictus_hoelldobleri_M200 Aenictus_fuchuanensis_M201 Aenictus_turneri_M135 Aenictus_gracilis_M199 Aenictus_cornutus_M230 Aenictus_currax_M245 Aenictus_rotundicollis_M232 Aenictus_laeviceps_M269 Aenictus_hodgsoni_M198 Aenictus_fergusoni_M223 Aenictus_ZA_M228 Aenictus_UG_M143 Aenictus_camposi_M222 Aenictus_levior_M231 Aenictus_bobaiensis_M197 Aenictus_latifemoratus_M266 Aenictus_yamanei_M265 Aenictus_silvestrii_M221 Dorylus_rubellus_M287 Dorylus_UG_M153 Dorylus_molestus_M290 Dorylus_mayri_M291 Dorylus_braunsi_M289 Dorylus_affinis_M177 Dorylus_kohli_M180 Dorylus_spininodis_M292 Dorylus_fulvus_M179 Dorylus_cf_fulvus_M149 Dorylus_fimbriatus_M288 Dorylus_orientalis_M244 Dorylus_conradti_M178 Dorylus_laevigatus_M157 Aenictogiton_ZM02_M181 Aenictogiton_UG_M189 Yunodorylus_eguchii_M247 Yunodorylus_TH_M191 Yunodorylus_paradoxus_M190 Yunodorylus_TH_M160 Chrysapace_cf_crawleyi_M262 Chrysapace_TH_M156 Chrysapace_cf_sauteri_M261 Chrysapace_MG_M155 Cerapachys_antennatus_M263 Cerapachys_TH_M203 Cerapachys_MY_M264 Cerapachys_sulcinodis_M243 Eburopone_MG_M214 Eburopone_MG_M213 Eburopone_MG_M195 Eburopone_MG_M130 Eburopone_UG_M259 Eburopone_CM02_D0788 Ooceraea_PG_M248 Ooceraea_FJ06_M168 Ooceraea_MY_M270 Ooceraea_biroi_Genome Ooceraea_australis_M138 Ooceraea_fragosa_D0842 Syscia_MY_M176 Syscia_MY_M147 Syscia_typhla_D0841 Syscia_augustae_M196 Syscia_GT_M127 Eusphinctus_TH_M158 Simopone_trita_M185 Simopone_rex_M133 Simopone_marleyi_M171 Simopone_conradti_M144 Simopone_dryas_M224 Simopone_grandidieri_M186 Simopone_cf_oculata_D0792 Tanipone_hirsuta_M279 Tanipone_aglandula_M280 Tanipone_zona_M182 Tanipone_scelesta_M159 Vicinopone_conciliatrix_M128 Parasyscia_wittmeri_M282 Parasyscia_UG_M218 Parasyscia_UG_M219 Parasyscia_dohertyi_M142 Parasyscia_PG_M204 Parasyscia_VN_M207 Parasyscia_MG_M212 Parasyscia_UG_M281 Zasphinctus_imbecilis_M170 Zasphinctus_PG_M285 Zasphinctus_trux_M136 Zasphinctus_sarowiwai_M227 Zasphinctus_TH_M192 Zasphinctus_wilsoni_M229 Lividopone_MG_M216 Lividopone_MG_M194 Lividopone_MG_M294 Lividopone_MG_M132 Lioponera_ruficornis_M165 Lioponera_clarus_M137 Lioponera_marginata_M249 Lioponera_PG_M250 Lioponera_cf_suscitata_M267 Lioponera_MY_M268 Lioponera_nr_mayri_M215 Lioponera_nr_kraepelinii_M131 Lioponera_vespula_M210 Lioponera_longitarsus_M193

Supplementary Figure S22: BAMM rate shift tree showing the overall best fit configuration. Red- filled circles signify placement of the shifts.

23 N

0.41 A 0.3 D

0.19

0.085

L

Supplementary Figure S23: BAMM rate shift tree showing net diversification rates. A: Aenictus, D: Dorylus, L: Lioponera, N: Neivamyrmex.

24 f = 0.21 f = 0.19 f = 0.16 N N N

A A A D D D

L L L

f = 0.047 f = 0.043 f = 0.035 N N N

A A A D D D

L L L

f = 0.033 f = 0.025 f = 0.02 N N N

A A A D D D

L L L

Supplementary Figure S24: BAMM plot showing nine most common shift configurations in the credible set. The ”f” number corresponds to the proportion of the posterior samples in which this configuration is present. A: Aenictus, D: Dorylus, L: Lioponera, N: Neivamyrmex.

