#NEXUS [!This data set was downloaded from TreeBASE, a relational database of phylogenetic knowledge. TreeBASE has been supported by the NSF, Harvard University, Yale University, SDSC and UC Davis. Please do not remove this acknowledgment from the Nexus file. Generated on May 18, 2024; 9:02 GMT TreeBASE (cc) 1994-2008 Study reference: Evans N. 2018. Molecular phylogenetics of swimming crabs (Portunoidea Rafinesque, 1815) supports a revised family-level classification and suggests a single derived origin of symbiotic taxa. PeerJ, 6:e4260: 56. TreeBASE Study URI: http://purl.org/phylo/treebase/phylows/study/TB2:S21486] BEGIN TAXA; TITLE Taxa; DIMENSIONS NTAX=123; TAXLABELS Arenaeus_cribrarius_OTU047 Bathynectes_maravigna_OTU022 Benthochascon_hemingi_OTU011 Callinectes_sapidus_OTU051 Cancer_pagurus_OTU001 Caphyra_bedoti_OTU091 Caphyra_cf_fulva_OTU093 Caphyra_loevis_OTU092 Caphyra_sp_B_OTU095 Caphyra_tridens_OTU096 Caphyra_yookadai_OTU097 Carcinus_maenas_OTU007 Carpilius_convexus_OTU002 Carupa_ohashii_OTU036 Carupa_tenuipes_var_A_OTU037 Chaceon_granulatus_OTU012 Charybdis_acuta_OTU098 Charybdis_annulata_OTU100 Charybdis_bimaculata_OTU101 Charybdis_callianassa_OTU102 Charybdis_feriata_OTU103 Charybdis_granulata_OTU110 Charybdis_hellerii_OTU104 Charybdis_hongkongensis_OTU105 Charybdis_japonica_OTU106 Charybdis_longicollis_OTU107 Charybdis_lucifera_OTU108 Charybdis_natator_OTU109 Charybdis_orientalis_OTU111 Charybdis_rathbuni_OTU113 Charybdis_variegata_OTU114 Coelocarcinus_foliatus_OTU010 Corystes_cassivelaunus_OTU003 Cronius_ruber_OTU116 Daldorfia_horrida_OTU005 Etisus_utilis_OTU006 Geryon_longipes_OTU013 Gonioinfradens_paucidentatus_OTU117 Goniosupradens_acutifrons_OTU118 Goniosupradens_hawaiensis_OTU120 Goniosupradens_obtusifrons_OTU121 Laleonectes_nipponensis_OTU052 Liocarcinus_corrugatus_OTU023 Liocarcinus_depurator_OTU024 Liocarcinus_holsatus_OTU025 Liocarcinus_maculatus_OTU026 Liocarcinus_navigator_OTU028 Lissocarcinus_arkati_OTU122 Lissocarcinus_holothuricola_OTU123 Lissocarcinus_laevis_OTU124 Lissocarcinus_orbicularis_OTU125 Lissocarcinus_polybiodes_OTU126 Lupocyclus_philippinensis_OTU054 Lupocyclus_rotundatus_OTU056 Macropipus_tuberculatus_OTU030 Menippe_rumphii_OTU004 Necora_puber_OTU031 Ovalipes_iridescens_OTU015 Ovalipes_punctatus_OTU016 Ovalipes_trimaculatus_OTU018 Parathranites_orientalis_OTU032 Pirimela_denticulata_OTU019 Podophthalmus_vigil_OTU046 Polybius_henslowii_OTU033 Portumnus_latipes_OTU008 Portunus_Achelous_ordwayi_OTU061 Portunus_Cycloachelous_orbitosinus_OTU068 Portunus_Lupocycloporus_gracilimanus_OTU069 Portunus_Monomia_argentatus_OTU070 