================== ASTRAL ===================== This is ASTRAL version 5.5.9 Gene trees are treated as unrooted 3191 trees read from Cetacea_ASTRAL_besttree.tre All output trees will be *arbitrarily* rooted at Phocoena_phocoena ======== Running the main analysis Number of taxa: 98 (87 species) Taxa: {Peponocephala_electra=[Pele], Balaenoptera_musculus=[Bmus49099], Inia_geoffrensis=[Igeo], Stenella_coeruleoalba=[Scoe], Balaenoptera_acutorostrata=[Bacu], Cephalorhynchus_heavisidii=[Chea7320], Lagenorhynchus_australis=[Laus], Kogia_brevirostris=[Kbre], Balaenoptera_edeni=[BedeAUS, Bede66737], Lipotes_vexillifer=[Lvex], Mesoplodon_perrini=[Mpni], Steno_bredanensis=[Sbre116871, Sbre18437], Bos_taurus=[Btau], Orcaella_brevirostris=[Obre], Tursiops_truncatus=[Ttru], Lagenodelphis_hosei=[Lhos452, Lhos30470], Physeter_macrocephalus=[Pmac], Ovis_aries=[Oari], Phocoena_phocoena=[Ppho], Globicephala_melas=[Gmel], Feresa_attenuata=[Fatt], Orcaella_heinsohnii=[Ohei], Balaenoptera_physalus=[Bphy_baits, Bphy], Mesoplodon_hectori=[Mhec], Lagenorhynchus_obscurus=[Lobs], Neophocaena_phocaenoides=[Npho], Balaenoptera_borealis=[Bbor], Phocoenoides_dalli=[Pdal], Mesolpodon_stejnegeri=[Mste], Vicugna_pacos=[Vpac], Orcinus_orca=[Oorc], Delphinapterus_leucas=[Dleu], Balaenoptera_bonaerensis=[BbonAUS], Equus_caballus=[Ecab], Gazella_arabica=[Gaar], Eubalaena_japonica=[Ejap43864], Hippopotamus_amphibius=[Hippo], Eubalaena_glacialis=[Egla13086], Grampus_griseus=[Ggri], Eubalaena_australis=[EausAUS], Sotalia_guianensis=[Sflu9837], Kogia_sima=[Ksim], Hyperoodon_ampullatus=[Hamp], Mesoplodon_bowdoini=[Mbow], Berardius_bairdii=[Bbai76728], Sus_scrofa=[Sscr], Stenella_clymene=[Scly1726, Scly1724], Lagenorhynchus_acutus=[Lacu], Balaena_mysticetus=[Bmys], Lissodelphis_peroni=[LperAUS], Lagenorhynchus_obliquidens=[Lobl], Phocoena_spinnipinis=[Pspi], Mesoplodon_carlhubbsi=[Mcar], Mesoplodon_grayii=[MgraAUS], Mesoplodon_gingkodens=[Mgin], Mesoplodon_densirostris=[Mden], Eschrictius_robustus=[Erob133443], Panthalops_hodgsonii=[Phod], Oryx_leucoryx=[Orle], Monodon_monoceros=[Mmon], Pontoporia_blainvillei=[Pbla7349], Caperea_marginata=[Cmar59905], Mesoplodon_layardi=[MlayAUS], Stenella_frontalis=[Sfro7782, Sfro7784], Camelus_bactrianus=[Cbac], Berardius_arnouxii=[Barn], Choeropsis_liberiensis=[Clib], Megaptera_novaeangliae=[Mnov], Lissodelphis_borealis=[Lbor], Mesoplodon_europaeus=[Meur], Mesoplodon_bidens=[Mbid], Globicephala_macrorhynchus=[Gmac39091], Stenella_attenuata=[Satt38219, Satt18473], Mesoplodon_peruvianus=[Mper], Lagenorhynchus_albirostris=[Lalb], Stenella_longirostris=[Slon24923, Slon16012], Sousa_chinensis=[Schi], Tursiops_aduncus=[Tadu79924], Pseudorca_crassidens=[Pcra123188], Ziphius_cavirostris=[Zcav], Phocoena_dioptrica=[Pdio], Tragelaphus_eurycerus=[Treu2], Tasmacetus_shepherdi=[Tshe], Cephalorhynchus_commersoni=[Ccom40], Hyperoodon_planifrons=[Hpla9120], Delphinus_delphis=[Dcap108471, Dcap79929, Ddeltrop4525, DdelSJR], Mesoplodon_mirus=[Mmir]} Taxon occupancy: {Ppho=3187, Satt38219=3168, Egla13086=3186, Lobl=3186, Gmel=3185, Bacu=3125, Lobs=3185, Bphy_baits=3182, MlayAUS=3178, Oorc=3189, Zcav=3180, Ggri=3185, Sbre116871=3186, Pdal=3075, Ejap43864=3184, Pdio=3184, Slon24923=3186, Btau=3143, Chea7320=3187, EausAUS=3184, Clib=3170, Obre=3185, Mcar=3182, Satt18473=3186, Igeo=3183, Mnov=2498, Npho=3174, Vpac=2370, Schi=3186, Bbor=3186, Hamp=3182, Sbre18437=3173, Scoe=3190, Dcap108471=3185, Sflu9837=3187, Pele=3185, Dcap79929=3172, Scly1726=3185, Meur=3182, Scly1724=3075, Lhos452=3191, Slon16012=3174, Dleu=3183, Ohei=3186, Mbow=3183, Pspi=3181, Mgin=3181, Ecab=3090, Mden=3178, Tadu79924=3184, Hippo=3179, Gmac39091=3188, Gaar=3152, Oari=3142, Ksim=3180, LperAUS=3187, Mste=3182, Mper=3181, Bbai76728=3184, Orle=3157, Mpni=3183, BedeAUS=3183, Bede66737=3173, Ccom40=3177, Erob133443=3183, Sfro7782=3172, Ddeltrop4525=3173, Mbid=3183, Sfro7784=3186, Hpla9120=2587, DdelSJR=3187, Fatt=3186, Mmon=3159, Mhec=3180, Ttru=3083, Barn=3150, Phod=3139, Sscr=2977, Kbre=3181, Mmir=3178, Lhos30470=3172, Pbla7349=3183, Laus=3186, Pmac=3164, Bmys=3020, Lbor=3184, MgraAUS=3149, Bphy=3097, Lacu=3184, Pcra123188=3185, BbonAUS=3185, Cmar59905=3190, Lalb=3185, Bmus49099=3183, Treu2=3145, Lvex=3022, Tshe=3186, Cbac=3149} Number of gene trees: 3191 1903 trees have missing taxa Calculating quartet distance matrix (for completion of X) Species tree distances calculated ... Will attempt to complete bipartitions from X before adding using a distance matrix. Building set of clusters (X) from gene trees In second round sampling 2 rounds will be done ------------------------------ gradient0: 101949 ------------------------------ gradient1: 13122 Number of Clusters after addition by distance: 115071 calculating extra bipartitions to be added at level 1 ... Adding to X using resolutions of greedy consensus ... Limit for sigma of degrees:2225 polytomy size limit : 22 discarded polytomies: [3, 3, 3, 3, 4, 4, 4, 5, 5, 5, 5, 7, 8, 9, 10, 14, 22] Threshold 0.0: Threshold 0.01: Threshold 0.02: polytomy of size 3; rounds with additions with at least 5 support: 0; clusters: 115071 Threshold 0.05: polytomy of size 4; rounds with additions with at least 5 support: 0; clusters: 115071 Threshold 0.1: polytomy of size 7; rounds with additions with at least 5 support: 0; clusters: 115071 polytomy of size 5; rounds with additions with at least 5 support: 0; clusters: 115071 Threshold 0.2: polytomy of size 3; rounds with additions with at least 5 support: 0; clusters: 115071 polytomy of size 5; rounds with additions with at least 5 support: 0; clusters: 115071 polytomy of size 10; rounds with additions with at least 5 support: 0; clusters: 115071 polytomy of size 8; rounds with additions with at least 5 support: 0; clusters: 115071 polytomy of size 9; rounds with additions with at least 5 support: 0; clusters: 115071 polytomy of size 3; rounds with additions with at least 5 support: 0; clusters: 115071 polytomy of size 4; rounds with additions with at least 5 support: 0; clusters: 115071 Threshold 0.3333333333333333: polytomy of size 5; rounds with additions