25 L DA N

N 1

A 0.5 D

0

L

Supplementary Figure S25: BAMM cohort plot. Blocks signify comparisons of shift regimes among species and clades, except across the diagonal which represents the comparison of a species to itself. A: Aenictus, D: Dorylus, L: Lioponera, N: Neivamyrmex.

26 N Neivamyrmex texanus M274 N Neivamyrmex californicus M272 N Neivamyrmex kiowapache M275 TN Neivamyrmex opacithorax M276 T Neivamyrmex sumichrasti M151 T Neivamyrmex asper M233 T Neivamyrmex compressinodis M235 N Neivamyrmex cf nyensis M296 TN Neivamyrmex melanocephalus M154 T Neivamyrmex impudens M237 T Neivamyrmex gibbatus M139 T Neivamyrmex distans M242 T Neivamyrmex alfaroi M240 T Neivamyrmex adnepos M236 T Neivamyrmex EC M175 TN Neivamyrmex swainsonii M169 T T Eciton rapax M145 T Eciton hamatum M293 N T Eciton burchellii M273 T Eciton lucanoides M239 P T Eciton vagans M184 T Eciton quadriglume M254 E T Eciton mexicanum M238 T Nomamyrmex hartigii M220 M TN Nomamyrmex esenbeckii M129 O T Labidus spininodis M172 T Labidus praedator M152 A TN Labidus coecus M173 T Cheliomyrmex cf morosus M217 TN T Cheliomyrmex cf andicola M174 T Cheliomyrmex megalonyx M146 TP T Leptanilloides gracilis M187 T Leptanilloides erinys M246 TE T Leptanilloides femoralis M188 TM T Leptanilloides nubecula M167 T Leptanilloides mckennae D0228 TO T Sphinctomyrmex stali M253 T Sphinctomyrmex cf marcoyi M202 TA T Acanthostichus serratulus M166 T Acanthostichus GF M208 NP T Acanthostichus BR M252 N Acanthostichus AZ M278 NE N Acanthostichus AZ M277 NM T Cylindromyrme x whymperi M271 T Cylindromyrmex darlingtoni M211 NO T Cylindromyrmex brasiliensis M140 T Cylindromyrmex meinerti D0778 NA T Neocerapachys cf splendens M251 T Neocerapachys BR M295 PE T Neocerapachys neotropicus M134 T Neocerapachys CR M209 PM O Aenictus hoelldobleri M200 O Aenictus fuchuanensis M201 PO A Aenictus turneri M135 PA O Aenictus gracilis M199 O Aenictus cornutus M230 EM A Aenictus currax M245 O Aenictus rotundicollis M232 EO O Aenictus laeviceps M269 O Aenictus hodgsoni M198 EA POAenictus fergusoni M223 E Aenictus ZA M228 MO E Aenictus UG M143 O Aenictus camposi M222 MA O Aenictus levior M231 OA O Aenictus bobaiensis M197 O Aenictus latifemoratus M266 TNP O Aenictus yamanei M265 O Aenictus silvestrii M221 TNE E Dorylus rubellus M287 E Dorylus UG M153 TNM E Dorylus molestus M290 E Dorylus mayri M291 TNO E Dorylus braunsi M289 TNA E Dorylus affinis M177 E Dorylus kohli M180 TPE E Dorylus spininodis M292 PE Dorylus fulvus M179 TPM E Dorylus cf fulvus M149 E Dorylus fimbriatus M288 TPO O Dorylus orientalis M244 E Dorylus conradti M178 TPA O Dorylus laevigatus M157 E Aenictogiton ZM02 M181 TEM E Aenictogiton UG M189 TEO O Yunodorylus eguchii M247 O Yunodorylus TH M191 TEA O Yunodorylus paradoxus M190 O Yunodorylus TH M160 TMO O Chrysapace cf crawleyi M262 O Chrysapace TH M156 TMA O Chrysapace cf sauteri M261 TOA M Chrysapace MG M155 O Cerapachys antennatus M263 NPE O Cerapachys TH M203 O Cerapachys MY M264 NPM O Cerapachys sulcinodis M243 M Eburopone MG M214 NPO M Eburopone MG M213 M Eburopone MG M195 NPA M Eburopone MG M130 E Eburopone UG M259 NEM E Eburopone CM02 D0788 NEO A Ooceraea PG M248 A Ooceraea FJ06 M168 NEA O Ooceraea MY M270 O Ooceraea biroi Genome NMO A Ooceraea australis M138 O Ooceraea fragosa D0842 NMA O Syscia MY M176 NOA O Syscia MY M147 O Syscia typhla D0841 PEM N Syscia augustae M196 T Syscia GT M127 PEO O Eusphinctus TH M158 M Simopone trita M185 PEA M Simopone rex M133 E Simopone marleyi M171 PMO E Simopone conradti M144 E Simopone dryas M224 PMA M Simopone grandidieri M186 POA O Simopone cf oculata D0792 M Tanipone hirsuta M279 EMO M Tanipone aglandula M280 M Tanipone zona M182 EMA M Tanipone scelesta M159 E Vicinopone conciliatrix M128 EOA E Parasyscia wittmeri M282 E Parasyscia UG M218 MOA E Parasyscia UG M219 O Parasyscia dohertyi M142 A Parasyscia PG M204 O Parasyscia VN M207 M Parasyscia MG M212 E Parasyscia UG M281 A Zasphinctus imbecilis M170 A Zasphinctus PG M285 A Zasphinctus trux M136 E Zasphinctus sarowiwai M227 O Zasphinctus TH M192 E Zasphinctus wilsoni M229 M Lividopone MG M216 M Lividopone MG M194 M Lividopone MG M294 M Lividopone MG M132 A Lioponera ruficornis M165 A Lioponera clarus M137 O Lioponera marginata M249 A Lioponera PG M250 O Lioponera cf suscitata M267 O Lioponera MY M268 M Lioponera nr mayri M215 M Lioponera nr kraepelinii M131 E Lioponera vespula M210 POLioponera longitarsus M193