Portunus_Monomia_gladiator_OTU071 Portunus_Monomia_pseudoargentatus_OTU073 Portunus_hastatus_OTU075 Portunus_inaequalis_OTU076 Portunus_pelagicus_OTU077 Portunus_trituberculatus_OTU080 Richerellus_moosai_OTU043 Scylla_serrata_OTU089 Sirpus_zariquieyi_OTU020 Thalamita_admete_OTU127 Thalamita_aff_admete_OTU128 Thalamita_aff_kukenthali_OTU144 Thalamita_aff_spinifera_OTU162 Thalamita_auauensis_OTU129 Thalamita_bevisi_OTU130 Thalamita_bouvieri_OTU131 Thalamita_cf_gatavakensis_sp_A_OTU138 Thalamita_cf_gatavakensis_sp_B_OTU137 Thalamita_chaptalii_OTU132 Thalamita_gloriensis_OTU151 Thalamita_granosimana_OTU140 Thalamita_integra_OTU141 Thalamita_kagosimensis_OTU142 Thalamita_malaccensis_OTU145 Thalamita_mitsiensis_OTU146 Thalamita_oculea_OTU147 Thalamita_parvidens_OTU149 Thalamita_philippinensis_OTU143 Thalamita_picta_OTU150 Thalamita_pseudoculea_OTU153 Thalamita_pseudopoissoni_OTU148 Thalamita_quadrilobata_OTU155 Thalamita_savignyi_OTU158 Thalamita_seurati_OTU159 Thalamita_sima_OTU160 Thalamita_stephensoni_OTU164 Thalamitoides_quadridens_OTU165 Thalamonyx_gracilipes_OTU139 Thia_scutellata_OTU034 Thranita_aff_rubridens_OTU157 Thranita_coeruleipes_OTU133 Thranita_crenata_OTU134 Thranita_danae_OTU135 Thranita_foresti_OTU136 Thranita_prymna_OTU152 Thranita_pseudopelsarti_OTU154 Thranita_spinicarpa_OTU161 Thranitaa_rubridens_OTU156 Trierarchus_cf_cooperi_sp_A_OTU168 Trierarchus_cf_cooperi_sp_B_OTU169 Trierarchus_rotundifrons_OTU170 Trierarchus_woodmasoni_OTU171 Zygita_longifrons_OTU172 Zygita_murinae_OTU173 ; END; BEGIN TREES; TITLE 'Portunoidea H3-only best ML topology'; LINK TAXA = Taxa; TREE 'H3-only best ML topology' = [&R] (Carpilius_convexus_OTU002:0.028882885,(Daldorfia_horrida_OTU005:0.06053672,((Cancer_pagurus_OTU001:0.10319764,Etisus_utilis_OTU006:0.1074162):0.0174459,((Corystes_cassivelaunus_OTU003:0.1669411,Menippe_rumphii_OTU004:0.09300037):0.01440993,((Benthochascon_hemingi_OTU011:0.03826651,(Chaceon_granulatus_OTU012:1.0E-8,Geryon_longipes_OTU013:1.0E-8):0.00559978):0.00645999,((Ovalipes_iridescens_OTU015:0.01341487,(Ovalipes_trimaculatus_OTU018:1.0E-8,Ovalipes_punctatus_OTU016:1.0E-8):0.00942317):0.03844755,((((Carcinus_maenas_OTU007:0.00773469,Portumnus_latipes_OTU008:0.01187977):0.01257631,(Pirimela_denticulata_OTU019:0.02199069,(Sirpus_zariquieyi_OTU020:0.03755405,Coelocarcinus_foliatus_OTU010:0.13584556):0.01022409):0.00471344):0.01330257,((Bathynectes_maravigna_OTU022:0.01029984,Thia_scutellata_OTU034:0.02412438):1.0E-8,((Liocarcinus_corrugatus_OTU023:0.00330633,(Macropipus_tuberculatus_OTU030:0.02511204,Necora_puber_OTU031:0.01463