with at least 5 support: 0; clusters: 115071 polytomy of size 22; rounds with additions with at least 5 support: 0; clusters: 115071 polytomy of size 3; rounds with additions with at least 5 support: 0; clusters: 115071 polytomy of size 14; rounds with additions with at least 5 support: 0; clusters: 115071 polytomy of size 5; rounds with additions with at least 5 support: 0; clusters: 115071 polytomy of size 4; rounds with additions with at least 5 support: 0; clusters: 115071 max k is :0 Number of Clusters after addition by greedy: 115071 gradient0 in heuristiic: 115071 calculating extra bipartitions to be added at level 1 ... Adding to X using resolutions of greedy consensus ... Limit for sigma of degrees:2225 polytomy size limit : 22 discarded polytomies: [3, 3, 3, 3, 4, 4, 4, 5, 5, 5, 5, 7, 8, 9, 10, 14, 22] Threshold 0.0: Threshold 0.01: Threshold 0.02: polytomy of size 3; rounds with additions with at least 5 support: 0; clusters: 115071 Threshold 0.05: polytomy of size 4; rounds with additions with at least 5 support: 0; clusters: 115071 Threshold 0.1: polytomy of size 7; rounds with additions with at least 5 support: 0; clusters: 115071 polytomy of size 5; rounds with additions with at least 5 support: 0; clusters: 115071 Threshold 0.2: polytomy of size 3; rounds with additions with at least 5 support: 0; clusters: 115071 polytomy of size 5; rounds with additions with at least 5 support: 0; clusters: 115071 polytomy of size 10; rounds with additions with at least 5 support: 0; clusters: 115071 polytomy of size 8; rounds with additions with at least 5 support: 0; clusters: 115071 polytomy of size 9; rounds with additions with at least 5 support: 0; clusters: 115071 polytomy of size 3; rounds with additions with at least 5 support: 0; clusters: 115071 polytomy of size 4; rounds with additions with at least 5 support: 0; clusters: 115071 Threshold 0.3333333333333333: polytomy of size 5; rounds with additions with at least 5 support: 0; clusters: 115071 polytomy of size 22; rounds with additions with at least 5 support: 0; clusters: 115071 polytomy of size 3; rounds with additions with at least 5 support: 0; clusters: 115071 polytomy of size 14; rounds with additions with at least 5 support: 0; clusters: 115071 polytomy of size 5; rounds with additions with at least 5 support: 0; clusters: 115071 polytomy of size 4; rounds with additions with at least 5 support: 0; clusters: 115071 max k is :0 Number of Clusters after addition by greedy: 115071 gradient1 in heuristiic: 0 partitions formed in 161.59 secs Dynamic Programming starting after 161.59 secs Using tree-based weight calculation. Using polytree-based weight calculation. Polytree max score: 10942595692 Polytree building time: 43.975 seconds. Number of quartet trees in the gene trees: 10941415490 Size of largest cluster: 98 Greedy score: 8516539286 estimationFactor: 1.2848641125848028 Calculated 100000 weights; time (seconds): 584 Calculated 200000 weights; time (seconds): 403 Sub-optimal score: 9064351857 Calculated 300000 weights; time (seconds): 404 Calculated 400000 weights; time (seconds): 406 Calculated 500000 weights; time (seconds): 398 Calculated 600000 weights; time (seconds): 395 Calculated 700000 weights; time (seconds): 403 Calculated 800000 weights; time (seconds): 425 Calculated 900000 weights; time (seconds): 444 Total Number of elements weighted: 937502 Normalized score (portion of input quartet trees satisfied before correcting for multiple individuals): 0.8608084698554849 Optimization score: 9418463126 Optimal tree inferred in 4031.097 secs. (Cephalorhynchus_heavisidii,(Lagenorhynchus_australis,(Cephalorhynchus_commersoni,(((Lagenorhynchus_obliquidens,Lagenorhynchus_obscurus),(Lissodelphis_peroni,Lissodelphis_borealis)),((((Orcaella_brevirostris,Orcaella_heinsohnii),(Steno_bredanensis,(Grampus_griseus,(Pseudorca_crassidens,((Globicephala_melas,Globicephala_macrorhynchus),(Peponocephala_electra,Feresa_attenuata)))))),(Sotalia_guianensis,(Sousa_chinensis,(Tursiops_truncatus,((Tursiops_aduncus,(Stenella_attenuata,Stenella_frontalis)),(Stenella_coeruleoalba,(Delphinus_delphis,(Lagenodelphis_hosei,(Stenella_longirostris,Stenella_clymene))))))))),(Lagenorhynchus_albirostris,(Orcinus_orca,(Lagenorhynchus_acutus,(((Delphinapterus_leucas,Monodon_monoceros),(Neophocaena_phocaenoides,(Phocoenoides_dalli,(Phocoena_phocoena,(Phocoena_dioptrica,Phocoena_spinnipinis))))),((Lipotes_vexillifer,(Inia_geoffrensis,Pontoporia_blainvillei)),(((Berardius_bairdii,Berardius_arnouxii),(Tasmacetus_shepherdi,(Ziphius_cavirostris,((Hyperoodon_ampullatus,Hyperoodon_planifrons),((Mesoplodon_bidens,(Mesoplodon_gingkodens,(Mesoplodon_europaeus,Mesoplodon_mirus))),((Mesoplodon_layardi,(Mesoplodon_carlhubbsi,Mesoplodon_bowdoini)),(Mesoplodon_hectori,(Mesoplodon_grayii,(Mesolpodon_stejnegeri,(Mesoplodon_densirostris,(Mesoplodon_peruvianus,Mesoplodon_perrini))))))))))),((Physeter_macrocephalus,(Kogia_sima,Kogia_brevirostris)),(((Choeropsis_liberiensis,Hippopotamus_amphibius),((Sus_scrofa,(Equus_caballus,(Vicugna_pacos,Camelus_bactrianus))),((Bos_taurus,Tragelaphus_eurycerus),(Gazella_arabica,(Oryx_leucoryx,(Ovis_aries,Panthalops_hodgsonii)))))),((Balaena_mysticetus,(Eubalaena_australis,(Eubalaena_glacialis,Eubalaena_japonica))),(Caperea_marginata,((Balaenoptera_acutorostrata,Balaenoptera_bonaerensis),(Eschrictius_robustus,((Balaenoptera_physalus,Megaptera_novaeangliae),(Balaenoptera_musculus,(Balaenoptera_borealis,Balaenoptera_edeni)))))))))))))))))))); Final quartet score is: 9499200228 Final normalized quartet score is: 0.8681875061487131 (Ppho,((Pdio,Pspi)1:0.525339604655167,(Pdal,(Npho,((Dleu,Mmon)1:0.9105705975645723,(((Lvex,(Igeo,Pbla7349)1:0.7849126322774105)1:0.15287298898612647,(((Bbai76728,Barn)1:1.545102964659641,(Tshe,(Zcav,((Hamp,Hpla9120)1:0.20024465054334448,((Mbid,(Mgin,(Meur,Mmir)1:0.1180106052527581)1:0.5661850597347461)0.99:0.03709271894105283,((MlayAUS,(Mcar,Mbow)1:0.18531296308165426)1:0.30004266938348323,(Mhec,(MgraAUS,(Mste,(Mden,(Mper,Mpni)1:0.35516847698879744)1:0.05056121382660242)1:0.26620075135102433)1:0.06946482