80 60 40 20 0 Ma Supplementary Figure S26: Relative likelihoods of ranges estimations from BioGeoBEARS under DEC+J, averaged over 100 posterior BEAST trees. Pie charts at the nodes correspond to ancestral state estimations and pie charts on the corners correspond to ranges immediately following speci- ation. The region names are abbreviated as follows: Neotropical (T), Nearctic (N), Palearctic (P), Afrotropical (E), Malagasy (M), Indomalayan (O), and Australasian (A). All ages in Ma.

27 N Neivamyrmex texanus M274 N Neivamyrmex californicus M272 N Neivamyrmex kiowapache M275 TNNeivamyrmex opacithorax M276 T Neivamyrmex sumichrasti M151 T Neivamyrmex asper M233 T Neivamyrmex compressinodis M235 N Neivamyrmex cf nyensis M296 TN Neivamyrmex melanocephalus M154 T Neivamyrmex impudens M237 T Neivamyrmex gibbatus M139 T Neivamyrmex distans M242 T Neivamyrmex alfaroi M240 T Neivamyrmex adnepos M236 T Neivamyrmex EC M175 TN Neivamyrmex swainsonii M169 T Eciton rapax M145 T Eciton hamatum M293 T Eciton burchellii M273 T Eciton lucanoides M239 T Eciton vagans M184 T Eciton quadriglume M254 T Eciton mexicanum M238 T Nomamyrmex hartigii M220 TN Nomamyrmex esenbeckii M129 T Labidus spininodis M172 T Labidus praedator M152 TN Labidus coecus M173 T Cheliomyrmex cf morosus M217 T Cheliomyrmex cf andicola M174 T Cheliomyrmex megalonyx M146 T Leptanilloides gracilis M187 T Leptanilloides erinys M246 T Leptanilloides femoralis M188 T Leptanilloides nubecula M167 T Leptanilloides mckennae D0228 T Sphinctomyrmex stali M253 T Sphinctomyrmex cf marcoyi M202 T Acanthostichus serratulus M166 T Acanthostichus GF M208 T Acanthostichus BR M252 N Acanthostichus AZ M278 N Acanthostichus AZ M277 T Cylindromyrmex whymperi M271 T Cylindromyrmex darlingtoni M21 T T Cylindromyrmex brasiliensis M140 N T Cylindromyrmex meinerti D0778 P T Neocerapachys cf splendens M251 T Neocerapachys BR M295 E T Neocerapachys neotropicus M134 M T Neocerapachys CR M209 O O Aenictus hoelldobleri M200 O Aenictus fuchuanensis M201 A A Aenictus turneri M135 TN O Aenictus gracilis M199 TP O Aenictus cornutus M230 A Aenictus currax M245 TE O Aenictus rotundicollis M232 TM O Aenictus laeviceps M269 TO O Aenictus hodgsoni M198 POAenictus fergusoni M223 TA E Aenictus ZA M228 NP E Aenictus UG M143 NE O Aenictus camposi M222 O Aenictus levior M231 NM O Aenictus bobaiensis M197 NO O Aenictus latifemoratus M266 NA O Aenictus yamanei M265 O Aenictus silvestrii M221 PE E Dorylus rubellus M287 PM E Dorylus UG M153 PO E Dorylus molestus M290 E Dorylus mayri M291 PA E Dorylus braunsi M289 EM E Dorylus affinis M177 EO E Dorylus kohli M180 E Dorylus spininodis M292 EA PE Dorylus fulvus M179 MO E Dorylus cf fulvus M149 MA E Dorylus fimbriatus M288 O Dorylus orientalis M244 OA E Dorylus conradti M178 TNP O Dorylus laevigatus M157 TNE E Aenictogiton ZM02 M181 E Aenictogiton