207):0.00297798):1.0E-8,((Liocarcinus_maculatus_OTU026:1.0E-8,Liocarcinus_navigator_OTU028:0.00659838):0.00336975,(Liocarcinus_holsatus_OTU025:1.0E-8,(Polybius_henslowii_OTU033:1.0E-8,Liocarcinus_depurator_OTU024:1.0E-8):1.0E-8):0.00674817):0.01360802):0.00336224):0.00981052):0.03435991,(Parathranites_orientalis_OTU032:0.10067265,(Podophthalmus_vigil_OTU046:0.0763971,(((Portunus_Monomia_pseudoargentatus_OTU073:0.00668808,Portunus_Monomia_gladiator_OTU071:1.0E-8):0.00123256,(Portunus_Monomia_argentatus_OTU070:0.00745865,Portunus_Cycloachelous_orbitosinus_OTU068:0.04144527):0.00570586):0.04341609,(((Portunus_trituberculatus_OTU080:1.0E-8,Portunus_pelagicus_OTU077:1.0E-8):0.04329824,(Arenaeus_cribrarius_OTU047:0.01633905,(Callinectes_sapidus_OTU051:0.02753049,Cronius_ruber_OTU116:0.0490457):0.01146101):0.00579379):0.01637624,(((Scylla_serrata_OTU089:0.02931435,(Lupocyclus_philippinensis_OTU054:1.0E-8,(Portunus_Lupocycloporus_gracilimanus_OTU069:1.0E-8,Lupocyclus_rotundatus_OTU056:0.00370887):1.0E-8):0.05884045):0.01319888,(Carupa_tenuipes_var_A_OTU037:0.03880754,(Laleonectes_nipponensis_OTU052:0.04689162,(Richerellus_moosai_OTU043:0.01881191,Carupa_ohashii_OTU036:0.00705806):1.0E-8):0.00368183):0.01304874):0.00436667,((Portunus_Achelous_ordwayi_OTU061:0.01611318,(Portunus_inaequalis_OTU076:1.0E-8,Portunus_hastatus_OTU075:1.0E-8):0.04531656):0.07134362,(Gonioinfradens_paucidentatus_OTU117:0.03270451,(((Goniosupradens_obtusifrons_OTU121:1.0E-8,(Goniosupradens_acutifrons_OTU118:1.0E-8,Goniosupradens_hawaiensis_OTU120:0.00371935):1.0E-8):0.0079295,(((Charybdis_acuta_OTU098:0.0291332,Charybdis_bimaculata_OTU101:0.00565767):0.00568847,(Charybdis_feriata_OTU103:0.00365707,(Charybdis_granulata_OTU110:0.00362509,(Charybdis_longicollis_OTU107:0.00407601,Charybdis_hongkongensis_OTU105:0.00348147):0.00375038):1.0E-8):0.00370505):1.0E-8,(Charybdis_variegata_OTU114:0.01097173,((Charybdis_lucifera_OTU108:1.0E-8,(Charybdis_orientalis_OTU111:0.01082185,(Charybdis_japonica_OTU106:0.00361796,Charybdis_callianassa_OTU102:0.01087932):1.0E-8):0.0035749):1.0E-8,(Charybdis_hellerii_OTU104:0.01083487,(Charybdis_natator_OTU109:1.0E-8,(Charybdis_annulata_OTU100:0.00405241,Charybdis_rathbuni_OTU113:0.00708037):0.00362708):1.0E-8):0.00739655):1.0E-8):0.00358506):0.02216147):0.01911153,((((Thalamita_bouvieri_OTU131:1.0E-8,Thalamita_mitsiensis_OTU146:1.0E-8):0.0039811,((Thranita_crenata_OTU134:1.0E-8,Thranita_spinicarpa_OTU161:1.0E-8):0.00356094,((Thranita_coeruleipes_OTU133:1.0E-8,Thranita_prymna_OTU152:0.00888496):1.0E-8,((Thranita_danae_OTU135:1.0E-8,Thranita_foresti_OTU136:1.0E-8