379047789)1:0.34321653031320404)1:0.16937192610729654)1:0.6036922123605899)1:0.2937159695082019)1:0.12112890016779564)1:0.5037721631324881)1:2.2268335398169627,((Pmac,(Ksim,Kbre)1:2.8242412379771697)1:2.117554949752784,(((Clib,Hippo)1:3.756815877309568,((Sscr,(Ecab,(Vpac,Cbac)1:3.35486522722958)1:0.30349919401870235)1:1.0184053721584447,((Btau,Treu2)1:0.9374032916706551,(Gaar,(Orle,(Oari,Phod)1:1.1176372231124907)1:0.774791323623576)1:1.1230797591247867)1:4.549656112985143)1:0.5530409239638551)1:2.7978048025226196,((Bmys,(EausAUS,(Egla13086,Ejap43864)1:0.24997769084618723)1:0.9802223951879331)1:1.719266003821556,(Cmar59905,((Bacu,BbonAUS)1:1.181554096471316,(Erob133443,(((Bphy_baits,Bphy)1:1.1173759425584133,Mnov)1:0.3645945684709462,(Bmus49099,(Bbor,(BedeAUS,Bede66737)1:0.8738182710998464)1:1.2867348727142727)1:0.39116287929735044)1:0.06316848574378342)1:0.11445931727552129)1:1.0536642363427131)1:0.49644915786519433)1:1.898724780153856)1:0.6041708337023514)1:0.8775838973172021)1:1.621631480751309)1:1.3850470991415513,(Lacu,(Oorc,(Lalb,((((Obre,Ohei)1:0.9368660796185334,((Sbre116871,Sbre18437)1:1.1603071459234422,(Ggri,(Pcra123188,((Gmel,Gmac39091)1:0.3873975471841627,(Pele,Fatt)1:0.09348697896573308)1:0.2106214381701413)1:0.1501147468742517)1:0.35544150986530676)1:0.2793965307490192)1:0.17334620178556281,(Sflu9837,(Schi,(Ttru,((Tadu79924,((Satt38219,Satt18473)1:0.0676046083139081,(Sfro7782,Sfro7784)1:0.17667675605308927)1:0.3238107960431748)1:0.05015661905077315,(Scoe,((Dcap108471,Dcap79929,Ddeltrop4525,DdelSJR)1:0.46631880028381045,((Lhos452,Lhos30470)1:0.3362527762156484,((Slon24923,Slon16012)1:0.19406805997985094,(Scly1726,Scly1724)0.31:0.0)1:0.10848481849960807)0.42:0.003792023892043208)1:0.07285642707675014)0.89:0.021961978308577823)1:0.09265889230521326)1:0.20035622731134514)1:0.13781440102881395)1:0.4625296103031585)1:0.089762247044118,(((Lobl,Lobs)1:0.5732200068461579,(LperAUS,Lbor)1:0.36701220541333857)0.8:0.03564214768968928,(Ccom40,(Laus,Chea7320)1:0.26969124758105045)1:0.37779615189144894)1:0.9648673902751742)1:0.13307774543580608)1:0.04781405511651782)1:0.2572541331030987)1:1.616258262075749)1:0.9678486735670344)1:1.524421528299792)1:0.12720096834509131)1:0.27812316159203093)); (Phocoena_phocoena,((Phocoena_dioptrica,Phocoena_spinnipinis)1:0.525339604655167,(Phocoenoides_dalli,(Neophocaena_phocaenoides,((Delphinapterus_leucas,Monodon_monoceros)1:0.9105705975645723,(((Lipotes_vexillifer,(Inia_geoffrensis,Pontoporia_blainvillei)1:0.7849126322774105)1:0.15287298898612647,(((Berardius_bairdii,Berardius_arnouxii)1:1.545102964659641,(Tasmacetus_shepherdi,(Ziphius_cavirostris,((Hyperoodon_ampullatus,Hyperoodon_planifrons)1:0.20024465054334448,((Mesoplodon_bidens,(Mesoplodon_gingkodens,(Mesoplodon_europaeus,Mesoplodon_mirus)1:0.1180106052527581)1:0.5661850597347461)0.99:0.03709271894105283,((Mesoplodon_layardi,(Mesoplodon_carlhubbsi,Mesoplodon_bowdoini)1:0.18531296308165426)1:0.30004266938348323,(Mesoplodon_hectori,(Mesoplodon_grayii,(Mesolpodon_stejnegeri,(Mesoplodon_densirostris,(Mesoplodon_peruvianus,Mesoplodon_perrini)1:0.35516847698879744)1:0.05056121382660242)1:0.26620075135102433)1:0.06946482379047789)1:0.34321653031320404)1:0.16937192610729654)1:0.6036922123605899)1:0.2937159695082019)1:0.12112890016779564)1:0.5037721631324881)1:2.2268335398169627,((Physeter_macrocephalus,(Kogia_sima,Kogia_brevirostris)1:2.8242412379771697)1:2.117554949752784,(((Choeropsis_liberiensis,Hippopotamus_amphibius)1:3.756815877309568,((Sus_scrofa,(Equus_caballus,(Vicugna_pacos,Camelus_bactrianus)1:3.35486522722958)1:0.30349919401870235)1:1.0184053721584447,((Bos_taurus,Tragelaphus_eurycerus)1:0.9374032916706551,(Gazella_arabica,(Oryx_leucoryx,(Ovis_aries,Panthalops_hodgsonii)1:1.1176372231124907)1:0.774791323623576)1:1.1230797591247867)1:4.549656112985143)1:0.5530409239638551)1:2.7978048025226196,((Balaena_mysticetus,(Eubalaena_australis,(Eubalaena_glacialis,Eubalaena_japonica)1:0.24997769084618723)1:0.9802223951879331)1:1.719266003821556,(Caperea_marginata,((Balaenoptera_acutorostrata,Balaenoptera_bonaerensis)1:1.181554096471316,(Eschrictius_robustus,((Balaenoptera_physalus:1.1173759425584133,Megaptera_novaeangliae)1:0.3645945684709462,(Balaenoptera_musculus,(Balaenoptera_borealis,Balaenoptera_edeni:0.8738182710998464)1:1.2867348727142727)1:0.39116287929735044)1:0.06316848574378342)1:0.11445931727552129)1:1.0536642363427131)1:0.49644915786519433)1:1.898724780153856)1:0.6041708337023514)1:0.8775838973172021)1:1.621631480751309)1:1.3850470991415513,(Lagenorhynchus_acutus,(Orcinus_orca,(Lagenorhynchus_albirostris,((((Orcaella_brevirostris,Orcaella_heinsohnii)1:0.9368660796185334,(Steno_bredanensis:1.1603071459234422,(Grampus_griseus,(Pseudorca_crassidens,((Globicephala_melas,Globicephala_macrorhynchus)1:0.3873975471841627,(Peponocephala_electra,Feresa_attenuata)1:0.09348697896573308)1:0.2106214381701413)1:0.1501147468742517)1:0.35544150986530676)1:0.2793965307490192)1:0.17334620178556281,(Sotalia_guianensis,(Sousa_chinensis,(Tursiops_truncatus,((Tursiops_aduncus,(Stenella_attenuata:0.0676046083139081,Stenella_frontalis:0.17667675605308927)1:0.3238107960431748)1:0.05015661905077315,(Stenella_coeruleoalba,(Delphinus_delphis:0.46631880028381045,(Lagenodelphis_hosei:0.3362527762156484,(Stenella_longirostris:0.19406805997985094,Stenella_clymene:0.0)1:0.10848481849960807)0.42:0.003792023892043208)1:0.07285642707675014)0.89:0.021961978308577823)1:0.09265889230521326)1:0.20035622731134514)1:0.13781440102881395)1:0.4625296103031585)1:0.089762247044118,(((Lagenorhynchus_obliquidens,Lagenorhynchus_obscurus)1:0.5732200068461579,(Lissodelphis_peroni,Lissodelphis_borealis)1:0.36701220541333857)0.8:0.03564214768968928,(Cephalorhynchus_commersoni,(Lagenorhynchus_australis,Cephalorhynchus_heavisidii)1:0.26969124758105045)1:0.37779615189144894)1:0.9648673902751742)1:0.13307774543580608)1:0.04781405511651782)1:0.2572541331030987)1:1.616258262075749)1:0.9678486735670344)1:1.524421528299792)1:0.12720096834509131)1:0.27812316159203093)); Weight calculation took 3700.972894361 secs ASTRAL finished in 4035.767 secs