UG M189 TNM O Yunodorylus eguchii M247 TNO O Yunodorylus TH M191 TNA O Yunodorylus paradoxus M190 O Yunodorylus TH M160 TPE O Chrysapace cf crawleyi M262 TPM O Chrysapace TH M156 TPO O Chrysapace cf sauteri M261 M Chrysapace MG M155 TPA O Cerapachys antennatus M263 TEM O Cerapachys TH M203 TEO O Cerapachys MY M264 O Cerapachys sulcinodis M243 TEA M Eburopone MG M214 TMO M Eburopone MG M213 TMA M Eburopone MG M195 M Eburopone MG M130 TOA E Eburopone UG M259 NPE E Eburopone CM02 D0788 NPM A Ooceraea PG M248 A Ooceraea FJ06 M168 NPO O Ooceraea MY M270 NPA O Ooceraea biroi Genome NEM A Ooceraea australis M138 O Ooceraea fragosa D0842 NEO O Syscia MY M176 NEA O Syscia MY M147 NMO O Syscia typhla D0841 N Syscia augustae M196 NMA T Syscia GT M127 NOA O Eusphinctus TH M158 PEM M Simopone trita M185 M Simopone rex M133 PEO E Simopone marleyi M171 PEA E Simopone conradti M144 PMO E Simopone dryas M224 M Simopone grandidieri M186 PMA O Simopone cf oculata D0792 POA M Tanipone hirsuta M279 EMO M Tanipone aglandula M280 M Tanipone zona M182 EMA M Tanipone scelesta M159 EOA E Vicinopone conciliatrix M128 MOA E Parasyscia wittmeri M282 E Parasyscia UG M218 E Parasyscia UG M219 O Parasyscia dohertyi M142 A Parasyscia PG M204 O Parasyscia VN M207 M Parasyscia MG M212 E Parasyscia UG M281 A Zasphinctus imbecilis M170 A Zasphinctus PG M285 A Zasphinctus trux M136 E Zasphinctus sarowiwai M227 O Zasphinctus TH M192 E Zasphinctus wilsoni M229 M Lividopone MG M216 M Lividopone MG M194 M Lividopone MG M294 M Lividopone MG M132 A Lioponera ruficornis M165 A Lioponera clarus M137 O Lioponera marginata M249 A Lioponera PG M250 O Lioponera cf suscitata M267 O Lioponera MY M268 M Lioponera nr mayri M215 M Lioponera nr kraepelinii M131 E Lioponera vespula M210 POLioponera longitarsus M193

80 60 40 20 0 Ma Supplementary Figure S27: Relative likelihoods of ranges from BioGeoBEARS under DEC+J estimated on the BEAST consensus tree. Pie charts at the nodes correspond to ancestral state esti- mations and pie charts on the corners correspond to ranges immediately following speciation. The region names are abbreviated as follows: Neotropical (T), Nearctic (N), Palearctic (P), Afrotropical (E), Malagasy (M), Indomalayan (O), and Australasian (A). All ages in Ma.

28 A

0.09

0.06 RCFV

0.03

B slow evolving homogeneous high bootstrap

0.8

0.6

0.4 Slope of r egression

0.2

0.0

slow evolving homogeneous high bootstrap Loci

Supplementary Figure S28: Box plots comparison of properties of slow-evolving, compositionally homogeneous, and ”high signal” or high average bootstrap loci. A: Relative composition frequency variability (RCFV), B: Slope of regression of p-distances against distances on ML tree from a locus. Higher RCFV signifies more compositional heterogeneity and higher slope of regression signifies less potential for saturation.