):0.00379781,(Thranita_pseudopelsarti_OTU154:1.0E-8,(Thranita_aff_rubridens_OTU157:1.0E-8,Thranitaa_rubridens_OTU156:0.00376841):1.0E-8):1.0E-8):1.0E-8):0.00396351):0.01671605):0.00391264,((Thalamita_philippinensis_OTU143:0.00794352,Thalamita_aff_kukenthali_OTU144:1.0E-8):0.01201995,(Thalamitoides_quadridens_OTU165:0.02782937,((Thalamita_picta_OTU150:0.01163488,Thalamita_seurati_OTU159:1.0E-8):0.03020843,((Thalamita_sima_OTU160:0.01909734,(Thalamita_kagosimensis_OTU142:0.00807768,Thalamita_pseudopoissoni_OTU148:0.00386289):0.00774035):0.00437689,(Thalamita_pseudoculea_OTU153:0.0192777,(Thalamita_malaccensis_OTU145:0.00369184,Thalamita_oculea_OTU147:1.0E-8):0.0077058):1.0E-8):0.01545135):0.00907649):0.00418436):1.0E-8):0.00740438,(Thalamita_aff_spinifera_OTU162:0.01559371,((Lissocarcinus_arkati_OTU122:0.01228443,(Lissocarcinus_laevis_OTU124:0.00384208,(Lissocarcinus_polybiodes_OTU126:1.0E-8,(Lissocarcinus_holothuricola_OTU123:1.0E-8,Lissocarcinus_orbicularis_OTU125:0.00370521):0.00379975):0.00785248):0.00331952):0.01683883,(((Trierarchus_cf_cooperi_sp_A_OTU168:0.01116033,(Zygita_longifrons_OTU172:0.00395489,Zygita_murinae_OTU173:1.0E-8):0.0036933):1.0E-8,(Trierarchus_woodmasoni_OTU171:0.0113863,(Trierarchus_cf_cooperi_sp_B_OTU169:0.00375332,(Trierarchus_rotundifrons_OTU170:0.02346748,(Caphyra_tridens_OTU096:1.0E-8,(Caphyra_sp_B_OTU095:0.01928865,((Caphyra_bedoti_OTU091:1.0E-8,Caphyra_yookadai_OTU097:1.0E-8):1.0E-8,(Caphyra_cf_fulva_OTU093:0.00446044,Caphyra_loevis_OTU092:1.0E-8):0.00761744):1.0E-8):1.0E-8):0.00754745):1.0E-8):1.0E-8):0.00374724):0.00759922,(Thalamonyx_gracilipes_OTU139:0.04033463,(((Thalamita_granosimana_OTU140:0.01285401,Thalamita_stephensoni_OTU164:0.01238459):0.00807966,(Thalamita_quadrilobata_OTU155:0.00388097,Thalamita_savignyi_OTU158:1.0E-8):0.00401392):0.00398114,(Thalamita_aff_admete_OTU128:0.01234386,(Thalamita_auauensis_OTU129:1.0E-8,((Thalamita_admete_OTU127:0.02072218,(Thalamita_bevisi_OTU130:0.01181015,Thalamita_gloriensis_OTU151:0.00375243):1.0E-8):0.00407478,(Thalamita_cf_gatavakensis_sp_A_OTU138:0.02217269,(Thalamita_cf_gatavakensis_sp_B_OTU137:1.0E-8,(Thalamita_parvidens_OTU149:0.0028975,(Thalamita_chaptalii_OTU132:0.02224085,Thalamita_integra_OTU141:1.0E-8):0.01314778):0.01751212):0.00908872):0.00291468):0.00379633):0.00800797):0.00353379):0.00815882):0.01237426):1.0E-8):0.00372961):1.0E-8):0.00479892):1.0E-8):0.03085297):0.017971):1.0E-8):0.01007489):0.01600426):0.03449171):0.02520183):0.01407):0.0047044):0.02759547):1.0E-8):0.02349471):0.028882885); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr106674] END;