29 Supplementary Table S1: Voucher specimens used in this study. CASENT numbers correspond to records on AntWeb.org.

Taxon Name Specimen Code Country Year Collected Acanthostichus AZ M277 CASENT0324689 United States 2010 Acanthostichus AZ M278 CASENT0324880 United States 2009 Acanthostichus BR M252 CASENT0732106 Brazil 2014 Acanthostichus GF M208 CASENT0732074 French Guiana 2006 Acanthostichus serratulus M166 CASENT0732042 Ecuador 2003 Aenictogiton UG M189 CASENT0317577 Uganda 2012 Aenictogiton ZM02 M181 CASENT0732056 Zambia 2005 Aenictus bobaiensis M197 CASENT0732068 China 2014 Aenictus camposi M222 CASENT0732087 Malaysia 2014 Aenictus cornutus M230 CASENT0732089 Malaysia 2014 Aenictus currax M245 CASENT0732104 Papua New Guinea 2010 Aenictus fergusoni M223 CASENT0732088 India 2001 Aenictus fuchuanensis M201 CASENT0732072 China 2013 Aenictus gracilis M199 CASENT0732070 Malaysia 2008 Aenictus hodgsoni M198 CASENT0732069 China 2012 Aenictus hoelldobleri M200 CASENT0732071 China 2013 Aenictus laeviceps M269 CASENT0702955 Malaysia 2014 Aenictus latifemoratus M266 CASENT0392370 Malaysia 2014 Aenictus levior M231 CASENT0732090 Malaysia 2014 Aenictus rotundicollis M232 CASENT0732091 Malaysia 2014 Aenictus silvestrii M221 CASENT0732086 Malaysia 2014 Aenictus turneri M135 CASENT0732016 Australia 2004 Aenictus UG M143 CASENT0732021 Uganda 2012 Aenictus yamanei M265 CASENT0385898 Malaysia 2014 Aenictus ZA M228 CASENT0764132 South Africa 2011 Cerapachys antennatus M263 CASENT0384548 Malaysia 2014 Cerapachys MY M264 CASENT0384921 Malaysia 2014 Cerapachys sulcinodis M243 CASENT0732102 China 2015 Cerapachys TH M203 CASENT0268115 Thailand 2006 Cheliomyrmex cf andicola M174 CASENT0732049 Ecuador 2009 Cheliomyrmex cf morosus M217 CASENT0732082 Honduras 2010 Cheliomyrmex megalonyx M146 CASENT0732024 Peru 2013 Chrysapace cf crawleyi M262 CASENT0391566 Malaysia 2014 Chrysapace cf sauteri M261 CASENT0385026 Malaysia 2014 Chrysapace MG M155 CASENT0304584 Madagascar 2013 Chrysapace TH M156 CASENT0278856 Thailand 2006 Cylindromyrmex brasiliensis M140 CASENT0731132 Venezuela 2008 Cylindromyrmex darlingtoni M211 CASENT0756069 Dominican Republic 2015 Cylindromyrmex meinerti D0778 JTLC000009430 Costa Rica 2003 Cylindromyrmex whymperi M271 CASENT0732116 Costa Rica 2003 Dorylus affinis M177 CASENT0732052 Kenya 2004 Dorylus braunsi M289 CASENT0732037 Kenya 2004 Dorylus cf fulvus M149 CASENT0732026 Uganda 2012 Dorylus conradti M178 CASENT0732053 Kenya 2004 Dorylus fimbriatus M288 CASENT0732036 Kenya 2004 Dorylus fulvus M179 CASENT0732054 Kenya 2008 Dorylus kohli M180 CASENT0732055 Kenya 2007 Dorylus laevigatus M157 CASENT0202245 Malaysia 2010 Dorylus mayri M291 CASENT0732123 Nigeria 2005 Dorylus molestus M290 CASENT0732122 Uganda 2012 Dorylus orientalis M244 CASENT0732103 China 2015

30 Supplementary Table S1: Continued. Voucher specimens used in this study. CASENT numbers correspond to records on AntWeb.org.

Taxon Name Specimen Code Country Year Collected Dorylus rubellus M287 CASENT0732035 Nigeria 2005 Dorylus spininodis M292 CASENT0732124 Uganda 2012 Dorylus UG M153 CASENT0732030 Uganda 2012 Eburopone CM02 D0788 CASENT0178891 Cameroon 2000 Eburopone MG M130 CASENT0732012 Madagascar 2013 Eburopone MG M195 CASENT0732066 Madagascar 2013 Eburopone MG M213 CASENT0732077 Madagascar 2013 Eburopone MG M214 CASENT0732078 Madagascar 2013 Eburopone UG M259 CASENT0352799 Uganda 2012 Eciton burchellii M273 CASENT0732118 Honduras 2007 Eciton hamatum M293 CASENT0732125 Mexico 2014 Eciton lucanoides M239 CASENT0732098 Panama 2015 Eciton mexicanum M238 CASENT0732097 Costa Rica 2013 Eciton quadriglume M254 CASENT0732108 Brazil 2011 Eciton rapax M145 CASENT0732023 Peru 2013 Eciton vagans M184 CASENT0732059 Costa Rica 2004 Eusphinctus TH M158 CASENT0285681 Thailand 2006 Labidus coecus M173 CASENT0732048 Ecuador 2009 Labidus praedator M152 CASENT0732029 Mexico 2014 Labidus spininodis M172 CASENT0732047 Ecuador 2009 Leptanilloides erinys M246 CASENT0234600 Ecuador 2009 Leptanilloides femoralis M188 CASENT0732063 Venezuela 2008 Leptanilloides gracilis M187 CASENT0732062 Mexico 2008 Leptanilloides mckennae D0228 CASENT0106086 Costa Rica 2003 Leptanilloides nubecula M167 CASENT0732043 Ecuador 2004 Lioponera cf suscitata M267 CASENT0386895 Malaysia 2014 Lioponera longitarsus M193 CASENT0732064 Bangladesh 2014 Lioponera marginata M249 CASENT0219054 Papua New Guinea 2009 Lioponera MY M268 CASENT0389090 Malaysia 2014 Lioponera nr kraepelinii M131 CASENT0732013 Madagascar 2013 Lioponera nr mayri M215 CASENT0732079 Madagascar 2013 Lioponera PG M250 CASENT0215868 Papua New Guinea 2009 Lioponera clarus M137 CASENT0732018 Australia 2006 Lioponera ruficornis M165 CASENT0732041 Australia 2005 Lioponera vespula M210 CASENT0234847 Uganda 2012 Lividopone MG M132 CASENT0732014 Madagascar 2013 Lividopone MG M194 CASENT0732065 Madagascar 2013 Lividopone MG M216 CASENT0732080 Madagascar 2013 Lividopone MG M294 CASENT0732126 Madagascar 2013 Neivamyrmex adnepos M236 CASENT0732095 Costa Rica 2006 Neivamyrmex alfaroi M240 CASENT0732099 Costa Rica 2013 Neivamyrmex asper M233 CASENT0732092 Costa Rica 2014 Neivamyrmex californicus M272 CASENT0732117 United States 2004 Neivamyrmex cf nyensis M296 CASENT0249496 United States 2003 Neivamyrmex compressinodis M235 CASENT0732094 Nicaragua 2011 Neivamyrmex distans M242 CASENT0732101 Costa Rica 1998 Neivamyrmex EC M175 CASENT0732050 Ecuador 2009 Neivamyrmex gibbatus M139 CASENT0732019 Venezuela 2008 Neivamyrmex impudens M237 CASENT0732096 Guatemala 2009 Neivamyrmex kiowapache M275 CASENT0732120 United States 2015 Neivamyrmex melanocephalus M154 CASENT0732031 Mexico 2014

31 Supplementary Table S1: Continued. Voucher specimens used in this study. CASENT numbers correspond to records on AntWeb.org.

Taxon Name Specimen Code Country Year Collected Neivamyrmex opacithorax M276 CASENT0732121 United States 2015 Neivamyrmex sumichrasti M151 CASENT0732028 Mexico 2014 Neivamyrmex swainsonii M169 CASENT0732045 United States 2004 Neivamyrmex texanus M274 CASENT0732119 United States 2015 Neocerapachys BR M295 CASENT0732127 Brazil 2014 Neocerapachys cf splendens M251 CASENT0732105 Brazil 2013 Neocerapachys neotropicus M134 CASENT0732015 Costa Rica 2014 Neocerapachys CR M209 CASENT0732075 Costa Rica 2004 Nomamyrmex esenbeckii M129 CASENT0732011 Mexico 2013 Nomamyrmex hartigii M220 CASENT0732085 Costa Rica 2006 Ooceraea australis M138 CASENT0106146 Australia 2006 Ooceraea FJ06 M168 CASENT0732044 Fiji 2006 Ooceraea fragosa D0842 CASENT0106215 Sri Lanka 2005 Ooceraea MY M270 CASENT0722573 Malaysia 2014 Ooceraea PG M248 CASENT0187824 Papua New Guinea 2009 Parasyscia dohertyi M142 CASENT0732020 Malaysia 2010 Parasyscia MG M212 CASENT0732076 Madagascar 2013 Parasyscia PG M204 CASENT0215652 Papua New Guinea 2009 Parasyscia UG M218 CASENT0732083 Uganda 2012 Parasyscia UG M219 CASENT0732084 Uganda 2012 Parasyscia UG M281 CASENT0352569 Uganda 2012 Parasyscia VN M207 CASENT0731211 Vietnam 2007 Parasyscia wittmeri M282 CASENT0263905 Saudi Arabia 2011 Simopone cf oculata D0792 CASENT0139634 Thailand 2006 Simopone conradti M144 CASENT0732022 Uganda 2012 Simopone dryas M224 CASENT0764130 Kenya 2006 Simopone grandidieri M186 CASENT0732061 Madagascar 2009 Simopone marleyi M171 CASENT0249324 South Africa 1986 Simopone rex M133 CASENT0731175 Madagascar 2013 Simopone trita M185 CASENT0732060 Madagascar 2003 Sphinctomyrmex cf marcoyi M202 CASENT0731146 Argentina 2013 Sphinctomyrmex stali M253 CASENT0732107 Brazil 2013 Syscia augustae M196 CASENT0732067 United States 2015 Syscia GT M127 CASENT0732010 Guatemala 2009 Syscia MY M147 CASENT0732025 Malaysia 2014 Syscia MY M176 CASENT0732051 Malaysia 2009 Syscia typhla D0841 CASENT0106214 Sri Lanka 2006 Tanipone aglandula M280 CASENT0052407 Madagascar 2003 Tanipone hirsuta M279 CASENT0147732 Madagascar 2008 Tanipone scelesta M159 CASENT0229662 Madagascar 2010 Tanipone zona M182 CASENT0732057 Madagascar 2003 Vicinopone conciliatrix M128 CASENT0731168 Uganda 2012 Yunodorylus eguchii M247 CASENT0731166 Vietnam 2004 Yunodorylus paradoxus M190 CASENT0731165 Malaysia 2006 Yunodorylus TH M160 CASENT0139796 Thailand 2006 Yunodorylus TH M191 CASENT0134717 Thailand 2006 Zasphinctus imbecilis M170 CASENT0732046 Australia 2005 Zasphinctus PG M285 CASENT0732033 Papua New Guinea 2000 Zasphinctus sarowiwai M227 CASENT0764121 Kenya 2012 Zasphinctus TH M192 CASENT0131746 Thailand 2006 Zasphinctus trux M136 CASENT0732017 Australia 2006 Zasphinctus wilsoni M229 MCZENT00512765 Mozambique 2012

32 Supplementary Table S2: Statistics of data matrices used in this study.

Proportion of Number Alignment Percent Alignment Name Parsimony AT Content of Taxa Length Missing Informative Sites Combined Data 164 892,761 15.476 0.478 0.530 ”High-Signal” Loci 164 177,947 17.534 0.565 0.578 Slow-Evolving Loci 164 178,662 10.245 0.348 0.486 Homogeneous Loci 164 97,849 10.177 0.369 0.488 No Aenictus 146 892,761 15.006 0.469 0.528 BEAST Matrix 155 44,079 16.489 0.466 0.531 Amino Acids 164 89,483 16.104 0.138 -

33 Supplementary Table S3: Calibration scheme used for penalized likelihood analyses in chronos. MRCA column refers to the most recent common ancestor of two tip names in the maximum likelihood tree obtained from slow-evolving loci matrix.

Clade MRCA Minimum Age (Ma) Maximum Age (Ma) Notes This calibration assumes that poneroids and formicoids shared the last common ancestor at least as early as Burmomyrma, a 94.3-99.7 Ma fossil from Burmese Amber. Harpeg- This taxon was has originally assigned to Aneuretinae (Dlussky, 1996) but recently its nathos_saltator_Genome, Root 94 135 placement has been questioned (LaPolla et al., 2013). Here I take a conservative view Acanthos- that it is at least a representative of stem formicoids. Maximum age is based on the tichus_serratulus_M166 upper bound of 95% confidence interval for this node in the time-calibrated phylogeny of the Formicidae by Moreau and Bell (2013). Kyromyrma neffi (Grimaldi and Agosti, 2000) is a 89.3-94.3 Ma old fossil from New Jersey Amber that shows a clearly preserved acidopore, a unique formicine feature. crown Campono- Kyromyrma is universally treated as a stem Formicinae. Although the upper 95% Formicinae plus tus_floridanus_Genome, 89.3 120 confidence interval for this node was only 95 Ma in Moreau and Bell (2013), the Myrmicinae Atta_cephalotes_Genome maximum age assumed here is more conservatively placed at 120 Ma to accommodate the fact that Ward et al. (2015) inferred ages of one of the constituent clades, the Myrmicinae, up to 110 Ma. Crown Mymicinae are here calibrated with the Baltic amber Myrmica (Radchenko 34 et al., 2007) from the Priabonian age of Eocene (33.9-37.2 Ma). Although Pogono- Pogonomyrmex was a lineage branching after Myrmica in the phylogeny by Ward et al. crown myrmex_barbatus_Genome, 33.9 110 (2015), the latest UCE-based results (Branstetter et al. (2016), M.G. Branstetter pers. Myrmicinae Atta_cephalotes_Genome comm.) suggest that Pogonomyrmex and Myrmica form a clade within the Myrmicinae. The maximum age is based on the upper bound of 95% confidence interval in time-calibrated phylogeny of (Ward et al., 2015). A recently discovered Baltic Amber fossil recognizable as Chrysapace (author’s personal observation) is used to calibrate the node of Cerapachys, Yunodorylus, and Cerapachys, Chrysapace_TH_M156, Chrysapace. Although the maximum likelihood tree places Cerapachys as sister to Chrysapace, and 33.9 85 Yunodorylus_TH_M191 Chrysapace, this relationship has low support, so a conservative approach calibrates the Yunodorylus next node down. Maximum age corresponds to the upper bound of 95% confidence interval in the time-calibrated tree of Brady et al. (2014). Cylin- Cylindromyrmex inopinatus from Dominican Amber is considered a sister species of crown dromyrmex_meinerti_D778, extant C. longiceps (De Andrade, 2001) and thus used here to calibrate crown 13.7 43 Cylindromyrmex Cylin- Cylindromyrmex. Maximum age is the upper bound of 95% confidence interval for dromyrmex_darlingtoni_M211 Cylindromyrmex age in Brady et al. (2014). Neivamyrmex ectopus (Wilson, 1985) is a Dominican Amber species that is somewhat difficult to place in the extant Neivamyrmex diversity. A potentially older fossil of crown New Eciton_hamatum_M293, Neivamyrmex comes from Mexican Amber, 16-23 Ma (Coty et al., 2014). The ancestor 16 46 World army ants Neivamyrmex_californicus_M272 of New World army ants is here dated with a minimum age of 16 Ma. Maximum age is based on upper bound of 95% confidence interval age for this clade in (Brady et al., 2014). Supplementary Table S4: Calibration scheme used for fossilized birth-death process analyses in BEAST. Total group refers to fossil that could be placed in either stem or crown group.

Sampling Deposit Species Group Calibrated Notes Time (Ma) Age (Ma) Chrysapace sp. total Chrysapace 36.6 33.9-37.2 See notes in Supplementary Table S3. Neivamyrmex total 19.2 13.7-20.4 See notes in Supplementary Table S3 ectopus Neivamyrmex Cylindromyrmex total This species was described together with C. electrinus by De Andrade (1998a). Both 19.5 13.7-20.4 antillanus Cylindromyrmex are used to calibrate total group Cylindromyrmex. This fossil was described by De Andrade (1998b) as similar to A. skwarrae, A. quirozi Acanthostichus total and A. arizonensis. Although it is possible that one of the male Acanthostichus 14.5 13.7-20.4 hispaniolicus Acanthostichus specimens sequenced here from Arizona corresponds to A. arizonensis, this fossil is used here to calibrate the total group Acanthostichus. Cylindromyrmex total 18.1 13.7-20.4 See C. antillanus notes above. electrinus Cylindromyrmex crown Cylindromyrmex Cylindromyrmex 14.2 13.7-20.4 See notes in Supplementary Table S3. inopinatus excl. C. meinerti total Neivamyrmex sp. 19.3 16-23 Coty et al. (2014) reported a Neivamyrmex species from Chiapas Amber. Neivamyrmex

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